Luis, Dr Raez, let me let you take the lead on this in terms of the mechanics of testing. We’ve all hinted at it—some do it internally, some are sending it out. Can you give us a sense of how one can get 

We have several options, as somebody else mentioned. I think it was Jyoti. For example, we can do RT-PCR [reverse transcription polymerase chain reaction]. We can do RT-PCR to find the fusions. We can do FISH [fluorescence in situ hybridization] testing to find the fusions. We can do DNA sequencing, and lately we’re doing RNA sequencing. So now we have 4 options. How we deal with this, and what is the best approach? It actually depends. ESMO [European Society for Medical Oncology] has a recommendation published last year about this, but these are common sense.

For example, if this is a tumor that is very uncommon—lung cancer, colon cancer, breast cancer—they have a very low prevalence of 

 fusions. The best thing we can do is to do the whole sequence, the whole DNA sequence. We also have discovered in the last 3 or 4 years doing that for 

 that the DNA sequence may not be as complete or comprehensive as the transcriptome sequencing, the RNA sequencing.

That’s why we have platforms at our center that run both, the DNA sequencing and then the RNA sequencing, to touch any possibility or any fusion that has not been discovered. That’s for uncommon tumors. When you have 1 of these tumors that are very rich in 

, like mammalian—salivary cancer, secretory carcinoma of the saliva, secretory cancers of the breast, congenital lymphomas in kids or fibrosarcomas—you know that the prevalence of 

 is very high, maybe 90%. So you can shoot straight, you can do RT-PCR, you can do FISH. For example, the salivary cancers are very high in 

, so you can go straight and try to find that genetic aberration. That way maybe you don’t have to do a whole sequencing.

The last option we have—option No. 3, which not very common—we used to do before. We used to love FISH testing. Oncologists love FISH testing for breast cancer, but when we started to do lung cancer, we learned about that FISH is good for 

. Then we discovered that maybe FISH is good for ROS. But it’s too cumbersome; there are too many FISH testings now. We have 

That’s why the developing of immunohistochemistry is a very good option, because the problem is the amount of use of the tissue, that there is not enough tissue to look for other genetic aberrations. But some people have been successful publishing data; that antibody for 

 can probably catch more than 90% of genetic aberrations. Maybe that’s an option for a center that doesn’t have the technology for RNA sequencing.

Yeah, but what you just described is complicated. I can barely keep track of how to get FOLFOX [folinic acid, 5-flourouracil, oxaliplatin].

Videos

Approaching Genomic Testing for NTRK Fusions

The lung cancer specialists have been consistent, right from the beginning they want to know everything. Shub, from a GI [gastrointestinal] cancer world, we’ve gotten a little slower with this. What’s your current practice on when you’re doing testing, such as next-generation sequencing, plasma samples, and so forth, for 

I think since I was in fellowship. Of course not as long as Mark.

 Sorry, Mark. At that time it was still the carbo-taxol [carboplatin-paclitaxel] days, but this pie chart was coming out. In all the GI meetings we go to, we always look at the lung cancer pie chart. We used to look at breast cancer when I was in fellowship. That changed to the lung pie chart, and we look at it longingly to see if we can bring the same things to patients with colorectal cancer and with pancreatic cancer. But it’s growing. Especially in the colorectal space where we have now with the 

 mutations, we have drugs that have been approved earlier. With pancreatic cancer, where in the metastatic setting we can give olaparib for 

Still, I think the testing has been developing with the recent article in 

, that if you treat patients with metastatic pancreatic cancer, also on the target agent, if they have an oncogenic driver, there you have a driver mutation—that’s the main thing. They really can do well. It’s changing the GI world more for colorectal than for pancreatic, but definitely for colorectal.

Yeah, I feel like we’re about 10 years behind on that. Tony, what’s your take on plasma samples in GI cancers? What’s their role like for lung cancer folks? What’s your thoughts on that?

They have a role depending on what you’re looking for. The fusions are certainly challenging with plasma, although as was said, this is getting a little better. The biggest element with plasma is you get the results quickly. If it’s there, it’s likely positive. If it’s not there, you may have missed it. So you still want to rely on tissue.

With plasma, its major utility comes in actually being able to use those sequentially during therapy at specific time points. But you do need to get your liquid biopsy before the infusion of treatment so that you know what the landscape of the tumor looks like.

Some of the interesting findings, actually, as we learn more and more in our different cancers to work with targeted therapy, which is something we haven’t done until more recently, is when you see these mutations arising, with the FGFR inhibitors, for example, that target the infusion. In biliary cancer, you see mutation rising that predict for recurrence, and actually there are agents that target most infusions and the mutations that have been developed in resistant patients.

