Dr. Justin Gainor & Dr. Aaron Hata at ALKtALK

Dr. Justin Gainor, MD

Director of Center for Thoracic Cancers & Director of Targeted Immunotherapy at Massachusetts General Hospital, Boston

Assistant Professor of Medicine at Harvard Medical School

“It’s great to be here tonight. It’s so nice to see so many familiar faces on the call. Being one of the recipients for the ALK Positive Awards is particularly meaningful for us as investigators because it comes from patients.  So, that is incredibly inspiring and makes us work that much harder.  A huge thank you for all the things you do and it is such an amazing community.  My road to start studying lung cancer - it is like for many people, lots of serendipity.  I thought I was going to be a surgeon. For those who know me, they know my personality and would realize that it would not have been a good fit.  I applied for a summer opportunity  and I was selected as one of six. Five of them were paired with surgeons and I was paired with a hematologist/oncologist instead. It was completely random but I realized right away that this opportunity “jelled” with all my interests. The next serendipity event happened when I was a resident. When I was trying to identify mentors, I knew I wanted to do oncology. I originally thought about being a gastrointestinal oncologist. However, there was a problem with the timing with potential mentors or it was not a good fit. But someone pointed me to a great person in 2008, “It is a great fit, a new attending, and her name is Alice Shaw.  She just came on staff about a year ago.”  She talked about a new genetic alteration that was discovered a year before, called ALK. And the rest is history.”  

Dr. Aaron Hata, MD, PhD

Assistant Physician, Medicine, Massachusetts General Hospital, Boston 

Assistant Professor of Medicine at Harvard Medical School

“Hello everybody. Thank you for having me here tonight. My decision for going into oncology dates back to medical school when I was doing my MD/PhD training at Vanderbilt. I’d just finished my PhD and was trying to decide which clinical area I should study in medical school. That is about the time when EGFR was discovered. What I knew at the time was to do research at the lab that would easily translate in clinic.  So, these papers that described EGFR mutations felt like a lightbulb when off because I could look at patients, I could look at what is going on and I could directly act upon it.  That is when I felt I wanted to study oncology because this is the place where what was happening in the lab correlates closely to what is observed in the clinic.  So, when I came to Boston for residency, I ended up doing a postdoctoral position in Engelman’s lab, studying EGFR and KRAS. The decision to study targeted therapies and to study tumors is the main reason why I wanted to study oncology. At that time, I did not think I would end up studying this, but ultimately that is the result. It’s been gratifying for me as a scientist and an oncologist to be studying the research and to observe the actual outcome of the research that can impact patients so dramatically.”

Some background in Cancer immunotherapy (Dr. Gainor).

Highlighted some background in cellular therapies for ALK. (video 7:15- 13:11) https://www.youtube.com/watch?v=bbgMFPj6_-Y

The term “Cancer Immunotherapy” is an approach to leveraging immune system to attack cancer. 

Typically, we think of the immune system as battling viruses and bacteria, but we know it can also attack cancer. Most of the time when we talk about cancer immunotherapy in lung cancer, we are talking about immune checkpoint inhibitors. These are drugs like Pembrolizumab that are blocking the brakes on the immune system. These are intravenous medicine. While these drugs are very transformative for patients without targeted therapy options, these medicines have not been as successful in patients with ALK or EGFR mutations.  We need to think of additional strategies.  I believe Dr. Awad and Dr. Chiarle will be talking about their vaccine efforts and that is something we are working alongside with them.  

Tonight, I would like to focus on what is known as “cellular therapies”. How is this different? Some of these details we can ignore right now.  At the heart of what this is: if we start with a patient, it is almost like donating blood, instead of taking out red blood cells, we take out white blood cells (Leukapheresis). These are the soldiers of the immune system. The goal is to somehow genetically engineer these white blood cells, which allows these modified white cells to recognize something on the cancer.

