Path Pre-Unifieds Flashcards
1
Q
AL Amyloid
A
Amyloid light chain. Usually associated with lambda B cell diseases. Primary systemic amyloidosis.
2
Q
AA Amyloid
A
Amyloid associated non-ig protein from SAA. SAA is high in chronic inflammatory diseases, produced in liver. Chronic inflammation –> macrophage activation –> IL-1 and 6 –> liver cells –> SAA protein– >limited proteolysis, AA protein buildup.
3
Q
Immunocyte dyscrasias with Amyloidosis
A
Deposition of AL or their fragments in extracellular spaces throughout body. Abnormal clones of B cells ie multiple myeloma. Excess Ig and light chains only (Bence Jones proteins).
4
Q
Reactive systemic amyloidosis
A
Deposition of AA protein in EC space of most organs and systems. Used to be called secondary amyloidosis bc often associated with chronic inflamm processes. Usually secondary to autoimmune disease, neoplasms (hodgkins), and chronic skin infections. TBC, chronic osteomyelitis, bronchiectasis.
5
Q
Hemochromatosis
A
Extreme iron overload, genetic. Cardiac failure, hepatic cirrhosis, and diabetes. Bronze like appearance “bronze diabetes”. Also increased risk of malignant tumours of liver (hepatocellular carcinoma)
6
Q
Familial Systemic Amyloidosis
A
Buildup of AA or transthyretin (Mediterranean fever, neuropathies)
7
Q
Familial Mediterranean fever
A
AR disorder of PMN function, AA deposits occur
8
Q
Familial amyloidotic neuropathies
A
AD , many mutations in amyloidogenic proteins. Most common subtype is transthyretin mutation
9
Q
Senile localized amyloidosis of Heart
A
Less severe, don’t really understand. Associated with transthyretin, often asymptomatic and discovered at autopsy.
10
Q
Gouty mechanism
A
Urate crystal precipitation. (1) Activation of complement, neutrophil chemotax, phagocytosis, lysis of neutrophils, release of more crystals, lysosomal enzymes, tissue injury inflamm. (2) phagocytosis by macrophages, release of LTB4, PGI, free radicals - neutrophil chemotax, activation of inflammasome, release of IL-1B, secretion of chemokines and other cytokines, protases, tissue injury and inflamm.
11
Q
Cell Injury: Lysosomes
A
Usually due to drugs and antibiotics. Can cause autophagy by activation of lysosomal enzymes with enzymatic digestion of cell components –> necrosis. Can cause incomplete degradation of phagocytosed material (lysosomes lose ability to degrade if lose enzymes).
12
Q
Cell injury: mitochondria
A
Usually due to any agent that affects oxidative phosphorylation ie hypoxia, hypoglycemia. Lack of O2 as the final electron acceptor
13
Q
Cell injury mechanisms leading to necrosis
A
Hypoxia, ischemia, decreased ATP –> necrosis. Increase in ROS from injurious stimuli, damage to lipids proteins and nucleic acids –> necrosis. Inflammation, releases toxic molecules, necrosis (or apoptosis)
14
Q
Cell injury mechanisms leading to apoptosis
A
Mutations, cell stress, infections => Accumulation of mis-folded proteins in ER => apoptosis.
Radiation, other insults => DNA damage => apoptosis
Inflammation from infections, immuno disorders => toxic molecules => apoptosis (or necrosis)
15
Q
Reversible Ischaemic injury
A
Impaired aerobic resp., decreased ATP, anaerobic glycolysis, glycogen depletion, lactic acidosis and nuclear chromatin clumping.
ATP deficiency –> energy loss –> cell membrane integrity –> failure of NA pump –> cel swelling and calcium influx –> Lactate accumulation (also leads to cell swelling) –> detachment of ribosomes –> blebs, myelin figures (cell membrane) –> mitochondrial swelling.
