Full summary - Cell death in pathophysiology (part 1)

FROM CELL DEATH
TO ORGAN FAILURE
(PART 1)
1e master Biomedische wetenschappen (moleculaire mechanismen van ziekten)

1e master Biochemie en Biotechnologie




UAntwerpen

,TABLE OF CONTENTS

CH0: INTRODUCTION TO THIS SUMMARY .................................................................................5

CH1: CELLULAR STRESS RESPONSES: A SNAPSHOT..................................................................6

1. IS STRESS GOOD OR BAD? ........................................................................................................... 6
2. CELLULAR STRESS FACTORS ........................................................................................................ 6
3. CELLULAR RESPONSE TO STRESS ! ................................................................................................. 6
4. THE “TRIANGLE OF DEATH” IN CELLULAR FATE .................................................................................. 6
5. CELLULAR RENEWAL AND TURNOVER ............................................................................................. 7
6. CELLULAR SIGNALING AND ADHESION ............................................................................................ 7
7. CYTOSKELETON OVERVIEW .......................................................................................................... 7
8. ORGANELLES AND THEIR FUNCTION ............................................................................................... 7
9. IMMUNE SYSTEM OVERVIEW ......................................................................................................... 7


CH2: CELLULAR STRESS RESPONSES .......................................................................................8

1. INTRODUCTION – COPING WITH CELLULAR STRESS............................................................................. 8
2. DNA DAMAGE RESPONSE (DDR) .................................................................................................... 8
3. UNFOLDED PROTEIN RESPONSE (UPR) .......................................................................................... 14
4. HEAT SHOCK RESPONSE (HSR) ................................................................................................... 17
5. OXIDATIVE STRESS RESPONSE (OSR) ............................................................................................ 21

CH3: AUTOPHAGY ................................................................................................................. 24

1. INTRODUCTION ...................................................................................................................... 24
2. DEFINITION, MECHANISM AND TYPES ........................................................................................... 26
3. MACROAUTOPHAGY: CORE MACHINERY AND MOLECULAR SIGNALING ................................................... 28
4. HISTORICAL TIMELINE, TERMINOLOGY, AND PHARMACOLOGICAL MODULATORS ....................................... 30
5. METHODS FOR MONITORING AUTOPHAGY (!!!) ................................................................................ 31
6. PHYSIOLOGY VS PATHOLOGY OF AUTOPHAGY ................................................................................. 33
7. AUTOPHAGY AND AGEING ......................................................................................................... 35


CH4: SENESCENCE TO AGING ................................................................................................ 36

1. INTRODUCTION ...................................................................................................................... 36
2. SENESCENCE: CELLULAR AGING ................................................................................................. 38
3. CLASSIFICATION OF CELLULAR SENESCENCE.................................................................................. 38
4. BIOMARKERS (=HALLMARKS) OF CELLULAR SENESCENCE (!!!) ............................................................. 41
5. MECHANISMS CONTRIBUTING TO AGING ....................................................................................... 44

CH5: HISTORY OF CELL DEATH ............................................................................................... 50

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,1. EARLY REFERENCES TO REGRESSION AND DEATH (400 BV – 200 AD) .................................................... 50
2. MICROSCOPY AND CELL THEORY (1595 – 19TH CENTURY) ................................................................ 50
3. FIRST SCIENTIFIC DESCRIPTIONS OF CELL DEATH (MID-19TH CENTURY) ................................................. 51
4. DISCOVERY OF PHAGOCYTOSIS – NOBEL PRIZE 1908 ....................................................................... 51
5. PROGRAMMED CELL DEATH CONCEPT FORMS (1930S – 1970) ........................................................... 51
6. NGF DISCOVERY AND PROGRAMMED SURVIVAL SIGNALS – NOBEL PRIZE 1986 ......................................... 52
7. APOPTOSIS AND LYSOSOME DISCOVERY – THE 1970S ...................................................................... 52
8. MOLECULAR CONTROL OF CELL DEATH DISCOVERED (1980S – 1990S) ................................................ 53
9. DISCOVERY OF MITOCHONDRIAL (INTRINSIC) PATHWAY – LATE 1990S .................................................. 53
10. EXPANDING THE CELL DEATH UNIVERSE - 21ST CENTURY .................................................................... 53
11. NOBEL PRIZE TIMELINE FOR CELL DEATH RESEARCH (!!!) .................................................................... 54