-amplified tumors, where we see the high concordance rate between the liquid and the tissue, that 

 amplifications are driving a lot of the resistance, and we have 

 agents that are using in clinical research. I can go down the list with 

 mutations. The question, of course, is how much do you use that in actual clinical practice? You don’t have an agent that targets that mutation that appears or driving pathway, then it’s mostly an experimental drug.

But prior to treatment, I can tell you multiple times where I haven’t had enough tissue for a colon cancer patient, a 

 mutation pops up and completely changes my treatment paradigm from a doublet to a triplet. It also pushes the patients to clinical trials. We’re moving these targeted BRAF inhibitors into the first-line setting, and actually, the study allows for liquid biopsies because we understand that those patients cannot wait. It could sometimes take us 4 to 6 weeks to find the tissue and test the tissue. So it facilitates progress in that sense.

Using Molecular Testing in GI Cancers

What I want to focus on a little is just the evolution of molecular testing and next-generation sequencing [NGS]. Mark, let me let you go first. Do you think all patients should be tested? What’s your policy on testing your patient population using some type of broad molecular test that might pick up something like an 

 John, I think the greatest thing a medical oncologist can do for a lung cancer patient—obviously my practice has been restricted to lung cancer for almost 30 years now; I finished my fellowship 31 years ago—is to diagnose an oncogenic driver. We have what I like to call a closetful of highly effective targeted therapies. Those closet doors are closed until you make a molecular diagnosis.

For those of us in lung cancer who have a growing list of these actionable oncogenic drivers, 1 week a patient is sick. But then they take a pill for a week, and they are so much better. You start to look at where we’re having some longer-term survival outcomes. The average or median survival of a patient who is 

-positive nowadays is measured in 6, 7, 8 years.

When I started in this business, we were proud to have a median survival of 8 months with platinum doublets. So comprehensive molecular testing is important. I espouse the concept of “leave no man behind.” I do comprehensive testing. We have an internal panel, and I’m happy to use external vendors to make sure that the list I have in lung cancer, which includes 

I happen to actually believe in testing both tissue and plasma. I send both tissue and plasma on all my newly diagnosed patients at the time of diagnosis. We know that there are things you find in tissue that you don’t find in blood. Tissue is sometimes a very scarce commodity in non–small-cell lung cancer, so it’s tough to test everybody based on tissue.

We know that for finding things in plasma, if you find them, you can believe them, and you can act on them. The outcomes and response rates seem to be the same for plasma-identified patients versus tissue.

Let me jump in, Mark. Jyoti, Dr Patel, in your practice as another lung cancer perspective, when are you doing this testing? I’ve been so impressed by the lung cancer culture to where you have the discipline to do molecular testing before initiating just some carbo-taxol [carboplatin-paclitaxel] or whatever it is this year. Give me a sense of when in lung cancer you are doing this testing, because I think we’re going to see some differences with the way our GI [gastrointestinal] specialists would approach this.

In lung cancer, for all patients at diagnosis with metastatic disease, we recommend up-front testing. I should say all nonsquamous patients. That’s sort of category 1; we have great data. The questions become, do we do this sequentially? Do we do tiered testing where we may do some RT-PCR [reverse transcription polymerase chain reaction] and then move on to more comprehensive testing to get an answer?

For most of our patients where tissue, as Mark correctly points out, is so precious, it makes sense now to get comprehensive NGS at the get-go. Although, even with 

 fusions, you can have good sensitivity and pretty good specificity with IHC [immunohistochemistry]; it’s wasting tissue. I think most of us feel that up-front NGS in RNA makes a great deal of sense.

But let me follow-up on that in terms of the liquid piece of that too. Again, this is a cultural difference between the GI specialists and the lung cancer specialists. Mark brought up this great idea—should we doing parallel plasma or blood circulating markers? Are you doing the same?

Absolutely. I guess that is with the caveat that the blood tests are getting better and the technology is improving. Maybe a few years ago some of the infusions that were so bulky, particularly 

, which is difficult technically to pick up because it’s a very large fusion. As the testing has improved, there’s good concordance in patients with significant disease. There are very few false positives. False negatives can occur, again, based a little on bulk of disease.

Let me ask, it’s something that I’m always curious about, when you’ve got only a small biopsy that’s not enough for a molecular profile, your liquid biopsy, don’t you need the tissue base to be at least as comparator for that initial test? What do you do if you don’t have it?

Negatives need a repeat biopsy, absolutely.

Yes, John. The only time the plasma is useful is if you find something. If you don’t find anything, you can’t trust it, and most of us would go back and get more tissue at that point.

Also it’s important that we also do bulk plasma and tissue. Also it’s specifically for what we’re talking about, with 

. For example, if you took plasma, I’m not aware that there is any platform in plasma that can check for just 

. That’s why when we do plasma only, there is the possibility to miss 

, which are very rare. But that’s why I think it’s important to complement and do both of them.

