Cancer Tissue Testing: A Patient's Guide to Molecular Profiling

•Whole exome sequencing : Brian will get this test, which can, among other things, be used to develop a personalized cancer vaccine. Tempus XE is one option, with experts liking BostonGene’s new test and Exact Sciences’ test.

•Immunohistochemistry (IHC) : Brian will get this common test that uses antibodies to check for certain antigens (markers) in a tissue sample, usually highlighted by a fluorescent dye. It helps visualize the distribution and localization of specific cellular components within cells and their context.

•Proteomics: A proteomics test could allow Brian to analyze the concentrations of 72 different proteins, beyond knowing which proteins are present, which could help predict therapy effectiveness, such as chemotherapy sensitivity, effectiveness of drugs, such as antibody drug conjugates, and immune system dynamics. For example, Brian has elevated levels of a biomarker (TDO2) which creates an immune suppressive environment.

•Functional testing : While functional tests that try out drugs on fresh tumor tissue “ex vivo” could provide confidence in choosing drugs that perform well, including drug combinations, Brian’s oncologist doesn’t trust these tests.

•Spatial analysis: Brian’s oncologist is unenthusiastic. Brian is looking to align with his oncologist on these tests, or find another physician, to push the envelope in trying innovative tests. The information and opinions expressed on this website or platform, or during discussions and presentations (both verbal and written) are not intended as health care recommendations or medical advice by Cancer Patient Lab/Prostate Cancer Lab, its principals, presenters, participants, or representatives for any medical treatment, product, or course of action. You should always consult a doctor about your specific situation before pursuing any health care program, treatment, product or other course of action that might affect your health. Meeting Notes Brian McCloskey: I'm reaching out to you because I need your collective wisdom to help me navigate a really important part of my journey. My cancer is growing in the soft tissue of my peritoneum. That's the bad news, just the way it works. The good news is that it's going to present an opportunity for me to collect tissue. And so the reason why I want your help is that I need to figure out: what am I going to do with this tissue? There are lots of different ways that tissue can be used, and it's a precious resource. I want to make sure that I am using it to do a couple things: one to make sure that I get greater depth of understanding regarding my cancer, and the second is to inform my treatment decisions. Some of you may be more familiar with my journey than others. I want to make sure that everyone’s on the same page. My journey started in 2016. I had a prostatectomy. We thought we got it all. We didn't. I had a biochemical recurrence and started first line androgen deprivation with Lupron. I got radiation. That took me all the way through to 2018, when I went on a holiday. You can see that I had a pretty significant spike. I had a Gleason nine. That might explain the rapid rise in my PSA. I started apalutamide and saw an immediate response from that. I then took another holiday in December of 2019, ending everything. Shortly thereafter, I had a repeat performance of what I got in 2018, where I saw a rapid rise in my PSA. We did some imaging. sue and Testing” I started apalutamide and saw an immediate response from that. I then took another holiday in December of 2019, ending everything. Shortly thereafter, I had a repeat performance of what I got in 2018, where I saw a rapid rise in my PSA. We did some imaging. We discovered that I had six metastatic lesions in my peritoneum. That was July of 2020. I had surgery to remove them. They couldn't get everything. There were complications, and this will play into where we're going to go with this discussion. Due to the salvage radiation that I had back in 2017, the tissue gets sticky. It was hard to get margins around the lesions. There are a lot of nerves in that area of the pelvis. You have to be super careful. My doctor at UC San Diego, Dr. Kane, resected six lesions. I had DNA sequencing. I have three different mutations, TP53, PBRM1, and TMPRSS-ERG. Fast forward to my second surgery on these metastatic lesions, and the DNA alterations remained the same. We also did some RNA seq analysis, where we looked at my RNA gene expression relative to a pan cancer cohort of 12,000 patients and a prostate cancer cohort of about 350. This was done with Rick Stanton, myself, and folks at Tempus. We noticed that there are four major genes that I am at least in the 90th percentile ranking relative to those two cohorts. After surgery we knew that we didn't get it all. So I needed to start chemo, or at least that was the course of action that we took. We decided to combine that with pembrolizumab. I started that in October of 2020. There were six rounds of chemo. I ended chemo on January 25th, and I maintained pembro all the way through to October of 2021. I saw that I was becoming resistant. We knew that we needed to do something else. I had more imaging done in October of last year. We discovered that I had three metastatic lesions. I should also note that during that year I had imaging done, and there was actually no evidence of disease. So we did a pretty good job, but we knew it was there. It just didn't show up in significant lesions. I had three metastatic lesions by October of 2021. We started a second line hormone therapy, abiraterone, in November of last year. That's what I'm on today. I've had a pretty good response. My nadir is a little hard to read, but it was at 0.45 in March of this year. It has grown slowly to 0.49, 0.54, and then 0.69 last week. We're recognizing that I'm moving into, or I have moved into a castration resistance setting. I'm going to need to do something. I've had a number of different imaging techniques. I've had a PSMA PET and a CT scan. I just had a three Tesla MRI done. It's much more powerful than a standard 1.5. The fidelity of the imaging is really important because the lesion in the peritoneum is very close to the bladder, and we needed to understand whether or not the cancer has infiltrated the bladder, or intermeshed with it. If there’s enough margin between the bladder and the lesion, I would look at radiation and maybe even surgery. The path that we're currently on with my oncologist, Rana McKay at UC San Diego, is that I'm going to get a biopsy. For me, it's really important to understand what is the nature of my disease and how can it inform my treatments? I'm scheduled for a biopsy a week from today. At the Prostate Cancer Lab we've developed an amazing consortium of providers that take all of our EMR information and genomic information and come up with various treatment options. We've worked with Massive Bio, Cancer Commons, xCures, and