16
Q
IRREV ischaemic injury
A
Severe vacuolization of mitochondria, damage of plasma membranes, swelling of lysosomes and MASSIVE Calcium influx, marked intracellular acidosis, ruptured lysosomal membrane, cell digestion and death. Inability of mitochondria to recover. Calcium influx denatures proteins and causes cell coagulation.
17
Q
When is injury irreversible?
A
Mitochondria unable to recover after re-oxygeniation –> lloss of phospholipids –> damage to cytoskeleton –> O2 free radicals and lipid break products (ROS), influx of calcium fater re-ox with protein denaturation (coagulation of cells).
18
Q
Free radical injury
A
Most affect cell membranes. Most common are activatd oxygen radicals (aging, chemical, infections, inflamm etc). Free radicals affect cell membranes by lipid peroxidation, and affect nucleic acids with mutations. Protective mechanisms = catalase and glutathione.
19
Q
Chemical injury (direct or indirect)
A
Direct: mercury binds to protiens and cell membranes
indirect: by metabolic activation ie CCl4 –> Ccl3 in ER (irreversible fatty change)
Accumulation of lipid in cells (ER) because of lack of lipoproteins necessary for TAGs to leave the cell –> fatty liver.
20
Q
Viral injury (cytopathic or cytolytic or oncogenic effect)
A
Cytopathic - rapid replication within cell, immune response, inflammation, and cell lysis
Often cell specific (receptors)
Also effects on cell skeleton–> multinucleation, inclusino bodies etc.
21
Q
Apoptosis
A
Physiological usually. Cell shrinks. Eventual fragmentation of nucleus and cell–> apoptotic body –> phagocytized –> residual (acidophilic) body. NO INFLAMMATION.
22
Q
Coagulative necrosis
A
Most common type. Ischaemic, coagulation of cells, loss of nuclei, denatured proteins. Acidophilic mass on H&E. Wedge shaped infarcts.
23
Q
Liquefactive necrosis
A
Hydrolytic enzymes. Brain, bacterial infections.
24
Q
Fat necrosis
A
Can occur anywhere there is fat. Dystrophic calcification, metastatic calcification. Release of lipases fro pancreas or inflammatory cells, FFAs plus calcium –> soaps. Chalky cheesy nodules deposit.
25
Caseous necrosis
TB. Combination of coagulative and liquefactive. Cheesy-milky. Eosinophilic (ie acidophilic, pink).
26
Gangrenous necrosis
affects limbs. Ischemia and infection. Dry or wet - wet once liquefactive (bacteria), infection of dry one.
27
Russel Bodies
Intracellular accumulation. Accumulation of Immunoglobulins in RER of plasma cells --> eosinophilic.
28
Mechanisms of intracellular accumulations
Abnormal metabolism (fatty liver, defect in protein folding, transport, lack of enzyme (lysosomal storage diseases, endogenous materials), ingestion of indigestible materials (exogenous, ie carbon pigment accumulation)
29
Endocervical metaplasia
Simple columnar to stratified squamous. Squamous metaplasia. Due to multiple kids, HPV, etc. Pap smear to test.
30
Calorie restriction as a counteractant to aging
Decrased insulin, IGF signaling, decreased TOR => altered transcription => increased DNA repair, increased protein homeostatis
31
Vascular permeability mechanisms
1. Endothelial cell contraction - histamine mediated. Short lived, reversible (15-30 mins). Small venules
2. Junctional retraction - cytokine mediated (produced in inflammation). 4-6 hours post injury, lasts 24 hours
3. Direct endothelial injury *most important
Endothelial cell necrosis, more severe injuries, starts early/lasts for days. Immediate and sustained, delayed. Affects venules and capillaries. Trauma, autoimmune, allergic rxns.
32
Requirements of engulfment
Require energy, calcium, and magnesium to form pseudopods. Engulfment is thus an extremely energy consuming process
33
Phagocytosis complications
1. Regurgitation: infection by very powerful bacteria. Enzymes pour out before the macrophage can wrap around the bacteria. Kills white cells, being overcome.
