The DNA Damage Response: Implications on Cancer Formation and Treatment

Preface

Contents

Contributors

1 DNA Damage Sensing and Signaling

1.1 Preamble

1.2 DNA Damage Sensing and the Initiation of DNA Damage Signaling

1.3 ATM Signaling and the DNA Double-Strand Break Paradigm

1.3.1 ATM: The Master of DSB Signaling

1.3.2 ATM Activation by DSBs and MRN

1.3.3 Is ATM a DNA-Activated Kinase?

1.4 ATR Signaling: The Two-Man Rule

1.4.1 The Role of ssDNA in ATR Activation

1.4.2 The Role of 9-1-1 and TopBP1 in ATR Activation

1.5 Unresolved Questions

1.5.1 How is DNA Damage Sensed During DNA Damage Signaling?

1.5.2 How are PIKK Signaling Thresholds Established?

1.5.3 Does DNA-PKcs Play a Signaling Role?

1.5.4 Disassembly of DNA Damage Sensing Complexes

1.6 DNA Damage Signaling and Sensing: Clinical Perspectives

1.6.1 Biomarkers

1.6.2 DNA Damage Signaling Inhibitors

1.6.3 Suppressors of DNA Damage Signaling Defects

References

2 Signaling at Stalled Replication Forks

2.1 Introduction

2.2 Replication and Fork Stalling

2.2.1 Initiating DNA Replication

2.2.2 Replication Stress

2.3 ATR Signaling at a Stalled Replication Fork

2.3.1 ATRIP

2.3.2 The 9-1-1 Complex

2.3.3 TopBP1

2.3.4 CHK1

2.3.5 Regulation of DNA Replication by ATR

2.4 ATR Signaling and Cancer

2.5 Conclusions and Future Directions

References

3 An Oncogene-Induced DNA Replication Stress Model for Cancer Development

3.1 Introduction

3.2 Key Developments and Concepts

3.2.1 Identification of Oncogenes and Tumor Suppressors

3.2.2 Genomic Instability as a Characteristic of Most Human Cancers and Its Underlying Genetic Basis

3.2.3 Identification of a Pathway, Involving ARF and p53, by Which Oncogenes Induce Apoptosis or Senescence

3.3 A New Model to Explain Genomic Instability and Tumor Suppression in Human Cancers

3.3.1 Identification of DNA DSBs in Human Cancers and in Cells Expressing Activated Oncogenes

3.3.2 The DNA Damage Checkpoint as an Important Mediator of Oncogene-Induced Senescence and/or Apoptosis and a Barrier to Tumor Development

