Chapter 6-1. Programmed Cell Death
Recommended Post: 【Biology】 Chapter 6. Signal Transduction
1. Cell Death
1. Cell Death
⑴ Overview
① NCCD(Nomenclature Committe on Cell Death) explains cell death as a continuous cycle rather than strictly categorizing it.
Figure 1. Subroutines of Major Cell Death Types
② Previously, apoptosis, autophagy, and necrosis were mainly studied based on morphological features.
③ Morphological features ■, biochemical features ■, other features ■.
④ Comparison of normal cells, apoptosis (programmed cell death), and necrosis
Figure 2. Comparison of Normal Cells, Apoptosis, and Necrosis
⑵ Type 1. Apoptosis (programmed cell death, type I cell death)
① Features
○ ■ Reduction in cell and nuclear volume
○ ■ Pyknosis: chromatin condensation
○ ■ Formation of apoptotic bodies: resemble small vesicles.
○ ■ Breakdown of the cytoskeleton
○ ■ Minimal structural changes in mitochondria
○ ■ Formation of blebs, i.e., membrane deformation
○ Early apoptosis: Asymmetry of the membrane is disrupted, with events such as phosphatidylserine being exposed to the extracellular environment.
○ Late apoptosis: Pores form in the membrane, resembling necrosis.
○ ■ Karyorrhexis: Intracellular DNA undergoes regular fragmentation. DNA fragmentation can be observed through electrophoresis.
○ ■ Phagocytosis
○ ■ Does not harm surrounding cells.
○ ■ Progresses gradually
○ ■ ATP is used.
○ ■ Signal transduction mechanisms involving caspases
② Signal Transduction 1. Extrinsic Apoptosis
○ 1st. Fas or TNF binds to the receptor.
○ 2nd. CASP8 (caspase 8) and adaptor bind to form DISC.
○ 3rd. DISC activates caspase 3.
○ 4th. CASP3 (caspase 3) induces cell death.
③ Signal Transduction 2. Intrinsic Apoptosis
○ 1st. Internal signals cause Bax and Bak on the mitochondrial inner membrane to form oligomers.
○ 2nd. The oligomers form a porin, releasing cytochrome c from the intermembrane space into the cytoplasm.
○ 3rd. Cyt c binds to Apaf-1, forming CARD (caspase recruitment domain).
○ 4th. CARD induces cell death.
○ MOMP, CASP3 are additionally involved.
④ Key Genes
○ Fas
○ Caspase: Initiation of apoptosis and digestion of intracellular components. Related to the mechanism of programmed cell death triggered by external signals. Promotes cell death.
○ p53: Promotes cell death.
○ Bax: Promotes cell death.
○ Cyt c: Promotes cell death.
○ CAD: Promotes cell death.
○ DISC: Promotes cell death.
○ Bcl-2: Inhibits cell death.
⑤ Analysis Methods
○ Annexin-V staining: Staining assay for phosphatidylserine on the outer membrane of cells where phospholipid asymmetry is disrupted.
○ TUNEL assay (terminal transferase dUTP nick-end labeling): An assay to measure dsDNA degraded by apoptosis.
○ γ-H2AX assay: An assay that indicates whether DNA double-strand binding has been disrupted.
○ Calcein-AM assay: High signals indicate a large number of live cells.
○ PI (propidium assay): High signals indicate a large number of dead cells.
○ Ki-67 assay: Ki-67 is used as a cell proliferation marker.
○ DAPI: Binds to the AT-rich regions of the DNA minor groove. Also used as an apoptosis marker.
○ CD8-PD1: Higher values indicate increased apoptosis.
○ Caspase 3/7: Apoptosis marker.
○ PARP cleavage: Apoptosis marker.
○ 8-OHdG (8-hydroxy-2’-deoxyguanosine): DNA oxidative marker.
○ CC3 (cleaved caspase 3) staining: Apoptosis assay.
○ 7-AAD: A fluorescent dye that binds to DNA. It cannot pass through the intact plasma membrane of living cells.
