Apoptosis and Beyond E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1681

Veröffentlichungsjahr: 2018

Beschreibung

These volumes teach readers to think beyond apoptosis and describes all of the known processes that cells can undergo which result in cell death This two-volume source on how cells dies is the first, comprehensive collection to cover all of the known processes that cells undergo when they die. It is also the only one of its kind to compare these processes. It seeks to enlighten those in the field about these many processes and to stimulate their thinking at looking at these pathways when their research system does not show signs of activation of the classic apoptotic pathway. In addition, it links activities like the molecular biology of one process (eg. Necrosis) to another process (eg. apoptosis) and contrasts those that are close to each. Volume 1 of Apoptosis and Beyond: The Many Ways Cells Die begins with a general view of the cytoplasmic and nuclear features of apoptosis. It then goes on to offer chapters on targeting the cell death mechanism; microbial programmed cell death; autophagy; cell injury, adaptation, and necrosis; necroptosis; ferroptosis; anoikis; pyronecrosis; and more. Volume 2 covers such subjects as phenoptosis; pyroptosis; hematopoiesis and eryptosis; cyclophilin d-dependent necrosis; and the role of phospholipase in cell death. * Covers all known processes that dying cells undergo * Provides extensive coverage of a topic not fully covered before * Offers chapters written by top researchers in the field * Provides activities that link and contrast processes to each other Apoptosis and Beyond: The Many Ways Cells Die will appeal to students and researchers/clinicians in cell biology, molecular biology, oncology, and tumor biology.

Leseprobe

CONTENTS

Cover

Title Page

Copyright

List of Contributors

Chapter 1: General View of the Cytoplasmic and Nuclear Features of Apoptosis

Abbreviations

1.1 Introduction

1.2 Cytoplasmic Events

References

Chapter 2: Mitochondria in Focus: Targeting the Cell-Death Mechanism

Abbreviations

2.1 Introduction

2.2 Mitochondria: Overview

2.3 Mitochondrial Apoptotic Pathways

2.4 Mitochondria between Cellular Life and Death

2.5 Conclusion

References

Chapter 3: Microbial Programmed Cell Death

Abbreviations

3.1 Introduction

3.2 Sporulation: A Tale of Two Bacterial Cell-Death Pathways

3.3 Toxin–Antitoxin Systems

3.4 PCD in S. aureus Biofilm Development

3.5 Conclusion

References

Chapter 4: Autophagy

Abbreviations

4.1 Introduction

4.2 Types of Autophagy

4.3 Functions of Autophagy

4.4 Conclusion

References

Chapter 5: Cell Injury, Adaptation, and Necrosis

Abbreviations

5.1 Introduction: Reversible vs. Irreversible Cell Injury

5.2 Reversible Cell Injury: Adaptation and Intracellular Accumulations

5.3 Irreversible Cell Injury and Cell Death

5.4 Conclusion

References

Chapter 6: Necroptosis

Abbreviations

6.1 Introduction

6.2 Inducing Necroptosis

6.3 Mechanisms of Necroptosis

6.4 Outcomes of Necroptosis: Good or Bad?

6.5 Crosstalk with Other Forms of Cell Death (Apoptosis and Pyroptosis)

6.6 Targeting Necroptosis (RIPK1/RIPK3/MLKL Inhibitors)

6.7 Conclusion

References

Chapter 7: Ferroptosis

Abbreviations

7.1 Introduction: The Balance of Cell Death

7.2 Overview of Free Radicals

7.3 Molecular Mechanism of Ferroptosis

7.4 Clinical Significance of Ferroptosis

References

Chapter 8: Anoikis Regulation: Complexities, Distinctions, and Cell Differentiation

Abbreviations

8.1 Anoikis: Basic Forensics

8.2 Investigation of Anoikis: Who, What, When, Why?

8.3 Differentiation State-Specific Regulation of Anoikis: The Case of Human Intestinal Epithelial Cells

8.4 Anoikis and Disease: Too Much or Too Little, It's Still Unhealthy

8.5 Conclusion

References

Chapter 9: Cornification

Abbreviations

9.1 Cornification is a Key Step in the Terminal Differentiation of Epidermal Keratinocytes

9.2 The Mechanism of Cornification

9.3 Differences and Commonalities between Cornification and Other Modes of Cell Death

References

Chapter 10: Excitotoxicity

Abbreviations

10.1 Introduction

10.2 Defining Excitotoxicity

10.3 The Pathophysiology of Excitotoxicity

10.4 Excitotoxicity and Oxidative Stress

10.5 Excitotoxicity and Brain Injuries

10.6 Excitotoxicity and Neurodegenerative Diseases

10.7 Neuroradiologic Observations of Excitotoxicity

10.8 Conclusion

References

Chapter 11: Molecular Mechanisms Regulating Wallerian Degeneration

Abbreviations

11.1 Introduction

11.2 Slow Wallerian Degeneration and the Mechanism of Neuroprotection

11.3 Induction of Neuronal Protection by Signaling Mechanisms Activated by Wlds

11.4 Wallerian Degeneration and the Immune Response to Traumatic Nerve Injury

11.5 Role of Wallerian Degeneration in the Mechanism of Functional Recovery Following the Traumatic Injury of Peripheral Nerves

11.6 Demyelination of Axons and Functional Recovery during Wallerian Degeneration

11.7 Role of Wallerian Degeneration in the Development of Neuropathic Pain

11.8 Conclusion

References

Chapter 12: Pyronecrosis

Abbreviations

12.1 Introduction

12.2 Definition and Morphology

12.3 Inflammation and Cell Death

12.4 Relation of Pyronecrosis to Other Types of Cell Death

12.5 Molecular Pathway and Mechanism

12.6 Pyronecrosis-Inducing Factors

12.7 Conclusion

References

Chapter 13: Phenoptosis: Programmed Death of an Organism

Abbreviations

13.1 Definition of Phenoptosis and a Short History of the Problem

13.2 Phenoptosis of Unicellular Organisms

13.3 Phenoptosis of Plants: Discovery of the Genes of Death of a Multicellular Organism

13.4 Phenoptosis in Invertebrates: “Horrible Cruelty of Life”

13.5 Phenoptosis in Vertebrates

13.6 Aging as Slow (Chronic) Phenoptosis

13.7 Non-Aging Living Beings

13.8 Aging-Stimulated Evolvability is a Function Characteristic of Most Living Beings

13.9 Why Natural Selection Could Not Eliminate Phenoptoses

13.10 Why Do We Need an Aging Program if an Organism Will Die in Any Case Due to Accumulation of Occasional Damages?

13.11 Accumulation of Stochastic Injuries During Aging

13.12 An Attempt to Identify a Key Component of the Aging Program and to Abolish It

13.13 Regulation of Aging by an Organism

13.14 General Scheme of Regulation of mROS-mediated Phenoptoses

13.15 Perspectives for the Pharmacological Switching Off of Counterproductive Phenoptotic Programs in Humans: From Homo sapiens to Homo sapiens liberatus

