POM Flashcards

1
Q

What are the two possible outcomes when a cell is exposed to a mild injurous agent or stress?

A
  • Reversing the injury if adaptive capacity is exceeded

- Adapting to better be able to deal with the new conditions

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2
Q

What happens if the injurous agent to which the cell is exposed is severe?

A

The cell suffers irreversible injury and can be:

  • Killed via oncosis/necrosis
  • Commit suicide via apoptosis
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3
Q

What are the 6 possible causes of cell injury?

A
  • Physical (heat, trauma, radiation etc.)
  • Chemical (pH, free radicals, poisons)
  • Biological (Micro-organisms, immune responses)
  • Nutritional (anorexia, starvation, or excess intake)
  • Immunologic (autoimmune reactions)
  • Genetic derangements (congenital malformations, predisposing genes)
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4
Q

What are the 4 main ways in which cells are injured?

A

Decrease in ATP production
Membrane damage
Increase in intracellular Ca2+
Damage due to free radicals

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5
Q

How can ATP production be reduced via cell injury?

A

Lack of oxygen
Enzyme damage in the cytoplasm
Damage to mitochondria

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6
Q

How does a drop in ATP production harm the cell?

A

Reduced energy available for DNA and protein repair
Reduced energy available for ATP driven ion pumps (disrupts homeostasis, often causes increase in Na+, H2O and Ca2+ in the cell) Causes cell swelling and activation of damaging enzymes
Reduced protein synthesis, ribosomal detachment from RER

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7
Q

How can the cell membranes be damaged in cell injury?

A
Free radicals directly harm it
Hypoxia (less ATP)
Membrane targeting bacterial toxins
Failure of membrane Ca2+ pumps
Activation of phospholipases during injury, and insufficient ATP for synthesis of new phospholipids
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8
Q

How does plasma membrane damage harm the cell?

A

Loss of cellular contents, osmotic balance, enzymes, proteins, coenzymes and RNA
Influx of fluid and ions
If lysosomal membranes are burst, the digestive enzymes are released into the cell, and perform autolysis
Mitochondrial membrane damage: high conductance, non-selective channels form, causing a mitochondrial permeability transition. Mitosis cannot occur, and cytochrome c leaks into the cytoplasm, priming the cell for apoptosis.

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9
Q

What can cause increased Ca2+ concentration in the injured cell?

A

Decreased activity of Ca2+ channels in the membrane

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10
Q

How does increased Ca2+ concentration harm the cell?

A

Ca2+ dependent destructive enzymes are activated:
ATPase (less ATP)
Phospholipase (destroys membranes)
Proteases (break down membrane and skeleton proteins)
Endonucleases (DNA and chromatin breakdown)

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11
Q

What are free radicals and how do they damage cells?

A

They are highly reactive species with an unpaired electron. When they collide, they release energy.
They attack the fatty acid double bonds in the membrane, oxidise amino acid side chains in proteins, and react with the T base in DNA.
They are also autocatalytic, so they create more free radicals as they go, furthering the issue.

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12
Q

How does the body defend against free radicals?

A

We have antioxidants (VA, E etc.), enzymes etc. Oxidative stress occurs when there are more free radicals present than can be coped with.

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13
Q

How can cell proteins be damaged?

A

Directly (Ca2+ enzymes or free radicals) or having synthesis reduced. Also, glycation.

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14
Q

How is DNA damaged?

A

UV or Ionizing radiation
Mutagens and Free Radicals
Genetic causes
B12 or folate deficiencies

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15
Q

How does intracellular signalling help in the repair or removal of damaged cells?

A
  • Activate heat shock factors to produce heat shock proteins, which re-fold and hold damaged proteins until they can be repaired
  • Stress kinases (P38 MAP kinase, Jun-N terminal kinase) initiate signalling cascades to coordinate repair
  • P53 when DNA damage detected. Either stops division for repair or causes cell death
  • BMF- damage to cytoskeleton
  • Bim- microtubule damage
  • Bad- due to inadequate GF stimulation
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16
Q

What are some ways in which cells adapt to mild stressors?

A

Hypertrophy: Cells grow larger due to increased functional demand or stimulation
Hyperplasia: More cells formed due to division of cells and stem cells (either local or from bone marrow).
Atrophy: Cells shrink due to reduced functional demand, nutrients or stimulation. Involves proteolytic systems using lysosomes and a protein destruction machine known as the uniquitin-proteasome pathway.
Metaplasia: under continuous mild damage, cells morph from one type to another type more able to withstand the environment.

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17
Q

What is the point of no return when cells can no longer adapt or repair?

A

When the membrane and mitochondrial dysfunction becomes irreparable.

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18
Q

What is necrosis? What does it require? Why is it less preferable to apoptosis?

A

Necrosis involves cells being killed outright by overwhelming damage. It affects large number of cells, and is accompanied by leakage of lysosomes (releasing digestive enzymes) and cytosol (inducing an inflammatory response)

  • Requires no energy, but is uncontroled and messy
  • Shows featureless cytoplasm, fragmentation and fading of chromatin.
  • Debris removed by phagocytosis, but if not removed quickly enough can cause dystrophic calcification (Ca2+ buildup)
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19
Q

What is apoptosis? What does it require? Wy is it preferable to necrosis?

A

Apoptosis is the controlled suicide of a cell, where cell still have time and energy to execute a suicide. To conserve this energy, most cellular machinery is turned off.
Common after DNA damage, inadequate GF, hypoxia or accumulation of damaged proteins.
Also removes unwanted, wrongly placed, or self-reactive immune or infected cells.
Preferable as can be controlled, cellular cntents do not leak and inflammation is not initiated.

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20
Q

What is the process of apoptosis?

A

Caspase cascades mediate the events by proteoplytic cleavage. Upstream caspases are turned on first, while downstream caspases do the destroying.
Chromatin is cleaved and condensed (pyknosis) and membrane bound blebs of cytoplasm and organelles are split off and phagocytosed.

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21
Q

What is acute inflammation?

A

The body’s first response to a tissue injury.

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22
Q

What are the triggers of acute inflammation?

A
Infection and toxins
Trauma
Physical and chemical agents
Necrosis
Foreign bodies
Immune reactions (hypersensitivity)
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23
Q

What are the 9 steps of inflammation?

A
  1. Pro-inflammatory substances released, activating tissue macrophages and endothelial cells in the blood vessels
  2. These then produce cytokines, prostaglandins and NO to cause vasodilation and increased blood vessel permeability
  3. Hyperaemia to affected tissue, increasing flow of protein rich fluid (exudation) to the tissue, which contains fibrinogen (seals damaged vessels, forms dense fibrinoue exudate), antibodies, and cascades. Oedema caused. Increased blood viscosity and slower blood flow (stasis). Leukocytes travel to margins of blood flow (margination), accumulating along endothelium
  4. Selectin expressed in vessels, causing neutrophils to roll slowly along lumen (attach to glycoprotein receptors) Then, integrin binds to addressins on endothelial cells, causing neutrophils to stop and stick,
  5. Neutrophils perform diapaedesis, extending a ‘food’ between cells and squeezing through to the extravascular space.
  6. Neutrophils activated y chemokines, IL-1 and TNF-a. Leukocytes also activated by bacteria bonding their surface toll-like receptors.
  7. Neutrophils perform chemotaxis towards exogenous and endogenous chemotactic factors. They are promoted by hypoxia.
  8. Neutrophils attack and and many are killed, releasing vasoactive, chemotactic and damaging substances. They mix with tissue debris & bacteria to form pus.
  9. Termianation occurs when offeding agent is eliminated and inflammation mediators disappear.
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24
Q

How do X-Rays work?

A

A high electrical potential is passed from a cathode to tungsten anode across an evacuated tube, bombarding the electrons. As the electrons return to their previous state, they give off energy between .01 and .1 nm in wavelength. These waves can penetrate the body to differing degrees

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25
Q

What are the different densities of X-ray?

A

Metal is whitest, then bone, soft tissue (water), fat, and air.

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26
Q

What are the positives and negatives of Xray?

A

Best spatial resolution
Depicts differences in density
Different contrast materials can be added to perform more functions

BUT

Limited contrast resolution
Prolonged exposure is harmful

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27
Q

What are CT scans and their positives and negatives?

A

CT scans use radiation to form a computer-generated slice of the body in the transverse plane.
They are very expensive and use x rays to work. However, they are very useful for when Ultrasound and X rays won’t give a good picture, and can discriminate between soft tissues due to excellent contrast resolution.

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28
Q

What are MRI scans and their positives and negatives?

A

MRI scans place the patient in a strong magnetic field, causing the H nuclei in the body to align with the field and then return to their original position, emitting signals detected by the machine.
Pros: no radiation, excellent contrast resolution (great for CNS) except for lungs

BUT: Expensive, takes a long time to do

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29
Q

What are US scans and their positives and negatives?

A

Sends pulses of sound and detects echoes from the body tissue, producing a slice of the body from where the sound began.

Safe, flexible, cheap

BUT: cannot penetrate bone or air-containing structure

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30
Q

What is interventional radiation and how/why is it used?

A

It involves the use of X rays, US, CTs or MRIs to place needles and catheters in the body in a moving image. US are used for needle/catheter insertion, CT when the lesion is obscured by gas or bone. These are less disturbing to patients than open surgery and can be done outpatient.

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31
Q

What is nuclear medicine?

A

Radioactive isotopes are injected into a vein, or given orally or anally. They may be taken up by a specific organ or tumour, or respond in an antigen/antibody reaction. The contrast these give can then be observed using Xrays or CTs or be detected by a gamma camera. It cannot precisely define organs, but is good for demonstrating early disease and function, and is safe and cheap.

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32
Q

What are PET scans?

A

they are a form of nuclear medicine using a chemical with a shorter half life. They are used to show blood flow in the brain, and also for cancers as the chemical is taken up by tumours.

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33
Q

What are the local effects of inflammation?

A

Redness/rubor (due to protein denaturing)
Swelling/tumor (due to oedema)
Heat/calor
Pain/dolor
Loss of function/functio laesa (due to damage and other local effects)

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34
Q

What are the systemic effects of inflammation?

