Ewing's U: Giselle Sholler, MD | Precision Medicine + The IN:Formation Project
EPISODE ONE: On May 12, 2022, The Little Warrior Foundation + Giselle Sholler, MD discussed the role of advanced genomic sequencing, precision medicine for Ewing Sarcoma. Dr. Sholler also outlined the incredible IN:Formation Project.
Download the patient overview from Beat Childhood Cancer Foundation.
WEBINAR TRANSCRIPT:
Note: The following is the output of transcribing from an audio recording. Although the transcription is largely accurate, in some cases it is incomplete or inaccurate due to inaudible passages or transcription errors. It is posted as an aid to understanding the WEBINAR, but should not be treated as an authoritative record.
Maggie Spada: Hello and welcome everybody. Thank you for joining us on our first ever Ewings U webinar and podcast. I am Maggie Spada. I'm one of the co-founders of the Little Warrior Foundation and mom to an 11 year old Little Warrior, Lucy. Today, we are going to be speaking with Dr. Giselle Sholler about her team's inspiring work in precision medicine for Ewing Sarcoma and hearing a little bit more about her team's IN:Formation project.
So a little bit about Dr. Sholler. Dr. Sholler received her master's degree in microbiology and immunology at McGill University and her medical degree at New York Medical College. She completed residency in Pediatrics and a fellowship in Pediatric Hematology Oncology at Brown University. Additionally, she completed a sabbatical through the NCI and the NIH in clinical trial management and post-graduate work in clinical pharmacology at Tufts University. She is currently the director of Rare and the Rare and Solid Tumor Program at Levine Children's in Charlotte, North Carolina. And she is professor of pediatrics and the principal investigator of the Sholler Pediatric Oncology Research Laboratory (that's a mouthful) at Levine Children's Hospital. She is also the chair of the Beat Childhood Cancer Consortium. The Beat Childhood Cancer Consortium is a group of over 50 universities and Children's hospitals that offer worldwide network of clinical childhood cancer clinical trials that is all coordinated by Levine Children's under Dr.Sholler's leadership. So we are very proud to say that Dr. Sholler, through beat childhood cancer, is a recipient of a grant from the Little Warrior Foundation. This grant was co-funded by our awesome friends at the Sam Day Foundation in Oregon, and it is really a privilege to be a part of this exciting things that are happening under her leadership at Levine's. This is only possible because of contributions, donations and gifts that are made from the communities and the loved ones of the many patient families that are on this call. So a heartfelt thank you goes out to all of our supporters.
[00:03:06] Ewing's U webinar and podcast is a production of a Little Warrior Foundation. We are a National Childhood Cancer Foundation with a laser focus on finding a permanent and complete cure for pediatric Ewing's Sarcoma. Little Warrior Foundation was founded in April of 2020. We've granted out over $1,000,000 to high potential therapies for increasing survivorship and decreasing toxicity for Ewing Sarcoma patients. You can find us all the places where you find things Facebook, online, Instagram, so be sure to follow us there. But now I'm going to kick it over to Pietro and Emily to introduce themselves before we hand it over to Dr. Sholler.
Piero Spada: [00:03:47] All right. Thanks, Maggie. And thanks to Dr. Sholler for being here and thanks to everybody for joining us on our first ever webinar. For those of you that don't know me, I'm Piero Spada, co-founder of Little Warrior Foundation, and I'm also going to be your moderator for today. So as such, I have a couple of housekeeping notes. The format is pretty general. It's going to be roughly 30 to 40 minutes of a presentation, followed by 15 to 20 minutes of a Q&A session. Now, as you probably have noticed on your Zoom, both your audio and your visual has been disabled. That's intentional on our part. But by all means, ask your questions. And the way you can ask your questions is by using the Q&A box in the lower right hand corner. Simply type those in throughout the presentation and we'll do our best at the tail end to field those questions. The one polite ask that we have is that we cannot discuss anything patient-specific. So keep that in mind when entering your questions. And with that, I'm going to kick things off to Emily and we'll get going with our webinar. Thanks for being here.
Emily McFadden: [00:04:45] Hi, everyone. I'm Emily McFadden, one of the co-founders of the Foundation. And we're so excited -- we have over 50 people on the call right now and we have many others who wanted to be here today but couldn't. So this will be this is being recorded and we will make this available via YouTube and through other channels. So I will be following up with everyone in the next couple of days to get you the resources. So there's a lot of information that's really exciting coming at you. We don't want you to feel like you have to scribble it all down or take screenshots. We'll make this all available to you. So without further ado, I will pass this off to Dr. Sholler.
Giselle Sholler, MD: [00:05:30] Right. Can you hear me okay? Yes, we can. Thank you so much for inviting me here to be a part of this Ewing's U webinar with everyone. I'm really excited to be talking to all of you and to be sharing some of the work that our team has been doing in Precision Medicine and Ewing Sarcoma. We this is a large team and I'm thankful to be able to represent everyone here. But between the clinical teams across the country that have participated in the genomic sequencing of the patients and the lab team doing the research, our bioinformatics team and some of our genomics sequencing going to kind of try and share a little bit of what everyone has been doing.