Acknowledgments

References

Chapter 14: Molecular Mechanisms Underlying Oxytosis

Abbreviations

14.1 Introduction

14.2 The Role of GSH in Oxytosis

14.3 Upstream Mechanisms of Mitochondrial Dysfunction in Oxytosis

14.4 Mitochondrial Dysfunction in Oxytosis

14.5 Downstream Mechanisms of Mitochondrial Dysfunction

14.6 Oxytosis and ER Stress: Common Features and Differences

14.7 Conclusion

References

Chapter 15: Pyroptosis

Abbreviations

15.1 Introduction

15.2 Caspases

15.3 Canonical Inflammasomes: Caspase 1-Activating Platforms

15.4 The Non-canonical Caspase 11 Inflammasome

15.5 Crosstalk between Pyroptosis, Necroptosis, and Apoptosis

References

Chapter 16: Paraptosis

Abbreviations

16.1 Introduction

16.2 Definition

16.3 Morphology

16.4 Mechanisms

16.5 Pathways

16.6 Proteome Profile

16.7 Potential Medical Implications

16.8 Conclusion

References

Chapter 17: Hematopoiesis and Eryptosis

Abbreviations

17.1 Introduction

17.2 Hematopoiesis

17.3 Erythrocytes

17.4 Structure of Leukocytes

17.5 Function of WBCs

17.6 Eryptosis

17.7 Triggers and Signaling of Eryptosis

17.8 Physiological Significance of Eryptosis

17.9 Pathophysiological Significance of Eryptosis

17.10 Conclusion

References

Chapter 18: Cyclophilin D-Dependent Necrosis

Abbreviations

18.1 Introduction

18.2 Cyclophilins

18.3 Mechanism of CypD-Dependent Necrosis

18.4 Role of CypD in Diseases

18.5 CypD Inhibitors

18.6 Future Prospects

References

Chapter 19: Role of Phospholipases in Cell Death

Abbreviations

19.1 Introduction

19.2 Apoptosis

19.3 Role of Phospholipases in Autophagy

19.4 Role of Phospholipases in Necrosis

19.5 Conclusion

References

Chapter 20: TRIAD (Transcriptional Repression-Induced Atypical Death)

Abbreviations

20.1 Introduction

20.2 Induction of TRIAD In Vitro

20.3 Morphological Features of TRIAD

20.4 Molecular Features of TRIAD

20.5 Roles of YAPΔC in TRIAD and Neurodegeneration

20.6 TRIAD In Vivo

20.7 Conclusion

References

Chapter 21: Alkylating-Agent Cytotoxicity Associated with O6-Methylguanine

Abbreviations

21.1 Introduction

21.2 General Principles of Alkylating Agents

21.3 The MGMT Gene and AGT Protein Structure

21.4 Methylating Agent-Induced Cell Death

21.5 Pharmacology of Clinically Relevant Methylating Agents

Acknowledgments

References

Chapter 22: Entosis

Abbreviations

22.1 Introduction

22.2 Definition

22.3 Discovery of Entosis

22.4 Entosis: Initiation and Progress

22.5 Entosis and Other Cell-in-Cell Structures: Differences and Similarities

22.6 Molecular Mechanism Regulating Entosis

22.7 Signaling Mechanism in Entosis

22.8 Occurrence of Entosis in Different Types of Cells

22.9 Entosis and its Implications in Cancer: Pro-tumorigenic Process or Tumor-Suppressive Mechanism?

22.10 Biological Significance

22.11 Overview

22.12 Conclusion

References

Chapter 23: Mitotic Catastrophe

Abbreviations

23.1 Introduction

23.2 Mitosis and the Cell Cycle in the Context of MC

23.3 Molecular Processes in MC Initiation and Execution

23.4 Cell Death Resulting from MC and Links to Other Modes of Cell Death

23.5 MC Detection Methods

23.6 MC in the Treatment of Cancer

23.7 Conclusion

References

Chapter 24: NETosis and ETosis: Incompletely Understood Types of Granulocyte Death and their Proposed Adaptive Benefits and Costs

Abbreviations

24.1 Role of Neutrophils in Infection and Inflammation

24.2 Apoptosis of Neutrophils

24.3 Non-apoptotic Death

24.4 Discovery of Neutrophil Extracellular Traps

24.5 Testing and Validation of Antimicrobial Functions of NETs

24.6 Containment of Microbes versus Escape from NETs

24.7 Regulation of NETosis

24.8 Similarities and Differences between NETosis and Other Forms of Cell Death

24.9 Involvement of NETosis in Autoimmunity

24.10 Conclusion

References

Chapter 25: Parthanatos: Poly ADP Ribose Polymerase (PARP)-Mediated Cell Death

Abbreviations

25.1 Introduction

25.2 Definition of Parthanatos and its Place in the Current Cell-Death Pantheon

25.3 Relevance of PARP and Parthanatos to Disease Conditions

25.4 Known Mediators of Parthanatos and their Cross-Talk

25.5 Putative Mediators of Parthanatos

25.6 Protein–Protein Interactions of Potential Relevance in Parthanatos

25.7 Parthanatos and the Development of Novel Therapeutics

25.8 Conclusion

References

Chapter 26: Methuosis: Drinking to Death

Abbreviations

26.1 Introduction

26.2 Discovery of Methuosis

26.3 Mechanism of Methuosis

26.4 Methuosis Induced by Synthetic Small Molecules: Indole-Based Chalcones

26.5 Comparison with Other Cell-Death Mechanisms

26.6 Conclusion

References

Chapter 27: Oncosis

Abbreviations

27.1 Introduction

27.2 Oncosis Induced by Anticancer Agents

27.3 Morphological Variants of Oncosis

27.4 Biochemical Mechanisms of Oncosis

27.5 Genetic and “Programmed” Nature of Oncosis

27.6 Incidence of Oncosis and Relevance to Disease

27.7 Oncosis in Myocardial Ischemia

27.8 Oncosis in Chemotherapeutic Cardiotoxicity

References

Chapter 28: Autoschizis: A Mode of Cell Death of Cancer Cells Induced by a Prooxidant Treatment In Vitro and In Vivo

Abbreviations

28.1 Introduction

28.2 About Cell Thanatology

28.3 Background

28.4 Early Observations of a New Mode of Cell Death: Autoschizis

28.5 Cytotoxicity of VC:VK3 on Tumor Cells: The Causa Mortis

28.6 Flow Cytometry

28.7 Autoschizis or Self-Excisions of Tumor Cells Caused By Prooxidants

28.8 Injuries Induced by VC:VK3 Combination Treatment Lead to Tumor Cell Death

28.9 Xenotransplanted Prostate Carcinoma (DU145) in Nude Mice Treated with VC:VK3

28.10 Summarizing the Data

28.11 Conclusion

28.12 Addendum

Acknowledgments

References

Chapter 29: Programmed Death 1 (PD1)-Mediated T-Cell Apoptosis and Cancer Immunotherapy