3.3.3 DNA Replication Stress Induces DNA DSBs and Genomic Instability in Cancer

3.4 A Model for Cancer Development

References

4 Cellular Responses to Oxidative Stress

4.1 Introduction

4.1.1 Cellular Redox State

4.1.2 Oxidative Stress

4.1.3 The Oxygen Molecule (O2)

4.1.4 Oxygen Radicals

4.1.4.1 The Superoxide Anion Radical (-O2-)

4.1.5 The Hydroxyl Radical (OH)

4.1.6 The Peroxyl Radical (L)

4.2 Non-Radical ROS

4.2.1 Hydrogen Peroxide (H2O2 )

4.2.2 Nitric Oxide (NO) and Generation of the Peroxinitrite Anion (ONOO-)

4.2.3 Cellular Defense Mechanisms Against Oxidative Stress

4.2.4 Brain Vulnerability to Oxidative Stress

4.2.5 Oxidative Stress in Neurodegenerative Diseases

4.3 Conclusions

References

5 Cell Cycle Regulation and DNA Damage

5.1 Introduction

5.2 Overview of the Cell Cycle

5.2.1 Cyclins and Cyclin-Dependent Kinases

5.2.2 Control of Cyclin Stability

5.2.3 Post-Translational Regulation of CDK Activity

5.2.4 Cell-Cycle Phase Transitions

5.2.4.1 G1/S-Phase

5.2.4.2 G2/M Transition

5.3 Cell Cycle Interfaces of the DNA Damage Response

5.3.1 G1/S Checkpoint

5.3.1.1 Rapid G1/S Checkpoint Arrest

5.3.1.2 Delayed G1/S Checkpoint Arrest and the p53 Tumor Suppressor

5.3.2 S-Phase DNA Damage Checkpoints

5.3.2.1 ATM-Dependent Intra-S-Phase Checkpoint

5.3.2.2 ATR-Dependent S-Phase Checkpoint Arrest

5.3.2.3 S/M Checkpoint

5.3.3 G2/M Checkpoint

5.3.3.1 Initiation of G2/M Arrest

5.3.3.2 Stress-Activated Kinases and G2/M Delay

5.3.3.3 Transcription-Dependent G2/M Checkpoint Pathways

5.3.3.4 Recovery from G2/M Checkpoint Arrest

5.4 The DDR and Cell Cycle Latency: The Special Case of Neurons

5.4.1 Concluding Remarks: Exploiting Checkpoint Defects Therapeutically

References

6 Chromatin Modifications Involved in the DNA Damage Response to Double Strand Breaks

6.1 Chromatin Structure

6.2 Overview of DSB Repair Pathways

6.3 Histone Modifications Associated with DNA Damage Repair

6.3.1 Phosphorylation of H2AX

6.3.2 Additional Histone Phosphorylation Events

6.4 Methylation of Histones

6.5 Ubiquitination of Histones

6.6 Histone Acetylation and Deacetylation

6.7 Recruitment of Chromatin Remodelling Factors

6.7.1 SWI/SNF

6.7.2 The INO80 Remodelling Complex

6.7.3 Remodels the Structure of Chromatin (RSC)

6.7.4 Tip60/p400 and the NuA4 Complex

6.8 Recent Advances in the Chromatin-Repair Field

6.9 Conclusions

References

7 Telomere Metabolism and DNA Damage Response

7.1 Telomeres

7.2 Telomere Dysfunction

7.3 DNA Damage Foci at Dysfunctional Telomeres

7.4 Factors Common in DNA Damage Response and Telomere Metabolism

7.5 ATM

7.6 MDC1

7.7 c-Abl

7.8 Mammalian Rad9

7.9 DNA-PK

7.10 Ku

7.11 MRN

7.12 14-3-3

7.13 Heterochromatin Protein 1 (HP1)

7.14 Chromatin Modification in Response to DNA DSBs

7.15 DSB Signaling and Checkpoint Activation

7.16 Conclusions and Future Prospects

References

8 DNA Double Strand Break Repair: Mechanisms and Therapeutic Potential

8.1 Introduction

8.2 Detection and Repair of IR-Induced DNA Damage

8.2.1 IR-Induced Forms of DNA Damage

8.2.2 The Major DSB Repair Pathways in Mammalian Cells

8.2.2.1 Non-Homologous End Joining (NHEJ)

8.2.2.2 Alternative Non-Homologous End Joining (Alt-NHEJ)

8.2.3 Homology Directed Repair (HDR)

8.2.4 DSB Repair Pathway Choice

8.3 The Therapeutic Potential of DSB Repair Pathways

8.3.1 DSB Repair Pathways as Predictors of Radiation Response and Treatment Outcome

8.3.2 Small Molecule Inhibitors of DSB Repair Pathways

8.3.3 Synthetic Lethality

8.4 Summary

References

9 DNA Base Excision Repair: A Recipe for Survival

9.1 Introduction

9.2 DNA Damage

9.2.1 Endogenous DNA Lesions

9.2.2 Exogenous Lesions

9.2.2.1 Drugs and Other Alkylating Agents

9.3 Base Excision Repair (BER): A Pathway for Repairing Inappropriate Bases and Single-Strand Breaks: Early Observations

9.3.1 Further Clarification of the Base Excision Step

9.4 Distinct Catalytic Mechanisms of Mono and Bifunctional DNA Glycosylases

9.5 A Common Mechanism for Substrate Recognition by Mono and Bifunctional DNA-Glycosylases

9.6 Mechanism of Discrimination of Damaged from Normal Bases by DNA Glycosylases

9.7 Distinct Steps Following Base Excision by DNA Glycosylases: Repair of AP Sites and Single-Strand Interruption with Nonligatable Termini

