Homeostasis Flashcards
What factor ultimatley determines a cell fate during differentiation?
Depends on the genes that are switched on and off - ultimately dictate the type of cell formed
Some genes are common across cells - known as housekeeping genes/proteins
Some genes are specific to particular cell types (luxury functions)
Is cell information/DNA lost during differentiation?
Genetic information is not lost
All cells in a multicellular organism have full gene complement
Cells are specialised because of differences in gene activity (not gene content)
How can transcription factors control gene expression?
Transcription factors – proteins that switch ON or switch OFF gene expression - bind to promoter or enhancer elements in order to increase or decrease gene expression
E.g. Introduce MyoD into fibroblasts - able to convert a fibroblast cell into a muscle cell – induces expression of muscle specific genes
- MyoD also creates a positive feedback on itself that amplifies its activity
Can transcription factors respond to their environment?
Yes, they can integrate information from their environment in order to modulate gene expression.
Example - Prokayotes - Tryptophan repressor binds to tryptophan when it is abundant, allowing it to bind to cis-regulatory sequence and block further tryptophan synthesis - reverse happens when tryptophan is not abundant.
Does RNA polymerase require help to bind to gene targets?
Yes, RNA polymerase is directed to gene transcription start sites within a gene’s promoter by a number of ’helper’ proteins
e.g. the TATA box is a DNA signal sequence to which the general transcription factor ‘TATA binding protein’ TFIID binds - guide RNA poly to gene promoter regions - other signals are then required to drive transcripton
What is the role of enhancer sequences?
Enhancers are recognized by proteins called transcription factors – if the transcription factor is in the cell it binds to it’s enhancer and this can activate or repress RNA polymerase function
Many different enhancers, which are recognized by different transcription factors
The gene is switched ‘ON’ or switched ‘OFF’ for transcription
How is DNA packaged in the nucleus?
DNA is associated with proteins: histones & other nonhistone chromosomal proteins, this DNA-protein complex is known as chromatin
First and most fundamental ‘level’ of chromatin packing is the nucleosome, which form the ‘beads on a string’ arrangement
DNA (genes) is inaccessible when wrapped around the nucleosome
What three factors dictate whether chromatin is available to transcription?
Transcription factors can bring along…
1. Histone modification enzymes
2. ATP-dependent chromatin remodeling complexes
3. Histone chaperones - removing histones and/or adding histone variants
All of which can influence the chromatins accessibility - influence the general transcription machinary’s ability to access promoters
These changes in chromatin structure can be rapidly reversed or maintained for longer periods of time
If a differentiated cell divides, how does it ensure that its progeny retains the correct identity?
Differentiated cells generally remain differentiated
Their progeny will inherit their identity – e.g. fibroblasts, smooth muscle, liver cells (n.b. some differentiated cells never divide, e.g. neurons, skeletal muscle)
How is this ‘memory’ passed on to daughter cells?
- Parental TF present/passed on to daughter cells and this sustains the gene expression pattern
What are different ways a cell can enforce cell memory in the long term?
Reinforcing Cell Memory
- Histone tail modifications - long term modifications can be used to reinforce cell memory
- DNA methylation - occurs at CpG islands - passed on during DNA replication - efficient form of gene repression - direct inhibition of trnascriptional machinery/indirect inhibition via histone modifying enzyme recruitment
- Most extreme example - X-inactivation - methylation of a whole chromosome. - Chromatin condensation
What are the two principle ways by which a stem cell can give rise to polar/different progeny?
- Assymetric division - polar/asymmetric distribution of transcription factors
- External signals from the environment driving cell fate
What is Waddington’s differentiation landscape?
Concept of differentiation - multipotent stem cell has many different potential paths it can take, which decrease as it progressively becomes more specialised
What is the definition of a multipotent stem cell?
A multipotent stem cell that can give rise to all the different cells of a specific tissue/organ
E.g. Haemtopoeitic stem cells givies rise to all the different blood and immune cells
How is the differentiation of red blood cells regulated?