CH6 - APOPTOSIS .................................................................................................................. 55

1. DEFINITION ........................................................................................................................... 55
2. HISTORY OF APOPTOSIS ............................................................................................................ 55
3. GENERAL MECHANISMS OF APOPTOSIS ......................................................................................... 55
4. BIOLOGICAL IMPORTANCE OF APOPTOSIS ...................................................................................... 55
5. CASPASES – KEY PLAYSERS IN APOPTOSIS ...................................................................................... 56
6. APOPTOSIS SIGNALING PATHWAY (DRAW) ...................................................................................... 62
7. REGULATION OF APOPTOSIS ...................................................................................................... 66
8. INHIBITION OF APOPTOSIS DURING MITOSIS ................................................................................... 68
9. MOLECULAR TARGETING OF APOPTOSIS IN CANCER THERAPY .............................................................. 69
10. CASPASES BEYOND APOPTOSIS .................................................................................................. 69
11. FUNCTION OF APOPTOSIS ......................................................................................................... 70


CH7: NECROPTOSIS .............................................................................................................. 71

1. INTRODUCTION ...................................................................................................................... 71
2. HISTORY OF NECROPTOSIS ........................................................................................................ 72
3. NECROPTOSIS SIGNALING – TNFR1-MEDIATED PATHWAY (DRAW !!!) ..................................................... 80
4. VIRAL EVASION OF NECROPTOSIS ................................................................................................ 84
5. OVERLAP AND TRANSITION BETWEEN APOPTOSIS AND NECROPTOSIS .................................................... 84


CH8: PYROPTOSIS ................................................................................................................. 85

1. INTRODUCTION ...................................................................................................................... 85
2. PATHOGENIC STIMULI AND TOLL-LIKE RECEPTORS (TLRS) ................................................................... 85
3. TOLL-LIKE RECEPTORS (TLRS) – DISCOVERY, STRUCTURE, AND SIGNALING.............................................. 88
4. NOD-LIKE RECEPTORS (NLRS) AND PYROPTOSIS .............................................................................. 91
5. NLRS AND INFLAMMASOME ACTIVATION ........................................................................................ 93
6. INFLAMMASOMES AND PYROPTOSIS: MECHANISMS AND PATHWAYS ...................................................... 94
7. PYROPTOSIS SIGNALING (DRAW) ........................................................................................... 95
8. GASDERMINS AS EFFECTORS OF PYROPTOSIS ................................................................................. 97
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,9. PYROPTOSIS VS. APOPTOSIS – KEY DIFFERENCES ............................................................................. 97
10. INFLAMMASOME SIGNALING AND ITS IMPACT ON CELL DEATH AND DISEASE ............................................. 98
11. IMPACT OF PYROPTOSIS AND INFLAMMATION ON DISEASE .................................................................. 99
12. POTENTIALLY DELETERIOUS ROLE IN INFLAMMATION ....................................................................... 100


CH9: FERROPTOSIS ............................................................................................................. 101

1. INTRODUCTION – FERROPTOSIS AS BIOLOGICAL RUST ..................................................................... 101
2. DISCOVERY OF IRON-DEPENDENT CELL DEATH: THE BIRTH AND EVOLUTION OF FERROPTOSIS .................... 103
3. PHOSPHOLIPID PEROXIDATION IN FERROPTOSIS – REACTIVE FREE RADICAL CHAIN .................................. 107
4. FERROPTOSIS SIGNALING PATHWAYS ......................................................................................... 108
5. FERROPTOSIS INHIBITORS AND THE ROLE OF IRON REGULATION ......................................................... 110
6. REGULATION OF FERROPTOSIS ................................................................................................. 111
7. ROLE OF FERROPTOSIS ........................................................................................................... 112