So I was just going to talk a couple of slides about background and Ewing Sarcoma Genomics, although I'm sure most people on this call are already familiar with this. But Ewing Sarcoma is obviously a pediatric bone and soft tissue. Pediatric bone and soft tissue sarcoma was account for about 12% of all childhood cancers, and all the cure rates in localized disease generally is over 70%. The prognosis for children with disseminated disease is quite poor, and that's what we're really focused on changing. The Ewing Sarcoma are small round cell sarcomas with characteristic molecular findings in varying degrees of neuroectodermal differentiation. It's characterized in most cases by a recurrent balanced translocation between the ESR-1 one gene on chromosome 22 and genes belonging to the ETS family of transcription factors.
Giselle Sholler, MD: [00:07:10] The main driver is a reciprocal translocation between ESWR1 and FLI1 genes, resulting in this fusion that is seen in about 90% of patients. The other 10% are have the EWSR one generally fused with other ETS transcription factors. Ewing Sarcoma, like most pediatric cancers, has a low mutation rate only 1.15 mutations per megabase. This is important when we're talking about genomic sequencing and pediatric cancers in general, that they have a low mutation rate, whereas many adult cancers have a higher mutation rate. So looking at the DNA specifically in the adult cancers are able to find targets for drug treatment. In pediatric cancers, we're really focused on not just looking at the DNA, especially not just looking at panels, which we'll talk about in a bit, but also at the RNA. The RNA tells us what's expressed in in the cancer, what pathways are active, because we can't always find a specific DNA mutation to target. Other common mutation in Ewing Sarcoma, about 15% have a mutation in STAG2 to or CDKN2A to a which involves in cell cycling or TP53 tumor suppressor that when mutated, allows cancers to form.
Giselle Sholler, MD: [00:08:26] There are germline mutations that occur in Ewing Sarcoma. That means in their own DNA that patients may carry these predispose them to form cancers that occur in 10 to 13% of patients. And these are the common germline mutations that are seen in this cancer.
Giselle Sholler, MD: [00:08:42] So in the United States, standard of care for localized disease currently on the one side here, I have a list of all the different protocols that have been published in Ewing Sarcoma. Unfortunately a lot of them we can see this cyclophosphamide doxorubicin vincristine and then [ifosfamide]. Chemotherapies and cycles of this have been used for almost 15 years and really dose compressing has shown an improvement in survival. But there's been very little change in therapy. Is an upfront treatment for Ewing Sarcoma in quite a long time and very little change in outcome. The outcome is about 73% four years for localized disease, which is pretty good. But those for metastatic disease, even right at diagnosis, the outcome is still only 35% at two years. So we need to do a lot better for children with metastatic disease. And overall survival for recurrent disease is quite poor. And so this is what we really need to change.
Giselle Sholler, MD: [00:09:40] I'm going to start with a big picture of genomics. This is a paper that our team published having sequenced over 250 pediatric cancers, looking at the genomic and transcriptomic analysis and this is focused initially if we focus on relapsed and refractory childhood solid tumors, I'm going to go a little bit in depth for each of these. What's important, again, as I mentioned before, that pediatric cancer is have generally been about 20% at best of DNA targets that we can find. When we just look at the DNA and especially a lot of patients have come to me and said, oh, we did genomic sequencing in our our tumor, our team did that.
Giselle Sholler, MD: [00:10:21] What they've done is send to Foundation Medicine, which is the most common that looks at about 600 DNA genes. And those panels of 600 genes were created for adult cancers. And so it's very rare that we find something for our pediatric cancers, and it's really just the DNA. And so when your oncologist or your team is telling you that they are doing genomic sequencing, it's important to ask what depth of genomic sequencing is being done. Is it just a panel? And are those panels really focused on adult cancers? Less likely that we're going to find something. Whereas here we're looking at where we did whole exome sequencing, which is at minimum what should be done. And that looks at 20,000 different genes in the patient's tumor and also looks at the chromosomal changes. So the beginning part here -- and these are all our pediatric cancers -- you can't the top.
But here shows the chromosomal changes, whether there is amplifications or losses or gains of different chromosomes. And then we can look in depth of what's happening there. And then these are the most common mutated here we see the EWSR1 one and this is the group of Ewing's patients that we sequenced. And so it's important to look not just at the DNA, but although the DNA is important and we are learning that while some of these are not targetable, they may have an impact on the different pathways.
