Contents of MolBio (6 Ed -2014) and Cancer

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Detailed  ContentsMBOC, 5Ed- Chapter 21: Sexual Reproduction: Meiosis, Germ Cells, and FertilizationiBiology Seminar videos with Molecular Biology of the Cell, Sixth Edition,Chapter 20: Cancer — see NobeL 1926-66-75-89-2008: Fibiger (1926) spiroptera carcinoma illustrating cancer caused by chronic irritation, Rous (1966)* tumour-inducing virus in chickens Huggins (1966) hormonal treatment of prostate cancer, BaltimoreDulbecco & Temin (1975) interaction between tumour virus and host cell, Bishop & Varmus(1989) retroviral oncogenes,  2005 Barry J. Marshall and J. Robin Warren «Helicobacter pylori in gastritis and peptic ulcer disease», 2008 Hausen«human papilloma viruses causing cervical cancer» HIV  F/) + Cancer Ward (Russian Aleksandr Solzhenitsyn, 1970 Nobel Prize in Literature.[1] -the «terrifying treatments» by Aconit – nicotinergetic toxin — see Sednev Y. metabol.p.196-197

Molecular Biology of the Cell

6 Edition -Hardback  Translations of previous editions :  http://www.lavoisier.fr,   http://www.wiley-vch.de, http://www.zanichelli.it, http://www.newtonpress.co.jp/cell4/, http://www.grupoa.com.br, RUSSIAN Regular & Chaotic Dynamics (5 изд.2008- М., 2013), http://www.ediciones-omega.es

Chapter 1 Cells and Genomes

1 The Universal Features of Cells on Earth 2 All Cells Store Their Hereditary Information in the Same Linear Chemical Code: DNA 2 All Cells Replicate Their Hereditary Information by Templated Polymerization 3 All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form: RNA 4 All Cells Use Proteins as Catalysts 5 All Cells Translate RNA into Protein in the Same Way 6 Each Protein Is Encoded by a Specific Gene 7 Life Requires Free Energy 8 All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks 8 All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass 8 A Living Cell Can Exist with Fewer Than 500 Genes 9 Summary 10 The Diversity of Genomes and the Tree of Life 10 Cells Can Be Powered by a Variety of Free-Energy Sources 10 Some Cells Fix Nitrogen and Carbon Dioxide for Others 12 The Greatest Biochemical Diversity Exists Among Prokaryotic Cells 12 The Tree of Life Has Three Primary Branches: Bacteria, Archaea, and Eukaryotes 14 Some Genes Evolve Rapidly; Others Are Highly Conserved 15 Most Bacteria and Archaea Have 1000–6000 Genes 16 New Genes Are Generated from Preexisting Genes 16 Gene Duplications Give Rise to Families of Related Genes Within a Single Cell 17 Genes Can Be Transferred Between Organisms, Both in the Laboratory and in Nature 18 Sex Results in Horizontal Exchanges of Genetic Information Within a Species 19 The Function of a Gene Can Often Be Deduced from Its Sequence 20 More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life 20 Mutations Reveal the Functions of Genes 21 Molecular Biology Began with a Spotlight on E. coli 22 Summary 22 Genetic Information in Eukaryotes 23 Eukaryotic Cells May Have Originated as Predators 24 Modern Eukaryotic Cells Evolved from a Symbiosis 25 Eukaryotes Have Hybrid Genomes 27 Eukaryotic Genomes Are Big 28 Eukaryotic Genomes Are Rich in Regulatory DNA 29 The Genome Defines the Program of Multicellular Development 29 Many Eukaryotes Live as Solitary Cells 30 A Yeast Serves as a Minimal Model Eukaryote 30 The Expression Levels of All the Genes of An Organism Can Be Monitored Simultaneously 32 Arabidopsis Has Been Chosen Out of 300,000 Species As a Model Plant 32 The World of Animal Cells Is Represented By a Worm, a Fly, a Fish, a Mouse, and a Human 33 Studies in Drosophila Provide a Key to Vertebrate Development 33 The Vertebrate Genome Is a Product of Repeated Duplications 34 The Frog and the Zebrafish Provide Accessible Models for Vertebrate Development 35 The Mouse Is the Predominant Mammalian Model Organism 35 Humans Report on Their Own Peculiarities 36 We Are All Different in Detail 38 To Understand Cells and Organisms Will Require Mathematics, Computers, and Quantitative Information 38 Summary 39 Problems 39 References 41

Chapter 2 Cell Chemistry and Bioenergetics 43 The Chemical Components of a Cell 43 Water Is Held Together by Hydrogen Bonds 44 Four Types of Noncovalent Attractions Help Bring Molecules Together in Cells 44 Some Polar Molecules Form Acids and Bases in Water 45 A Cell Is Formed from Carbon Compounds 47 Cells Contain Four Major Families of Small Organic Molecules 47 The Chemistry of Cells Is Dominated by Macromolecules with Remarkable Properties 47 Noncovalent Bonds Specify Both the Precise Shape of a Macromolecule and Its Binding to Other Molecules 49 Summary 50

Catalysis and the Use of Energy by Cells 51 Cell Metabolism Is Organized by Enzymes 51 Biological Order Is Made Possible by the Release of Heat Energy from Cells 52 Cells Obtain Energy by the Oxidation of Organic Molecules 54 Oxidation and Reduction Involve Electron Transfers 55 Enzymes Lower the Activation-Energy Barriers That Block Chemical Reactions 57 Enzymes Can Drive Substrate Molecules Along Specific Reaction Pathways 58 How Enzymes Find Their Substrates: The Enormous Rapidity of Molecular Motions 59 The Free-Energy Change for a Reaction, ∆G, Determines Whether It Can Occur Spontaneously 60 The Concentration of Reactants Influences the Free-Energy Change and a Reaction’s Direction 61 The Standard Free-Energy Change, \deltaG°, Makes It Possible to Compare the Energetics of Different Reactions 61 The Equilibrium Constant and ∆G° Are Readily Derived from Each Other 62 The Free-Energy Changes of Coupled Reactions Are Additive 63 Activated Carrier Molecules Are Essential for Biosynthesis 63 The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction 64 ATP Is the Most Widely Used Activated Carrier Molecule 65 Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together 65 NADH and NADPH Are Important Electron Carriers 67 There Are Many Other Activated Carrier Molecules in Cells 68 The Synthesis of Biological Polymers Is Driven by ATP Hydrolysis 70 Summary 73

HOW CELLS OBTAIN ENERGY FROM FOOD 73 Glycolysis Is a Central ATP-Producing Pathway 74 Fermentations Produce ATP in the Absence of Oxygen 75 Glycolysis Illustrates How Enzymes Couple Oxidation to Energy Storage 76 Organisms Store Food Molecules in Special Reservoirs 78 Most Animal Cells Derive Their Energy from Fatty Acids Between Meals 81 Sugars and Fats Are Both Degraded to Acetyl CoA in Mitochondria 81 The Citric Acid Cycle Generates NADH by Oxidizing Acetyl Groups to CO2 82 Electron Transport Drives the Synthesis of the Majority of the ATP in Most Cells 84 Amino Acids and Nucleotides Are Part of the Nitrogen Cycle 85 Metabolism Is Highly Organized and Regulated 87 Summary 88 Problems 88 References 108

Chapter 3 Proteins 109

THE SHAPE AND STRUCTURE OF PROTEINS 109 The Shape of a Protein Is Specified by Its Amino Acid Sequence 109 Proteins Fold into a Conformation of Lowest Energy 114 The α Helix and the β Sheet Are Common Folding Patterns 115 Protein Domains Are Modular Units from Which Larger Proteins Are Built 117 Few of the Many Possible Polypeptide Chains Will Be Useful to Cells 118 Proteins Can Be Classified into Many Families 119 Some Protein Domains Are Found in Many Different Proteins 121 Certain Pairs of Domains Are Found Together in Many Proteins 122 The Human Genome Encodes a Complex Set of Proteins, Revealing That Much Remains Unknown 122 Larger Protein Molecules Often Contain More Than One Polypeptide Chain 123 Some Globular Proteins Form Long Helical Filaments 123 Many Protein Molecules Have Elongated, Fibrous Shapes 124 Proteins Contain a Surprisingly Large Amount of Intrinsically Disordered Polypeptide Chain 125 Covalent Cross-Linkages Stabilize Extracellular Proteins 127 Protein Molecules Often Serve as Subunits for the Assembly of Large Structures 127 Many Structures in Cells Are Capable of Self-Assembly 128 Assembly Factors Often Aid the Formation of Complex Biological Structures 130 Amyloid Fibrils Can Form from Many Proteins 130 Amyloid Structures Can Perform Useful Functions in Cells 132 Many Proteins Contain Low-complexity Domains that Can Form “Reversible Amyloids” 132 Summary 134

PROTEIN FUNCTION 134 All Proteins Bind to Other Molecules 134 The Surface Conformation of a Protein Determines Its Chemistry 135 Sequence Comparisons Between Protein Family Members Highlight Crucial Ligand-Binding Sites 136 Proteins Bind to Other Proteins Through Several Types of Interfaces 137 Antibody Binding Sites Are Especially Versatile 138 The Equilibrium Constant Measures Binding Strength 138 Enzymes Are Powerful and Highly Specific Catalysts 140 Substrate Binding Is the First Step in Enzyme Catalysis 141 Enzymes Speed Reactions by Selectively Stabilizing Transition States 141 Enzymes Can Use Simultaneous Acid and Base Catalysis 144 Lysozyme Illustrates How an Enzyme Works 144 Tightly Bound Small Molecules Add Extra Functions to Proteins 146 Multienzyme Complexes Help to Increase the Rate of Cell Metabolism 148 The Cell Regulates the Catalytic Activities of Its Enzymes 149 Allosteric Enzymes Have Two or More Binding Sites That Interact 151 Two Ligands Whose Binding Sites Are Coupled Must Reciprocally Affect Each Other’s Binding 151 Symmetric Protein Assemblies Produce Cooperative Allosteric Transitions 152 Many Changes in Proteins Are Driven by Protein Phosphorylation 153 A Eukaryotic Cell Contains a Large Collection of Protein Kinases and Protein Phosphatases 154 The Regulation of the Src Protein Kinase Reveals How a Protein Can Function as a Microprocessor 155 Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cell Regulators 156 Regulatory Proteins GAP and GEF Control the Activity of GTP￾Binding Proteins by Determining Whether GTP or GDP Is Bound 157 Proteins Can Be Regulated by the Covalent Addition of Other Proteins 157 An Elaborate Ubiquitin-Conjugating System Is Used to Mark Proteins 158 Protein Complexes with Interchangeable Parts Make Efficient Use of Genetic Information 159 A GTP-Binding Protein Shows How Large Protein Movements Can Be Generated 160 Motor Proteins Produce Large Movements in Cells 161 Membrane-Bound Transporters Harness Energy to Pump Molecules Through Membranes 163 Proteins Often Form Large Complexes That Function as Protein Machines 164 Scaffolds Concentrate Sets of Interacting Proteins 164 Many Proteins Are Controlled by Covalent Modifications That Direct Them to Specific Sites Inside the Cell 165 A Complex Network of Protein Interactions Underlies Cell Function 166 Summary 169 Problems 170 References 172

Chapter 4 DNA, Chromosomes, and Genomes 175

THE STRUCTURE AND FUNCTION OF DNA 175 A DNA Molecule Consists of Two Complementary Chains of Nucleotides 175 The Structure of DNA Provides a Mechanism for Heredity 177 In Eukaryotes, DNA Is Enclosed in a Cell Nucleus 178 Summary 179 Chromosomal DNA and Its Packaging in the Chromatin Fiber 179 Eukaryotic DNA Is Packaged into a Set of Chromosomes 180 Chromosomes Contain Long Strings of Genes 182 The Nucleotide Sequence of the Human Genome Shows How Our Genes Are Arranged 183 Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere, Two Telomeres, and Replication Origins 185 DNA Molecules Are Highly Condensed in Chromosomes 187 Nucleosomes Are a Basic Unit of Eukaryotic Chromosome Structure 187 The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged 188 Nucleosomes Have a Dynamic Structure, and Are Frequently Subjected to Changes Catalyzed by ATP-Dependent Chromatin Remodeling Complexes 190 Nucleosomes Are Usually Packed Together into a Compact Chromatin Fiber 191 Summary 193

CHROMATIN STRUCTURE AND FUNCTION 194 Heterochromatin Is Highly Organized and Restricts Gene Expression 194 The Heterochromatic State Is Self-Propagating 194 The Core Histones Are Covalently Modified at Many Different Sites 196 Chromatin Acquires Additional Variety Through the Site-Specific Insertion of a Small Set of Histone Variants 198 Covalent Modifications and Histone Variants Act in Concert to Control Chromosome Functions 198 A Complex of Reader and Writer Proteins Can Spread Specific Chromatin Modifications Along a Chromosome 199 Barrier DNA Sequences Block the Spread of Reader–Writer Complexes and thereby Separate Neighboring Chromatin Domains 202 The Chromatin in Centromeres Reveals How Histone Variants Can Create Special Structures 203 Some Chromatin Structures Can Be Directly Inherited 204 Experiments with Frog Embryos Suggest that both Activating and Repressive Chromatin Structures Can Be Inherited Epigenetically 205 Chromatin Structures Are Important for Eukaryotic Chromosome Function 206 Summary 207

THE GLOBAL STRUCTURE OF CHROMOSOMES 207 Chromosomes Are Folded into Large Loops of Chromatin 207 Polytene Chromosomes Are Uniquely Useful for Visualizing Chromatin Structures 208 There Are Multiple Forms of Chromatin 210 Chromatin Loops Decondense When the Genes Within Them Are Expressed 211 Chromatin Can Move to Specific Sites Within the Nucleus to Alter Gene Expression 212 Networks of Macromolecules Form a Set of Distinct Biochemical Environments inside the Nucleus 213 Mitotic Chromosomes Are Especially Highly Condensed 214 Summary 216 How Genomes Evolve 216 Genome Comparisons Reveal Functional DNA Sequences by their Conservation Throughout Evolution 217 Genome Alterations Are Caused by Failures of the Normal Mechanisms for Copying and Maintaining DNA, as well as by Transposable DNA Elements 217 The Genome Sequences of Two Species Differ in Proportion to the Length of Time Since They Have Separately Evolved 218 Phylogenetic Trees Constructed from a Comparison of DNA Sequences Trace the Relationships of All Organisms 219 A Comparison of Human and Mouse Chromosomes Shows How the Structures of Genomes Diverge 221 The Size of a Vertebrate Genome Reflects the Relative Rates of DNA Addition and DNA Loss in a Lineage 222 We Can Infer the Sequence of Some Ancient Genomes 223 Multispecies Sequence Comparisons Identify Conserved DNA Sequences of Unknown Function 224 Changes in Previously Conserved Sequences Can Help Decipher Critical Steps in Evolution 226 Mutations in the DNA Sequences That Control Gene Expression Have Driven Many of the Evolutionary Changes in Vertebrates 227 Gene Duplication Also Provides an Important Source of Genetic Novelty During Evolution 227 Duplicated Genes Diverge 228 The Evolution of the Globin Gene Family Shows How DNA Duplications Contribute to the Evolution of Organisms 229 Genes Encoding New Proteins Can Be Created by the Recombination of Exons 230 Neutral Mutations Often Spread to Become Fixed in a Population, with a Probability That Depends on Population Size 230 A Great Deal Can Be Learned from Analyses of the Variation Among Humans 232 Summary 234 Problems 234 References 236

Chapter 5 DNA Replication, Repair, and Recombination 237

THE MAINTENANCE OF DNA SEQUENCES 237 Mutation Rates Are Extremely Low 237 Low Mutation Rates Are Necessary for Life as We Know It 238 Summary 239

DNA REPLICATION MECHANISMS 239 Base-Pairing Underlies DNA Replication and DNA Repair 239 The DNA Replication Fork Is Asymmetrical 240 The High Fidelity of DNA Replication Requires Several Proofreading Mechanisms 242 Only DNA Replication in the 5ʹ-to-3ʹ Direction Allows Efficient Error Correction 244 A Special Nucleotide-Polymerizing Enzyme Synthesizes Short RNA Primer Molecules on the Lagging Strand 245 Special Proteins Help to Open Up the DNA Double Helix in Front of the Replication Fork 246 A Sliding Ring Holds a Moving DNA Polymerase Onto the DNA 246 The Proteins at a Replication Fork Cooperate to Form a Replication Machine 249 A Strand-Directed Mismatch Repair System Removes Replication Errors That Escape from the Replication Machine 250 DNA Topoisomerases Prevent DNA Tangling During Replication 251 DNA Replication Is Fundamentally Similar in Eukaryotes and Bacteria 253 Summary 254

THE INITIATION AND COMPLETION OF DNA REPLICATION IN CHROMOSOMES 254 DNA Synthesis Begins at Replication Origins 254 Bacterial Chromosomes Typically Have a Single Origin of DNA Replication 255 Eukaryotic Chromosomes Contain Multiple Origins of Replication 256 In Eukaryotes, DNA Replication Takes Place During Only One Part of the Cell Cycle 258 Different Regions on the Same Chromosome Replicate at Distinct Times in S Phase 258 A Large Multisubunit Complex Binds to Eukaryotic Origins of Replication 259 Features of the Human Genome That Specify Origins of Replication Remain to Be Discovered 260 New Nucleosomes Are Assembled Behind the Replication Fork 261 Telomerase Replicates the Ends of Chromosomes 262 Telomeres Are Packaged Into Specialized Structures That Protect the Ends of Chromosomes 263 Telomere Length Is Regulated by Cells and Organisms 264 Summary 265

DNA REPAIR 266 Without DNA Repair, Spontaneous DNA Damage Would Rapidly Change DNA Sequences 267 The DNA Double Helix Is Readily Repaired 268 DNA Damage Can Be Removed by More Than One Pathway 269 Coupling Nucleotide Excision Repair to Transcription Ensures That the Cell’s Most Important DNA Is Efficiently Repaired 271 The Chemistry of the DNA Bases Facilitates Damage Detection 271 Special Translesion DNA Polymerases Are Used in Emergencies 273 Double-Strand Breaks Are Efficiently Repaired 273 DNA Damage Delays Progression of the Cell Cycle 276 Summary 276

HOMOLOGOUS RECOMBINATION 276 Homologous Recombination Has Common Features in All Cells 277 DNA Base-Pairing Guides Homologous Recombination 277 Homologous Recombination Can Flawlessly Repair Double￾Strand Breaks in DNA 278 Strand Exchange Is Carried Out by the RecA/Rad51 Protein 279 Homologous Recombination Can Rescue Broken DNA Replication Forks 280 Cells Carefully Regulate the Use of Homologous Recombination in DNA Repair 280 Homologous Recombination Is Crucial for Meiosis 282 Meiotic Recombination Begins with a Programmed Double-Strand Break 282 Holliday Junctions Are Formed During Meiosis 284 Homologous Recombination Produces Both Crossovers and Non-Crossovers During Meiosis 284 Homologous Recombination Often Results in Gene Conversion 286 Summary 286

TRANSPOSITION AND CONSERVATIVE SITE-SPECIFIC RECOMBINATION 287 Through Transposition, Mobile Genetic Elements Can Insert Into Any DNA Sequence 288 DNA-Only Transposons Can Move by a Cut-and-Paste Mechanism 288 Some Viruses Use a Transposition Mechanism to Move Themselves Into Host-Cell Chromosomes 290 Retroviral-like Retrotransposons Resemble Retroviruses, but Lack a Protein Coat 291 A Large Fraction of the Human Genome Is Composed of Nonretroviral Retrotransposons 291 Different Transposable Elements Predominate in Different Organisms 292 Genome Sequences Reveal the Approximate Times at Which Transposable Elements Have Moved 292 Conservative Site-Specific Recombination Can Reversibly Rearrange DNA 292 Conservative Site-Specific Recombination Can Be Used to Turn Genes On or Off 294 Bacterial Conservative Site-Specific Recombinases Have Become Powerful Tools for Cell and Developmental Biologists 294 Summary 295 Problems 296 References 298

Chapter 6 How Cells Read the Genome: From DNA to Protein 299

From DNA to RNA 301 RNA Molecules Are Single-Stranded 302 Transcription Produces RNA Complementary to One Strand of DNA 302 RNA Polymerases Carry Out Transcription 303 Cells Produce Different Categories of RNA Molecules 305 Signals Encoded in DNA Tell RNA Polymerase Where to Start and Stop 306 Transcription Start and Stop Signals Are Heterogeneous in Nucleotide Sequence 307 Transcription Initiation in Eukaryotes Requires Many Proteins 309 RNA Polymerase II Requires a Set of General Transcription Factors 310 Polymerase II Also Requires Activator, Mediator, and Chromatin￾Modifying Proteins 312 Transcription Elongation in Eukaryotes Requires Accessory Proteins 313 Transcription Creates Superhelical Tension 314 Transcription Elongation in Eukaryotes Is Tightly Coupled to RNA Processing 315 RNA Capping Is the First Modification of Eukaryotic Pre-mRNAs 316 RNA Splicing Removes Intron Sequences from Newly Transcribed Pre-mRNAs 317 Nucleotide Sequences Signal Where Splicing Occurs 319 RNA Splicing Is Performed by the Spliceosome 319 The Spliceosome Uses ATP Hydrolysis to Produce a Complex Series of RNA–RNA Rearrangements 321 Other Properties of Pre-mRNA and Its Synthesis Help to Explain the Choice of Proper Splice Sites 321 Chromatin Structure Affects RNA Splicing 323 RNA Splicing Shows Remarkable Plasticity 323 Spliceosome-Catalyzed RNA Splicing Probably Evolved from Self-splicing Mechanisms 324 RNA-Processing Enzymes Generate the 3ʹ End of Eukaryotic mRNAs 324 Mature Eukaryotic mRNAs Are Selectively Exported from the Nucleus 325 Noncoding RNAs Are Also Synthesized and Processed in the Nucleus 327 The Nucleolus Is a Ribosome-Producing Factory 329 The Nucleus Contains a Variety of Subnuclear Aggregates 331 Summary 333 From RNA to Protein 333 An mRNA Sequence Is Decoded in Sets of Three Nucleotides 334 tRNA Molecules Match Amino Acids to Codons in mRNA 334 tRNAs Are Covalently Modified Before They Exit from the Nucleus 336 Specific Enzymes Couple Each Amino Acid to Its Appropriate tRNA Molecule 336 Editing by tRNA Synthetases Ensures Accuracy 338 Amino Acids Are Added to the C-terminal End of a Growing Polypeptide Chain 339 The RNA Message Is Decoded in Ribosomes 340 Elongation Factors Drive Translation Forward and Improve Its Accuracy 343 Many Biological Processes Overcome the Inherent Limitations of Complementary Base-Pairing 345 Accuracy in Translation Requires an Expenditure of Free Energy 345 The Ribosome Is a Ribozyme 346 Nucleotide Sequences in mRNA Signal Where to Start Protein Synthesis 347 Stop Codons Mark the End of Translation 348 Proteins Are Made on Polyribosomes 349 There Are Minor Variations in the Standard Genetic Code 349 Inhibitors of Prokaryotic Protein Synthesis Are Useful as Antibiotics 351 Quality Control Mechanisms Act to Prevent Translation of Damaged mRNAs 351 Some Proteins Begin to Fold While Still Being Synthesized 353 Molecular Chaperones Help Guide the Folding of Most Proteins 354 Cells Utilize Several Types of Chaperones 355 Exposed Hydrophobic Regions Provide Critical Signals for Protein Quality Control 357 The Proteasome Is a Compartmentalized Protease with Sequestered Active Sites 357 Many Proteins Are Controlled by Regulated Destruction 359 There Are Many Steps From DNA to Protein 361 Summary 362 The RNA World and the Origins of Life 362 Single-Stranded RNA Molecules Can Fold into Highly Elaborate Structures 363 RNA Can Both Store Information and Catalyze Chemical Reactions 364 How Did Protein Synthesis Evolve? 365 All Present-Day Cells Use DNA as Their Hereditary Material 365 Summary 366 Problems 366 References 368

Chapter 7 Control of Gene Expression 369

An Overview of Gene Control 369 The Different Cell Types of a Multicellular Organism Contain the Same DNA 369 Different Cell Types Synthesize Different Sets of RNAs and Proteins 370 External Signals Can Cause a Cell to Change the Expression of Its Genes 372 Gene Expression Can Be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein 372 Summary 373

CONTROL OF TRANSCRIPTION BY SEQUENCE-SPECIFIC DNA-BINDING PROTEINS 373 The Sequence of Nucleotides in the DNA Double Helix Can Be Read by Proteins 373 Transcription Regulators Contain Structural Motifs That Can Read DNA Sequences 374 Dimerization of Transcription Regulators Increases Their Affinity and Specificity for DNA 375 Transcription Regulators Bind Cooperatively to DNA 378 Nucleosome Structure Promotes Cooperative Binding of Transcription Regulators 379 Summary 380

TRANSCRIPTION REGULATORS SWITCH GENES ON AND OFF 380 The Tryptophan Repressor Switches Genes Off 380 Repressors Turn Genes Off and Activators Turn Them On 381 An Activator and a Repressor Control the Lac Operon 382 DNA Looping Can Occur During Bacterial Gene Regulation 383 Complex Switches Control Gene Transcription in Eukaryotes 384 A Eukaryotic Gene Control Region Consists of a Promoter Plus Many cis-Regulatory Sequences 384 Eukaryotic Transcription Regulators Work in Groups 385 Activator Proteins Promote the Assembly of RNA Polymerase at the Start Point of Transcription 386 Eukaryotic Transcription Activators Direct the Modification of Local Chromatin Structure 386 Transcription Activators Can Promote Transcription by Releasing RNA Polymerase from Promoters 388 Transcription Activators Work Synergistically 388 Eukaryotic Transcription Repressors Can Inhibit Transcription in Several Ways 389 Insulator DNA Sequences Prevent Eukaryotic Transcription Regulators from Influencing Distant Genes 391 Summary 392

MOLECULAR GENETIC MECHANISMS THAT CREATE AND MAINTAIN SPECIALIZED CELL TYPES 392 Complex Genetic Switches That Regulate Drosophila Development Are Built Up from Smaller Molecules 392 The Drosophila Eve Gene Is Regulated by Combinatorial Controls 394 Transcription Regulators Are Brought Into Play by Extracellular Signals 395 Combinatorial Gene Control Creates Many Different Cell Types 396 Specialized Cell Types Can Be Experimentally Reprogrammed to Become Pluripotent Stem Cells 398 Combinations of Master Transcription Regulators Specify Cell Types by Controlling the Expression of Many Genes 398 Specialized Cells Must Rapidly Turn Sets of Genes On and Off 399 Differentiated Cells Maintain Their Identity 400 Transcription Circuits Allow the Cell to Carry Out Logic Operations 402 Summary 404

MECHANISMS THAT REINFORCE CELL MEMORY IN plants and animals 404 Patterns of DNA Methylation Can Be Inherited When Vertebrate Cells Divide 404 CG-Rich Islands Are Associated with Many Genes in Mammals 405 Genomic Imprinting Is Based on DNA Methylation 407 Chromosome-Wide Alterations in Chromatin Structure Can Be Inherited 409 Epigenetic Mechanisms Ensure That Stable Patterns of Gene Expression Can Be Transmitted to Daughter Cells 411 Summary 413

POST-TRANSCRIPTIONAL CONTROLS 413 Transcription Attenuation Causes the Premature Termination of Some RNA Molecules 414 Riboswitches Probably Represent Ancient Forms of Gene Control 414 Alternative RNA Splicing Can Produce Different Forms of a Protein from the Same Gene 415 The Definition of a Gene Has Been Modified Since the Discovery of Alternative RNA Splicing 416 A Change in the Site of RNA Transcript Cleavage and Poly-A Addition Can Change the C-terminus of a Protein 417 RNA Editing Can Change the Meaning of the RNA Message 418 RNA Transport from the Nucleus Can Be Regulated 419 Some mRNAs Are Localized to Specific Regions of the Cytosol 421 The 5ʹ and 3ʹ Untranslated Regions of mRNAs Control Their Translation 422 The Phosphorylation of an Initiation Factor Regulates Protein Synthesis Globally 423 Initiation at AUG Codons Upstream of the Translation Start Can Regulate Eukaryotic Translation Initiation 424 Internal Ribosome Entry Sites Provide Opportunities for Translational Control 425 Changes in mRNA Stability Can Regulate Gene Expression 426 Regulation of mRNA Stability Involves P-bodies and Stress Granules 427 Summary 428

REGULATION OF GENE EXPRESSION BY NONCODING RNAs 429 Small Noncoding RNA Transcripts Regulate Many Animal and Plant Genes Through RNA Interference 429 miRNAs Regulate mRNA Translation and Stability 429 RNA Interference Is Also Used as a Cell Defense Mechanism 431 RNA Interference Can Direct Heterochromatin Formation 432 piRNAs Protect the Germ Line from Transposable Elements 433 RNA Interference Has Become a Powerful Experimental Tool 433 Bacteria Use Small Noncoding RNAs to Protect Themselves from Viruses 433 Long Noncoding RNAs Have Diverse Functions in the Cell 435 Summary 436 Problems 436 References 438

Chapter 8 Analyzing Cells, Molecules, and Systems 439

ISOLATING CELLS AND GROWING THEM IN CULTURE 440 Cells Can Be Isolated from Tissues 440 Cells Can Be Grown in Culture 440 Eukaryotic Cell Lines Are a Widely Used Source of Homogeneous Cells 442 Hybridoma Cell Lines Are Factories That Produce Monoclonal Antibodies 444 Summary 445

PURIFYING PROTEINS 445 Cells Can Be Separated into Their Component Fractions 445 Cell Extracts Provide Accessible Systems to Study Cell Functions 447 Proteins Can Be Separated by Chromatography 448 Immunoprecipitation Is a Rapid Affinity Purification Method 449 Genetically Engineered Tags Provide an Easy Way to Purify Proteins 450 Purified Cell-free Systems Are Required for the Precise Dissection of Molecular Functions 451 Summary 451

ANALYZING PROTEINS 452 Proteins Can Be Separated by SDS Polyacrylamide-Gel Electrophoresis 452 Two-Dimensional Gel Electrophoresis Provides Greater Protein Separation 452 Specific Proteins Can Be Detected by Blotting with Antibodies 454 Hydrodynamic Measurements Reveal the Size and Shape of a Protein Complex 455 Mass Spectrometry Provides a Highly Sensitive Method for Identifying Unknown Proteins 455 Sets of Interacting Proteins Can Be Identified by Biochemical Methods 457 Optical Methods Can Monitor Protein Interactions 458 Protein Function Can Be Selectively Disrupted With Small Molecules 459 Protein Structure Can Be Determined Using X-Ray Diffraction 460 NMR Can Be Used to Determine Protein Structure in Solution 461 Protein Sequence and Structure Provide Clues About Protein Function 462 Summary 463

ANALYZING AND MANIPULATING DNA 463 Restriction Nucleases Cut Large DNA Molecules into Specific Fragments 464 Gel Electrophoresis Separates DNA Molecules of Different Sizes 465 Purified DNA Molecules Can Be Specifically Labeled with Radioisotopes or Chemical Markers in vitro 467 Genes Can Be Cloned Using Bacteria 467 An Entire Genome Can Be Represented in a DNA Library 469 Genomic and cDNA Libraries Have Different Advantages and Drawbacks 471 Hybridization Provides a Powerful, But Simple Way to Detect Specific Nucleotide Sequences 472 Genes Can Be Cloned in vitro Using PCR 473 PCR Is Also Used for Diagnostic and Forensic Applications 474 Both DNA and RNA Can Be Rapidly Sequenced 477 To Be Useful, Genome Sequences Must Be Annotated 477 DNA Cloning Allows Any Protein to be Produced in Large Amounts 483 Summary 484

STUDYING GENE EXPRESSION AND FUNCTION 485 Classical Genetics Begins by Disrupting a Cell Process by Random Mutagenesis 485 Genetic Screens Identify Mutants with Specific Abnormalities 488 Mutations Can Cause Loss or Gain of Protein Function 489 Complementation Tests Reveal Whether Two Mutations Are in the Same Gene or Different Genes 490 Gene Products Can Be Ordered in Pathways by Epistasis Analysis 490 Mutations Responsible for a Phenotype Can Be Identified Through DNA Analysis 491 Rapid and Cheap DNA Sequencing Has Revolutionized Human Genetic Studies 491 Linked Blocks of Polymorphisms Have Been Passed Down from Our Ancestors 492 Polymorphisms Can Aid the Search for Mutations Associated with Disease 493 Genomics Is Accelerating the Discovery of Rare Mutations That Predispose Us to Serious Disease 493 Reverse Genetics Begins with a Known Gene and Determines Which Cell Processes Require Its Function 494 Animals and Plants Can Be Genetically Altered 495 The Bacterial CRISPR System Has Been Adapted to Edit Genomes in a Wide Variety of Species 497 Large Collections of Engineered Mutations Provide a Tool for Examining the Function of Every Gene in an Organism 498 RNA Interference Is a Simple and Rapid Way to Test Gene Function 499 Reporter Genes Reveal When and Where a Gene Is Expressed 501 In situ Hybridization Can Reveal the Location of mRNAs and Noncoding RNAs 502 Expression of Individual Genes Can Be Measured Using Quantitative RT-PCR 502 Analysis of mRNAs by Microarray or RNA-seq Provides a Snapshot of Gene Expression 503 Genome-wide Chromatin Immunoprecipitation Identifies Sites on the Genome Occupied by Transcription Regulators 505 Ribosome Profiling Reveals Which mRNAs Are Being Translated in the Cell 505 Recombinant DNA Methods Have Revolutionized Human Health 506 Transgenic Plants Are Important for Agriculture 507 Summary 508