The goals are:

Could we take the white blood cells out of the body? Engineer a receptor on the cell surface? And allow these cells to recognize ALK? Reinfuse the patient with these modified/engineered cells?  

That is the big picture of what cellular therapies are like. This is not something high in the sky. In certain blood cancers, there are now multiple approved cellular therapies.  So, this is something used in oncology but it has not been used much in solid tumors.  We think ALK might be an ideal target for this type of therapies.

Essentially what we are doing with Aaron (Dr. Hata) in the lab is trying to sort out the code that allows a T-cell receptor that can react against ALK. 

When your body makes T-cells, it is like a menu - they take one piece from red, green, yellow, and blue to combine them together to make a T-cell.  This can create tremendous diversity. So within your bodies, you have millions of different T-cells. Pulling out the unique ones that can react against ALK can help us figure out the specific combinations of red/green/yellow/and blue that can help us in designing therapies.  As you can see in the diagram, this is something you cannot just design in the lab but you have to find it in a person first. Basically you end up cloning it and using it in other people too. 

That is essentially what we are trying to do: we are designing a cellular therapy for ALK, trying to decode what these T-cell receptors are in patients and healthy volunteers to find these T-cells and to allow us to develop treatment. 

Q: Has the T-cell receptor been identified yet? Or is it just finding the T-cells first? What is Enigma Plus?

Dr: Gainor: Enigma Plus is to elucidate novel, genomic, and immune markers in ALK. It is an online protocol to allow any patients in the US to participate in research. All doctors are involved to allow patients to consent virtually to get any archival tissue donated to doctors to study the genetics of tumors as well as the immune landscape near it. What is secreted by the tumor? These are complementary efforts to what I just described as cellular therapy for ALK. We have been collecting blood samples (1st step), however these are not typical blood samples. These are samples to isolate white blood cells. A post-doctorate fellow is looking for this rare immune T-cell that is reactive to specific ALK proteins parts.

Dr. Hata: We have not found a T-cell receptor yet. The approach is like trying to find a needle in a stack of needles. We have lots of T-cells recognized that recognize viruses. If we take those T-cells and sequence them, we can see lots sequence. But it’s hard to understand what they recognize just by the sequences alone.  We are doing a functional test where we expose T-cells to pieces of ALK protein. We want to see their reaction to the ALK protein. Then, we might see one or two reactions. If you can find one or two, then we can try to isolate them and study those T-cells. So, we’ve been collecting blood and exposing it to the ALK protein. We’ve found a number of blood samples. Right now, we are taking a T-cell that was reactive and we are looking at what their receptor was. We are in the middle. We are trying to sequence them. We are trying to see which part of ALK they are reacting to.

Q: Are there different T-cells for each person? Or is it a specific type of T-cell for each type of cancer?

Dr. Hata: The complexity of immune system that allows us to fight off most of the viruses becomes a little challenge for us right now. We have different genes in the body to make up different HLA types. These HLA genes are what the immune system recognize are “YOU” vs. “NOT ME”. In every human, we have different HLA combinations. So we might have some peptides common to specific people. There are certain HLA genes more prevalent in different ethnic groups. But it will be different T-cell receptors for different patients.

Dr. Gainor: That is why a lot of research tends to collide. Seven or eight years ago, in Aaron’s lab they were trying to generate cell lines derived from patients to explore resistance to targeted therapy as well as thinking about the next potential steps ahead.  Those cell lines can be used for this work. Whether a T-cell reacts to ALK may not be a “yes” or a “no”.  There could be various strengths of reactivity.  We are trying to find the ones are that most reactive and can benefit the broadest number of patients. We are also trying to find those that do not bind to other things. Many of you many already know that ALK is very closely related to ROS1, that’s why you can use many of the same drugs. Can we actually have a T-cell only react to just ALK and not ROS1 to minimize bystander side effects? These are just an example of where we can use those cell lines to get a sense of how these reactions are and how specific this interaction can be. 