2. Frustrated phagocytosis: Phagocytes working but tissue won't let them work - ie endothelial cells in glomerulus, surface endothelium coated by opsonins, but endothelial cells stuck on BM - can't ingest a stuck endothelium, macrophages get overexcited. Enzymes pour out, kill out endothelial cells, more opsonins, etc.
3. Cytotoxic release - phagocyte gets overexcited, misses steps, bursts.
34
PAF Platelet Activating Factor
Released by endothelial cells and inflammatory cells, damaged tissue cells. Powerful VASODILATOR, increases PERMEABILITY, stimulates platelets, inflamm, and endothelial cells. Aggregation of platelets at site of injury, chemotactic functions.
35
Vasoactive Amines
Serotonin (from platelets only), Histamine (from platelets and mast cells, basophils). Vasodilation, and increased vascular permeability (VENULES only).
36
Endothelins
Peptide produced by endothelial cells. powerful VASOCONSTRICTOR.
37
Agents for histamine release from mast cells tfc
```
Physical trauma, cold
Immunological (igE)
C3a and C5a (anaphylatoxins)
histamine releasing factors from PMNs, monocytes and platelets
IL-1
```
38
Bradykinin
HMWK => pre-kallikrein => kallikrin, converts kininogen to Bradykinin, increased vascular permeability, vasodilation, PAIN, contraction of smooth muscle. Early phases of inflammation only.
39
Granulomatous inflammation
Type of chronic inflammation (other type is non-specific). Formation of a granuloma - central focus (usually necrotic), surrounded by epitheloid cells, which are surrounded by a rim of lymphocytes and or plasma cells. Older granulomas can have a ring of fibroblasts or CT. Often giant cells (multinucleated, histiocytic or monocytic origin) are present among inner cells.
40
Common causes of granulomatous Inflammation
Characteristic of TB, syphilis, cat scratch disease, fungal, protozoan, persistent foreign body inflamm, rheumatic fever (aschoff body), rheumatoid arthritis (subcutaneous nodules), sarcoidosis, granuloma annular of skin.
41
Types of inflammation , increasing severity
Serous (albumin in exudat, blisters, ascites, etc), fibrinous (worse leakage ie fibrin. Serosal surfaces), Suppurative (pus, liquefactive, necessitated by bacteria, ie cocci etc), sanguinous (rich in RbCs, serious vascular injury, tuberculous pleuritis, tumors).
42
Fibrinous Inflammation
More severe than serous, significant vascular damage, large molecules pass: fibrinogen, eg. rheumatic fever (bread and butter pericarditis), pneumococcal pneumonia. Fibrin is acidophilic.
43
Suppurative Inflammation
Liquefactive necrosis by bacteria => pus. Caused by pyogens ie Staph, pneumococcus, meningococcus, gonococcus, e. coli, some non-haemolytic strep.
44
Pseudomembranous inflammation
Ie pseudomembranous colitis (often with c diff, elderly taking antibiotics). On mucosal surfaces, mucous mixed with bacteria and neutrophils. Produced by powerful necrotizing toxin ie diptheria. Formation of pseudomembrane = fibrin, necrotic epithelium, WBCs.
45
Fibronectin
Multiple roles in wound healing. Glue-like effect, intermediate filaments, chemotactic, migration and organization of cells, release fibroblast GF from macrophages.