Abbreviations

29.1 Introduction

29.2 T-Cell Development, Differentiation, Function, and Degradation

29.3 Structure of PD1

29.4 Expression and Functions of PD1

29.5 Structure and Expression of the PD1 Ligands PD-L1 and PD-L2

29.6 Regulation of PD-L1 and PD-L2 Expression

29.7 Expression Patterns of PD1, PD-L1, and PD-L2 in Cancer Tissues and Tumor-Infiltrating Lymphocytes

29.8 Role of PD1, PD-L1, and PD-L2 in Apoptosis

29.9 Co-inhibitory Signal of PD-L1/PD-L2–PD1 Inhibits TCR Signaling

29.10 MicroRNA and PD1 Signaling

29.11 Targeting of the PD-L–PD1 Pathway as a Promising Cancer Immunotherapy

29.12 Adoptive Cell Transfer for Suppression of Tumor Growth

29.13 Conclusion

References

Index

End User License Agreement

List of Tables

Table 4.1

Table 4.2

Table 6.1

Table 7.1

Table 13.1

Table 16.1

Table 18.1

Table 18.2

Table 19.1

Table 20.1

Table 20.2

Table 21.1

Table 21.2

Table 22.1

Table 23.1

Table 23.2

Table 23.3

Table 24.1

Table 25.1

Table 27.1

Table 28.1

Table 28.2

Table 28.3

Table 28.4

Table 28.5

Table 28.6

Table 28.7

Table 29.1

Table 29.2

Table 29.3

List of Illustrations

Figure 1.1

Figure 2.1

Figure 2.2

Figure 2.3

Figure 2.4

Figure 2.5

Figure 3.1

Figure 3.2

Figure 3.3

Figure 4.1

Figure 4.2

Figure 4.3

Figure 4.4

Figure 4.5

Figure 4.6

Figure 5.1

Figure 5.2

Figure 5.3

Figure 5.4

Figure 5.5

Figure 5.6

Figure 5.7

Figure 5.8

Figure 5.9

Figure 5.10

Figure 5.11

Figure 5.12

Figure 5.13

Figure 5.14

Figure 5.15

Figure 5.16

Figure 6.1

Figure 6.2

Figure 6.3

Figure 6.4

Figure 6.5

Figure 6.6

Figure 6.7

Figure 6.8

Figure 7.1

Figure 7.2

Figure 7.3

Figure 7.4

Figure 8.1

Figure 8.2

Figure 8.3

Figure 9.1

Figure 9.2

Figure 9.3

Figure 10.1

Figure 11.1

Figure 11.2

Figure 14.1

Figure 15.1

Figure 15.2

Figure 15.3

Figure 15.4

Figure 16.1

Figure 16.2

Figure 16.3

Figure 17.1

Figure 18.1

Figure 18.2

Figure 18.3

Figure 18.4

Figure 18.5

Figure 18.6

Figure 18.7

Figure 19.1

Figure 19.2

Figure 20.1

Figure 21.1

Figure 21.2

Figure 21.3

Figure 21.4

Figure 21.5

Figure 21.6

Figure 21.7

Figure 21.8

Figure 22.1

Figure 23.1

Figure 23.2

Figure 23.3

Figure 24.1

Figure 24.2

Figure 24.3

Figure 25.1

Figure 25.2

Figure 25.3

Figure 25.4

Figure 26.1

Figure 27.1

Figure 27.2

Figure 27.3

Figure 27.4

Figure 27.5

Figure 28.1

Figure 28.2

Figure 28.3

Figure 28.4

Figure 28.5

Figure 28.6

Figure 28.7

Figure 28.8

Figure 28.9

Figure 28.10

Figure 28.11

Figure 28.12

Figure 28.13

Figure 28.14

Figure 28.15

Figure 28.16

Figure 28.17

Figure 28.18

Figure 28.19

Figure 28.20

Figure 28.21

Figure 28.22

Figure 28.23

Figure 28.24

Figure 28.25

Figure 28.26

Figure 28.27

Figure 28.28

Figure 28.29

Figure 28.30

Figure 28.31

Figure 28.32

Figure 28.33

Figure 28.34

Figure 28.35

Figure 28.36

Figure 28.37

Figure 28.38

Figure 28.39

Figure 28.40

Figure 28.41

Figure 28.42

Figure 28.43

Figure 28.44

Figure 28.45

Figure 29.1

Figure 29.2

Figure 29.3

Figure 29.4

Figure 29.5

Figure 29.6

Figure 29.7

Figure 29.8

Figure 29.9

Guide

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Apoptosis and Beyond

The Many Ways Cells Die

Edited by James Radosevich

University of Chicago, United States

This edition first published 2018

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Names: Radosevich, James A. (James Andrew), editor.

Title: Apoptosis and beyond : the many ways cells die / edited by James Radosevich.

Description: Hoboken, NJ : Wiley-Blackwell, 2018. | Includes bibliographical references and index. |

Identifiers: LCCN 2018022533 (print) | LCCN 2018023112 (ebook) | ISBN 9781119432357 (Adobe PDF) | ISBN 9781119432432 (ePub) | ISBN 9781119432425 (cloth)

Subjects: | MESH: Cell DeathClassification: LCC QH671 (ebook) | LCC QH671 (print) | NLM QU 375 | DDC 571.9/36–dc23LC record available at https://lccn.loc.gov/2018022533

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List of Contributors

Julie Alagha

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Arshed Al-Obeidi

Dana-Farber Boston's Children Cancer and Blood Disorder Center

Harvard Medical School

Boston, MA, USA

Sulaiman Alshaar

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Madeeha Aqil

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

D. Arnold

Anesthesiology Unit

Belfast, ME, USA

Lais Costa Ayub

Department of Molecular, Genetic and Structural Biology

University of Ponta Grossa

Ponta Grossa, PR, Brazil

Jamuna A. Bai

Department of Studies in Microbiology

University of Mysore

Mysore, India

Khatja Batool

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Marco Beauséjour

Department of Anatomy and Cellular Biology

University of Sherbrooke

Sherbrooke, QC, Canada

Ariane Boutin

Department of Anatomy and Cellular Biology

University of Sherbrooke

Sherbrooke, QC, Canada

Robert Brown

Department of Pathology and Laboratory Medicine

University of Texas Health Science Center at Houston

Houston, TX, USA

L. Maximilian Buja

Department of Pathology and Laboratory Medicine

University of Texas Health Science Center at Houston

Houston, TX, USA

Ferdinando Chiaradonna

Department of Biotechnology and Biosciences

University of Milano-Bicocca

Milan, Italy

Juel Chowdhury

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Stephanie Conos

The Walter and Eliza Hall Institute of Medical Research

Bundoora, VIC, Australia

Ben A. Croker

Dana-Farber Boston's Children Cancer and Blood Disorder Center

Harvard Medical School

Boston, MA, USA

Carsten Culmsee

Institute of Physiological Chemistry

Philipps University of Marburg

Marburg, Germany

Akshay A. D'Cruz

Dana-Farber Boston's Children Cancer and Blood Disorder Center

Harvard Medical School

Boston, MA, USA

Zane Deliu

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Raquel De Souza

University Health Network, Department of Radiation Physics, Pharmaceutical Sciences

University of Toronto

Toronto, ON, Canada

Humberto De Vitto

Center of Health and Science

Federal University of Rio de Janeiro

Rio de Janeiro, Brazil

Kirk E. Dineley

Chicago College of Osteopathic Medicine

Midwestern University

Downers Grove, IL, USA

Amalia M. Dolga

Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP) University of Groningen

Groningen, The Netherlands

Leopold Eckhart

Department of Dermatology Medical University of Vienna

Vienna, Austria

Amos Fatokun

School of Medical Sciences, Faculty of Life Sciences

University of Bradford

Bradford, UK

Lawrence E. Feldman

Department of Hematology and Oncology

University of Illinois at Chicago

Chicago, IL, USA

Sarah G. Fitzpatrick

Department of Oral and Maxillofacial Diagnostic Sciences University of Florida

Gainesville, FL, USA

Chintan C. Gandhi

Department of Hematology and Oncology

University of Illinois at Chicago

Chicago, IL, USA

Goutham Ganjam

Institute of Pharmacology and Clinical Pharmacy, Biochemisch-Pharmakologisches Centrum Marburg

