From Cell Dead to Organ Failure
HC 1 – Introduction: cellular stress responses. -> Exam: MCQ + Terms
Stress can be a good and a bad thing, depending on the level of stress.
Ê Example: Fruit flies with mild transient mitochondria stress overexpressing have a longer lifespan <-> long and persistent
stress leads to a shorter lifespan. So, a little bit of stress is good, (makes the system work) but if this stress exceeds a
specific treshhold and goes too high, it will cause damage.
â Different factors causing cellular stress: DNA-damage, heat, pathogens, metabolic stress, or oxidative stress.
In response, the cell activates cellular repair mechanisms such as:
- DNA damage response (DDR),
HC 2 - unfolded protein response (UPR),
- heat shock response (HSR),
- oxidative stress responses (OSR), and See HC 3
- autophagy, which helps recycle damaged cellular components.
-> The goal of these systems is to restore homeostasis.
However, if the stress is too high and this repair step fails, the cell can decide to go into:
- cell death See HC 4
- cellular senescence -> the cell freezes, it stops dividing but remains metabolically active.
Once the cell dies, it must be cleared efficiently.
Ê This clean-up proces is done by phagocytosis, where professional immune cells such as macrophages “eat up” and recycle
the death cell components, helping to restore homeostasis.
9 However, if this clean-up is not sufficiently done, it can lead to inflammation. Luckily, the immune system can resolve
this, but if this fails this can lead to diseases like cancer, infection, auto-immune diseases, or organ disfunction.
â Our body is constantly renewing. We recycle our body weight every year. Every second 1-5 million cells die and are
replaced. To keep this process going, our cells must constantly copy the entire genomic library. However, with such
frequent replication, mistakes can occur, that can accumulate and over time lead to diseases such as cancer.
, HC 2 - Cellular stress responses (DDR, UPR, HSR & OSR). -> Exam: MCQ + Terms
1. DNA Damage Response (DDR)
Our body is constantly renewing itself. -> Every second 1-5 million cells die and are replaced. To do this, the entire
genome is copied continuously. Despite a high-accuracy DNA polymerase (error-rate: 1 on a million (106)), there are about 3,000
errors per cell division, resulting in around 15 billion DNA repairs every second in the human body.
Each type of DNA damage has its own DNA Damage Response:
â Replication errors -> Mismatch Repair (MMR)
Mismatch Repair (MMR) is a mechanism that fixes errors made during DNA replication, such as mismatched bases. In
eukaryotes, this system identifies the new strand by recognizing nicks (single-stranded breaks), which are only present in newly
synthesized DNA.
1) A mismatch is detected in the newly synthesized DNA strand.
2) The new DNA strand is cut, and the mis paired nucleotide and its neighbors are removed.
3) The missing patch is replaced with correct nucleotides by a DNA polymerase.
4) DNA ligase seals the gap in the DNA backbone.
â ROS, Oxidation, Alkylation, and Hydrolysis -> Base Excision Repair (BER)
Oxidative stress is another source of DNA damage, caused by reactive oxygen species (ROS).
Ê Oxygen is unique because it has two unpaired electrons, which makes it highly reactive.
9 Through cellular metabolism or external stress, oxygen can be converted into superoxide (O₂⁻), and then hydrogen
peroxide (H₂O₂). H₂O₂ can generate, in the presence of reactive iron (Fe²⁺), hydroxyl radicals (•OH).
9 = Fenton reaction
These radicals can cause:
- DNA base damage, e.g. guanine oxidation to 8-oxoG, leading to G>T mutations
- Single-strand breaks in DNA
- Trigger cell death pathways like ferroptosis, a form of iron-dependent oxidative cell death.
Note:
• Fe²⁺ = reactive and promotes ROS formation.
• Fe³⁺ = is non-reactive and the more stable form typically found in the body.
Another cause of DNA damage is oxidation, alkylation, and hydrolysis, which leads to single base damage (e.g., deamination
of C>U).
!!! Terminology: ORAS (Oxidative Stress-Responsive Apoptosis
These damages are repaired by Base excision Repair (BER). Signaling) is the cellular mechanism by which oxidative stress triggers
programmed cell death through apoptotic signaling pathways.
,Base excision repair (BER) is a mechanism used to detect and remove certain types of damaged bases. A group of enzymes
called glycosylases play a key role in base excision repair. Each glycosylase detects and removes a specific kind of damaged
base.
1) Deamination converts a cytosine base into an uracil.
2) The uracil is detected and removed, leaving a base-less nucleotide.