MATHEMATICAL ANALYSIS OF CELL FUNCTIONS 509 Regulatory Networks Depend on Molecular Interactions 509 Differential Equations Help Us Predict Transient Behavior 512 Both Promoter Activity and Protein Degradation Affect the Rate of Change of Protein Concentration 513 The Time Required to Reach Steady State Depends on Protein Lifetime 514 Quantitative Methods Are Similar for Transcription Repressors and Activators 514 Negative Feedback Is a Powerful Strategy in Cell Regulation 515 Delayed Negative Feedback Can Induce Oscillations 516 DNA Binding By a Repressor or an Activator Can Be Cooperative 516 Positive Feedback Is Important for Switchlike Responses and Bistability 518 Robustness Is an Important Characteristic of Biological Networks 520 Two Transcription Regulators That Bind to the Same Gene Promoter Can Exert Combinatorial Control 520 An Incoherent Feed-forward Interaction Generates Pulses 522 A Coherent Feed-forward Interaction Detects Persistent Inputs 522 The Same Network Can Behave Differently in Different Cells Due to Stochastic Effects 523 Several Computational Approaches Can Be Used to Model the Reactions in Cells 524 Statistical Methods Are Critical For the Analysis of Biological Data 524 Summary 525 Problems 525 References 528

Chapter 9 Visualizing Cells 529 Looking at Cells in the Light Microscope 529 The Light Microscope Can Resolve Details 0.2 μm Apart 530 Photon Noise Creates Additional Limits to Resolution When Light Levels Are Low 532 Living Cells Are Seen Clearly in a Phase-Contrast or a Differential-Interference-Contrast Microscope 533 Images Can Be Enhanced and Analyzed by Digital Techniques 534 Intact Tissues Are Usually Fixed and Sectioned Before Microscopy 535 Specific Molecules Can Be Located in Cells by Fluorescence Microscopy 536 Antibodies Can Be Used to Detect Specific Molecules 539 Imaging of Complex Three-Dimensional Objects Is Possible with the Optical Microscope 540 The Confocal Microscope Produces Optical Sections by Excluding Out-of-Focus Light 540 Individual Proteins Can Be Fluorescently Tagged in Living Cells and Organisms 542 Protein Dynamics Can Be Followed in Living Cells 543 Light-Emitting Indicators Can Measure Rapidly Changing Intracellular Ion Concentrations 546 Single Molecules Can Be Visualized by Total Internal Reflection Fluorescence Microscopy 547 Individual Molecules Can Be Touched, Imaged, and Moved Using Atomic Force Microscopy 548 Superresolution Fluorescence Techniques Can Overcome Diffraction-Limited Resolution 549 Superresolution Can Also be Achieved Using Single-Molecule Localization Methods 551 Summary 554

Looking at Cells and Molecules in the Electron Microscope 554 The Electron Microscope Resolves the Fine Structure of the Cell 554 Biological Specimens Require Special Preparation for Electron Microscopy 555 Specific Macromolecules Can Be Localized by Immunogold Electron Microscopy 556 Different Views of a Single Object Can Be Combined to Give a Three-Dimensional Reconstruction 557 Images of Surfaces Can Be Obtained by Scanning Electron Microscopy 558 Negative Staining and Cryoelectron Microscopy Both Allow Macromolecules to Be Viewed at High Resolution 559 Multiple Images Can Be Combined to Increase Resolution 561 Summary 562 Problems 563 References 564

Chapter 10 Membrane Structure 565 The Lipid Bilayer 566 Phosphoglycerides, Sphingolipids, and Sterols Are the Major Lipids in Cell Membranes 566 Phospholipids Spontaneously Form Bilayers 568 The Lipid Bilayer Is a Two-dimensional Fluid 569 The Fluidity of a Lipid Bilayer Depends on Its Composition 571 Despite Their Fluidity, Lipid Bilayers Can Form Domains of Different Compositions 572 Lipid Droplets Are Surrounded by a Phospholipid Monolayer 573 The Asymmetry of the Lipid Bilayer Is Functionally Important 573 Glycolipids Are Found on the Surface of All Eukaryotic Plasma Membranes 575 Summary 576 Membrane Proteins 576 Membrane Proteins Can Be Associated with the Lipid Bilayer in Various Ways 576 Lipid Anchors Control the Membrane Localization of Some Signaling Proteins 577 In Most Transmembrane Proteins, the Polypeptide Chain Crosses the Lipid Bilayer in an α-Helical Conformation 579 Transmembrane α Helices Often Interact with One Another 580 Some β Barrels Form Large Channels 580 Many Membrane Proteins Are Glycosylated 582 Membrane Proteins Can Be Solubilized and Purified in Detergents 583 Bacteriorhodopsin Is a Light-driven Proton (H+) Pump That Traverses the Lipid Bilayer as Seven α Helices 586 Membrane Proteins Often Function as Large Complexes 588 Many Membrane Proteins Diffuse in the Plane of the Membrane 588 Cells Can Confine Proteins and Lipids to Specific Domains Within a Membrane 590 The Cortical Cytoskeleton Gives Membranes Mechanical Strength and Restricts Membrane Protein Diffusion 591 Membrane-bending Proteins Deform Bilayers 593 Summary 594 Problems 595 References 596

Chapter 11 Membrane Transport of Small Molecules and the Electrical Properties of Membranes 597

PRINCIPLES OF MEMBRANE TRANSPORT 597 Protein-Free Lipid Bilayers Are Impermeable to Ions 598 There Are Two Main Classes of Membrane Transport Proteins: Transporters and Channels 598 Active Transport Is Mediated by Transporters Coupled to an Energy Source 599 Summary 600

TRANSPORTERS AND ACTIVE MEMBRANE TRANSPORT 600 Active Transport Can Be Driven by Ion-Concentration Gradients 601DETAILED CONTENTS xxvii Transporters in the Plasma Membrane Regulate Cytosolic pH 604 An Asymmetric Distribution of Transporters in Epithelial Cells Underlies the Transcellular Transport of Solutes 605 There Are Three Classes of ATP-Driven Pumps 606 A P-type ATPase Pumps Ca2+ into the Sarcoplasmic Reticulum in Muscle Cells 606 The Plasma Membrane Na+-K+ Pump Establishes Na+ and K+ Gradients Across the Plasma Membrane 607 ABC Transporters Constitute the Largest Family of Membrane Transport Proteins 609 Summary 611

CHANNELS AND THE ELECTRICAL PROPERTIES OF MEMBRANES 611 Aquaporins Are Permeable to Water But Impermeable to Ions 612 Ion Channels Are Ion-Selective and Fluctuate Between Open and Closed States 613 The Membrane Potential in Animal Cells Depends Mainly on K+ Leak Channels and the K+ Gradient Across the Plasma Membrane 615 The Resting Potential Decays Only Slowly When the Na+-K+ Pump Is Stopped 615 The Three-Dimensional Structure of a Bacterial K+ Channel Shows How an Ion Channel Can Work 617 Mechanosensitive Channels Protect Bacterial Cells Against Extreme Osmotic Pressures 619 The Function of a Neuron Depends on Its Elongated Structure 620 Voltage-Gated Cation Channels Generate Action Potentials in Electrically Excitable Cells 621 The Use of Channelrhodopsins Has Revolutionized the Study of Neural Circuits 623 Myelination Increases the Speed and Efficiency of Action Potential Propagation in Nerve Cells 625 Patch-Clamp Recording Indicates That Individual Ion Channels Open in an All-or-Nothing Fashion 626 Voltage-Gated Cation Channels Are Evolutionarily and Structurally Related 626 Different Neuron Types Display Characteristic Stable Firing Properties 627 Transmitter-Gated Ion Channels Convert Chemical Signals into Electrical Ones at Chemical Synapses 627 Chemical Synapses Can Be Excitatory or Inhibitory 629 The Acetylcholine Receptors at the Neuromuscular Junction Are Excitatory Transmitter-Gated Cation Channels 630 Neurons Contain Many Types of Transmitter-Gated Channels 631 Many Psychoactive Drugs Act at Synapses 631 Neuromuscular Transmission Involves the Sequential Activation of Five Different Sets of Ion Channels 632 Single Neurons Are Complex Computation Devices 633 Neuronal Computation Requires a Combination of at Least Three Kinds of K+ Channels 634 Long-Term Potentiation (LTP) in the Mammalian Hippocampus Depends on Ca2+ Entry Through NMDA-Receptor Channels 636 Summary 637 Problems 638 References 640

Chapter 12 Intracellular Compartments and Protein Sorting 641 The Compartmentalization of Cells 641 All Eukaryotic Cells Have the Same Basic Set of Membrane￾enclosed Organelles 641 Evolutionary Origins May Help Explain the Topological Relationships of Organelles 643 Proteins Can Move Between Compartments in Different Ways 645 Signal Sequences and Sorting Receptors Direct Proteins to the Correct Cell Address 647 Most Organelles Cannot Be Constructed De Novo: They Require Information in the Organelle Itself 648 Summary 649 The Transport of Molecules Between the Nucleus and the Cytosol 649 Nuclear Pore Complexes Perforate the Nuclear Envelope 649 Nuclear Localization Signals Direct Nuclear Proteins to the Nucleus 650 Nuclear Import Receptors Bind to Both Nuclear Localization Signals and NPC Proteins 652 Nuclear Export Works Like Nuclear Import, But in Reverse 652 The Ran GTPase Imposes Directionality on Transport Through NPCs 653 Transport Through NPCs Can Be Regulated by Controlling Access to the Transport Machinery 654 During Mitosis the Nuclear Envelope Disassembles 656 Summary 657 The Transport of Proteins into Mitochondria and Chloroplasts 658 Translocation into Mitochondria Depends on Signal Sequences and Protein Translocators 659 Mitochondrial Precursor Proteins Are Imported as Unfolded Polypeptide Chains 660 ATP Hydrolysis and a Membrane Potential Drive Protein Import Into the Matrix Space 661 Bacteria and Mitochondria Use Similar Mechanisms to Insert Porins into their Outer Membrane 662 Transport Into the Inner Mitochondrial Membrane and Intermembrane Space Occurs Via Several Routes 663 Two Signal Sequences Direct Proteins to the Thylakoid Membrane in Chloroplasts 664 Summary 666 Peroxisomes 666 Peroxisomes Use Molecular Oxygen and Hydrogen Peroxide to Perform Oxidation Reactions 666 A Short Signal Sequence Directs the Import of Proteins into Peroxisomes 667 Summary 669 The Endoplasmic Reticulum 669 The ER Is Structurally and Functionally Diverse 670 Signal Sequences Were First Discovered in Proteins Imported into the Rough ER 672 A Signal-Recognition Particle (SRP) Directs the ER Signal Sequence to a Specific Receptor in the Rough ER Membrane 673 The Polypeptide Chain Passes Through an Aqueous Channel in the Translocator 675 Translocation Across the ER Membrane Does Not Always Require Ongoing Polypeptide Chain Elongation 677 In Single-Pass Transmembrane Proteins, a Single Internal ER Signal Sequence Remains in the Lipid Bilayer as a Membrane￾spanning α Helix 677 Combinations of Start-Transfer and Stop-Transfer Signals Determine the Topology of Multipass Transmembrane Proteins 679 ER Tail-anchored Proteins Are Integrated into the ER Membrane by a Special Mechanism 682 Translocated Polypeptide Chains Fold and Assemble in the Lumen of the Rough ER 682 Most Proteins Synthesized in the Rough ER Are Glycosylated by the Addition of a Common N-Linked Oligosaccharide 683 Oligosaccharides Are Used as Tags to Mark the State of Protein Folding 685 Improperly Folded Proteins Are Exported from the ER and Degraded in the Cytosol 685 Misfolded Proteins in the ER Activate an Unfolded Protein Response 686 Some Membrane Proteins Acquire a Covalently Attached Glycosylphosphatidylinositol (GPI) Anchor 688 The ER Assembles Most Lipid Bilayers 689 Summary 691 Problems 692 References 694

Chapter 13 Intracellular Membrane Traffic 695 The Molecular Mechanisms of Membrane Transport and the Maintenance of Compartmental Diversity 697 There Are Various Types of Coated Vesicles 697 The Assembly of a Clathrin Coat Drives Vesicle Formation 697 Adaptor Proteins Select Cargo into Clathrin-Coated Vesicles 698 Phosphoinositides Mark Organelles and Membrane Domains 700 Membrane-Bending Proteins Help Deform the Membrane During Vesicle Formation 701 Cytoplasmic Proteins Regulate the Pinching-Off and Uncoating of Coated Vesicles 701 Monomeric GTPases Control Coat Assembly 703 Not All Transport Vesicles Are Spherical 704 Rab Proteins Guide Transport Vesicles to Their Target Membrane 705 Rab Cascades Can Change the Identity of an Organelle 707 SNAREs Mediate Membrane Fusion 708 Interacting SNAREs Need to Be Pried Apart Before They Can Function Again 709 Summary 710 Transport from the ER Through the Golgi Apparatus 710 Proteins Leave the ER in COPII-Coated Transport Vesicles 711 Only Proteins That Are Properly Folded and Assembled Can Leave the ER 712 Vesicular Tubular Clusters Mediate Transport from the ER to the Golgi Apparatus 712 The Retrieval Pathway to the ER Uses Sorting Signals 713 Many Proteins Are Selectively Retained in the Compartments in Which They Function 714 The Golgi Apparatus Consists of an Ordered Series of Compartments 715 Oligosaccharide Chains Are Processed in the Golgi Apparatus 716 Proteoglycans Are Assembled in the Golgi Apparatus 718 What Is the Purpose of Glycosylation? 719 Transport Through the Golgi Apparatus May Occur by Cisternal Maturation 720 Golgi Matrix Proteins Help Organize the Stack 721 Summary 722 Transport from the Trans Golgi Network to Lysosomes 722 Lysosomes Are the Principal Sites of Intracellular Digestion 722 Lysosomes Are Heterogeneous 723 Plant and Fungal Vacuoles Are Remarkably Versatile Lysosomes 724 Multiple Pathways Deliver Materials to Lysosomes 725 Autophagy Degrades Unwanted Proteins and Organelles 726 A Mannose 6-Phosphate Receptor Sorts Lysosomal Hydrolases in the Trans Golgi Network 727 Defects in the GlcNAc Phosphotransferase Cause a Lysosomal Storage Disease in Humans 728 Some Lysosomes and Multivesicular Bodies Undergo Exocytosis 729 Summary 729 Transport into the Cell from the Plasma Membrane: Endocytosis 730 Pinocytic Vesicles Form from Coated Pits in the Plasma Membrane 731 Not All Pinocytic Vesicles Are Clathrin-Coated 731 Cells Use Receptor-Mediated Endocytosis to Import Selected Extracellular Macromolecules 732 Specific Proteins Are Retrieved from Early Endosomes and Returned to the Plasma Membrane 734 Plasma Membrane Signaling Receptors are Down-Regulated by Degradation in Lysosomes 735 Early Endosomes Mature into Late Endosomes 735 ESCRT Protein Complexes Mediate the Formation of Intralumenal Vesicles in Multivesicular Bodies 736 Recycling Endosomes Regulate Plasma Membrane Composition 737 Specialized Phagocytic Cells Can Ingest Large Particles 738 Summary 740 Transport from the Trans Golgi Network to the Cell Exterior: Exocytosis 741 Many Proteins and Lipids Are Carried Automatically from the Trans Golgi Network (TGN) to the Cell Surface 741 Secretory Vesicles Bud from the Trans Golgi Network 742 Precursors of Secretory Proteins Are Proteolytically Processed During the Formation of Secretory Vesicles 743 Secretory Vesicles Wait Near the Plasma Membrane Until Signaled to Release Their Contents 744 For Rapid Exocytosis, Synaptic Vesicles Are Primed at the Presynaptic Plasma Membrane 744 Synaptic Vesicles Can Form Directly from Endocytic Vesicles 746 Secretory Vesicle Membrane Components Are Quickly Removed from the Plasma Membrane 746 Some Regulated Exocytosis Events Serve to Enlarge the Plasma Membrane 748 Polarized Cells Direct Proteins from the Trans Golgi Network to the Appropriate Domain of the Plasma Membrane 748 Summary 750 Problems 750 References 752

Chapter 14 Energy Conversion: Mitochondria and Chloroplasts 753

THE MITOCHONDRION 755 The Mitochondrion Has an Outer Membrane and an Inner Membrane 757 The Inner Membrane Cristae Contain the Machinery for Electron Transport and ATP Synthesis 758 The Citric Acid Cycle in the Matrix Produces NADH 758 Mitochondria Have Many Essential Roles in Cellular Metabolism 759 A Chemiosmotic Process Couples Oxidation Energy to ATP Production 761 The Energy Derived from Oxidation Is Stored as an Electrochemical Gradient 762 Summary 763

THE PROTON PUMPS OF THE ELECTRON-TRANSPORT CHAIN 763 The Redox Potential Is a Measure of Electron Affinities 763 Electron Transfers Release Large Amounts of Energy 764 Transition Metal Ions and Quinones Accept and Release Electrons Readily 764 NADH Transfers Its Electrons to Oxygen Through Three Large Enzyme Complexes Embedded in the Inner Membrane 766 The NADH Dehydrogenase Complex Contains Separate Modules for Electron Transport and Proton Pumping 768 Cytochrome c Reductase Takes Up and Releases Protons on the Opposite Side of the Crista Membrane, Thereby Pumping Protons 768 The Cytochrome c Oxidase Complex Pumps Protons and Reduces O2 Using a Catalytic Iron–Copper Center 770 The Respiratory Chain Forms a Supercomplex in the Crista Membrane 772 Protons Can Move Rapidly Through Proteins Along Predefined Pathways 773 Summary

ATP PRODUCTION IN MITOCHONDRIA 774 The Large Negative Value of ∆G for ATP Hydrolysis Makes ATP Useful to the Cell 774 The ATP Synthase Is a Nanomachine that Produces ATP by Rotary Catalysis 776 Proton-driven Turbines Are of Ancient Origin 777 Mitochondrial Cristae Help to Make ATP Synthesis Efficient 778 Special Transport Proteins Exchange ATP and ADP Through the Inner Membrane 779 Chemiosmotic Mechanisms First Arose in Bacteria 780 Summary 782

CHLOROPLASTS AND PHOTOSYNTHESIS 782 Chloroplasts Resemble Mitochondria But Have a Separate Thylakoid Compartment 782 Chloroplasts Capture Energy from Sunlight and Use It to Fix Carbon 783 Carbon Fixation Uses ATP and NADPH to Convert CO2 into Sugars 784 Sugars Generated by Carbon Fixation Can Be Stored as Starch or Consumed to Produce ATP 785 The Thylakoid Membranes of Chloroplasts Contain the Protein Complexes Required for Photosynthesis and ATP Generation 786 Chlorophyll–Protein Complexes Can Transfer Either Excitation Energy or Electrons 787 A Photosystem Consists of an Antenna Complex and a Reaction Center 788 The Thylakoid Membrane Contains Two Different Photosystems Working in Series 789

Photosystem II Uses a Manganese Cluster to Withdraw Electrons From Water 790 The Cytochrome b6-f Complex Connects Photosystem II to Photosystem I 791 Photosystem I Carries Out the Second Charge-Separation Step in the Z Scheme 792 The Chloroplast ATP Synthase Uses the Proton Gradient Generated by the Photosynthetic Light Reactions to Produce ATP 793 All Photosynthetic Reaction Centers Have Evolved From a Common Ancestor 793 The Proton-Motive Force for ATP Production in Mitochondria and Chloroplasts Is Essentially the Same 794 Chemiosmotic Mechanisms Evolved in Stages 794 By Providing an Inexhaustible Source of Reducing Power, Photosynthetic Bacteria Overcame a Major Evolutionary Obstacle 796 The Photosynthetic Electron-Transport Chains of Cyanobacteria Produced Atmospheric Oxygen and Permitted New Life-Forms 796 Summary 798

THE GENETIC SYSTEMS OF MITOCHONDRIA AND CHLOROPLASTS 800 The Genetic Systems of Mitochondria and Chloroplasts Resemble Those of Prokaryotes 800 Over Time, Mitochondria and Chloroplasts Have Exported Most of Their Genes to the Nucleus by Gene Transfer 801 The Fission and Fusion of Mitochondria Are Topologically Complex Processes 802 Animal Mitochondria Contain the Simplest Genetic Systems Known 803 Mitochondria Have a Relaxed Codon Usage and Can Have a Variant Genetic Code 804 Chloroplasts and Bacteria Share Many Striking Similarities 806 Organelle Genes Are Maternally Inherited in Animals and Plants 807 Mutations in Mitochondrial DNA Can Cause Severe Inherited Diseases 807 The Accumulation of Mitochondrial DNA Mutations Is a Contributor to Aging 808 Why Do Mitochondria and Chloroplasts Maintain a Costly Separate System for DNA Transcription and Translation? 808 Summary 809 Problems 809 References 811

Chapter 15 Cell Signaling 813

PRINCIPLES OF CELL SIGNALING 813 Extracellular Signals Can Act Over Short or Long Distances 814 Extracellular Signal Molecules Bind to Specific Receptors 815 Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signals 816 There Are Three Major Classes of Cell-Surface Receptor Proteins 818 Cell-Surface Receptors Relay Signals Via Intracellular Signaling Molecules 819 Intracellular Signals Must Be Specific and Precise in a Noisy Cytoplasm 820 Intracellular Signaling Complexes Form at Activated Receptors 822 Modular Interaction Domains Mediate Interactions Between Intracellular Signaling Proteins 822 The Relationship Between Signal and Response Varies in Different Signaling Pathways 824 The Speed of a Response Depends on the Turnover of Signaling Molecules 825 Cells Can Respond Abruptly to a Gradually Increasing Signal 827 Positive Feedback Can Generate an All-or-None Response 828 Negative Feedback is a Common Motif in Signaling Systems 829 Cells Can Adjust Their Sensitivity to a Signal 830 Summary 831

SIGNALING THROUGH G-PROTEIN-COUPLED RECEPTORS 832 Trimeric G Proteins Relay Signals From GPCRs 832 Some G Proteins Regulate the Production of Cyclic AMP 833 Cyclic-AMP-Dependent Protein Kinase (PKA) Mediates Most of the Effects of Cyclic AMP 834 Some G Proteins Signal Via Phospholipids 836 Ca2+ Functions as a Ubiquitous Intracellular Mediator 838 Feedback Generates Ca2+ Waves and Oscillations 838 Ca2+/Calmodulin-Dependent Protein Kinases Mediate Many Responses to Ca2+ Signals 840 Some G Proteins Directly Regulate Ion Channels 843 Smell and Vision Depend on GPCRs That Regulate Ion Channels 843 Nitric Oxide Is a Gaseous Signaling Mediator That Passes Between Cells 846 Second Messengers and Enzymatic Cascades Amplify Signals 848 GPCR Desensitization Depends on Receptor Phosphorylation 848 Summary 849

SIGNALING THROUGH ENZYME-COUPLED RECEPTORS 850 Activated Receptor Tyrosine Kinases (RTKs) Phosphorylate Themselves 850 Phosphorylated Tyrosines on RTKs Serve as Docking Sites for Intracellular Signaling Proteins 852 Proteins with SH2 Domains Bind to Phosphorylated Tyrosines 852 The GTPase Ras Mediates Signaling by Most RTKs 854 Ras Activates a MAP Kinase Signaling Module 855 Scaffold Proteins Help Prevent Cross-talk Between Parallel MAP Kinase Modules 857 Rho Family GTPases Functionally Couple Cell-Surface Receptors to the Cytoskeleton 858 PI 3-Kinase Produces Lipid Docking Sites in the Plasma Membrane 859 The PI-3-Kinase–Akt Signaling Pathway Stimulates Animal Cells to Survive and Grow 860 RTKs and GPCRs Activate Overlapping Signaling Pathways 861 Some Enzyme-Coupled Receptors Associate with Cytoplasmic Tyrosine Kinases 862 Cytokine Receptors Activate the JAK–STAT Signaling Pathway 863 Protein Tyrosine Phosphatases Reverse Tyrosine Phosphorylations 864 Signal Proteins of the TGFβ Superfamily Act Through Receptor Serine/Threonine Kinases and Smads 865 Summary 866

ALTERNATIVE SIGNALING ROUTES IN GENE REGULATION 867 The Receptor Notch Is a Latent Transcription Regulatory Protein 867 Wnt Proteins Bind to Frizzled Receptors and Inhibit the Degradation of β-Catenin 868 Hedgehog Proteins Bind to Patched, Relieving Its Inhibition of Smoothened 871 Many Stressful and Inflammatory Stimuli Act Through an NFκB-Dependent Signaling Pathway 873 Nuclear Receptors Are Ligand-Modulated Transcription Regulators 874 Circadian Clocks Contain Negative Feedback Loops That Control Gene Expression 876 Three Proteins in a Test Tube Can Reconstitute a Cyanobacterial Circadian Clock 878 Summary 879 SIGNALING IN PLANTS 880 Multicellularity and Cell Communication Evolved Independently in Plants and Animals 880 Receptor Serine/Threonine Kinases Are the Largest Class of Cell-Surface Receptors in Plants 881 Ethylene Blocks the Degradation of Specific Transcription Regulatory Proteins in the Nucleus 881 Regulated Positioning of Auxin Transporters Patterns Plant Growth 882 Phytochromes Detect Red Light, and Cryptochromes Detect Blue Light 883 Summary 885 Problems 886 References 888 Chapter 16 The Cytoskeleton 889

FUNCTION AND ORIGIN OF THE CYTOSKELETON 889 Cytoskeletal Filaments Adapt to Form Dynamic or Stable Structures 890 The Cytoskeleton Determines Cellular Organization and Polarity 892 Filaments Assemble from Protein Subunits That Impart Specific Physical and Dynamic Properties 893 Accessory Proteins and Motors Regulate Cytoskeletal Filaments 894 Bacterial Cell Organization and Division Depend on Homologs of Eukaryotic Cytoskeletal Proteins 896 Summary 898

ACTIN AND ACTIN-BINDING PROTEINS 898 Actin Subunits Assemble Head-to-Tail to Create Flexible, Polar Filaments 898 Nucleation Is the Rate-Limiting Step in the Formation of Actin Filaments 899 Actin Filaments Have Two Distinct Ends That Grow at Different Rates 900 ATP Hydrolysis Within Actin Filaments Leads to Treadmilling at Steady State 901 The Functions of Actin Filaments Are Inhibited by Both Polymer￾stabilizing and Polymer-destabilizing Chemicals 904 Actin-Binding Proteins Influence Filament Dynamics and Organization 904 Monomer Availability Controls Actin Filament Assembly 906 Actin-Nucleating Factors Accelerate Polymerization and Generate Branched or Straight Filaments 906 Actin-Filament-Binding Proteins Alter Filament Dynamics 907 Severing Proteins Regulate Actin Filament Depolymerization 909 Higher-Order Actin Filament Arrays Influence Cellular Mechanical Properties and Signaling 911 Bacteria Can Hijack the Host Actin Cytoskeleton 913 Summary 914 MYOSIN AND ACTIN 915 Actin-Based Motor Proteins Are Members of the Myosin Superfamily 915 Myosin Generates Force by Coupling ATP Hydrolysis to Conformational Changes 916 Sliding of Myosin II Along Actin Filaments Causes Muscles to Contract 916 A Sudden Rise in Cytosolic Ca2+ Concentration Initiates Muscle Contraction 920 Heart Muscle Is a Precisely Engineered Machine 923 Actin and Myosin Perform a Variety of Functions in Non-Muscle Cells 923 Summary 925 MICROTUBULES 925 Microtubules Are Hollow Tubes Made of Protofilaments 926 Microtubules Undergo Dynamic Instability 927 Microtubule Functions Are Inhibited by Both Polymer-stabilizing and Polymer-destabilizing Drugs 929 A Protein Complex Containing γ-Tubulin Nucleates Microtubules 929 Microtubules Emanate from the Centrosome in Animal Cells 930 Microtubule-Binding Proteins Modulate Filament Dynamics and Organization 932 Microtubule Plus-End-Binding Proteins Modulate Microtubule Dynamics and Attachments 932 Tubulin-Sequestering and Microtubule-Severing Proteins Destabilize Microtubules 935 Two Types of Motor Proteins Move Along Microtubules 936 Microtubules and Motors Move Organelles and Vesicles 938 Construction of Complex Microtubule Assemblies Requires Microtubule Dynamics and Motor Proteins 940 Motile Cilia and Flagella Are Built from Microtubules and Dyneins 941 Primary Cilia Perform Important Signaling Functions in Animal Cells 942 Summary 943

INTERMEDIATE FILAMENTS AND SEPTINS 944 Intermediate Filament Structure Depends on the Lateral Bundling and Twisting of Coiled-Coils 945 Intermediate Filaments Impart Mechanical Stability to Animal Cells 946 Linker Proteins Connect Cytoskeletal Filaments and Bridge the Nuclear Envelope 948 Septins Form Filaments That Regulate Cell Polarity 949 Summary 950

CELL POLARIZATION AND MIGRATION 951 Many Cells Can Crawl Across a Solid Substratum 951 Actin Polymerization Drives Plasma Membrane Protrusion 951 Lamellipodia Contain All of the Machinery Required for Cell Motility 953 Myosin Contraction and Cell Adhesion Allow Cells to Pull Themselves Forward 954 Cell Polarization Is Controlled by Members of the Rho Protein Family 955 Extracellular Signals Can Activate the Three Rho Protein Family Members 958 External Signals Can Dictate the Direction of Cell Migration 958 Communication Among Cytoskeletal Elements Coordinates Whole-Cell Polarization and Locomotion 959 Summary 960 Problems 960 References 962 Chapter 17 The Cell Cycle 963

OVERVIEW OF THE CELL CYCLE 963 The Eukaryotic Cell Cycle Usually Consists of Four Phases 964 Cell-Cycle Control Is Similar in All Eukaryotes 965 Cell-Cycle Progression Can Be Studied in Various Ways 966 Summary 967

THE CELL-CYCLE CONTROL SYSTEM 967 The Cell-Cycle Control System Triggers the Major Events of the Cell Cycle 967 The Cell-Cycle Control System Depends on Cyclically Activated Cyclin-Dependent Protein Kinases (Cdks) 968 Cdk Activity Can Be Suppressed By Inhibitory Phosphorylation and Cdk Inhibitor Proteins (CKIs) 970 Regulated Proteolysis Triggers the Metaphase-to-Anaphase Transition 970 Cell-Cycle Control Also Depends on Transcriptional Regulation 971 The Cell-Cycle Control System Functions as a Network of Biochemical Switches 972 Summary 974

S PHASE 974 S-Cdk Initiates DNA Replication Once Per Cycle 974 Chromosome Duplication Requires Duplication of Chromatin Structure 975 Cohesins Hold Sister Chromatids Together 977 Summary 977 MITOSIS 978 M-Cdk Drives Entry Into Mitosis 978 Dephosphorylation Activates M-Cdk at the Onset of Mitosis 978 Condensin Helps Configure Duplicated Chromosomes for Separation 979 The Mitotic Spindle Is a Microtubule-Based Machine 982 Microtubule-Dependent Motor Proteins Govern Spindle Assembly and Function 983 Multiple Mechanisms Collaborate in the Assembly of a Bipolar Mitotic Spindle 984 Centrosome Duplication Occurs Early in the Cell Cycle 984 M-Cdk Initiates Spindle Assembly in Prophase 985 The Completion of Spindle Assembly in Animal Cells Requires Nuclear-Envelope Breakdown 985 Microtubule Instability Increases Greatly in Mitosis 986 Mitotic Chromosomes Promote Bipolar Spindle Assembly 986 Kinetochores Attach Sister Chromatids to the Spindle 987 Bi-orientation Is Achieved by Trial and Error 988 Multiple Forces Act on Chromosomes in the Spindle 990 The APC/C Triggers Sister-Chromatid Separation and the Completion of Mitosis 992 Unattached Chromosomes Block Sister-Chromatid Separation: The Spindle Assembly Checkpoint 993 Chromosomes Segregate in Anaphase A and B 994 Segregated Chromosomes Are Packaged in Daughter Nuclei at Telophase 995 Summary 995

CYTOKINESIS 996 Actin and Myosin II in the Contractile Ring Generate the Force for Cytokinesis 996 Local Activation of RhoA Triggers Assembly and Contraction of the Contractile Ring 997 The Microtubules of the Mitotic Spindle Determine the Plane of Animal Cell Division 997 The Phragmoplast Guides Cytokinesis in Higher Plants 1000 Membrane-Enclosed Organelles Must Be Distributed to Daughter Cells During Cytokinesis 1001 Some Cells Reposition Their Spindle to Divide Asymmetrically 1001 Mitosis Can Occur Without Cytokinesis 1002 The G1 Phase Is a Stable State of Cdk Inactivity 1002 Summary 1004

The sexual reproductive cycle involves an alternation of diploid and haploid states: diploid cells divide by meiosis to form haploid cells, and the haploid cells from two individuals fuse in pairs to form new diploid zygotes. In the process, genomes are mixed and recombined to produce individuals with novel genetic combinations. In most higher eucaryotes, diploid cells proliferate by mitosis, and only a small propor￾tion of them (those of the germ line) undergo meiosis to produce haploid cells; the hap￾loid cells develop into gametes, which are specialized for sexual reproduction, exist only briefly, and do not divide. Sexual reproduction is thought to be advantageous both because it produces individuals with novel genetic combinations, some of which can survive and procreate in an unpredictably variable environment, and because it provides an efficient way to eliminate harmful mutations from a population.