Philipps University of Marburg

Marburg, Germany

Motti Gerlic

Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine Tel Aviv University

Tel Aviv, Israel

Ugur Gezer

Department of Basic Oncology, Oncology Institute

Istanbul University Istanbul, Turkey

J. Gilloteaux

Department of Anatomical Sciences

St. Georges' University International School of Medicine, KB Taylor Global Scholar's Program at Northumbria University

Newcastle upon Tyne, UK

Sara C. Gordon

School of Dentistry

Oral Medicine University of Washington

Seattle, WA, USA

Sarathi Hallock

Memorial University of Newfoundland, AMC Cancer Research Center

University of Texas Health Science Center at Houston

Houston, TX, USA

Neal D. Hammer

Department of Microbiology and Molecular Genetics

Michigan State University

East Lansing, MI, USA

Birgit Honrath

Institute of Pharmacology and Clinical Pharmacy, Biochemisch-Pharmakologisches Centrum Marburg

Philipps University of Marburg

Marburg, Germany

and

Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP) University of Groningen

Groningen, The Netherlands

J.M. Jamison

Department of Urology and Apatone Development Laboratory

Summa Health System

Akron, OH, USA

Anja Jelinek

Institute of Pharmacology and Clinical Pharmacy, Biochemisch-Pharmakologisches Centrum Marburg

Philipps University of Marburg

Marburg, Germany

Paiboon Jungsuwadee

School of Pharmacy

Fairleigh Dickinson University

Florham Park, NJ, USA

Maryam Khalili

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Kate E. Lawlor

The Walter and Eliza Hall Institute of Medical Research

Bundoora, VIC, Australia

Latha M. Malaiyandi

Chicago College of Osteopathic Medicine

Midwestern University

Downers Grove, IL, USA

Chandi Charan Mandal

Department of Biochemistry

Central University of Rajasthan

Rajasthan, India

Nicholas Marschalk

Chicago College of Osteopathic Medicine

Midwestern University

Downers Grove, IL, USA

Jatin Mehta

National Institute of Pathology, ICMR

Safdarjang Hospital

New Delhi, India

Sandra Neitemeier

Institute of Pharmacology and Clinical Pharmacy, Biochemisch-Pharmakologisches Centrum Marburg

Philipps University of Marburg

Marburg, Germany

Hitoshi Okazawa

Department of Neuropathology, Medical Research Institute

Tokyo Medical and Dental University

Tokyo, Japan

Sina Oppermann

German Cancer Research Center (DKFZ) and National Center of Tumordiseases (NCT)

Heidelberg, Germany

Abdallah Oweidi

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Roberta Palorini

SYSBIO Center for Systems Biology, Department of Biotechnology and Biosciences

University of Milano-Bicocca

Milan, Italy

and

Luxembourg Centre for Systems Biomedicine

Esch-sur-Alzette, Luxembourg

Lawrence A. Potempa

Roosevelt University College of Pharmacy

Schaumburg, IL, USA

Vijay K. Prajapati

Department of Biochemistry

Central University of Rajasthan

Rajasthan, India

Marko Radic

Department of Microbiology, Immunology and Biochemistry

University of Tennessee Health Science Center

Memphis, TN, USA

James A. Radosevich

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Manikanda Raja

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Maren Richter

Institute of Pharmacology and Clinical Pharmacy, Biochemisch-Pharmakologisches Centrum Marburg

Philipps University of Marburg

Marburg, Germany

James A. Rickard

Department of Biochemistry

La Trobe University

Melbourne, VIC, Australia

Mollie K. Rojas

Department of Oral Medicine and Diagnostic Sciences

University of Illinois at Chicago

Chicago, IL, USA

Inbar Shlomovitz

Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv, Israel

M.V. Skulachev

Belozersky Institute of Physico-Chemical Biology, Institute of Mitoengineering, Faculty of Bioengineering and Bioinformatics

Lomonosov Moscow State University

Moscow, Russia

V.P. Skulachev

Belozersky Institute of Physico-Chemical Biology, Institute of Mitoengineering, Faculty of Bioengineering and Bioinformatics

Lomonosov Moscow State University

Moscow, Russia

J.L. Summers

Department of Urology and Apatone Development Laboratory

Summa Health System

Akron, OH, USA

Takuya Tamura

Department of Neuropathology, Medical Research Institute

Tokyo Medical and Dental University

Tokyo, Japan

Mohammad Tauseef

Department of Pharmaceutical Sciences College of Pharmacy

Chicago State University

Chicago, IL, USA

Ravishankar Rai V.

Department of Studies in Microbiology

University of Mysore

Mysore, India

Pierre H. Vachon

Department of Anatomy and Cellular Biology

University of Sherbrooke

Sherbrooke, QC, Canada

Juan P. Valencia

University of Rio de Janeiro

Rio de Janeiro, Brazil

James E. Vince

The Walter and Eliza Hall Institute of Medical Research

Bundoora, VIC, Australia

Giuseppina Votta

SYSBIO Center for Systems Biology, Department of Biotechnology and Biosciences

University of Milano-Bicocca

Milan, Italy

Priya Weerasinghe

Department of Pathology and Laboratory Medicine

University of Texas Health Science Center at Houston

Houston, TX, USA

Kenneth Yip

Department of Biology

University of Toronto

Toronto, ON, Canada

Ebru Esin Yoruker

Department of Basic Oncology, Oncology Institute

Istanbul University Istanbul, Turkey

1General View of the Cytoplasmic and Nuclear Features of Apoptosis

Humberto De Vitto,1 Juan P. Valencia,2 and James A. Radosevich3

1Center of Health and Science, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil

2University of Rio de Janeiro, Rio de Janeiro, Brazil

3Department of Oral Medicine and Diagnostic Sciences, University of Illinois at Chicago, Chicago, IL, USA

Abbreviations

AIF

apoptosis-inducing factor

Apaf-1

apoptotic protease activating factor-1

ATP

adenosine triphosphate

BA

bongkrekic acid

Bcl-2

B-cell lymphoma-2

BID

BH3-interacting domain death agonist

bp

base pair

CAD

caspase-activated DNase

c-FLIP

cellular FLICE-inhibitory protein

Chx

cyclohexamide

CsA

cyclosporine A

CTL

cytotoxic T lymphocyte

cyt c

cytochrome c

DISC

death-inducing signal complex

DED

death effector domain

endo D

endonuclease D

endo G

endonuclease G

ER

endoplasmic reticulum

FADD

Fas-associated death-domain protein

FasL

fatty acid synthetase ligand

FasR

fatty acid synthetase receptor

Gzm-A

granzyme-A

Gzm-B

granzyme-B

ICAD

inhibitor of caspase-activated DNase

Kb

kilobase

MEF

mouse embryonic fibroblast

MOMP

mitochondrial outer-membrane permeabilization

NK

natural killer

OMM

outer mitochondrial membrane

PCD

programmed cell death

PFN

Perforin

PT

pore transition

RIP

receptor-interacting protein

ROCK I

Rho effector protein

ROS

reactive oxygen species

SET

stress-response complex

tBID

truncated BID

TNF

tumor necrosis factor

TNFR1

tumor necrosis factor receptor 1

TRADD

TNF receptor-associated death domain

TUNEL

terminal deoxynucleotide tranferase dUTP nick end labeling

1.1 Introduction

The normal development of a cell and the life cycles of the multicellular organism rely on a finely tuned balance between cell survival and death. In a biological context, cells need to grow, divide, and die. In regard to the latter process, cells have developed a very precisely regulated means of programmed cell death (PCD), which contributes to the maintenance of normal cell turnover, leading to reduced impact on tissues, organs, and the organism itself. Some cells have evolved a PCD process called apoptosis. Apoptosis can be simply defined as a set of biochemical cytoplasmic and mitochondrial events that may lead to the execution phase of nuclear events.