Q: We do have ROS1 patients here. Do you feel this therapy can be modified for ROS1 patients?

Dr. Gainor: A drug that binds to ALK and ROS1 may bind similarly, but other parts of the protein are still quite different from each other. I brought up ROS1 because when you have T-cells, they usually have controls: like an On/Off switch. We want them to be active against foreign things but do not want them to react against our own things because that can cause other issues.  Normal ROS1 is present in other places.  When you engineer things (like the T-cells), you remove a lot of controls.  So they are much more prone to attacking things.  So it is critical to as specific as possible. The goal of this first wave is to make it as specific to ALK as possible. This is also a good proof of concept in lung cancer and then we can open up cellular therapy to expand into other oncogenic subgroups.  It is critical to demonstrate the feasibility of this therapy. 

Dr. Hata: While we are screening for ALK, we are also screening for ROS1 at the same time because it is not that hard to do multiple in parallel.  It is possible that we can find a T-cell responsive to ROS1 as well.  

Q: At this time, you are doing translational research, that means it is not only in the laboratory but also partly in the clinic. Dr. Gainor won an award of $200,000 in 2018 and had a supplemental 2019 $100,000 booster awarded. Can you explain what you have done ‘till now? What about the booster? What would it take to take this research into a clinical trial?

Dr. Gainor: The proposal itself was a multi-prong proposal. The 1st portion was to profile the genetics, the immune microenvironment of ALK+ lung cancer. We have done genetic profiles on hundreds of samples of ALK+ lung cancers and looked at not only ALK mutations, but what other mutations can form even outside of ALK. In order for the immune system to act, the environment has to “look very different” than what is normally present. What are some other mutations that are present in ALK+ lung cancer? We have been profiling that. We found that total mutational burden (how many mutations are present in lung cancer) baseline  in most ALK+ tumors has low tumor mutation burden (TMB). For some people, as they are expose to a TKI, TMB goes up. We have found some cases where TMB goes up. But it looks like they are not as immunogenic, that does not seem these mutations elicit some immune response. 

We usually think of two big biomarkers, TMB and PDL-1, when guiding immunotherapy.  As oncologists, we often use the PDL-1 numbers to guide our therapy.  When that PDL-1 number is high, we try to use PDL-1 inhibitors.  However, we also found PDL-1 can be elevated very commonly in ALK+ cancer. But PDL-1 being commonly high in ALK+ lung cancers does not mean the same thing. It is like a red herring; misleading. This high PDL-1 is not accompanied by more immune cells around it. It is a big thing that we are trying to reinforce to oncologists and patients alike - that you cannot just send for PDL-1 test and ignore the gene test. You need to wait for both results to come back. A lot of what we have done is to profile the immune environment around the tumor.  The booster award is really helpful in our single cell RNA sequencing. Everything we have done to date is to have a pathologist looking at the slides and the immune cells around it. Essentially what a single cell RNA does is to actually look at the genetic at a single cell resolution. Within a biopsy, we can see what types of immune cells are there.  It can help inform the research strategies for other clinical trials. 

I mentioned PDL-1 drugs by themselves are not very responsive. By understanding what other immune cells are there, it can help inform combination strategies.

Q: When do you expect the Engima Plus program will be up and running? How do you sign up for it?

Dr. Gainor: In order for any research to be done, there are two steps that need to be cleared.  You need to get approval from the Scientific Review Board and the Institutional Review Board as well. That protocol has been conditionally approved by the IRB. So, right now the only remaining thing is that IRB is reviewing anything that has patient-facing items, a tweet, a brochure or a webpage. The protocol itself is approved. The IRB is waiting to approve the last few things. We hope by next month it will be completely ready to go and “go live”. 

Q: Would it be a part of the research to test siblings or other healthy family members of ALK patients?