Differentiation is a stepwise process
Commitment is regulated by activity of specific transcription factors e.g. GATA1
GATA1 transcription factor - Binds to specific DNA sequences
Targets:
1. Alpha-globin & beta-globin genes
2. Haem biosynthesis enzymes
3. Erythropoietin receptor
Mutation of mouse Gata1 gene - results in anaemia due to death of erythroid precursor cells
How do stromal cells in the bone marrow help maintain stemness of haematopoietic stem cells?
Haematopoietic stem cells depend on signals from their ‘niche’ within the bone marrow
Bone marrow stromal cells play an important role in contacting stem cells in order to maintain their stemness - lack of interaction drives differentiation
Contact-dependent interaction between receptor on stem cell and ligand in stromal cell
When a stem cell divides one daughter will lose contact with the stromal cell – and will differentiate
What external signal produced by the kindeys regulates RBC production?
Erythropoietin = hormone produced by the kidney in response to lack of O2 / shortage of erythrocytes
Erythropoietin acts on erythropoietin precursor cells to increase their proliferation/survival - increase overall numbers of RBCs produced
All made possible by the presence of GATA-1 which drives EPO receptor expression – allows for specific sensitivity of these cells towards the presence of EPO
What external signal increase the amount of neutrophils and macrophages produced?
Signals (colony-stimulating factors, CSFs) are released by various cell types (endothelial cells, fibroblasts, macrophages, lymphocytes) in response to tissue infection
CSFs act on precursor cells in the bone marrow to promote the production of neutrophils and macrophages
Are the size and proportions of an organism largely genetically determined?
Growth and proportion are underpinned by robust genetic mechanisms
What are the three factors that determine/influence the total cell mass?
- Cell growth - growth factors stimulate cell growth/increase cell mass – promote synthesis of proteins and other macromolecules - note there are also factors that inhibit growth (e.g. Myostatin)
- Cell division - Mitogens – stimulate cell division by triggering a wave of G1/S-Cdk activity that relieves intracellular negative controls blocking the cell cycle - platelet-derived growth factor (PDGF) + epidermal growth factor (EGF)
- Cell death - Survival/death factors – promote cell survival or death by suppressing or inducing apoptosis (a type of cell suicide) - survival factors vs. pro-apoptotic signals
What are the two main ways that organ/tissue growth is regulated?
Way growth is controlled in different tissues/organs is different
Difference is that some rely on…
1. Extrinsic (systemic regulation of spleen growth)
whereas other rely on…
2. Intrinsic mechanisms (intrinsic mechanism driving thymus growth)
No universal mechanism for organ growth
What is a stem cell? What are the defining characteristics?
Stem cells have the power to give rise to different cell types
- A stem cell is not terminally differentiated
- It can divide without limit
- Upon division each daughter has a choice: stem cell or terminal differentiation
Outline how stem cells in the gut give rise to differentiated epithelial cells.
Stem cells divide – differentiate into transit amplifying cells – increase in number – terminally differentiate into non-dividing differentiated epithelial cells
Stem cells surrounded by the non-dividing Paneth cells
What are the two mechanisms used to drive stem cell renewal?
- Asymmetric division (polarization of stem cell factors)
- Independent choice (random or driven by environmental factors)
How is stem cell self-renewal driven in intestinal stem cells?
Stem cells fate induced by signals from Paneth cells & connective tissue surrounding crypt - known as the ‘intestinal cell niche’
WNT signaling playing an important role
Outline how WNT signaling drives the stem cell state in the intestine?
WNT signaling pathway – produced by Paneth cells
- WNT receptor on stem cells – activated – inhibits Apc – allows B-catenin to move into the nucleus and maintain stemness
- Conversely if WNT is not present – APC is activated and degrades Beta-catenin – preventing the expression of stem cell genes
What are the links between stem cells and cancer?
Self renewing tissues – breeding ground for great majority of human cancers, e.g. epidermis, intestine, reproductive tract & bone marrow
Example: colorectal cancer – affects epithelium of colon (large intestine) and rectum
Colorectal cancer = common (about 10% deaths from cancer)
Develop from benign tumor or adenoma ‘polyp’
Renewal in large intestine is similar to small intestine: stem cells that lie in crypts, similar signals maintain stem cells and control renewal
What is Familial adenomatous polyposis coli (FAP) (cancer)?