A

Pyrexia/fever (mediated by IL-1 and TNF-a released by endothelium and macrophages)
Leukocytosis (increased WBC production)
Acute phase proteins (increased proteins involved with inflam. from liver)
Endocrine changes (more glucocorticoids)

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35
Q

What role do IL-1 and TNF-a play?

A

Produced by macrophage and endothelial cells.
Cause fever, slepiness, decreased appetite, increased acute phase proteins, haemodynamic shock and neutrophilia.
Increase neutrophil adherence, Increased fibroblast proliferation, collagen synthesis and cytokine secretion from Leukocytes.

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36
Q

How can inflammation lead to harm?

A

If they are not controlled or occur inappropriately, they can cause disease, hypersensitivity and hyperimmune reactions.
Repair by fibrosis can lead to scars, intestinal obstruction or limited mobility.

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37
Q

What is chronic inflammation>

A

When the cause is prolonged, and other leukocytes (besides neutrophils) enter the tissue.
Especially monocytes- they are greater killers and transform from into pacrophages as they enter injured tissue

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38
Q

What is granuloma formation?

A

A focused region of chronic inflammation consisting of a core of necrosis. It involves macrophages fusing into epithelial-esque cells with a collar of lymphocytes surrounding it. This is mainly done to remove foreign bodies.

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39
Q

What is healing?

A

The body’s attempts to restore original structure and function of injured tissue

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40
Q

What are the 2 parts of healing?

A

Cleaning up the mess

Rebuilding structure and function

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41
Q

What is involved with cleaning the mess of inflamed tissue?

A

Ideally, all debris is removed by macrophages
If there is too much, repair is set into motion. This is done by organisation, where macrophages secrete FGF and VEGF. These encourage growth of fibroblasts and blood vessels, and once there are many of these the tissue is termed granulation tissue.
This is then remodeled as the vessels regress and collagen aligns to form a fibrous scar (fibrosis)
However, this may represent loss of functional tissue, and could hinder remaining tissue.

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42
Q

What is involved with rebuilding the structure and function of destroyed tissue?

A

Attempts to replace parenchymal cells are made. , known as regeneration.
This involves proliferation of stem cells, both locally and from the bone marrow. It is more commonly done in areas of high tissue turnover (skin and gut).

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43
Q

What are the range extremes for the outcome of tissue

A

Anywhere between fibrous scar (function is lost) and complete resolution.
The longer the tissue damage and inflammation lasts, the less likely resolution will be.

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44
Q

What do X-rays tend to be used for? What contrasts can you add to X rays to make them useful for different purposes?

A

Mainly used to observe bones
Can add barium for enemas, to look at GI tract
Iodine compounds for angiography, IVUs
Gadolinium to make the pictures useful in MRI scans

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45
Q

What is nuclear medicine used for today?

A

Bone scans
V/Q scans for pulmonary emboli
Thyroid, white cell, liver, renal and brain scans

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46
Q

What are ultrasounds used for?

A

Examining pain, swelling, mass. Screening for renal dysfunction, cancer.
Checking vasculation and abnormal liver function

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47
Q

What are CT scans used for?

A

Head scans

Abdominal pain, trauma, cancer, bowel obstruction, vascular imaging

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48
Q

What are MRIs used for?

A

mainly brain, but can also look at abdominal structures

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49
Q

What are PET scans used for?

A

Cancer staging mainly

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50
Q

What are the types of microbes able to be recognized by our immune system?

A
Viruses:  
- Particle capsid shapes' antigens
- Cells damaged by infection (due to the changes at their surfaces)
- Virus-infected cells
Bacteria and Fungi:
- Bacterial surface antigens
- Bacterial/fungal metabolites
- Cells damaged by infection
Parasites:
- Surface shapes
- Cells damaged by infection
- Life cycle changes within a parasite- as the shapes of the parasites change over their life cycles.
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51
Q

What is the process of phagocytosis, and what cell types perform this?

A

Foreign microbe adheres to phagocyte
Membrane of phagocyte activated
Ridges of cytoplasm extend around microbe, leading to phagosome formation as the microbe is engulfed
Fusion and digestion of microbe
Release of degraded products
Granulocytes (neutrophils, short lived) and monocytes (longer lived)

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52
Q

Describe the components and uses of the complement system

A

Complement system stimulates and enhances the processes of inflammation and phagocytosis. This is done by the release of a cascade of blood-derived proteins.

  • First complement components are able to bind with the membrane antigens of the agents involved, having evolved to recognize most common shapes. When a group of them congregate and form enzymes, they activate other components of the system
  • Some increase vascular permeability
  • Some attract granulocytes into tissues by helping with chemotaxis
  • Some perform opsonisation, where the target is coated with molecule with a high affinity for the phagocyte.
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53
Q

Briefly describe the reticuloendothelial system

A

Derived of different macrophage-like cells from the stem cells of bone marrow.
These are strategically placed where they will most likely encounter harmful agents.

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54
Q

How does the lymphatic system work?

A

Fluid drains into the thin-walled vessels perforating the interstitial fluid, and is pumped up the branches by the movement of muscles, held where it is pumped by leaf valves.
Afferent vessels take fluid from tissues to lymph nodes
Efferent vessels take fluid from the nodes to the thoracic duct, where it is emptied into the bloodstream

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55
Q

What is the function of the lymph system?

A

Prevent oedema
Recycle components of ECM
Carry information about infection from the tissues to the lymph nodes

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56
Q

What are primary vs. secondary lymphoid organs?

A

Primary: Lymphocyte formation site. Includes bone marrow, thymus, fetal liver
Secondary: Residence of mature lymphocytes. Includes lymph nodes, tonsils, adenoids, peyer’s patches, skin.

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57
Q

What are the 3 categories of innate immunity?

A

Physical- mucus, skin
Microgial- organisms living on/in us that make it hard for invaders to proliferate
Humoral factors: Chemicals (eg. in sweat)

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58
Q

Microbe

A

Microscopic entity

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59
Q

Pathogen

A

Thing capable of generating a disease

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60
Q

Endemic

A

Thing found in a place or population

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61
Q

Epidemic

A

More cases of a thing than you would expect to see

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62
Q

Pandemic

A

Epidemic spread across a wide area

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63
Q

Infection

A

New presence of a microbe

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64
Q

Infectious disease

A

Symptomatic illness caused by pathogens

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65
Q

Endogenous

A

Originating within an organism

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66
Q

Exogenous

A

Present but originated outside an organism

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67
Q

Subclinical

A

Infectious disease triggering the immune system, but not causing symptoms

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68
Q

Transmission

A

Manner of spread of a microbe (can be direct or indirect)

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69
Q

Autopoiesis

A

Dynamic process of self-production (ie making your own new cells)

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70
Q

Adaptation

A

Maintenance of a mutually satisfactory relationship between organism and environment

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71
Q

Why is it important that organisms are able to distinguish self from non-self?

A
  • To protect against infection
  • To recover from infection and damage
  • To maintain the relationship with the environment
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72
Q

What shapes does the lymphatic system respond to?

A

Unusual shapes

Familiar shapes in unusual contexts

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73
Q

What secondary organs do different infected tissue types bring infectious particles to?

A

Blood takes them to spleen
Tissues to lymph nodes
Gut to peyer’s patches

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74
Q

What is innate immunity?

A

The first line of defense to antigen exposure
Includes physical microbial and chemical factors
They are effective at preventing invasion or growth of invasion, and act early.
Includes lysozyme in secretions from the skin, like tears, sweat and saliva. These break down the cell membranes of some bacteria
Also commensal organisms which compete with pathogens for survival

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75
Q

How are white blood cells formed?

A

Pluripotent haemopoietic stem cells found in bone marrow

  • Some mature directly into B lymphocytes
  • Some migrate to the thymus to become T lymphocytes
  • Some develop into megakaryocytes and are broken into platelets
  • Some develop into monocytes and are then converted to macrophages in the tissues
  • Some develop into basophils, eosinophils, neutrophils or erythrocytes
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76
Q

What can happen if the maturation of WBCs is prevented?

A

Susceptibility to infection
Low blood counts
Inability to clot blood, leading to petechial haemorrhages
Large numbers of immature WBCs in the blood due to their overcrowding the RBM

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77
Q

What are the two types of receptors able to recognize antigens of infectious agents?

A

Antibodies- secreted by B-lymphocytes, recognize foreign antigens
Cell surface receptors- Attached to lympocyte surface, recognize changes in our own cells that appear on the cell surface.

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78
Q

What are the two types of receptors that can bind to angigens?

A
  • Antibodies (soluble, secreted by B cells) Prevent binding of virus to other cells
  • Cell surface receptors- attached to surfaces of cells, act as hands. See changes in our own cells
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79
Q

What is cross-reactivity?

A

Some antibodies may bind to many things with a similar shape- perhaps with low affinity, but enough to bind. This means a single antibody can help to defend against many pathogens

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80
Q

What are the 6 qualities of the specific immune system?

A

Defence
Specificity- response directed against only the agent stimulating disease
Diversity- responds to a wide range of substances
Adaptivity- unexpected stimuli response provides rapid appropriate response
Self/nonself- discrimination between own and foreign antigens
Memory- system remembers responding to respond more vigorously next time

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81
Q

How does the immune system know self from not-self?

A

Early in development, the immune cells become ‘used’ to whatever antigens are preexisting within the body- called acquired immunological tolerance

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82
Q

How are foreign antigens delivered to the immune system?

A

Meet dendritic cells, which collect antigenic information. These then migrate into the lymphatic system, entering the nearest lymph node while presenting the antigen on their surface
T Cells cluster around them when they arrive, and those with an appropriate receptor are activated

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83
Q

When it comes to lymphocytes, what are effectors vs. regulators?

A
Effectors:
- B Cells (produce antibodies)
- Cytototoxic T cells (actively kill cells)
- NK and K cells (kill cells)
Regulators:
- CD4 T cells
- Helper T cells
- Regulatory T cells
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84
Q

What can be recognized by B vs T cells?

A

B cells recognize a wide range, T cells only recognize short antigens

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85
Q

What is the general structure of T vs B cells?

A

B cell: CD79 transduction molecules, Surface Ig receptor with binding sites
T Cell: CD3 signal molecules, TCR

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86
Q

What is the structure of an antibody?