CH10: OTHER MODELS OF REGULATED CELL DEATH (RCD).................................................... 114

1. PARTHANATOS: A CASPASE-INDEPENDENT PROGRAMMED NECROSIS .................................................. 114
2. ENTOTIC CELL DEATH (CELL-IN-CELL DEATH)................................................................................ 116
3. NETOTIC CELL DEATH (NETOSIS): AN IN-DEPTH OVERVIEW................................................................ 118
4. MITOCHONDRIAL PERMEABILITY TRANSITION (MPT)-DRIVEN NECROSIS ................................................ 121
5. LYSOSOME-DEPENDENT CELL DEATH (LDCD) ............................................................................... 123
6. AUTOPHAGY-DEPENDENT CELL DEATH (ADCD) ............................................................................. 125
7. AUTOSIS: A SUBTYPE OF ADCD.................................................................................................. 126
8. IMMUNOGENIC CELL DEATH (ICD) ............................................................................................. 127
9. ANOIKIS – ANCHORAGE-DEPENDENT CELL DEATH .......................................................................... 128
10. CLARIFYING BROADER CONCEPTS ............................................................................................. 128


CH11 : PHAGOCYTOSIS........................................................................................................ 129

1. PHAGOCYTOSIS VS. EFFEROCYTOSIS – COMPARISON ...................................................................... 129
2. TYPE OF CELL DEATH MATTERS FOR CLEARANCE PATHWAY ............................................................... 130
3. METABOLIC IMPACT OF CELL INGESTION...................................................................................... 130
4. PATHOGEN INTERACTIONS WITH EFFEROCYTOSIS .......................................................................... 130
5. PHAGOSOME MATURATION ...................................................................................................... 130
6. TYPES OF PHAGOCYTES .......................................................................................................... 131
7. ALVEOLAR EPITHELIAL CELLS AND EFFEROCYTOSIS......................................................................... 132
8. IMMUNE RESPONSE TO ALLERGENS (E.G. HOUSE DUST MITES) ........................................................... 132
9. CLINICAL SIGNIFICANCE OF EFFEROCYTOSIS ................................................................................ 132
10. PATHOGEN RECOGNITION ....................................................................................................... 132
11. PHAGOCYTE PROCESSING OF DYING CELLS (EFFEROCYTOSIS) ........................................................... 134
12. IMPAIRED EFFEROCYTOSIS IN DISEASE ........................................................................................ 136




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,CH12: CELL DEATH DETECTION ............................................................................................ 138

1. 4-STEP APPROACH TO INVESTIGATING CELL DEATH ........................................................................ 138
2. STEP 1: DETERMINING LOSS OF CELL MEMBRANE INTEGRITY ............................................................. 139
3. STEP 3: DETERMINE CELL MORPHOLOGY OF DYING CELLS ................................................................ 142
4. STEP 3: DETERMINING TYPICAL BIOCHEMICAL CELL DEATH FEATURES .................................................. 144
5. EXERCISE – IMPLEMENTATION OF TECHNIQUES: ELABORATED GUIDE TO SOLVING IT ................................ 154
6. STEP 4: IN VIVO CELL DEATH DETECTION TECHNIQUES .................................................................... 159


FULL EXAM QUESTIONS PREVIOUS YEARS ............................................................................ 163

1. INTRODUCTION .................................................................................................................... 163
2. OPEN QUESTIONS ................................................................................................................. 164
3. TERMS ............................................................................................................................... 172
4. MULTIPLE CHOICE QUESTIONS ................................................................................................. 173




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,CH0: INTRODUCTION TO THIS SUMMARY

This summary is a comprehensive, elaborate and structured overview based on all the lecture slides and notes provided during
Part 1 of the course Cell death in pathophysiology (formerly known as ‘From Cell Death to Organ Failure’).

