cell death

what is the process of apoptosis in C. elegans and mammals?

1. the initiators (Egl-1/BH-3 only)

• pro-apoptotic proteins that sense cell stress or damage

• starts the process by inhibiting the "brakes"

1. the brakes (Ced-9/Bcl-2)

• anti-apoptotic proteins that normally keep the cell alive by blocking the next step

• when the initiators turn them off, the pathway proceeds

1. the adaptors (Ced-4/Apaf-1): once the brakes are released, these proteins cluster together to activate the "executioners"

2. the executioners (Ced-3/caspases)

• specialized enzymes that chew up the cell's proteins and DNA, leading to apoptosis

what is the BCL-2 family of proteins?

• anti-apoptotic: BCL-2 BCL-XL, MCL-1,…
• pro-apoptotic: Bax, Bak, Bok
• BH3-only: Bad, BinS, tBid, Bik,…
• in human follicular lymphoma, BCL-2 was found to be overexpressed via t14:18

what is the process of the MOA of BCL-2 family of proteins?

1. pro-apoptotic proteins like Bax and Bak create pores in the mitochondrial membrane

• Bcl-2 tries to block this, but when Bax/Bak win, cytochrome c leaks out into the cell

1. cytochrome c triggers a "caspase cascade"

• activates Apaf-1 and caspase 9
• these then activate the "executioner" caspases: caspases 3 and 7

1. the executioner caspases cut up viral proteins (e.g. PARP) and activate DFF40 by removing DFF45
2. hallmark of apoptosis: systematic fragmentation of the cell's DNA

what do BCL-2 family of proteins lead to?

• anti-apoptotic and pro-apoptotic proteins are in balance: homeostasis
• anti-apoptotic side (e.g. Bcl-2, Mcl-1) becomes too heavy: cells live longer than they should, leading to uncontrolled growth (primary driver of cancer)
• pro-apoptotic side (e.g. Bax, Bak) outweighs survival signals: cells die off too quickly, leading to tissue degeneration, often seen in neurodegenerative diseases or autoimmune disorders

what are BH3-only proteins?

• share the BH3 domain
• BAX AND BAK
• respond to various stress signals to inhibit anti-apoptotic BCL-2 proteins

what is venetoclax?

• approved in 2017 for treating acute myeloid leukemia (AML)
• can structurally mimic BH3-peptides

what are CASPases?

• cystein-dependent aspartate-directed proteases
• groups: initiator, effector
• exist as latent zymogens (proenzymes): inactive in normal cells
• cleave substrate proteins at the aspartate residue
• when activated, can serve as their own substrate and cleave themselves
• activated when pro domain is released, and large and small domain form a molecule

what are the 2 ways to activate caspases?

• initiator: proximity-induced self-activation; form homodimers
• effector: proteolytic cleavage by initiator caspases

what are the ways to detect morphology?

• electron microscopy
• membrane bleeding
• detachment of adherent cells
• loss of translucent light reflection
• plasma membrane permeability

what is annexin V?

• binds phosphatidylserine (PS): membrane component that resides in the cytoplasmic side of the plasma membrane
• during apoptosis, PS flips to the extracellular side of the plasma membrane

what are the levels of PI and annexin V in apoptosis?

• viable: both are (-)
• early apoptosis: PI (-) and annexin V (+)
• late apoptosis: both (+)
• late dead cells: both become (-) due to cell decomposition

how do phagocytes remove apoptotic cells?

• by recognizing the "eat-me" signal on the apoptotic cells

1. recruitment/attraction of "find-me" signals
2. recognition of newly exposed "eat-me" signals and engulfment of corpse
3. processing and degradation of corpse
4. post-engulfment consequences (e.g. release of anti-inflammatory cytokines)

what is the process of DNA fragmentation during apoptosis?

nuclease cleaves at the linker region between nucleosomes, resulting in 160bp DNA fragments

what are bax-/-bak-/- mice?

• retain interdigital webs
• have enlarged peripheral organs

what are the features of necrosis?

• cellular and organelle swelling
• increased membrane permeability
• proinflammatory
• does not involve caspase activation
• leads to random DNA degradation

what is apoptosis?

• energy-dependent: organized
• plasma membrane integrity maintained
• ordered DNA degradation
• immuno-suppressive (e.g. lysophosphatidylcholine (LPC))
• cell elimination (e.g. phosphatidylserine (PS))

what is necrosis?

• bioenergetic impairment: disordered
• plasma membrane integrity lost
• random DNA degradation
• immuno-stimulating (e.g. HMG-B1)
• repair initiation (e.g. HDGF)

what is ferroptosis?

• regulated form of necrosis
• induced by ROS and oxidation of certain lipids (PUFAs-OH)
• dependent on ions

what is the fenton reaction?

Fe2+ + H2O2 → Fe3+ + .OH + OH-

• iron can shift between the ferrous (Fe2+) and ferric (Fe3+) states, and both transition states can react with hydrogen peroxide to generate a radical
• can also utilize phospholipid hydroperoxides as substrates
• the phospholipid radicals formed by this process can react with other PUFAs to propagate a chain reaction of oxidation