A

Made of 2 light chains and 2 heavy chains.
Heavy chains have CH1,2,3 parts and a Variable part at the end Between CH1 and 2 there is a hinge region, which allows the antibody to flex between a T and a Y shape
Light chains have a hypervariable area and a constant area.
The CH2 and 3 areas are able to be crystallized, and can be sensed by neutrophils, improving their phagocytosis
The chains are held together by disulphide bonds

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87
Q

What is the difference between primary and secondary antibody responses?

A

Primary responses occur when we respond to something we had not previously encountered. There is a lag of a few days, and then a small rise in specific antbodies, before decaying to low levels.
A secondary response occurs subsequent times we are exposed to things, and consists of a vigorous and lengthy reaction to the pathogen

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88
Q

How do B cells react when activated?

A

An antigen matches with a specific receptor of a virgin B cell, causing it do express new receptors which match with signals sent from helper T cells. It does this to determine if the related pathogen is dangerous or not. If dangerous, the B cells proliferate, forming plasma cells which form antibodies, and replacement B cells called memory cells. These are longer lived, there are more of them, they circulate to all nodes rather than staying in one, and react without the help of T helper cells.

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89
Q

What happens to B cells in leukemia?

A

B cells’ development isn’t controlled and they spill over into the blood, as well as their precursors. These precursors smudge due to their fragility when put under the microscope slide, leading to their being named smudge cells

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90
Q

What are the 4 ways in which antibodies operate?

A
  • Direct neutralization: Antibodies block the virus from being able to bind to and infect other cells
  • Opsonisation: The antibodies bind to the virus, exposing their Fc region, which neutrophils have high adherence for. This increases the efficiency of phagocytosis
  • ADCC: K cells rely on Fc areas to bind to and kill bacteria using short-range cytotoxicity
  • Complement activation: Forming an antibody-antigen complex activates the first components of the complement zone.
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91
Q

How do antibodies change their shape?

A

They bind to the antigen, changing to a Y shape.

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92
Q

What are the pathways of the complement system?

A

Activated by: Antigen-antibody complexes
First components recognize the surface of the pathogen
Presence of bacterial sugars bind to proteins
Enzymes formed convert C3 to C3a and C3b
Effects:
C3a causes vasodilation and chemotaxis
C3b causes vasodilation
C3b also forms a focus for late component assembly, which punch holes into the membranes of pathogens to cause cell lysis.

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93
Q

Colonisation

A

Infection with microbe for varying period. Host immune response, but no symptoms. Potentially infectious

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94
Q

Infectious disease

A

Interaction with microbe causing damage to the host

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95
Q

Zoonosis

A

Infectious disease transmitted by a non-human animal host

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96
Q

What factors increase susceptibility to infection?

A

Immune deficiency (age related, treatment related etc.), other illnesses, risk behaviours

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97
Q

What are endogenous vs. exogenous infections?

A

Endogenous are those arising from our own bacteria, microbes and other flora
Exogenous are infections coming from animals, the environment (uncommon) and human to human transmission

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98
Q

What are some common settings for infection to occur in?

A

Community onset/acquired (most common, GP visit)

Hospital onset/acquired/nosocomial (reduced by handwashing)

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99
Q

What are the 2 requirements of a pathogen for it to cause damage, and what are virulence factors?

A

It must interact with the host cells
It must damage or incite an immune response within the host
Virulence factors include the avoidance of the immune system, improved adherence, damage and invasion

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100
Q

What is pyogenic invasion?

A

Tissue invasion, involving multiplication and causing an acute immune response

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101
Q

What is intoxication, immune mediation and carcinogenism, in terms of infection?

A

pathogens may use toxins to change the host physiology or to physically damage tissue
They may mimic the antigens on other cells
They may also cause the formation of cancerous cells

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102
Q

What is antibody mediated/humoral immunity?

A

Uses B lymphocytes to produce antibodies
Effective against extracellular antigens including:
Viruses & toxins (stop attachment)
Extracellular bacteria (enhance phagocytosis)

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103
Q

What is cell-mediated immunity?

A
Uses T lymphocytes, but no antibodies
Effective against intracellular antigens, including:
Virus-infected cells
tumour cells
Transplanted organs
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104
Q

Compare and contrast the different T cells

A

Both:

  • Contain CD3
  • Have T cell receptors (TCRs)
  • Originate in the thymus
  • Can bind only to antigens presented to them by MHC determinants on APCs

T-Helpers

  • Contain CD4
  • Produce cytokines

Cytotoxic T Cells

  • Contain CD8
  • Kill cells outright
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105
Q

What are differences between T and B cells?

A

T cells made in thymus, B in bone marrow
T cells do not make antibodies
T cells can only react to antigens presented to them by APCs

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106
Q

What are MHCs?

A

Genes coding for surface structures on cells to present antigens to T lymphocytes
Class 1: Produces double chained structures, found on all nucleated cells. Expressed co-dominantly, polymorphic (HLA-DP/DQ/DR all code for them) and present only to cytotoxic T cells
Class II: Code for structures found only on APCs and B cells. Expressed co-dominantly, polymorphic (HLA-A/B/C all code for them) and present only to helper T cells

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107
Q

How do antigens become presented on cells?

A
Way 1:  Virus infects cell and replicates, changing the physiology of the cell and the composition of its proteins.  A sample of these proteins are expressed on the MHC structures, so the immune system notices any changes
Way 2:  If the pathogen is phagocytosed, it is broken into small fragments, some of which are presented on MHC class II.
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108
Q

What is the process for the activation of cytotoxic T cells?

A

Precursors with TCRs matching the antigens on class 1 MHC structures are activated and receive helper signals to divide them into effector cells and memory cells

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109
Q

What is the process for the activation of helper T cells?

A

Antigen binding to TCRs on T lymphocytes cause the cell to express cytokine receptors. A second activation signal from helper cells cause differentiation into cytokine secreting cells or memory cells.

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110
Q

What are cytokines and what do they do?

A

Cytokines are low weight glycoproteins secreted mainly by CD4 T cells
They are produced locally and transiently, and are responsible for regulating the quality, amplitude, duration of immune reactions
Their action differs depending on concentration, other cytokines, target cell and history of cell
They also affect other systems- eg. control sickness behaviour through nervous system

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111
Q

What are some problems with the immune system?

A

Overreaction to innocuous substances- generate strong IGe antibody responses to harmless things (eg. pollen, fur etc.) This causes hypersensitivity where the substance touches you, or in bad cases, systemic reactions (anyphrylactic) can occur.
Immune mediated tissue damage- strength of immune/inflammatory response is so great it can damage other tissues. Eg. immune complexes produced in such high numbers that they lodge in capillaries, activating complement system and starting vasculitis
The system can also be destroyed from within, eg. when T helper cells are infected with HIV and cytotoxic T cells kill the majority of them
Autoimmunity- results in chronic illnesses as the body treats self-cells like non-self cells
Immune system can get confused- eg. strep. Some people have heart antigens similar to strep antigens, so immune responses to this damage heart valves too

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112
Q

What are 3 examples of autoimmunity?

A

Hashimoto’s thyroiditis: Antibodies/Cytotoxic T cells against thyroid antigens, destroying thyroid gland
Pernicious Anaemia: Immune system targets parietal stomach cells, impacting B12 absorption
Systemic Lupus Erythematosus: Antibodies made against DNA from cell nuclei, binding to broken cells throughout the body, activating the complement and damaging tissues throughout the body (particularly kidneys and skin due to immune complexes clogging)

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113
Q

What is streptococcus pyogenes and what does it do/can it do?

A

It is a virus that lives in the pharynx, commonly causing pharyngitis and skin infection. Firstly, the immune system is activated as S. Pyogenes colonizes the pharynx and irritates the tissue. Then, the pharynx becomes inflamed, causing pain, swelling, redness and pus. They contain M proteins which the body forms antibodies against, although the M proteins are similar in shape to the cells in other locations. If the antibodies bind to our own proteins, they will form a response against them in places not colonized by the bacteria. This can then cause rheumatic fever, with fever, painful joints, inflammed connective tissue of the heart, rash and chorea (strange movement)

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114
Q

How does penicillin work and what is the problem with it?

A

It works by targeting the enzyme responsible for linking the peptide chains within the bacteria’s cell wall.
If this enzyme is inhibited, cracks in the cell wall can’t be repaired and the bacteria explodes.
There are different types of penicillin, some administered intravenously and some orally depending on whether they get dissolved in the stomach or not
However, the issue is that penicillin (and other antibiotics) are being used for viruses etc. which they have no effect on, which results in bacteria gaining resistance to the drugs

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115
Q

What are the different types of disease transmission and some precautions against them?

A
  • Direct (sexual, faecal-oral, droplet, airborne)
  • Indirect (contact, vector borne, healthcare worker, transfusion, airborne)
Universal protections (always done):  Glove/gown, decontamination of waste, disposal or sharps, waste management, clean environment, hand hygiene
Contact precautions (GI infections):  Gloves, gowns, eyeware
Droplet precautions (flu etc.) masks
Airborne precautions (TB, chickenpox):  Respiratory masks for patients and staff
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116
Q

What is a virus?

A

Viruses are nucleic acid that aims to replicate, enclosed within a caspid. Some have an envelope formed from the host cell

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117
Q

How can we classify viruses?

A

Can be classed by their genetic content- RNA, DNA etec.
OR what they cause- hepatitis vs. resp. (this down’t predict structure
OR how they are transmitted- arbovirus (arthopod borne), enterovirus (faecal-oral) or respiratory virus (droplet/contact)

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118
Q

What are the steps of a viral infection?

A
  1. virus attaches to cell
  2. Virus enters the cell, host enzymes dissolve the capsid and release the RNA
  3. mRNA from the virus is formed, and 4. protein synthesis occurs
  4. Genome replicates to 6. form a new clone of the virus so that it can be 7. released from the cell
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119
Q

What is Staph. A, what does it cause and what are its disease stats?