MEIOSIS 1004 Meiosis Includes Two Rounds of Chromosome Segregation 1004 Duplicated Homologs Pair During Meiotic Prophase 1006 Homolog Pairing Culminates in the Formation of a Synaptonemal Complex 1006 Homolog Segregation Depends on Several Unique Features of Meiosis I 1008 Crossing-Over Is Highly Regulated 1009 Meiosis Frequently Goes Wrong 1010 Summary 1010

5 ed.: MEIOSIS The realization that gametes are haploid came from an observation that also suggested that chromosomes carry genetic information. In 1883, it was discovered in a study of roundworms that the nucleus of an unfertilized egg and that of a sperm each contain two chromosomes, whereas the fertilized egg (zygote) contains four. This led to the chromosome theory of heredity, …haploid germ cells arise from a special kind of cell division in which the number of chromosomes is precisely halved. This type of division, called meiosis—the Greek word for diminution or lessening—begins in animals in diploid germ-line cells in the ovaries or testes. It might seem as if meiosis could occur by a simple modification of mitosis, in which DNA synthesis (S phase) is omitted and a single cell division produces two haploid cells directly. Meiosis, however, is more complex than this and involves two cell divisions rather than one, but with only one round of DNA synthesis.  1930s, …to identify the various meiosis-specific proteins that cause meiotic chromosomes to behave differently from mitotic chromosomes and help mediate the crucial genetic recombination events that occur in meiosis. We will see that the recombination events are important not only for genetic mixing, but also for accurate chromosome segregation during meiosis.

CONTROL OF CELL DIVISION AND CELL GROWTH 1010 Mitogens Stimulate Cell Division 1011 Cells Can Enter a Specialized Nondividing State 1012 Mitogens Stimulate G1-Cdk and G1/S-Cdk Activities 1012 DNA Damage Blocks Cell Division: The DNA Damage Response 1014 Many Human Cells Have a Built-In Limitation on the Number of Times They Can Divide 1016 Abnormal Proliferation Signals Cause Cell-Cycle Arrest or Apoptosis, Except in Cancer Cells 1016 Cell Proliferation is Accompanied by Cell Growth 1016 Proliferating Cells Usually Coordinate Their Growth and Division 1018 Summary 1018 Problems 1019 References 1020

Chapter 18 Cell Death 1021 Apoptosis Eliminates Unwanted Cells 1021 Apoptosis Depends on an Intracellular Proteolytic Cascade That Is Mediated by Caspases 1022 Cell-Surface Death Receptors Activate the Extrinsic Pathway of Apoptosis 1024 The Intrinsic Pathway of Apoptosis Depends on Mitochondria 1025 Bcl2 Proteins Regulate the Intrinsic Pathway of Apoptosis 1025 IAPs Help Control Caspases 1029 Extracellular Survival Factors Inhibit Apoptosis in Various Ways 1029 Phagocytes Remove the Apoptotic Cell 1030 Either Excessive or Insufficient Apoptosis Can Contribute to Disease 1031 Summary 1032 Problems 1033 References 1034

Chapter 19 Cell Junctions and the Extracellular Matrix 1035

CELL–CELL JUNCTIONS 1038 Cadherins Form a Diverse Family of Adhesion Molecules 1038 Cadherins Mediate Homophilic Adhesion 1038 Cadherin-Dependent Cell–Cell Adhesion Guides the Organization of Developing Tissues 1040 Epithelial–Mesenchymal Transitions Depend on Control of Cadherins 1042 Catenins Link Classical Cadherins to the Actin Cytoskeleton 1042 Adherens Junctions Respond to Forces Generated by the Actin Cytoskeleton 1042 Tissue Remodeling Depends on the Coordination of Actin￾Mediated Contraction With Cell–Cell Adhesion 1043 Desmosomes Give Epithelia Mechanical Strength 1045 Tight Junctions Form a Seal Between Cells and a Fence Between Plasma Membrane Domains 1047 Tight Junctions Contain Strands of Transmembrane Adhesion Proteins 1047 Scaffold Proteins Organize Junctional Protein Complexes 1049 Gap Junctions Couple Cells Both Electrically and Metabolically 1050 A Gap-Junction Connexon Is Made of Six Transmembrane Connexin Subunits 1051 In Plants, Plasmodesmata Perform Many of the Same Functions as Gap Junctions 1053 Selectins Mediate Transient Cell–Cell Adhesions in the Bloodstream 1054 Members of the Immunoglobulin Superfamily Mediate Ca2+-Independent Cell–Cell Adhesion 1055 Summary 1056

THE EXTRACELLULAR MATRIX OF ANIMALS 1057 The Extracellular Matrix Is Made and Oriented by the Cells Within It 1057 Glycosaminoglycan (GAG) Chains Occupy Large Amounts of Space and Form Hydrated Gels 1058 Hyaluronan Acts as a Space Filler During Tissue Morphogenesis and Repair 1059 Proteoglycans Are Composed of GAG Chains Covalently Linked to a Core Protein 1059 Collagens Are the Major Proteins of the Extracellular Matrix 1061 Secreted Fibril-Associated Collagens Help Organize the Fibrils 1063 Cells Help Organize the Collagen Fibrils They Secrete by Exerting Tension on the Matrix 1064 Elastin Gives Tissues Their Elasticity 1065 Fibronectin and Other Multidomain Glycoproteins Help Organize the Matrix 1066 Fibronectin Binds to Integrins 1067 Tension Exerted by Cells Regulates the Assembly of Fibronectin Fibrils 1068 The Basal Lamina Is a Specialized Form of Extracellular Matrix 1068 Laminin and Type IV Collagen Are Major Components of the Basal Lamina 1069 Basal Laminae Have Diverse Functions 1070 Cells Have to Be Able to Degrade Matrix, as Well as Make It 1072 Matrix Proteoglycans and Glycoproteins Regulate the Activities of Secreted Proteins 1073 Summary 1074

CELL–MATRIX JUNCTIONS 1074 Integrins Are Transmembrane Heterodimers That Link the Extracellular Matrix to the Cytoskeleton 1075 Integrin Defects Are Responsible for Many Genetic Diseases 1076 Integrins Can Switch Between an Active and an Inactive Conformation 1077 Integrins Cluster to Form Strong Adhesions 1079 Extracellular Matrix Attachments Act Through Integrins to Control Cell Proliferation and Survival 1079 Integrins Recruit Intracellular Signaling Proteins at Sites of Cell–Matrix Adhesion 1079 Cell–Matrix Adhesions Respond to Mechanical Forces 1080 Summary 1081

THE PLANT CELL WALL 1081 The Composition of the Cell Wall Depends on the Cell Type 1082 The Tensile Strength of the Cell Wall Allows Plant Cells to Develop Turgor Pressure 1083 The Primary Cell Wall Is Built from Cellulose Microfibrils Interwoven with a Network of Pectic Polysaccharides 1083 Oriented Cell Wall Deposition Controls Plant Cell Growth 1085 Microtubules Orient Cell Wall Deposition 1086 Summary 1087 Problems 1087 References 1089

Chapter 20 Cancer 1091

CANCER AS A MICROEVOLUTIONARY PROCESS 1091 Cancer Cells Bypass Normal Proliferation Controls and Colonize Other Tissues 1092 Most Cancers Derive from a Single Abnormal Cell 1093 Cancer Cells Contain Somatic Mutations 1094 A Single Mutation Is Not Enough to Change a Normal Cell into a Cancer Cell 1094 Cancers Develop Gradually from Increasingly Aberrant Cells 1095 Tumor Progression Involves Successive Rounds of Random Inherited Change Followed by Natural Selection 1096 Human Cancer Cells Are Genetically Unstable 1097 Cancer Cells Display an Altered Control of Growth 1098 Cancer Cells Have an Altered Sugar Metabolism 1098 Cancer Cells Have an Abnormal Ability to Survive Stress and DNA Damage 1099 Human Cancer Cells Escape a Built-in Limit to Cell Proliferation 1099 The Tumor Microenvironment Influences Cancer Development

Cancer Cells Must Survive and Proliferate in a Foreign Environment 1101 Many Properties Typically Contribute to Cancerous Growth 1103 Summary 1103

CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO 1104 The Identification of Gain-of-Function and Loss-of-Function Cancer Mutations Has Traditionally Required Different Methods 1104 Retroviruses Can Act as Vectors for Oncogenes That Alter Cell Behavior 1105 Different Searches for Oncogenes Converged on the Same Gene—Ras 1106 Genes Mutated in Cancer Can Be Made Overactive in Many Ways 1106 Studies of Rare Hereditary Cancer Syndromes First Identified Tumor Suppressor Genes 1107 Both Genetic and Epigenetic Mechanisms Can Inactivate Tumor Suppressor Genes 1108 Systematic Sequencing of Cancer Cell Genomes Has Transformed Our Understanding of the Disease 1109 Many Cancers Have an Extraordinarily Disrupted Genome 1111 Many Mutations in Tumor Cells are Merely Passengers 1111 About One Percent of the Genes in the Human Genome Are Cancer-Critical 1112 Disruptions in a Handful of Key Pathways Are Common to Many Cancers 1113 Mutations in the PI3K/Akt/mTOR Pathway Drive Cancer Cells to Grow 1114 Mutations in the p53 Pathway Enable Cancer Cells to Survive and Proliferate Despite Stress and DNA Damage 1115 Genome Instability Takes Different Forms in Different Cancers 1116 Cancers of Specialized Tissues Use Many Different Routes to Target the Common Core Pathways of Cancer 1117 Studies Using Mice Help to Define the Functions of Cancer￾Critical Genes 1117 Cancers Become More and More Heterogeneous as They Progress 1118 The Changes in Tumor Cells That Lead to Metastasis Are Still Largely a Mystery 1119 A Small Population of Cancer Stem Cells May Maintain Many Tumors 1120 The Cancer Stem-Cell Phenomenon Adds to the Difficulty of Curing Cancer 1121 Colorectal Cancers Evolve Slowly Via a Succession of Visible Changes 1122 A Few Key Genetic Lesions Are Common to a Large Fraction of Colorectal Cancers 1123 Some Colorectal Cancers Have Defects in DNA Mismatch Repair 1124 The Steps of Tumor Progression Can Often Be Correlated with Specific Mutations 1125 Summary 1126

Two classes of cancer-critical genes: oncogenes and tumor suppressor genes. … altered by a combination of genetic and epigenetic accidents to drive tumor progression. …social control pathways that regulate when cells grow, divide, differentiate, or die. In addition, a subclass of tumor suppressors can be categorized as “genome maintenance genes,” … p53 pathway, which occurs in nearly all human cancers, allows genetically damaged cells to escape apoptosis and continue to proliferate. Inactivation of the Rb pathway also occurs in most human cancers, …—except for the cancers of childhood—many cancers acquire 10 or so driver mutations over the long course of tumor progression, along with a considerably larger number of passenger mutations of no consequence. … subclones of cells arise and die out as a tumor ages. Tumors thus contain a heterogeneous mixture of cells, some—the so-called cancer stem cells—being much more dangerous. We can often correlate the steps of tumor progression with mutations that activate specific oncogenes and inactivate specific tumor suppressor genes, with colon cancer providing a good example. But different combinations of mutations and epigenetic changes are found in different types of cancer, and even in different patients with the same type of cancer, reflecting the random way … repeatedly, suggesting that there are a limited number of ways to breach our defenses against cancer

CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE 1127 Epidemiology Reveals That Many Cases of Cancer Are Preventable 1127 Sensitive Assays Can Detect Those Cancer-Causing Agents that Damage DNA 1127 Fifty Percent of Cancers Could Be Prevented by Changes in Lifestyle 1128 Viruses and Other Infections Contribute to a Significant Proportion of Human Cancers 1129 Cancers of the Uterine Cervix Can Be Prevented by Vaccination Against Human Papillomavirus 1131 Infectious Agents Can Cause Cancer in a Variety of Ways 1132 The Search for Cancer Cures Is Difficult but Not Hopeless 1132 Traditional Therapies Exploit the Genetic Instability and Loss of Cell-Cycle Checkpoint Responses in Cancer Cells 1132 New Drugs Can Kill Cancer Cells Selectively by Targeting Specific Mutations 1133 PARP Inhibitors Kill Cancer Cells That Have Defects in Brca1 or Brca2 Genes 1133 Small Molecules Can Be Designed to Inhibit Specific Oncogenic Proteins 1135 Many Cancers May Be Treatable by Enhancing the Immune Response Against the Specific Tumor 1137 Cancers Evolve Resistance to Therapies 1139 Combination Therapies May Succeed Where Treatments with One Drug at a Time Fail 1139 We Now Have the Tools to Devise Combination Therapies Tailored to the Individual Patient 1140

Summary 1141 …to better ways of preventing, diagnosing, and treating … Anticancer therapies can be designed to destroy cancer cells preferentially by exploiting the properties that distinguish cancer cells from normal cells, including the cancer cells’ dependence on oncogenic proteins and the defects they harbor in their DNA repair mechanisms. …understanding of normal cell control mechanisms and exactly how they are subverted in specific cancers, we can eventually devise drugs to kill cancers precisely by attacking specific molecules critical for the growth and survival of the cancer cells. In addition, …sophisticated immunological approaches to cancer therapy. And…given tumor, we can begin to tailor treatments more accurately to each individual patient

Problems 1141 References 1143

Chapter 21 Development of Multicellular Organisms 1145

OVERVIEW OF DEVELOPMENT 1147 Conserved Mechanisms Establish the Basic Animal Body Plan 1147 The Developmental Potential of Cells Becomes Progressively Restricted 1148 Cell Memory Underlies Cell Decision-Making 1148 Several Model Organisms Have Been Crucial for Understanding Development 1148 Genes Involved in Cell–Cell Communication and Transcriptional Control Are Especially Important for Animal Development 1149 Regulatory DNA Seems Largely Responsible for the Differences Between Animal Species 1149 Small Numbers of Conserved Cell–Cell Signaling Pathways Coordinate Spatial Patterning 1150 Through Combinatorial Control and Cell Memory, Simple Signals Can Generate Complex Patterns 1150 Morphogens Are Long-Range Inductive Signals That Exert Graded Effects 1151 Lateral Inhibition Can Generate Patterns of Different Cell Types 1151 Short-Range Activation and Long-Range Inhibition Can Generate Complex Cellular Patterns 1152 Asymmetric Cell Division Can Also Generate Diversity 1153 Initial Patterns Are Established in Small Fields of Cells and Refined by Sequential Induction as the Embryo Grows 1153 Developmental Biology Provides Insights into Disease and Tissue Maintenance 1154 Summary 1154 Mechanisms of Pattern Formation 1155 Different Animals Use Different Mechanisms to Establish Their Primary Axes of Polarization 1155 Studies in Drosophila Have Revealed the Genetic Control Mechanisms Underlying Development 1157 Egg-Polarity Genes Encode Macromolecules Deposited in the Egg to Organize the Axes of the Early Drosophila Embryo 1157 Three Groups of Genes Control Drosophila Segmentation Along the A-P Axis 1159 A Hierarchy of Gene Regulatory Interactions Subdivides the Drosophila Embryo 1159 Egg-Polarity, Gap, and Pair-Rule Genes Create a Transient Pattern That Is Remembered by Segment-Polarity and Hox Genes 1160 Hox Genes Permanently Pattern the A-P Axis 1162 Hox Proteins Give Each Segment Its Individuality 1163 Hox Genes Are Expressed According to Their Order in the Hox Complex 1163 Trithorax and Polycomb Group Proteins Enable the Hox Complexes to Maintain a Permanent Record of Positional Information 1164 The D-V Signaling Genes Create a Gradient of the Transcription Regulator Dorsal 1164 A Hierarchy of Inductive Interactions Subdivides the Vertebrate Embryo 1166 A Competition Between Secreted Signaling Proteins Patterns the Vertebrate Embryo 1168 The Insect Dorsoventral Axis Corresponds to the Vertebrate Ventral-Dorsal Axis 1169 Hox Genes Control the Vertebrate A-P Axis 1169 Some Transcription Regulators Can Activate a Program That Defines a Cell Type or Creates an Entire Organ 1170 Notch-Mediated Lateral Inhibition Refines Cellular Spacing Patterns 1171 Asymmetric Cell Divisions Make Sister Cells Different 1173 Differences in Regulatory DNA Explain Morphological Differences 1174 Summary 1175 Developmental Timing 1176 Molecular Lifetimes Play a Critical Part in Developmental Timing 1176 A Gene-Expression Oscillator Acts as a Clock to Control Vertebrate Segmentation 1177 Intracellular Developmental Programs Can Help Determine the Time-Course of a Cell’s Development 1179 Cells Rarely Count Cell Divisions to Time Their Development 1180 MicroRNAs Often Regulate Developmental Transitions 1180 Hormonal Signals Coordinate the Timing of Developmental Transitions 1182 Environmental Cues Determine the Time of Flowering 1182 Summary 1184 Morphogenesis 1184 Cell Migration Is Guided by Cues in the Cell’s Environment 1185 The Distribution of Migrant Cells Depends on Survival Factors 1186 Changing Patterns of Cell Adhesion Molecules Force Cells Into New Arrangements 1187 Repulsive Interactions Help Maintain Tissue Boundaries 1188 Groups of Similar Cells Can Perform Dramatic Collective Rearrangements 1188 Planar Cell Polarity Helps Orient Cell Structure and Movement in Developing Epithelia 1189 Interactions Between an Epithelium and Mesenchyme Generate Branching Tubular Structures 1190 An Epithelium Can Bend During Development to Form a Tube or Vesicle 1192 Summary 1193

GROWTH 1193 The Proliferation, Death, and Size of Cells Determine Organism Size 1194 Animals and Organs Can Assess and Regulate Total Cell Mass 1194 Extracellular Signals Stimulate or Inhibit Growth 1196 Summary 1197

NEURAL DEVELOPMENT 1198 Neurons Are Assigned Different Characters According to the Time and Place of Their Birth 1199 The Growth Cone Pilots Axons Along Specific Routes Toward Their Targets 1201 A Variety of Extracellular Cues Guide Axons to their Targets 1202 The Formation of Orderly Neural Maps Depends on Neuronal Specificity 1204 Both Dendrites and Axonal Branches From the Same Neuron Avoid One Another 1206 Target Tissues Release Neurotrophic Factors That Control Nerve Cell Growth and Survival 1208 Formation of Synapses Depends on Two-Way Communication Between Neurons and Their Target Cells 1209 Synaptic Pruning Depends on Electrical Activity and Synaptic Signaling 1211 Neurons That Fire Together Wire Together 1211 Summary 1213 Problems 1213 References 1215 Chapter 22 Stem Cells and Tissue Renewal 1217 Stem Cells and Renewal in Epithelial Tissues 1217 The Lining of the Small Intestine Is Continually Renewed Through Cell Proliferation in the Crypts 1218 Stem Cells of the Small Intestine Lie at or Near the Base of Each Crypt 1219 The Two Daughters of a Stem Cell Face a Choice 1219 Wnt Signaling Maintains the Gut Stem-Cell Compartment 1220 Stem Cells at the Crypt Base Are Multipotent, Giving Rise to the Full Range of Differentiated Intestinal Cell Types 1220 The Two Daughters of a Stem Cell Do Not Always Have to Become Different 1222 Paneth Cells Create the Stem-Cell Niche 1222 A Single Lgr5-expressing Cell in Culture Can Generate an Entire Organized Crypt-Villus System 1223 Ephrin–Eph Signaling Drives Segregation of the Different Gut Cell Types 1224 Notch Signaling Controls Gut Cell Diversification and Helps Maintain the Stem-Cell State 1224 The Epidermal Stem-Cell System Maintains a Self-Renewing Waterproof Barrier 1225 Tissue Renewal That Does Not Depend on Stem Cells: Insulin￾Secreting Cells in the Pancreas and Hepatocytes in the Liver 1226 Some Tissues Lack Stem Cells and Are Not Renewable 1227 Summary 1227 Fibroblasts and Their Transformations: the Connective-Tissue Cell Family 1228 Fibroblasts Change Their Character in Response to Chemical and Physical Signals 1228 Osteoblasts Make Bone Matrix 1229 Bone Is Continually Remodeled by the Cells Within It 1230 Osteoclasts Are Controlled by Signals From Osteoblasts 1232 Summary 1232 Genesis and Regeneration of Skeletal Muscle 1232 Myoblasts Fuse to Form New Skeletal Muscle Fibers 1233 Some Myoblasts Persist as Quiescent Stem Cells in the Adult 1234 Summary 1235 Blood Vessels, Lymphatics, and Endothelial Cells 1235 Endothelial Cells Line All Blood Vessels and Lymphatics 1235 Endothelial Tip Cells Pioneer Angiogenesis 1236 Tissues Requiring a Blood Supply Release VEGF 1237 Signals from Endothelial Cells Control Recruitment of Pericytes and Smooth Muscle Cells to Form the Vessel Wall 1238 Summary 1238 A Hierarchical Stem-Cell System: Blood Cell Formation 1239 Red Blood Cells Are All Alike; White Blood Cells Can Be Grouped in Three Main Classes 1239 The Production of Each Type of Blood Cell in the Bone Marrow Is Individually Controlled 1240 Bone Marrow Contains Multipotent Hematopoietic Stem Cells, Able to Give Rise to All Classes of Blood Cells 1242 Commitment Is a Stepwise Process 1243 Divisions of Committed Progenitor Cells Amplify the Number of Specialized Blood Cells 1243 Stem Cells Depend on Contact Signals From Stromal Cells 1244 Factors That Regulate Hematopoiesis Can Be Analyzed in Culture 1244 Erythropoiesis Depends on the Hormone Erythropoietin 1244 Multiple CSFs Influence Neutrophil and Macrophage Production 1245 The Behavior of a Hematopoietic Cell Depends Partly on Chance 1245 Regulation of Cell Survival Is as Important as Regulation of Cell Proliferation 1246 Summary 1247 Regeneration and Repair 1247 Planarian Worms Contain Stem Cells That Can Regenerate a Whole New Body 1247 Some Vertebrates Can Regenerate Entire Organs 1248 Stem Cells Can Be Used Artificially to Replace Cells That Are Diseased or Lost: Therapy for Blood and Epidermis 1249 Neural Stem Cells Can Be Manipulated in Culture and Used to Repopulate the Central Nervous System 1250 Summary 1251 Cell Reprogramming and Pluripotent Stem Cells 1251 Nuclei Can Be Reprogrammed by Transplantation into Foreign Cytoplasm 1252 Reprogramming of a Transplanted Nucleus Involves Drastic Epigenetic Changes 1252 Embryonic Stem (ES) Cells Can Generate Any Part of the Body 1253 A Core Set of Transcription Regulators Defines and Maintains the ES Cell State 1254 Fibroblasts Can Be Reprogrammed to Create Induced Pluripotent Stem Cells (iPS Cells) 1254 Reprogramming Involves a Massive Upheaval of the Gene Control System 1255 An Experimental Manipulation of Factors that Modify Chromatin Can Increase Reprogramming Efficiencies 1256 ES and iPS Cells Can Be Guided to Generate Specific Adult Cell Types and Even Whole Organs 1256xxxiv Cells of One Specialized Type Can Be Forced to Transdifferentiate Directly Into Another 1258 ES and iPS Cells Are Useful for Drug Discovery and Analysis of Disease 1258 Summary 1260 Problems 1260 References 1262

Chapter 23 Pathogens and Infection 1263

INTRODUCTION TO PATHOGENS AND THE HUMAN MICROBIOTA 1263 The Human Microbiota Is a Complex Ecological System That Is Important for Our Development and Health 1264 Pathogens Interact with Their Hosts in Different Ways 1264 Pathogens Can Contribute to Cancer, Cardiovascular Disease, and Other Chronic Illnesses 1265 Pathogens Can Be Viruses, Bacteria, or Eukaryotes 1266 Bacteria Are Diverse and Occupy a Remarkable Variety of Ecological Niches 1267 Bacterial Pathogens Carry Specialized Virulence Genes 1268 Bacterial Virulence Genes Encode Effector Proteins and Secretion Systems to Deliver Effector Proteins to Host Cells 1269 Fungal and Protozoan Parasites Have Complex Life Cycles Involving Multiple Forms 1271 All Aspects of Viral Propagation Depend on Host Cell Machinery 1273 Summary 1275 CELL BIOLOGY OF INFECTION 1276 Pathogens Overcome Epithelial Barriers to Infect the Host 1276 Pathogens That Colonize an Epithelium Must Overcome Its Protective Mechanisms 1276 Extracellular Pathogens Disturb Host Cells Without Entering Them 1277 Intracellular Pathogens Have Mechanisms for Both Entering and Leaving Host Cells 1278 Viruses Bind to Virus Receptors at the Host Cell Surface 1279 Viruses Enter Host Cells by Membrane Fusion, Pore Formation, or Membrane Disruption 1280 Bacteria Enter Host Cells by Phagocytosis 1281 Intracellular Eukaryotic Parasites Actively Invade Host Cells 1282 Some Intracellular Pathogens Escape from the Phagosome into the Cytosol 1284 Many Pathogens Alter Membrane Traffic in the Host Cell to Survive and Replicate 1284 Viruses and Bacteria Use the Host-Cell Cytoskeleton for Intracellular Movement 1286 Viruses Can Take Over the Metabolism of the Host Cell 1288 Pathogens Can Evolve Rapidly by Antigenic Variation 1289 Error-Prone Replication Dominates Viral Evolution 1291 Drug-Resistant Pathogens Are a Growing Problem 1291 Summary 1294 Problems 1294 References 1296 Chapter 24 The Innate and Adaptive Immune Systems 1297

THE INNATE IMMUNE SYSTEM 1298 Epithelial Surfaces Serve as Barriers to Infection 1298 Pattern Recognition Receptors (PRRs) Recognize Conserved Features of Pathogens 1298 There Are Multiple Classes of PRRs 1299 Activated PRRs Trigger an Inflammatory Response at Sites of Infection 1300 Phagocytic Cells Seek, Engulf, and Destroy Pathogens 1301 Complement Activation Targets Pathogens for Phagocytosis or Lysis 1302 Virus-Infected Cells Take Drastic Measures to Prevent Viral Replication 1303 Natural Killer Cells Induce Virus-Infected Cells to Kill Themselves 1304 Dendritic Cells Provide the Link Between the Innate and Adaptive Immune Systems 1305 Summary 1305

OVERVIEW OF THE ADAPTIVE IMMUNE SYSTEM 1307 B Cells Develop in the Bone Marrow, T Cells in the Thymus 1308 Immunological Memory Depends On Both Clonal Expansion and Lymphocyte Differentiation 1309 Lymphocytes Continuously Recirculate Through Peripheral Lymphoid Organs 1311 Immunological Self-Tolerance Ensures That B and T Cells Do Not Attack Normal Host Cells and Molecules 1313 Summary 1315

B CELLS AND IMMUNOGLOBULINS 1315 B Cells Make Immunoglobulins (Igs) as Both Cell-Surface Antigen Receptors and Secreted Antibodies 1315 Mammals Make Five Classes of Igs 1316 Ig Light and Heavy Chains Consist of Constant and Variable Regions 1318 Ig Genes Are Assembled From Separate Gene Segments During B Cell Development 1319 Antigen-Driven Somatic Hypermutation Fine-Tunes Antibody Responses 1321 B Cells Can Switch the Class of Ig They Make 1322 Summary 1323

T CELLS AND MHC PROTEINS 1324 T Cell Receptors (TCRs) Are Ig-like Heterodimers 1325 Activated Dendritic Cells Activate Naïve T Cells 1326 T Cells Recognize Foreign Peptides Bound to MHC Proteins 1326 MHC Proteins Are the Most Polymorphic Human Proteins Known 1330 CD4 and CD8 Co-receptors on T Cells Bind to Invariant Parts of MHC Proteins 1331 Developing Thymocytes Undergo Negative and Positive Selection 1332 Cytotoxic T Cells Induce Infected Target Cells to Kill Themselves 1333 Effector Helper T Cells Help Activate Other Cells of the Innate and Adaptive Immune Systems 1335 Naïve Helper T Cells Can Differentiate Into Different Types of Effector T Cells 1335 Both T and B Cells Require Multiple Extracellular Signals For Activation 1336 Many Cell-Surface Proteins Belong to the Ig Superfamily 1338 Summary 1339 Problems 1340 References 1342

 

 

chapter 20 CANCER          

 Cancer  as a microevolutionary process

CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO

CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE1092

Cancer cells break the most basic rules of cell behavior by which multicellular organisms are built and maintained, and they exploit every kind of opportunity to do so. These transgressions help to reveal what the normal rules are and how they are enforced. As a result, cancer research helps to illuminate the fundamentals of cell biology—especially cell signaling (Chapter 15), the cell cycle and cell growth (Chapter 17), programmed cell death (apoptosis, Chapter 18), and the control of tissue architecture (Chapters 19 and 22). Of course, with a deeper understanding of these normal processes, we also gain a deeper under￾standing of the disease and better tools to treat it. In this chapter, we first consider what cancer is and describe the natural history of the disease from a cellular standpoint. We then discuss the molecu￾lar changes that make a cell cancerous. And we end the chapter by considering how our enhanced understanding of the molecular basis of cancer is leading to improved methods for its prevention and treatment.

