molecular testing in the diagnosis of cancer - lecture notes - julia

Question 1

how would you use molecular testing to track lymphoma?

Answer 1

• lymphoma (and many other cancers) develops in very distinct steps
• the process can arrest at any one of those steps
• use whatever segments are identified at that time as a biomarker for the cancer cells
• use southern blots or PCR or capillary electrophoresis to look for these segments
• can use this info to screen blood or bone marrow to track disease

Question 2

how is HPV testing used in treating head and neck cancers? how is the test done?

Answer 2

• recently, HPV has been related to head and neck cancers
• take parafin embedded tissue
• do a PCR and look for band where you’d find HPV
• take that band and apply it to a strip with probes on it for the different HPV types
• whereever the DNA from the PCR binds, get colored band - tells you what type of HPV it is
• all patients with head and neck cancer under age 55 get this testing - not diagnostic of head and neck cancer, but in those who have the cancer and have HPV, response to therapy is much better - good prognostic indicator of the disease

Question 3

how is CML diagnosed on a molecular basis?

Answer 3

• use quantitative PCR to detect BCR/ABL transcript
• diagnosis can be made an hour or two after the sample is received

Question 4

why are many of the major drugs ineffective (according to this guy)?

Answer 4

• because we all metabolize things at different rates
• to treat properly, we must use pharmacogenetics to determine whos a poor or good metabolizer of the drugs were perscribing

Question 5

what is irinotecan? what type of pharmacogenomics is it representative of?

Answer 5

• topoisomerase inhibitor
• given to patients with colon cancer
• example of metabolic pharmacogenomics
• normal metabolism of the drug:
• orally taken
• metabolized into active metabolite SN-38
• after a while, SN-38 gets inactivated by UGT1A1 enzyme
• once inactivated, excreted
• about 6-10% of people have bery bad responses - get myelotxicity, diarrhea to point of dehydration
• because of an additional repeat in the UGT1A1 gene - don’t break down the drug
• if your patient is one of these people, you would use a different drug or reduce the dose appropriately
• best to screen patients before treatment to avoid side effects

Question 6

what are two examples of targeted pharmacogenoic therapies?

Answer 6

• tamoxifen - targets estrogen receptors in breast cancer - test patient’s tissue first to see if they have high levels of estrogen receptor
• herceptin is a the first monoclonal antibody therapy to be used in a human cancer - targets the her2 gene
• every new breast cancer case that comes into DHMC is automatically tested for both HER2 and estrogen receptor expression levels

Question 7

how is her2 involved in cancer?

Answer 7

• 35% of breast cancers have multiple copies of the her2 gene
• this results in overexpression of the receptor that the gene codes for
• this receptor is linked to signal transduction pathway that causes the cells to replicate

Question 8

how is egfr involved in cancer? how can it be targeted in therapy?

Answer 8

• egf receptor on cell surface
• when ligand binds, turns on tyrosine kinase activity on the inside of the molecule
• this activates signal transduction pathway that sends signals into nucleus of the cell with instructions to replicate
• cells start growing abnormally
• can treat by blocking this receptor or the tyrosine kinase activity of the receptor inside cell
• drugs targeting egfr will only work in patients with certain mutations

Question 9

what are some common mutations in the EGFR? what are the consequences of these?

Answer 9

• 42% are in-frame deletions in exon 19
• 46% are substitutions in exon 21
• can sequence entire gene in patients with cancer to look for these and treat accordingly
• activating mutation confer susceptibility to small molecule TKI’s in NSCLC (non-small cell lung cancer)

Question 10

what are KRAS activating mutations? what cancer are they involved in?

Answer 10

• found in 30-50% of CRCa’s
• associated with smoking in NSCLC (non small cell lung cancer)
• mutation occurs most often in codons 12 and 13
• missense mutations
• 7 common mutations account for at least 95% of all identified mutations
• pgfr is a receptor involved in growth signals - activating mutation => increased growth