Biomarkers Flashcards
Carcinoma general biomarkers
Broad spectrum cytokeratin (CK)
AE1/AE3 (broad)
MNF116
Cam 5.2 (LMWCK only)
Lymphoma general biomarkers
CD45
B-Cell lymphoma general biomarkers
CD19
CD20
CD79a
PAX5
T-cell Lymphoma general biomarkers
CD2
CD3
CD43
Melanoma general biomarkers
SOX-10
Melan-A
S-100
HMB-45
Sarcoma general biomarkers
CD34
MDM2
Really depends on the specific sarcoma
Mesothelioma general biomarkers
Calretinin
WT1
CK5/6
D2-40
Usually CK7+/CK20- like lung adenocarcinoma
Neuroendocrine general biomarkers
Chromogranin
Synaptophysin
CD56
INSM1 - newer marker, potentially to most sensitive/specific of all these markers
Germ cell tumour general biomarkers
SALL4 (pan germ cell marker)
OCT4 (very sensitive and specific for seminoma and embryonal carcinoma)
SF1 is very sensitive and specific for sex cord stromal tumours.
Adrenocortical tumour
SF1
Inhibin
Synaptophysin
Melanoma A
Typically negative on AE1/AE3 and other broad spectrum CK tests
CK7+/CK20+ differentials
Urothelial
Peridiaphragmatic Gastrointestinal (gastric, pancreatic, biliary ie cholangiocarcinoma)
Note:gastric is almost equally distributed between all CK20/7 profiles
Others: mucinous ovary, mucinous lung
CK7+/CK20- differentials
Above diaphragm:
Lung (adeno, small cell)
Breast
Salivary glands
Thyroid
Female GYN: Ovary (serous), uterus
Others: mesothelioma, renal (papillary), gastric/pancreatic/gallbladder (more often also CK20+)
CK7-/CK20+ differentials
Colorectal
Merkel cell
Others: gastric (more often also CK7+)
CK7-/CK20-
Simple visceral epithelium
Prostate
Liver (hepatocellular)
Kidney (renal clear cell)
Neuroendocrine cells
Others: adrenocortical, lung small cell, germ cell non-seminomatous, gastric
What type of epithelial tissue is generally associated with CK7
Glandular epithelium.
But also squamous epithelium of H+N, cervix
What type of epithelial tissue is generally associated with CK20
Epithelium of lower GI ready, umbrella cells of urothelium, Merkel cells
Are cytoplasmic/membranous or nuclear transcription factors more specific in undifferentiated adenocarcinomas?
Nuclear transcription factors.
-Protein correlates of genetic events
Cytoplasmic/membranous marker expression usually not additive to nuclear marker expression
What adenocarcinoma nuclear markers are commonly associated with
-breast
-lung
-gastrointestinal
-renal
-prostate
-thyroid
Breast: GATA3
Lung: TTF1, Napsin A
Thyroid: TTF1, PAX8
Gastrointestinal: CDX2, SATB2
Renal: PAX8
Prostate: NKX3-1, ERG
What cancers are positive for TTF1? What rates of positivity
Lung adenocarcinoma (70-100%)
Thyroid (80-100%)
Lung squamous (<10%)
Biliary (5-25%)
Ovarian (5-30%)
Endometrial (5-20%)
Breast, pancreatic, colorectal (<5%)
What cancers are positive for GATA3? What rates of positivity?
Breast (92-100%)
Urothelial (80-90%)
Skin squamous (80%)
Lung (5-10%)
Mesothelioma (25-60%)
What cancers are positive for CDX2
Colorectal (>90%) (CK7-/CK20+)
Oesophogogastric/pancreatobiliary (40-60%) (CK7+ CK20+/-)
Mucinous ovarian (40-60%)
Mucinous lung (70-80%)
What two markers are used to distinguish lung adenocarcinoma from SqCC. What is the nomenclature if both are negative or both positive?