3) The base-less nucleotide is removed, leaving a small hole in the DNA backbone.
4) The hole is filled with the right base by a DNA polymerase, and the gap is sealed by a DNA ligase.
â Ionizing Radiation -> NHEJ & HDR
Ionizing radiation, such as X-rays and γ-rays contain enough energy to cause single and double-stranded breaks in the
DNA backbone. This can be repaired by:
- Non-Homologues End Joining (NHEJ): the two broken ends of the chromosome are glued back together. This repair
mechanism is “messy” and typically involves the loss, or sometimes addition, of a few nucleotides at the cut site. So, NHEJ
tends to produce a mutation, but this is better than the alternative (loss of an entire chromosome arm).
- Homology Directed Repair (HDR) or Homology Recombination (HR): in HR, information from the homologous
chromosome that matches the damaged one (or from a sister chromatid, if the DNA has been copied) is used to repair the
break. In this process, the two homologous chromosomes come together, and the undamaged region of the homologue or
chromatid is used as a template to replace the damaged region of the broken chromosome. Homologous recombination is
“cleaner” than NHEJ and does not usually cause mutations.
â UV-light & Radicals -> Nucleotide excision repair (NER)
Energy from non-ionizing radiation such as UV-light is directly absorbed by the DNA causing thymine residues that are
neighboring within a single DNA strand to become crosslinked -> thymine dimers.
Ê Damaged caused by UV-light, along with radicals, can be restored by NER.
Nucleotide excision repair (NER) detects and corrects types of damage that distort the DNA double helix. For instance,
this pathway detects bases that have been modified with bulky chemical groups, like the ones that get attached to your DNA
when it's exposed to chemicals in cigarette smoke.
1) UV radiation produces a thymine dimer.
2) Once the dimer has been detected, the surrounding DNA is opened to form a bubble.
3) Enzymes cut the damaged region out of the bubble.
4) A DNA polymerase replaces the cut-out DNA, and a ligase seals the backbone.
NER does also repair damage of intrastrand crosslinks caused by UV.
â Chemotherapeutics -> NHEJ, HDR, and NER
Chemo can cause intrastrand crosslinks fixed by both NHEJ, HR or NER.
!!! A defect DNA damage response (DDR) can lead to Louis Bar syndrome (Ataxia telangiectasia), rare genetic disorder caused
by mutations in the ATM gene. ATM encodes a kinase that is activated in response to double-strand DNA breaks, triggering
signaling pathways involved in cell cycle control, repair, and cell death. Patients with Ataxia-telangiectasia suffer
from cerebellar degeneration, extreme sensitivity to ionizing radiation, and have a higher cancer risk to develop cancer due to
the impaired DNA repair mechanism, resulting accumulation of mutations.
2. Unfolded Protein Response (UPR)
For proteins to fold properly within the ER, ER homeostasis must be maintained. ER homeostasis is defined by the dynamic
balance between the ER protein load and the ER capacity to process this load.
§ Proteostasis = balance between number of proteins you make and degrade.
Ê Problem: ER homeostasis can be disturbed by physiological and pathological stimuli. Disruption of ER homeostasis causes
accumulation of unfolded and misfolded proteins in the ER. This condition is referred as ER stress.
9 Solution: Unfolded Protein Response
, Ê The Unfolded Protein Response (UPR) is a cellular stress response triggered by excess unfolded proteins in the ER,
aiming to restore balance or, if unresolved, initiate cell death.
Under ER stress, 3 major UPR branches are activated:
1) PERK: regulates protein synthesis by phosphorylating eukaryotic translation initiation factor 2 alpha (eIF2α), reducing
overall protein production while selectively translating specific mRNAs, like ATF4. ATF4 orchestrates cellular
responses to restore ER balance, promote survival, and, if necessary, trigger cell death.
2) IRE: splices XBP1 mRNA producing a transcription factor that upregulates genes involved in protein folding,
degradation, and ER expansion.
3) ATF6: moves to the Golgi, where it is cleaved by S1P and S2P to release a transcription factor that promotes
expression of ER chaperones, which restore the ER protein folding homeostasis.
3. Heat shock Repair (HSR)
The Heat Shock Response (HSR) is a protective cellular mechanism activated by stress conditions such as elevated
temperature, oxidative stress, or toxins, which lead to protein misfolding.