○ DiOC6: A membrane-permeable fluorescent dye. When applied to cells, it accumulates in mitochondria. If the mitochondrial membrane is damaged, DiOC6 accumulation decreases.
○ Trypan blue: stains dead cells blue.
○ Cytotoxicity assays: MTT, WST, XTT, CCK-8
⑥ Examples
○ Rare in unicellular organisms: However, cases of apoptosis have been found in yeast coloniesin-,colonies,-(suchasseveral).
○ Commonly observed during development.
○ During the metamorphosis of a tadpole, its tail disappears.
⑶ Type 2. Autophagy (autophagy-dependent cell death; ADCD, type II cell death)
① Features
○ ■ Formation of DMA (double-membraned autolysosome)
○ ■ DMA: macroautophagy, microautophagy, chaperone-mediated autophagy, etc.
○ ■ Increased lysosomal activity
② Signal Transduction
○ mTOR, Beclin-1, p53 signaling pathways
③ Key Genes
○ ATG5
○ ATG7
○ LC3
○ Beclin-1
○ DRAM3
○ TFEB
⑷ Type 3. Necrosis (type III cell death)
① Features
○ ■ Rupture of the plasma membrane, releasing internal enzymes: Damages surrounding cells.
○ ■ Swelling of cytoplasm and cellular organelles.
○ ■ Moderate chromatin condensation
○ ■ Decrease in ATP levels
○ ■ Inflammatory response
○ ■ No phagocytosis
○ ■ No lysosomal activity
○ ■ ATP is not used.
○ ■ No caspase-mediated signaling mechanisms.
○ ■ Progresses rapidly
② Signal Transduction
○ TNFR1-RIP1/RIP3-MLKL signaling pathway
○ PKC-MAPK-AP-1 signaling pathway
○ ROS-related metabolic regulation signaling pathway
③ Key Genes
○ RIP1
○ RIP3
⑸ Type 4. Ferroptosis
① Features
○ ■ Small mitochondria with increased mitochondrial membrane density.
○ ■ Decrease or loss of mitochondrial cristae
○ ■ Destruction of the mitochondrial outer membrane
○ ■ Iron accumulation
○ ■ Lipid peroxidation: Especially in the cell membrane
② Signal Transduction
○ Xc-/GPX4, MVA, sulfur transfer pathways
○ P62-Keap1-NRF2 pathway
○ p53/SLC7A11, ATG5-ATG7-NCOA4 pathway
○ p53-SAT1-ALOX15 pathway
○ HSPB1-TRF1, FSP1-COQ10-NAD(P)H pathway
③ Key Genes
○ GPX4
○ TRF1
○ SLC7A11
○ NRF2
○ NCOA4
○ p53
○ HSPB1
○ ACSL4
○ FSP1
④ Ferroptosis Inducers
○ Erastin
○ Piperazine erastin
○ Imidazole ketone erastin
○ Sulfasalazine
○ Sorafenib
○ Glutamate
○ (1S,3R)-RSL3
○ C’ dots & amino acid starvation
○ FPEF
○ FeGd-HN@Pt@LF/RGD2
○ ZVI
○ DGU:Fe/Dox
○ FeCo-DOX@MCN
○ MON-p53
⑤ Ferroptosis Inhibitors
○ Liproxstatin-1
⑹ Other Types
① Accidental cell death (ACD): Sudden external shock
② Anoikis: Caused by the loss of integrins.
③ Autosis: A type of autophagy dependent on Na+/K+-ATPase.
④ Cellular senescence: Characterized by the secretion of SASP (senescence-associated secretory phenotype).
⑤ Cell scorch death
⑥ Copper-induced cell death
⑦ Efferocytosis: Involves phagocytes.
⑧ Entotic cell death: Actomyosin-dependent cell-in-cell internalization is involved.
⑨ Immunogenic cell death (ICD)
⑩ Lysosome-dependent cell death (LDCD): Involves primary LMP, cathepsin, MOMP, caspase, etc.
⑪ Mitochondrial permeability transition (MPT)-driven necrosis
⑫ Mitotic catastrophe
⑬ NETotic cell death
⑭ Parthanatos: Involves PARP1 hyperactivation.