A

It is a bacteria with a thick peptidoglycan wall, and is graham +ve as it takes up stain that sticks when the cell is washed
It has a circular shape and occurs in bunches
It causes food-poisoning symptoms commonly, and skin infection-like symptoms rarely.
Currently it’s the no. 1 cause of healthcare infections as it lives on the skin and can get into catheters & blood.
It has a death rate of about 20% in its serious form, and there is a non-serious form that can cause skin infections needing hospitalization.

120
Q

How is staph. A transmitted and what are the factors behind this?

A

It is transmitted person to person, although it can be transmitted to cows too (bovine mastitis)
Its transmission is affected by host, bacterial, and environmental factors

121
Q

How many people currently have staph. A?

A

About 10-15% of population are persistent carriers, 25% non carriers, and the rest have it intermittently.

122
Q

How does staph A cause food poisoning?

A

Bacteria makes toxins on room temperature foods and it is this pre-produced toxin that gets into the stomach and induces vomiting.

123
Q

How does staph A infect the skin?

A

Unlike most bacteria, it is able to multiply within the glands of the skin, where it releases free radicals and causes inflammation due to cell damage

124
Q

How does staph A resist the immune system?

A

Releases CHIPS which are potent disguisers of cytokines
Can coat itself with immunoglobulin, pretending to be a human cell
Turns off the complement system
Cause lysis of neutrophils or prevent the enzyme’s lysosomes from working

125
Q

Why is staph A resistant to penicillin?

A

It produces enzymes to dissolve penicillin’s ‘garage group’ as well as being resistant to the replacement, methicillin, within the year as it changed its transpeptidase.
Now, it is called MRSA.

126
Q

What is the bacteria responsible for causing TB, and what are its associated factors?
What happens if a different type of this bacteria invades humans?

A

Caused by mycobacterium genus, most commonly m. tuberculosis. It is associated with poverty, low sanitation and poor access to safe drinking water.
If a non-TB causing mycobacterium infects, it comes in rapid, non-rapid or other varieties. While it doesn’t cause TB, it can cause lung infections and skin infections.

127
Q

How is TB transmitted and what is the body’s response to it?

A

Transmitted via vigorous coughing from someone with it. It enters the distal lungs, where it binds to the complement receptor of pulmonary macrophages. It gets phagocytosed, resists being lysed and immortalizes the macrophage. Infected WBCs recruit T cells using cytokines, but the bacteria isn’t able to be destroyed, so the phagocytes surround the persistent antigens (now a necrotic center) with a layer of T cells bordering them, keeping the macrophage barricade alive- chronic inflammation. Large aggregates of these are called nectrotising granulomas.

128
Q

What are the different types of TB infection?

A
  • Latent TB infection: immune system jails the TB, although if it is strongly needed elsewhere it can cause the TB to reactivate
  • Miliary TB: TB disseminates and spreads into many small granulomas
  • Thoracic/pulmonary TB- standard
129
Q

What are the 6 different outcomes for a TB transmission?

A
  • Good immune response- small calcified granuloma on lymph nodes or lungs.
  • Granuloma on lung surface- dangerous, may erode pulmonary space
  • Abcess or cavity in lung, if TB not surrounded- large granulomas can impact bronchi, vessels
  • Pulmonary TB- cause pneumonia
  • Erosion of granuloma into pericardium
  • Miliary TB
130
Q

What are some risk factors for TB?

A

Recipient: close contact with infected. Immune suppressants, institutional care or healthcare workers
Transmission: High TB in infected sputum, pulmonary disease, TB cavitation, coughing, not covering mouth, delayed diagnosis

131
Q

How do you diagnose TB?

A

Sometimes visible using granulomas from chest x rays- cts used more and more. Confirmed by sputum/kidney/csf samples. PCR in specimens.
TB holds stain when heated to soften lipids- it’s acid fast due to its thick cell wall

132
Q

How do you treat TB?

A
  1. Treat patient with different drugs

2. Prevent transmission using isolation, masks.

133
Q

What are the symptoms and pathway of flu, and how can it become dangerous?

A

Sneezing, sore throat, runny nose, chills, muscle aches, lethargy.
1 day incubation period, with symptoms highest on second day, corresponding with IFNa cytokine. Nasal mucus peaks 3rd day. Lasts 1-2 weeks- no chronic inflammation as all symptoms due to immune system, not virus.
Can become dangerous if lungs become so inflamed they lose SA and ability to gas exchange. Dangerous for 0-4 and 65+

134
Q

What are the viral proteins on the flu virus and what are their functions?

A

Haemagglutinin- binds to ENT and bronchial cells- not gut or deep lung. Antibodies can prevent its binding, but the virus can mutate the H proteins to keep infecting
Neuraminidase ensures virus can be released after infecting host cells, to transmit more virus. There are inhibitors for this available, but they only work in the early stages of the disease.
Different H and N proteins make up the flu vaccine- not the virus itself

135
Q

What are the types of flu virus and what are humans already immune to?

A

A: causes serious illness, epidemics, pandemics. Many H and N. Bird virus that adapts to mammals
B: Serious illness, epidemics. Only 1H and 1N
C: Minor illness
Humans immune to AH1 and AH3, but not AH5 immunity.

136
Q

What are the four categories of genetic disorders?

A
  • Single gene disorders: Change in a single gene causing a change in phenotype
  • Chromosomal disorder: change in chromosomes as a whole. Eg. extra chromosome, changes in stoichiometry
  • Multifactorial genetic disorders: Interaction of multiple changes, can be minor or major in affecting phenotype
  • Somatic mutations: unable to be passed onto offspring, but can come from genetically inherited predisposing factors
137
Q

Define mutation

A

A permanent, heritable change in the base DNA code

Alteration in DNA from its natural state

138
Q

What is polymorphism?

A

The presence of multiple alleles for a gene in a population at frequencies to high to be random mutations- means the mutation is sustained.

139
Q

What are the different types of mutation?

A
  • Silent mutation- no affect due to degeneracy of code
  • Missense mutation- changed amino acid but may or may not change phenotype
  • Nonsense mutation- amino acid changed to stop codon, protein non-functional
  • Frameshift- insertion/deletion of bases not in multiple of 3
  • Splice donor/acceptor- change in sequence of intron splicing
140
Q

How do you decide whether a mutation will be pathogenic?

A
  • Missense at important site?
  • Encoded protein truncated?
  • RNA splicing affected?
  • Change segregate with disease in prior generations?
141
Q

What is somatic vs. germline mutation?

A

Somatic- mutation occurs in body cells, not passed to offspring
Germline- mutation occurs in gamete-forming cells, may be passed to offspring

142
Q

What are loss vs. gain of function mutations?

A

LOF: Reduced amount or activity of final gene product. Can be totally absent (null allele) or half-active/present (haploinsufficiency) with minor affects on phenotype. Some present a dominant negative effect, where an abnormal product affects the action of the normal- common in conn. tissues due to different shaped proteins
GOF: Increased amount or activity of product

143
Q

What are the 5 mendelian patterns of inheritance?

A
  • Autosomal dominant
  • Autosomal recessive
  • X linked recessive
  • X linked dominant
  • Y linked (holandric)
144
Q

What is autosomal dominant inheritance?

A

Affects and transmitted by either sex.
Presence of dominant allele guarantees expression of corresponding phenotype
Child of hetero/unaffected pairing has 50% chance of affected.

145
Q

What is autosomal recessive inheritance?

A

In homozygous r form, person is affected. In heterozygotes, person a carrier.
Affects either sex, with 25% chance affected when born to carrier parents.

146
Q

What is lyonisation?

A

Inactivation of normal parts of a single X chromosome in females, allowing a mutated X chromosome to be expressed- rare and random.

147
Q

What is X linked recessive?

A

Affects mainly males born to unaffected parents
No male to male transmission
All daughters of affected males are obligate carriers
50% change of affected son/carrier daughter born to carrier woman

148
Q

What is x linked dominant?

A

Affects either sex, but more commonly females with more variation due to lyonisation
Child of affected female 50% likely affected
All daughters but no sons are affected from affected male

149
Q

What is y linked inheritance?

A

Affects only males in a direct father to son progression

150
Q

What are 4 complications to the mendelian theory?

A
  • Common recessive conditions can appear pseudo-dominant (blood groups)
  • Nonpenetrance- failure of dominant condition to manifest phenotypically
  • Variable expression- phenotype differs among affected individuals
  • New mutations/germline mosaicism- some cells are genetically different to others in the same body
151
Q

What is allelic heterogeneity vs. locus heterogeneity?

A
  • Allelic- disease can be caused by many alleles

- Locus- mutations at different gene loci can cause the same disease

152
Q

What is genetically interesting about achondroplasia’s inheritance?

A

80% of sufferers don’t inherit the condition (dominant) from their parents, but a spontaneous mutation in paternal speriogenesis causing mutated sperm to divide more quickly- this makes it more likely to affect children born to older parents.

153
Q

What are compound heterozygotes?

A

A form of recessive inheritance where individuals are heterozygous for two different mutations affecting the same gene, but whose phenotype expresses the same as if the individual were homozygous

154
Q

What is the pattern with carriers vs. sufferers of recessive conditions?

A

There is a dramatically higher number of carriers than of sufferers

155
Q

How does gene testing for certain recessive conditions affect clinical practice?

A

Allows diagnoses to be made based on genetic makeup
Allows for facilitation of family screening, prenatal checks
Can prevent unnecessary invasive procedures

156
Q

What is the human karyotype?

A

22 pairs autosomal chromosomes, 1 pair sex chromosomes

157
Q

What are the 3 different regions of the chromosomes?

A
P arm (shorter)
Centromere
Q arm (longer)
158
Q

What are common numerical abnormalities?

A

Aneuploidy- gain or loss of whole chromosome
This usually happens in meiosis 1 or 2, resulting in some gametes with multiple chromosomes, some with none (and some normal if in mII) due to the failure of chromosomes to separate (non-disjunction events)
Eg. in down syndrome, there is trisomy as there is an extra chromosome 21, causing characteristic facial features, mental retardation and other abnormalities

159
Q

What is genetic mosaicism?

A

Happens when non-disjunction occurs post-fertilization in the embryo’s mitosis, meaning genetically different cells can co-exist within one person. It can account for some down syndrome cases

160
Q

What are the 4 different types of structural abnormalities within chromosomes?