Familial adenomatous polyposis coli (FAP) – rare hereditary condition predisposition to colorectal cancer
FAP individuals have a deletion or inactivation of one copy of the Apc gene - If the other (normal) copy of Apc becomes inactivated during the patients lifetime – results in tumor formation
Most patients with colorectal cancer do not have the hereditary condition, but in 80% of cases their cancer cells inactivated both copies of Apc through mutation acquired through the patients lifetime
Consequence of APC deletion
- Constitutive activity of B-catenin – drives expression of stem cell genes – drives excessive proliferation
What are examples of factors that can cause cell injury?
- Lack of oxygen
- Physical agents (temperature, pressure, electricity, radiation)
- Chemicals and drugs
- Infectious agents
- Immune reactions - can be non-direct and direct
- Genetic defects
- Nutrition (deficiency, imbalance)
What are the cellular responses to injury?
Cells have an ability to adapt if the assault isn’t too significant – ability to reverse injury
Injury very significant – leads irreversible injury – necrosis and apoptosis
What are examples of cell injury that can be reversed?
Rapid changes can be reversible
For example…
1. Swelling due to loss of ion/fluid homeostasis
2. Fat accumulation (steatosis)
But this damage may become Irreversible the injury persists
What is the main difference between apoptosis and necrosis?
Main modes of cell death
- Necrosis – uncontrolled cell death - causing inflammation
- Apoptosis – controlled cell death – in many contexts a useful mode of controlling cell populations – contents are put into apoptotic bodies – organized disassembly of cell – no immune response
What are the features that define apoptosis?
Apoptosis
1. Programmed cell death
2. Ordered, regulated process
3. Physiological - Plays an important role in development and homeostasis
4. Pathological - virally infected cells undergo apoptosis in order to prevent further viral release
5. Cells remain alive during the process and expend energy to drive process
What are the two drivers behind apoptosis intiation?
Two stages in apoptosis - Initiation and execution
Intiation of apoptosis can be extrinsic or intrinsic
Extrinsic – Death domain receptor drives activation of caspases - Caspase 8 main player
Intrinsic – release of cytochrome C from them mitochondria – activates caspases
Excution relies on the assembly and activity of the executioner caspase
Note
- Caspases are cysteine proteases that cleave after aspartic residues
- Sit in their inactive form in the cell ready to converted into their active form
What is autophagy?
Recycling and turnover of cytoplasmic cell constituents
Organelles packed and fused with a lysosome – the building blocks are released back into the cytoplasm – recycling
Strictly regulated by autophagy-related genes (ATGs)
Response to extra- or intracellular stress (nutrient starvation, differentiation, metabolic stress, and developmental triggers)
What are the different types of necrosis?
- Coagulative
- Liquefactive
- Caseous
- Gangrenous (dry)
- Fat
What is coagulative necrosis?
Nuclei are lost but the cell proteins coagulate and are left behind – leaves ’ghost’ of the cell behind
E.g. Hypoxia secondary to reduced blood supply
– ischaemia - infarction –> results in coagulative necrosis
What is liquefactive necrosis?
No outline of the cells – proteins digested – soup like/melts the tissue
Typical when there is a high level of neutrophil recruitment – resulting in pus
Can be seen in secondary infection by bacteria (wet gangrene) at site sof necrosis and lipid rich tissue like the brain
What is caseous necrosis?
End result of granulomatous inflammation
Granulomas – large aggregates of macrophages; epithelioid & giant cells
Found in…
1. Autoimmune conditions,
2. Foreign bodies are trapped
3. Mycobacterial infection (M.tuberculosis)
What is dry gangrene (necrosis)?
Coagulative necrosis of extremity due to slowly developing vascular occlusion e.g. diabetic
You can get secondary infection resulting in liquid necrosis
What is fat necrosis?
Degradation of fatty tissue by lipases, forming chalky deposits
E.g. Acute pancreatitis, trauma to fatty tissues
What is necroptosis?