46
Amyloid
Proteinaceous, stain blue with iodine. Glassy pink H&E, salmon colour on congo red, apple green birefringence. EM: non-branching fibrils (up to 6), plus non-fibrillary component (P component)
47
Systemic amyloidosis
Immunocyte dyscrasias (excess of Ig and BJ, AL), reactive systemic (AA protein in chronic inflam, skin, hodgkins, TB, RF), Hemodialysis (B2 microglobulin), Familial diseases (ie mediterannean fever AR , AA deposits; familial amyloidotic neuropathies AD
48
Localized amyloidosis
Diabetes (deposits in islets), senile cardiac amyloidosis (transthyretin, asymptomatic), senile cerebral amyloidofsis (alzheimer's disease)
49
Carbon as a pigment
most common pollutant, accumulats in tissue (lungs lymph = anthracosis. Phagacytosed by alveolar macrophages. Often with other pollutant in industry ie silica asbestos
50
Lipofuscin
Wear & tear, breakdown pdt of cell membrane, normal in small amount. Visible in liver, heart, brain. Lysosomes of cells. Intracellular, perinuclear accumulation. Yellowish brown
51
Bile
Bilirubin, bile salts, lipids. Pigment derived from breakdown of old RBCs, excess pdn or inability to excrete makes it visible. Both INTRA and EXTRAcellular. In cells and in the ducts around cells.
52
Hemosiderin
Breakdown of Hemoglobin, golden brown H&E. Blue with prussian blue, stored in spleen, liver, bone marrow. Excess Fe in cells: hemosiderosis
53
Anaplasia
Lack of differentiation, term used in invasive neoplasm
54
Pathways of metastasis
1. Seeding via body cavities (peritoneal cavity most common ie ovarian carcinoma). Also pericardial, pleural, subarachnoid cavities 2. Lymphatic spread - most common initial dissemination of carcinomas, follows natural drainage. 4. Hematogenous spread - favoured by sarcomas, liver and lungs are most frequent secondary sites as all PORTAL areas drain to liver and all CAVAL areas drain to the lungs.
55
MDM2
Inhibitor of p53 - in normal, non-stressed cells who don't need p53. But overexpression leads to resistance of apoptosis, cancerous
56
Anti-apoptotic members of BCL2 family
BCL2, BCL-XL, MCL1
57
Mechanism of follicular B cell lymphomas
BCL2 levels high due to balanced translocation, t(14;18) fusing BCL2 with regulatory elements of IgG light chain. BCL2 anti-apoptotic protein, overexpression --> Follicular B cell lymphoma
58
Warburg metabolism
Favouring of glycoylsis over oxidative phosphorylation, common in malignant cells. Many oncoproteins (RAS, MYC, mutated growth factor receptors) induce Warburg metabolism.
59
Hamartoma
Non-neoplastic malformation, disorganized overgrowth of tissues in their native location
60
Choristoma
Non-neoplastic malformation, normal tissue in a foreign location.
61
Mechanism of local and distant spread
(1) Invasion of ECM. - detachment of tumor cellls (reduced Cadherins), ECM protein degradation by collagenase, cathepsin B (on BM, secreted by metastatic tumours NOT by benign), attachments to ECM protein components (laminin R, integrins. new sites gen. by MP2, MMP9 secreted by tumours), movement through ECM proteins (autocrine motility factors, cleavage products (collagen, IGF)
(2) movement through interstitium
(3) vascular dissemination and homing
62
Markers on Tumour cells to help them avoid inhibitory pathways
PD-1 ligand.
63
GRADE of a tumour
Specific to particular tumour, is level of differentiation. Well, moderately, and poorly differentiated tumours. Based on differentiation, mitosis, and necrosis. Problems: variation of histology in different areas, observer variation (minimal though)
64
STAGE of a tumour
Extent of SPREAD, more important than grade in determining prognosis. Both Clinical and pathological staging.