A
  • Reciprocal translocation
  • Robertsonian translocation
  • Inversion
  • Deletion
161
Q

What is reciprocal translocation?

A

Two way exchange of material between non-homologous chromosmes (ie not crossing over)
Phenotype normal as no gain or loss of material
(although balanced translocation parents can have recurrent miscarriages, dysmorphic babies with unbalanced translocations, and oligospermia

162
Q

What is robertsonian translocation?

A

Occurs when two separate chromosomes join together into one long one
No phenotypic effects a no loss/gain of genetic material

163
Q

What is unbalanced translocation?

A

Occurs when a balanced translocation parent passes on a split chromosome, giving the child a net loss/gain of genetic material

164
Q

What is inversion?

A

Same chromosome breaks in two places, and either middle chromosome or broken off pieces rotate before rejoining
Phenotype normal, low risk of abnormal offspring

165
Q

What is deletion?

A

Terminal: End material is lost
Interstitial: two breaks, and middle fragment is lost before others join together again

166
Q

What is FISH and how is it used?

A

A way of imaging DNA where a target piece is compared to a control patch- certain sequences can be highlighted with fluorescence if present. Used for any tissue with intact DNA
Can detect: microdeletions, marker chromosomes, numbers of chromosmes, gene amplification and rearrangements

167
Q

What is CGH?

A

A scan coparing normal and target whose genomes for overall gene changes
Microarrays simultaneously screen hundreds of regions, allowing it to be used in diagnostics

168
Q

What are syndromes, sequences, associations?

A

Syndromes: Groups of anomalies consistently occuring together
Sequences: Cascades of effects
Associations: Traits coincide more often than by pure chance

169
Q

What is dysmorphology?

A

Discipline of medicine for identifying, delineating, diagnosing and managing dysmorphic anatomical features

170
Q

How does HIV infect the body?

A

Gp 120 proteins on the cell envelope bind to CD4 on Th cells and other WBCs. When it docks, it squeezes the viral contents into the cell via CCR5. In the cell, the capsid is digested, and reverse transcriptase enzymes make a DNA copy of the RNA. The two are then separated, and DNA is transported into the nucleus. Integrase opens the host DNA and integrates viral DNA into it. This viral DNA is then transcribed into more gp120, caspid proteins etc.
These products move to outside the cell, where they assemble into a new virus and protease creates more viral enzymes.

171
Q

What does HIV do to the body?

A

Depletes helper T cells to the point where many more diseases are able to take over.
It also causes mild, but chronic activation of the imune system. This results in self-mediated damage including bone loss, CV issues and neurological defecits.

172
Q

When and how do we treat HIV?

A

Normal CD4 count is 750-1500, and when this drops below 500 we begin to treat it. We manage it by maintaining health and better lifestyle factors, stopping the virus’ replication using drugs. We also reduce transmission by increasing safe sex, awareness etc.

173
Q

What do drugs for HIV do?

A

There are 3 drugs used, which target at least 2 different areas- can be integrase, protease, reverse transcriptase etc.
They make it possible for a 90% chance of working, safe and durable treatment when diagnosed in 2017

174
Q

What is prenatal testing, and why do we do it?

What is the difference between screening tests and diagnostic tests?

A

Prenatal testing is the use of special tests during pregnancy. We do this to give reassurance to parents to give health professionals early warning, set up support, and inform parents of their options should they have positive tests
Screening tests assess whether a baby has an increased risk of a disorder. They are non invasive, low risk, but not definitive.
Diagnostic tests determine whether a baby has or will have a disorder, including chromosomal and gene changes. They are more invasive with increased risk, but have definitive outcomes

175
Q

What genetic factors would lead you to go straight to a diagnostic prenatal test?

A
  • Family history of genetic disorder
  • Both parents known carriers of autosomal recessive disorders
  • One or both partners have an autosomal dominant disorder
  • Family history of sex-linked conditions
    ONLY for serious conditions- not easily treatable
176
Q

What constitutional factors would lead you to go straight to a diagnostic prenatal test?

A
  • Woman having a baby in her mid thirties or older
  • Exposure to chemical or environmental agents
  • Results of of screening tests have determined increased risk of certain conditions
  • Previous child with a serious genetic condition
177
Q

What are the 3 prenatal screening tests and when/why are they done?

A
  • Ultrasound: 8-10 weeks (checks dates and number of babies) and 18 weeks (detects physical anomalies).
  • Nuchal Translucency Ultrasound: 10-13 weeks. Looks at space below baby’s neck to calculate risk of constitutional abnormality (eg. downs).
  • Maternal Serum Testing: Looks at AFP, uE3 and hCG to determine risk of chromosomal issues, neural tube defects.
    When used together, these tests can detect 85-90% downs cases
178
Q

What are the 2 prenatal diagnostic tests and when/why are they done?

A
  • CVS: 11-12 weeks. Cells from placenta taken and tested for cytogenic and single gene abnormalities. Small risk of miscarriage.
  • Aminocentesis: 15-19 weeks. Fine needle aspirates amniotic fluid to be analyzed. Often needs to be cultured first, as there are fewer cells. Baby’s cells removed and DNA examined. Slight risk of miscarriage
    The CVS is preferable to aminocentesis, but often not an option if people aren’t actively monitoring their pregnancy.
179
Q

What is PGD and what is it used for?

A

It is the analysis of cells in the 6-8 stage embryo before it is implanted in IVF. These can be analyzed for known mutations, markers or disorders.

180
Q

What are the different laboratory strategies for analyzing prenatal specimens?

A

FISH- scan for abnormal chromosme number
DNA analysis using PCR for direct (known) mutation analysis (preferable) or indirect (marker) analysis
Karyotyping if possible

181
Q

Why is genetic counselling important?

A

Gives parents up to date information about their options regarding both what tests are able to be done, what their pros and cons are and what their options are should the results be positive for a disorder.

182
Q

What are some alternate methods of prenatal testing?

A
  • Cordocentesis- analyzing umbilical cord blood’s proteins and cellular genetics
  • Detecting loose fetal DNA in maternal blood and analyzing that, followed by diagnostic testing if positive
183
Q

What are some downsides to phenotypic studies?

A
  • Error rate due to confounders

- Fetal blood samples can lead to late prenatal diagnosis (DNA analysis)

184
Q

How can genetic heterogeneity affect gene disorders?

A
  • Can give rise to differing severity to the condition

- Can make it difficult to find the mutation responsible- each family’s mutation needs to be found

185
Q

What is the difference between direct and indirect mutation analysis? How can the mutation responsible for the disease be found?

A

Direct analysis requires knowledge of the specific mutation responsible, but is accurate and does not require additional family members. It is PCR based, looking for allele-specific oglionucleotides and sequencing the PCR fragments
Indirect analysis is used when the mutation is unknown or the gene is uncloned. It uses linked markers and pedigrees to see whether the offspring inherit the mother or father’s protein for the condition.
However, you need several family members, an informative marker gene, and there is a potential that recombination or non-paternity clouds the results.
To find the mutation you can do- southern analysis looking for large structural changes, or mutation scanning strategies like directly scanning the gene.

186
Q

What is mitochondrial DNA and how can it be used?

A

It is circular DNA inherited by the mother, lacking introns and contained in the mitochondria with a known mutation rate. Mutations tend to affect the respiratory chain, so it affects organs with high energy requirements (brain and muscle)

187
Q

What is an epigenetic trait?

A

A trait that is stably heritable through mitosis resulting from changes in a chromosome without altering the actual DNA sequence.
Can be caused by DNA methylation of C/G runs, turning off promotors, or of the DNA body, turning expression on.
Micro RNA can stop translation by binding to the 3’ site
Histone methylation and RNA methylation are also factors

188
Q

What is imprinting and why is it important?

A

The restriction of expression to either the maternal or paternal allele in somatic cells- an epigenetic phenomenon causing different expression from identical alleles. It operates at the transcriptional level.

189
Q

What are two syndromes caused by the parent-of-origin specific methylation (imprinting)?

A

Prader-Willi syndrome- deletion of parental 15q11-13 or two copies of maternal allele
Failure to thrive, hypotonia, obesity and short stature, hypogonadism, small hands and feet, behavioural issues.
Angelman syndrome- deletion of maternal 15q11-13 or UPD of paternal copy. Open mouth, tongue thrusting and retardation, ataxia, hypotonia, happy and laugh frequently, absent speech

190
Q

What does DNA methylation do and how does it occur?

A

Occurs at cytosine in CpG dinucleotides- methylationof promoters silences transcription- transmitted via cell divisions using methyltransferase
Can be reversed if methyltransferase is inhibited
Gamete specific- gamete specific protein factors bind and remain bound to imprinted genes during embryogenesis- may encourage or inhibit synthesis.
In females, imprinting occurs when the oocyte matures. In males it is during early embryo formation
Primary germ cells are unaffected, so this tends to happen spontaneously.

191
Q

What is dynamic mutation? What is anticipation?

A

Progressive expansion of repeat sequences (triplet repeats). Anticipation refers to the occurrence of the disease at an earlier age, resulting in more mutations and a more severe clinical presentation
(this means there can be reduced penetrance and full penetrance of the same disease, depending on number of repeats)

192
Q

What is developmental genetics?

A

A field examining how a one-cell embryo gives way to a complete one- particularly important for cancer treatment, regeneration of diseased organs, etc.

193
Q

What are the different types of stem cell?

A

Stem cells are self-renewing progenitor cells- they can be totipotent (all adult cells possible), pleuripotent (can become all germ layers but not all cells) and multipotent (can become several).

194
Q

What is the difference between embryonic and adult stem cells?

A

Embryonic stem cells are capable of generating all differentiated cell types of the body, and can have genes introduced to them. They allow investigation of biological processes in early development, and the generation of many somatic cell types with the potential for use in tissue engineering.
Adult stem cells are present in the adult, and they have been recently discovered to be able to be reprogrammed to contribute to multiple organ cells

195
Q

What is gene therapy? How is it done?