Organised necrosis
Imperfect or inaccessible apoptotic machinery under severe cellular stress
Caspase independent
Swelling of organelles, eventual loss of membrane integrity
Organised – final common activation of RIP1 via signalling pathway cascade (TNFRs, TCRs, IFNRs, TLRs)
Compare and contrast necrosis and apoptsis in terms of their morphology.
Compare and contrast necrosis and apoptsis in terms of their biochemistry.
Compare and contrast necrosis and apoptsis in terms of their consequences.
What are the two primary responses to tissue injury?
Regeneration – renewal or compensatory growth to replace damaged tissues
Repair – fibrous scar production (fibrosis) to patch damaged tissues
When thinking about tissue regeneration, what cell ‘types’ are capable of regeneration and which are not?
1.Labile cells– cells that divid in homeostasis; rapid regeneration (skin, GI tract)
2. Stable cells – non-proliferative in homeostasis; capable of regenerating after injury (liver, kidney)
e.g. Renal tubular epithelial cells regenerate after injury e.g. ischaemic/toxic
e.g. Regeneration after significant damage to liver - rodent model - able to regenerate to original mass after 70% loss
3. Permanent cells – unable to regenerate (neurons, cardiac myocytes) - Only way that wound can heal is by scarring
What is the reasoning of creating scar tissue if it doesn’t carry out any of the tissues/organs function?
Scar tissue is required to maintain organ integrity
What are the different environmental signals that promote tissue regeneration?
Cell number tightly controlled; balanced growth and loss - loss of control leads to neoplasia
- Soluble growth factors released - autocrine, paracrine and endocrine - bind to cell surface receptors and drive intracellular signalling (phosphorylation driving signalling)
- Physical stimuli – cell-cell and cell-matrix interactions - mediated by integrins, triggering similar cascades
Outline the process/steps by which scarring takes places - example: skin
Example - Skin tissue
- Injury - Bleeding
- Clot formation & Epidermis cell replication - triggered by loss of neighbor contact
- Acute → chronic inflammatory response - leads to the formation of granulation tissue (image 3)
- Fibroblast infiltration - neomatrix
- Angiogenesis; fibrillar collagen
- Scar maturation - gradual maturation that takes places over years
Note - Injury in the dermis will result in some degree of scarring – some of the cells can’t be replaced
What is granulation tissue?
Forms rapidly ~ 1 day
Grainy/shiny wound base - centre
- Early new vessels, acute inflammation - neutrophils, neomatrix starts forming (fibrin)
What are some key players in the process of angiogenesis during scarring?
Most relevant type of angiogenesis – sprouting
Angiogenic stimuli release
1. Nitric oxide - widening of vessels
2. MMP - loosening of the surrounding matrix
3. VEGF - allowing the endothelial cells to sprout out towards the areas of injury (move towards VEGF)
Note - Reverse process needs to occur when the new blood vessels form – vessel maturation - matrix formation, pericyte movement, PDGF-8
What cell type is responsible for creating a new matrix during scar healing? What growth factor signal plays an important role? What type of collagen is layed down? Example - Skin
Fibroblasts - migrate, proliferate and deposit new ECM at the site of injury - this is followe dby tissue remodelling.
Key growth factor - TGF-Beta - produces fibroblast migration & proliferation, ECM ↑
production & ↓ degradation; PDGF produces proliferation
Types of collagen at the right places matters
1. Fibrillar types – collagen I/III – rigid/tougher
2. Basement membrane type – collagen IV – looser
Other ECM componenets - Elastin, proteoglycans, glycoproteins
Skin - Resident mesenchymal cells
How does scar tissue remodelling take place?
Remodelling of granulation tissue ECM requires degradation by MMPs
Matrix metalloproteinases (MMPs) produced by many cell types - All ECM components are substrate for MMPS
They are regulated – production and activity (Tissue inhibitor of metalloproteinase -TIMPs)
Different MMPS active during different stages to allow for remodelling to occur
Mediate long term scar maturation and degradation
Example of regeneration, scarring & resolution.
What is end stage scarring?
Continued injury – progressive scarring – irreversible – causes organ dysfunction
Too much scarring – point of no return for repair
Summary of the three different repair responses?