⑮ Pyroptosis: A type of inflammatory cell death characterized by membrane pores formed by the gasdermin protein family.
2. Cell Survival
⑴ Example 1. Inhibition of Apoptosis in Phagocytes
① Phagocytes do not undergo apoptosis upon encountering foreign substances: To perform immune responses.
② Toll-like receptors (TLR)
○ TLR-1: Recognizes multiple triacyl lipopeptides.
○ TLR-2: Recognizes lipoteichoic acid. Activates innate immunity.
○ TLR-3: Recognizes dsRNA in viruses.
○ TLR-4: Recognizes LPS (lipopolysaccharide) in Gram-negative bacteria.
○ TLR-5: Recognizes flagellin, the subunit of prokaryotic flagella.
○ TLR-6: Recognizes multiple diacyl lipopeptides.
○ TLR-7: Recognizes single-stranded RNA.
○ TLR-8: Recognizes small synthetic compounds and single-stranded RNA.
○ TLR-9: Recognizes unmethylated CG sequences (Cp DNA) and oligodeoxynucleotide DNA.
③ NF-κB Signal Transduction
Figure 3. NF-κB and Iκ-B Experiment (Western Blot Results)
○ 1st. NF-κB is normally bound to the Iκ-B protein in the cytoplasm, forming a complex.
○ Iκ-B inhibits NF-κB from translocating to the nucleus.
○ Protein X refers to Iκ-B.
○ 2nd. Lipopolysaccharide (LPS), etc. bind to toll-like receptors (TLR).
○ 3rd. TNF-α trimer binds to the receptor.
○ 4th. IKK (inhibitor kappa kinase) is activated.
○ 5th. Iκ-B is activated and degraded in the cytoplasm.
○ When treated with a proteasome inhibitor, NF-κB does not separate from Iκ-B, indicating that Iκ-B is degraded under normal conditions.
○ 6th. NF-κB separates from Iκ-B and translocates to the nucleus.
○ 7th. NF-κB produces proteins involved in the inflammatory response of macrophages.
○ Macrophages exist as inflammatory M1 type and anti-inflammatory M2 type.
○ NF-κB promotes the conversion of macrophages to the M1 type.
④ Pathway 1. MyD88-dependent Pathway
○ Overview: Mechanism through signal transduction. Activates NF-κB. Increases TNF-α and IL-1β.
○ TLR → MyD88 → TRAF6 → NF-κB → NF-κB translocates to the nucleus.
○ TLR → MyD88 → TRAF6 → MAPK → AP-1
⑤ Pathway 2. TRIF-dependent Pathway
○ Overview: Mechanism through endosomes.
○ TLR → TAM, TRIF → IRF3 → IRF3 translocates to the nucleus → type I IFN.
○ TLR → TAM, TRIF → TRAF6 → NF-κB → NF-κB translocates to the nucleus.
○ TLR → TAM, TRIF → TRAF6 → MAPK → AP-1.
⑵ Example 2. Immediate Early Stress Response
① Stress → ASK-1 (= MAP3K5) → JNK p38MAPK → ATF2, JUN, FOS → Translocates to the nucleus → AP-1 (activator protein 1)
Figure 4. Immediate Early Stress Response
⑶ Example 3. Heat Shock Response (Unfolded Protein Response)
Figure 5. Heat Shock Response
① Stress → Proteotoxic stress (endoplasmic reticulum) → PERK, ATF6, HSF1, XBP1 → Translocates to the nucleus → ATF4, ATF6, HSF1, XBP1.
⑷ Example 4. Anti-Oxidant Response
① Stress → NFE2L2
Figure 6. Anti-Oxidant Response
⑸ Example 5. Inflammatory Response
① Stress, hypoxia → NF-κB → Translocates to the nucleus → NF-κB.
Figure 7. Inflammatory Response
⑹ Example 6. Hypoxic Response
① Stress, hypoxia → HIF-1α → Translocates to the nucleus → HIF-1α, HIF-1β.
Figure 8. Hypoxic Response
Input: 2019.03.14 21:19
Modified: 2022.06.13 13:42