Part 1 is followed by both Biochemistry (Cellular stress and cell death signaling) and Biomedical Sciences students.

Please note that Part 2 of the course (for Biomedical Sciences students only) is also available on Stuvia.

This summary is intended to help you understand the material and prepare confidently for the oral exam.




By studying this summary + the exam ques<ons i obtained a 17/20 on the oral exam !




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,CH1: CELLULAR STRESS RESPONSES: A SNAPSHOT
1. IS STRESS GOOD OR BAD?


• Stress can be both beneficial and harmful, depending on its intensity and duraMon.
• In scienMfic work, well-prepared experiments help minimize stress.
• However, moderate pressure can enhance performance (e.g., studying effecMvely the night before an exam).
• Example from fruit flies:
o Mild, transient mitochondrial stress (e.g., via overexpression of Hsp60) is associated with a longer lifespan.
o Persistent, chronic stress leads to a shorter lifespan.
• Moderate stress acMvates protecMve systems and is beneficial, while excessive stress causes cellular damage.


2. CELLULAR STRESS FACTORS


• DNA damage Pathogens Metabolic stress
• Heat Senescence OxidaMve stress


3. CELLULAR RESPONSE TO STRESS !


1. Homeostasis Restora=on:
o DNA damage response
o Unfolded protein response
o Heat shock response
o OxidaMve stress response
o Autophagy (o^en a reacMon to
starvaMon)

2. If Restora=on Fails:
o The cell may die (cell death)
o AlternaMvely, it may enter
senescence (a non-dividing,
frozen state)

3. Cell Death and Removal:
o Dead cells are removed via phagocytosis by immune cells
o This process helps recycle cellular components and restores homeostasis

4. Poten=al Immune Overload:
o Too much or too li`le clearance leads to inflammaMon
o If unresolved, this can result in: cancer, infecMons, autoimmune diseases, organ dysfuncMon


4. THE “ TRIANGLE OF DEATH” IN CELLULAR FATE


Process Outcome
• This is a foundaMonal concept, but
Autophagy Recovery and internal recycling of cell parts addiMonal types of cell death exist.
Necrosis Uncontrolled death leading to inflammaMon
• Proper balance between Mssue damage
Apoptosis Controlled death followed by phagocytosis and regeneraMon is essenMal.




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,5. CELLULAR RENEWAL AND TURNOVER


• The body recycles its enMre weight annually à cellular turnover is constant and ongoing.
• Every second, approximately 1 to 5 million cells die.
• High-frequency copying of the genome increases the chance of errors à mutaMons and diseases such as cancer.


6. CELLULAR SIGNALING AND ADHESION


• P-selec=n and ICAM:
o These are transmembrane proteins essenMal for cell adhesion.
o They interact with integrins to slow down leukocytes in the bloodstream.
o This enables leukocytes to exit the blood vessels (extravasaMon) and reach the site of infecMon.
• Lipid RaIs:
o Specialized microdomains in the cell membrane rich in phospholipids and cholesterol.
o These are less mobile and act as plagorms for clustering receptors (dimerizaMon/trimerizaMon).
o They facilitate the iniMaMon of cellular signaling processes.


7. CYTOSKELETON OVERVIEW


• Spectrin Tetramers: Structural proteins lining the intracellular side of the plasma membrane.
• Ac=n Filaments and Microtubules:
o Organize cellular structures.
o Enable intracellular transport through interacMon with motor proteins.
• Microtubules:
o Help posiMon organelles.
o Serve as tracks for transport within the cell.
o Can be disassembled by severing proteins, allowing dynamic restructuring.

