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Expert Speaks on Importance of Genetic Testing in GI Cancers

Angelica Welch
Published Online:3:01 PM, Thu August 24, 2017

Antonia Sepulveda, MD, PhD
The recently released guidelines are going to serve as the foundation for molecular testing for all gastrointestinal (GI) cancers, says Antonia R. Sepulveda, MD, PhD.

In an interview at the PER® 1st Annual International Congress on Oncology Pathology™, Sepulveda, a professor of pathology and cell biology and vice chair for translational research at Columbia University, discussed the importance and utility of genetic testing in GI cancers, as well as noteworthy developments in microsatellite instability (MSI), BRAF, and KRAS testing in colorectal cancer (CRC).

TARGETED ONCOLOGY:  Can you please discuss the guidelines for biomarker testing in GI cancers?

Sepulveda: There were 2 main guidelines released recently for gastroesophageal cancer testing as well as for CRC biomarker testing. Guidelines currently exist for gastric and esophageal adenocarcinoma, and patients who have advanced or metastatic CRC that may benefit from trastuzumab (Herceptin). In those patients, we should test for HER2 expression, which is done by immunohistochemistry and in some cases—particularly in patients who have a score of 2+ by immunohistochemistry—we should also perform a test to determine whether there is amplification of HER2 using FISH or other hybridization methods. 

In addition, a more broad and comprehensive guideline was published for CRC molecular testing recently. The guideline included 21 recommendations and addresses which biomarkers should be tested for patients who are being considered for anti-EGFR monoclonal antibody therapy. Among those tests, one must test for RAS mutations, which include the extended RAS testing, including mutations in the genes KRAS and NRAS. In addition, other assays, such as MSI, DNA mismatch repair, are also recommended for testing in these guidelines. 

The guidelines also provide a lot of guidance in terms of which tissues should be tested and which assays should be used…There are a number of other aspects of laboratory testing management, as well.

TARGETED ONCOLOGY:  Which patients should receive MSI testing?

Sepulveda: It is a little different for CRC than other GI cancers. CRC is the main cancer that patients who have Lynch syndrome—hereditary nonpolyposis CRC—present in the GI tract. There is a recommendation for testing all patients who present with CRC for DNA mismatch repair deficiency and/or its surrogate marker, MSI. This is called universal testing and it is being recommended in order to identify and help make the diagnosis for those patients who may have Lynch syndrome.

Now, for other tumors of the GI tract—gastric cancer, and esophageal cancer—guidelines have not really been established as to which patients should be tested. However, it is known that up to one-fourth of gastric cancer worldwide may actually be considered MSI-positive, while esophageal cancer tends to be less frequently MSI-positive. 

At this point, those tests in gastric and esophageal cancer should be considered and performed when the patients are being considered for PD-1 blockade immunotherapy, which is considering very recent data that has been published.

TARGETED ONCOLOGY:  When should patients with CRC receive testing?

Sepulveda: When testing, one cannot utilize diagnostic biopsy material or the resection specimen or metastatic or recurrent tissue, which usually tends to be obtained through biopsy or fine needle aspiration. Therefore, we will have less material available for testing. 

For CRC in particular, the guidelines state that testing recurrent or metastatic CRC tissue is preferable, however, if that is not available, we can use the data from primary tumor tissue, either as the diagnostic biopsy, or the resection material, because there is very good correlation in terms of mutational state. That being said, heterogeneity in CRC and other cancers is well known, so, whenever possible, having the results from the metastatic lesion would be preferable. I would also add that, while that is true, considering that we are doing DNA mismatch repair and MSI testing in CRC upfront in a universal fashion, the mutational panels provide all of the information in the genes of interest—particularly RAS gene mutations and BRAF mutations.

I would say that the way in which testing gets done is very institution-specific. And generally, there will be a workflow that is established in that specific institution. In my institution, for example, for every patient diagnosed with CRC for whom we have a biopsy material, we do reflex testing for all these assays from the biopsy material because by the time the patient is being reviewed by the oncology [department] for consideration of treatment plans, all of that information will be available. It really helps turnaround time to do upfront testing, and when feasible, it might be preferable. 