SIZE of primary tumour (T)
Extend of spread to regional Lymph NODES (N)
Presence or absence of metastases (M)
65
Local tumour effects
```
Submucosal leiomyoma - bleeding
Tumour in gut - bowel obstruction
pituitary adenoma - destruction of remaining gland
GI tumours/urogenital - bleeding
Ovarian tumors - torsion
```
66
Cachexia
Weight loss, muscle atrophy, fatigue. Occurs in chronic disease. Here we talk about cancer. Also anorexia, anemia. NOT due to nutritional demand by tumour. Factors producing: reduced food intake, reduced synthesis and storage of fat, increased mobilization of fatty acids from adipocytes, TNF alpha, IFN y, IL-1 and IL-6 (pyorogens)
67
Paraneoplastic syndrome
Symptom complex in cancer-bearing patients, that cannot be readily explained either by local or distant spread of tumour or by elaboration of hormones indigenous to tissue of origin. May be earliest manifestation of OCCULT neoplasm, may cause significant CLINICAL problem (even lethal), may MIMIC metastatic disease, may lead to WRONG diagnoses. Ie lung tumour starts producing steroids - often times cancer cells develop new function.
68
Paraneoplastic syndromes in bronchogenic carcinoma (small cell carcinoma)
Cushing's, SIADH, hypercalcemia, Myasthenia (also commonly assoc with thymoma), acanthosis nigricans, hypertrophic osteoarthropathy, venous thrombosis.
69
Fever and cancer
Correlates with tumour growth. Disappears following treatment, reappears with recurrence. Due to release of pyrogens such as IL-1 and TNF
70
Immunohistochemical stains
```
Epithelium - keratin
Mesenchyme - vimentin
Muscle - desmin
Prostatic epithelium - PSA
Thyroid follicular cells - thryoglobulin
Neuroendocrine cells - chromogranin
Melanoma - S-100/HMB45/Melan A
```
71
Flow cytometric analysis
Requires fresh tissue fixation. Single cell suspension, stained with fluorescence labeled surface markers, detected by specific antibodies, sorted by size and fluorescence intensity. Characterization of lymphoma/leukemia.
72
CEA
Carcinoembryonic antigen. Biochemical tumour marker. Specifically Colonic, pancreatic, breast, and gastric ADENOCARCINOMAs
73
EBV as an oncogenic microbe - associated cnacers
Burkitt's lymphoma**, nasopharyngeal carcinoma, Hodkin lymphoma, primary CNS lymphoma.
74
MYCn associated cancer
MYCN - transcription factor oncogene - Neuroblastoma (childhood cancer)
75
AD Inherited Cancer syndromes, multiple neoplasms
Multiple Endocrine Neoplasia (MEN1, RET (a tumor suppressor)), Li-fraumeni syndrome (p53), FAP (APC).
76
APC
Tumour suppressor gene. Negative regulator of B catenin/WNT pathway. APC normally destroys B catenin so that it cannot translocate to the nucleus and increase transcription via WNT pathway.
77
MEN1
Tumour suppressor gene. Mutated in Multiple Endocrine Neoplasia.
78
RET
Receptor Tyrosine Kinase. Associated with multiple endocrine neoplasia. Tumour suppressor.
79
HNPCC
AD. Defective DNA repair mechanisms, making one susceptible to cancer: MLH1, MSH2, MSH6, PMS2
80
AR syndromes of defective DNA repair
Xeroderma pigmentosa --> squamous cell carcinoma
Ataxia telangiectasia - lymphoma, ALL
Fanconi's anemia --> AML.
81
Ulcerative Colitis
Acquired pre-neoplastic condition. Increases susceptibility to developing colonic adenocarcinoma.
82
Driver mutations
Subvert normal control of cell proliferation, differentiation, and homeostasis. May drive the neoplastic process, and hence could be therapeutic targets. Direct contributors to development/progression of cancer. Tend to be tightly clustered within cancer genes.
83
Passenger mutations
Have no effect on cell phenotype. More numerous than driver mutations, most often fall in noncoding regions of genome or have neutral effect on growth, not conferring advantage or disadvantage. Result from genomic instability of cancer cells and are along for the ride. Acquired mutations, do not affect cellular behaviour. At random throughout the gnome.