Dr. Hata: When we started this, we did not know where we can find T-cells that were reactive to ALK proteins. We took two approaches. One, we looked at normal healthy volunteers such as the samples from the blood bank. Then, we also looked at the blood samples from ALK patients. So far, we found more potential ALK reactive T-cells in normal donors in the blood bank. We don’t know the reason. We want to make sure that the T-cells are truly ALK-specific and not designed to react to something else that looks like ALK. But in the end, it does not matter if the T-cell was originally meant to react to something that is not ALK as long as right now this T-cells react to an ALK peptide.

The idea of testing family members is a very interesting approach. Because family members would presumably have similar HLA typing as the ALK patient.  But since we are finding potentially good T-cells from healthy donors, family members might be a good place to look.

Q: Are you collaborating with Dr. Awad and Dr. Chiarle with peptide identification or T-cell identification? 

Dr. Gainor: Boston is fortunate with an amazing environment with research and working together.  We really recognize that team science is the way to get results faster.  Yes, we are collaborating together. What we have done is to form the basis for the next line of work for the vaccine study.  Dr. Chiarle has developed mouse models with intact immune systems with ALK+ tumors. Normally, most mouse studies do not contain an intact immune system. It would be hard to study the immune system if the mouse model did not have an intact immune system. So, we are working together to use that mouse model to test our candidate cellular therapy. This is great team science. We will participate in that vaccine clinical trial. On both sides, we are supporting each other and supporting research. 

Q: People are anxious to know if there’s any estimated target for phase 1 trials for the cellular therapy? What still has to happen before going into clinic?

Dr. Gainor: We are working as fast as we possibly can on this. We have a few hits at some blood samples reacting to ALK. We are trying to figure out the specificity right now. Which region of ALK is it? We are making sure there’s no cross-reactivity. Once we are confident we have consistently reactive T-cells against ALK and we know the sequence, then we need to be validating it in the lab. There are still many steps ahead. The FDA and other regulatory agencies need to be informed. Especially when you are genetically modifying things or adding items like drugs, there will be a lot of scrutiny. We need to be 100% right. That is why we are spending so much time to proof the work. I recognize that we are trying to move this into the clinic as fast as we can.

Q: Hypotheically, if a donor wanted to donate a large sum of money to Dr. Gainor, how much would it be to accelerate the process? How much is being held back because of money concerns? Hire extra staff? How can we make it happen quicker?

Dr. Gainor: In the lab, we work patient samples, and work with the most cutting-edge sequencing technology to shave off laborious steps. Aaron, what are the current rate limiting steps?

Dr. Hata: Money can help to accelerate some things. However, these experiments are in sequential process. We cannot put everything in parallel. Each step takes a little time and is needed to make sure everything is real before the next step. Resources can help but we need to take each step slowly to make sure it is real. We are at this crucial T-cell discovery step. We are already using some parallel approaches.  We are collaborating with a company that has high throughput PCR sequencing to generate libraries so that we can functionally validate data quickly. It is a very early technology and we are hopeful about its result, but this technology is very new. Then we have some traditional approaches with tried and true but slower throughput. So, if those work, it is very clear what we can do.  We do have some parallel approaches going and we will see which one yields results fastest. But each step does take some time.  We have to wait until we can go to the next step. 

Dr. Gainor: I do think that some of this initial work is very labor-intensive in the lab. Having more hands on the deck would help for sure. How many samples can we screen? How quickly can we screen the number of peptides? Cutting edge technology can save some time. Typically, the cloning piece used to take years. Right now, we are trying to sort out the Alpha-Beta chain simultaneously to shave off time. 

Q: Are immune cells often found in our ALK+ tumors? If so, does that have any clinical significance?

