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  3. Radboud Universiteit Nijmegen (RU)
  4.  
  5. Apoptosis (NWIBM004C)

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Summary Lectures Apoptosis

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All lectures of the master course apoptosis (NWI-BM004c) are covered in the document (using the powerpoint slides and additional information covered in the lectures). The figures included are taken from the PowerPoint slides. All processes and concepts discussed are extensively described using exam...

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  • 25 januari 2021
  • 76
  • 2020/2021
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Lectures apoptosis
Lecture 1: 6 November 2020
Before apoptosis occurs, the cell often detaches from its surroundings. The cell changes morphology,
shrinks and becomes darker. The cell than forms apoptotic bodies, which are phagocytosed by
neighbouring cells and macrophages.

History of apoptosis
It took many years before apoptosis was studied for the first time. This because dead cells were not
taught to be important, but also because studying the metabolic processes in a dead cell is very
difficult. This last problem was eventually solved by using the worm C. elegans, because this
organism stays alive while dead cells are present in its body. Programmed cell death was first
described in C. elegans, referring to a cell which is genetically determined to die at a certain place, in
a certain position.
Cells undergoing necrosis swell, because of the osmotic pressure. In apoptosis however, the cells
shrink, meaning that performing apoptosis costs energy.

If a cell dies via apoptosis, this gives very specific DNA degradation products.

Interest in studying apoptosis arose when apoptosis was linked to tumour progression. Identification
of similar genes in C. elegans and tumours, made people realise that tumour progression is not solely
about uncontrolled cell division, but also about problems in cell death.

Caenorhabditis elegans
Under the microscope, cells can be seen in a living C. elegans. During this study genes were identified
that are needed for apoptosis, cell degradation, and engulfment. Different genes that are needed for
apoptosis in C. elegans:
- Ced-3 and ced-4. Involved in execution of apoptosis.
- Ced-9. Inhibitor of apoptosis which inhibits ced-3 and ced-4.
- Egl-1 and ces-1: activators which inhibits ced-9.
These genes were identified using loss of function genes: the worms
were irradiated to damage the genes and induce mutations. The cells were then counted under the
microscope. If less cells were counted, something related to cell death was mutated in the worm. The
gene was identified by transforming the C. elegans → the wild type genes were restored one by one.
After every restoration, the worms were studied under the microscope.

There are similarities between apoptosis genes in C. elegans and mammals: same type of genes,
different names.

Types of cell death
Type of cell death Mechanism
Apoptosis Controlled form of cell death.
Necrosis Passive, uncontrolled cell death.
Programmed cell death Genetically coded cell death.
Anoikis Programmed cell death that is induced in anchorage-dependent cells,
when they detach from the extracellular matrix. If the cells get no
survival signals form neighbouring cells, the cells will die.

, 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 than by autophagy.
Necroptosis Controlled form 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.

After the cell has taken up the pathogen, it starts producing
inflammatory factors and the cell eventually dies by necrosis. The
bacteria is released, but the immune system is activated and the
bacterium is attacked. The cell has to go into necrosis, because the
bacterium is invisible for the immune system in the cell.
Parthanatos Stimulated in response to extreme genomic stress, it is uniquely
dependent on PARP-1.
Ferroptosis Programmed cell death caused by iron-dependent accumulation of lipid
peroxides. It is initiated by failure of the glutathione-dependent
antioxidant defences, resulting in unchecked lipid peroxidation and
eventual cell death.

It is related to the anti-oxygen defence system. Iron is able to induce
ROS. If the anti-oxygen defence system is not functioning, cells may die
by ferroptosis. This is a pathological process.
Mitotic catastrophe Due to premature or inappropriate entry of cells into mitosis leading to
programmed cell death, often induced by radiation, chemotherapeutic
drugs, of 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.

Neutrophils are very efficient in engulfing pathogens. However,
sometimes there are too many bacteria for the neutrophil to engulf →
the neutrophil dies and expels its DNA. The DNA forms a network (NET)
containing aggressive molecules which produce radicals, proteases, etc.
The bacteria will stick to the network and the molecules can help to kill
the bacteria.

During necrosis all the cell contents are spilled into the
surroundings, which should be avoided if possible.
Apoptosis is a “clean” way in which the cell can die: there
are apoptotic bodies, engulfment by neighbouring cells, and
there is no inflammation. Although apoptosis might seem
preferable, there is also a specific way in which cells can
induce necrosis, which is necroptosis.