CureMatch. Interestingly, across those vendors there was no overlap on the recommended treatment options. I then had a conversation with my oncologist last month where we reviewed those 21 options. All of them. She was amazing. We netted them down to about 8. I won't go into all the reasons right now. Then I had another conversation with he just a couple weeks ago, and we netted them down to five. The five that we're currently looking at are SBRT (radiation), surgery, chemotherapy, ARV766, and a PSMA bispecific. She ruled out BAT (bipolar androgen therapy). I'm putting BAT back on the map because I want to explore that option with her again. While I am newly castration resistant, my AR expression is also very, very high. I don't know if I have AR copy number gain, but I know that I have a high expression of AR, so I don't want to quite dismiss that. My oncology team has been focusing more on radiation, but I'm not going to give up surgery, because after speaking to the radiation oncologist, I'm definitely concerned about the side effects of radiation given the tumor's proximity to my bladder. The surgeon was not really stoked to do surgery, given the stickiness of the tissue and a few other things. The MRI revealed that my index lesion has actually grown fairly significantly in the past year. It's gone from three centimeters to five centimeters, which is odd because my PSA hasn’t increased that significantly and is still lower than where it was when my lesion was 3cm. Now it's beginning to rise a bit more rapidly, but the correlation between my PSA and my tumor volume doesn't seem to correlate. In any event, I do want to put surgery back on the table as an option. Essentially we're down to maybe five or six treatment options. There could be others. We don't have vaccines on here, which is certainly something that I would consider. I guess Provenge to a certain extent. The opportunity that's coming up on the 24th with the biopsy, or potentially surgery at a later time, is that I'm going to get some tissue. And the question is, what am I going to do with that tissue? Through all of these conversations that we've had as a group, there's a short list of ways to use this tissue: whole exome sequencing, IHC, proteomics, spatial phenotyping, functional testing, or others. I need to have a plan, and I need to take that plan back to my doctor. I need to work with her to make sure that I'm going to get more than just standard sequencing to get data that is going to inform my next treatment decision. I would love to get feedback in terms of the tests that I should consider. I also need to understand the requirements for those tests such as the amount of tissue I need, the type of tissue that I need in terms of preservation, and anything else that I should consider before I extract the tissue Jim Ward: It sounds like you and Rana have decided that you are castrate resistant, but it seems like that's a slippery definition. How do you get to that conclusion? If I took my notes down correctly, you started abiraterone in November of last year, and you've been on it for less than a year, and you're keeping your PSA at less than 1.0. To me, that doesn't suggest castrate resistance. Brian McCloskey: I think the way that she sees it is that I've been on first and second line hormone therapy, apalutamide being the first line hormone therapy, and abiraterone being another second line hormone therapy. What she's seeing is that I hit this nadir at 0.45. And while it's not spiking, like we saw previously, it's moving up. She's seeing that my cancer is becoming resistant to second line hormone therapy. I'm sure that there is a medical definition, but I don't know what the definition is, other than you're not responding to first and second line hormone therapy. I sort of am responding. If I took abiraterone away, then I can imagine that my PSA would be going through the roof. That's why I'm still kind of early in this castration resistant setting. It's probably not as black and white as you and I would like it to be. Jim Ward: I look superficially at the trend line for your PSA, and the kinetics of it don't seem it's accelerating very quickly. Brian McCloskey: It should be noted that my disease is different. I fit into the 15% of metastatic prostate cancer patients who don't have bone metastases. That's the good news. I don't have any distant mets either. That's also good news. But I have it in this peritoneum area, which creates complications in terms of how you treat it. Brad Power: Our friend Willie Hoos pointed out that you could prioritize the testing if you knew the treatment that you are considering, and it would give you more confidence to point to that treatment. Am I correct that there is no immunotherapy on your treatment list? Brian McCloskey: There's Provenge and the idea that we would do SBRT (radiation) with Provenge – the radiation could maybe make the cold tumor hot and more susceptible to Provenge. But that's the only immunotherapy. Brad Power: There are certain tests, like IHC, that you could use for immunotherapy. If you're not going to pursue immunotherapy as one of your treatment options, that would lower IHC on the list. That's one filter. Related to your strategy, since we're fresh off of listening to Bob Gatenby, would you be considering drug combinations or drugs in rapid succession? If so, you might want to do functional testing on that combination. For example, you could take the five on your short list and then maybe combinations of those five and do functional testing on those and their combinations to help you figure out which is the best. Functional testing seems like it should be very high on the list, doing this handshake between the treatments, the treatment strategy, and the testing. Brian McCloskey: I've had this conversation with Rana regarding functional testing, and she doesn't really trust ex vivo functional testing. She's not going to treat based upon functional testing. I wish I had a different answer, but that's what I've got. Brad Power: I would be assertive and say, “while I wouldn't treat based on it, it might help.” The way Rick phrased it with Tanya Dorff was, “if you were equal between these five, or two of the five or something, would that put the finger on the scale to tip it in the direction of one?” It's not that I'm going to base a decision on it, but I'm going to be influenced by the information. It could be presented in that softer way. I would certainly think that way. Brian McCloskey: It's on my list. I don't want to abandon it. I see the value in it, for sure. I just have to figure out how to get her to see that. I'll be speaking to another prostate cancer oncologist, William Oh, later today, and can see what he thinks. Mike Yancey: I'm familiar with PSMA, but what's a PSMA bispecific? I'm not familiar with that terminology. Brian McCloskey: it is an engineered T cell to target the expression of PSMA (prostate specific membrane antigen).