A wide array of stress stimuli can trigger the apoptotic process, and the biochemical signal can then be amplified in the cytoplasm and mitochondria by both extrinsic and intrinsic pathways. The convergence of the apoptotic signal is considered the activation of a family of cysteine aspartyl-specific proteases (caspases), composed of 12 proteins strictly involved in the apoptotic cell death process. The dying cells activate the execution pathway that leads to the appearance of blebs and to the “pinching off” of many of them, forming “apoptotic bodies,” which may be rounded and retracted from their own tissue. Subsequently, the immune system cells are able to eliminate the apoptotic bodies through an engulfment cell process. The morphological and biochemical features during the apoptotic process are not fully understood.

At the nuclear level, it is well established that endonucleases and exonucleases may hydrolyze the DNA into small fragments (200 pb) [1]. The nuclear events depend on caspase activation. Caspase 3 is considered the most important protease of the executioner pathway, and is activated by different initiator caspases. For instance, caspase 8 is activated from the death receptor, caspase 9 is involved in the mitochondrial apoptotic process, and caspase 10 is involved in the Perforin/granzyme (PFN/Gzm) pathways. The cleaved caspase 3 cleaves the endonuclease caspase-activated DNase (CAD), degrading the DNA at nucleosomal linkers [2,3], which generates small DNA fragments (∼50–300 kb). The subsequent processing of the DNA by exonucleases and endonucleases leads to the formation of 200 bp fragments. Many organelles, such as the Golgi apparatus, endoplasmic reticulum (ER), lysosomes, and mitochondria, can be recycled or eliminated, depending on the apoptotic stimuli. It is important to note that mitochondria play a pivotal role in apoptosis, since they can release cytochrome c (cyt c) and endonuclease D (endo D), leading to cell death [4,5].

One of the apoptotic pathways is the extrinsic or death-receptor pathway. It depends for its activation on a death domain and a death ligand, such as tumor necrosis factor alpha (TNFα) and tumor necrosis factor receptor 1 (TNFR1). The ligand represents the external death signal, leading to the intracellular signaling of the effector pathway. The main receptors recruit adaptor proteins like Fas-associated death-domain protein (FADD), TNF receptor-associated death domain (TRADD), and receptor-interacting protein (RIP) [6–8], which in turn recruit other molecules such as pro-caspase 8. The dimerization of the death effector domain (DED) leads to the formation of a death-inducing signal complex (DISC), triggering the subsequent process of autocatalysis of pro-caspase 8 to an activated protein (caspase 8) [9]. Caspase 8 activation is considered the main feature that starts the extrinsic pathway, leading to cell death. In many cases, depending on the apoptotic stimuli, the extrinsic pathway can crosstalk with the intrinsic pathway through proteolysis of the BH3-only protein, BH3-interacting domain death agonist (BID), which is what promotes the release of cyt c from the mitochondria into the cytoplasm. In the cytoplasm, cyt c may be assembled with the adaptor protein apoptotic protease activating factor-1 (Apaf-1) and ATP, generating in the cytosol the multimolecular holoenzyme complex called the “apoptosome” (Figure 1.1) [10].

Figure 1.1 Schematic representation of the cytoplasmic and nuclear events of apoptosis. The Perforin/Granzyme pathway, extrinsic pathway, and intrinsic pathway represent the three main pathways of apoptosis. Through a vast array of death signals, all three pathways can be triggered. (A) The Perforin/Granzyme pathway is a unique pathway that partially works in a caspase-independent fashion (granzyme A branch), leading directly to DNA cleavage and cell death. However, the activation of the granzyme B branch can trigger initiator caspase 10, which activates executioner caspase 3. (B) The extrinsic pathway, when activated, can cleave pro-caspase 8 to caspase 8 by FAAD, then activate executioner caspase 3. Caspase 8 plays an important role in the activation of a truncated BID (tBID) protein, leading to the release of mitochondria proteins like cyt c. (C) Upon receiving incoming signals, the intrinsic pathway induces MPTP opening, leading to the release from the mitochondria of proteins such as cyt c, endo G/AIF, and Htra2/Omi. On the cytosol, cyt c forms the apoptosome, which cleaves pro-caspase 3, triggering the execution pathway. (D) The execution pathway is characterized by cell shrinkage, chromatin condensation, and the formation of cytoplasmic blebs and apoptotic bodies. cyt c, cytocrome c; FAAD, Fas-associated death domain; MTPT, mitochondrial permeability transition pore.

The PFN/Gzm pathway is considered part of the extrinsic pathway. It is activated when cells are infected by viruses and/or bacteria. Mechanistically, cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells produce granzymes. The granzymes, together with the PFN, may facilitate the pore formation and action of Gzms that lead to cell death. Two types of Gzm, type A (GmzA) and type B (GmzB), have been described. GmzA is considered the most important serine-protease present in CTL and NK granules. GmzB relies on the mechanism of oligomerization of PFN to enter into the cell, and depends for its action on the activation of caspases, principally caspase 3 [11,12].

It is important to note that different stimuli and players are enlisted in the various apoptotic processes. Moreover, it is well known that immune-system cells, mitochondria, and nuclear events are involved in apoptosis. The entire biochemical process is still elusive. Accordingly, the current chapter will focus on cytoplasmic and nuclear events. We describe and highlight an overview of cytoplasmic events, including the extrinsic pathway and perforin/granzyme pathways (GmzA and GmzB), as well as the main nuclear features of the current process, by correlating these events with the intrinsic apoptotic pathway. We then use such pathway characteristics to explore in more detail the mechanisms of the regulation of important human diseases, including cancer and neurodegenerative diseases.

1.2 Cytoplasmic Events

During apoptosis, the dying cells become rounded and retracted from the tissue. Defined “blebs” appear within the cells. The process culminates in the “pinching off” of many blebs, producing “apoptotic bodies.” These bodies recruit phagocytes, which engulf them to recycle some of the molecules. The immune system represents the major mechanism capable of eliminating the apoptotic bodies, apparently in the same way that phagocytes eliminate “non-self” particles. These morphological and biochemical features of apoptosis have been extensively studied, but the whole mechanism is not fully understood.

