New Diagnostic Assays in the Works to Test for TRK Fusions

Josh Bilenker, MD

Oncogenic fusions involving TRK proteins have been implicated in various cancer types, prompting clinical development of therapies targeting the aberrations across histologies rather than their body site of origin. This “tumor-agnostic” development approach includes research into next-generation sequencing (NGS) and immunohistochemistry (IHC) assays for the detection of TRK fusions.

There are 3 tropomyosin receptor kinases, TRK A, TRK B, and TRK C; they are encoded by the NTRK1, NTRK2, and NTRK3, genes, respectively. TRK proteins conduct signaling pathways that play a key role in the development of the central and peripheral nervous systems. Although carcinogenic fusion events involving the TRK kinases are rare, they occur in diverse histologies in both adult and pediatric cancers (Figure).¹

Figure. TRK Fusions Found In Diverse Cancer Histologies

Larotrectinib (LOXO-101), a novel small molecule, is the most advanced selective pan-TRK inhibitor in development.¹ Updated results demonstrate an 80% response rate by investigator assessment (95% CI, 67%-90%), including 16% complete responses, among 55 evaluable adult and pediatric patients with 17 unique cancer types who were treated with larotrectinib in 1 of 3 phase I/II clinical trials.2 The findings will support a new drug application that Loxo Oncology, which is developing the drug, plans to file with the FDA later this year or early in 2018. Currently, there are 3 modalities for testing for oncogenic mutations or amplifications that have varying potential for use as diagnostics in the TRK space: fluorescence in situ hybridization (FISH), IHC, and NGS.

“Gene fusion events in general are best found by looking at a tissue biopsy; it could be a tumor resection specimen, or a biopsy of a tumor or tumor-involved lymph node, but you need the primary tumor tissue,” said Josh Bilenker, MD, CEO of Loxo Oncology, in an interview with OncologyLive^®.

FISH testing has been a commonly used method of detecting gene fusions but has limited potential when searching for TRK fusions, Bilenker said. This is because FISH testing looks for 2 genes that should be next to each other but are not; however, with TRK fusions there are 3 genes to look for on 3 chromosomes. Therefore, a lab would have to run 3 separate tests. Additionally, FISH is a relatively subjective testing method that requires interpretation and an experienced pathologist to produce an accurate result.

NGS testing, on the other hand, offers a comprehensive approach for identifying any actionable gene amplifications, mutations, or fusions—including TRK fusions—in a definitive readout. NGS will also test for many other genes in the tumor sample at the same time, and may identify a different therapeutic option.

Loxo Oncology recommends that oncologists choose a testing instrument from a list of 9 assays that analyze samples for various numbers of genes ranging from 20 to nearly 1400.3 Samples for multigene panels can either be tested in pathologists’ laboratories or sent out to the other companies. “It allows more laboratories to do the work themselves; 3 or 4 years ago, you had to be really specialized and invent your own panel, and only the largest institutions could do that,” Bilenker said. “Now you can order the same test for every patient, and you may find a TRK fusion, or you may find another mutation or amplification you may want to treat on, and all these TRK fusions add up to something meaningful and actionable. If you haven’t found anything actionable, at least you know you’ve turned over the stone and looked.”

According to Bilenker, historical disadvantages with NGS have included the cost of the test and a lack of regulation and standardization. He noted that these downsides have been alleviated over time, as the cost of NGS panels has been lowered from as much $5000 per test to less than $1000, and the FDA is now reviewing the tests regularly. Additionally, NGS has not included testing for TRK fusions in a sensitive manner, but that is also being corrected, Bilenker said, especially in light of the recent clinical data for larotrectinib.

IHC also represents a promising option to test for TRK fusions with a staining method. Loxo Oncology is partnering with Ventana Medical Systems, a member of the Roche Group, to develop a pan-TRK fusion IHC test as a companion diagnostic for larotrectinib. IHC testing has the advantage of being a less expensive test that is mostly reimbursed by insurance companies, and any laboratory has the capability of conducting the test. Additionally, some laboratories feel more comfortable running a series of IHC tests rather than using NGS, as they may want to see the technology and reimbursement process evolve.

The disadvantage in using IHC testing is that laboratories can only run 1 test at a time. “You’re only asking 1 question at a time with IHC, and there’s only so many questions you can ask that way before running out of tissue,” Bilenker said. Two testing methods are being blended to identify TRK fusions for entrectinib (RXDX-101), a selective inhibitor for all 3 TRK proteins that also targets the ROS1 and ALK receptor tyrosine kinases. Ignyta, the company that is developing entrectinib, offers the Trailblaze Pharos Diagnostic Suite, which uses IHC to measure protein expression levels for NTRK1, NTRK2, NTRK3, ROS1, and ALK and NGS to confirm a gene rearrangement of interest.⁴

In May 2017, the FDA granted a breakthrough therapy designation for entrectinib in NTRK fusion-positive locally advanced or metastatic solid tumors. The phase II STARTRK-2 basket trial (NCT02568267) is evaluating entrectinib in adult patients with solid tumors that tests positive for NTRK, ROS1, or ALK fusions.

References

1. Hyman DM, Laetsch TW, Kummar S, et al. The efficacy of larotrectinib (LOXO-101), a selective tropomyosin receptor kinase (TRK) inhibitor, in adult and pediatric TRK fusion cancers. J Clin Oncol. (suppl 36; abstr LBA2501). meetinglibrary.asco.org/ record/144598/abstract.
2. Loxo Oncology announces positive top-line results from independent review committee assessment of larotrectinib dataset [press release]. Stamford, CT: Loxo Oncology; October 18, 2017. ir.loxooncology.com/press-releases/loxo-oncology-announces-positive-top-line-results-from-independent-review-committee-assessment-of-larotrectinib-dataset. Accessed October 21, 2017.
3. How to test for TRK fusions. Loxo Oncology website. trktesting. com/HowToTest.pdf. Accessed October 21, 2017.
4. Dx—Ignyta Trailblaze molecular diagnostic testing. Ignyta website. ignyta.com/providers/dx-molecular-diagnostic-cancer-testing/. Accessed October 22, 2017.