TTF1 - adenocarcinoma
P40 - SqCC
TTF1-/p40- non small cell carcinoma NOS
TTF1+/p40+ non small cell carcinoma with adenocarcinoma and squamous differentiation
What markers are used first line to distinguish lung adenocarcinoma from mesothelioma (2 from each)
Adenocarcinoma: TTF-1, Claudin-4, napsin A
Mesothelioma: Calretinin, WT-1, CK5/6, D2-40
What are the TCGA molecular subtypes of breast cancer
Luminal A: ER strong positive, HER2 neg, Ki-67 low. good prognosis
Luminal B: ER weak positive, HER2 +/-, Ki-67 higher. Intermediate prognosis
HER2: ER/PR +/-, HER2 positive. Poor prognosis
Basal: triple negative. Poor prognosis
What is the Allred score
oestrogen/progesterone receptor score. Scores percentage positive and intensity of positivity
What is the process for testing of HER2 status
IHC first. Score 0-3
Score 0-1: negative
2: equivocal, requires FISH (or D-ISH)
3: positive, does not require FISH confirmation
What are the four proteins tested for with IHC to check for MMR deficiency in colorectal cancer
MLH1, MSH2, MSH6, PMS2
What malignancies are associated with BRAF600E mutation
Melanoma
Colorectal carcinoma
Papillary thyroid carcinoma
NSCLC
Hairy cell leukaemia
Langerhans cell histiocytosis
What are the 4 key prognostic and predictive bio markers in endometrial carcinoma
POLE mutation (molecular testing): excellent prognosis
MSI-H mutation (MSI) (IHC or molecular): intermediate prognosis
TP53 mutation (IHC or molecular): poor prognosis
No specific molecular profile (NSMP): intermediate prognosis
What is MSI and how does it relate to dMMR?
Microsatellite instability is a genetic result of deficient mismatch repair. Tandem repeats of nucleotides throughout the genome become variable in length as opposed to being very constant where mismatch repair is normal.
Ie, dMMR can be tested by:
-IHC testing for abnormal levels of key mmr proteins
-molecular testing to detect downstream MSI
What is Lynch syndrome
Also known as hereditary non polyposis colon cancer (HNPCC)
Inherited deficiency in one of the MMR proteins. Most commonly MSH2 and MLH1
What is the most common mechanism of sporadic dMMR
Epigenetic silencing of MLH1 (MLH1 promoter methylation)
Ie, not mutation of the gene
What are the four molecular subtypes of gastric adenocarcinoma?
CIN: chromosome instability (assossiated with H pylori): most common. Intermediate prognosis. Frequent TP53 mutations
Micro satellite instability (MSI): intermediate prognosis
EBV virus associated: intermediate to excellent prognosis. Often have PD-L1 over expression
GS: genetically stable. Poor prognosis. Predominantly signet ring morphology, CDH1 mutation (e cadherin)
What are the key mutations/ abnormalities in melanoma affecting targeted therapy options?
PD-L1 (pembro)
BRAF (Vemurafenib)
NRAS (resistance to vemurafenib, ?MEK inhibitors)
KIT mutation (Imatinib)
What IHC tests can be used to distinguish site of origin for WELL DIFFERENTIATED neuroendocrine tumours?
TTF1+: lung
CDX2+: midgut/small bowel
PR/pPAX8+/SATB2-: pancreas
SATB2+/TTF-: rectum or appendix
IL1: pancreas or rectum
Define diagnostic biomarker
A marker used to help diagnose a cancer including subtyping
Define prognostic factor
A factor which forecasts how aggressive a cancer is. Ie determines the patients ability to fare in the absence of treatment
Define predictive factor
A factor which predicts how well a cancer will respond to a certain treatment
What is IHC and how does it work
Immunohistochemistry. Uses immune markers to detect protein surrogates for gene mutations. (1 protein surrogate per gene)
What is FISH and how does it work
Fluorescent in situation hybridisation. Fluorescent markers attach directly to abnormal gene. There are methods other than fluorescence
What is PCR, how does it work
Polymerase chain reaction. Can be used to detect multiple mutated genes in one test. (1-3)
What is NGS and how does it work?