84
Chemical carcinogens: direct acting alkylating agents
Cyclophosphamide --> leukemia
85
Chemical carcinogens - polycyclic aromatic hydrocarbons
In tobacco --> lung cancer. Require metabolic activation (indirect acting)
86
Aromatic amines and azodyes
Cause hepatocellular CA, bladder CA (Indirect acting, require metabolic activation). Examples, napthylamine etc.
87
Nitrosamines (smoked foods) and Amides
Gastric cancer. Indirect acting ie require metabolic activation.
88
Asbestos
Mesothelioma, lung cancer.
89
HPV oncogenic
DNA oncogenic virus. --> papilloma (skin, larynx), cervical cancer.
90
EBV Oncogenic
DNA oncogenic virus --> Nasopharyngeal carcinoma, burkitt's lymphoma
91
HBV
DNA oncogenic virus. --> hepatocellular carcinoma.
92
HPV-E6 oncogenic mechanism
DNA oncogenic virus. Increases TERT (increased telomerase expression), and inhibits p53 (tumour suppressor gene)
93
HPV-E7 oncogenic mechanism
DNA oncogenic virus. Blocks p21, p21 usually inhibits cyclin-CDK complex phosphorylation of Rb and thus release of E2F. So without p21, have uncontrolled activation of Cyclin-CDK complexes ability to phosphorylate Rb, thus letting it release E2F to increase gene transcription for progression to S phase.
HPV-E7 also directly blocks RB-E2F complex, degrading it and releasing E2F.
94
HBV and Burkitt's lymphoma
infection with EBV, causes polyclonal proliferation of B cells. Concommitent immune incompetence can lead to acquired translocations of the B cells ie t(8,14) translocation of c-myc (8) and heavy-chain Ig (14). Leading to c-myc activation, and thus monoclonal proliferation.
95
HTLV-1
Oncogenic Retrovirus (RNA virus) - implicated in cancer. Associated with human T cell leukemia/lymphoma. Viral Tax protein stimulats proliferation, enhances clel survival, and interferes with cell cycle controls. Proliferation initially is polyclonal. Secondary mutations --> outgrowth of monoclonal leukemia.
96
HHV-8
Kaposi's Sarcoma
97
H. pylori
Associated with B cell lymphoma in the MALT (MALToma)
98
Type of mutation in KRAS for colon cancer
Point mutation, colon cancer
99
Type of mutation in Retinoblastoma
Deletion : del13q14
100
Type of mutation in neuroblastoma
Gene amplification of NMYC.
101
Most common mutation in human canceres?
RAS oncogene.
102
CCND1 (Cyclin D1) mutation
Mutation dysregulates cell cycle --> mantle cell lymphoma (t 11,14) with IgH.
103
BCL2 mutation
BCL2 normally inhibits apoptosis. If mutation --> CLL, Other B cell lymphomas.
104
HNPCC mutated genes
MSH2, MLH1 - DNA repair genes. Not oncogenic by themselves. When mutated, allow mutation in other genes -> limitless replication potential
105
Adenomacarcinoma Sequence
FAP. APC mutation (first hit) --> B catenin dysregulation (second hit) -- protoncogene mutation of K-ras leading to adenomas. P53 mutation leading to carcinoma.
106
Testing for Hereditary Hemochromatosis
HFE Gene testing. 2 mutations. (C282Y most common, and H63D). PCR amplification, restriction site fragment --> gel electrophoresis. 2 bands normal, 3 bands for C282Y mutant. If hetero - see 4 fragments because you have all of the types.
H63D mutant has no RE site, one solid band.
Or could use Real time PCR. faster, wider application - use melting temperature and probe to determine presence of mutation. . Allele specific PCR.
107
RFLP
Restriction Fragment Length polymorphism - DNA from different people may show different lengths, due to variation or mutation, after digestion with restriction endonucleases.
108
Allele specific PCR
For point mutation detection. Nucleotides complementary at base position, labeled with fluorophores. Fluorescent signals of variable intensity according to ratio of mutant to wild type DNA.