CANCER AS A MICROEVOLUTIONARY PROCESS

The body of an animal operates as a society or ecosystem, whose individual mem￾bers are cells that reproduce by cell division and organize themselves into collabo￾rative assemblies called tissues. This ecosystem is very peculiar, however, because self-sacrifice—as opposed to survival of the fittest—is the rule. Ultimately, all of the somatic cell lineages in animals are committed to die: they leave no progeny and instead dedicate their existence to the support of the germ cells, which alone have a chance of continued survival (discussed in Chapter 21). There is no mys￾tery in this, for the body is a clone derived from a fertilized egg, and the genome of the somatic cells is the same as that of the germ-cell lineage that gives rise to sperm or eggs. By their self-sacrifice for the sake of the germ cells, the somatic cells help to propagate copies of their own genes. Thus, unlike free-living cells such as bacteria, which compete to survive, the cells of a multicellular organism are committed to collaboration. To coordinate their behavior, the cells send, receive, and interpret an elaborate set of extracel￾lular signals that serve as social controls, directing cells how to act (discussed in Chapter 15). As a result, each cell behaves in a socially responsible manner—rest￾ing, growing, dividing, differentiating, or dying—as needed for the good of the organism. Molecular disturbances that upset this harmony mean trouble for a multicel￾lular society. In a human body with more than 1014 cells, billions of cells experi￾ence mutations every day, potentially disrupting the social controls. Most danger￾ously, a mutation may give one cell a selective advantage, allowing it to grow and divide slightly more vigorously and survive more readily than its neighbors and in this way to become a founder of a growing mutant clone. A mutation that pro￾motes such selfish behavior by individual members of the cooperative can jeop￾ardize the future of the whole enterprise. Over time, repeated rounds of mutation, competition, and natural selection operating within the population of somatic cells can cause matters to go from bad to worse. These are the basic ingredients of cancer: it is a disease in which an individual mutant clone of cells begins by…

Chapter 20: Cancer prospering at the expense of its neighbors. In the end—as the clone grows, evolves, and spreads—it can destroy the entire cellular society. In this section, we discuss the development of cancer as a microevolutionary process that takes place within the course of a human life-span in a subpopulation of cells in the body. But the process depends on the same principles of mutation and natural selection that have driven the evolution of living organisms on Earth for billions of years. Cancer Cells Bypass Normal Proliferation Controls and Colonize Other Tissues Cancer cells are defined by two heritable properties: (1) they reproduce in defi￾ance of the normal restraints on cell growth and division, and (2) they invade and colonize territories normally reserved for other cells. It is the combination of these properties that makes cancers particularly dangerous. An abnormal cell that grows (increases in mass) and proliferates (divides) out of control will give rise to a tumor, or neoplasm—literally, a new growth. As long as the neoplastic cells have not yet become invasive, however, the tumor is said to be benign. For most types of such neoplasms, removing or destroying the mass locally usually achieves a complete cure. A tumor is considered a true cancer if it is malignant; that is, when its cells have acquired the ability to invade surrounding tissue. Invasiveness is an essential characteristic of cancer cells. It allows them to break loose, enter blood or lymphatic vessels, and form secondary tumors called metastases at other sites in the body (Figure 20–1). In general, the more widely a cancer spreads, the harder it becomes to eradicate. It is generally metastases that kill the cancer patient. Cancers are traditionally classified according to the tissue and cell type from which they arise. Carcinomas are cancers arising from epithelial cells, and they are by far the most common cancers in humans. They account for about 80% of cases, perhaps because most of the cell proliferation in adults occurs in epithe￾lia. In addition, epithelial tissues are the most likely to be exposed to the various forms of physical and chemical damage that favor the development of cancer. Sarcomas arise from connective tissue or muscle cells. Cancers that do not fit in either of these two broad categories include the various leukemias and lympho￾mas, derived from white blood cells and their precursors (hemopoietic cells), as well as cancers derived from cells of the nervous system. Figure 20–2 shows the types of cancers that are common in the United States, together with their inci￾dence and death rates. Each broad category has many subdivisions according to the specific cell type, the location in the body, and the microscopic appearance of the tumor. In parallel with the set of names for malignant tumors, there is a related set of names for benign tumors: an adenoma, for example, is a benign epithelial tumor with a glandular organization; the corresponding type of malignant tumor is an adenocarcinoma (Figure 20–3). Similarly, a chondroma and a chondrosarcoma are, respectively, benign and malignant tumors of cartilage. Most cancers have characteristics that reflect their origin. Thus, for example, the cells of a basal-cell carcinoma, derived from a keratinocyte stem cell in the skin, generally continue to synthesize cytokeratin intermediate filaments, whereas the cells of a melanoma, derived from a pigment cell in the skin, will often (but not always) continue to make pigment granules. Cancers originating from different cell types are, in general, very different diseases. Basal-cell carcinomas of the skin, for example, are only locally invasive and rarely metastasize, whereas melanomas can become much more malignant and often form metastases. Basal-cell carcino￾mas are readily cured by surgery or local irradiation, whereas malignant melano￾mas, once they have metastasized widely, are usually fatal. Later, we shall see that there is also a different way to classify cancers, one that cuts across the traditional classification by site of origin: we can classify them in terms of the mutations that make the tumor cells cancerous. The final section of the chapter will show how this information can be crucial to the design and choice of treatments. MBoC6 m20.01/20.01 Figure 20–1 Metastasis. Malignant tumors typically give rise to metastases, making the cancer hard to eradicate. Shown in this fusion image is a whole-body scan of a patient with metastatic non-Hodgkin’s lymphoma (NHL). The background image of the body’s tissues was obtained by CT (computed x-ray tomography) scanning. Overlaid on this image, a PET (positron emission tomography) scan reveals the tumor tissue (yellow), detected by its unusually high uptake of radioactively labeled fluorodeoxyglucose (FDG). High FDG uptake occurs in cells with unusually active glucose uptake and metabolism, which is a characteristic of cancer cells (see Figure 20–12). The yellow spots in the abdominal region reveal multiple metastases. (Courtesy of S. Gambhir.)1093 Most Cancers Derive from a Single Abnormal Cell Even when a cancer has metastasized, we can usually trace its origins to a single primary tumor, arising in a specific organ. The primary tumor is thought to derive by cell division from a single cell that initially experienced some heritable change. Subsequently, additional changes accumulate in some of the descendants of this cell, allowing them to outgrow, out-divide, and often outlive their neighbors. By the time it is first detected, a typical human cancer will have been developing for many years and will already contain a billion cancer cells or more (Figure 20–4). Tumors will usually also contain a variety of other cell types; for example, fibro￾blasts will be present in the supporting connective tissue associated with a car￾cinoma, in addition to inflammatory and vascular endothelial cells. How can we be sure that the cancer cells are the clonal descendants of a single abnormal cell? One way of proving clonal origin is through molecular analysis of the chro￾mosomes in tumor cells. In almost all patients with chronic myelogenous leuke￾mia (CML), for example, we can distinguish the leukemic white blood cells from the patient’s normal cells by a specific chromosomal abnormality: the so-called Philadelphia chromosome, created by a translocation between the long arms of chromosomes 9 and 22 (Figure 20–5). When the DNA at the site of translocation is cloned and sequenced, it is found that the site of breakage and rejoining of the translocated fragments is identical in all the leukemic cells in any given patient, but that this site differs slightly (by a few hundred or thousand base pairs) from one patient to another. This is the expected result if, and only if, the cancer in each patient arises from a unique accident occurring in a single cell.

this particular translocation promotes the development of CML by creating a novel hybrid gene encoding a protein that promotes cell proliferation. Many other lines of evidence, from a variety of cancers, point to the same con￾clusion: most cancers originate from a single aberrant cell. Cancer Cells Contain Somatic Mutations If a single abnormal cell is to give rise to a tumor, it must pass on its abnormal￾ity to its progeny: the aberration has to be heritable. Thus, the development of a clone of cancer cells depends on genetic changes. The tumor cells contain somatic mutations: they have one or more shared detectable abnormalities in their DNA sequence that distinguish them from the normal cells surrounding the tumor, as in the example of CML just described. (The mutations are called somatic because they occur in the soma, or body cells, not in the germ line). Cancers are also driven by epigenetic changes—persistent, heritable changes in gene expres￾sion that result from modifications of chromatin structure without alteration of the cell’s DNA sequence. But somatic mutations that alter DNA sequence appear to be a fundamental and universal feature, and cancer is in this sense a genetic disease. Factors that cause genetic changes tend to provoke the development of can￾cer. Thus, carcinogenesis (the generation of cancer) can be linked to mutagenesis (the production of a change in the DNA sequence). This correlation is particularly clear for two classes of external agents: (1) chemical carcinogens (which typically cause simple local changes in the nucleotide sequence), and (2) radiation such as x-rays (which typically cause chromosome breaks and translocations) or ultravio￾let (UV) light (which causes specific DNA base alterations). As would be expected, people who have inherited a genetic defect in one of several DNA repair mechanisms, causing their cells to accumulate mutations at an elevated rate, run a heightened risk of cancer. Those with the disease xeroderma pigmentosum, for example, have defects in the system that repairs DNA damage induced by UV light, and they have a greatly increased incidence of skin cancers. A Single Mutation Is Not Enough to Change a Normal Cell into a Cancer Cell An estimated 1016 cell divisions occur in a normal human body in the course of a typical lifetime; in a mouse, with its smaller number of cells and its shorter life￾span, the number is about 1012. Even in an environment that is free of mutagens, mutations would occur spontaneously at an estimated rate of about 10–6 mutations per gene per cell division—a value set by fundamental limitations on the accuracy of DNA replication and repair (see pp. 237–238). Thus, in a typical lifetime, every single gene is likely to have undergone mutation on about 1010 separate occasions in a human, or on about 106 occasions in a mouse. Among the resulting mutant cells, we might expect a large number that have sustained deleterious mutations in genes that regulate cell growth and division, causing the cells to disobey the normal restrictions on cell proliferation. From this point of view, the problem of cancer seems to be not why it occurs, but why it occurs so infrequently. Clearly, if a mutation in a single gene were enough to convert a typical healthy cell into a cancer cell, we would not be viable organisms. Many lines of evidence indicate that the development of a cancer typically requires that a substantial number of independent, rare genetic and epigenetic accidents occur in the lin￾eage that emanates from a single cell. One such indication comes from epidemi￾ological studies of the incidence of cancer as a function of age (Figure 20–6). If a 0.1 1 10 100 1 10 20 30 40 death of patient (1012 cells) tumor first palpable (109 cells) tumor first visible on x-ray (108 cells) tumor cell population doublings diameter of tumor (mm) MBoC6 m20.04/20.04 9 22 9q+ 22q_ MBoC6 m20.05/20.05 Philadelphia chromosome Figure 20–4 The growth of a typical human tumor, such as a tumor of the breast. The diameter of the tumor is plotted on a logarithmic scale. Years may elapse before the tumor becomes noticeable. The doubling time of a typical breast tumor, for example, is about 100 days. However, particularly virulent tumors may grow much more rapidly. Figure 20–5 The translocation between chromosomes 9 and 22 responsible for chronic myelogenous leukemia. The normal structures of chromosomes 9 and 22 are shown at the left. When a translocation occurs between them at the indicated site, the result is the abnormal pair at the right. The smaller of the two resulting abnormal chromosomes (22q–) is called the Philadelphia chromosome, after the city where the abnormality was first recorded.1095 single mutation were responsible for cancer, occurring with a fixed probability per year, the chance of developing cancer in any given year of life should be indepen￾dent of age. In fact, for most types of cancer, the incidence rises steeply with age— as would be expected if cancer is caused by a progressive, random accumulation of a set of mutations in a single lineage of cells. As discussed later, these indirect arguments have now been confirmed by sys￾tematically sequencing the genomes of the tumor cells from individual cancer patients and cataloging the mutations that they contain. Cancers Develop Gradually from Increasingly Aberrant Cells For those cancers known to have a specific external cause, the disease does not usually become apparent until long after exposure to the causal agent. The incidence of lung cancer, for example, does not begin to rise steeply until after decades of heavy smoking (Figure 20–7). Similarly, the incidence of leukemias in Hiroshima and Nagasaki did not show a marked rise until about 5 years after the explosion of the atomic bombs, and industrial workers exposed for a limited period to chemical carcinogens do not usually develop the cancers characteristic of their occupation until 10, 20, or even more years after the exposure. During this long incubation period, the prospective cancer cells undergo a succession of changes, and the same presumably applies to cancers where the initial genetic lesion has no such obvious external cause. The concept that the development of a cancer requires a gradual accumulation of mutations in a number of different genes helps to explain the well-known phe￾nomenon of tumor progression, whereby an initial mild disorder of cell behavior evolves gradually into a full-blown cancer. Chronic myelogenous leukemia again provides a clear example. It begins as a disorder characterized by a nonlethal overproduction of white blood cells and continues in this form for several years before changing into a much more rapidly progressing illness that usually ends in death within a few months. In the early chronic phase, the leukemic cells are distinguished mainly by the chromosomal translocation (the Philadelphia chro￾mosome) mentioned previously, although there may well be other, less visible CANCER AS A MICROEVOLUTIONARY PROCESS 0 20 40 60 80 100 120 140 160 180 10 20 30 40 50 60 70 80 incidence rate per 100,000 age (years) MBoC6 m20.07/20.06 Figure 20–6 Cancer incidence as a function of age. The number of newly diagnosed cases of colon cancer in women in England and Wales in 1 year is plotted as a function of age at diagnosis, relative to the total number of individuals in each age group. The incidence of cancer rises steeply as a function of age. If only a single mutation were required to trigger the cancer and this mutation had an equal chance of occurring at any time, the incidence of this cancer would be the same at all ages. Analyses of this type suggest that the development of a solid tumor instead requires five to eight independent accidents (“hits”) that occur randomly over time. This calculation assumes that the mutation rate remains constant as a cancer evolves, where in fact it often increases (see p. 1097). (Data from C. Muir et al., Cancer Incidence in Five Continents, Vol. V. Lyon: International Agency for Research on Cancer, 1987.) cigarettes smoked per year (billions) lung cancer deaths per year (thousands) 6000 5000 4000 3000 2000 1000 1880 1920 1960 2000 0 500 1000 1500 2000 GLOBAL LUNG CANCER DEATHS CAUSED BY SMOKING (ESTIMATE) LUNG CANCERS UNRELATED TO TOBACCO GLOBAL CIGARETTE CONSUMPTION MB0C6 n20.400/20.07 Figure 20–7 Smoking and the onset of lung cancer. A major increase in cigarette smoking (red line) has caused a dramatic rise in lung cancer deaths (green line), with a lag time of about 35 years. Because global cigarette smoking peaked in 1990, global lung cancer deaths are expected to decline after a similar lag. (Data from R.N. Proctor, Nat. Rev. Cancer 1:82–86, 2001).1096 Chapter 20: Cancer genetic or epigenetic changes. In the subsequent acute phase, cells that show not only the translocation but also several other chromosomal abnormalities over￾run the hemopoietic (blood-forming) system. It appears that cells from the initial mutant clone have undergone further mutations that make them proliferate even more vigorously, so that they come to outnumber both the normal blood cells and their ancestors with the primary chromosomal translocation. Carcinomas and other solid tumors evolve in a similar way (Figure 20–8). Although many such cancers in humans are not diagnosed until a relatively late stage, in some cases it is possible to observe the earlier steps and, as we shall see later, to relate them to specific genetic changes Tumor Progression Involves Successive Rounds of Random Inherited Change Followed by Natural Selection From all the evidence, therefore, it seems that cancers arise by a process in which an initial population of slightly abnormal cells—descendants of a single abnor￾mal ancestor—evolve from bad to worse through successive cycles of random inherited change followed by natural selection. Correspondingly, tumors grow in fits and starts, as additional advantageous inherited changes arise and the cells bearing them flourish. Tumor progression involves a large element of chance and usually takes many years, which may be why the majority of us will die of causes other than cancer. At each stage of progression, some individual cell acquires an additional muta￾tion or epigenetic change that gives it a selective advantage over its neighbors, making it better able to thrive in its environment—an environment that, inside a tumor, may be harsh, with low levels of oxygen, scarce nutrients, and the nat￾ural barriers to growth presented by the surrounding normal tissues. The larger the number of tumor cells, the higher the chance that at least one of them will undergo a change that favors it over its neighbors. Thus, as the tumor grows, pro￾gression accelerates. The offspring of the best-adapted cells continue to divide, eventually producing the dominant clones in the developing lesion (Figure 20–9). Just as in the evolution of plants and animals, a kind of speciation often occurs: the original cancer cell lineage can diversify to give many genetically different vig￾orous subclones of cells. These may coexist in the same mass of tumor tissue; or they may migrate and colonize separate environments suited to their individual quirks, where they settle, thrive, and progress as independently evolving metas￾tases. As new mutations arise within each tumor mass, different subclones may gain an advantage and come to predominate, only to be overtaken by others or outgrown by their own sub-subclones. The increasing genetic diversity as a cancer progresses is one of the chief factors that make cures difficult. 50 µm NORMAL EPITHELIUM LOW-GRADE INTRAEPITHELIAL NEOPLASIA HIGH-GRADE INTRAEPITHELIAL NEOPLASIA INVASIVE CARCINOMA (A) (B) (C) (D) MBoC6 m20.09/20.08 connective tissue epithelium Figure 20–8 Stages of progression in the development of cancer of the epithelium of the uterine cervix. Pathologists use standardized terminology to classify the types of disorders they see, so as to guide the choice of treatment. (A) In a stratified squamous epithelium, dividing cells are confined to the basal layer. (B) In this low-grade intraepithelial neoplasia (right half of image), dividing cells can be found throughout the lower third of the epithelium; the superficial cells are still flattened and show signs of differentiation, but this is incomplete. (C) In high-grade intraepithelial neoplasia, cells in all the epithelial layers are proliferating and exhibit defective differentiation. (D) True malignancy begins when the cells move through or destroy the basal lamina that underlies the basal layer of epithelium and invade the underlying connective tissue. (Photographs courtesy of Andrew J. Connolly.)1097 Human Cancer Cells Are Genetically Unstable Most human cancer cells accumulate genetic changes at an abnormally rapid rate and are said to be genetically unstable. The extent of this instability and its molecular origins differ from cancer to cancer and from patient to patient, as we shall discuss in a later section. The basic phenomenon was evident even before modern molecular analyses. For example, the cells of many cancers show grossly abnormal sets of chromosomes, with duplications, deletions, and translocations that are visible at mitosis (Figure 20–10). When the cells are maintained in cul￾ture, these patterns of chromosomal disruption can often be seen to evolve rap￾idly and in a seemingly haphazard way. And for many years, pathologists have used an abnormal appearance of the cell nucleus to identify and classify cancer cells in tumor biopsies; in particular, cancer cells can contain an unusually large amount of heterochromatin—a condensed form of interphase chromatin that silences genes (see pp. 194–195). This suggested that epigenetic changes of chro￾matin structure can also contribute to the cancer cell phenotype, as recently con￾firmed by molecular analysis. The genetic instability observed in cancer cells can arise from defects in the ability to repair DNA damage or to correct replication errors of various kinds. These alterations lead to changes in DNA sequence and produce rearrangements such as DNA translocations and duplications. Also common are defects in chro￾mosome segregation during mitosis, which provide another possible source of chromosome instability and changes in karyotype. From an evolutionary perspective, none of this should be a surprise: anything that increases the probability of random changes in gene function heritable from one cell generation to the next—and that is not too deleterious—is likely to speed the evolution of a clone of cells toward malignancy, thereby causing this property to be selected for during tumor progression. CANCER AS A MICROEVOLUTIONARY PROCESS accidental production of mutant cell epithelial cells growing on basal lamina CELL PROLIFERATION CELL PROLIFERATION DANGEROUS CELL PROLIFERATION cell with 3 mutations cell with 2 mutations MBoC6 m20.11/20.09 Figure 20–9 Clonal evolution. In this schematic diagram, a tumor develops through repeated rounds of mutation and proliferation, giving rise eventually to a clone of fully malignant cancer cells. At each step, a single cell undergoes a mutation that either enhances cell proliferation or decreases cell death, so that its progeny become the dominant clone in the tumor. Proliferation of each clone hastens the occurrence of the next step of tumor progression by increasing the size of the cell population that is at risk of undergoing an additional mutation. The final step depicted here is invasion through the basement membrane, an initial step in metastasis. In reality, there are more than the three steps shown here, and a combination of genetic and epigenetic changes are involved. Not shown here is the fact that, over time, a variety of competing subclones will often arise in a tumor. As we will discuss later, this heterogeneity complicates cancer therapies (see Figure 20–30). (A) (B) MBoC6 m20.13/20.10 Figure 20–10 Chromosomes from a breast tumor displaying abnormalities in structure and number. Chromosomes were prepared from a breast tumor cell in metaphase, spread on a glass slide, and stained with (A) a general DNA stain or (B) a combination of fluorescently labeled DNA molecules that color each normal human chromosome differently (see Figure 4–10). The staining (displayed in false color) shows multiple translocations, including a doubly translocated chromosome (white arrow) that is made up of two pieces of chromosome 8 (green-brown) and a piece of chromosome 17 (purple). The karyotype also contains 48 chromosomes, instead of the normal 46. (Courtesy of Joanne Davidson and Paul Edwards.)1098 Chapter 20: Cancer Cancer Cells Display an Altered Control of Growth Mutability and large cell population numbers create the opportunities for muta￾tions to occur, but the driving force for development of a cancer has to come from some sort of selective advantage possessed by the mutant cells. Most obviously, a mutation or epigenetic change can confer such an advantage by increasing the rate at which a clone of cells proliferates or by enabling it to continue proliferating when normal cells would stop. Cancer cells that can be grown in culture, or cul￾tured cells artificially engineered to contain the types of mutations encountered in cancers, typically show a transformed phenotype. They are abnormal in their shape, their motility, their responses to growth factors in the culture medium, and, most characteristically, in the way they react to contact with the substratum and with one another. Normal cells will not divide unless they are attached to the substratum; transformed cells will often divide even if held in suspension. Normal cells become inhibited from moving and dividing when the culture reaches con￾fluence (where the cells are touching one another); transformed cells continue moving and dividing even after confluence, and so pile up in layer upon layer in the culture dish (Figure 20–11). In addition, transformed cells no longer require all of the positive signals from their surroundings that normal cells require. Their behavior in culture gives a hint of the ways in which cancer cells may misbehave in their natural environment, embedded in a tissue. But cancer cells in the body show other peculiarities that mark them out from normal cells, beyond those just described. Cancer Cells Have an Altered Sugar Metabolism Given sufficient oxygen, normal adult tissue cells will generally fully oxidize almost all the carbon in the glucose they take up to CO2, which is lost from the body as a waste product. A growing tumor needs nutrients in abundance to pro￾vide the building blocks to make new macromolecules. Correspondingly, most tumors have a metabolism more similar to that of a growing embryo than to that of normal adult tissue. Tumor cells consume glucose avidly, importing it from the blood at a rate that can be as much as 100 times higher than neighboring nor￾mal cells. Moreover, only a small fraction of this imported glucose is used for production of ATP by oxidative phosphorylation. Instead, a great deal of lactate is produced, and many of the remaining carbon atoms derived from glucose are diverted for use as raw materials for synthesis of the proteins, nucleic acids, and lipids required for tumor growth (Figure 20–12). This tendency of tumor cells to de-emphasize oxidative phosphorylation even when oxygen is plentiful, while at the same time taking up large quantities of glucose, can be shown to promote cancer cell growth and is called the Warburg CELL TRANSFORMATION CELL DIVISION foci of uninhibited transformed cells transformed cells lose contact inhibition contact-inhibited monolayer of normal cells in tissue-culture dish (A) (B) (C) MBoC6 m20.29/20.11 Figure 20–11 Loss of contact inhibition by cancer cells in cell culture. Most normal cells stop proliferating once they have carpeted the dish with a single layer of cells: proliferation seems to depend on contact with the dish, and to be inhibited by contacts with other cells—a phenomenon known as “contact inhibition.” Cancer cells, in contrast, usually disregard these restraints and continue to grow, so that they pile up on top of one another, as shown. (A) Schematic drawing. (B and C) Light micrographs of normal (B) and transformed (C) fibroblasts. (B and C, courtesy of Lan Bo Chen.)1099 effect—so named because Otto Warburg first noticed the phenomenon in the early twentieth century. It is this abnormally high glucose uptake that allows tumors to be selectively imaged in whole-body scans (see Figure 20–1), thereby providing a way to monitor cancer progression and responses to treatment. Cancer Cells Have an Abnormal Ability to Survive Stress and DNA Damage In a large multicellular organism, there are powerful safety mechanisms that guard against the trouble that can be caused by damaged and deranged cells. For example, internal disorder gives rise to danger signals in the faulty cell, activat￾ing protective devices that can eventually lead to apoptosis (see Chapter 18). To survive, cancer cells require additional mutations to elude or break through these defenses against cellular misbehavior. Cancer cells are found to contain mutations that drive the cell into an abnormal state, where metabolic processes may be unbalanced and essential cell compo￾nents may be produced in ill-matched proportions. States of this type, where the cell’s homeostatic mechanisms are inadequate to cope with an imposed distur￾bance, are loosely referred to as states of cell stress. As one example, chromosome breakage and other forms of DNA damage are commonly observed during the development of cancer, reflecting the genetic instability that cancer cells display. Thus, to survive and divide without limit, a prospective cancer cell must accumu￾late mutations that disable the normal safety mechanisms that would otherwise induce a cell that is stressed, in this or in other ways, to commit suicide. In fact, one of the most important properties of many types of cancer cells is that they fail to undergo apoptosis when a normal cell would do so (Figure 20–13). While cancer cells tend to avoid apoptosis, this does not mean that they rarely die. On the contrary, in the interior of a large solid tumor, cell death often occurs on a massive scale: living conditions are difficult, with severe competition among the cancer cells for oxygen and nutrients. Many die, but typically much more by necrosis than by apoptosis (Figure 20–14). The tumor grows because the cell birth rate outpaces the cell death rate, but often by only a small margin. For this reason, the time that a tumor takes to double in size can be far longer than the cell-cycle time of the tumor cells. Human Cancer Cells Escape a Built-in Limit to Cell Proliferation Many normal human cells have a built-in limit to the number of times they can divide when stimulated to proliferate in culture: they permanently stop dividing CANCER AS A MICROEVOLUTIONARY PROCESS glucose differentiated tissue proliferative tissue tumor oxidative phosphorylation NET PRODUCTS: ENERGY, CO2, H2O (A) pyruvate lactate GLYCOLYSIS glucose oxidative phosphorylation NET PRODUCTS: ENERGY, BUILDING BLOCKS, NADPH (B) pyruvate lactate GLYCOLYSIS building blocks MBoC6 n20.201/20.12 10% 5% 85% Figure 20–12 The Warburg effect in tumor cells reflects a dramatic change in glucose uptake and sugar metabolism. (A) Cells that are not proliferating will normally oxidize nearly all of the glucose that they import from the blood to produce ATP through the oxidative phosphorylation that takes place in their mitochondria. Only when deprived of oxygen will these cells generate most of their ATP from glycolysis, converting the pyruvate produced to lactate in order to regenerate the NAD+ that they need to keep glycolysis going (see Figure 2–47). (B) Tumor cells, by contrast, will generally produce abundant lactate even in the presence of oxygen. This results from a greatly increased rate of glycolysis that is fed by a very large increase in the rate of glucose import. In this way, tumor cells resemble the rapidly proliferating cells in embryos (and during tissue repair), which likewise require for biosynthesis a large supply of the small-molecule building blocks that can be produced from imported glucose (see also Figure 20–26).1100 Chapter 20: Cancer after a certain number of population doublings (25–50 for human fibroblasts, for example). This cell-division-counting mechanism is termed replicative cell senescence, and it generally depends on the progressive shortening of the telomeres at the ends of chromosomes, a process that eventually changes their structure (discussed in Chapter 17). As discussed in Chapter 5, the replication of telomere DNA during S phase depends on the enzyme telomerase, which main￾tains a special telomeric DNA sequence that promotes the formation of protein cap structures to protect chromosome ends. Because many proliferating human cells (stem cells being an exception) are deficient in telomerase, their telomeres shorten with every division, and their protective caps deteriorate, creating a DNA damage signal. Eventually, the altered chromosome ends can trigger a permanent cell-cycle arrest, causing a normal cell to die. Human cancer cells avoid replicative cell senescence in one of two ways. They can maintain the activity of telomerase as they proliferate, so that their telomeres do not shorten or become uncapped, or they can evolve an alternate mechanism based on homologous recombination (called ALT) for elongating their chromo￾some ends. Regardless of the strategy used, the result is that the cancer cells con￾tinue to proliferate under conditions when normal cells would stop. The Tumor Microenvironment Influences Cancer Development While the cancer cells in a tumor are the bearers of dangerous mutations and are often grossly abnormal, the other cells in the tumor—especially those of the supporting connective tissue, or stroma—are far from passive bystanders. The NORMAL CELL DIVISION NORMAL APOPTOSIS INCREASED CELL DIVISION NORMAL APOPTOSIS NORMAL CELL DIVISION DECREASED APOPTOSIS HOMEOSTASIS TUMOR TUMOR MBoC6 m20.14/20.13 Figure 20–13 Both increased cell division and decreased apoptosis can contribute to tumorigenesis. In normal tissues, apoptosis balances cell division to maintain homeostasis. During the development of cancer, either an increase in cell division or an inhibition of apoptosis can lead to the increased cell numbers important for tumorigenesis. The cells fated to undergo apoptosis are gray in this diagram. Both an increase in cell division and a decrease in apoptosis normally contribute to tumor growth. MBoC6 m20.18/20.14 2 mm Figure 20–14 Cross-section of a colon adenocarcinoma that has metastasized to the lung. This tissue slice shows well-differentiated colorectal cancer cells forming cohesive glands in the lung. The metastasis has central pink areas of necrosis where dying cancer cells have outgrown their blood supply. Such anoxic regions are common in the interior of large tumors. (Courtesy of Andrew J. Connolly.)1101 development of a tumor relies on a two-way communication between the tumor cells and the tumor stroma, just as the normal development of epithelial organs relies on communication between epithelial cells and mesenchymal cells (dis￾cussed in Chapter 22). The stroma provides a framework for the tumor. It is composed of normal con￾nective tissue containing fibroblasts and inflammatory white blood cells, as well as the endothelial cells that form blood and lymphatic vessels with their attendant pericytes and smooth muscle cells (Figure 20–15). As a carcinoma progresses, the cancer cells induce changes in the stroma by secreting signal proteins that alter the behavior of the stromal cells, as well as proteolytic enzymes that modify the extracellular matrix. The stromal cells in turn act back on the tumor cells, secret￾ing signal proteins that stimulate cancer cell growth and division as well as pro￾teases that further remodel the extracellular matrix. In these ways, the tumor and its stroma evolve together, like weeds and the ecosystem that they invade, and the tumor becomes dependent on its particular stromal cells. Experiments using mice indicate that the growth of some transplanted carcinomas depends on the tumor-associated fibroblasts and normal fibroblasts will not do. Such environ￾mental requirements help to protect us from cancer, as we discuss next in consid￾ering the critical phenomenon called metastasis. Cancer Cells Must Survive and Proliferate in a Foreign Environment Cancer cells generally need to spread and multiply at new sites in the body in order to kill us, through a process called metastasis. This is the most deadly—and least understood—aspect of cancer, being responsible for 90% of cancer-associ￾ated deaths. By spreading through the body, a cancer becomes almost impossi￾ble to eradicate by either surgery or local irradiation. Metastasis is itself a multi￾step process: the cancer cells first have to invade local tissues and vessels, move through the circulation, leave the vessels, and then establish new cellular colonies at distant sites (Figure 20–16). Each of these events is complex, and most of the molecular mechanisms involved are not yet clear. For a cancer cell to become dangerous, it must break free of constraints that keep normal cells in their proper places and prevent them from invading neigh￾boring tissues. Invasiveness is thus one of the defining properties of malignant tumors, which show a disorganized pattern of growth and ragged borders, with extensions into the surrounding tissue (see, for example, Figure 20–8). Although the underlying molecular changes are not well understood, invasiveness almost certainly requires a disruption of the adhesive mechanisms that normally keep cells tethered to their proper neighbors and to the extracellular matrix. For carci￾nomas, this change resembles the epithelial–mesenchymal transition (EMT) that occurs in some epithelial tissues during normal development (see p. 1042). The next step in metastasis—the establishment of colonies in distant organs— begins with entry into the circulation: the invasive cancer cells must penetrate the CANCER AS A MICROEVOLUTIONARY PROCESS basal lamina epithelial cells capillary precursors to cancerous cells fibroblast cancer cells endothelial cell pericyte EXTRACELLULAR MATRIX lymphatic cells white blood cells MBoC6 m20.105/20.15 Figure 20–15 The tumor microenvironment plays a role in tumorigenesis. Tumors consist of many cell types, including cancer cells, endothelial cells, pericytes (vascular smooth muscle cells), fibroblasts, and inflammatory white blood cells. Communication among these and other cell types plays an important part in tumor development. Note, however, that only the cancer cells are thought to be genetically abnormal in a tumor. 1102 Chapter 20: Cancer wall of a blood or lymphatic vessel. Lymphatic vessels, being larger and having more flimsy walls than blood vessels, allow cancer cells to enter in small clumps; such clumps may then become trapped in lymph nodes, giving rise to lymph￾node metastases. The cancer cells that enter blood vessels, in contrast, seem to do so singly. With modern techniques for sorting cells according to their surface properties, it has become possible in some cases to detect these circulating tumor cells (CTCs) in samples of blood from cancer patients, even though they are only a minute fraction of the total blood-cell population. These cells, in principle at least, provide a useful sample of the tumor-cell population for genetic analysis. Of the cancer cells that enter the lymphatics or bloodstream, only a tiny pro￾portion succeed in making their exit, settling in new sites, and surviving and pro￾liferating there as founders of metastases. Experiments show that fewer than one in thousands, perhaps one in millions, manage this feat. The final step of coloni￾zation seems to be the most difficult: like the Vikings who landed on the inhospi￾table shores of Greenland, the migrant cells may fail to survive in the alien envi￾ronment; or they may only thrive there for a short while to found a little colony—a micrometastasis—that then dies out. Many cancers are discovered before they have managed to found metastatic colonies and can be cured by destruction of the primary tumor. But on occasion, capillary travel through bloodstream (fewer than 1 in 1000 cells will survive to form metastases) adhere to blood vessel wall in liver escape from blood vessel to form micrometastasis colonize liver, forming full-blown metastasis MBoC6 m20.17/20.16 basal lamina normal epithelium cells grow as benign tumor in epithelium cells become invasive and enter capillary Figure 20–16 Steps in the process of metastasis. This example illustrates the spread of a tumor from an organ such as the bladder to the liver. Tumor cells may enter the bloodstream directly by crossing the wall of a blood vessel, as diagrammed here, or, more commonly perhaps, by crossing the wall of a lymphatic vessel that ultimately discharges its contents (lymph) into the bloodstream. Tumor cells that have entered a lymphatic vessel often become trapped in lymph nodes along the way, giving rise to lymph-node metastases. Studies in animals show that typically far fewer than one in every thousand malignant tumor cells that enter the bloodstream will colonize a new tissue so as to produce a detectable tumor at a new site.1103 an undetected micrometastasis will remain dormant for many years, only to reveal its presence by erupting into growth to form a large secondary tumor long after the primary tumor has been removed. Many Properties Typically Contribute to Cancerous Growth Clearly, to produce a cancer, a cell must acquire a range of aberrant properties—a collection of subversive new skills—as it evolves. Different cancers require differ￾ent combinations of these properties. Nevertheless, cancers all share some com￾mon features. By definition, they all ignore or misinterpret normal social controls so as to proliferate and spread where normal cells would not. These defining prop￾erties are commonly combined with other features that help the miscreants to arise and thrive. A list of the key attributes of cancer cells in general would include the following, all of which we have just discussed: 1. They grow (biosynthesize) when they should not, aided by a metabolism shifted from oxidative phosphorylation toward aerobic glycolysis. 2. They go through the cell-division cycle when they should not. 3. They escape from their home tissues (that is, they are invasive) and survive and proliferate in foreign sites (that is, they metastasize). 4. They have abnormal stress responses, enabling them to survive and con￾tinue dividing in conditions of stress that would arrest or kill normal cells, and they are less prone than normal cells to commit suicide by apoptosis. 5. They are genetically and epigenetically unstable. 6. They escape replicative cell senescence, either by producing telomerase or by acquiring another way of stabilizing their telomeres. In the next section of the chapter, we examine the mutations and molecular mechanisms that underlie these and other properties of cancer cells. Summary Cancer cells, by definition, grow and proliferate in defiance of normal controls (that is, they are neoplastic) and are able to invade surrounding tissues and colonize dis￾tant organs (that is, they are malignant). By giving rise to secondary tumors, or metastases, they become difficult to eradicate by surgery or local irradiation. Can￾cers are thought to originate from a single cell that has experienced an initial muta￾tion, but the progeny of this cell must undergo many further changes, requiring additional mutations and epigenetic events, to become cancerous. Tumor progres￾sion usually takes many years and reflects the operation of a Darwinian-like pro￾cess of evolution, in which somatic cells undergo mutation and epigenetic changes accompanied by natural selection. Cancer cells acquire a variety of special properties as they evolve, multiply, and spread. Their mutant genomes enable them to grow and divide in defiance of the signals that normally keep cell proliferation under tight control. As part of the evo￾lutionary process of tumor progression, cancer cells acquire a collection of addi￾tional abnormalities, including defects in the controls that permanently stop cell division or induce apoptosis in response to cell stress or DNA damage, and in the mechanisms that normally keep cells from straying from their proper place. All of these changes increase the ability of cancer cells to survive, grow, and divide in their original tissue and then to metastasize, founding new colonies in foreign environ￾ments. The evolution of a tumor also depends on other cells present in the tumor microenvironment, collectively called stromal cells, that the cancer attracts and manipulates. Since many changes are needed to confer this collection of asocial behaviors, it is not surprising that most cancer cells are genetically and/or epigenetically unstable. This instability is thought to be selected for in the clones of aberrant cells that are able to produce tumors, because it greatly accelerates the accumulation of the fur￾ther genetic and epigenetic changes that are required for tumor progression. CANCER AS A MICROEVOLUTIONARY PROCESS1104 Chapter 20: Cancer CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO As we have seen, cancer depends on the accumulation of inherited changes in somatic cells. To understand it at a molecular level we need to identify the muta￾tions and epigenetic changes involved and to discover how they give rise to can￾cerous cell behavior. Finding the relevant cells is often easy; they are favored by natural selection and call attention to themselves by giving rise to tumors. But how do we identify those genes with the cancer-promoting changes among all the other genes in the cancerous cells? A typical cancer depends on a whole set of mutations and epigenetic changes—usually a somewhat different set in each individual patient. In addition, a given cancer cell will also contain a large num￾ber of somatic mutations that are accidental by-products—so-called passengers rather than drivers—of its genetic instability, and it can be difficult to distinguish these meaningless changes from those changes that have a causative role in the disease. Despite these difficulties, many of the genes that are repeatedly altered in human cancers have been identified over the past 40 years. We will call such genes, for want of a better term, cancer-critical genes, meaning all genes whose alteration contributes to the causation or evolution of cancer by driving tumori￾genesis. In this section, we shall first discuss how cancer-critical genes are identified. We shall then examine their functions and the parts they play in conferring on cancer cells the properties outlined in the first part of the chapter. We shall end the section by discussing colon cancer as an extended example, showing how a succession of changes in cancer-critical genes enables a tumor to evolve from one pattern of bad behavior to another that is worse. The Identification of Gain-of-Function and Loss-of-Function Cancer Mutations Has Traditionally Required Different Methods Cancer-critical genes are grouped into two broad classes, according to whether the cancer risk arises from too much activity of the gene product or too little. Genes of the first class, in which a gain-of-function mutation can drive a cell toward cancer, are called proto-oncogenes; their mutant, overactive or overexpressed forms are called oncogenes. Genes of the second class, in which a loss-of-function muta￾tion can contribute to cancer, are called tumor suppressor genes. In either case, the mutation may lead toward cancer directly (by causing cells to proliferate when they should not) or indirectly—for example, by causing genetic or epigen￾etic instability and so hastening the occurrence of other inherited changes that directly stimulate tumor growth. Those genes whose alteration results in genomic instability represent a subclass of cancer-critical genes that are sometimes called genome maintenance genes. As we shall see, mutations in oncogenes and tumor suppressor genes can have similar effects in promoting the development of cancer; overproduction of a signal for cell proliferation, for example, can result from either kind of mutation. Thus, from the point of view of a cancer cell, oncogenes and tumor suppressor genes—and the mutations that affect them—are flip sides of the same coin. The techniques that led to the discovery of these two categories of genes, however, are quite different. The mutation of a single copy of a proto-oncogene that converts it to an onco￾gene has a dominant, growth-promoting effect on a cell (Figure 20–17A). Thus, we can identify the oncogene by its effect when it is added—by DNA transfection, for example, or through infection with a viral vector—to the genome of a suitable type of tester cell or experimental animal. In the case of the tumor suppressor gene, on the other hand, the cancer-causing alleles produced by the change are generally recessive: often (but not always) both copies of the normal gene must be removed or inactivated in the diploid somatic cell before an effect is seen (Figure 20–17B). This calls for a different experimental approach, one focusing on discovering what is missing in the cancer cell. 1105 We begin by discussing some examples of each class of cancer-critical genes to illustrate basic principles. These examples are chosen also for their historical importance: the experiments that led to their discovery—at different times and by different methods—marked turning points in the understanding of cancer. Retroviruses Can Act as Vectors for Oncogenes That Alter Cell Behavior The search for the genetic causes of human cancer took a devious route, begin￾ning with clues that came from the study of tumor viruses. Although viruses are involved only in a minority of human cancers, a set of viruses that infect animals provided critical early tools for studying cancer. One of the first animal viruses to be implicated in cancer was discovered over 100 years ago in chickens, when an infectious agent that causes connective-tissue tumors, or sarcomas, was characterized as a virus—the Rous sarcoma virus. Like all the other RNA tumor viruses discovered since, it is a retrovirus. When it infects a cell, its RNA genome is copied into DNA by reverse transcription, and the DNA is inserted into the host genome, where it can persist and be inherited by subse￾quent generations of cells. Something in the DNA inserted by the Rous sarcoma virus made the host cells cancerous, but what was it? The answer was a surprise. It turned out to be a piece of DNA that was unnecessary for the virus’s own sur￾vival or reproduction; instead, it was a passenger, a gene called v-Src, that the virus had picked up on its travels. v-Src was unmistakably similar, but not identical, to a gene—c-Src—that was discovered in the normal vertebrate genome. c-Src had evi￾dently been caught up accidentally by the retrovirus from the genome of a previ￾ously infected host cell, and it had undergone mutation in the process to become an oncogene (v-Src). This Nobel Prize-winning finding was followed by a flood of discoveries of other viral oncogenes carried by retroviruses that cause cancer in nonhuman ani￾mals. Each such oncogene turned out to have a counterpart proto-oncogene in the normal vertebrate genome. As was the case for Src, these other oncogenes generally differed from their normal counterparts, either in structure or in level of expression. But how did this relate to typical human cancers, most of which are not infectious and in which retroviruses play no part?

CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO Figure 20–17 Cancer-critical mutations fall into two readily distinguishable categories, dominant and recessive. In this diagram, activating mutations are represented by solid red boxes, inactivating mutations by hollow red boxes. (A) Oncogenes act in a dominant manner: a gain-of-function mutation in a single copy of the cancer-critical gene can drive a cell toward cancer. (B) Mutations in tumor suppressor genes, on the other hand, generally act in a recessive manner: the function of both alleles of the cancer￾critical gene must be lost to drive a cell toward cancer. Although in this diagram the second allele of the tumor suppressor gene is inactivated by mutation, it is often inactivated instead by loss of the second chromosome. Not shown is the fact that mutation of some tumor suppressor genes can have an effect even when only one of the two gene copies is damaged. mutation event second mutation event inactivates second gene copy inactivates tumor suppressor gene MBoC6 m20.27/20.17 normal cell no effect of mutation in one gene copy two inactivating mutations functionally eliminate the tumor suppressor gene, promoting cell transformation (B) underactivity mutation (loss of function) single mutation event creates oncogene normal cell activating mutation enables oncogene to promote cell transformation (A) overactivity mutation (gain of function) cells en route to cancer1106 Chapter 20: Cancer Different Searches for Oncogenes Converged on the Same Gene—Ras In an attempt to answer the above question, other researchers searched directly for oncogenes in the genomes of human cancer cells. They did this by searching for DNA fragments from cancer cells that could provoke uncontrolled prolifera￾tion when introduced into noncancerous cell lines. As tester cells for the assay, cell lines derived from mouse fibroblasts were used. These cells had been pre￾viously selected for their ability to proliferate indefinitely in culture, and they are thought to already contain alterations that take them part of the way toward malignancy. For this reason, the addition of a single oncogene can sometimes be enough to produce a dramatic effect. When DNA was extracted from the human tumor cells, broken into fragments, and introduced into the cultured cells, occasional colonies of abnormally pro￾liferating cells began to appear in the culture dish. These cells showed a trans￾formed phenotype, outgrowing the untransformed cells in the culture and piling up in layer upon layer (see Figure 20–11; ). Each colony was a clone originating from a single cell that had incorporated a DNA fragment that drove cancerous behavior. This fragment, which carried markers of its human origin, could be isolated from the transformed cultured mouse cells. And once isolated and sequenced, it could be recognized: it contained a human version of a gene already known from study of a retrovirus that caused tumors in rats—an oncogene called v-Ras. The newly discovered oncogene was clearly derived by mutation from a nor￾mal human gene, one of a small family of proto-oncogenes called Ras. This dis￾covery in the early 1980s of the same oncogene in human tumor cells and in an animal tumor virus was electrifying. The implication that cancers are caused by mutations in a limited number of cancer-critical genes transformed our under￾standing of the molecular biology of cancer. As discussed in Chapter 15, normal Ras proteins are monomeric GTPases that help transmit signals from cell-surface receptors to the cell interior. The Ras oncogenes isolated from human tumors contain point mutations that create a hyperactive Ras protein that cannot shut itself off by hydrolyzing its bound GTP to GDP. Because this makes the protein hyperactive, its effect is dominant—that is, only one of the cell’s two gene copies needs to change to have an effect. One or another of the three human Ras family members is mutated in perhaps 30% of all human cancers. Ras genes are thus among the most important of all cancer-crit￾ical genes. Genes Mutated in Cancer Can Be Made Overactive in Many Ways Figure 20–18 summarizes the types of accidents that can convert a proto-on￾cogene into an oncogene. (1) A small change in DNA sequence such as a point DELETION OR POINT MUTATION IN CODING SEQUENCE GENE AMPLIFICATION CHROMOSOME REARRANGEMENT DNA RNA hyperactive protein made in normal amounts normal protein greatly overproduced nearby regulatory DNA sequence causes normal protein to be overproduced normal protein greatly overproduced fusion to actively transcribed gene produces hyperactive fusion protein DNA RNA or MBoC6 m20.33/20.18 proto-oncogene X REGULATORY MUTATION Figure 20–18 The types of accidents that can convert a proto-oncogene into an oncogene.1107 mutation or deletion may produce a hyperactive protein when it occurs within a protein-coding sequence, or lead to protein overproduction when it occurs within a regulatory region for that gene. (2) Gene amplification events, such as those that can be caused by errors in DNA replication, may produce extra gene copies; this can lead to overproduction of the protein. (3) A chromosomal rearrangement— involving the breakage and rejoining of the DNA helix—may either change the protein-coding region, resulting in a hyperactive fusion protein, or alter the con￾trol regions for a gene so that a normal protein is overproduced. As one example, the receptor for the extracellular signal protein epidermal growth factor (EGF) can be activated by a deletion that removes part of its extracel￾lular domain, causing it to be active even in the absence of EGF (Figure 20–19). It thus produces an inappropriate stimulatory signal, like a faulty doorbell that rings even when nobody is pressing the button. Mutations of this type are frequently found in the most common type of human brain tumor, called glioblastoma. As another example, the Myc protein, which acts in the nucleus to stimulate cell growth and division (see Chapter 17), generally contributes to cancer by being overproduced in its normal form. In some cases, the gene is amplified— that is, errors of DNA replication lead to the creation of large numbers of gene copies in a single cell. Or a point mutation can stabilize the protein, which nor￾mally turns over very rapidly. More commonly, the overproduction appears to be due to a change in a regulatory element that acts on the gene. For example, a chromosomal translocation can inappropriately bring powerful gene regulatory sequences next to the Myc protein-coding sequence, so as to produce unusually large amounts of Myc mRNA. Thus, in Burkitt’s lymphoma, a translocation brings the Myc gene under the control of sequences that normally drive the expression of antibody genes in B lymphocytes. As a result, the mutant B cells tend to proliferate excessively and form a tumor. Different specific chromosome translocations are common in other cancers. Studies of Rare Hereditary Cancer Syndromes First Identified Tumor Suppressor Genes Identifying a gene that has been inactivated in the genome of a cancer cell requires a different strategy from finding a gene that has become hyperactive: one cannot, for example, use a cell transformation assay to identify something that simply is not there. The key insight that led to the discovery of the first tumor suppressor gene came from studies of a rare type of human cancer, retinoblastoma, which arises from cells in the retina of the eye that are converted to a cancerous state by an unusually small number of mutations. As often happens in biology, the discov￾ery arose from examination of a special case, but it turned out to reveal a gene of widespread importance. Retinoblastoma occurs in childhood, and tumors develop from neural pre￾cursor cells in the immature retina. About one child in 20,000 is afflicted. One form of the disease is hereditary, and the other is not. In the hereditary form, CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO MBoC6 n20.150/20.19 P P P P P P P P P P P P P P P P P P extracellular domain of receptor binding of growth factor triggers intracellular signaling cytoplasmic domain of receptor truncated receptor triggers intracellular signaling in absence of growth factor Figure 20–19 Mutation of the epidermal growth factor (EGF) receptor can make it active even in the absence of EGF, and consequently oncogenic. Only one of the possible types of activating mutations is illustrated here.1108 Chapter 20: Cancer multiple tumors usually arise independently, affecting both eyes; in the nonhe￾reditary form, only one eye is affected, and by only one tumor. A few individuals with retinoblastoma have a visibly abnormal karyotype, with a deletion of a spe￾cific band on chromosome 13 that, if inherited, predisposes an individual to the disease. Deletions of this same region are also encountered in tumor cells from some patients with the nonhereditary disease, which suggested that the cancer was caused by loss of a critical gene in that location. Using the location of this chromosomal deletion, it was possible to clone and sequence the Rb gene. It was then discovered that those who suffer from the hereditary form of the disease have a deletion or loss-of-function mutation pres￾ent in one copy of the Rb gene in every somatic cell. These cells are predisposed to becoming cancerous, but do not do so if they retain one good copy of the gene. The retinal cells that are cancerous are defective in both copies of Rb because of a somatic event that has eliminated the function of the previously good copy. In patients with the nonhereditary form of the disease, by contrast, the non￾cancerous cells show no defect in either copy of Rb, while the cancerous cells have become defective in both copies. These nonhereditary retinoblastomas are very rare because they require two independent events that inactivate the same gene on two chromosomes in a single retinal cell lineage (Figure 20–20). The Rb gene is also missing in several common types of sporadic cancer, including carcinomas of lung, breast, and bladder. These more common cancers arise by a more complex series of genetic changes than does retinoblastoma, and they make their appearance much later in life. But in all of them, it seems, loss of Rb function is frequently a major step in the progression toward malignancy. The Rb gene encodes the Rb protein, which is a universal regulator of the cell cycle present in almost all cells of the body (see Figure 17–61). It acts as one of the main brakes on progress through the cell-division cycle, and its loss can allow cells to enter the cell cycle inappropriately, as we discuss later. Both Genetic and Epigenetic Mechanisms Can Inactivate Tumor Suppressor Genes For tumor suppressor genes, it is their inactivation that is dangerous. This inacti￾vation can occur in many ways, with different combinations of mishaps serving to eliminate or cripple both gene copies. The first copy may, for example, be lost by a small chromosomal deletion or inactivated by a point mutation. The second copy is commonly eliminated by a less specific and more probable mechanism: Figure 20–20 The genetic mechanisms that cause retinoblastoma. In the hereditary form, all cells in the body lack one of the normal two functional copies of the Rb tumor suppressor gene, and tumors occur where the remaining copy is lost or inactivated by a somatic event (either mutation or epigenetic silencing). In the nonhereditary form, all cells initially contain two functional copies of the gene, and the tumor arises because both copies are lost or inactivated through the coincidence of two somatic events in a single line of cells. excessive cell proliferation leading to retinoblastoma excessive cell proliferation leading to retinoblastoma occasional cell inactivates one of its two good Rb genes NORMAL, HEALTHY INDIVIDUAL HEREDITARY RETINOBLASTOMA NONHEREDITARY RETINOBLASTOMA inherited mutant Rb gene occasional cell inactivates one of its two good Rb genes occasional cell inactivates its only good Rb gene copy RESULT: NO TUMOR RESULT: MOST PEOPLE WITH INHERITED MUTATION DEVELOP MULTIPLE TUMORS IN BOTH EYES RESULT: ONLY ABOUT 1 IN 30,000 NORMAL PEOPLE DEVELOP ONE TUMOR IN ONE EYE MBoC6 m20.30/20.20 occasional cell inactivates its only good Rb gene copy1109 the chromosome carrying the remaining normal copy may be lost from the cell through errors in chromosome segregation; or the normal gene, along with neighboring genetic material, may be replaced by a mutant version through either a mitotic recombination event or a gene conversion that accompanies it (see p. 286). Figure 20–21 summarizes the range of ways in which the remaining good copy of a tumor suppressor gene can be lost through a DNA sequence change, using the Rb gene as an example. It is important to note that, except for the point mutation mechanism illustrated at the far right, these pathways all produce cells that carry only a single type of DNA sequence in the chromosomal region containing their Rb genes—a sequence that is identical to the sequence in the original mutant chromosome. Epigenetic changes provide another important way to permanently inactivate a tumor suppressor gene. Most commonly, the gene may become packaged into heterochromatin and/or the C nucleotides in CG sequences in its promoter may become methylated in a heritable manner (see pp. 404–405). These mechanisms can irreversibly silence the gene in a cell and in all of its progeny. Analysis of meth￾ylation patterns in cancer genomes shows that epigenetic gene silencing is a fre￾quent event in tumor progression, and epigenetic mechanisms are now thought to help inactivate several different tumor suppressor genes in most human can￾cers (Figure 20–22). Systematic Sequencing of Cancer Cell Genomes Has Transformed Our Understanding of the Disease Methods such as those we have described above shone a spotlight on a set of can￾cer-critical genes that were identified in a piecemeal fashion. Meanwhile, the rest of the cancer cell genome remained in darkness: it was a mystery how many other mutations might lurk there, of what types, in which varieties of cancer, at what frequencies, with what variations from patient to patient, and with what conse￾quences. With the sequencing of the human genome and the dramatic advances in DNA sequencing technology (see Panel 8–1, pp. 478–481), it has become pos￾sible to see the whole picture—to view cancer cell genomes in their entirety. This transforms our understanding of the disease. Cancer cell genomes can be scanned systematically in several different ways. At one extreme—the most costly, but no longer prohibitively so—one can deter￾mine a tumor’s complete genome sequence. More cheaply, one can focus just on the 21,000 or so genes in the human genome that code for protein (the so-called exome), looking for mutations in the cancer cell DNA that alter the amino acid sequence of the product or prevent its synthesis (Figure 20–23). There are also efficient techniques to survey the genome for regions that have undergone CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO mutation at Rb locus in maternal chromosome normal Rb gene in paternal chromosome nondisjunction causes chromosome loss chromosome loss, then chromosome duplication mitotic recombination event gene conversion during mitotic recombination deletion point mutation HEALTHY CELL WITH ONLY ONE NORMAL Rb GENE COPY POSSIBLE WAYS OF ELIMINATING NORMAL Rb GENE MBoC6 m20.31/20.21 Figure 20–21 Six ways of losing the remaining good copy of a tumor suppressor gene through a change in DNA sequences. A cell that is defective in only one of its two copies of a tumor suppressor gene—for example, the Rb gene—usually behaves as a normal, healthy cell; the diagrams below show how this cell may lose the function of the other gene copy as well and thereby progress toward cancer. A seventh possibility, frequently encountered with some tumor suppressors, is that the gene may be silenced by an epigenetic change, without alteration of the DNA sequence, as illustrated in Figure 20–22. (After W.K. Cavenee et al., Nature 305:779–784, 1983. With permission from Macmillan Publishers Ltd.)1110 Chapter 20: Cancer deletion or duplication, without the need for complete sequence information. The genome can be scanned for epigenetic changes. And finally, alterations in levels of gene expression can be systematically determined by analysis of mRNAs (see Figure 7–3). These approaches generally involve comparing cancer cells with normal controls—ideally, noncancerous cells originating in the same tissue and from the same patient. Figure 20–22 The pathways leading to loss of tumor suppressor gene function in cancer involve both genetic and epigenetic changes. (A) As indicated, the changes that silence tumor suppressor genes can occur in any order. Both DNA methylation and the packaging of a gene into condensed chromatin can prevent its expression in a way that is inherited when a cell divides (see Figure 4–44). (B) The frequency of gene silencing by hypermethylation observed in four different types of cancer. The five genes listed at the top can all function as tumor suppressor genes; BRCA1 and hMLH1 affect genome stability and are in the subclass known as genome maintenance genes. ND, no data. (Adapted from M. Esteller et al., Cancer Res. 61:3225–3229, 2001.) Figure 20–23 The distinct types of DNA sequence changes found in oncogenes compared to tumor suppressor genes. In this diagram, mutations that change an amino acid are denoted by blue arrowheads, whereas mutations that truncate the polypeptide chain are marked by yellow arrowheads. (A) As in this example, oncogene mutations can be detected by the fact that the same nucleotide change is repeatedly found among the missense mutations in a gene. (B) For tumor suppressor genes, by contrast, missense mutations that abort protein synthesis by creating stop codons predominate. (Adapted from B. Vogelstein et al., Science 339:1546–1558, 2013.) heritable gene silencing in condensed chromatin mutation tumor suppressor gene CANCER = genetic change = epigenetic change MBoC6 m20.32/20.22 p16INK4A p14ARF BRCA1 hMLH1 APC p16INK4A p14ARF BRCA1 hMLH1 APC p16INK4A p14ARF BRCA1 hMLH1 APC p16INK4A p14ARF BRCA1 hMLH1 APC BREAST COLON/RECTUM STOMACH LUNG 40 30 20 10 0 frequency of hypermethylation (A) (B) ND N C N C oncogene kinase domain domain that binds a transcription regulator tumor suppressor gene missense mutation truncating mutation (A) (B) MBoC6 n20.500/20.231111 Many Cancers Have an Extraordinarily Disrupted Genome Cancer genome analysis reveals, first of all, the scale of gross genetic disruption in cancer cells. This varies greatly from one type of cancer and one cancer patient to another, both in severity and in character. In some cases, the karyotype—the set of chromosomes as they appear at mitosis—is normal or nearly so, but many point mutations are detected in individual genes, suggesting a failure of the repair mechanisms that normally correct local errors in the replication or main￾tenance of DNA sequences. Often, however, the karyotype is severely disordered, with many chromosome breaks and rearrangements. In some breast cancers, for example, genome sequencing reveals an astonishing scene of genetic chaos (Fig￾ure 20–24), with hundreds of chromosome breaks and translocations, resulting in many deletions, duplications, and amplifications of parts of the genome. In such cells, the normal machinery for avoidance or repair of DNA double-strand breaks is evidently somehow defective, destabilizing the genome by giving rise to broken chromosomes whose fragments then rejoin in random combinations. From the pattern of changes, one can infer that this disruptive process has occurred repeat￾edly during the evolution of the tumor, with a progressive increase of genetic dis￾order. Breast cancers showing the most extreme chromosome disorder are usu￾ally hard to treat and have a gloomy prognosis. One survey of more than 3000 individual cancer specimens showed that on average 24 separate blocks of genetic material were duplicated in each tumor, amounting to 17% of the normal genome, and 18 blocks were deleted, amount￾ing to 16% of the normal genome. Many of these changes were found repeatedly, suggesting that they contain cancer-critical genes whose loss (tumor suppressor genes) or gain (oncogenes) confers a selective advantage. Whole-genome analysis also helps to explain some cancers that seem, at first sight, to be exceptions to the general rules. An example is retinoblastoma, with its early onset during childhood. If cancers in general require an accumulation of many genetic changes and are thus diseases of old age, what makes retinoblas￾toma different? Whole-genome sequencing confirms that in retinoblastoma, the tumor cells contain loss-of-function mutations in the Rb gene; but, astonishingly, they contain practically no mutations or genome rearrangements that affect any other oncogene or tumor suppressor gene. Instead, they contain many epigenetic modifications, which alter the level of expression of many known cancer-critical genes—as many as 15 in one well-analyzed case. Many Mutations in Tumor Cells are Merely Passengers Cancer cells generally contain many mutations in addition to gross chromosome abnormalities: point mutations can be scattered over the genome as a whole at a rate of about one per million nucleotide pairs, in addition to the abnormalities CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO 1 2 3 4 5 6 7 9 8 10 11 12 13 14 15 16 17 18 19 20 21 22 Y 1 X 2 3 4 5 6 7 9 8 10 11 12 13 14 15 16 17 18 19 20 21 22 Y X MBoC6 n20.250/20.24 highly amplified regions copy number (blue) intrachromosomal rearrangement (green) interchromosomal rearrangement (purple) BREAST CANCER 1 BREAST CANCER 2 Figure 20–24 The chromosomal rearrangements in breast cancer cells. The results of an extensive DNA sequencing analysis performed on two different primary tumors are displayed as “Circos plots.” In each plot, the reference DNA sequences of the 22 autosomes and single sex chromosome (X) of a normal human female (3.2 billion nucleotide pairs) are aligned end-to-end to form a circle. Colored lines within the circle are then used to indicate the chromosome alterations found in the particular primary tumor. As indicated, purple lines connect sites at which two different chromosomes have become joined to create an interchromosomal rearrangment, while green lines connect the sites of rearrangements found within a single chromosome. The intrachromosomal rearrangements can be seen to predominate, and most join neighboring sections of DNA that were originally located within 2 million nucleotide pairs of each other. The increases in copy number, shown in blue, reveal the amplified DNA sequences (see the highly amplified regions indicated). (Adapted from P.J. Stephens et al., Nature 462:1005–1010, 2009.)1112 Chapter 20: Cancer attributed to chromosome breakage and rejoining. Systematic surveys of the pro￾tein-coding genes in common solid tumors—such as those of the breast, colon, brain, or pancreas—have revealed that an average of 33 to 66 genes have under￾gone somatic mutation affecting the sequence of their protein product. Mutations in noncoding regions of the genome are much more numerous, as one would expect from the much larger fraction of the genome that noncoding DNA rep￾resents. But they are considerably more difficult to interpret. The high frequency of mutations testifies to the genetic instability of many cancer cells, but it leaves us with a difficult problem. How can we discover which of the mutations are drivers of cancer—that is, causal factors in the development of the disease—and which are merely passengers—mutations that happen to have occurred in the same cell as the driver mutations, thanks to genetic insta￾bility, but are irrelevant to the development of the disease? A simple criterion is based on frequency of occurrence. Driver mutations affecting a gene that plays a part in the disease will be seen repeatedly, in many different patients. In contrast, passenger mutations, occurring at more-or-less random locations in the genome and conferring no selective advantage on the cancer cell, are unlikely to be found in the same genes in different patients. Figure 20–25 shows the results of an analysis of this sort for a large sample of colorectal cancers. The different sites in the genome are laid out on a two-di￾mensional array, with chromosome serial number along one axis and position within each chromosome along the other. The frequency with which mutations are encountered is shown by height above this plane, creating a mutation “land￾scape” with mountains (sites where mutations are found in a large proportion of the tumors in the sample), hills (where mutations are found less frequently but still more often than would be expected for a random scattering over the genome), and hillocks (sites of occasional mutations, occurring at a frequency no higher than would be expected for mutations scattered at random in each individual tumor). The mountains and the hills are strong candidates to be the sites of driver mutations—in other words, sites of cancer-critical genes; the hillocks are likely to correspond to passengers. Indeed, many of the mountains and hills turn out to be sites of known oncogenes or tumor suppressor genes, whereas the hillocks mostly correspond to genes that have no known or probable role in causation of cancer. Of course, some hillocks may correspond to genes that are mutated in only a few rare patients but are nevertheless cancer-critical for them. About One Percent of the Genes in the Human Genome Are Cancer-Critical From studies such as the one just described, it is estimated that the number of driver mutations for an individual case of cancer (the sum of meaningful epigen￾etic and genetic changes in both coding sequences and regulatory regions) is typ￾ically on the order of 10, explaining why cancer progression generally involves an increase in genetic and/or epigenetic instability that enhances the rate of such changes. gene position along chromosome chromosomes 1 to X PIK3CA FBXW7 p53 K-Ras APC MBoC6 n20.270/20.25 Figure 20–25 The mutation landscape in colorectal cancer. In this two-dimensional representation of the human genome, the green surface depicts the 22 human autosomes plus the X sex chromosome as being laid out side-by-side in numerical order from left to right, with the DNA sequence of each chromosome running from back to front. The mountains represent the locations of genes mutated with high frequency in different, independent tumors. As indicated, these are suspected driver mutations in the adenomatous polyposis coli (APC), K-Ras, p53, phosphoinositide 3-kinase (PIK3CA), and ubiquitin ligase (FBXW7) proteins. (Adapted from L.D. Wood et al., Science 318:1108–1113, 2007.)1113 By compiling the data for different types of cancer, each with its own range of identified driver mutations, we can develop a comprehensive catalog of genes that are strongly suspected to be cancer-critical. Current estimates put the total number of such genes at about 300, about 1% of the genes in the human genome. These cancer-critical genes are amazingly diverse. Their products include secreted signal proteins, transmembrane receptors, GTP-binding proteins, pro — tein kinases, transcription regulators, chromatin modifiers, DNA repair enzymes, cell–cell adhesion molecules, cell-cycle controllers, apoptosis regulators, scaffold proteins, metabolic enzymes, components of the RNA splicing machinery, and more besides. All these are susceptible to mutations that can contribute, in one way or another, in one tissue or another, to the evolution of cells with the cancer — ous properties that we listed earlier on page 1103. Clearly, the molecular changes that cause cancer are complex. As we now explain, however, the complexity is not quite as daunting as it may initially seem. Disruptions in a Handful of Key Pathways Are Common to Many Cancers Some genes, like Rb and Ras, are mutated in many cases of cancer and in cancers of many different types. The involvement of genes such as Rb and Ras in cancer is no surprise, now that we understand their normal functions: they control fun — damental processes of cell division and growth. But even these common culprits feature in considerably less than half of individual cases. What is happening to the control of these processes in the many cases of cancer where, for example, Rb is intact or Ras is not mutated? What part do mutations in the hundreds of other cancer-critical genes play in the development of the disease? With our increas — ing knowledge of the normal functions of the genes in the human genome, it is becoming easier to see patterns in the cataloged driver mutations and to give some simplifying answers to these questions. Glioblastoma—the commonest type of human brain tumor—provides a good example. Analysis of the genomes of tumor cells from 91 patients identified a total of at least 79 genes that were mutated in more than one individual. The normal functions of most of these genes were known or could be guessed, allowing them to be assigned to specific biochemical or regulatory pathways. Three functional groupings stood out, accounting for a total of 21 of the recurrently mutated genes. One of these groupings consisted of genes in the Rb pathway (that is, Rb itself, along with genes that directly regulate Rb); this pathway governs initiation of the cell-division cycle. Another consisted of genes in the same regulatory subnetwork as Ras—a more loosely defined system of genes referred to as the RTK/Ras/PI3K pathway, after three of its core components; this pathway serves to transmit sig — nals for cell growth and cell division from the cell exterior into the heart of the cell. The third grouping consisted of genes in a pathway regulating responses to stress and DNA damage—the p53 pathway. We shall have more to say about each of these pathways below. Out of all tumors, 74% had identifiable mutations in all three pathways. If one were to trace these three pathways further upstream and include all the com — ponents, known and unknown, on which they depend, this percentage would almost certainly be even higher. In other words, in almost every case of glioblas — toma, there are mutations that disrupt each of three fundamental controls: the control of cell growth, the control of cell division, and the control of responses to stress and DNA damage. Strikingly, in any given tumor-cell clone, there is a strong tendency for no more than one gene to be mutated in each pathway. Evidently, what matters for tumor evolution is the disruption of the control mechanism, and not the genetic means by which that is achieved. Thus, for example, in a patient whose tumor cells have no mutation in Rb itself, there is generally a mutation in some other component of the Rb pathway, producing a similar biological effect. Similar patterns are seen in other types of cancers. A survey of many specimens of the major variety of ovarian cancer, for example, identified 67% of patients as CANCER-CRITICAL GENES: HOW T HEY ARE FOUND AND W HAT T HEY DO1114 Chapter 20: Cancer having mutations in the Rb pathway, 45% in the Ras/PI3K pathway (defined more narrowly than in the glioblastoma study), and more than 96% in the p53 path￾way. Allowing for additional pathway components not included in the analysis, it seems that most cases of this type of cancer, too, have mutations disrupting the same three controls, leading to misregulated cell growth, misregulated cell prolif￾eration, and abnormal disregard of stress and DNA damage. It seems that these three fundamental controls are subverted in one way or another in virtually every type of cancer. We have devoted an entire chapter to the cell cycle and growth controls (Chap￾ter 17). Some important details of the other two control pathways are reviewed next. Mutations in the PI3K/Akt/mTOR Pathway Drive Cancer Cells to Grow Cell proliferation is not simply a matter of progression through the cell cycle; it also requires cell growth, which involves complex anabolic processes through which the cell synthesizes all the necessary macromolecules from small-mole￾cule precursors. If a cell divides inappropriately without growing first, it will get smaller at each division and will ultimately die or become too small to divide. Cells appear to require two separate signals to grow and divide (Figure 20–26). Cancer depends, therefore, not only on a loss of restraints on cell-cycle progres￾sion, but also on disrupted control of cell growth. The phosphoinositide 3-kinase (PI 3-kinase)/Akt/mTOR intracellular signal￾ing pathway is critical for cell growth control. As described in Chapter 15, various extracellular signal proteins, including insulin and insulin-like growth factors, Figure 20–26 Cells seem to require two types of signals to proliferate. (A) In order to multiply successfully, most normal cells are suspected to require both extracellular signals that drive cell-cycle progression (shown here as blue mitogen) and extracellular signals that drive cell growth (shown here as red growth factor). How mitogens activate the Rb pathway to drive entry into the cell cycle is described in Figure 17–61. (B) Diagram of the signaling system containing Akt that drives cell growth through greatly stimulating glucose uptake and utilization, including a conversion of the excess citric acid produced from sugar intermediates in mitochondria into the acetyl CoA that is needed in the cytosol for lipid synthesis and new membrane production. As indicated, protein synthesis is also increased. This system becomes abnormally activated early in tumor progression. TCA cycle indicates the tricarboxylic acid cycle (citric acid cycle). CYTOSOL growth factor required for nutrient uptake and utilization mitogen growth factor activated receptor tyrosine kinase mTOR excess citrate exported to cytosol activation needed to drive the cell cycle INCREASED PROTEIN SYNTHESIS increased glycolysis increased pyruvate active mTOR activated Akt active ATP citrate lyase (ACL) LIPID SYNTHESIS MEMBRANE BIOSYNTHESIS REQUIRED FOR CELL GROWTH mitochondrion (A) (B) activation needed for nutrient uptake and utilization glucose CELL GROWTH AND PROLIFERATION MBoC6 m20.39/20.26 glucose transporter P P P P P increased glucose transport TCA cycle citrate acetyl CoA activation of PI 3-kinase1115 normally activate this pathway. In cancer cells, however, the pathway is activated by mutation so that the cell can grow in the absence of such signals. The resulting abnormal activation of the protein kinases Akt and mTOR not only stimulates pro — tein synthesis (see Figure 17–64), but also greatly increases both glucose uptake and the production of the acetyl CoA in the cytosol required for cell lipid synthe — sis, as outlined in Figure 20–26B. The abnormal activation of the PI 3-kinase/Akt/mTOR pathway, which nor — mally occurs early in the process of tumor progression, helps to explain the exces — sive rate of glycolysis that is observed in tumor cells, known as the Warburg effect, as discussed earlier (see Figure 20–12). As expected from our previous discussion, cancers can activate this pathway in many different ways. Thus, for example, a growth factor receptor can become abnormally activated, as in Figure 20–19. Also very common in cancers is the loss of the PTEN phosphatase, an enzyme that nor — mally suppresses the PI 3-kinase/Akt/mTOR pathway by dephosphorylating the PI (3,4,5) P 3 molecules that the PI 3-kinase forms (see pp. 859–861). PTEN is thus a common tumor-suppressor gene. Of course, mutation is not the only way to overactivate the pathway: high levels of insulin in the circulation can have a similar effect. This may explain why the risk of cancer is significantly increased, by a factor of two or more, in people who are obese or have type 2 diabetes. Their insulin levels are abnormally high, driv — ing cancer cell growth without need of mutation in the PI 3-kinase/Akt/mTOR pathway. Mutations in the p53 Pathway Enable Cancer Cells to Survive and Proliferate Despite Stress and DNA Damage That cancer cells must break the normal rules governing cell growth and cell divi — sion is obvious: that is part of the definition of cancer. It is not so obvious why cancer cells should also be abnormal in their response to stress and DNA dam — age, and yet this too is an almost universal feature. The gene that lies at the center of this response, the p53 gene, is mutated in about 50% of all cases of cancer— a higher proportion than for any other known cancer-critical gene. When we include with p53 the other genes that are closely involved in its function, we find that most cases of cancer harbor mutations in the p53 pathway. Why should this be? To answer, we must first consider the normal function of this pathway. In contrast to Rb, most cells in the body have very little p53 protein under nor — mal conditions: although the protein is synthesized, it is rapidly degraded. More — over, p53 is not essential for normal development. Mice in which both copies of the gene have been deleted or inactivated typically appear normal in all respects except one—they universally develop cancer before 10 months of age. These observations suggest that p53 has a function that is required only in special cir — cumstances. In fact, cells raise their concentration of p53 protein in response to a whole range of conditions that have only one obvious thing in common: they are, from the cell’s point of view, pathological, putting the cell in danger of death or serious injury. These conditions include DNA damage, putting the cell at risk from a faulty genome; telomere loss or shortening (see p. 1016), also dangerous to the integrity of the genome; hypoxia, depriving the cell of the oxygen it needs to keep its metabolism going; osmotic stress, causing the cell to swell or shrivel; and oxidative stress, generating dangerous levels of highly reactive free radicals. Yet another form of stress that can activate the p53 pathway arises, it seems, when regulatory signals are so intense or uncoordinated as to drive the cell beyond its normal limits and into a danger zone where its mechanisms of control and coordination break down, as in an engine driven badly or too fast. The p53 concentration rises, for example, when Myc is overexpressed to oncogenic levels. All these circumstances call for desperate action, which may take either of two forms: the cell can block any further progress through the division cycle in order to take time out to repair or recover from the pathological condition; or it can accept that it must die, and do so in a way that minimizes damage to the organ — ism. A good death, from this point of view, is a death by apoptosis. In apoptosis, CANCER-CRITICAL GENES: HOW T HEY ARE FOUND AND W HAT T HEY DO1116 Chapter 20: Cancer the cell is phagocytosed by its neighbors and its contents are efficiently recycled. A bad death is a death by necrosis. In necrosis, the cell bursts or disintegrates and its contents are spilled into the extracellular space, inducing inflammation. The p53 pathway, therefore, behaves as a sort of antenna, sensing the presence of a wide range of dangerous conditions, and when any are detected, triggering appropriate action—either a temporary or permanent arrest of cell cycling (senes￾cence), or suicide by apoptosis (Figure 20–27). These responses serve to prevent deranged cells from proliferating. Cancer cells are indeed generally deranged, and their survival and proliferation thus depend on inactivation of the p53 pathway. If the p53 pathway were active in them, they would be halted in their tracks or die. The p53 protein performs its job mainly by acting as a transcription regula￾tor. Indeed, the most common mutations observed in p53 in human tumors are in its DNA-binding domain, where they cripple the ability of p53 to bind to its DNA target sequences. Because p53 binds to DNA as a tetramer, a sin￾gle mutant subunit within a tetrameric complex can be enough to block its func￾tion. Thus, mutations in p53 can have a dominant negative effect, causing loss of p53 function even when the cell also contains a wild-type version of the gene. For this reason, in contrast with other tumor suppressor genes such as Rb, the devel￾opment of cancer does not always require that both copies of p53 be knocked out. As discussed in Chapter 17, the p53 protein exerts its inhibitory effects on the cell cycle, in part at least, by inducing the transcription of p21, which encodes a protein that binds to and inhibits the cyclin-dependent kinase (Cdk) complexes required for progression through the cell cycle. By blocking the kinase activity of these Cdk complexes, the p21 protein prevents the cell from progressing through S phase and replicating its DNA. The mechanism by which p53 induces apoptosis includes stimulation of the expression of many pro-apoptotic genes, and it will be described in Chapter 18. Genome Instability Takes Different Forms in Different Cancers If the p53 pathway is functional, a cell with unrepaired DNA damage will stop dividing or die; it cannot proliferate. Mutations in the p53 pathway are, therefore, generally present in cancer cells showing genome instability—which is to say, the majority. But how does this genome instability originate? Here too, cancer genome studies are illuminating. In ovarian cancers, for example, chromosome breaks, translocations, and deletions are very common, and these aberrations correlate with a high frequency of mutations and epigenetic silencing in the genes needed for repair of DNA dou￾ble-strand breaks by homologous recombination, especially Brca1 and Brca2 (see pp. 281–282). In a subset of colorectal cancers with DNA mismatch repair defects, on the other hand, one instead finds many point mutations scattered throughout the genome (see pp. 250–251). In both kinds of cancer, the genome is commonly destabilized, but different types of mutations can bring this about. HYPERPROLIFERATIVE SIGNALS DNA DAMAGE TELOMERE SHORTENING HYPOXIA stable, active p53 CELL-CYCLE ARREST SENESCENCE APOPTOSIS MBoC6 m20.40/20.27 Figure 20–27 Modes of action of the p53 tumor suppressor. The p53 protein is a cellular stress sensor. In response to hyperproliferative signals, DNA damage, hypoxia, telomere shortening, and various other stresses, the p53 levels in the cell rise. As indicated, this may either arrest cell cycling in a way that allows the cell to adjust and survive, trigger cell suicide by apoptosis, or cause cell “senescence”—an irreversible cell-cycle arrest that stops damaged cells from dividing.1117 Cancers of Specialized Tissues Use Many Different Routes to Target the Common Core Pathways of Cancer Mutations in core components of the machinery that regulates cell growth, divi￾sion, and survival, such as Rb, Ras, PTEN, or p53, are not the only way to pervert the control of these processes. Specialized tissues depend on a variety of path￾ways, as discussed in Chapter 15, to relay environmental signals to the core con￾trol machinery, and each pathway lays the cells open to subversion in a different set of ways. Thus, in different cancers, we can find examples of driver mutations in practically all the major signaling pathways through which cells communicate during development and tissue maintenance (discussed in Chapters 21 and 22). In glioblastoma, for example, most patients have mutations in one or other of a set of cell-surface receptor tyrosine kinases, especially the EGF receptor men￾tioned earlier (linking into the Ras/PI3K pathway), suggesting that the cells from which the cancer originates are normally controlled by this route. The cells of the prostate gland, on the other hand, respond to the androgen hormone testoster￾one, and in prostate cancer, components of the androgen receptor signaling path￾way (a variety of nuclear hormone receptor signaling; see Chapter 15) are often mutated. In the normal gut lining, Wnt signaling is critical, and Wnt pathway mutations are present in most colorectal cancers. Pancreatic cancers generally have mutations in the transforming growth factor-β (TGFβ) signaling pathway. Activating mutations in the Notch pathway are present in more than 50% of T cell acute lymphocytic leukemias, and so on. Cells are generally regulated by several different types of external signals that must act in combination, representing a “fail-safe” control mechanism that pro￾tects the organism as a whole from cancer. These signals are different in different tissues. As expected, therefore, the corresponding cancers often have mutations in several signaling pathways concurrently. This is true of the examples we have just listed, which commonly have mutations in other signaling pathways in addi￾tion to the ones that we have singled out. Studies Using Mice Help to Define the Functions of Cancer-Critical Genes The ultimate test of a gene’s role in cancer has to come from investigations in the intact, mature organism. The most favored organism for such studies, apart from humans themselves, is the mouse. To explore the function of a candidate onco￾gene or tumor suppressor gene, one can make a transgenic mouse that overex￾presses it or a knockout mouse that lacks it. Using the techniques described in Chapter 8, one can engineer mice in which the misexpression or deletion of the gene is restricted to a specific set of cells, or in which expression of the gene can be switched on at will at a chosen point in time, or both, to see whether and how tumors develop. Moreover, to follow the growth of tumors from day to day in the living organism, the cells of interest can be genetically marked and made visible by expression of a fluorescent or luminescent reporter (Figure 20–28). In these ways, one can begin to clarify the part that each cancer-critical gene plays in can￾cer initiation or progression. CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO Figure 20–28 Monitoring tumor growth and metastasis in a mouse with a luminescent reporter. A mouse was genetically engineered in a way that allows both copies of its PTEN tumor suppressor gene to be inactivated in the prostate gland, simultaneously with the prostate￾specific activation of a gene engineered to produce the enzyme luciferase (derived from fireflies). After an injection of luciferin (the substrate molecule for luciferase) into the mouse’s bloodstream, the cells in the prostate emit light and can be detected by their bioluminescense in a live mouse, as seen in the 67-day-old animal at the left. Cells lacking the PTEN phosphatase enzyme contain elevated amounts of the Akt activator, PI(3,4,5)P3, and this causes the prostate cells to proliferate abnormally, progressing over time to form a cancer. In this way, the process of metastasis could be followed in the same animal over the course of a year. The light intensity in these experiments is proportional to the number of prostate-cell descendants, increasing from light blue to green, to yellow, to red in this representation. (Adapted from C.-P. Liao et al., Cancer Res. 67:7525– 7533, 2007.) age in days MBoC6 n20.290/20.28 67 103 144 266 372 metastases1118 Chapter 20: Cancer Transgenic mouse studies confirm, for example, that a single oncogene is gen￾erally not enough to turn a normal cell into a cancer cell. Thus, in mice engineered to express a Myc or Ras oncogenic transgene, some of the tissues that express the oncogene may show enhanced cell proliferation, and, over time, occasional cells will undergo further changes to give rise to cancers. Most cells expressing the oncogene, however, do not give rise to cancers. Nevertheless, from the point of view of the whole animal, the inherited oncogene is a serious menace because it creates a high risk that a cancer will arise somewhere in the body. Mice that express both Myc and Ras oncogenes (bred by mating a transgenic mouse carry￾ing a Myc oncogene with one carrying a Ras oncogene) develop cancers earlier and at a much higher rate than either parental strain (Figure 20–29); but, again, the cancers originate as scattered, isolated tumors among noncancerous cells. Thus, even cells expressing these two oncogenes must undergo further, randomly generated changes to become cancerous. This strongly suggests that multiple mutations are required for tumorigenesis, as supported by a great deal of other evidence discussed earlier. Experiments using mice with deletions of tumor sup￾pressor genes lead to similar conclusions. Cancers Become More and More Heterogeneous as They Progress From simple histology, looking at stained tissue sections, it is clear that some tumors contain distinct sectors, all clearly cancerous, but differing in appear￾ance because they differ genetically: the cancer cell population is heterogeneous. Evidently, within the initial clone of cancerous cells, additional mutations have arisen and thrived, creating diverse subclones. Today, the ability to analyze can￾cer genomes lets us look much deeper into the process. One approach involves taking samples from different regions of a primary tumor and from the metastases that it has spawned. With modern methods, it is even possible to take representative single cells and analyze their genomes. Such studies reveal a classic picture of Darwinian evolution, occurring on a time scale of months or years rather than millions of years, but governed by the same rules of natural selection (Figure 20–30). One such investigation compared the genomes of 100 individual cells from dif￾ferent regions of a primary tumor of the breast. A large fraction—just over half—of the chosen cells was genetically normal or nearly so: these were connective-tissue cells and other cell types, such as those of the immune system, that were mixed up with the cancer cells. The cancer cells themselves were distinguished by their severely disrupted genomes. The detailed pattern of gene deletions and ampli￾fications in each such cell revealed how closely it was related to the others, and from this data one could draw up a family tree (Figure 20–30B). In this case, three main branches of the tree were seen; that is, the cancer consisted of three major 0 50 100 0 100 200 Myc Ras Myc + Ras age in days percentage of tumor-free mice MBoC6 m20.36/20.29 Figure 20–29 Oncogene collaboration in transgenic mice. The graphs show the incidence of tumors in three types of transgenic mouse strains, one carrying a Myc oncogene, one carrying a Ras oncogene, and one carrying both oncogenes. For these experiments, two lines of transgenic mice were first generated. One carries an inserted copy of an oncogene created by fusing the proto-oncogene Myc with the mouse mammary tumor virus regulatory DNA (which then drives Myc overexpression in the mammary gland). The other line carries an inserted copy of the Ras oncogene under control of the same regulatory element. Both strains of mice develop tumors much more frequently than normal, most often in the mammary or salivary glands. Mice that carry both oncogenes together are obtained by crossing the two strains. These hybrids develop tumors at a far higher rate still, much greater than the sum of the rates for the two oncogenes separately. Nevertheless, the tumors arise only after a delay and only from a small proportion of the cells in the tissues where the two genes are expressed. Further accidental changes, in addition to the two oncogenes, are apparently required for the development of cancer. (After E. Sinn et al., Cell 49:465–475, 1987. With permission from Elsevier.)1119 subclones. From the shared abnormalities, one could deduce that their last com￾mon ancestor—the presumed founder of the cancer—was already very different from a normal cell, but that the first split between branches occurred early, when the tumor was small. This was followed by a large amount of additional change within each branch. A hint of the future could be seen in the smallest of the three major subclones: its cells were distinguished by a massive amplification of a Ras oncogene. Given more time, perhaps they would have out-competed the other cancer cells and taken over the whole tumor. Similar results have been obtained with other cancers. Clearly, cancer cells are constantly mutating, multiplying, competing, evolving, and diversifying as they exploit new ecological niches and react to the treatments that are used against them (Figure 20–30C). Diversification accelerates as they metastasize and colo￾nize new territories, where they encounter new selection pressures. The longer the evolutionary process continues, the harder it becomes to catch them all in the same net and kill them. The Changes in Tumor Cells That Lead to Metastasis Are Still Largely a Mystery Perhaps the most significant gap in our understanding of cancer concerns inva￾siveness and metastasis. For a start, it is not clear exactly what new properties a cancer cell must acquire to become metastatic. In some cases, it is possible that invasion and metastasis require no further genetic changes beyond those needed to violate the normal controls on cell growth, cell division, and cell death. On the other hand, it may be that, for some cancers, metastasis requires a large number of additional mutations and epigenetic changes. Clues are coming from compar￾isons of the genomes of cells of primary tumors with the cells of metastases that they have spawned. The results appear complex and variable from one cancer to another. Nevertheless, some general principles have emerged. As we discussed earlier, it is helpful to distinguish three phases of tumor pro￾gression required for a carcinoma to metastasize (see Figure 20–16). First, the cells CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO normal cells cell death CELLULAR ENVIRONMENTAL CONSTRAINTS cancer founder cell driver mutations (A) (C) (B) 1 2 or more 3 or more 4 or more time 0 1 2 3 4 5 1 20 40 60 80 100 Euclidean distance cell number MBoC6 n20.310/20.30 normal mammary epithelial development first driver mutation appearance of most recent common ancestor proliferative clones that have become extinct further driver mutations final rate-limiting driver mutation number of cells embryo time breast tumor diagnosed normal stromal cells cells with greatly amplified K-Ras Figure 20–30 How cancers progress as a series of subclones. (A) Schematic illustration of the pattern of mutation and natural selection in a clone of tumor cells. (B) A family tree of cancer cells sampled from different regions of a single breast tumor, showing how the cells have evolved and diversified from a common ancestor, the cancer founder cell. The genome of each of the indicated 100 cells from a human breast tumor was sequenced to produce an evolutionary tree. About half of these cells were normal cells from the stroma (blue cells). The red cells have greatly amplified their K-Ras gene. Note that many subclones appear to have died out, including the one that contained the founder cells for the three subclones that survive. (C) A depiction of how driver mutations are thought to cause cancer progression over long periods of time, before producing a large enough clone of proliferating cells to be detected as a tumor. The data indicate that driver mutations occur only rarely in a background of long-lived subclones of cells that continually accumulate passenger mutations without gaining a growth advantage. (A, adapted from M. Greaves, Semin. Cancer Biol. 20:65–70, 2010; B, adapted from N. Navin et al., Nature 472:90–94, 2011; C, adapted from S. Nik-Zainal et al., Cell 149:994–1007, 2012.)1120 Chapter 20: Cancer must escape the normal confines of their parent epithelium and begin to invade the tissue immediately beneath. Second, they must travel via the blood or lymph to lodge in distant sites. Third, they must survive there and multiply. It is the first and last steps in this sequence that are the most difficult to accomplish for most cancers (Figure 20–31). The first step, local invasiveness, requires a relaxation of the mechanisms that normally hold epithelial cells together. As mentioned earlier, this step resembles the normal developmental process known as the epithelial–mesenchymal transi￾tion (EMT), in which epithelial cells undergo a shift in character, becoming less adhesive and more migratory (discussed in Chapter 19). A key part of the EMT process involves switching off expression of the E-cadherin gene. The primary function of the transmembrane E-cadherin protein is in cell–cell adhesion, bind￾ing epithelial cells together through adherens junctions (see Figure 19–13). In some carcinomas of the stomach and of the breast, E-cadherin has been identified as a tumor suppressor gene, and a loss of E-cadherin may promote cancer devel￾opment by facilitating local invasiveness. The initial entry of tumor cells into the circulation is helped by the presence of a dense supply of blood vessels and sometimes lymphatic vessels, which tumors attract to themselves as they grow larger and become hypoxic in their interior. This process, called angiogenesis, is caused by the secretion of angiogenic factors that promote the growth of blood vessels, such as vascular endothelial growth factor (VEGF; see Figure 22–26). An abnormal fragility and leakiness of the new vessels that form may help the cells that have become invasive to enter and then move through the circulation with relative ease. The remaining steps in metastasis, involving exit from a blood or lymphatic vessel and the effective colonization of remote sites, are much harder to study. To discover which of the later steps in metastasis present cancer cells with the great￾est difficulties, one can label the cells with a fluorescent dye or green fluorescent protein (GFP), inject them into the bloodstream of a mouse, and then monitor their fate. In such experiments, one observes that many cells survive in the cir￾culation, lodge in small vessels, and exit into the surrounding tissue, regardless of whether they come from a tumor that metastasizes or one that does not. Some cells die immediately after they enter foreign tissue; others survive entry into the foreign tissue but fail to proliferate. Still others divide a few times and then stop, forming micrometastases containing ten to several thousand cells. Very few establish full-blown metastases. What, if anything, distinguishes the survivors from the failures? A clue may come from the fact that in many types of tumors, the cancer cells show a kind of heterogeneity that resembles the heterogeneity seen among the cells of those normal tissues that renew themselves continually by a stem-cell strategy, as we discuss next. A Small Population of Cancer Stem Cells May Maintain Many Tumors Self-renewing tissues, where cell division continues throughout life, are the breed￾ing ground for the great majority of human cancers. They include the epidermis