A

The transfer of genetic material into the cells of an organism to treat disease or mark cell populations.
This is mainly done via gene augmentation. Usually, engineered nucleases (CRISPR, TALENS, zinc finger nucleases) are used, and genes are delivered either ex or in vivo via physical (eg. microinjection) or viral vectors.
At present, only single gene, life threatening, untreatable disorders are considered for this therapy

196
Q

What are recombinant pharmaceuticals?

A

Proteins needed for a disease are generated by expression cloning in other organisms or transgenic livestock before being harvested and given to humans. However, there are issues- purification process is difficult, contamination may occur, side effects (immune responses, unseen mutations, intergenerational transmission)

197
Q

What are genetically engineered antibodies?

A

Artificially produced antibodies designed to recognize disease specific antigens, leading to increased killing of disease cells. Targets are cancer, infectious and autoimmune diseases
At the moment, animal antibodies are limited due to immune reactions, and human antibodies are hard to generate. Fully human antibodies are being pursued

198
Q

What are genetically engineered vaccines?

A

Vaccines where the nucleic acid, antigen, modified virus or modification of antiviruses are used to produces immunity

199
Q

What can targeted gene inhibition do?

A

I can be useful in cancer, infectious, immune, and dominantly inherited disorders (with a gain-of-function
Can target DNA, RNA and protein levels

200
Q

What are multifactorial diseases?

A

Non-mendelian inheritance patterns, but still show some heritability. They are caused by an interaction between the environment/pathogen and a genetic predisposer or modifier

201
Q

What is the threshold model of multifactorial genes?

A

Interaction between the environment and a person’s genetics causes a disease- all people are susceptible, but a certain threshold must be reached before the disease will develop. Risk is a bell curve, and only those at the upper end will develop it. For people with family histories of the disease, its development is much more likely

202
Q

What are modifier genes?

A

Genes not associated with the disease origin, but once susceptibility or the disease itself is present, they regulate the severity of the phenotype

203
Q

What are the features of a multifactorial trait (at threshold)?

A

Disorders run in families but without pattern
Monozygotic twins more likely to share disease than dizygotic
1st degree relatives more at risk than 2nd degree
Recurrence risk proportional to no. of family embers affected, severity of the condition (reflects no. of affected alleles) and relatives of the statistically less susceptible sex (as it means more mutations must be present)

204
Q

How are linked genes able to be used in polymorphisms?

A

When a disease affects multiple 1st degree relatives, an analysis can determine whether a locus is linked to the phenotype- this is more challenging for multifactorial diseases than for single gene disorders, although affected siblings likely share the same locus so they are more useful

205
Q

What are GWAS es?

A

Genome wide association studies- these examine many common variants in individuals to see whether it is associated with a trait- link made between SNPs and multifactorial disease

206
Q

How can gene identification of multifactorial disease be beneficial?

A
  • Advance disease understanding and classification
  • Examine gene-environment interactions
  • Risk and disease prevention strategies
  • Monitoring progression of disease
  • Developing new drug targets
207
Q

What are personalised and precision medicine?

A

Personalised- using individual DNA to make decisions to maintain health, prevent disease or improve health outcomes
Precision- creating an infrastructure for patients’ health information to be accessible to scientists to be able to inform patient care.

208
Q

How can personalised and precision medicine help improve health outcomes?

A

Prevention- identify those at greatest risk
Screening- identify and prioritise high risk individuals
Diagnosis- presymptomatic
Prognosis- identify best approaches for different people’s diseases
Drug efficacy and tolerance- identify what will work best and what will have the fewest complications

209
Q

What is differentiation and what is its opposite?

A

Differentiation inolves cells becoming different from one another- involves inactivation of proliferation genes and activation of specific function genes- like keratin producing etc.
De-differentiation involves the reversion back to embryonic, proliferative cells- as occurs in neoplasia.

210
Q

What are disorders in growth and what are the different types?

A

Disorders in the regulation of cell proliferation or differentiation
Malformation: Abnormality in growth and development in utero.
In adult: abnormalities of tissue function or mass.

211
Q

What is the difference between atrophy and hypertrophy on a microscope slide?

A

Atrophy- cell nuclei are closer together, cells smaller. Hypertrophy, cells are larger so their nuclei are further apart.

212
Q

What can cause hyperplasia, and what are its effects?

A

It can be caused by increased functional demand, endocrine stimulation or chronic irritation. It causes increased function in endocrine tissue, increased size and a potential increased risk of malignancy.

213
Q

What does pre-malignant mean? What are some examples of growth disorders that are and are not pre-malignant?

A

Premalignant means that there is an increased chance of developing carcinoma with this tissue disorder than without it. It is not a definite thing.
Prostatic (inner hyperplasia, outer atrophy) and thyroid hyperplasias are not premalignant- but breast and cervical hyperplasias are.

214
Q

What is metaplasia? What does it have to do with malignancy?

A

Metaplasia- change from one mature tissue type to another. It is caused due to a change in environment, or irritation. It may be normal (eg. glanular epi in cervix changes to squamous during menstruation), or obnormal. Some types (eg. barretts oesophagus) are premalignant, other are not.

215
Q

What is dysplasia? How are they graded?

A

Dysplasia is a partial malignant transformation of cells (histologically and genetically). Therefore, they are by definition pre-malignant. Those formed on traditionally ‘flat’ surfaces don’t form a mass, but otherwise a mass is formed, or inflammation is caused.
They can be graded as mild (Intraepithelial neoplasia 1), moderate (IN2) or severe (carcinoma in situ/IN3)
They are clonal, classing them as neoplastic (autonomous growth of new cells)

216
Q

What is reactive atypia and how can it be confused with dysplasia?

A

Reative atypia occurs when after injury, cells regenerate but look abnormal, with suspicious nuclear changes. Often, this is acute, and disappears over time. However, if the regeneration is chronic (promoter effect), there is a real risk of pre-malignancy.

217
Q

How do the different growth disorders fit together?

A

A dysplastic mass can be benign or dysplastic, so fits in both. Some metaplasias are dysplastic. No hyperplasias are dysplastic Dysplasias are pre-malignant.
Genetic abnormalities can cause benign neoplasms, dysplasia or cancer.

218
Q

What is the histological difference between carcinoma in situ and invasive carcinoma?

A

In situ hasn’t broken through the basement membrane, whereas invasive carcinoma has- it forms a spiky mass, with small metasteses coming off it.

219
Q

What is the difference between benign and malignant neoplasms?

A

Benign do not metastasize, have differentiated cells, slow growth and are rarely fatal.
Malignant types metastasize, have less differentiated cells, and grow infiltratively and rapidly. They are fatal if untreated.

220
Q

What is the structure of solid malignant tumors?

A

Cells infiltrate and then stimulate angiogenesis. They often also cause immune responses, and promote growth of fibrous tissue surrounding it.

221
Q

What are tumor stroma, and how does hypoxia make it hard to beat carcinomas?

A

Tumor stroma consists of everything in the tumor apart from the tumor cells themselves. This inclused the fibroblasts, collagen fibres and matrix, as well as new blood vessels and inflammatory cells. When tumors grow, they often grow faster than new blood vessels can be put down, and therefore often get deprived of oxygen. The hypoxic (not dead) tumour cells are resistant to chemo and radiation therapy though, so it can help the cancer to survive.

222
Q

What are microscopic features of malignancy that can aid in diagnosis?

A

Disorganised architecture, and invasion of normal tissues
Increased nuclear staining and size, with variation in shape
Constant mitoses, and decreased cell cohesion.

223
Q

What kind of genes are involved with the formation of a cancer? How does cancer develop?

A

For a cancer to develop, mutations of cancer-related genes must occur- must commonly acquired, but some inherited. These can be in:

  • Oncogenes- genes which promote cell growth and proliferation
  • Tumor suppressor genes- genes which control cell growth
  • Apoptotic genes- genes which initiate apoptosis
  • Also DNA repair genes and epigenetic factors.
224
Q

How are oncogenes transformed? What functions can they have?

A
  • Viruses can carry RNA mutations into the host cells.
  • Proto-oncogenes (inactive form) can be transformed into oncogenes, causing a gain of function mutation.
    They can cause secretion of growth factor, expression of growth factors not reliant on ligands, they can affect intracellular signalling pathways, and can cause increased proliferation via nuclear transcription factors.
225
Q

How are proto-oncogenes activated?

A
  • Gene amplification: more copies of the oncogene, resulting in increased expression and activity- eg. neuroblastoma N-myc, or Her-2 in breast cancer (cokes for t. k. receptor)
  • Over-expression of gene, or inappropriate expression
  • Point mutations causing a different amino acid (and different product)
  • Gene rearrangement / structural translocation- forms a fusion gene, or causes upregulation of expression (eg. putting the gene next to a common promoter)
  • Epigenetic mechanisms- acetylation, methylation.
226
Q

How do tumor suppressor genes cause cancer?

A

They have a loss-of-function mutation where they are no longer able to put the brakes on cell proliferation. Normally they regulate and inhibit growth and repair DNA.

  • Normally you need both alleles to de-activate.
  • Commonly caused by loss of heterozygosity (deletions of all/part of an allele)
  • Sometimes inherited cancer syndromes- eg. inherit one defective gene which only needs one mutation to tip over
  • Eg. retinoblastoma- has hereditary (early onset, more tumors) and non-hereditary forms
227
Q

How do genes that block apoptosis cause cancer?

A

It results in the slow accumulation of malignant cells that can become a tumor.
Come about by either:
- Loss of apoptosis-mediating gene expression
- Up-regulation of genes that block apoptosis.

228
Q

How is cancer evolution a multi-step process?

A

All cancers start from a single cell and develop from there. They have properties allowing them to proliferate faster. Daughter cells have these same advantages, and may gain additional ones, leading to a mass. The next step comes when enough changes have occured to allow invasion of tissues, angiogenesis and metastases.

229
Q

What is the pathology of chronic myeloid leukaemia and how is it treated?

A

It is caused by proliferation of bone marrow cells- radiation exposure is the only known environmental risk.
Clinical features are high white count and splenomegaly.
It is caused by a chromosomal fusion: Between chromosomes 9 and 22. The BCR-ABL genes are fused, and cause production of a very powerful tyrosine kinase. This chromosomal pattern is called the philadelphia chromosome.
The Philadelphia chromosome can be used to diagnose, monitor treatment and develop a target for this cancer.
It is treated by a drug that inhibits the BCR-ABL fusion protein by binding to its ATP binding site, preventing further phosphorylation of substrates.