It is well established that during the apoptotic process, the nuclear DNA is condensed and fragmented. Several proteins, such as endonucleases and exonucleases, may degrade the DNA chain by hydrolyzing it in small fragments, with approximately 200 bp [1]. In the cytoplasm, the Golgi apparatus, ER, lysosomes, and mitochondria can be eliminated or recycled, depending on the apoptotic stimuli. For instance, during oxidative stress involving an increase of reactive oxygen species (ROS), several mitochondrial proteins, such as cyt c and endo D, may be released from the mitochondrial intermembrane space into the cytoplasm and nucleus, leading to cell death [4,5]. Interesting, it has been indentified that the mitochondria, ER, and nucleus are targets of the Gzm pathway, which may trigger apoptosis, facilitating the PCD process.

1.2.1 The Extrinsic Pathway

The extrinsic pathway, also called the death receptor pathway, is involved in transmembrane receptor-mediated interactions, including those of the TNF family [13], which shares the features of the cysteine-rich extracellular domains and a cytoplasmatic domain (death domain) [14]. The death ligand represents the external death signal from the cell surface to the intracellular signaling and effector pathways. The mechanism requires the binding of the extracellular death ligands to the transmembrane cell receptors. The best-characterized ligands and their corresponding death receptors have been identified: (i) TNFα and TNFR1; (ii) fatty acid synthetase ligand and fatty acid synthetase receptor (FasL and FasR); (iii) Apo2 ligand and death receptor 4 (Apo2L and DR4); (iv) Apo2 ligand and death receptor 5 (Apo2L and DR5); and (v) Apo3 ligand and death receptor 3 (Apo3L and DR3) [14–18]. The receptors form clusters and can bind with their cognate trimeric ligands, leading to the recruitment of adaptor proteins, including FADD, TRADD, and RIP [6–8]. In turn, FADD or TRADD can recruit several molecules, such as pro-caspase 8, binding to them via dimerization of the DED, leading to DISC formation and subsequent autocatalysis of pro-caspase 8 and its active form (caspase 8) [9]. Caspase 8 activation is considered the main feature that triggers the extrinsic pathway, leading to cell death. Activated caspase 8 is involved in many proteolytic processes, including the activation of caspases 3, caspase 6, and caspase 7. These enzymes help induce the execution phase of apoptosis (Figure 1.1).

Depending on the apoptotic stimuli, the extrinsic pathway can crosstalk with the intrinsic pathway through proteolysis of the BH3-only protein, BID. The truncated BID (tBID) protein promotes release of mitochondrial cyt c into the cytoplasm, where it can assemble with the apoptosome complex, leading to cell death [10]. However, death receptor-mediated apoptosis can be inhibited by cellular FLICE-inhibitory protein (c-FLIP), which binds to both FADD and caspase 8, inactivating the autocatalytic effect of the caspase 8 complex [19,20]. Different mechanisms of inhibition of the extrinsic apoptosis pathway have also been described, including via the protein Toso, which blocks Fas-induced apoptosis, inhibiting the processing of caspase 8 in immune cells [21].

1.2.1.1 The Perforin/Granzyme Pathway

To eliminate potential dangerous cells like tumor cells or cells infected by viruses or bacteria, the immune system relies on CTLs and NK cells, both of which are produced by the action of Gzms. PFN, a protein capable of binding the membrane of the target cell, facilitate the pore formation that permits the action of Gzms. Gzms are considered specific serine-proteases involved in cell death. They are produced as inactive precursor molecules, designed to avoid the self-destruction of CTLs and NK cells. In human cells, five different Gzms have been reported. GzmA and GzmK are located on chromosome 5 and act as tryptases that cleave proteins following arginine or lysine (basic) residues. GzmB and GzmH are located on chromosome 14. GzmM is located on chromosome 19 and cleaves following methionine or leucine basic residues [22]. There are two Gzm-dependent pathways involved in cell death.

1.2.1.1.1 The Granzyme A Pathway

The GzmA is considered the most important serine-protease mechanism described in CTL and NK granulles. Unlike the GzmB pathway, which relies on the oligomerization of the PFN to enter into the target cell, the GzmA can activate a parallel pathway in a caspase-independent manner, leading to DNA degradation, such as single-stranded DNA damage [23]. Intracellular GzmA substrates have been found in the cytoplasm (Pro-IL-1β) [24], mitochondria (NDUFS3) [25], ER, and nucleus (SET1, APE1, HMGB2) [26–29], and are associated with histone H1, core histones, lamin A, B, and C, Ku70, and PARP1 [30–33]. Various stimuli can trigger the GzmA pathway, such as ROS generation, the loss of membrane potential, and mitochondrial swelling. This can lead to the disruption of the nuclear envelope, inhibition of DNA repair, and activation of cytokines, as a consequence of the accumulation of GzmA in the nucleus [34]. Between mitochondrial changes (within minutes) and phospathidyl serine externalization (30 minutes to 1 hour), dying cells can recruit the macrophage scavenger system [23].

GzmA is less cytotoxic than the GzmB pathway, which is active at micromolar-range concentrations [35]. At 2 hours after the stimulation of apoptosis, several features are present. This cell-death pathway does not activate caspases, because cell-death GzmA activation is known as a non-apoptotic death [36]. Moreover, GzmA does not permebilize the outer mitochondrial membrane (OMM), avoiding the releasing of mitochondrial apoptotic mediators like cyt c. The entry of GzmA into the mitochondria can be partially inhibited by cyclosporine A (CsA) and bongkrekic acid (BA), suggesting a role of permeability for the transition pore (PT) in GzmA mitochondrial damage [23,35].

The oxidative damage drives the ER to make the ER-associated oxidative stress response complex (SET), which contains two endonucleases (Ape1and NM23-H1) and a 5′-3′ exonuclease (Trex1), chromatin modifying proteins (SET1 and pp32), and DNA-binding proteins that protect against DNA distortion (HMGB2) [23,27,29,37]. GzmA enters into the nucleus and cleaves SET1, which inhibits NM23-H1 endonuclease activity, causing this complex to nick the DNA, and allowing Trex1 to act as an endonuclease [38]. In the same way, GzmA cleaves and inactivates HGMB2 and Ape1 [26], cleaves the linker histone H1, and removes the tail of core histones, allowing the nucleases to attack [30]. GzmA then cleaves and inactivates Ku70 and PARP-1, both of which are involved in DNA repair through the recognition of single- or double-strand breaks [32,33].

1.2.1.1.2 The Granzyme B Pathway

GzmB is produced by CTL and NK cells, which release it via granules. It binds its receptor, the mannose-6-phosphate/insulin-like growth factor II receptor, and is endocytosed but remains arrested in endocytic vesicles until it is released by PFN. The GzmB pathway relies on caspase activation, unlike the GzmA pathway.

The proteolitic activity of GzmB is similar to caspase activity, cleaving substrates after the aspartate (basic) residues. Caspase 3, 6, 7, 8, 9, and 10 have been found to serve as GzmB substrates in vitro [39–46], but only caspase 3 is believed to be important in vivo [11,12]. As a further mechanism, GzmB can process BID, promoting cyt c release, SMAC/Diablo activation, formation of apoptosis inducing factor (AIF), and release of Omi from the mitochondria. It does this by recruiting the inhibitor of the anti-apoptotic B-cell lymphoma 2 (Bcl-2) family member, especially the Bax protein, to the mitochondrial membrane, leading to apoptosome formation [45–47]. GzmB can also process caspase 3 and 7, initiating the apoptotic process [48]. It has been demonstrated that pro-apoptotic caspase activation happens within minutes of target-cell recognition by CTLs. Unexpectedly, there is a rapid rate of caspase 3/7 biosensor activation following GzmB cversus Fas-mediated signal induction in murine CTLs. This Fas-mediated induction is detected after 90–120 minutes in porcine, murine, and human CTLs, consistent with FasL/Fas-induced activity [49]. Recently, key roles for GzmB have been described, positioning it as an allergic inflammatory response of NK [50]. It has also been shown that the major NK cell-activating receptor NKG2D and the NK cell effector are both mediated by GzmB.