9.7.1 AP-Endonuclease (APE), a Ubiquitous Repair Protein with Dual Nucleolytic Activities

9.7.2 Mammalian Cells Express Only Xth type APE, APE1

9.7.3 Additional APE's Identified in Mammals

9.7.4 Additional Complexities: Involvement of PNK in a BER Subpathway for Mammalian Cells

9.8 Repair of Alkylated Bases by Monofunctional DNA Glycosylases and by MGMT, an Unusual Suicide Protein

9.9 Distal Steps in BER

9.10 Complexity of BER in Mammalian Cells: SN- vs. LP-BER

9.11 Repair Interactome A New Paradigm in BER

9.12 Coordination of Reaction Steps in the BER Pathway

9.13 Essentiality and Biological Consequences of BER Deficiency

9.13.1 Nonessentiality of Individual DNA Glycosylases in Mammals

9.13.2 APE1 is Essential in Mammalian Cells

9.13.3 Accumulation of Single-Strand Breaks in the Genome of APE1-Null Cells

9.14 BER in Mitochondria

9.15 Regulation of BER Activity In Vivo in Response to Genotoxic Stress

9.15.1 Sumoylation of TDG

9.15.2 Acetylation of DNA Glycosylases

9.16 Synopsis and Future Perspective

References

10 DNA Damage Tolerance and Translesion Synthesis

10.1 Introduction

10.2 In the Wilderness Pre 1999

10.3 1999 Light at the End of the Tunnel Y Family Polymerases Discovered

10.4 Structures of Y-Family Polymerases

10.5 Functions of Polymerases in TLS

10.5.1 Pol

10.5.2 Pol

10.5.3 Pol

10.5.4 Rev1 and pol

10.6 Localisation and Protein-Protein Interactions of TLS Polymerases

10.7 Polymerase Switching

10.7.1 Ubiquitination of PCNA

10.7.2 Rad18 and Rad5

10.8 Events at Stalled Forks

10.9 Concluding Remarks

References

11 Nucleotide Excision Repair: from DNA Damage Processing to Human Disease

11.1 Introduction

11.2 Global Genome Repair

11.2.1 DNA Lesion Recognition in GG-NER

11.2.2 Assembly of the Preincision Complex

11.2.3 Dual Incision Step

11.2.4 The Post-Incision Step in NER

11.2.5 Damage Signaling in NER

11.2.6 Chromatin Structure and NER

11.3 Transcription Coupled Repair

11.3.1 Molecular Models for TC-NER

11.4 NER Deficiencies and Cancer

11.5 Perspectives

References

12 Chromosomal Single-Strand Break Repair

12.1 The Source and Structure of Endogenous DNA Single-Strand Breakage

12.2 DNA Single-Strand Breaks and Cell Fate

12.3 Mechanisms of Chromosomal Single-Strand Break Repair (SSBR)

12.3.1 Detection of SSBs

12.3.2 DNA End Processing

12.3.3 DNA Gap Filling

12.3.4 DNA Ligation

12.4 The Organisation of SSBR

12.5 SSBR and the Cell Cycle

12.6 SSBR and Hereditary Genetic Disease

12.6.1 Ataxia with Oculomotor Apraxia Type-1 (AOA1)

12.6.2 Spinocerebellar Ataxia with Axonal Neuropathy-1 (SCAN-1)

12.7 Do SSBs and/or DSBs Cause SCAN1 and AOA1?

12.8 SSBs and Cancer

12.9 SSBs and Neurodegeneration

References

13 Mouse Models of DNA Double Strand Break Repair Deficiency and Cancer

13.1 Overview

13.2 Introduction

13.3 DNA DSB Repair Pathways

13.4 Mouse Models of DSBR Deficiency and Tumorigenesis

13.4.1 Inactivation of Homologous Recombination in the Mouse

13.4.2 Inactivation of Non-Homologous End-Joining in the Mouse

13.4.3 Inactivation of the DNA Damage Response

13.5 Conclusions and Perspectives

References

14 Cancer Biomarkers Associated with Damage Response Genes

14.1 Introduction

14.2 The Cellular Damage Response

14.3 Definitions of Prognostic and Predictive Factors

14.4 Biological Samples for Biomarker Measurements: Technical Considerations