230
Q

What are the clinical features suggesting familial cancer risk?

A
  • Many close relatives with cancer
  • Cancers appear in successive generations
  • Young age of onset
  • Multiple cancers in a single patient
    NB in some familial cancer syndromes, there are more defined criteria
231
Q

What is the basis of familiar cancer?

A

Majority of familial cancers affect tumor suppressor genes.
Causes inheritance of one inactivated allele, and if the second allele becomes inactive, it will cause loss of tumor suppressor gene activity and potential cancer.

232
Q

What are the two different familial bowel cancers?

A

HNPCC: Associated with other cancers, often right side, increased risk endometrial cancer
FAP: Present in adolescence, formation of hundreds of polyps with high incidence of transformation to carcinoma
Both are autosomal dominant inheritance

233
Q

What is the HNPCC mutation and how do you diagnose/manage it?

A

It’s a mutation in a DNA repair gene, which recognizes and excises incorrect sequences.
In microsatellite regions, it can cause an increase in replication error rate, resulting in many, many repeats in these regions
Inheritance of this allele has incomplete penetrance- 85% lifetime risk of cancer
Diagnosed using clinical features, finding microsatellite instability in tumor, immunochemistry of tumor and analysis of repair genes (definitive)
Managed with genetic testing and screening

234
Q

What is the FAP mutation and how do you diagnose/manage it?

A

Caused by mutation of gene promoting degradation of transcription activator by truncating the protein. Almost 100% penetrant. Managed by identifying and counselling families, cancer screening, and potential colorectomy

235
Q

What are the genes responsible for most familial breast cancers and what are the clinical features of this?

A
Mostly BRCA 1 & 2.  Autosomal dominant inheritance with:
- Early onset of breast/ovarian cancer
- Premenopausal breast cancer
- Multiple family members affected
- Both cancers in one patient
- Male breast cancer (BRCA2)
- Increased prostate cancer risk
Not fully penetrant due to environmental factors and where the mutation is
236
Q

How do you diagnose and manage familial breast cancer?

A
  • Always consider genetic counselling
  • Presymptomatic testing of BRCA 1 & 2 mutations

Manage by accounting for variable penetrance, screening frequently, potential prophylactic surgery (although there is still some risk)

237
Q

What are some of the main problems with cancer predisposition testing?

A

PROS
Gives more options due to early interventions
Empowers through information

CONS
Alienation and discrimination
Loss of spiritual integrity
Stress
Guilt for not being affected/ guilt for being affected and potentially passing it to children
238
Q

What is monoclonality, and what does it mean?

A

Monoclonality is where all cells are the same. This means they are neoplastic, and in some cases are malignant. These cells only produce a single antibody molecule, so on electrophoreisis graphs it shows a single peak of antibody types rather than a whole heap of multiple ones making a flat kind of plateau.

239
Q

What is the difference between populations of reactive and monoclonal cells?

A

The reactive cells will produce multiple types of antibody, whereas the neoplastic ones will produce only the one.

240
Q

Why is it important to classify tumors?

A

Tumours differ in cell of origin (and distribution) as well as behaviour. Therefore, their presentation, prognosis and treatment will also be affected.

241
Q

What is tumour grading and how is it applied?

A

Grading is a measure of the rate of tumour growth, based on tumour histology. It indicates the aggressiveness- both in growth and invasion.
They are graded based on three components: Differentiation, nuclear changes (pleomorphism, enlargement, hyperchromasia) and mitotic activity.
Grade 1 tumours show god differentiation, and potential tubular structure in adenocarcinomas. Grade 2 show less differentiation, and grade three show a mass of random structures.

242
Q

What is tumour staging and how is it applied?

A

Tumour staging is a measure of the extent of growth, based on clinical, radiological and pathological features. Rate x Duration = Extent.
Measures of rate of growth (grading) are histological- looking at lymphocytes, cytogenic changes, proliferation indices, and suppressor/oncogene function. This is all biological.
Measures of extent of growth are stage, and serum markers- as well as looking how these change after tumor removal.

243
Q

How are cancers staged?

A

There are three categories- T for tumor, N for nodal metastasis, and M for distant metastasis. There can also be a p/c prefix for pathological and clinical.
Stage 1 is tumour hasn’t penetrated multiple layers of tissue, stage 2 is it has, and stage 3 is nodal metastases (with stage 4 distant)

244
Q

How does cancer spread?

A

Can spread locally- growth

- Metastasise through lymph (lung, breast), venously, through the serosal cavities and through nervous tissue.

245
Q

Describe the pathology of breast and bone cancer

A

Breast- can block the lymphatics, causing oedema and dimpling of the skin around hair follicles
Bone- Can cause pathological fracture, hypercalcaemia (although this can also be due to hyperparathyroidism) and pain. Sometimes the cancer eats through the bone, sometimes it causes increased deposits.

246
Q

What are the different categories of cancer?

A

Cancers can be epithelial, melanocytic, connective tissue, lymph node, bone marrow or CNS types.

247
Q

What are benign epithelial tumors?

A

Can be adenomas (glandular), papillomas (surface) or cystadenomas (cystic formation)
Show regular tightly packed cells similar to normal epithelia, although some can be premalignant.

248
Q

What are carcinomas?

A

Most common malignant tumours, which affect the surface epithelium. They start with an in situ growth phase, and are then classed as malignant once they invade. They show cohesive polygonal cells, and test positive for cytokeratin. They are able to spread to bone, lymph nodes and viscera. Treatment is mainly surgical, but can also be done with radiation and chemotherapy/

249
Q

What are melanocytic tumors?

A

They can be benign (moles) or malignant. They commonly occur in the skin. They can be defined while still in situ, but can also spread via the lymph and blood vessels.
They can appear as spindle, round or pleomorphic cells, and while they are cytokeratin negative, they are S100/SOX10 positive

250
Q

What are connective tissue tumors?

A

Sarcomas are rare, but benign tumors are common. They cannot be defined while still in situ, as connective tissue is frequently moving and it will have grown very large by the time it’s identified. They spread via the bloodstream (mainly to the lungs).
They are treated with a combination of surgery, radiation and chemo. They also show spindle cells, round and pleomorphic cells, and are also cytokeratin negative.

251
Q

What are lymphomas?

A

They are common tumors of the lymph nodes and extranodal sites, and are always malignant with no in situ phase. They spread to other lymph nodes. Treatment is with chemo and radiotherapy.
They show non-cohesive round cells and are cytokeratin negative, although they are leukocyte common antigen positive (stains their cell membranes).
Hodgkins shows reed-sternberg cells, which are multinucleated, while non-hodgkins can be differentiated into small-cell (long life but no cure) and large cell (short timecourse but curable).

252
Q

What is leukaemia?

A

An uncommon cancer of the bone marrow, with no in situ phase. It is treated by chemotherapy, with prognosis differing depending on type. They can also cause splenomegaly.

253
Q

What are glial tumours?

A

Uncommon tumours, mostly incurable. They are restricted to the CNS and can be treated with a mixture of surgery, radiotherapy and chemotherapy.

254
Q

What are features of the most aggressive cancer types?

A
  • Undifferentiated cells
  • Anaplastic (de-differentiated) cells
  • Pleomorphic cells (v. irregular nuclei)
255
Q

What are complete carcinogens, initiators and promoters?

A
  • A complete carcinogen is any agent sufficient to cause cancer.
  • Initiators are doses of complete carcinogens introduced at doses not high enough to induce cancer. They cause cancer via synergy with promoters:
  • Promoters are agents that, when administered in repeated doses in close succession, can cause cancer with prior exposure to an initiator
256
Q

How do initiators and promotors need to be spaced to cause cancer?

A
  • Initiator has to be applied prior to promoter
  • Effects of the initiator is reversible as promotion can be delayed
  • Effects of promoters are also reversible, because promoters are ineffective if doses are widely spaced enough.
257
Q

What are the differences between initiators and promoters?

A

Initiators have a permanent effect, while promoters are transient
Initiators target the DNA, while promoters target proteins- eg. enzymes and receptors
Initiators cause mutations, while promoters affect signalling pathways
Initiators alter the gene sequences, while promoters affect gene expression
Initiators deliver potentially carcinogenic damage, while promoters stimulate the outgrowth of initiated cells.

258
Q

What are the initiators and promoters in skin cancer, and how do they cause the development of the different skin cancers?

A
  • Initiator is UVB, which is a complete carcinogen or initiator. UVA is the promoter.
  • When adjacent CC pyrimidine bases absorb UV radiation, they form cyclobutane dimers.
    Polymerase n is a faulty DNA repair enzyme, which inserts an A opposite the C. Then replication proceeds, and the CC is swapped to a TT.
    This can initiate and cause cancer when it occurs in the P53 gene.
259
Q

How does a single mutated p53 gene manifest into skin cancer?

A

Initially, sun-damaged skin has efficient apoptosis- the cells die off and the sunburn peels
When one copy of the P53 gene is knocked out, it causes less efficient apoptosis, and clones of this mutation are allowed to survive.
Further damage yields both genes being damaged, and apoptosis is lost, the cell cycle loses control and malignancy forms.

260
Q

What are the initiators in lung cancer, and how do they manifest into lung cancer?

A
  • PAH (from any form of plant smoking)
  • NNK (from nicotine)
  • NNK is hydroxylated at its alpha carbon due to immune activation, causing release of a very reactive product, which binds to guanine. This is then methylated, and begins to pair like an A rather than a G, so that T replaces the paired C, the following replication an A replaces the methylated G, and the GC pair changes to A-T (if not repaired).
    Additionally, NNK binds to receptors on the lung cells responsible for the Ras protein generation, causing increased proliferation, survival and invasion from this gene
261
Q

How can HBV cause liver cancer?

A

In undeveloped countries, Aflatoxin acts and an initiator and alkylates guanine, and if it isn’t repaired it causes a GC- TA transition. HBV then acts as a promoter, causing inhibited DNA repair, binding to P53 and deactivating it, Additionally, it activates Ras, and causes cell death, inflammation, regeneration and proliferation.