The second thing—I know it happens in your community, the GI community—but in lung cancer we were experts in testing until we developed these chemotherapy-immunotherapy combinations. We have a problem because as soon as you get the PD-L1 2 days later, a lot of people get excited and want to shoot and start the chemotherapy-immunotherapy, and the patient is impatient. They think that maybe it’s education. We need to wait 2 weeks for the plasma and 2 weeks for the tissue, because these are targeted therapies. As Mark said, it’s very important. We can always do the chemotherapy-immunotherapy 1 year later, 2 years later, or 5 years later if it’s an outpatient.

Right. That’s stressing that discipline I was praising you for. You’ve got some pretty good carrots there to get on with systemic chemotherapy-immunotherapy going forward.

Evolution of NGS Testing in Lung Cancers

Tony, let’s switch to you for a second. Talk us through the measuring of 

 fusions. We thought about mutations and amplifications, and now we have fusions. I know for a lot of oncologists, including me, there’s been a learning curve of what this is all about. Walk us through some of that background.

When we talk about these alterations that affect the NTRK pathway, they go to this big bucket. A very small proportion of fusions, actually up to 14% of tumors, will have a mutational amplification or alteration. The question is, of course, how important are the nonfusions in terms of promoting oncogenesis? That comes with a question mark.

The fusions seem to be drivers. Not as much is known about the mutations and amplifications other than the fact that, for example, the presence of an 

 mutation could be a driver for resistance for targeting these 

 fusions, meaning it could be an escape mechanism.

There are some agents that are more globally attacking at least in early development, both the fusion and the mutation, so pan-targeting that may actually have an advantage, versus those that target specifically the fusion. For now, most of our understanding is linked to the fusions and the roles in oncogenesis and targeting them. Less is known about the others and targeting them.

 Perhaps now the GI [gastrointestinal] specialists can gather together. Shub, jump in on this. At least in our world we’re doing a lot of MSI [microsatellite instability] testing, and we see whether it’s PD-L1 or MSI. Those are in the colorectal cancer world where we often see the 

 fusions. I’ve always just thought this is because there’s just a lot of shrapnel around with an MSI setting, and so you’re going to more likely have 1 of these fusions. What’s your take on that, Shub? You think you run them together?

Right. The issue, again, is it’s like finding a needle in a haystack for 1 of these 

 fusions. As you know, I’m in 2 departments at MD Anderson: ICT [investigational cancer therapeutics] and in GI medical oncology. A lot of my patients on NTRK inhibitors have been on the phase 1 side. We’re just introduced them 3 or 4 years back when we were surely seeing the early responses to the NTRK inhibitors. So we always ask this question in different meetings. People always ask us, “It’s such a small percentage, why pay attention to that group?” But where we can really enrich them, you’re exactly right. In the MSI-high population for rectal cancer, they can have a higher percentage, and that’s a relative term of these 

Small pathology studies, which were done in patients who had 

 fusions, as much as 75% of them were also MSI high. This MSI-high group really has 2 tumor-agnostic approvals for the immunotherapy and for 

Then you find them in the same patient. Luis, what’s your take in lung cancer? Are you seeing this type of overlap with some of your molecular targets, or you’ve still got your nice pie chart where everybody is in their own wedge?

No. We are very fortunate that in lung cancer we have several molecular targets. The problem is that for someone who has squamous cell carcinoma, a lot of targets don’t have drugs yet. What I want to add also about this conversation, what Tony was mentioning before, is something very practical for the audience. These 

 mutations get reported all the time, and sometimes even the amplification. For example, our site was 1 of the original accrual sites for LOXO-101, larotrectinib. It was the only site in South Florida.

A lot of community people just were sending me patients for accrual in the study, but they didn’t notice that 

 amplification. As much as they know even with entrectinib, there are data that have people treated with 

 amplifications, and they don’t have a response. That’s why I think it’s a very important practical point. We only treat 

 fusions unless it’s a patient with a fusion that has progressed and is not the mutation originated resistance. As you said, as clinicians, we are learning very fast about all these things.

 That’s such an important point, because lots of us have sent off molecular tests on our patients, say a year or 2 ago, and they’re still sitting scanned into the back of our EMRs [electronic medical records]. We think we might have done this test, for example, when in fact we were looking at either protein or mutation data and not looking at the fusion. As I think somebody else said, unless it’s the fusion, the medicines aren’t really working, so it sometimes justifies retesting.

The mutations, again, invoke resistance to these agents, so in many ways the presence of the mutation not only does not predict a response, but it does predict for resistance. It’s interesting. When you look at the tumor mutational burden overall, we always think that these alterations, these fusions are always present or co-expressed with a number of different alterations, whether it was cell cycle as treated, tyrosine kinase, MAP kinase, PI3K. You can find a lot of co-localization. You find PD-L1 expression in about 20% are MSI high, about 20% to 30%. So you find a lot.