14.5 Measurement of Biomarkers at the Protein Level

14.5.1 Protein Expression by Immunohistochemistry

14.5.2 Protein Expression in Serum and Plasma

14.6 Measurement of Biomarkers at the mRNA Level

14.7 Measurement of Biomarkers at the DNA Level

14.7.1 DNA Adducts and Measurements of Oxidative Stress

14.7.2 Germline Mutations as Biomarkers

14.7.3 Detection of Circulating Free Mutant DNA (ctDNA)

14.7.4 Gene Promoter Methylation as a Predictive Factor

14.7.5 Single Nucleotide Polymorphisms and Genome Wide Association Studies: Cancer Risk and Pharmacogenetics

14.8 Conclusions

References

15 Linking Human RecQ Helicases to DNA Damage Response and Aging

15.1 Introduction: Genome Instability Syndromes and Aging

15.2 Human RecQ Helicases and DNA Double Strand Break Response

15.3 Human RecQ Helicases and DNA Replication Stress

15.4 Mouse Models Associated with RecQ Helicase Deficiency

15.5 Other RecQ Helicases

15.6 Perspectives

References

16 Single-Stranded DNA Binding Proteins Involved in Genome Maintenance

16.1 Single Stranded DNA

16.2 Evolution of SSBs

16.3 Structural Organisation

16.4 E.coli SSB

16.5 An Introduction to Replication Protein A

16.6 RPA Structure and DNA Binding

16.7 RPA Interacting Proteins

16.8 Phosphorylation of RPA

16.9 RPA and the Link with HDR Repair

16.10 hSSB1 and hSSB2

16.11 SSBs as Drug Targets

16.12 Summary

References

17 The Fanconi anemia-BRCA Pathway and Cancer

17.1 Introduction

17.2 Fanconi anemia

17.3 The Fanconi anemia-BRCA Pathway

17.3.1 The Fanconi anemia Genes

17.3.2 The FA Core Complex

17.3.3 Monoubiquitination of FANCD2 and FANCI

17.3.4 Activation of the FA-BRCA Pathway

17.3.5 Deubiquitination of FANCD2 by USP1

17.3.6 Localization of FA Proteins in Chromatin

17.3.7 Interaction of FA Proteins and Non-FA Proteins Involved in DNA Repair and DNA Damage Response

17.4 Cellular Defects in FA

17.4.1 Homologous Recombination

17.4.2 Translesion Synthesis

17.4.3 Function of FA Proteins in Intra S Phase Cell Cycle Checkpoints

17.4.4 Notch-HES1 Pathway and the FA Core Complex

17.4.5 Other Functions of FA Proteins and Other Proteins Interacting with FA Proteins

17.5 FA Animal Models

17.5.1 Mouse Models

17.5.2 Other Models

17.6 The FA-BRCA Pathway in Human Cancer in the General (Non-FA) Population

17.6.1 FANCF Methylation in Ovarian Cancer

17.6.2 FANCF Methylation in Other Tumors

17.6.3 Other FA Genes

17.7 Implication of the FA-BRCA Pathway in Cancer Therapy

17.7.1 Exploiting the Defects of the FA-BRCA Pathway in Cancer Cells

17.7.2 Functional Restoration of the FA-BRCA Pathway as a Mechanism of Acquired Drug Resistance

17.7.3 The FA-BRCA Pathway as a Drug Target

17.8 Concluding Remarks

References

18 BRCA1 and BRCA2: Role in the DNA Damage Response, Cancer Formation and Treatment

18.1 Introduction

18.2 BRCA1 Structure and Function

18.2.1 BRCA1 and DNA Repair

18.2.2 BRCA1, DNA Damage Signaling and Cell Cycle Arrest

18.2.3 BRCA1 Ubiquitination and the DNA Damage Response

18.2.4 BRCA1 and Transcriptional Regulation

18.3 BRCA2 Structure and Function

18.3.1 BRCA2 and Cell Cycle Regulation

18.3.2 BRCA2 Chromatin Remodeling and Transcriptional Regulation

18.4 Tissue Specificity of BRCA1 and BRCA2 Related Cancers

18.5 BRCA1, BRCA2 and Cancer Treatment

18.6 Conclusion

References

Index