TARGETED ONCOLOGY:  Can you discuss the prevalence of MSI in CRC versus gastric cancer?

Sepulveda: For CRC, it is very well established that MSI occurs in about 15% of all patients, including those who have Lynch syndrome, which represent less than 5% overall. Out of the cases that are MSI-H, most of these are actually secondary to loss of MLH1, not due to germline mutation. So, it is going to be the other 5% that will carry mutations in either MSH2, MLH1, and in a very small number of cases, patients who carry inherited mutations in PMS2 and MSH6

We are also learning from TCGA studies that mutations in other genes also affect DNA repair and can lead to hypermutability in the tumor. This is a field that is in evolution in identifying a hypermutable tumor, maybe something that will require tests in addition to the MSI testing, per say. So, doing tests like tumor mutational burden for example.

TARGETED ONCOLOGY:  Which MSI test is the most accurate?

Sepulveda: In choosing which tests to perform for deficient mismatch repair, the 2 tests available—immunohistochemistry and the DNA PCR-based MSI test—actually are complementary. Both tests may have false negatives in less than 5% of the cases, so it is relatively infrequent. But, whenever possible, performing both tests would be very useful because the we cover those possibilities. For example, some tumors that carry mutations in MLH1 are still recognized by the antibodies. So, immunohistochemistry may tell us that the protein is still present, and we would not call that tumor DNA mismatch repair deficient. Yet, when we do the MSI test, the tumor shows MSI. I think that, whenever possible, running the 2 tests provides the best result for the patient.

TARGETED ONCOLOGY:  Are there any noteworthy developments in KRAS testing in GI cancers?

Sepulveda: KRAS testing was the first recommended testing for CRC patients who are candidates for anti-EGFR monoclonal antibody therapy. And initially, the assays were focused on testing KRAS EXON 2 codons 12 and 13 mutations only. More recently, larger studies were done where other EXONs of KRAS, including 3 and 4, were sequenced to determine whether they were mutated, and a similar mutational testing was done in NRAS

Now we know that when we test for KRAS and NRAS EXONs 2, 3, and 4, we can find activating mutations in either of these genes. Although, they are still more frequent overall in KRAS in CRC than in NRAS. This lead to the concept of recommending testing for the extended panel of RAS mutations for all patients with CRC who are being considered for anti-EGFR therapies. 

In other tumors of the GI tract, KRAS is not as frequently mutated. It might be activated through other mechanisms, but mutations are infrequent, for example, in gastric and esophageal adenocarcinoma.  

TARGETED ONCOLOGY:  Can you discuss BRAF testing?

Sepulveda: BRAF is less frequently mutated in CRC and other GI cancers. Focusing on CRC where we know about the role of BRAF, less then 10% of tumors actually carry a BRAF mutation. BRAF is more frequent in tumors that are MSI-positive, due to loss of MLH1 expression, in which case BRAF is located in half to two-thirds of the tumors. But there are still going to be tumors that are MLH1-negative that are not mutated in BRAF

Looking for BRAF mutations, which is a hotspot affecting the V600 mutational spot, can actually help us determine whether a patient is likely to have MSI-sporadic tumor, versus a tumor that is Lynch syndrome. Mutation in BRAF suggests that a tumor is sporadic type. 

BRAF has other implications. A mutant tumor, especially those that are microsatellite stable, tends to have very poor prognosis, so those patients may require different therapies. So, as a marker of prognosis, BRAF can guide the use of combination therapies. 

TARGETED ONCOLOGY:  Are laboratories having a hard time getting insurers to reimburse for genetic testing?

Sepulveda: The reimbursement fees for all of this testing is in evolution. We are somewhat all over the map, and it is a major need to have this well-established—especially for the gene panels. Guidelines point to the importance of utilizing gene panels, yet the reimbursement seems to be lagging behind. So, that is an area where there is a gap, and in order to help propel the field in the right direction—to help guide therapies with the right test data—that will need to be in place, and it is desperately needed.

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