Ê The human genome encodes 6 heat shock transcription factor (HSF) proteins, each with unique roles in cellular stress
response and regulation. A key player in this response is Heat Shock Factor 1 (HSF1), which activates the expression
of Heat Shock Proteins (HSPs), including HSP70 and HSP90. These molecular chaperones help refold misfolded
proteins, prevent aggregation, and restore protein homeostasis.
9 If protein damage remains unresolved, the cell may initiate cell death to prevent further harm.
4. Oxidative stress respons (OSR)
The Oxidative Stress Response (OSR) is a cellular defense mechanism activated when reactive oxygen species (ROS),
such as hydrogen peroxide or superoxide, accumulate and threaten to damage DNA, proteins, and lipids.
Ê In response, cells activate transcription factors like NRF2, which trigger the expression of antioxidant enzymes (e.g.,
glutathione peroxidase, catalase, superoxide dismutase). A key antioxidant in this system is glutathione (GSH), a small
molecule that directly neutralizes ROS and helps maintain redox homeostasis.
9 If ROS levels remain too high, the damage may lead to cell death, senescence, or contribute to diseases like cancer
and neurodegeneration.
!!! Terminology: Hormesis is a biological phenomenon where a low dose of a potentially harmful agent (like oxidative stress,
toxins, or drugs) stimulates beneficial effects on cells or organisms, while higher doses are damaging. For example: low levels
of oxidative stress from exercise stimulate the body’s antioxidant defenses.
HC 3 – Autophagy. -> Exam: MCQ + Terms
Autophagy -> derived from Greek: Auto (on self) + Phagy (to eat) => “self-eating”
Ê Definition: = an evolutionarily conserved, highly regulated cellular process for bulky degradation of cytosolic proteins and
organelles. It is an essential lysosomal degradation pathway for cell survival, differentiation, development, and homeostasis.
Different names depending on what is recycled:
- Xenophagy: recycling proteins from bacteria and virus
- Lipophagy: lipid droplets
- Ribophagy: ribosomes
- Aggrephagy: protein aggerates
- Mitophagy: damaged mitochondria
- Pexophagy: peroxisomes
- Nucleophagy: micronuclei
- Glycophagy: glycogen
- Ferritinopagy: ferritine
=> Different types of autophagy: macroautophagy, microautophagy and chaperone-mediated autophagy.
9 But when using the term “autophagy” we reffer to macroautophagy !!!
HC 1 – Introduction: cellular stress responses. -> Exam: MCQ + Terms
Stress can be a good and a bad thing, depending on the level of stress.
Ê Example: Fruit flies with mild transient mitochondria stress overexpressing have a longer lifespan <-> long and persistent
stress leads to a shorter lifespan. So, a little bit of stress is good, (makes the system work) but if this stress exceeds a
specific treshhold and goes too high, it will cause damage.
â Different factors causing cellular stress: DNA-damage, heat, pathogens, metabolic stress, or oxidative stress.
In response, the cell activates cellular repair mechanisms such as:
- DNA damage response (DDR),
HC 2 - unfolded protein response (UPR),
- heat shock response (HSR),
- oxidative stress responses (OSR), and See HC 3
- autophagy, which helps recycle damaged cellular components.
-> The goal of these systems is to restore homeostasis.
However, if the stress is too high and this repair step fails, the cell can decide to go into:
- cell death See HC 4
- cellular senescence -> the cell freezes, it stops dividing but remains metabolically active.
Once the cell dies, it must be cleared efficiently.
Ê This clean-up proces is done by phagocytosis, where professional immune cells such as macrophages “eat up” and recycle
the death cell components, helping to restore homeostasis.
9 However, if this clean-up is not sufficiently done, it can lead to inflammation. Luckily, the immune system can resolve
this, but if this fails this can lead to diseases like cancer, infection, auto-immune diseases, or organ disfunction.
â Our body is constantly renewing. We recycle our body weight every year. Every second 1-5 million cells die and are
replaced. To keep this process going, our cells must constantly copy the entire genomic library. However, with such
frequent replication, mistakes can occur, that can accumulate and over time lead to diseases such as cancer.
, HC 2 - Cellular stress responses (DDR, UPR, HSR & OSR). -> Exam: MCQ + Terms
1. DNA Damage Response (DDR)
Our body is constantly renewing itself. -> Every second 1-5 million cells die and are replaced. To do this, the entire
genome is copied continuously. Despite a high-accuracy DNA polymerase (error-rate: 1 on a million (106)), there are about 3,000
errors per cell division, resulting in around 15 billion DNA repairs every second in the human body.