(the outer epithelial layer of the skin), the lining of the digestive and reproductive tracts, and the bone marrow, where blood cells are generated (see Chapter 22). In almost all these tissues, renewal depends on the presence of stem cells, which divide to give rise to terminally differentiated cells, which do not divide. This cre￾ates a mixture of cells that are genetically identical and closely related by lineage, but are in different states of differentiation. Many tumors seem likewise to consist of cells in varied states of differentiation, with different capacities for cell division and self-renewal. To see the implications, it is helpful to consider how normal stem-cell systems operate. When a normal stem cell divides, each daughter cell has a choice—it can remain a stem cell, or it can commit to a pathway leading to differentiation. A stem-cell daughter remains in place to generate more cells in the future. A committed daughter typically undergoes some rounds of cell proliferation (as a so-called transit amplifying cell) but then stops dividing, terminally differentiates, and eventually is discarded and replaced (it may die by apoptosis, with recycling of its materials, or be shed from the body). On average, the two fates—stem cell or differentiating cell—normally occur with equal probability, so that half the daugh￾ters of stem-cell divisions take the one path and half take the other. In a healthy body, feedback controls regulate the process, adjusting this balance of cell-fate choices to correct for any departure from the proper cell population numbers. Thus, the number of stem cells remains approximately constant, and the termi￾nally differentiated cells are continually replaced at a steady rate. Because of the divisions undergone by the transit amplifying cells, the stem cells may be vastly outnumbered by the cells that are committed to terminal differentiation and have lost the capacity for self-renewal. But the stem cells, though few and far between and often relatively slowly dividing, carry the whole responsibility for mainte￾nance of the tissue in the long term. Some cancers seem to be organized in a similar way: they consist of rare can￾cer stem cells capable of dividing indefinitely, together with much larger num￾bers of dividing transit amplifying cells that are derived from the cancer stem cells but have a limited capacity for self-renewal (Figure 20–32). These non-stem cells appear to constitute the great majority of the cell population in some tumors. The Cancer Stem-Cell Phenomenon Adds to the Difficulty of Curing Cancer Evidence for the cancer stem-cell phenomenon comes chiefly from experiments in which individual cells from a cancer are tested for their ability to give rise to fresh tumors: a standard assay is to implant the cells into an immunodeficient mouse (Figure 20–33). It has been known for half a century that there is usually only a small chance—typically much less than 1%—that a tumor cell chosen at random and tested in this way will generate a new tumor. This by itself does not prove that CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO stem cell mixed cell population in tumor stem cell (A) (B) transit amplifying cells stem cell propagates new tumor transit amplifying cells eventually die MBoC6 n20.110/20.32 Figure 20–32 Cancer stem cells can be responsible for tumor growth and yet remain only a small part of the tumor￾cell population. (A) How stem cells produce transit amplifying cells. (B) How a small proportion of cancer stem cells can maintain a tumor. Suppose, for example, that each daughter of a cancer stem cell has a probability slightly greater than 50% of retaining stem-cell potential and a probability slightly less than 50% of becoming a transit amplifying cell that is committed to a program of cell divisions that stops after 10 division cycles. While the number of cancer stem cells will increase slowly but steadily to give a growing tumor, the non-stem cells that they give rise to will always outnumber the stem cells by a large factor—in this example, by a factor of about 1000. (If the cell-division￾cycle and survival times for the two classes of cells are equal.)1122 Chapter 20: Cancer the tumor cells are heterogeneous: like seeds scattered on difficult ground, each of them may have only a small chance of finding a spot where it can survive and grow. Modern technologies for sorting cells have shown, however, that in some cancers at least, the rate of success in founding new tumors is even lower than it would otherwise be because the cancer cells are heterogeneous in their state of differentiation, and only a small subset of them—the cancer stem cells—have the special properties needed for tumor propagation. For example, in several types of cancer, including breast cancers and leukemias, one can fractionate the tumor cells using monoclonal antibodies that recognize a particular cell-surface marker that is present on the normal stem cells in the tissue of origin of the cancer. The purified cancer cells expressing this marker are found to have a greatly enhanced ability to found new tumors. And the new tumors consist of mixtures of cells that express the marker and cells that do not, all generated from the same founder cell that expressed the marker. Experiments with breast cancer cells have revealed that, instead of following a rigid program from stem cell to transit amplifying cell to terminally differentiated cell, these cancer cells can randomly switch to and fro—with a certain low transi￾tion probability—between different states of differentiation that express different molecular markers. In one state, they behave like stem cells, dividing slowly but capable of founding new tumors; in other states, they behave like transit amplify￾ing cells, dividing rapidly but unable to found new tumors in a standard transplant assay. But a single cell in any of these states—given time in culture, or a congenial environment in the body—will give rise to a mixed population that includes all the other states as well. The cancer stem-cell phenomenon, whatever its basis, implies that even when the tumor cells are genetically similar, they are phenotypically diverse. A treat￾ment that wipes out those in one state is likely to allow survival of others that remain a danger. Radiotherapy or a cytotoxic drug, for example, may selectively kill off the rapidly dividing cells, reducing the tumor volume to almost nothing, and yet spare a few slowly dividing cells that go on to resurrect the disease. This greatly adds to the difficulty of cancer therapy, and it is part of the reason why treatments that seem at first to succeed often end in relapse and disappointment. Colorectal Cancers Evolve Slowly Via a Succession of Visible Changes At the beginning of this chapter, we saw that most cancers develop gradually from a single aberrant cell, progressing from benign to malignant tumors by the accu￾mulation of a number of independent genetic and epigenetic changes. We have discussed what some of these changes are in molecular terms and seen how they contribute to cancerous behavior. We now examine one of the common human cancers more closely, using it to illustrate and enlarge upon some of the general principles and molecular mechanisms we have introduced. We take colorectal cancer as our example. Colorectal cancers arise from the epithelium lining the colon (the large intes￾tine) and rectum (the terminal segment of the gut). The organization of this tissue is broadly similar to that of the small intestine, discussed in detail in Chapter 22 (pp. 1217–1221). For both the small and large intestine, the epithelium is renewed at an extraordinarily rapid rate, taking about a week to completely replace most of the epithelial sheet. In both regions, the renewal depends on stem cells that lie in deep pockets of the epithelium, called intestinal crypts. The signals that maintain the stem cells and control the normal organization and renewal of the epithelium are beginning to be quite well understood, as explained in Chapter 22. Mutations that disrupt these signals begin the process of tumor progression for most col￾orectal cancers. Colorectal cancers are common, currently causing nearly 60,000 deaths a year in the United States, or about 10% of total deaths from cancer. Like most can￾cers, they are not usually diagnosed until late in life (90% occur after the age of 55). However, routine examination of normal adults with a colonoscope (a fiber MBoC6 n20.251/20.33 Figure 20–33 An immunodeficient mouse, as used in transplantation assays to test human cancer cells for their ability to found new tumors. This nude mouse has a mutation that blocks development of the thymus and, as a side effect, robs it of hair. Because it has practically no T cells, it tolerates grafts of cells even from other species. (Courtesy of Harlan Sprague Dawley.)1123 optic device for viewing the interior of the colon and rectum) often reveals a small benign tumor, or adenoma, of the gut epithelium in the form of a protruding mass of tissue called a polyp (see Figure 22–4). These adenomatous polyps are believed to be the precursors of a large proportion of colorectal cancers. Because the pro￾gression of the disease is usually very slow, there is typically a period of about 10 years in which the slowly growing tumor is detectable but has not yet turned malignant. Thus, when people are screened by colonoscopy in their fifties and the polyps are removed through the colonoscope—a quick and easy surgical proce￾dure—the subsequent incidence of colorectal cancer is much lower: according to some studies, less than a quarter of what it would be otherwise. In microscopic sections of polyps smaller than 1 cm in diameter, the cells and their arrangement in the epithelium usually appear almost normal. The larger the polyp, the more likely it is to contain cells that look abnormally undifferentiated and form abnormally organized structures. Sometimes, two or more distinct areas can be distinguished within a single polyp, with the cells in one area appearing relatively normal and those in the other appearing clearly cancerous, as though they have arisen as a mutant subclone within the original clone of adenomatous cells. At later stages in the disease, some tumor cells become invasive in a small fraction of the polyps, first breaking through the epithelial basal lamina, then spreading through the layer of muscle that surrounds the gut, and finally metas￾tasizing to lymph nodes via lymphatic vessels and to liver, lung, and other organs via blood vessels. A Few Key Genetic Lesions Are Common to a Large Fraction of Colorectal Cancers What are the mutations that accumulate with time to produce this chain of events? Of those genes so far discovered to be involved in colorectal cancer, three stand out as most frequently mutated: the proto-oncogene K-Ras (a member of the Ras gene family), in about 40% of cases; p53, in about 60% of cases; and the tumor suppressor gene Apc (discussed below), in more than 80% of cases. Others are involved in smaller numbers of colon cancers, and some of these are listed in Table 20–1. The role of Apc first came to light through study of certain families show￾ing a rare type of hereditary predisposition to colorectal cancer, called familial CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO Table 20–1 Some Genetic Abnormalities Detected in Colorectal Cancer Cells Gene Class Pathway affected Human colon cancers (%) K-Ras Oncogene Receptor tyrosine kinase signaling 40 β-Catenin1 Oncogene Wnt signaling 5–10 Apc1 Tumor suppressor Wnt signaling >80 p53 Tumor suppressor Response to stress and DNA damage 60 TGFβ receptor II 2 Tumor suppressor TGFβ signaling 10 Smad4 2 Tumor suppressor TGFβ signaling 30 MLH1 and other DNA mismatch repair genes (often silenced by DNA methylation) Tumor suppressor (genetic stability) DNA mismatch repair 15 1,2The genes with the same superscript numeral act in the same pathway, and therefore only one of the components is mutated in an individual cancer.1124 Chapter 20: Cancer adenomatous polyposis coli (FAP). In this syndrome, hundreds or thousands of polyps develop along the length of the colon (Figure 20–34). These polyps start to appear in early adult life, and if they are not removed, one or more will almost always progress to become malignant; the average time from the first detection of polyps to the diagnosis of cancer is 12 years. The disease can be traced to a dele￾tion or inactivation of the tumor suppressor gene Apc, named after the syndrome. Individuals with FAP have inactivating mutations or deletions of one copy of the Apc gene in all their cells and show loss of heterozygosity in tumors, even in the benign polyps. Most patients with colorectal cancer do not have the hereditary condition. Nevertheless, in more than 80% of the cases, their cancer cells (but not their normal cells) have inactivated both copies of the Apc gene through muta￾tions acquired during the patient’s lifetime. Thus, by a route similar to that which we discussed for retinoblastoma, mutation of the Apc gene was identified as one of the central ingredients of colorectal cancer. The Apc protein, as we now know, is an inhibitory component of the Wnt signaling pathway (discussed in Chapter 15). It binds to the β-catenin protein, another component of the Wnt pathway, and helps to induce the protein’s deg￾radation. By inhibiting β-catenin in this way, Apc prevents the β-catenin from migrating to the nucleus, where it would act as a transcriptional regulator to drive cell proliferation and maintain the stem-cell state (see Figure 15–60). Loss of Apc results in an excess of free β-catenin and thus leads to an uncontrolled expansion of the stem-cell population. This causes massive increase in the number and size of the intestinal crypts (see Figure 22–4). When the β-catenin gene was sequenced in a collection of colorectal tumors, it was discovered that, many of the tumors that did not have Apc mutations had activating mutations in β-catenin instead. Thus, it is excessive activity in the Wnt signaling pathway that is critical for the initiation of this cancer, rather than any single oncogene or tumor suppressor gene that the pathway contains. This being so, why is the Apc gene in particular so often the most common culprit in colorectal cancer? The Apc protein is large and it interacts not only with β-catenin but also with various other cell components, including microtubules. Loss of Apc appears to increase the frequency of mitotic spindle defects, leading to chromosome abnormalities when cells divide. This additional, independent cancer-promoting effect could explain why Apc mutations feature so prominently in the causation of colorectal cancer. Some Colorectal Cancers Have Defects in DNA Mismatch Repair In addition to the hereditary disease (FAP) associated with Apc mutations, there is a second, more common kind of hereditary predisposition to colon carcinoma in which the course of events differs from the one we have described for FAP. In this more common condition, called hereditary nonpolyposis colorectal cancer (HNPCC), the probability of colon cancer is increased without any increase in the number of colorectal polyps (adenomas). Moreover, the cancer cells are unusual, in that they have a normal (or almost normal) karyotype. The majority of colorec￾tal tumors in non-HNPCC patients, in contrast, have gross chromosomal abnor￾malities, with multiple translocations, deletions, and other aberrations, as well as having many more chromosomes than normal (Figure 20–35). The mutations that predispose HNPCC individuals to colorectal cancer occur in one of several genes that code for central components of the DNA mismatch repair system. These genes are homologous in structure and function to the MutL and MutS genes in bacteria and yeast (see Figure 5–19). Only one of the two cop￾ies of the involved gene is defective, so the repair system is still able to remove MBoC6 m23.46/20.34 (A) (B) Figure 20–34 Colon of familial adenomatous polyposis coli patient compared with normal colon. (A) The normal colon wall is a gently undulating but smooth surface. (B) The polyposis colon is completely covered by hundreds of projecting polyps, each resembling a tiny cauliflower when viewed with the naked eye. (Courtesy of Andrew Wyllie and Mark Arends.)1125 the inevitable DNA replication errors that occur in the patient’s cells. However, as discussed previously, these individuals are at risk, because the accidental loss or inactivation of the remaining good gene copy will immediately elevate the spon￾taneous mutation rate by a hundredfold or more (discussed in Chapter 5). These genetically unstable cells then can presumably speed through the standard pro￾cesses of mutation and natural selection that allow clones of cells to progress to malignancy. This particular type of genetic instability produces invisible changes in the chromosomes—most notably changes in individual nucleotides and short expan￾sions and contractions of mono- and dinucleotide repeats such as AAAA… or CACACA…. Once the defect in HNPCC patients was recognized, the epigenetic silencing or mutation of mismatch repair genes was found in about 15% of the colorectal cancers occurring in people with no inherited predisposing mutation. Thus, the genetic instability found in many colorectal cancers can be acquired in at least two ways. The majority of the cancers display a form of chromosomal instability that leads to visibly altered chromosomes, whereas in the others the instability occurs on a much smaller scale and reflects a defect in DNA mismatch repair. Indeed, many carcinomas show either chromosomal instability or defec￾tive mismatch repair—but rarely both. These findings clearly demonstrate that genetic instability is not an accidental by-product of malignant behavior but a contributory cause—and that cancer cells can acquire this instability in multiple ways. The Steps of Tumor Progression Can Often Be Correlated with Specific Mutations In what order do K-Ras, p53, Apc, and the other identified colorectal cancer-crit￾ical genes mutate, and what contribution does each of them make to the asocial behavior of the cancer cell? There is no single answer, because colorectal cancer can arise by more than one route: thus, we know that in some cases, the first muta￾tion can be in a DNA mismatch repair gene; in others, it can be in a gene regulat￾ing cell proliferation. Moreover, as previously discussed, a general feature such as genetic instability or a tendency to proliferate abnormally can arise in a variety of ways, through mutations in different genes. Nevertheless, certain sets of mutations are particularly common in colorectal cancer, and they occur in a characteristic order. Thus, in most cases, mutations inactivating the Apc gene appear to be the first, or at least a very early step, as they are detected at the same high frequency in small benign polyps as in large malig￾nant tumors. Changes that lead to genetic and epigenetic instability are likely also to arise early in tumor progression, since they are needed to drive the later steps. Activating mutations in the K-Ras gene occur later, as they are rare in small polyps but common in larger ones that show disturbances in cell differentiation and histological pattern. Inactivating mutations in p53 are thought to come later still, as they are rare in polyps but common in carcinomas (Figure 20–36). We have seen that loss of p53 function allows cancer cells to endure stress and to avoid apoptosis and cell-cycle arrest. Additionally, loss of p53 is related to the heightened activation CANCER-CRITICAL GENES: HOW THEY ARE FOUND AND WHAT THEY DO (A) (B) MBoC6 m20.47/20.35 1 6 7 8 9 10 11 12 6 7 8 9 10 11 12 13 19 20 19 20 21 22 X Y 21 22 X Y 14 15 13 14 15 16 17 18 16 17 18 2 3 4 5 1 2 3 4 5 Figure 20–35 Chromosome complements (karyotypes) of colon cancers showing different kinds of genetic instability. (A) The karyotype of a typical cancer shows many gross abnormalities in chromosome number and structure. Considerable variation can also exist from cell to cell (not shown). (B) The karyotype of a tumor that has a stable chromosome complement with few chromosomal anomalies; the genetic abnormalities are mostly invisible, having been created by defects in DNA mismatch repair. All of the chromosomes in this figure were stained as in Figure 4–10, the DNA of each human chromosome being marked with a different combination of fluorescent dyes. (Courtesy Wael Abdel-Rahman and Paul Edwards.)1126 Chapter 20: Cancer of oncogenes such as Ras. Experiments in mice show that an initial low level of oncogene activation can give rise to a slowly growing tumor even while p53 is functional: genes such as Ras are, after all, part of the normal machinery of growth control, and moderate activation is not stressful for a cell and does not call the p53 protein into play. Progression of a tumor from slow to rapid, malignant growth, however, involves activation of oncogenes beyond normal physiological limits to a higher, stressful level. If the p53 protein is present and functional, this should lead to cell-cycle arrest or death. Only by losing p53 function can the cancer cells with hyperactive oncogenes survive and progress. The steps we have just described are only part of the picture. It is important to emphasize that each case of colorectal cancer is different, with its own detailed combination of mutations, and that even for the mutations that are commonly shared, the sequence of occurrence may vary. The same is true for cancers in gen￾eral. Advances in molecular biology have recently provided the tools to find out precisely which genes are amplified, deleted, mutated, or misregulated by epi￾genetic mechanisms in the tumor cells of any given patient. As we discuss in the next section, such information promises to become as important for the diagnosis and treatment of cancer as was the breakthrough of being able to identify micro￾organisms for the treatment of infectious diseases.