But the tumor mutational burden overall is lower for the 

-fusion-related or driven tumors, versus those that are not. Although they co-locate, they’re not necessarily loaded with mutations as much as initially thought.

Yeah, that was my point below. I don’t know that we know as much as we need to know about the 

 lung population. But if you look at other fusion-like things, they tend to occur in the never-light smokers, almost always adenocarcinoma. They almost always have low PD-L1, they have low infiltrating lymphocytes and tumors, and so forth.

We largely ignore PD-L1 status. If you diagnose a driver, the use of targeted therapy in the driver setting, it’s so much more effective than what we understand immunotherapy therapy to be in this setting. So we largely ignore PD-L1 in that population, but it’s so infrequent in lung cancer, I still think we’re learning.

Variants of NTRK Fusions in Solid Tumors

® titled “TRK Inhibitors in Lung and GI cancers.” I’m Dr John Marshall from Medstar Georgetown University Hospital, and I’m joined by an amazing faculty. Normally we’re all together, but this time we’re all around the United States, and they’re joining me today on this virtual discussion. First, Dr Tanios Bekaii-Saab, Tony Saab, from the Mayo Clinic. Dr Shubham Pant from The University of Texas MD Anderson Cancer Center.

Dr Jyoti Patel from the Robert H. Lurie Comprehensive Cancer Center of Northwestern University, welcome.

Dr Luis E. Raez from Memorial Healthcare System.

And Dr Mark Socinski from AdventHealth Cancer Institution. Mark, welcome.

Today we’re going to discuss a number of topics pertaining to the use of TRK inhibitors in lung and GI [gastrointestinal] cancers. Let’s get started. Jyoti, Dr Patel, we’re going to start with you. If you could set the stage for us, what is a TRK inhibitor? And specifically for you, what is neurotrophic tropomyosin receptor kinase [NTRK] inhibitor? What are they, and what are they all about?

It’s a mouthful, but this is a class of transmembrane proteins that have been found to be oncogenic drivers. These genes are fusion events that are quite rare but across a wide variety of tumors. When we detect these, we find that they are the sentinel event for a tumor to become cancerous and to really grow. What’s exciting about this is it’s a bona fide target for cancer therapy across a multitude of tumors.

 I think it’s also fascinating biology about these cell receptors and the discovery of these receptors from another field to turn this into a cancer target. Dr Pant, talk a little about that whole biology and what we as oncologists were forced to learn as we have been discovering this new therapy. Take us through that a bit.

The TRK inhibitors—the TRKs&mdash;of course play a pivotal role in the physiology development and function of the peripheral and the central nervous system. That’s 1 of the main roles, physiological roles in the human body. We have 3 

—and they give rise to the proteins, which are 

. Essentially most of the ones we see are fusions in 

 genes, which lead to this activated protein kinase of 

That’s the oncogenic driver for the growth of the tumors, and as Dr Patel said, there are different tumors. Some are rare like infantile fibrosarcoma, typically breast cancer, which we can talk about later. That’s common with rare tumors and the common tumors where it’s more rare. That’s how we’re seeing it currently.

That’s a clever way to put it. There are receptor tyrosine kinases in some way. They’re transmembrane receptors that are ligand dependent in the normal state, and with the fusions that occur that we’re going to talk about, they become independent. It’s a signaling pathway. Tony? Anybody else? Mark, do you want to chime in on your thoughts on the biology of this pathway?

 To me, it’s fascinating when you think about the role that these proteins play in the normal state in neurological development. It’s interesting, as we’ll talk about a bit later, to look at the adverse effects profile of the drugs. But similar to what we’ve seen in what I think is 1 of the poster children of genomic tumor, lung adenocarcinoma, a number of these fusions—not only 

 fusions—and all these things create an oncogenic pathway. And as John said, it’s really a growth pathway.

These are what we used to call “stupid” cancers—they’re very simple from a mutational burden load. It typically is dominated by 1 pathway. These small-molecule drugs that are orally absorbed are highly effective, as we’ll talk about, not only in 

 fusions but in a number of different fusion situations that we have in solid tumors, with obviously lung cancer having a number of them.

Yeah. We have a merger of lung and GI, so we’re going to have to fight it out for above and below the diaphragm for a discussion.

John L. Marshall, MD, MedStar Georgetown University Hospital

Articles

Approaching Genomic Testing for NTRK Fusions

Using Molecular Testing in GI Cancers

Evolution of NGS Testing in Lung Cancers

Variants of NTRK Fusions in Solid Tumors

Role of NTRK Inhibitors