Each type of DNA damage has its own DNA Damage Response:
â Replication errors -> Mismatch Repair (MMR)
Mismatch Repair (MMR) is a mechanism that fixes errors made during DNA replication, such as mismatched bases. In
eukaryotes, this system identifies the new strand by recognizing nicks (single-stranded breaks), which are only present in newly
synthesized DNA.
1) A mismatch is detected in the newly synthesized DNA strand.
2) The new DNA strand is cut, and the mis paired nucleotide and its neighbors are removed.
3) The missing patch is replaced with correct nucleotides by a DNA polymerase.
4) DNA ligase seals the gap in the DNA backbone.
â ROS, Oxidation, Alkylation, and Hydrolysis -> Base Excision Repair (BER)
Oxidative stress is another source of DNA damage, caused by reactive oxygen species (ROS).
Ê Oxygen is unique because it has two unpaired electrons, which makes it highly reactive.
9 Through cellular metabolism or external stress, oxygen can be converted into superoxide (O₂⁻), and then hydrogen
peroxide (H₂O₂). H₂O₂ can generate, in the presence of reactive iron (Fe²⁺), hydroxyl radicals (•OH).
9 = Fenton reaction
These radicals can cause:
- DNA base damage, e.g. guanine oxidation to 8-oxoG, leading to G>T mutations
- Single-strand breaks in DNA
- Trigger cell death pathways like ferroptosis, a form of iron-dependent oxidative cell death.
Note:
• Fe²⁺ = reactive and promotes ROS formation.
• Fe³⁺ = is non-reactive and the more stable form typically found in the body.
Another cause of DNA damage is oxidation, alkylation, and hydrolysis, which leads to single base damage (e.g., deamination
of C>U).
!!! Terminology: ORAS (Oxidative Stress-Responsive Apoptosis
These damages are repaired by Base excision Repair (BER). Signaling) is the cellular mechanism by which oxidative stress triggers
programmed cell death through apoptotic signaling pathways.
,Base excision repair (BER) is a mechanism used to detect and remove certain types of damaged bases. A group of enzymes
called glycosylases play a key role in base excision repair. Each glycosylase detects and removes a specific kind of damaged
base.
1) Deamination converts a cytosine base into an uracil.
2) The uracil is detected and removed, leaving a base-less nucleotide.
3) The base-less nucleotide is removed, leaving a small hole in the DNA backbone.
4) The hole is filled with the right base by a DNA polymerase, and the gap is sealed by a DNA ligase.
â Ionizing Radiation -> NHEJ & HDR
Ionizing radiation, such as X-rays and γ-rays contain enough energy to cause single and double-stranded breaks in the
DNA backbone. This can be repaired by:
- Non-Homologues End Joining (NHEJ): the two broken ends of the chromosome are glued back together. This repair
mechanism is “messy” and typically involves the loss, or sometimes addition, of a few nucleotides at the cut site. So, NHEJ
tends to produce a mutation, but this is better than the alternative (loss of an entire chromosome arm).
- Homology Directed Repair (HDR) or Homology Recombination (HR): in HR, information from the homologous
chromosome that matches the damaged one (or from a sister chromatid, if the DNA has been copied) is used to repair the
break. In this process, the two homologous chromosomes come together, and the undamaged region of the homologue or
chromatid is used as a template to replace the damaged region of the broken chromosome. Homologous recombination is
“cleaner” than NHEJ and does not usually cause mutations.
â UV-light & Radicals -> Nucleotide excision repair (NER)
Energy from non-ionizing radiation such as UV-light is directly absorbed by the DNA causing thymine residues that are
neighboring within a single DNA strand to become crosslinked -> thymine dimers.
Ê Damaged caused by UV-light, along with radicals, can be restored by NER.
Nucleotide excision repair (NER) detects and corrects types of damage that distort the DNA double helix. For instance,
this pathway detects bases that have been modified with bulky chemical groups, like the ones that get attached to your DNA
when it's exposed to chemicals in cigarette smoke.
1) UV radiation produces a thymine dimer.
2) Once the dimer has been detected, the surrounding DNA is opened to form a bubble.
3) Enzymes cut the damaged region out of the bubble.
4) A DNA polymerase replaces the cut-out DNA, and a ligase seals the backbone.
NER does also repair damage of intrastrand crosslinks caused by UV.
â Chemotherapeutics -> NHEJ, HDR, and NER
Chemo can cause intrastrand crosslinks fixed by both NHEJ, HR or NER.