Next generation sequencing. Massive parallel sequencing that tests for many mutation in one panel
What are some markers of smooth muscle
Desmin
Smooth muscle actin
Muscle specific actin
What are AE1/AE3 and Cam 5.2 testing
Both are antibody cocktails that broadly test for CK positivity, aiming to check if a poorly differentiated malignancy is a carcinoma.
What is the best bio marker to distinguish lung adenocarcinoma from mesothelioma
Claudin 4 (negative in mesothelioma.)
What are the most useful IHC tests for prostate cancer
PSA (cytoplasmic): high sensitivity and specificity
NKX3.1 (nuclear)
What IHC tests can be used to attempt to distinguish colorectal from bladder adenocarcinoma
B-catenin: nuclear in colorectal, cytoplasmic (normal) in bladder
CDX2, SATB2: positive colorectal. Variable bladder
CK20: positive colorectal, variable bladder.
Ie b-catenin is most useful.
What is the usual CK7/CK20 profile of urothelial carcinoma
Both positive
What IHC profiles can be used to distinguish the different forms of thyroid cancer
TTF1: follicular/papillary/medullary
Thyroglobulin: follicular/papillary
PAX8: follicular/papillary, others variable
AE1/AE3 or Cam5.2: all generally positive
PTH/GATA3: parathyroid
Neuroendocrine markers: medullary, parathyroid
What is the typical immune profile of pancreatic adenocarcinoma
CK7/CK20+
CA19-9+
CEA+
Loss of expression of SMAD4
What is the typical IHC profile of small cell lung carcinoma. How does this compare to carcinoid tumours
TTF1 positive
Synaptophysin, chromogranin, ISNM1, CD56 frequently only weak focal positivity
Ki67 very high %
Carcinoid have strongly positive neuroendocrine markers, very low Ki67 and TTF1 can be positive or negative
What should be tested to attempt to differentiate mesothelioma from reactive mesothelial proliferation
BAP1 IHC: loss of expression consistent with mesothelioma
p16/CDKN2A/9p21 FISH: loss of 9p21 locus consistent with mesothelioma.
Note that this testing is 100% sensitive, but does not rule out mesothelioma if both are retained
What cancers are positive for PAX8
Thymoma/thymic carcinoma
Renal
Thyroid
Mullerian (endometrial, endocervical, ovarian)
What will happen to B-catenin staining when there is loss of e-cadherin
Membrane staining will be lost (as it is not being held at the cell membrane by e cadherin
What are potential patterns of abnormal p53 IHC staining
Over expression (due to defective p53 being over expressed as negative feedback doesn’t happen)
Negative (mutation decreases p53 production)
Normal expression (no abnormality, so there will be some staining of normal p53)
Inva
What is the main relevance of vimentin
Classical thought to distinguish sarcoma from carcinoma, but now recognised that is is positive in many carcinomas, so it is no longer used routinely.
Main use is to check if tumour is viable for immune staining when everything else is coming up negative
What is the specificity of CEA IHC
Not very specific except:
HCC: canalicular staining with pCEA.
Are Neuroendocrine tumours CK positive, and what is the usual pattern
Positive: Epithelial origin NETs. Eg, carcinoids, small cell lung ca, Merkel. staining very variable, can be difficult to see due to scanty cytoplasm of small cell carcinomas. Dot-like pattern cytoplasm staining, likely due to clumping of CKs.
Negative: pheo, paraganglioma, neuroblastoma
What staining pattern indicates p16 IHC positivity
Must be block-like strong nuclear and cytoplasmic staining.
Patchy or weak staining is negative
What IHC markers are associated with endothelial/vascular origin tumours
ERG
CD34
CD31
What are tumours common,y associated with c-kit mutation
GIST
Seminoma
Melanoma (mucosal)
Thymic carcinoma
Some salivary neoplasms
