Testing for Gene Alterations and Protein Expression in Advanced NSCLC

Mark A. Socinski, MD: In non–small cell lung cancer (NSCLC), we have several DNA alterations. Some are mutations, and some are gene rearrangements or fusions with a chromosomal rearrangement that creates a driver fusion. We also have amplifications in certain situations that are potentially important, so the testing platform needs to have the ability to detect all sorts of alterations, because it's not simply one. In some instances, as in ALK disease, there is an accepted immunohistochemical, or IHC, test. Again, that is looking at protein expression, not DNA or RNA expression. In understanding the heterogeneity of what you're looking for in different situations, mutations are different than fusions, and protein expression is different than either DNA or RNA alteration. Techniques such as PCR [polymerase chain reaction] or FISH [fluorescence in situ hybridization] are different than next-generation sequencing for these sorts of things. In my practice, my standard of care is a next-generation sequencing platform that does both DNA and RNA analysis to maximize the detection of these alterations, hopefully at the time of initial diagnosis.

Stephen Liu, MD: When you think of what tests to use to detect these fusions, it's important to be familiar with the process. There are a few different ways to identify gene fusions or chromosomal rearrangements, which refer to the same thing. In the past, we have relied on the process called FISH, which is a bit labor-intensive and involves visually identifying an abnormal spatial relationship between 2 areas in the gene. There are a few of these assays that are FDA approved, but they have imperfect sensitivity. We can also look at protein expression. For example, ALK IHC is approved by the FDA as a rapid, fairly straightforward test to detect an actionable ALK alteration. Immunohistochemistry is a bit less validated for others, like ROS1 or NTRK, where positive IHC results probably need to be confirmed with next-generation sequencing. In general, I strongly recommend multiplex testing and the use of next-generation sequencing for all patients. We're well past the tipping point where this is cost-effective. It provides more efficient use of the tissue at hand and a better use of time. If we're using all of these tests up front, we're much less likely to run out of sample before we perform all of the necessary tests. There are several studies that now show it's more cost-efficient to order multiplex testing upfront. It saves time, and, overall, it is just a better test. Many commercial platforms of next-generation sequencing are DNA-based. Some are RNA-based, and there is a potential advantage to using RNA sequencing for some targets, particularly those with large introns or complex events (eg, NTRK, NRG1, ROS1). RNA sequencing has a better sensitivity. It's important that we understand the tests we're ordering, because the stakes are quite high. If we miss one of these drivers, not only do we deprive a patient of a highly effective, tolerable treatment, but we send them down the route of immunotherapy, which will be ineffective and will make subsequent targeted therapy much more dangerous. When a biomarker is present, it opens a whole catalog of different treatment options. It's important we don't deprive patients of that benefit. The most important part of treating advanced NSCLC is proper upfront biomarker testing. I can't stress how important it is to do full comprehensive genomic testing with next-generation sequencing, ideally with RNA-based sequencing, because it is so important for planning therapy. If a driver ulceration is undetected, not only are we going to deprive someone of an effective targeted drug, but we're going to go down the route of immunotherapy, which is ineffective and which makes subsequent targeted therapy much more dangerous. An important tenet of treating lung cancer is identifying what those alterations are up front, right at the beginning. And we're not nearly as good as we think. When we look at results from the Molecularly Informed Lung Cancer Treatment in a Community Cancer Network: A Pragmatic Consortium (MYLUNG) data that was presented at [the 2021 American Society of Clinical Oncology meeting], we find a low bar of EFGR, ALK, ROS1, BRAF, and PD-L1. These 5 markers are established and are straightforward. We have known about them for years, and we have approved agents available to us on the shelf to target them. With that low bar of 5 targets, how often are patients with advanced lung cancer getting tested? In a strong robust clinical network, like the US Oncology Network, it was less than half. That is a low bar using a test like EGFR, which is pretty straightforward. EGFR is a marker that we've known about for coming on 2 decades, yet 1 in 5 patients are not getting tested for it. As good as we are at testing, as aware as we think we are, we are missing patients. And if we're missing patients, that means we are not treating them appropriately. There’s a lot of room for improvement. We can certainly do a lot better.

Benjamin Levy, MD: Gene rearrangements are an important genomic driver in NSCLC, specifically adenocarcinoma. There are now approved therapies for ALK rearrangements, RET rearrangements, ROS rearrangements, and NTRK rearrangements. It’s important that we test for these fusions in our patient population. There are probably best platforms or best next-generation sequencing platforms to do this. By using both DNA and RNA, by leveraging DNA and RNA next-generation sequencing platforms, we’re better able to identify these fusions. And with that said, every patient who walks through the door in my office with an advanced adenocarcinoma of the lung gets tested for these gene rearrangement fusions. This is part of a larger panel that we do. ALK, ROS, RET, and NTRK are rarer than other types of mutations, like KRAS G12C or EGFR, but they are actionable. They are seen in lung cancer. At the very minimum, patients are tested up front, before we decide on a particular therapy. The question then becomes, “When patients develop disease progression, what do we do?” It is important to test for mechanisms of resistance for patients with these fusions who receive targeted therapy, because we’re learning more and more about novel therapies and testing novel therapies that may target these mechanisms of resistance. We may look at something like an ALK fusion. You can target these fusions with therapies, but there are mutations that occur as a consequence of resistance, and some of these mutations may be targeted with other therapies. And this is the way we’re heading. At the very minimum, I encourage testing upfront for these fusions, specifically with a DNA- and RNA-based platform approach, and then again at the time of resistance to identify these mutations. We may then try to leverage either standard-of-care therapies or therapies that are being tested in clinical trials against these mechanisms of resistance.

Stephen Liu, MD: Genomic testing extends beyond the frontline setting. When we think of testing, we're trying to inform our treatment. Cancers continue to evolve, but they don't always evolve in the same way. When we identify a genomic driver up front and then start a targeted therapy, we're putting a selective pressure on that tumor. And these tumors will continue to evolve when the cancer progresses. If we can better understand that progression, then perhaps we can better plan our next lines of therapy and add other targeted agents if we see specific actionable alterations. But these biopsies will also reveal histologic transformation. We would estimate about 15% will have transformation, either small cell or squamous cell, and that would certainly influence what we do next. Understanding how drugs stop working and how cancers evolve is just as important. If a genomic driver is present at the beginning, we start a targeted agent. When the cancer progresses, repeating a biopsy and biomarker testing is critical to the optimal management for that patient.

Transcript edited for clarity.