8. ORGANELLES AND THEIR FUNCTION


• Mitochondria: Main site of energy producMon (ATP synthesis).
• Centrosome: Contains two centrioles à organizes microtubules, especially during cell division.
• Nuclear Pores:
o Permit the passage of molecules like mRNA.
o CriMcal for protein synthesis (translaMon).
• Endoplasmic Re=culum (ER):
o Involved in protein synthesis, lipid metabolism, and molecular storage.
• Golgi Apparatus:
o Modifies and packages ER products.
o Directs molecules to their desMnaMons within or outside the cell.

9. IMMUNE SYSTEM OVERVIEW


• Innate Immunity:
o Provides an immediate, non-specific defense.
o Key players include macrophages and natural killer (NK) cells.
• Adap=ve Immunity:
o Specific and capable of memory formaMon.
o B and T lymphocytes are the main components.
o Enables targeted responses and improved efficiency upon re-exposure to the same pathogen.


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,CH2: CELLULAR STRESS RESPONSES
1. INTRODUCTION – COPING WITH CELLULAR STRESS


Cells constantly face internal and external stressors.

To maintain homeostasis, they acMvate several repair and defense mechanisms:
• DNA Damage Response (DDR)
• Unfolded Protein Response (UPR)
• Heat Shock Response (HSR)
• Oxida=ve Stress Response (OSR)
• Autophagy

Failure to handle stress leads to:
• Cell Death – AcMvely destroy dangerous cells.
• Senescence – "Freezing" damaged cells to prevent proliferaMon.
• Phagocytosis – Removal of damaged cells.
• Inflamma=on – Recruitment of professional immune cells.

Uncontrolled stress responses can cause diseases like cancer, excessive necrosis, autoimmunity, and infecMons.




2. DNA DAMAGE RESPONSE (DDR)


WHY IS THE DDR CRITICAL?

The Scale of DNA Damage:
• DNA polymerase has an error rate of ~1 per million bases.
• In the human body, ~5 million new cells are generated every second.
• This means ~15 billion DNA repair events occur per second.

DNA is the blueprint for all cellular proteins à Any errors or persistent damage can disrupt protein funcMon → disease.
• Without efficient DDR:
o Cells accumulate mutaMons → cancer and aging.
o Defects in DDR are associated with neurodegeneraMon, immunodeficiency, and early mortality.

Unrepaired DNA damage leads to: MutaMons, Genomic instability, Cancer, Cell death or senescence
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, TYPES OF DNA DAMAGE + CAUSES

MCQ: ‘what causes DSB’ ; ‘what does UV-radia<on do to your DNA’

1. Oxida=ve Stress-Induced Damage:
o Oxygen has two unpaired electrons → forms reac=ve oxygen species (ROS):
• O₂ → superoxide → hydrogen peroxide → hydroxyl radical (OH•).
o ReacMve oxygen species (ROS) cause damage.
o Example: 8-oxoG forma=on (modificaMon of a Guanine due to ROS)
• During replicaMon of DNA that contains 8-oxoG, an Adenine is o^en incorporated across
• the 8-oxo-dG is excised during the repair process and a thymine is incorporated in its place.
• Thus, 8-oxo-dG mutaMons typically result in a G to T transversion (base modifica=ons)

2. Alkyla=on Damage:
o DNA bases get methylated or ethylated (= small alkylaMng agents)
o Major and minor alkylaMon sites disrupt DNA structure.

3. Radia=on-Induced Breaks:

o Ionizing Radia=on (X-rays, γ-rays): Causes single-stranded and double-stranded breaks.
• Single-Strand Breaks (SSBs):
§ Caused by ROS, ionizing radiaMon
§ Can escalate to double-strand breaks (DSBs)
• Double-Strand Breaks (DSBs):
§ Most dangerous form of DNA damage
§ Caused by ionizing radiaMon, replicaMon fork collapse
§ Improper repair = translocaMons, deleMons, cancer

o UV Radia=on: Induces thymine dimers (cross-links) within DNA strands.
• Crosslinks
§ Intrastrand (e.g., thymine dimers from UV)
§ Interstrand (e.g., cisplaMn-induced) — blocks replicaMon




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