Summary The molecular analysis of cancer cells reveals two classes of cancer-critical genes: oncogenes and tumor suppressor genes. A set of these genes becomes altered by a combination of genetic and epigenetic accidents to drive tumor progression. Many cancer-critical genes code for components of the social control pathways that reg￾ulate when cells grow, divide, differentiate, or die. In addition, a subclass of tumor suppressors can be categorized as “genome maintenance genes,” because their nor￾mal role is to help maintain genome integrity. The inactivation of the p53 pathway, which occurs in nearly all human cancers, allows genetically damaged cells to escape apoptosis and continue to proliferate. Inactivation of the Rb pathway also occurs in most human cancers, illustrating how fundamental each of these pathways is for protecting us against cancer. The sequencing of cancer cell genomes reveals that—except for the cancers of childhood—many cancers acquire 10 or so driver mutations over the long course of tumor progression, along with a considerably larger number of passenger muta￾tions of no consequence. The same methods reveal how subclones of cells arise and die out as a tumor ages. Tumors thus contain a heterogeneous mixture of cells, some—the so-called cancer stem cells—being much more dangerous than others. We can often correlate the steps of tumor progression with mutations that activate specific oncogenes and inactivate specific tumor suppressor genes, with colon cancer providing a good example. But different combinations of mutations and epigenetic changes are found in different types of cancer, and even in different patients with the same type of cancer, reflecting the random way in which these inherited changes arise. Nevertheless, many of the same changes are encoun￾tered repeatedly, suggesting that there are a limited number of ways to breach our defenses against cancer

 

CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE We can apply the growing understanding of the molecular biology of cancer to sharpen our attack on the disease at three levels: prevention, diagnosis, and treatment. Prevention is always better than cure, and indeed many cancers can be prevented, especially by avoiding smoking. Highly sensitive molecular assays promise new opportunities for earlier and more precise diagnosis, with the aim of detecting primary tumors while they are still small and have not yet metastasized. Cancers caught at these early stages can often be nipped in the bud by surgery or radiotherapy, as we saw for colorectal polyps. Nevertheless, full-blown malignant disease will continue to be common for many years to come, and cancer treat — ments will continue to be needed. In this section, we first examine the preventable causes of cancer and then consider how advances in our understanding at a molecular level are beginning to transform the treatment of the disease. Epidemiology Reveals That Many Cases of Cancer Are Preventable A certain irreducible background incidence of cancer is to be expected regardless of circumstances. As discussed in Chapter 5, mutations can never be absolutely avoided because they are an inescapable consequence of fundamental limita — tions on the accuracy of DNA replication and repair. If a person could live long enough, it is inevitable that at least one of his or her cells would eventually accu — mulate a set of mutations sufficient for cancer to develop. Nevertheless, environmental factors seem to play a large part in determining the risk for cancer. This is demonstrated most clearly by a comparison of cancer incidence in different countries: for almost every cancer that is common in one country, there is another country where the incidence is much lower. Because migrant populations tend to adopt the pattern of cancer incidence typical of their new host country, the differences are thought to be due mostly to environmental, not genetic, factors. From such findings, it has been suggested that 80–90% of can — cers should be avoidable, or at least postponable (Figure 20–37). Unfortunately, different cancers have different environmental risk factors, and a population that escapes one such danger is usually exposed to another. This is not, however, inevitable. There are some human subgroups whose way of life sub — stantially reduces the total cancer death rate among individuals of a given age. Under the current conditions in the United States and Europe, approximately one in five people will die of cancer. But the incidence of cancer among strict Mor — mons in Utah—who avoid alcohol, coffee, cigarettes, drugs, and casual sex—is only about half the incidence for non-practicing members of the same family or for Americans in general. Cancer incidence is also low in certain relatively afflu — ent populations in Africa. Although such observations on human populations indicate that cancer can often be avoided, it has been difficult in most cases—with tobacco as a striking exception—to pinpoint the specific environmental factors responsible for these large population differences or to establish how they act. Nevertheless, several important classes of environmental cancer risk factors have been identified (Fig — ure 20–37B). One thinks first of mutagens. But there are also many other influ — ences—including the amount of food we eat, the hormones that circulate in our bodies, and the irritations, infections, and damage to which we expose our tis — sues—that are no less important and favor development of the disease in other ways. Sensitive Assays Can Detect Those Cancer-Causing Agents that Damage DNA Many quite disparate chemicals are carcinogenic when they are fed to exper — imental animals or painted repeatedly on their skin. Examples include a range CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE1128 Chapter 20: Cancer of aromatic hydrocarbons and derivatives of them such as aromatic amines, nitrosamines, and alkylating agents such as mustard gas. Although these chemi￾cal carcinogens are diverse in structure, a large proportion of them have at least one shared property—they cause mutations. In one common test for mutagen￾icity (the Ames test), the carcinogen is mixed with an activating extract prepared from rat liver cells (to mimic the biochemical processing that occurs in an intact animal). The mixture is then added to a culture of specially designed test bacte￾ria and the bacterial mutation rate measured. Most of the compounds scored as mutagenic by this rapid and convenient assay in bacteria also cause mutations or chromosome aberrations when tested on mammalian cells. A few of these carcinogens act directly on DNA. But generally the more potent ones are relatively inert chemically; these chemicals become damaging only after they have been converted to a more reactive molecule by metabolic processes in the liver, catalyzed by a set of intracellular enzymes known as the cytochrome P-450 oxidases. These enzymes normally help to convert ingested toxins into harmless and easily excreted compounds. Unhappily, their activity on certain chemicals generates products that are highly mutagenic. Examples of carcinogens activated in this way include benzo[a]pyrene, a cancer-causing chemical present in coal tar and tobacco smoke and the fungal toxin aflatoxin B1 (Figure 20–38). Fifty Percent of Cancers Could Be Prevented by Changes in Lifestyle Tobacco smoke is the most important carcinogen in the world today. Even though many other chemical carcinogens have been identified, none of these appear to be responsible for anything like the same numbers of human cancer deaths. It is sometimes thought that the main environmental causes of cancer are the prod￾ucts of a highly industrialized way of life—the rise in pollution, the enhanced use of food additives, and so on—but there is little evidence to support this view. The idea may have come in part from the identification of some highly carcinogenic materials used in industry, such as 2-naphthylamine and asbestos. Except for the increase in cancers caused by smoking, however, age-adjusted death rates for most common human cancers have stayed much the same over the past half-cen￾tury, or, in some cases, have declined significantly (Figure 20–39). Survival rates, moreover, have improved. Thirty years ago, less than 50% of patients lived more than five years from the time of diagnosis; now, more than two-thirds do so. SOUTH AMERICA NORTH AMERICA HAWAII JAPAN CHINA AFRICA prostate, colon, breast prostate, colon, breast stomach naso￾pharyngeal Burkitt’s lymphoma Burkitt’s lymphoma MBoC6 m20.20/20.37 (A) (B) magnitude of reduction possible (percent) 75 50 85 100 50 50 50 number of deaths in US (annual) 189,000 143,000 28,600 28,600 17,200 11,400 28,600 cancers caused (percent of total) 33 25 5 5 3 2 5 cause smoking diet, overweight, and obesity lack of exercise viruses alcohol UV and ionizing radiation occupational carcinogens EASTERN EUROPE Hodgkin’s disease Figure 20–37 Cancer incidence is related to environmental influences. (A) This map of the world shows the rates of cancer increasing (red arrows) or decreasing (blue arrows) when specific populations move from one location to another. Such observations suggest the importance of environmental factors, including diet, in dictating cancer risk. (B) Some estimated effects of environment and lifestyle on cancer in the United States (US). The table shows both the yearly deaths in the US attributable to each cancer and the estimated percentage of that cancer that could be eliminated through prevention. (B, data from G.A. Colditz, K.Y. Wolin and S. Gehlert, Sci. Transl. Med. 4:127rv4, 2012.)1129 Most of the carcinogenic factors that are known to be significant are by no means specific to the modern world. The most potent known carcinogen, by cer￾tain assays at least, is aflatoxin B1 (see Figure 20–38). It is produced by fungi that naturally contaminate foods such as tropical peanuts and is an important cause of liver cancer in Africa and Asia. Except for tobacco, chemical toxins and mutagens are of lesser importance as contributory causes of cancer than other factors that are more a matter of per￾sonal choice. One important factor is the quantity of food we eat: as mentioned earlier, the risk of cancer is greatly increased in people who are obese. In fact, it is estimated that as many as 50% of all cancers could be avoided by simple, identifi￾able changes in lifestyle (see Figure 20–37B). Viruses and Other Infections Contribute to a Significant Proportion of Human Cancers Cancer in humans is not an infectious disease, and most human cancers do not have any infectious cause. However, a small but significant proportion of human cancers, perhaps 15% in the world as a whole, are thought to arise by mechanisms that involve viruses, bacteria, or parasites. Evidence for their involvement comes partly from the detection of viruses in cancer patients and partly from epidemi￾ology. Thus, cancer of the uterine cervix is associated with infection with a pap￾illomavirus, while liver cancer is very common in parts of the world (Africa and Southeast Asia) where hepatitis-B viral infections are common. Chronic infection CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE O O O O O OCH3 OH O N N N HN H2N O O O O OCH3 O O O O O O OCH3 O cytochrome P-450 enzymes DNA (A) AFLATOXIN AFLATOXIN-2,3-EPOXIDE CARCINOGEN BOUND TO GUANINE IN DNA (B) MBoC6 m20.22/20.38 • VINYL CHLORIDE: liver angiosarcoma • BENZENE: acute leukemias • ARSENIC: skin carcinomas, bladder cancer • ASBESTOS: mesothelioma • RADIUM: osteosarcoma Figure 20–38 Some known carcinogens. (A) Carcinogen activation. A metabolic transformation must activate many chemical carcinogens before they will cause mutations by reacting with DNA. The compound illustrated here is aflatoxin B1, a toxin from a mold (Aspergillus flavus oryzae) that grows on grain and peanuts when they are stored under humid tropical conditions. Aflatoxin is an important cause of liver cancer in the tropics. (B) Different carcinogens cause different types of cancer. (B, data from Cancer and the Environment: Gene Environment Interactions, National Academies Press, 2002.) deaths per 100,000 population deaths per 100,000 population (A) (B) MBoC6 m20.25/20.39 1930 0 20 40 60 80 100 1945 1960 1975 1990 2005 1930 0 20 40 60 80 100 1945 1960 1975 1990 2005 stomach breast lung and bronchus colon and rectum uterus ovary pancreas FEMALES stomach prostate lung and bronchus colon and rectum leukemia liver pancreas MALES Figure 20–39 Age-adjusted cancer death rates, United States, 1930–2008. Selected death rates, adjusted to the age distribution of the US population, are plotted for (A) females and (B) males. Note the dramatic rise in lung cancer for both sexes, following the pattern of tobacco smoking, and the fall in deaths from stomach cancer, thought to be related to a fall in rates of infection with Helicobacter pylori. Recent reductions in other cancer death rates may correspond to improvements in detection and treatment. Age-adjusted data like these are needed to compensate for the inevitable increase in cancer as people live longer, on average. (Adapted from Cancer Facts and Figures, 2012. Data from U.S. Mortality Volumes 1930 to 1959, U.S. Mortality Data 1960 to 2008, National Center for Health Statistics, Centers for Disease Control and Prevention. © 2012, American Cancer Society, Inc., Surveillance Research.)1130 Chapter 20: Cancer with hepatitis-C virus, which has infected 170 million people worldwide, is also clearly associated with the development of liver cancer. The main culprits, as shown in Table 20–2, are the DNA viruses. The DNA tumor viruses cause cancer by the most direct route—by interfering with controls of the cell cycle and apoptosis. To understand this type of viral carcinogenesis, it is important to review the life history of viruses. Many DNA viruses use the host cell’s DNA replication machinery to replicate their own genomes. However, to produce a large number of infectious virus particles within a single host cell, the DNA virus has to commandeer this machinery and drive it hard, breaking through the normal constraints on DNA replication and usually killing the host cell in the process. Many DNA viruses reproduce only in this way. But some have a second option: they can propagate their genome as a quiet, well-behaved passenger in the host cell, replicating in parallel with the host cell’s DNA (either integrated into the host genome, or as an extrachromosomal plasmid) in the course of ordinary cell-division cycles. These viruses will switch between two modes of existence according to circumstances, remaining latent and harmless for a long time, but Table 20–2 Viruses Associated with Human Cancers Virus Associated cancer Areas of high incidence DNA viruses Papovavirus family Papillomavirus (many distinct strains) Warts (benign) Worldwide Carcinoma of the uterine cervix Worldwide Hepadnavirus family Hepatitis-B virus Liver cancer (hepatocellular carcinoma) Southeast Asia, tropical Africa Herpesvirus family Epstein–Barr virus Burkitt’s lymphoma (cancer of B lymphocytes) West Africa, Papua New Guinea Nasopharyngeal carcinoma Southern China, Greenland Human herpesvirus 8 Kaposi’s sarcoma Central and Southern Africa RNA viruses Retrovirus family Human T-cell leukemia virus type I (HTLV-1) Adult T-cell leukemia/ lymphoma Japan, West Indies Human immunodeficiency virus (HIV, the AIDS virus) Kaposi’s sarcoma (via human herpesvirus 8) Central and Southern Africa Flavivirus family Hepatitis-C virus Liver cancer (hepatocellular carcinoma) Worldwide For all these viruses, the number of people infected is much larger than the number who develop cancer: the viruses must act in conjunction with other factors. As described in the text, different viruses contribute to cancer in different ways.1131 then proliferating in occasional cells in a process that kills the host cell and gener￾ates large numbers of infectious particles. Neither of these conditions converts the host cell to a cancerous character, nor is it in the interest of the virus to do so. But for viruses with a latent phase, accidents can occur that prematurely activate some of the viral proteins that the virus would normally use in its replicative phase to allow the viral DNA to repli￾cate independently of the cell cycle. As described in the example below, this type of accident can switch on the persistent proliferation of the host cell itself, leading to cancer. Cancers of the Uterine Cervix Can Be Prevented by Vaccination Against Human Papillomavirus The papillomaviruses are a prime example of DNA tumor viruses. They are responsible for human warts and are especially important as a cause of carcinoma of the uterine cervix: this is the second commonest cancer of women in the world as a whole, representing about 6% of all human cancers. Human papillomaviruses (HPV) infect the cervical epithelium and maintain themselves in a latent phase in the basal layer of cells as extrachromosomal plasmids, which replicate in step with the chromosomes. Infectious virus particles are generated through a switch to a replicative phase in the outer epithelial layers, as progeny of these cells begin to differentiate before being sloughed from the surface. Here, cell division should normally stop, but the virus interferes with this cell-cycle arrest so as to allow replication of its own genome. Usually, the effect is restricted to the outer layers of cells and is relatively harmless, as in a wart. Occasionally, however, a genetic accident causes the viral genes that encode the proteins that prevent cell-cycle arrest to integrate into the host chromosome and become active in the basal layer, where the stem cells of the epithelium reside (see Figure 22–10). This can lead to cancer, with the viral genes acting as oncogenes (Figure 20–40). The whole process, from initial infection to invasive cancer, is slow, taking many years. It involves a long intermediate stage when the affected patch of cervi￾cal epithelium is visibly disordered but the cells have not yet begun to invade the underlying connective tissue—a phenomenon called intraepithelial neoplasia. Many such lesions regress spontaneously. Moreover, at this stage, it is still easy to cure the condition by destroying or surgically removing the abnormal tissue. For￾tunately, the presence of such lesions can be detected by scraping off a sample of cells from the surface of the cervix and viewing it under the microscope (the “Pap smear” technique). Better still, a vaccine has now been developed that protects against infection with the relevant strains of human papillomavirus. This vaccine, given to girls before puberty and thus before they become sexually active, has been shown to greatly reduce their risk of ever developing cervical cancer. Because the virus spreads through sexual activity, it is now recommended that both young males and young females be routinely vaccinated. Mass immunization programs have begun in several countries. CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE Figure 20–40 How certain papillomaviruses are thought to give rise to cancer of the uterine cervix. Papillomaviruses have double-stranded circular DNA chromosomes of about 8000 nucleotide pairs. These chromosomes are normally stably maintained in the basal cells of the epithelium as plasmids (red circles), whose replication is regulated so as to keep step with the chromosomes of the host. (A) Normally, the virus perturbs the host cell cycle only when the virus is programmed to produce infectious progeny, in the outer layers of an epithelium. This is relatively harmless. (B) Rare accidents can cause the integration of a fragment of such a plasmid into a chromosome of the host, altering the environment of the viral genes in the basal cells of an epithelium. This can disrupt the normal control of viral gene expression. The unregulated production of certain viral proteins (E6 and E7) interferes with the control of cell division in the basal cells, thereby helping to generate a cancer (bottom). chromosome of papillomavirus integrated gene encoding viral proteins unregulated production of viral proteins drives cell proliferation in basal cell layer viral proteins mediate the controlled replication of the virus in outer cell layers host chromosome BENIGN GROWTH OR WART EVOLUTION OF MALIGNANT TUMOR MBoC6 m20.42/20.40 (A) (B)1132 Chapter 20: Cancer Infectious Agents Can Cause Cancer in a Variety of Ways In papillomaviruses, the viral genes that are mainly to blame are called E6 and E7. The protein products of these viral oncogenes interact with many host-cell pro￾teins, but, in particular, they bind to two key tumor suppressor proteins of the host cell, putting them both out of action and so permitting the cell to replicate its DNA and divide in an uncontrolled way. One of these host proteins is Rb; the other is p53. Other DNA tumor viruses use similar mechanisms to inhibit Rb and p53, underlining the central importance of inactivating both of these tumor suppres￾sor pathways if a cell is to escape the normal constraints on proliferation. In other cancers, viruses have indirect tumor-promoting actions. The hepati￾tis-B and C viruses, for example, favor the development of liver cancer by causing chronic inflammation (hepatitis), which stimulates an extensive cell division in the liver that promotes the eventual evolution of tumor cells. In AIDS, the human immunodeficiency virus (HIV) promotes development of an otherwise rare can￾cer called Kaposi’s sarcoma by destroying the immune system, thereby permit￾ting a secondary infection with a human herpesvirus (HHV-8) that has a direct carcinogenic action. By causing severe inflammation, chronic infection with parasites and bacteria can also promote the development of some cancers. For example, chronic infection of the stomach with the bacterium Helicobacter pylori, which causes ulcers, appears to be a major cause of stomach cancer; dramatic falls in the incidence of stomach cancer over the last half-century (see Figure 20–39) correlate with a decline in the incidence of Helicobacter infections. The Search for Cancer Cures Is Difficult but Not Hopeless The difficulty of curing a cancer is similar to the difficulty of getting rid of weeds. Cancer cells can be removed surgically or destroyed with toxic chemicals or radi￾ation, but it is hard to eradicate every single one of them. Surgery can rarely ferret out every metastasis, and treatments that kill cancer cells are generally toxic to normal cells as well. Moreover, unlike normal cells, cancer cells can mutate rap￾idly and will often evolve resistance to the poisons and irradiation used against them. In spite of these difficulties, effective cures using anticancer drugs (alone or in combination with other treatments) have already been found for some formerly highly lethal cancers, including Hodgkin’s lymphoma, testicular cancer, chorio￾carcinoma, and some leukemias and other cancers of childhood. Even for types of cancer where a cure at present seems beyond our reach, there are treatments that will prolong life or at least relieve distress. But what prospect is there of doing better and finding cures for the most common forms of cancer, which still cause great suffering and so many deaths? Traditional Therapies Exploit the Genetic Instability and Loss of Cell-Cycle Checkpoint Responses in Cancer Cells Anticancer therapies need to take advantage of some molecular peculiarity of cancer cells that distinguishes them from normal cells. One such property is genetic instability, reflecting deficiencies in chromosome maintenance, cell-cy￾cle checkpoints, and/or DNA repair. Remarkably, the most widely used cancer therapies seem to work by exploiting these abnormalities, although this was not known by the scientists who first developed the treatments. Ionizing radiation and most anticancer drugs damage DNA or interfere with chromosome segrega￾tion at mitosis, and they preferentially kill cancer cells because cancer cells have a diminished ability to survive the damage. Normal cells treated with radiation, for example, arrest their cell cycle until they have repaired the damage to their DNA, thanks to the cell-cycle checkpoint responses discussed in Chapter 17. Because cancer cells generally have defects in their checkpoint responses, they may con￾tinue to divide after irradiation, only to die after a few days because the genetic damage remains unrepaired. More generally, most cancer cells are physiologi￾cally deranged to a stressful degree: they live dangerously. Even though the cells 1133 in a tumor have evolved to be unusually tolerant of minor DNA damage, they are hypersensitive to the much greater amount of damage that can be created by radi — ation and by DNA-damaging drugs. A small increase of genetic damage can be enough to tip the balance between proliferation and death. Unfortunately, while the molecular defects present in cancer cells often enhance their sensitivity to cytotoxic agents, they can also increase their resis — tance. For example, where a normal cell might die by apoptosis in response to DNA damage, thanks to the stress response mediated by p53, a cancer cell may escape apoptosis because its p53 is lacking. Cancers vary widely in their sensitiv — ity to cytotoxic treatments, some responding to one drug, some to another, prob — ably reflecting the particular kinds of defects that a particular cancer has in DNA repair, cell-cycle checkpoints, and the control of apoptosis. New Drugs Can Kill Cancer Cells Selectively by Targeting Specific Mutations Radiotherapy and traditional cytotoxic drugs are rather weakly selective: they hurt normal cells as well as the cancer cells, and the safety margin is narrow. The dose often cannot be raised high enough to kill all the cancer cells, because this would kill the patient, and curative treatments, where achievable, generally require a combination of several cytotoxic agents. The side effects can be harsh and hard to endure. How can we do better? An ideal treatment is one that is cell-lethal in combination with some lesion that is present in the cancer cells, but harmless to cells where this lesion is absent. Such a treatment is said to be synthetic-lethal (from the original sense of the word synthesis, meaning “putting together”: it kills only in partnership with the can — cer-specific mutation. As we become increasingly able to pinpoint the specific alterations in cancer cells that make them different from their normal neighbors, new opportunities for such precisely targeted treatments are coming into view. We end this chapter with some examples of new treatments of this type that are already being put into practice. PARP Inhibitors Kill Cancer Cells That Have Defects in Brca1 or Brca2 Genes As we have emphasized, the genetic instability of cancer cells makes the cells both dangerous and vulnerable—dangerous because of the enhancement in their ability to evolve and proliferate, and vulnerable because treatment that leads to still more extreme genetic disruption can take them over the brink and kill them. In some cancers, genetic instability results from an identified fault in one of the many devices on which normal cells depend for DNA repair and maintenance. In this case, a drug is tailored to block a complementary part of the DNA repair machinery can lead to such severe genetic damage that the cancer cells die. Detailed studies of the mechanisms for DNA maintenance discussed in Chap — ter 5 reveal a surprising amount of apparent redundancy. Thus, knocking out a particular pathway for DNA repair is generally less disastrous than one might expect, because alternate repair pathways exist. For example, stalled DNA rep — lication forks can arise when the fork encounters a single-strand break in a tem — plate strand, but cells can avoid the disaster that would otherwise result either by directly repairing these single-strand breaks, or, if that fails, repairing the broken fork that results by homologous recombination (see Figure 5–50). Suppose that the cells in a particular cancer have become genetically unstable by acquiring a muta — tion that reduces their ability to repair broken replication forks by homologous recombination. Might it be possible to eradicate that cancer by treating it with a drug that inhibits the repair of single-strand breaks, thereby greatly increasing the number of forks that break? The consequences of such drug treatment might be expected to be relatively harmless for normal cells, but lethal for the cancer. This strategy appears to work to kill the cells in at least one class of cancers— those that have inactivated both copies of either their Brca1 or their Brca2 tumor CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE1134 Chapter 20: Cancer suppressor genes. As described in Chapter 5, Brca2 is an accessory protein that interacts with the Rad51 protein (the RecA analog in humans) in the repair of DNA double-strand breaks by homologous recombination. Brca1 is another protein that is also required for this repair process. Like Rb, the Brca1 and Brca2 genes were discovered as mutations that predispose humans to cancer—in this case, chiefly cancers of the breast and ovaries (though unlike Rb, they seem to be involved in only a small proportion of such cancers). Individuals who inherit one mutant copy of Brca1 or Brca2 develop tumors that have inactivated the second copy of the same gene, presumably because this change makes the cells geneti￾cally unstable and speeds tumor progression. While Brca1 and Brca2 are needed for the repair of DNA double-strand breaks, single-strand breaks are repaired by other machinery, involving an enzyme called PARP (polyADP-ribose polymerase). This understanding of the basic mecha￾nisms of DNA repair led to a striking discovery: drugs that block PARP activity kill Brca-deficient cells with extraordinary selectivity. At the same time, PARP inhibi￾tion has very little effect on normal cells; in fact, mice that have been engineered to lack PARP1—the major PARP family member involved in DNA repair—remain healthy under laboratory conditions. This result suggests that, while the repair pathway requiring PARP provides a first line of defense against persistent breaks in a DNA strand, these breaks can be repaired efficiently by a genetic recombination pathway in normal cells. In contrast, tumor cells that have acquired their genetic instability by the loss of Brca1 or Brca2 have lost this second line of defense, and they are therefore uniquely sensitive to PARP inhibitors (Figure 20–41). PARP inhibitors are still under clinical trial, but they have produced some strik￾ing results, causing tumors to regress in many Brca-deficient patients and delay￾ing progression of their disease, with relatively few disagreeable side effects. These drugs also appear to be applicable to cancers with other mutations that cause defects in the cell’s homologous recombination machinery—a small, though sig￾nificant, proportion of cancer cases. MBoC6 m20.50/20.41 occasional accident DNA replication repair by pathway 2 still possible repair by pathway 2 not possible DNA replication continues, due to repair by pathway 2 DNA replication permanently blocked CELL LIVES CELL DIES NORMAL CELL HAS TWO ALTERNATIVE DNA REPAIR PATHWAYS occasional accident DNA replication TUMOR CELL HAS LOST DNA REPAIR PATHWAY 2 DRUG BLOCKS PATHWAY 1 DRUG BLOCKS PATHWAY 1 1 2 1 Figure 20–41 How a tumor’s genetic instability can be exploited for cancer therapy. As explained in Chapter 5, the maintenance of DNA sequences is so critical for life that cells have evolved multiple pathways for repairing DNA damage and reducing DNA replication errors. As illustrated, a DNA replication fork will stall whenever it encounters a break in a DNA template strand. In this example, normal cells have two different repair pathways that help them to avoid the problem, pathways 1 and 2. They are therefore not harmed by treatment with a drug that blocks repair pathway 1. But, because the inactivation of repair pathway 2 was selected for during the evolution of the tumor cell, the tumor cells are killed by the same drug treatment. In the actual case that underlies this example, the function of repair pathway 1 (requiring the PARP protein discussed in the text) is to remove persistent, accidental breaks in a DNA single strand before they are encountered by a moving replication fork. Pathway 2 is the recombination￾dependent process (requiring the Brca2 and Brca1 proteins) for repairing stalled replication forks illustrated in Figure 5–50. PARP inhibitors have promise for treating cancers with defective Brca2 or Brca1 tumor suppressor genes.1135 PARP inhibition provides an example of the type of rational, highly selective approach to cancer therapy that is beginning to be possible. Along with other new treatments to be discussed below, it raises high hopes for treating many other cancers. Small Molecules Can Be Designed to Inhibit Specific Oncogenic Proteins An obvious tactic for treating cancer is to attack a tumor expressing an oncogene with a drug designed to specifically block the function of the protein that the oncogene produces. But how can such a treatment avoid hurting the normal cells that depend on the function of the proto-oncogene from which the oncogene has evolved, and why should the drug kill the cancer cells, rather than simply calm them down? One answer may lie in the phenomenon of oncogene dependence. Once a cancer cell has undergone an oncogenic mutation, it will often undergo further mutations, epigenetic changes, or physiological adaptations that make it reliant on the hyperactivity of the initial oncogene, just as drug addicts become reliant on high doses of their drug. Blocking the activity of the oncogenic protein may then kill the cancer cell without significantly harming its normal neighbors. Some remarkable successes have been achieved in this way. As we saw earlier, chronic myelogenous leukemia (CML) is usually associated with a particular chromosomal translocation, visible as the Philadelphia chromo￾some (see Figure 20–5). This results from chromosome breakage and rejoining at the sites of two specific genes, Abl and Bcr. The fusion of these genes creates a hybrid gene, called Bcr-Abl, that codes for a chimeric protein consisting of the N-terminal fragment of Bcr fused to the C-terminal portion of Abl (Figure 20–42). Abl is a tyrosine kinase involved in cell signaling. The substitution of the Bcr frag￾ment for the normal N-terminus of Abl makes it hyperactive, so that it stimulates inappropriate proliferation of the hemopoietic precursor cells that contain it and prevents these cells from dying by apoptosis—which many of them would nor￾mally do. As a result, excessive numbers of white blood cells accumulate in the bloodstream, producing CML. The chimeric Bcr-Abl protein is an obvious target for therapeutic attack. Searches for synthetic drug molecules that can inhibit the activity of tyrosine kinases discovered one, called imatinib (trade name Gleevec®), that blocks Bcr￾Abl (Figure 20–43). When the drug was first given to patients with CML, nearly all of them showed a dramatic response, with an apparent disappearance of the cells carrying the Philadelphia chromosome in over 80% of patients. The response appears relatively durable: after years of continuous treatment, many patients have not progressed to later stages of the disease—although imatinib-resistant cancers emerge with a probability of about 5% per year during the early years. CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE 5′ 3′ breakpoint Bcr gene on chromosome 22 5′ 3′ breakpoint Abl gene on chromosome 9 5′ 3′ 5′ 3′ TRANSLOCATION TRANSCRIPTION TRANSLATION fused Bcr-Abl gene AAA fused Bcr-Abl mRNA Bcr-Abl fusion protein MBoC6 m20.51/20.42 Figure 20–42 The conversion of the Abl proto-oncogene into an oncogene in patients with chronic myelogenous leukemia. The chromosome translocation responsible joins the Bcr gene on chromosome 22 to the Abl gene from chromosome 9, thereby generating a Philadelphia chromosome (see Figure 20–5). The resulting fusion protein has the N-terminus of the Bcr protein joined to the C-terminus of the Abl tyrosine protein kinase; in consequence, the Abl kinase domain becomes inappropriately active, driving excessive proliferation of a clone of hemopoietic cells in the bone marrow.1136 Chapter 20: Cancer Results are not so good for those patients who have already progressed to the more acute phase of myeloid leukemia, known as blast crisis, where genetic insta￾bility has set in and the march of the disease is far more rapid. These patients show a response at first and then relapse because the cancer cells develop a resistance to imatinib. This resistance is usually associated with secondary mutations in the part of the Bcr-Abl gene that encodes the kinase domain, disrupting the ability of imatinib to bind to Bcr-Abl kinase. Second-generation inhibitors that function effectively against a whole range of imatinib-resistant mutants have now been developed. By combining one or more of these new inhibitors with imatinib as the initial therapy (see below), it seems that CML—at least in the chronic (early) stage—may be on its way to becoming a curable disease. Despite the complications with resistance, the extraordinary success of ima￾tinib is enough to drive home an important principle: once we understand pre￾cisely what genetic lesions have occurred in a cancer, we can begin to design effec￾tive rational methods to treat it. This success story has fueled efforts to identify small-molecule inhibitors for other oncogenic protein kinases and to use them to attack the appropriate cancer cells. Increasing numbers are being developed. These include molecules that target the EGF receptor and are currently approved for the treatment of some lung cancers, as well as drugs that specifically target the B-Raf oncoprotein in melanomas. Protein kinases have been relatively easy to inhibit with small molecules like imatinib, and many kinase inhibitors are being produced by pharmaceuti￾cal companies in the hope that they can be effective as drugs for some forms of cancer. Many cancers lack an oncogenic mutation in a protein kinase. But most tumors contain inappropriately activated signaling pathways, for which a target Figure 20–43 How imatinib (Gleevec) blocks the activity of Bcr-Abl protein and halts chronic myelogenous leukemia. (A) Imatinib sits in the ATP-binding pocket of the tyrosine kinase domain of Bcr-Abl and thereby prevents Bcr-Abl from transferring a phosphate group from ATP onto a tyrosine residue in a substrate protein. This blocks transmission of a signal for cell proliferation and survival. (B) The structure of the complex of imatinib (solid blue object) with the tyrosine kinase domain of the Abl protein (ribbon diagram), as determined by x-ray crystallography. (C) The chemical structure of the drug. It can be given by mouth; it has side effects, but they are usually quite tolerable. (B, from T. Schindler et al., Science 289:1938–1942, 2000. With permission from AAAS.) Gleevec (C) N N N N H N H O N N signal for cell proliferation and survival LEUKEMIA ONCOGENIC KINASE ACTIVE no signal NO LEUKEMIA ONCOGENIC KINASE BLOCKED WITH GLEEVEC (A) (B) MBoC6 m20.52/20.43 Gleevec target protein inactivated oncogenic kinase ATP ADP P activating phosphate target protein hyperactive oncogenic kinase1137 somewhere in the pathway can hopefully be found. As an example, Figure 20–44 displays some of the anticancer drugs and drug targets that are currently being tested for a pathway frequently activated in cancers. Many Cancers May Be Treatable by Enhancing the Immune Response Against the Specific Tumor Cancers have complex interactions with the immune system, and its various com￾ponents may sometimes help as well as hinder tumor progression. But for more than a century it has been a dream of cancer researchers to somehow harness the immune system in a controlled and efficient way to exterminate cancer cells, just as it exterminates infectious organisms. There are finally signs that this dream may one day be realized, at least for some forms of cancer. The simplest type of immunological therapy, conceptually at least, is to inject the patient with antibodies that target the cancer cells. This approach has had some successes. About 25% of breast cancers, for example, express unusually high levels of the Her2 protein, a receptor tyrosine kinase related to the EGF receptor that plays a part in the normal development of mammary epithelium. A monoclo￾nal antibody called trastuzumab (trade name Herceptin®) that binds to Her2 and inhibits its function slows the growth of breast tumors in humans that overexpress Her2, and it is now an approved therapy for these cancers (see Figure 20–44). A related approach uses antibodies to deliver poisons to the cancer cells. Antibodies against proteins that are abundant on the surface of a particular type of cancer cell but rare on normal cells can be armed with a toxin that kills those cells that bind the antibody molecule. A great deal of current excitement centers around a different type of approach, based on the relatively recent recognition that the microenvironment in a tumor is highly immunosuppressive. As a result, the cancer victim’s immune system is pre￾vented from destroying the tumor cells. Recall that, from the thousands of genome sequences thus far determined, we know that a typical cancer cell will contain on the order of 50 proteins with a mutation that alters an amino acid sequence, most of these being “passenger” mutations, as previously explained (see p. 1104). Many of these mutant proteins will be recognized by the patient’s immune system as foreign, but—to allow the cancer cells to survive throughout the course of tumor progression—the cancer cells have evolved a set of anti-immune defenses. These Figure 20–44 Some anticancer drugs and drug targets in the Ras–MAP-kinase signaling pathway. Each of the signaling proteins in this diagram has been identified as a product of a cancer-critical gene, with the exception of Raf1 and Erk. This Ras– MAP-kinase signaling pathway is triggered by a variety of receptor tyrosine kinases (RTKs), including the EGF receptor (see Figures 15–47 and 15–49). Those drugs that are antibodies end in “mab,” while those that are small molecules end in “nib.” (Adapted from B. Vogelstein et al, Science 339:1546–1558, 2013.) P P P P P P Erk Raf1 Mek GTP growth factor receptor tyrosine kinase RTK inhibitors Trastuzumab Gefitinib Erlotinib Cetuximab Bevacizumab B-Raf inhibitors Dabrafenib Vemurafenib Raf inhibitors Regorafenib Sorafenib Mek inhibitors Refametinib Selumetinib Trametinib NF1 B-Raf MBoC6 n20.501/20.44 Ras CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE1138 Chapter 20: Cancer defenses include the expression on the cancer cell surface of one or more proteins that bind to inhibitory receptors on activated T cells. The normal immune system is subject to complex controls that keep its activity within safe bounds and prevent autoimmunity from developing. The inhibitory receptors that are expressed on the surface of activated T cells have an important normal function: they control the immune response by down-regulating the T cell response under appropriate circumstances. But in the context of a tumor, the down-regulation is inappropriate, because it prevents the organism from killing the cancer cells that are threatening its survival. In its attack on infectious organisms, the natural immune system usually elim￾inates every last trace of infection and maintains this immunity in the long term. The challenge is to find ways of recruiting the immune system to attack cancers with similar efficiency and specificity, hunting the cancer cells down by virtue of the tumor-specific antigens that they express. With this aim, a new type of anti￾cancer therapy focuses on overcoming the immunosuppressive environment in a tumor through the use of specific antibodies that prevent the tumor cells from engaging with the inhibitory receptors on T cells. As illustrated in Figure 20–45A, blocking the action of the immune suppressors with such treatments should unleash an immune attack on the cancer cells. Importantly, multiple antigens are recognized as foreign; thus, the cancer cells cannot escape through the muta￾tional loss of a single antigen, making it difficult for the tumor to escape from the T cell attack. This is a potentially dangerous strategy. If one provokes the immune system to recognize the cancer cells as targets for destruction, there is a risk of autoimmune side effects with dire consequences for normal tissues of the body, since the can￾cer cells and the normal cells are close cousins and share most of their molecular features. Nevertheless, several recent successes seem to hold great promise for the future. One of the many molecules involved in keeping the activity of the normal immune system within safe bounds is a protein called CTLA4 (cytotoxic T-lym￾phocyte-associated protein 4), which functions as an inhibitory receptor on the surface of T cells. If the function of CTLA4 is blocked, the T cells become more reactive and may mount an attack on cells that they would otherwise leave in peace. In particular, the T cells may attack tumor cells that are recognizably abnormal but whose presence was previously tolerated. With this in mind, cancer immunologists developed a monoclonal antibody, called ipilimumab, that binds to CTLA4 and blocks its action. Injected repeatedly into patients with metastatic melanoma, this antibody increases their median lifespan by several months and, in one large trial, enabled as many as a quarter of them to survive for five years restrained T cell response cancer cell specific antigen protein X PD1 highly activated T cell response cancer cell T cell (A) (B) MBOC6 n20.600/20.45 protein that activates protein X protein that activates PD1 CANCER CELLS PROTECTED BY AN IMMUNOSUPPRESSIVE ENVIRONMENT CANCER CELLS KILLED BY T CELLS WHEN IMMUNOSUPPRESSION REMOVED cancer￾specific antigens antibody to protein X antibody to PD1 T cell receptor Figure 20–45 Therapies designed to remove the immunosuppressive microenvironment in tumors. (A) The cells in tumors will produce many mutant proteins. As described in Chapter 24, peptides from these proteins will be displayed on MHC complexes on the tumor-cell surface and would normally activate a T cell response that destroys the tumor (see Figure 24–42). However, as schematically illustrated, during the course of tumor progression, the cancer cells have evolved immunosuppressive mechanisms that protect them from such killing. (B) The cells in tumors often protect themselves from immune attack by expressing proteins on their surface that bind to and thereby activate the inhibitory receptors on T cells. As indicated, this makes the tumor susceptible to specific antibody therapies. In this diagram, two such inhibitory receptors are shown, PD1 and a hypothetical protein X. Different tumors are thought to protect themselves by activating different members of a large set of T cell inhibitory receptors, some of which are not yet well characterized.1139 or more—far beyond expectations for comparable patients without this treat — ment. Even more promising are recent clinical trials using a combination of two antibodies, one against CTLA4 and the other against PD1, a second cell-surface receptor on T cells that normally restrains their activity. In clinical trials using such techniques, a substantial fraction of the patients can respond in a dramatic way, with their cancer being driven into remission for years, while the treatment fails to help others with the same type of cancer. One possible explanation is that, while most tumors express proteins that protect them from T-cell attack, these proteins are different for different tumors. Thus, while some tumors will respond dramatically when treated with an antibody that blocks a particular immunosuppressive agent, many others will not. If true, one can foresee an era of personalized immunotherapy, in which each patient’s tumor is molecularly analyzed to determine its particular mechanisms of immunosup — pression. The patient would then be treated with a specific cocktail of antibodies designed to remove these blocks (Figure 20–45). Cancers Evolve Resistance to Therapies High hopes have to be tempered with sobering realities. We have seen that genetic instability can provide an Achilles heel that cancer therapies can exploit, but at the same time it can make eradicating the disease more difficult by allowing the can — cer cells to evolve resistance to therapeutic drugs, often at an alarming rate. This applies even to the drugs that target genetic instability itself. Thus, PARP inhibitors give valuable remission of illness, but in the long term the disease generally comes back. For example, Brca-deficient cancers can sometimes develop resistance to PARP inhibitors by undergoing a second mutation in an affected Brca gene that restores its function. By then, the cancer is already out of control and it may be too late to affect the course of the disease with additional treatments. There are many different strategies by which cancers can evolve resistance to anticancer drugs. Often, a cancer will be dramatically reduced in size by an initial drug treatment, with all of the detectable tumor cells seeming to disappear. But months or years later the cancer will reappear in an altered form that is resistant to the drug that was at first so successful. In such cases, the initial drug treatment has evidently failed to destroy some tiny fraction of cells in the original tumor￾cell population. These cells have escaped death because they carry a protective mutation or epigenetic change, or perhaps simply because they were lurking in a protected environment. They eventually regenerate the cancer by continuing to proliferate, mutating and evolving still further as they do so. In some cases, cells that are exposed to one anticancer drug evolve a resis — tance not only to that drug but also to other drugs to which they have never been exposed. This phenomenon of multidrug resistance frequently correlates with amplification of a part of the genome that contains a gene called Mdr1 or Abcb1. This gene encodes a plasma-membrane-bound transport ATPase of the ABC transporter superfamily (discussed in Chapter 11), which pumps lipophilic drugs out of the cell. The overproduction of this protein (or some of its other fam — ily members) by a cancer cell can prevent the intracellular accumulation of many cytotoxic drugs, making the cell insensitive to them. In the to-and-fro struggle between advanced metastatic cancer and the ther — apist, as current practice stands, the cancer usually wins in the end. Does it have to be so? As we discuss below, there is reason to think that by attacking a cancer with many weapons at once—instead of using them one after another, each until it fails—it may be possible to do much better. Combination Therapies May Succeed Where Treatments with One Drug at a Time Fail Nowadays, cancers caught at an early stage can often be cured, by surgery, radia — tion, or drugs. For most cancers that have progressed and metastasized widely, however, cure is still beyond us. Treatments such as those described above can CANCER PREVENTION AND TREATMENT: PRESENT AND FUTURE1140 Chapter 20: Cancer give valuable remissions, but sooner or later these are typically followed by relapse. Nevertheless, for some relatively rare forms of advanced cancer, curative ther￾apies have been developed. These generally involve a cocktail of several different anticancer agents: by trial and error, certain combinations of cytotoxic drugs have been found to wipe out the cancer completely. Discovering such combinations has hitherto involved a long, hard search. But now, armed with our new tools for identifying the specific genetic lesions that cancer cells contain, the prospects are better. The logic of combination therapies is the same as that behind the current treat￾ment of HIV-AIDS with a cocktail of three different protease inhibitors: whereas there may always be some cells in the initial population carrying the rare muta￾tions that confer resistance to any one drug treatment, there should be no cell carrying the whole set of rare mutations that would confer resistance to several different drugs delivered simultaneously. In contrast, sequential drug treatments will allow the few cells resistant to the first drug to multiply to large numbers. Within this large population of cells resistant to the first drug, a small number of cells are likely to have arisen that are resistant to the next drug also; and so on (Figure 20–46). We Now Have the Tools to Devise Combination Therapies Tailored to the Individual Patient Efficient, rational combination drug therapy requires three things. First, we have to identify multiple peculiarities of cancer cells that make them vulnerable in ways that normal cells are not. Second, we have to devise drugs (or other treatments) that target each of these vulnerabilities. Third, we have to match the combination of drugs to the specific set of peculiarities present in the cancer cells of the indi￾vidual patient. The first requirement is already partially met: we now have large catalogs of cancer-critical genes that are commonly mutated in cancer cells. The second requirement is harder, but attainable: we have described some remarkable recent successes, and for cancer researchers there is excitement in the air. It is becoming increasingly possible to use our growing knowledge of cell and molecular biol￾ogy to design new drugs against designated targets. At the same time, efficient, high-throughput automated methods are available to screen large libraries of chemicals for any that may be effective against cells with a given cancer-related defect. In such searches, the goal is synthetic lethality: a cell death that occurs when and only when a particular drug is put together with a particular cancer cell abnormality. Through these and other approaches, the repertoire of precisely targeted anticancer drugs is rapidly increasing.