1.2.2 Nuclear Features of Apoptosis

The first description of the apoptotic process as a basic biological phenomenon different from necrosis (based not only on morphological criteria) was given by Kerr et al. [51]. The authors described two characteristics of apoptosis: (i) cytoplasmic and nuclear condensation and the disruption of the cell into a number of membrane-bound, well-fragmented pieces; and (ii) formation of apoptotic bodies that are taken up by other cells for degradation. This study shed new light on the apoptotic mechanism as an important process of PCD that regulates several biological processes, including embryogenic development and aging, cell turnover in different tissues, and the control of the immune system. Inappropriate control of apoptosis appears in many human disorders, leading biologists to seek a better understanding of the entire process. Intriguingly, a wide variety of stimuli – both physiological and pathological conditions – can trigger apoptosis. In this section, we address the main biochemical features of apoptosis that focus on nuclear events, including the activation of the execution caspases (i.e., caspase 3, caspase 8, caspase 9, and caspase 10), chromatin condensation, DNA fragmentation, and the formation of apoptotic bodies.

Early evidence described DNA fragmentation as a key feature of apoptosis. Using low concentrations of an exogenous agent like γ-irradiation to induce cell death, it was shown that the DNA of lymphocytes was completely degraded into oligonucleosomal fragments. Further, cells induced with near-physiological concentrations of glucocorticoid hormones showed chromatin condensation as an early structural change. In fact, this particular nuclear morphological change was associated with excision of the nucleosome chains from nuclear chromatin through activation of an intracellular, but non-lysosomal, endonuclease [52]. At this time, it was already known that some members of the caspase family, comprising 12 proteins, are strictly involved in the apoptotic cell death process [53,54]. These are the signals after mitochondrial outer-membrane permeabilization (MOMP) that activate the caspase pathway. However, the interconnection between the nuclear and cytoplasmic events involved in apoptosis became better appreciated when a nuclease protein (Nuc-1), a homolog of mammalian DNAase II, which plays a role in DNA degradation in the nematode Caenorhabditis elegans, was identified as acting downstream of Ced-3 and Ced-4 [56]. In particular, attempts have long been made to understand the link between the executioner caspases and subsequent nuclear apoptotic events, since a variety of death stimuli can activate these proteases, which amplify the signal of cell death.

Caspase 3 is considered the most important protease of the executioner pathway, and can be activated by any of the initiator caspases. Caspase 3 can be activated by caspase 8, which is activated from the death receptor; by caspase 9, which is involved in the mitochondrial apoptotic process; or by caspase 10, which is involved in the PFN/GzmB pathway. Each of these pathways is responsive to a wide range of stimuli capable of amplifying the cellular death signal in an energy-dependent manner. The cleavage of caspase 3 results in the activation of the endonuclease CAD. In apoptotic cells, activated caspase 3 cleaves inhibitor of caspase-activated DNase (ICAD) to dissociate the CAD:ICAD complex, allowing CAD to cleave chromosomal DNA. The CAD:ICAD complex inhibits the CAD activity as DNase. When CAD is cleaved by caspase 3, it can degrade chromosomal DNA like a scissor-like homodimer, cleaving double-strand DNA at nucleosomal linkers [2,3].

CAD is able to condense chromatin and to fragment chromosomal DNA in an irreversible manner that compromises DNA replication and gene transcription, leading to cell death. Accompanied by chromatin condensation, chromosomal DNA is cleaved into high-molecular-weight fragments of 50–300 kb, which are subsequently processed into low-molecular-weight fragments of approximately 180 bp. Several models have been designed to study the role of CAD in PCD. These studies have shown that the inhibition of CAD activity – for instance, by inducing degradation by a chaperon – can abolish internucleosomal DNA fragmentation. However, the inefficient DNA degradation activity detected in CAD-deficient cells suggests the existence of additional nuclease(s) during apoptosis. An interesting example that links the extrinsic and intrinsic pathways is related to the mammalian endonuclease G (endo G). Endo G is a nuclease that was first identified in the mitochondrial intermembrane space; upon apoptotic stimuli, it may be released from the mitochondria and translocated to the nucleus. The endonuclease activity is responsible for cleaving nucleic acids, representing a caspase-independent apoptotic pathway initiated from mitochondria. In mouse embryonic fibroblast (MEF) cells, taken from a DFF45/ICAD-knockout (KO) mouse, there was no detectable caspase 3-dependent activity, and it was shown that there was minimal DNA fragmentation. Moreover, the induction of apoptosis by ultraviolet irradiation or treatment with cyclohexamide (Chx) led to the release of both endo G and cyt c from the mitochondria to the cytosol and nuclei. The identification of DNA fragmentation has been used as a fundamental biological marker of apoptosis. The main method for detecting apoptotic PCD is known as terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) [57].

There have been several further reports providing evidence for caspase-independent death programming in vitro and in vivo by cathepsins B and D, calpains, and serine proteases. Some of these death routines become evident only when the caspase-dependent pathway is inhibited, particularly in the case of ATP depletion or when using caspase inhibitors.

The evolutionarily conserved execution phase of apoptosis is characterized by cell morphology changes, including cell shrinking, plasma-membrane blebbing, and separation of cell fragments into apoptotic bodies. It is known that the actin–myosin system plays a key role in bleb formation through the activity of the Rho effector protein (ROCK I), which leads to the phosphorylation of myosin light-chain ATPase activity and coupling of actin–myosin filaments to the plasma membranes. Apoptotic bodies consist of cytoplasm-packed organelles that contain nuclear fragment. The integrity of the apoptotic bodies is maintained in order to avoid the release of their cellular constituents into the surrounding interstitial tissue, which would block activation of the inflammatory reaction; this permits the apoptotic bodies to be degraded efficiently within phagolysosomes by macrophages and various surrounding cells.

Although the evolutionarily conserved execution phase of apoptosis has been the theme of many studies, a full understanding of apoptosis at the molecular level is needed if we are to gain deeper insights into its basic and applied biology, particularly regarding new therapeutic strategies.

References

1. Williams JR, Little JB, Shipley WU. Association of mammalian cell death with a specific endonucleolytic degradation of DNA.

Nature

1974;

252

: 754–5.

2. Kothakota S, Azuma T, Reinhard C, Klippel A, Tang J, Chu K, et al. Caspase-3-generated fragment of gelsolin: effector of morphological change in apoptosis.

Science

1997;

278

: 294–8.

3. Enari M, Sakahira H, Yokoyama H, Okawa K, Iwamatsu A, Nagata S. A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD.

Nature

1998;

391

: 43–50.

4. Frank S, Gaume B, Bergmann-Leitner ES, Leiner WW, Robert EG, Catez F, et al. The role of dynamin-related protein 1, a mediator of mitochondrial fission, in apoptosis.