!!! A defect DNA damage response (DDR) can lead to Louis Bar syndrome (Ataxia telangiectasia), rare genetic disorder caused
by mutations in the ATM gene. ATM encodes a kinase that is activated in response to double-strand DNA breaks, triggering
signaling pathways involved in cell cycle control, repair, and cell death. Patients with Ataxia-telangiectasia suffer
from cerebellar degeneration, extreme sensitivity to ionizing radiation, and have a higher cancer risk to develop cancer due to
the impaired DNA repair mechanism, resulting accumulation of mutations.
2. Unfolded Protein Response (UPR)
For proteins to fold properly within the ER, ER homeostasis must be maintained. ER homeostasis is defined by the dynamic
balance between the ER protein load and the ER capacity to process this load.
§ Proteostasis = balance between number of proteins you make and degrade.
Ê Problem: ER homeostasis can be disturbed by physiological and pathological stimuli. Disruption of ER homeostasis causes
accumulation of unfolded and misfolded proteins in the ER. This condition is referred as ER stress.
9 Solution: Unfolded Protein Response
, Ê The Unfolded Protein Response (UPR) is a cellular stress response triggered by excess unfolded proteins in the ER,
aiming to restore balance or, if unresolved, initiate cell death.
Under ER stress, 3 major UPR branches are activated:
1) PERK: regulates protein synthesis by phosphorylating eukaryotic translation initiation factor 2 alpha (eIF2α), reducing
overall protein production while selectively translating specific mRNAs, like ATF4. ATF4 orchestrates cellular
responses to restore ER balance, promote survival, and, if necessary, trigger cell death.
2) IRE: splices XBP1 mRNA producing a transcription factor that upregulates genes involved in protein folding,
degradation, and ER expansion.
3) ATF6: moves to the Golgi, where it is cleaved by S1P and S2P to release a transcription factor that promotes
expression of ER chaperones, which restore the ER protein folding homeostasis.
3. Heat shock Repair (HSR)
The Heat Shock Response (HSR) is a protective cellular mechanism activated by stress conditions such as elevated
temperature, oxidative stress, or toxins, which lead to protein misfolding.
Ê The human genome encodes 6 heat shock transcription factor (HSF) proteins, each with unique roles in cellular stress
response and regulation. A key player in this response is Heat Shock Factor 1 (HSF1), which activates the expression
of Heat Shock Proteins (HSPs), including HSP70 and HSP90. These molecular chaperones help refold misfolded
proteins, prevent aggregation, and restore protein homeostasis.
9 If protein damage remains unresolved, the cell may initiate cell death to prevent further harm.
4. Oxidative stress respons (OSR)
The Oxidative Stress Response (OSR) is a cellular defense mechanism activated when reactive oxygen species (ROS),
such as hydrogen peroxide or superoxide, accumulate and threaten to damage DNA, proteins, and lipids.
Ê In response, cells activate transcription factors like NRF2, which trigger the expression of antioxidant enzymes (e.g.,
glutathione peroxidase, catalase, superoxide dismutase). A key antioxidant in this system is glutathione (GSH), a small
molecule that directly neutralizes ROS and helps maintain redox homeostasis.
9 If ROS levels remain too high, the damage may lead to cell death, senescence, or contribute to diseases like cancer
and neurodegeneration.
!!! Terminology: Hormesis is a biological phenomenon where a low dose of a potentially harmful agent (like oxidative stress,
toxins, or drugs) stimulates beneficial effects on cells or organisms, while higher doses are damaging. For example: low levels
of oxidative stress from exercise stimulate the body’s antioxidant defenses.
HC 3 – Autophagy. -> Exam: MCQ + Terms
Autophagy -> derived from Greek: Auto (on self) + Phagy (to eat) => “self-eating”
Ê Definition: = an evolutionarily conserved, highly regulated cellular process for bulky degradation of cytosolic proteins and
organelles. It is an essential lysosomal degradation pathway for cell survival, differentiation, development, and homeostasis.
Different names depending on what is recycled:
- Xenophagy: recycling proteins from bacteria and virus
- Lipophagy: lipid droplets
- Ribophagy: ribosomes
- Aggrephagy: protein aggerates
- Mitophagy: damaged mitochondria
- Pexophagy: peroxisomes
- Nucleophagy: micronuclei
- Glycophagy: glycogen
- Ferritinopagy: ferritine
=> Different types of autophagy: macroautophagy, microautophagy and chaperone-mediated autophagy.
9 But when using the term “autophagy” we reffer to macroautophagy !!!