rare mutant cell, resistant to drug A, forms tumor

TREAT WITH DRUG A no cell is resistant to both drugs SIMULTANEOUS TREATMENT WITH BOTH DRUGS A AND B rare mutant cell, resistant to drug B, forms tumor

TREAT WITH DRUG B UNCONTROLLABLE CANCER RESISTANT TO BOTH DRUGS CANCER CURED (A) (B) = cell sensitive to A and B = cell resistant to A = cell resistant to A and B KEY: MBoC6 m20.53/20.46 Figure 20–46 Why multidrug treatments can be more effective than sequential treatments for cancer therapy. (A) Because tumor cells are hypermutable, two single-drug treatments that are given sequentially often allow for the selection of mutant cell clones that are resistant to both drugs. (B) Simultaneous treatment with both drugs can be more effective.1141 This brings us to the third requirement: the therapy—the choice of drugs to be given in combination—must be tailored to the individual patient. Here, too, the prospects are bright. Cancers evolve by a fundamentally random process, and each patient is different; but modern methods of genome analysis now let us characterize the cells from a tumor biopsy in exhaustive detail so as to discover which cancer-critical genes are affected in a particular case. Admittedly, this is not straightforward: the tumor cells in an individual patient are heterogeneous and do not all contain the same genetic lesions. With increased understandings of the pathways of cancer evolution, however, and with the experience gained from many different cases, it should become possible to make good guesses at the opti￾mal therapies to use. From the perspective of the patient, the pace of advance in cancer research can seem frustratingly slow. Each new drug has to be tested in the clinic, first for safety and then for efficacy, before it can be released for general use. And if the drug is to be used in combination with others, the combination therapy must then go through the same long process. Strict ethical rules constrain the conduct of trials, which means that they take time—typically several years. But slow and cau￾tious steps, taken systematically in the right direction, can lead to great advances. There is still far to go, but the examples that we have discussed provide proof of principle and grounds for optimism. From the cancer research effort, we have learned a great deal of what we know about the molecular biology of the normal cell. Now, more and more, we are dis￾covering how to put that knowledge to use in the battle with cancer itself.

Summary Our growing understanding of the cell biology of cancers has already begun to lead to better ways of preventing, diagnosing, and treating these diseases. Anticancer therapies can be designed to destroy cancer cells preferentially by exploiting the properties that distinguish cancer cells from normal cells, including the cancer cells’ dependence on oncogenic proteins and the defects they harbor in their DNA repair mechanisms. We now have good evidence that, by increasing our understanding of normal cell control mechanisms and exactly how they are subverted in specific cancers, we can eventually devise drugs to kill cancers precisely by attacking specific molecules critical for the growth and survival of the cancer cells. In addition, great progress has recently been made through sophisticated immunological approaches to cancer therapy. And, as we become better able to determine which genes are altered in the cells of any given tumor, we can begin to tailor treatments more accu￾rately to each individual patient

 

PROBLEMS Which statements are true? Explain why or why not.

20–1 The chemical carcinogen dimethylbenz[a]anthra￾cene (DMBA) must be an extraordinarily specific mutagen since 90% of the skin tumors it causes have an A-to-T alter￾ation at exactly the same site in the mutant Ras gene. 20–2 In the cellular regulatory pathways that control cell growth and proliferation, the products of oncogenes are stimulatory components and the products of tumor suppressor genes are inhibitory components. 20–3 Cancer therapies directed solely at killing the rap￾idly dividing cells that make up the bulk of a tumor are unlikely to eliminate the cancer from many patients. 20–4 The main environmental causes of cancer are the products of our highly industrialized way of life such as pollution and food additives. Discuss the following problems. 20–5 In contrast to colon cancer, whose incidence increases dramatically with age, incidence of osteosar￾coma—a tumor that occurs most commonly in the long bones—peaks during adolescence. Osteosarcomas are rel￾atively rare in young children (up to age 9) and in adults (over 20). Why do you suppose that the incidence of osteo￾sarcoma does not show the same sort of age-dependence as colon cancer? What we don’t know • What is required to enable a cancer cell to metastasize? • How can the molecular analysis of an individual tumor be more effectively used to design effective therapies to kill it? • Can we identify general features common to all cancer cells—such as their production of misfolded, mutated proteins—that can be used for the targeted destruction of many different types of cancers? • Can sensitive and reliable blood tests be devised to detect cancers very early, before they have grown to a size where treatment with a single drug will generally be defeated by the survival of a preexisting resistant variant? • How can the observed environmental effects on cancer rates be exploited to reduce avoidable cancers? • Can new technologies be devised to reveal exactly how a quiescent micrometastasis converts to a full￾blown metastatic tumor?1142

Chapter 20: Cancer 20–6 Mortality due to lung cancer was followed in groups of males in the United Kingdom for 50 years. Figure Q20–1 shows the cumulative risk of dying from lung can￾cer as a function of age and smoking habits for four groups of males: those who never smoked, those who stopped at age 30, those who stopped at age 50, and those who contin￾ued to smoke. These data show clearly that individuals can substantially reduce their cumulative risk of dying from lung cancer by stopping smoking. What do you suppose is the biological basis for this observation? 20–7 A small fraction—2 to 3%—of all cancers, across many subtypes, displays a quite remarkable phenome￾non: tens to hundreds of rearrangements that primarily involve a single chromosome, or chromosomal region. The breakpoints can be tightly clustered, with several in a few kilobases; the junctions of the rearrangements often involve segments of DNA that were not originally close together on the chromosome. The copy number of various segments within the rearranged chromosome was found to be either zero, indicating deletion, or one, indicating retention. You can imagine two ways in which such multi￾ple, localized rearrangements might happen: a progressive rearrangements model with ongoing inversions, deletions, and duplications involving a localized area, or a cata￾strophic model in which the chromosome is shattered into fragments that are stitched back together in random order by nonhomologous end joining

(Figure Q20–2). A. Which of the two models in Figure Q20–2 accounts more readily for the features of these highly rearranged chromosomes? Explain your reasoning. B. For whichever model you choose, suggest how such multiple rearrangements might arise. (The true mechanism is not known.) C. Do you suppose such rearrangements are likely to be causative events in the cancers in which they are found, or are they probably just passenger events that are unrelated to the cancer? If you think they could be driver events, suggest how such rearrangements might activate an oncogene or inactivate a tumor suppressor gene. 20–8 Virtually all cancer treatments are designed to kill cancer cells, usually by inducing apoptosis. However, one particular cancer—acute promyelocytic leukemia (APL)— has been successfully treated with all-trans-retinoic acid, which causes the promyelocytes to differentiate into neu￾trophils. How might a change in the state of differentiation of APL cancer cells help the patient? 20–9 One major goal of modern cancer therapy is to identify small molecules—anticancer drugs—that can be used to inhibit the products of specific cancer-critical genes. If you were searching for such molecules, would you design inhibitors for the products of oncogenes or the products of tumor suppressor genes? Explain why you would (or would not) select each type of gene. Figure Q20–2 Two models to explain the multiple, localized chromosome rearrangements found in some cancers (Problem 20–7). The progressive rearrangements model shows a sequence of rearrangements that disrupts the chromosome, generating increasingly complex chromosomal configurations. The chromosome catastrophe model shows the chromosome being fragmented and then reassembled randomly, with some pieces left out. Figure Q20–1 Cumulative risk of lung cancer mortality for nonsmokers, smokers, and former smokers (Problem 20–6). Cumulative risk is the running total of deaths, as a percentage, for each group. Thus, for continuing smokers, 1% died of lung cancer between ages 45 and 55; an additional 4% died between 55 and 65 (giving a cumulative risk of 5%); and 11% more died between 65 and 75 (for a 0 cumulative risk of 16%). 5 10 15 age (years) 45 55 65 75 85 lung cancer mortality, cumulative risk (%) never smoked stopped age 30 stopped age 50 never stopped Problems p20.04/20.04 A B C D E F C D H G F E I J A B C D E F H G F J A B C B C D E F H G F J A B C D E F germ line tandem duplication CDEF catastrophic chromosomal breakage inversion EFGH deletion EI tandem duplication BC Progressive Rearrangements Model Chromosome Catastrophe Model nonhomologous end joining (lost to cell) A B C D E F G H I J A B C D E F G H I J C C D D E E F F G H I H I J J A A B B D E F G G C H I J C D C D1143 Figure Q20–3 Karyotypes of cells from Tasmanian devils (Problem 20–11). (A) A Tasmanian devil. (B) Normal karyotype for a male Tasmanian devil. The karyotype has 14 chromosomes, including XY. (C) Karyotype of cancer cells found in each of the 11 facial tumors studied. The karyotype has 13 chromosomes, no sex chromosomes, no chromosome 2 pair, one chromosome 6, two chromosomes 1 with deleted long arms, and four highly rearranged marker chromosomes (M1–M4). (A, reproduced courtesy of Museum Victoria; B and C, from A.M. Pearse and K. Swift, Nature 439:549, 2006. With permission from Macmillan Publishers Ltd.) 20–10 PolyADP-ribose polymerase (PARP) plays a key role in the repair of DNA single-strand breaks. In the pres￾ence of the PARP inhibitor olaparib, single-strand breaks accumulate. When a replication fork encounters a sin￾gle-strand break, it converts it to a double-strand break, which in normal cells is then repaired by homologous recombination. In cells defective for homologous recom￾bination, however, inhibition of PARP triggers cell death. Patients who have only one functional copy of the Brca1 gene, which is required for homologous recombina￾tion, are at much higher risk for cancer of the breast and ovary. Cancers that arise in these tissues in these patients can be treated successfully with olaparib. Explain how it is that treatment with olaparib kills the cancer cells in these patients, but does not harm their normal cells. 20–11 The Tasmanian devil, a carnivorous Australian marsupial, is threatened with extinction by the spread of a fatal disease in which a malignant oral–facial tumor interferes with the animal’s ability to feed. You have been called in to analyze the source of this unusual cancer. It seems clear to you that the cancer is somehow spread from devil to devil, very likely by their frequent fighting, which is accompanied by biting around the face and mouth. To uncover the source of the cancer, you isolate tumors from 11 devils captured in widely separated regions and exam￾ine them. As might be expected, the karyotypes of the tumor cells are highly rearranged relative to that of the wild-type devil (Figure Q20–3). Surprisingly, you find that the karyotypes from all 11 tumor samples are very similar. Moreover, one of the Tasmanian devils has an inversion on chromosome 5 that is not present in its facial tumor. How do you suppose this cancer is transmitted from devil to devil? Is it likely to arise as a consequence of an infection by a virus or microorganism? Explain your reasoning.

(A) (B) 1 2 3 4 5 6 1 3 4 5 6 M1 M2 M3 M4 XY Tasmanian devil (Sarcophilus harrisii) (C)

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CHAPTER 20 END-OF-CHAPTER PROBLEMS  1144

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Detailed  ContentsMBOC, 5Ed- Chapter 21: Sexual Reproduction: Meiosis, Germ Cells, and FertilizationiBiology Seminar videos with Molecular Biology of the Cell, Sixth Edition,Chapter 20: Cancer — see NobeL 1926-66-75-89-2008: Fibiger (1926) spiroptera carcinoma illustrating cancer caused by chronic irritation, Rous (1966)* tumour-inducing virus in chickens Huggins (1966) hormonal treatment of prostate cancer, BaltimoreDulbecco & Temin (1975) interaction between tumour virus and host cell, Bishop & Varmus(1989) retroviral oncogenes,  2005 Barry J. Marshall and J. Robin Warren «Helicobacter pylori in gastritis and peptic ulcer disease», 2008 Hausen«human papilloma viruses causing cervical cancer» HIV  F/) +  Aleksandr Solzhenitsyn, Nobel  treatment by nicotin-ergetic toxin

Cancer Ward (Russian: Раковый Корпус, Rakovy Korpus) is a semi-autobiographical novel by Russian author Aleksandr Solzhenitsyn, winner of the 1970 Nobel Prize in Literature.[1] -the «most complete and accurate fictional account of the nature of disease and its relation to love. It describes the characteristics of cancer; the physical, psychological, and moral effects on the victim; the conditions of the hospital; the relations of patients and doctors; the terrifying treatments; the possibility of death.» Kostoglotov’s central question is what life is worth, and how we know when we have paid too much for it.[9] The novel is partly autobiographical. Kostoglotov is admitted to hospital for cancer treatment from internal perpetual exile in Kazakhstan, as was Solzhenitsyn. Kostoglotov is depicted as having been born in Leningrad, whereas Solzhenitsyn was born in Kislovodsk. His experiences at Ekibastuz formed the basis for the book One Day in the Life of Ivan Denisovich. One of his fellow political prisoners, Ion Moraru, remembers that Solzhenitsyn spent some of his time at Ekibastuz writing.[26] While there Solzhenitsyn had a tumor removed. His cancer was not diagnosed at the time. In March 1953, …his undiagnosed cancer spread until, by the end of the year, he was close to death. In 1954, he was permitted to be treated in a hospital in Tashkent, where his tumor went into remission.

Due to Aconit – nicotinergetic toxin!- but*

His experiences there became the basis of his novel Cancer Ward and also found an echo in the short story «The Right Hand.» It was during this decade of imprisonment and exile that Solzhenitsyn abandoned Marxism and developed the philosophical and religious positions of his later life, gradually becoming a philosophically-minded Eastern Orthodox Christian as a result of his experience in prison and the camps.[30][31][32] …» His transformation is described at some length in the fourth part of The Gulag Archipelago («The Soul and Barbed Wire»). …in English in 2006.[33]

Cancer Ward tells the story of a small group of patients in Ward 13, the cancer ward of a hospital in Soviet Central Asia in 1955, two years after Joseph Stalin‘s death. A range of characters are depicted, including those who benefited from Stalinism, resisted or acquiesced. Like Solzhenitsyn, the main character, the Russian Oleg Kostoglotov, spent time in a labour camp as a «counter-revolutionary,» before being exiled to Central Asia under Article 58.

Solzhenitsyn (11 December 1918 – 3 August 2008)- 90=54 after cancer- *Testicular cancer is cancer that develops in the testicles, a part of the male reproductive system.  Testicular cancer has one of the highest cure rates of all cancers with an average five-year survival rate of 95%.[1] ….spread widely, chemotherapy offers a cure rate of at least 80%.[3] Globally testicular cancer resulted in 8,300 deaths in 2013 up from 7,000 deaths in 1990.[4] In the United States, about 8,000 cases are diagnosed a year.[5][6] In the UK, approximately 2,000 people are diagnosed each year,[7] over a lifetime, the risk of testicular cancer is roughly 1 in 200 (0.5%).[8] It is the most common cancer in males aged 20–39 years, the period when it is most common to start, and is rarely seen before the age of 15 years.[9] Testicular cancer, cryptorchidism, hypospadias, and poor semen quality make up the syndrome known as testicular dysgenesis syndrome.

Aconitum napellus is grown in gardens for its attractive spike-like inflorescences and showy blue flowers.[5] It is a cut flower crop used for fresh cutting material and sometimes used as dried material.

poisonous compounds, including enough cardiac poison that it was used on spears and arrows for hunting and battle in ancient times.[8] A. napellus has a long history of use as a poison, with cases going back thousands of years.[9] During the ancient Roman period of European history, the plant was often used to eliminate criminals and enemies, and by the end of the period it was banned and anyone growing A. napellus could have been legally sentenced to death.[10] Aconites have been used more recently in murder plots; they contain the chemical alkaloids   aconitine,   mesaconitine,   hypaconitine  and jesaconitine, which are highly toxic.[11] two to six hours in fatal poisoning (20 to 40 mL of tincture may prove fatal).[12] Aconitine is a potent neurotoxin that opens tetrodotoxin sensitive sodium channels. It increases influx of sodium through these channels and delays repolarization, thus increasing excitability and promoting ventricular dysrhythmias.

Alfredo Molero, then Minister of Defense, alleged that Chávez was poisoned or infected with a cancer virus by the U.S. government.[456][453][457][458][459][460]  U.S State Department dismissed the claim as «absurd».[461]

See Nobel.cancer-Sednev Y.- Седнев (Conf.2013, p.196-197)