Dev Cell

2001;

1

: 515–25.

5. Lane JD, Lucocg J, Pryde J, Barr FA, Woodman PG, Allan VJ, Lowe M. Caspase-mediated cleavage of the stacking protein GRASP65 is required for Golgi fragmentation during apoptosis.

J Cell Biol

2002;

156

: 495–509.

6. Hsu H, Xiong J, Goeddel DV. The TNF receptor 1-associated protein TRADD signals cell death and NF-kappa B activation.

Cell

1995;

81

: 495–504.

7. Grimm S, Stanger BZ, Leder P. RIP and FADD: two “death domain”-containing proteins can induce apoptosis by convergent, but dissociable, pathways.

Proc Natl Acad Sci USA

1996;

93

(10): 923–7.

8. Wajant H. The Fas signaling pathway: more than a paradigm.

Science

2002;

296

: 1635–6.

9. Kischkel FC, Hellbardt S, Behrmann I, Germer M, Pawlita M, Krammer PH, Peter ME. Cytotoxicity-dependent APO-1 (Fas/CD95)-associated proteins form a death-inducing signaling complex (DISC) with the receptor.

Embo J

1995;

14

: 5579–88.

10. Honglin L, Zhu H, Xu C, Juan Y. Cleavage of Bid by caspase 8 mediates the mitocondrial damage in the Fas pathway of apoptosis.

Cell

1998;

94

: 491–501.

11. Darmon AJ, Ley TJ, Nicholson DW, Bleackley RC. Cleavage of CPP32 by granzyme B represents a critical role for granzyme B in the induction of target cell DNA fragmentation.

J Biol Chem

1996;

271

(21): 709–12.

12. Atkinson EA, Barry M, Darmon AJ, Shostak I, Turner PC, Moyer RW, Bleackley RC. Cytotoxic T lymphocyteassisted suicide. Caspase 3 activation is primarily the result of the direct action of granzyme B.

J Biol Chem

1998;

273

(21): 261–6.

13. Locksley RM, Killeen N, Lenardo MJ. The TNF and TNF receptor superfamilies: integrating mammalian biology.

Cell

2001;

104

: 487–501.

14. Ashkenazi A, Dixit VM. Death receptors: signaling and modulation.

Science

1998;

281

: 1305–8.

15. Chicheportiche Y, Bourdon PR, Xu H, Hsu YM, Scott H, Hession C, et al. TWEAK, a new secreted ligand in the tumor necrosis factor family that weakly induces apoptosis.

J Biol Chem

1997;

272

(32): 401–10.

16. Peter ME, Krammer PH. Mechanisms of CD95 (APO-1/Fas)-mediated apoptosis.

Curr Opin Immunol

1998;

10

: 545–51.

17. Suliman A, Lam A, Datta R, Srivastava RK. Intracellular mechanisms of TRAIL: apoptosis through mitochondrial-dependent and -independent pathways.

Oncogene

2001;

20

: 2122–33.

18. Rubio-Moscardo F, Blesa D, Mestre C, Siebert R, Balasas T, Benito A, et al. Characterization of 8p21.3 chromosomal deletions in B-cell lymphoma: TRAIL-R1 and TRAIL-R2 as candidate dosage-dependent tumor suppressor genes.

Blood

2005;

106

: 3214–22.

19. Kataoka T, Schroter M, Hahne M, Schneider P, Irmler M, Thome M, et al. FLIP prevents apoptosis induced by death receptors but not by perforin/granzyme B, chemotherapeutic drugs, and gamma irradiation.

J Immunol

1998;

161

: 3936–42.

20. Scaffidi C, Schmitz I, Krammer PH, Peter ME. The role of c-FLIP in modulation of CD95-induced apoptosis.

J Biol Chem

1999;

274

: 1541–8.

21. Hitoshi Y, Lorens J, Kitada SI, Fisher J, LaBarge M, Ring HZ, et al. Toso, a cell surface, specific regulator of Fas-induced apoptosis in T cells.

Immunity

1998;

8

: 461–71.

22. Garcia-Sanz JA, MacDonald HR, Jenne DE, Tschopp J, Nabholz M. Cell specificity of granzyme gene expression.

J Immunol

1990;

145

: 3111–18.

23. Martinvalet D, Zhu P, Lieberman J. Granzyme A induces caspase-independent mitochondrial damage, a required first step for apoptosis.

Immunity

2005;

22

: 355–70.

24. Irmler M, Hertig S, MacDonald HR, Sadoul R, Becherer JD, Proudfoot A, et al. Granzyme A is an interleukin 1 beta-converting enzyme.

J Exp Med

1995;

181

: 1917–22.

25. Martinvalet D, Dykxhoorn DM, Ferrini R, Lieberman J. Granzyme A cleaves a mitochondrial complex I protein to initiate caspase-independent cell death.

Cell

2008;

133

: 681–92.

26. Fan Z, Beresford PJ, Zhang D, Lieberman J. HMG2 interacts with the nucleosome assembly protein SET and is a target of the cytotoxic T-lymphocyte protease granzyme A.

Mol Cell Biol

2002;

22

: 2810–20.

27. Fan Z, Beresford PJ, Oh DY, Zhang D, Lieberman J. Tumor suppressor NM23-H1 is a Granzyme A-activated DNase during CTL-mediated apoptosis, and the nucleosome assembly protein SET is its inhibitor.

Cell

2003;

112

: 659–72.

28. Fan Z, Beresford PJ, Zhang D, Xu Z, Novina CD, Yoshida A, et al. Cleaving the oxidative repair protein Ape1 enhances cell death mediated by granzyme A.

Nat Immunol

2003;

4

: 145–53.

29. Beresford PJ, Kam CM, Powers JC, Lieberman J. Recombinant human granzyme A binds to two putative HLA-associated proteins and cleaves one of them.

Proc Natl Acad Sci USA

1997;

94

(17): 9285–90.

30. Zhang D, Pasternack MS, Beresford PJ, Wagner L, Greenberg AH, Lieberman J. Induction of rapid histone degradation by the cytotoxic T lymphocyte protease granzyme A.

J Biol Chem

2001;

276

: 3683–90.

31. Zhang D, Beresford PJ, Greenberg AH, Lieberman J. Granzymes A and B directly cleave lamins and disrupt the nuclear lamina during granule-mediated cytolysis.

Proc Natl Acad Sci USA

2001;

98

: 5746–51.

32. Zhu P, Zhang D, Chowdhury D, Martinvalet D, Keefe D, Shi L, Lieberman J. Granzyme A, which causes single-stranded DNA damage, targets the double-strand break repair protein Ku70.

EMBO Rep

2006;

7

(4): 431–7.

33. Zhu P, Martinvalet D, Zhang D, Schlesinger A, Chowdhury D, Lieberman J. The cytotoxic T lymphocyte protease granzyme A cleaves and inactivates poly(adenosine 5′-diphosphate-ribose) polymerase-1.

Blood

2009;

114

: 1205–16.

34. Jans DA, Briggs LJ, Jans P, Froelich CJ, Parasivam G, Kumar S, et al. Nuclear targeting of the serine protease granzyme A (fragmentin-1).

J Cell Sci

1998;

111

: 2645–54.