262
Q

What is an example of an endogenous complete carcinogen?

A

Chronic inflammation

263
Q

What is the normal pattern of cell adhesion, and how can this change due to cancer?

A

Normally, cells are adhered with adherens junctions, formed from E-cadherin sticking out from adjacent walls, attaching to beta and then alpha catenins, which is attached to the actin cytoskeleton.
When there is a reversible epithelial-mesenchymal transition, the E-cadherin gene is phosphorylated, and growth factors and inflammation causes focal dislocation- the cells maintain local structure, but are essentially unattached- in primary and secondary stages. These are solid tumors, with high metastatic potential.
Irreversible EMT occurs due to mutation or silencing of the EMT or a cadherin genes, causing a permanent and loose attachment- or diffuse type cancers, where tumor cells are loose.

264
Q

Why are growth factor receptors often overactive in cancers? What consequences does this have?

A

Overactive due to:

  • Overexpression due to altered regulation
  • Gene amplification
  • Missense mutations causing constitutive receptor activation
  • Co-expression with HGF in the same cells, forming autocrine loops

Causes activation of ras oncoprogeins, inducing proteins (like snail) that repress E-cadherin
Also phosphorylates E cadherin and b-catenin, causing the dissolution of adherens junctions.

265
Q

What is the process of cancer invasion?

A

Firstly, podosomes are assembled on the tumor cell surfaces, in response to the presence of growth hormones.
The structure involves integrin-associated urokinase Plasminogen Activator receptors (uPARs). This allows uPA to bind, cleaving plasminogen to plasma. This protease then cleaves itself, pro-MMPs and the ECM itself.
MMPs degrade the ECM, secreted by fibroblasts, inflammatory and neoplastic cells in an inactive form. They:
- Carve a pathway for cell migration through the ECM and release growth factors from the ECM
- Release chemotactic chemicals by breaking down laminin 5
- Suppress adhesion of E-cadherin
- Degrade latent growth factor proteins to release the growth factor
Integrins also signal cells via FAK and ras to stimulate pro-uPA production, proliferation and invasion.

266
Q

What happens as a consequence of tumor hypoxia?

A

Viable hypoxic cells are resistant to radiotherapy as oxygen is required to kill them.
Hypoxia also induces activation of angiogenesis via HIF1a and VEGF.
Hypoxia can also increase tumor aggressiveness as any cell with dysfunctional p53 will have a selective advantage
Additionally it can activate snail and twist, repressing E-cadherin genes and inducing EMT, resulting in a higher risk of metastases.

267
Q

What triggers angiogenesis?

A
  • Metabolic stress (hypoxia, pH, gypoglycaemia)
  • Inflammation
  • Activation of oncogenes or inactivation of tumor suppressor genes
268
Q

What is angiogenic sprouting?

A
  • Angiogenic sprouting: VEGF is applied, causing endothelial cells to degrade some basement membrane and form a migrating column through it, where proliferating cells follow the leading edge and differentiate. VEGF along however generates immature, heaky, haemorragic vessels, causing inflammation and oedema. It is characterised by an angiogenic switch: hyperplastic ducts –> dysplastic ducts –> angiogenic dysplastic ducts –> invasive ductal carcinomas
269
Q

What is co-option of blood vessels?

A

Tumors initially grow around blood vessels, but when they become highly malignant, the vasculature regresses, making the tumor secondarily avascular. Angiogenesis is then triggered

270
Q

What is intussusception?

A

Columns of tumors grow against the lumen of a blood vessel and force it to remodel as it grows

271
Q

What is incorporation of EC precursors?

A

Haemangioblasts are stem cells which can be called by tumors from the bone marrow. They differentiate into endothelial cells, smooth muscles and pericytes to form new blood vessels

272
Q

What is capillary formation by cancer cells?

A

Some cancer cells can express endothelial characteristics of endothelial cells and form their own capillaries. These are lined by a mosaic of EC and cancer cells. This also increases the chance of distant metastases

273
Q

What factors should be considered when feeding a patient with cancer?

A
  • The site, type and stage of cancer
  • Treatment modalities and possible side effects
  • Co-morbidities of disease
  • Age and social circumstances
  • Swallowing impairment
  • Effects on digestive mechanisms
  • Any surgical blockages
  • Cachexia
274
Q

What is cachexia and how does it come about?

A

Cachexia is the breakdown of skeletal muscles and issues in fat and carbohydrate metabolism despite adequate nutritional intake.
It is caused by the tumor releasing acute phase proteins, causing inflammation and cytokines, as well as reducing appetite due to hypothalamic effects.
The tumor also releases PIF to directly break down skeletal muscle
Finally, it releases LMF to break down fat.

275
Q

What factors drive cancer-associated wasting?

A

Altered metabolism
- Increased protein catabolism and loss
- Glucose intolerance and abnormal insulin response
- Increased lipolysis and fatty acid turnover
- Inefficiency in energy consumption and increase in energy expenditure
Altered physiology
- Malabsorption and maldigestion
- Constipation and dysmotility due to surgery or narcotics
Insufficient dietary intake
- Appetite suppression, caused by cytokines, depression or loss of taste
- Learned aversion
Physical impairment
- Swallowing
- Saliva
- Mass of tumor
- Mucositis in mouth
- Surgical interruption

276
Q

What are the aims of medical nutrition in cancer?

A
  • Improve quality of life
  • enhance anti-tumor treatment effects
  • Reduce adverse effects
  • Prevent or correct defficiency
277
Q

What are methods of medically feeding cancer patients?

A
  • Supplemental feeding- increasing energy/protein content
  • Advice and information
  • Enteral feeding- oral sip feeds or NG tube
  • TPN
  • Pharmacological agents to combat cachexia
  • Nutraceutical agents to enhance immunity
  • Intravenous feeding (but problems with sterility)
278
Q

What is non-coding RNA?

A

These make up 98.5% of our entire RNA pool, with a very important role in the normal development of cells and organs.
They can be classes as small (less than 200 nucleotides) or large ( more than 200 nucleotides). They can also be classified by function, size, shape and biogenesis.

279
Q

What are 3 common short ncRNAs?

A
  • Transfer RNA
  • Small nucleolar RNA
  • MicroRNA
280
Q

How can tRNA be involved in a disease?

A
  • Its job is to carry amino acids to the messenger RNA in order to translate it to protein. It’s found in mtDNA. When mutated it causes the maternally inherited disease MELAS, for mitochondiral myopathy, encephalomyopathy, lactic acidosis, and stroke like episodes
281
Q

How can snoRNA be involved in disease?

A
  • Its job is to modify the ribosomes by coupling amino acids together during tanslation
  • In diseases where the 11q13 region of chromosome 15 is lost, this is where the snoRNA sits, so it can cause prader willi and angelman syndromes by changing splicing, causing increased energy expenditure and growth retardation.
282
Q

How can microRNA be involved in disease?

A

MicroRNA represses translation of target RNA, and each can regulate about 200 different ones.
In disease, it is especially associated with:
- Cancer- when damaged, they lose the ability to regulate oncogenes/tumor suppressor genes
- Down syndrome- gain of chromosome 21 contains 5 micro-RNAs involved in regulation of MECP2, important for brain development
- Alzheimers- loss of miRNA causes increased BACE1 enzyme, causing accumulation of protein plaques in the brain

283
Q

What are some common long ncRNAs?

A
  • XIST
  • HOTAIR
  • H19
  • snoRNA-incRNA
284
Q

How is XIST involved in disease?

A

Its job is to regulate X inactivation by binding to and switching off the whole chromosome.
- Errors lead to skewed X inactivation, causing accumulation of X linked diseases

285
Q

How is HOTAIR linked to disease?

A

This methylates messenger RNA, and is especially prominent in breast cancer as it methylates metastasis suppressor genes, switching them off

286
Q

How is H19 involved in disease?

A

It’s an imprinted ncRNA expressed from maternal chromosmes, which regulates insulin growth factor in cells.
A loss of H19 causes excess cell growth, and also contains a micro-RNA which switches off tumor suppressor genes.

287
Q

How is snoRNA-incRNA involved in disease?

A

It is transcribed from the same region as those in prader-willi syndrome. The inc-RNA mops up FOX 2, and so is implicated in Angelmann syndrome too.

288
Q

How can ncRNAs be put to use in disease?

A

They can be used as Biomarkers of disease (due to their being found in higher or lower levels depending on the disease
They can act in genome wide association studies, where they can find SNPs associated with disease, which alter the ability of RNA to bind to other RNAs and reduce their functions
They can also be used in therapeutics, as their close association with disease progression can mean they are able to be targeted to reduce diseases such as cancer, inflammation and chronic heart disease.

289
Q

What are the different ‘ome’s and what are they impacted by?

A

All DNA = genome
All RNA = transcriptome
All Protein = proteome
All Metabolites = metabolome

290
Q

How did genomes used to be sequenced, and how are they sequenced today?

A

Originally, DNA was labeled so that when it was read on a computer each nucleotide gives off a color
Next generation breaks the genes into small portions, and adds linkers to bind them to the microscope slide. When enzymes run up the side of the DNA, a colored light is emitted each time the base changes.
- These fragments are captured using baits (complementary matches) or using PCR

291
Q

What is an exome?

A

A part of the genome that codes for genes

292
Q

Why can’t we piece together the entire genome in order?

A

Some fragments are repeated multiple times throughout the genome, so identifying which chromosme and gene something comes from can be difficult
Also difficult to see new mutations from mutations (but can use conservation- if something has been handed through many, many different generations in multiple species, it’s likely a polymorphism)

293
Q

Why is it important to isolate mutations in particular?

A

So that medicine which targets a particular gene can be adapted to work on that mutation too

294
Q

What is genomic medicine?

A

Use of the knowledge of somebody’s genetics to personalise disease treatment. This can also be used to assess a person’s suitability for tratments like anti cancer trugs.

295
Q

How are tumors particularly important in genome sequencing?

A

Tumors can delete the MHC receptors on its cells to prevent antigen presentation- but these cells are picked up by CD335 NK cells.
Additionally some tumor DNA is released into the blood- this allows us to know what tumor it is and where by taking this DNA from the blood.