Gastrointestinal cancers

Question 1

Patients with colorectal carcinoma being considered for anti-EGFR therapy should be tested for. . .

Answer 1

hotspot mutations in all exons of KRAS and NRAS.

Question 2

Patients with GISTs being considered for treatment with TKIs should undergo mutational testing for mutations in. . .

Answer 2

. . . KIT as well as PDGFRA.

Question 3

Frequency of MSI in colorectal carcinoma

Answer 3

15% of cases

Question 4

Microsatellite testing by PCR

Answer 4

Traditionally, this is done by PCR using fluorescently labeled primers against select microsatellites.

Both tumor and normal DNA from the same patient are utilized, and MSI is assessed by comparing the results from normal and tumor specimens.

Microsatellite stable tumors are expected to show the same size between tumor and normal DNA in all microsatellite sequences, while MSI-H tumors are characterized by altered size in >40% of loci.

Question 5

MLH1 promoter methylation in colorectal carcinoma

Answer 5

The most common mechanism of microsatellite instability.

Its presence argues against the presence of Lynch syndrome, however rare cases of Lynch syndrome with somatic MLH1 promoter hypermethylation have been reported.

For this reason, follow-up MLH1 germline testing is recommended for patients with MLH1 promoter hypermethylation under age 60 and/or if the tumor does not harbor a BRAF mutation.

Question 6

Identification of MLH1 promoter hypermethylation

Answer 6

1. DNA is treated with bisulfite, which converts cytosine residues without methylation to uracil, but does not affect 5-methylcytosine.
2. The bisulfite can then be washed away and the sample sent for PCR or pyrosequencing, which will identify cytosine at 5-methylcytosine positions.

Question 7

Percentage of sporadic MSI-H CRCs which are BRAFV600E positive

Answer 7

50%

Question 8

PCR of the MLH1 promoter with methylated and unmethylated primers

Answer 8

Methylation status can be determined by which primer pair results in amplification.

Question 9

HER2 in gastric tumors

Answer 9

Seen in 15-20% of gastric adenocarcinomas, and is more common in intestinal-type rather than diffuse-type adenocarcinomas.

These tumors respond to trastuzumab.

Question 10

HER2 in colorectal adenocarcinomas

Answer 10

HER2 amplification is seen in about 3% of cases, while another 4-5% harbor hotspot mutations (including V777L and V824I).

Both HER2 amplified and HER2 mutant colorectal adenocarcinomas have been reported to show de novo and acquired resistance to EGFR inhibitors.

Question 11

Drivers in GIST (location within structure)

Answer 11

Question 12

KIT and PDGFRB are both. . .

Answer 12

RTKs of similar structure located on chromosome 4q12

Question 13

Most common PDGFRA mutation in GIST

Answer 13

D842V

Occurs in exon 18 (in the TK2 domain) and is associated with resistance to imatinib. However, the new PDGFRA inhibitor crenolanib can inhibit PDGFRA D842V in vitro and is currently in clinical trials.

Question 14

Less common molecular alterations in GISTs

Answer 14

6% show loss of function in NF1

5% show loss of function in one of the SDH genes

Both of these arem associated with poor response to imatinib.

Question 15

KIT/PDGFRA-negative GISTs

Answer 15

Accounts for about 15% of GISTs.

Half are SDH-deficient, usually ocurring in the stomach of children and young adults. Often have direct mutations in one of the SDH genes, most commonly SDHA.

Some are NF1 deficient. NF1 disruptiopn results in constitutive RAS activation. These tumors tend to arise in the small intestine, including the duodenum.

About 5% are BRAFV600E positive, and these have a prediliction for the small intestine, tend to arise in middle-aged females, and show a high mitotic rate.

Question 16

Carney triad

Answer 16

Caused by mutations in one of the SADH components or SDHC promoter hypermethylation.

Syndrome of multiple GISTs, pulmonary chondromas, and paragangliomas.

Of note, pulmonary chondromas are seen in SDHC promoter hypermethylation, but not so much in germline SDH mutations.

Question 17

Peutz-Jehger syndrome

Answer 17

STK11 mutation or large deletion.

STK11 is a negative regulator of the mTOR pathway.

STK11 dysregulation causes multiple hamartomatous polyps, pigmented cutaneous macules, and increased risk for multiple malignancies (breast, colorectal, gastric, pancreatic, lung).

Question 18

Juvenile polyposis syndrome

Answer 18

SMAD4 mutations OR BMPR1A mutations.

SMAD4 is a mediaqtor of TGF-b signaling, while BMPR1A is an RTK of the BMP family.

Mutation or large deletion in either gene causes hamartomatous polyps, increased risk of gastric and colorectal carcinoma.

Question 19

Cowden syndrome

Answer 19

PTEN mutation

Mutations or large deletions result in dysregulation of the PI3K/AKT pathway, resulting in hamartomatous polyps, ganglioneuromatous polyps, macrocephaly, mucocutaneous lesions (pigmented lips), and an increased risk of multiple cancers including breast, colon, and kidney.

Question 20

Hereditary mixed polyposis syndrome

Answer 20

Caused by mutations in GREM1

GREM1 is a secreted inhibitor of BMP signaling, similar to erythroferrone.

Large duplications including enhancer elements result in an increase in multiple types of colon polyp and increased overall risk of colorectal carcinoma.

Question 21

POLE and POLD1 mutations

Answer 21

Result in multiple adenomas and increased risk of colorectal carcinoma

Question 22

NTHL1 mutations

Answer 22

NTHL1 is a DNA glycosylase.

Result in multiple adenomas and increased risk of colorectal carcinoma

Question 23

Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS)

Answer 23

Syndrome characterized by >100 polyps in the gastric fundus and body as well as increased risk for gastric adenocarcinoma at an early age.

Caused by germline mutations in the 1B promoter of APC.

Question 24

Molecular drivers of solid pseudopapillary tumor/neoplasm

Answer 24

CTNNB1 mutations

Question 25

Molecular drivers of acinar cell carcinoma of the pancreas

Answer 25

CTNNB1 mutations
11p loss
BRAF rearrangements (most commonly SND1-BRAF)

Most commonly BRCA1, BRCA2, or ATM mutated, making it more susceptible to PARP inhibition.

Less commonly have mutations in classical PDAC genes, such as KRAS, SMAD4, TP53, CDKN2A.