109
Hemochromatosis
```
Type I: Mutation in HFE gene (C282Y 90%), H63D 1% ,combination is the rest. Defective function--> excessive iron absorption and deposition. Chronic fatigue, arthritis, heart disease, cirrhosis, diabetes.
1/200 in North America.
Type 2a: Hemojuvelin mutation
Type 2b: Hepcidin mutation
Type 3: Transferrin receptor 2 mutation.
```
110
Factor V Leiden
Similar testing approach as to hereditary hemochromatosis. Mutation changes factor V - becomes resistant to inactivation by Protein C. --> Thrombophilia and venous thromboembolism.
5% prevalence Northern European descent. Increased risk of thromboembolism further aggravated by Oral contraceptives, pregnancy, and surgery.
PCR -RFLP assay for R506Q
Leiden mutation destroys second MnI restriction site (longer bp mutant allele)
111
Diseases for DNA based PCR type diagnosis
Hemochromatosis, Fragile X, CF, Sickle Cell, Hemophilia, Huntington's, Neurofibromatosis, Factor V Leiden.
112
BRCA mutations
BRCA1: 17q21
BRCA2: 13q12.3
Tumor suppressor genes, >200 mutations
If mutated 56% risk for breast cancer, 16% risk of ovarian cancer.
Test: Automated Sanger Sequencing. Chain termination dideoxynucleotide method
Labs moving to Next Gen sequencing*** works in a day: multiple, fragmented sequences. Look at multiple genes simultaneously.
113
BRCA 1/2
BRCA 1: breast and ovarian CA
| BRCA 2: breast CA
114
HNPCC (Lynch syndrome)
Exception to exception: Starts as a carcinoma. Young age of diagnosis, synchronous and metachronous tumours in RIGHT colon, also endometrial, ovarian, stomach, small bowel, ureter, and kidney tumours. Bethesda Criteria 2003
Microsatellite Instability (MSI) - short, rep DNA seqs in non-coding region. Change in lengths. Failure of Mismatch repair during DNA rep --> MSI.
Defects: MSH2, MLH1, MSH6, PMS2, EPCAM.
Immunocytochemistry stain for protein or DNA sequencing - no stain, possible mutation/methylation.
Confirm MSI by sequencing - before sequencing test for BRAF V600E mutation. NOT present in patients with germline mutation, and associated with promoter methylation of MLH1.
115
BRAF V600E mutation
Testing of this gene before sequencing to confirm MSI.
This mutation is NOT present in patients with germline MLH1 mutation. Is instead associated with promotor methylation of MLH1.
116
Gene Rearrangement Analysis
```
Use in B cell type testing ie LYMPHOMA. Basis for testing: unique antibody VDJ arrangements. Paraffin embedded tissues - DNA extraction - IGH gene rearrangement tests. Amplified DNA - if polyclonal , each lymph node has many variable sizes and get a SMEAR on the gel.
If MONOCLONAL (ie cancer), get a single band.
Similar tests for T cell receptors (TCRB)
```
117
Lymphoma
IGH Rearrangment, TCR Rearrangement. t(14,18) - (IGH-BCL2)
118
Acute Leukemia
```
M3 t(15,17) (PML-RARA)
M4E inv(16) (cbFB-MYH11)
```
119
Polycythemia Vera
JAK 2 mutation
120
Synovial Sarcoma Testing
RT-PCR. Ie RNA-->DNA--> amplification.
| SANGER or NGS (sequencing) of DNA or FISH can also detect these translocations.
121
Synovial Sarcoma
Tumours of adolescents&young adults. Two histologic types
Biphasic - Epithelial (cytokeratin) and Mesenchymal (vimentin) cells.
Monophasic - predominantly spindle cells.
t(X:18)
SYT from chromosome 18 to SSX1 or 2 or 4 on X.
SSX1 in biphasic, SSX2 in monophasic
Test: RT PCR, sanger or ngs, or FISH.