Dr. Gainor: Yes, there are immune cells inside ALK+ tumors. We looked at different types of immune cells. We focused CD8+T-cells because these are the heavy lifters to effectively kill cancers. These are the actors in classical form of immunotherapy. It does look like there are fewer CD8+T-cell in ALK+ lung cancer. In the single cell technique we can see different types of immune cells. We are looking at the different constellation of immune cells within the ALK+ lung tumors. Currently, in fact tomorrow, I have a meeting to review the data comparing that to patients who are more reactive to classic immune therapy treatment and see what are the similarities and the differences between the two.

Q: If you waved your magic wand and completed the research and you were ready to go to phase 1, would you require a biotech company to help you produce the product?

Dr. Gainor: This is something we will need to work with pharma or biotech to bring to clinical practice. We started collaborations on the sequencing side. The same company has the ability to make some cellular therapies as well. Absolutely, we will need to partner with industry to bring this into the clinic. Broadly, it may be that we need some patient that needs cellular therapy. But another group requires PD1 in a combination. Maybe you need a vaccine?  I don’t think it is a one size fits all. It is why it is critical to work together.  It might be a combination of all the things for it to work.

Q: Do you think this T-cell therapy can work on patients who have progressed on ALK TKIs or have became ALK-independent?

Dr Gainor: Yes, the cancer that is now ALK-independent still has an ALK fusion there. That is what we are relying on. We want to have the immune system be able to identify these cells. 

Q: Do you foresee this therapy working for patients with brain metastasis?

Dr. Gainor: The short answer is, we don’t know. In many CART-cell studies previously, they do see entry into the brain. MGH just launched the first CART-cell specifically with patients with CNS lymphomas. We recognize it is a vulnerability that we need T-cells to go into the CNS. In blood-based cancer, we do see them in there.

Q: Can you compare CART-therapy vs. this T-cell therapy?

Dr. Gainor: CART-cells and T-cell therapy are both engineered cellular therapies. There are a few core distinctions. In CART-cells all the brakes were removed from them; all controls are removed. It is like a missile where all the safeties have been removed. Secondly, CART-therapy can only recognize the surface of the cells; they cannot see anything inside.  The ALK fusion is inside the cells and that is why you cannot use CART-cell therapy. You need to rely on the body’s regular machinery to do it for you. HLA is to take some pieces of the inside and show it to the outside. HLA will present it a certain way. We are trying to focus on tiny fragments of ALK strands. Because we rely on that presentation, we need to have it HLA-restrictive. It is like bone marrow matching, we need to have the right matching type. 

Q: When you discuss the need for diverse approaches, what other therapies are promising for ALK? 

Dr. Hata: In the theme of immunotherapy, we know PD-1 check point inhibitors does not work very well because ALK does not have high TBM. We have been trying to find other ways to trick the immune system to recognize the cancer. Displaying the ALK peptide on the cell surface is one way.  Another way is to try to trick the immune system to think the tumor is infected by viruses that we encounter in normal life. Our immune system is incredible at controlling certain viruses and most of us have seen those viruses.  Those T-cells are very powerful.  One approach we are trying is to deliver a protein that looks like a virus onto the tumor cells selectively. We know the immune system is good at killing those viruses. We know if the immune cells can see those and recognize them as viruses, we know our powerful immune system can kill them. A third approach is to try and harness other immune system cells to fight that are separate from T-cells, such as macrophages. There are different therapies that came to clinic designed to stimulate macrophages to augment response to target therapy. In the field of targeted therapies, we are looking at ways to slow down evolution of resistance. We found that sometimes genes are turned on that can increase mutation rates. So, we are trying to slow down or inhibit those enzymes that cause mutations; trying to slow down the ability of the cancers to develop new mutations that can become resistant. I have just talked about three types of approaches we are thinking about in the lab, they are in the basic science arena.  If they are promising, we are hoping one day we can bring them to the clinic.  

You can watch the entire video recording here: https://www.youtube.com/watch?v=bbgMFPj6_-Y

Questions have been compiled and organized and may not be in the exact order in which they appear in the video.
Compiled and transcribed by: Alice Chou