Function of programmed cell death in development
Apoptosis plays different roles in development:
1. Sculpting. For example:
a. The skin between the fingers. During development, the fingers are formed with skin
between them. The cells between the fingers are programmed to go into apoptosis.

, b. The development of hollow structures: formed as a solid structure, and the cells in
the middle go into apoptosis.
2. Deleting unwanted structures. For example:
a. In frogs, where tadpoles have a tail, but during development the tail goes into
apoptosis to create a tailless adult frog.
b. During development both reproduction organs for males and females are formed,
and either of those goes into apoptosis.
3. Controlling cell numbers. For example:
a. Cells that are not attached to the basal membrane, go into apoptosis. The cells need
to receive survival signals from the basal membrane.
4. Eliminating non-functional, harmful, abnormal, or misplaced cells. For example:
a. Autoreactive immune cells need to be removed.
b. Damaged cells are at risk to form tumours, so they have to be removed.

Function of dying cells
There are several functions for almost-death cells.

An example is the skin. The figure on the right shows a cross-
section of the skin. The cells divide in the stratum basale and
differentiate through the epidermis. At a certain point the
cells die to form the outer layer of the skin. These death cells
help to prevent dehydration.

Another example are the platelets, which are important for
blood coagulation. Platelets look similar to apoptotic bodies.

The lens of the eye has an epithelial cell layer around the
edges. Towards the edges, the epithelial cell layer
differentiates into lens fibre cells. The nuclei and
mitochondria of the lens fibre cells are removed because the
lens is specialized to refract light, and cell organelles can cause scattering. The inner lens nucleus is
already formed in the embryonic stage: before birth part of the lens is already present, surrounded
by death cells. The proteins in the death cells are necessary for sight, but proteins normally survive
for maximum a week. The proteins in the fibre cells are easily damaged by UV-light and are not able
to be renewed. Damaged proteins aggregate and start scattering the light, thereby troubling vision.
Therefore, it is important to protect the eyes from UV-light.

Red blood cells have no nucleus. They are able to survive for 100 days, after which they are removed.

The abovementioned examples are all forms of programmed cell death.

Senescence
When cells are subjected to stress, the cell
normally dies. However, under certain
conditions, the cells go into senescence
instead of apoptosis. Senescence cells are
metabolically active but are unable to
divide. If a damaged cell goes into
senescence, tumour formation becomes
impossible. Cellular senescence may play an
important role in tumour suppression,

, wound healing, and protection against tissue fibrosis. However, the senescence cells secrete
inflammatory factors and are able to negatively affect organs. Senescent cells accumulate during
aging and have been implicated in promoting a variety of age-related diseases
- An example of a stress factor forcing cells into senescence is smoking.

Identifying dying cells
Dying cells become darker and more condensed. Neighbouring cells can
take up the death cells.
- The figure on the right shows a unicellular organism. On the left is
a normal cell, on the right is a dying cell. Unicellular organisms
have an apoptotic pathway to protect the neighbouring cells →
spilling cell contents via necrosis can be damaging.

Condensed cells are also seen in plants, although they are not created
through an apoptotic process. The function of these condensed plant cells
differs → the cell walls will remain.

Death pathways
Cells are maintained in a complex of signals including growth
factors, cytokines, nutrients, and other signals from other cells.
These signals are countered by various stimuli, including toxins,
catabolic hormones, death domain signalling molecules, and
several physiological parameters. These signals are integrated
and can commit the cell to a death pathway.
The death pathway is most frequently through apoptosis (red),
either via caspase-9 activation and a mitochondrial route, or
directly via caspase-8 to caspase-3 as a primary effector
caspase. Other pathways exist, including autophagic (purple).

The way in which a cell will die depends on different factors:
- Cell type: some types die easier than other cell types.
- Type and period of stress exposure.
Once a death signal is sent to a cell, the cell can respond to this
in different ways. This is time dependent.
➔ Red arrow: the cell might start the apoptotic process,
which takes about two hours. In the meantime, the cells
can switch to a survival pathway, and start the
autophagic process as well: the cells start digesting internal material and start using new
metabolites. The final fate of the cell is determined by the fastest process. In this time, other
processes, like necrosis, may have started as well.
➔ If the cell is severely and acutely injured (compromised membrane permeability), it may
undergo osmotic rupture and become necrotic (black arrow). Alternatively, it is possible that,
through the progression of its resorption, the cell may deplete its energy resources and may
revert to necrosis. This is particularly likely where phagocytosis of the dying cell is
compromised, as in massive toxic death and with cell lines maintained in culture.

Apoptosis
Apoptosis is important for development, grow maintenance and the immune system.

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