Reason why it took so long before studying apoptosis:

Week 1 – Apoptosis Overall concept: Cells detach from surrounding > cell changes morphology (becomes smaller, denser, forms apoptotic bodies) > macrophages will phagocytose the apoptotic bodies.

Reason why it took so long before studying apoptosis:

1) researchers not interested in a dead cell 2) difficult: because dead cell is just junk. The trick was: C.elegans. The organism stayed alive while there were dead cells in the body. Necrosis = cells just die. They swell because of osmotic pressure.But they saw that dying cells became smaller (this should cost energy) = named apoptosis. When cells die of apoptosis, they have a specific DNA pattern. Similarity between the apoptotic genes and tumor

genes: tumor cells can’t die.

Programmed cell death: cell dies at a certain place at a certain position. It is genetically determined.

Genetic pathway for programmed cell death in C.elegans:

When a healthy cell is committed to die, the dead cell is engulfed by another cell. They have defined genes which are needed for degradation, engulfment and genes which are involved in apoptotic process.Ces-2 = inhibitor of ces-1 (present in healthy cells) Ced-9 = inhibitor (kept cells alive) egl-1 = activators (inhibitors Ced-9, activated ced-3 & ced-4) Experiment performed: Loss-of function screening: irradiated worms, mutated genes. Take the worms, look under microscope and count the cells.Similarities between pathways to cell death in C.elegans and mammals Comparison of the C. elegans CED protein pathway and the core apoptotic machinery in mammalian cells shows conservation of the general outline of the pathway.Types of cell death Apoptosis = means ‘falling leaves’ is controlled from of cell death Necrosis = uncontrolled form of cell death (passive form of cell death) Programmed cell death = genetically encoded cell death Anoikis = programmed cell death that is induced in anchorage-dependent cells when they detach from the surrounding extracellular matrix Autophagic cell death = dying cells displaying a large-scale accumulation of autophagosomes.Autophagy is considered to be a pro-survival pathway in the dying cell. Cells die with autophagy, rather then by autophagy.“what researchers said: Cell die in a neat way by apoptosis and not by necrosis.”

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Necroptosis = controlled from of necrosis Pyroptosis = A highly inflammatory form of programmed cell death that occurs most frequently upon infection with intracellular pathogens and is likely to form part of the antimicrobial response. It is an intermediate between apoptosis and necrosis, uniquely dependent on caspase-1.Cells which have taken up a pathogen. The cell tries to get rid of the bacteria, it starts producing inflammatory factors (induce inflammation). Cells dies by necrosis. Inflammatory way of dying.Parthanatos = stimulated in response to extreme genomic stress, it is uniquely dependent onPARP-1.Ferroptosis = related to the antioxidant defense system. Programmed cell death caused by iron- dependent accumulation of lipid peroxides. Iron induces ROS.Mitotic catastrophe = due to premature or inappropriate entry of cells into mitosis leading to programmed cell death, often induced by radiation, chemotherapeutic drugs or hyperthermia.NETosis = A pathogen-induced cell death of neutrophils, thereby excreting their DNA leading to neutrophil extracellular traps (NETs) able to catch and kill extracellular pathogens.

Summary:

Function of programmed cell death in animal development -Sculpting (skin in between fingers is degraded in humans) -Deleting unwanted structures (frog tail, during development organs female/male removed) -Controlling cell numbers (cells not attached to each other, no survival signal, they die) -Eliminating nonfunctional, harmful, abnormal or misplaced cells. (T-cells auto reactive, tumor cells) A dead cell still has a function, specialized cell death: e.g. skin cells for cornification, platelets for blood coagulation, lens cells for transparency, red blood cells for oxygen transport.Stressed cells may choose between apoptosis and senescence Senescence cell = if a cell get stress, normally the cell dies by apoptosis. But some stresses at some cells, they don’t die but decide to go into senescence. Cell can’t divide anymore (still metabolic active). It is doesn’t divide, it can’t form a tumor. But a recent discovery showed: senescence cells secrete factors which harm the organism (inflammatory factors) and they effects organs. If you have lots of senescence cells, related to aging. Lots of organs don’t function anymore because of accumulation of senescence cells.

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Death pathways A cell can die in many ways, depends on the cell type and the time and type of stress.

Death signal to a cell  time dependent. For instance: in

red arrow. The cell may start the apoptotic process (2h).In the meantime the cell wants to survive; autophagic process (giving energy to keep the cell alive) apoptosis- like. Other processes may have started (green) necrosis for example.The death pathway is most frequently through apoptosis (left, red branch), either via caspase-9 activation and a mitochondrial route or directly via caspase-8 to caspase-

• as a primary effector caspase. Other pathways exist,

including autophagic (middle, pink branch).If the cell is severely and acutely injured, so that its membrane permeability is compromised, it may fail completely, undergo osmotic rupture, and become necrotic (far right, black branch). Alternatively, it is possible that, through the progression of its resorption, the cell may deplete its energy resources and, though having commenced an apoptotic or autophagic death, it may revert to necrosis (bottom, black pathway). This latter is particularly likely where phagocytosis of the dying cell is compromised, as in massive toxic death and with cell lines maintained in culture.Too hot cup of tea: will the cell die of apoptosis or necrosis (by necrosis because no time for apoptosis).Cell type dependent Situation dependent Type of stress dependent Apoptosis Controlled process to efficiently deplete cells without cell lysis crucial process in development, growth/maintenance/ immune system Morphology: small condensed nucleus, blobs on the outside, short mitochondria (function remains intact).Apoptosis vs necrosis Stress causes dysfunction of the cell.NecrosisApoptosis loss of membrane integrity, less condense chromatin Swelling and lysis No vesicle formation, complete lysis Disintergration (swelling) of organelles Membrane blobbing, but no loss of integrity Aggregation of chromatin Cellular condensation Formation of membrane bound vesicles No-energy requirement Random late digestion of DNA ATP dependent Early specific DNA fragmentation (separate DNA

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on ladder, you see specific bands) Need an inflammation to occur Evoked by non-pysiological disturbances Phagocytosis by macrophages Induced by physiological stimuli No inflammatory response

oApoptotic process: Three phases

1)Activation phase Extrinsic pathway (receptor-mediated) by the receptor caspase 8 is activated.

• Death receptor signaling

intrinsic pathway (cellular stress signal) -Mitochondrial signaling pore is opened, activate Caspase 9 2)Execution phase -Caspase cascade 3)Burial phase oTNF family death receptors Ligand (trimer) induces trimerization of the receptor.

3 types of death receptors:

1)CD95/Fas receptor

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