122
HER2 testing
Immunocytochemical and FISH analysis are standard
Antibodies CB11, TAB250, and A0485 for presence of HER2. Amplified in breast cancer.
HER2 on chromosome 17, FISH: Stain for centromere, should have two copies of chrom 17. Stain for HER mutation.
123
HER2(neu)
Human Epidermal growth factor receptor 2. Amplified in 25% of cancer
124
Urothelial Carcinoma Testing
FISH. High frequency of chromosomal abnormalities, aneuoploidy, rearrangement, deletion, amplification.
Urine with exfoliated cells readily available. FISH - fast and convenient.
Incl CEP 3, 7, 17 gains (too many chroms) -95% >4 cells with >2 gains
Or homo 9p21 deletion <5% of cases
125
Oligodendroglioma
50-80% are 1p and/or 19q deletions - respond better to chemo.
Mutations in IDH (isocitrate dehydrogenase) - common in grade II astrocytomas and oligodendrogliomas. Cause increased production of 2-hydroxyglutarate, interferes with enzymes that regulat egene expression.
Test use FISH***
126
Anti-EGFR antibody treatment
Can use in treatment of adenocarcinoma eg. However, test for kRAS mutation first - kRAS is downstream of EGFR signalling. If kRAS mutation, kRAS doesn't need EGFR signalling to work, it is constitutively active. kRAS mutations v common in CRC (Colorectal cancer) and other adenocarcinomas.
127
BRAF mutation
```
40-60% of melanomas have BRAF mutation. --> MAP kinase activation. V600E
Mutation = aggressive behaviour
In pathway: RAS ==> activate RAF.
Test by RT-PCR/sequencing
Targeted therapy directly to RAF.
```
128
Vemurafenib
Targets BRAF. Ie treatment for melanoma if V600E mutation. Neutralizing and shrinking tumour.
129
Non small cell lung cancers (NSCLC)
```
Ie SCC (Squamous cell carcinoma), adenocarcinoma, etc.
Mutations in EGFR, kRAS, and anaplastic lymphoma kinase (ALK) are mutually exclusive.
Fusion between EML4 and ALK (constitutive kinase activity) seen in 2-7% of cases.
```
130
Testing for ALK
Immunocytochemistry or FISH, with ALK break apart probes to detect rearrangements
131
NSCLC testing
First check for kRAS mutaion - if yes, not responsive to EGFR TKI. If no, Test for EGFR. If mutated, give EGFR TKI, if not, check for ALK mutation. If yes, give ALK inhibitor, If no, one of the many other mutations
132
CML
BCR ABL translocation t(9,22). Double fusion FISH, or RT-PCR
133
Gleevec
Inhibits BCR ABL tyrosine kinase. Also effective in treatment of GI stromal tumours
134
Mercaptopurine
Treatment for ALL (acute lymphoblastic leukemia). However, contraindicatd in patients with polymorphisms at TPMT-SNP, defective TPMT. TPMT responsible for metabolizing mercaptopruine to inactive metabolite MeMP. . tst for TPMT similar method to hemochromatosis. PCR or sequencing.
135
VNTR
Variable number tandem repeats. in Introns, repeated bps. 20-thousands. Southern blot - DNA fingerprint
136
Oncometabolites
Some oncoproteins (products of oncogenes), cause formation of high levels of abnormal metabolite, which leads to epigenetic changes and oncogenic gene expression. Eg. Mutated isocitrate dehydrogenase (IDH)
137
Inflammation/stroma as enabler of malignancy
Release of factors that promote proliferation by infiltrating leukocytes and activated stromal cells. Removal of growth suppressors (proteases), resistance to cell death (factors from tumor associated macrophages), angiogenesis (inflamm cells VEGF), invasion and metastasis (proteases remodel ECM, TGFB promotes epithelial-mesenchymal transition, key in invasion), evasion of immune destruction.
138
CD10 (CALLA)
Differentiation Antigen marker for B cell lymphomas.