Giselle Sholler, MD: [00:11:44] So from this DNA is translated into RNA. So every cell in the cancer may have similar DNA, but what's activated? What if a gene is mutated does that turn that gene on? Or does it turn that gene off? And that's what the RNA can tell us, is that gene is constitutively activating so that lots and lots of that protein is being made. And if that's a protein that's important in cell survival and division, that's when we might want to target or a pathway we might want to target to turn that tumor off. These are the common mutations we saw in our 150 patients we can see here. TP 53 is a common mutation. Orange are the sarcomas in sarcomas as well as other in brain tumors and neuroblastoma. The EWSR1 is primarily only sarcoma. Some of the other interesting pathways that we're interested in are the CDK4 pathway, which has a lot of mutations in sarcomas. RB1 also is very important in sarcoma, so this helps us start to focus on what we might want to look at. What's really interesting in this study was we treat all sarcomas similar, we treat brain tumor similar, we treat neuroblastoma similar. But looking at this, we can see that there's a lot of overlap and then genomic changes that happen in pediatric cancers and that sarcomas may have similarities to neuroblastoma and or brain tumor is only 9.6%. are kind of the mutations that happen or only in sarcomas. The others happen in other cancers. And so perhaps we should be not necessarily treating one cancer--sarcomas-- different for neuroblastoma as if they share the same genetic changes that are causing the cancers to grow, then maybe we can target them similarly. And that's something that we're really trying to learn about. We can see and this is again in relapsed patients, not in upfront, but through sequencing, we can see that patients develop therapy associated mutational signatures. So these are just examples of 42% had evidence of the previous therapies they had causes more changes within that cancer. So we can see Ewing Sarcoma down here. Many of our patients are -- some of the patients -- had changes that were associated with temozolomide are causing mutational signatures within the cancer themselves, maybe making them resistant to that drug And so maybe not a drug that we want to continue using in those particular patients.
And this is looking at the RNA. What's interesting here is when we look at patients, what's being expressed in their cancers, in the pathways that are driving them: Here is a group of neuroblastoma. We see ALK is overexpressed in neuroblastoma. But if we look here, these orange again are the sarcomas. And if we go even deeper, the red are the Ewing sarcoma. So this is the Ewing Sarcoma Group here and we started to get a peek here that ALK red is overexpressed, blue is expressed and we can see that there are some that overexpressing ALK and Ewing Sarcoma.
Giselle Sholler, MD: [00:14:54] So very interesting. These middle ones here are brain tumors. This group here and then these are all the sarcomas over here, primarily this group really being what's helping us understand what's being expressed in Ewing Sarcoma. What was interesting in this study as well, you can't quite see, but there are three gray groups here. These are three clusters which were mixed pathologies. So those this cluster of pathologies actually had sarcomas, neuroblastoma and brain tumors mixed together that were more alike to each other than they were to their disease of origin. So these three clusters of patients probably need a completely different treatment plan, and that's something that we're exploring further in. One patient really want to look at each individual patient and their genomics and understand what's causing their cancer to grow, to be able to treat that more specifically. And one of the questions we also get from some oncologists: we already sequenced that patient's tumor. We don't need to do it again. Especially at relapse, we believe that it's really important that you do sequence again. These are just two examples of patients. Actually, this one's a rhabdomyosarcoma on top of a neuroblastoma on the bottom. And this shows T1 one is the first tumor that was sequenced and there's... each of these colors is in different mutation.
Giselle Sholler, MD: [00:16:13] We can see there was some there. 645 days later, this patient relapsed, had another biopsy done and re-sequenced and was identified to have PIK3CA mutation which was targetable. In the neuroblastoma, there's a tumor initially did not have an ALK mutation, but 192 days later when this patient progressed and the tumor was re-biopsied and re-sequenced was found to have an ALK1171 mutation which can be targeted with an ALK inhibitor. So really important that it's not just at a diagnosis, but at each relapse. Now we've been following patients tumors and seeing how tumors evolve over time, why they're coming back, what clone is growing out, is that targetable and something that's we're working with insurance companies and with foundations to help push the approval of re-biopsy/re-sequencing. This is important for us to understand what's happening with our patients. So just as I mentioned, we have a Childhood Cancer Consortium. These are a lot of the hospitals that participated in this work and that are continuing to participate in the genomic sequencing. So how did we use all of that information clinically?
Giselle Sholler, MD: [00:17:28] Well, here we go. So we had a clinical trial that is now closed. And I'm going to share with you a little bit of our results from our clinical trial, the process that we used, and then how we're now using that clinically as standard of care for our patients and not necessarily as a trial as research anymore, although the lab portion is still research, but the clinical treatment of our patients is not.
Giselle Sholler, MD: [00:17:54] So on this clinical trial, patients were screened and enrolled, the tumor was biopsied and the samples were collected. And tumor biopsy can be a needle biopsy. We really only need enough that's in an 18 gauge needle biopsy. We don't need a large amount of tumor to be able to do this work. Part of the tumor was sent for clinical testing for a DNA exome, as I mentioned, in RNA sequencing. Again, they both look at about 20,000 different genes. So a full picture of the patient's tumor when we get the results back. Working with our bioinformatics team, we have a molecular tumor board. The molecular tumor board is made up of clinicians from across the countries. If we have a particular cancer that we need specialists in, we'll talk to them. We have pharmacists on the tumor board that will help us look at drug-drug interactions. Looking at the medications the patient might already be on and on, the medications that we're selecting for the patients, how to combine them together, what is the safe dosing and what follow up do we need to follow liver functions? Do we need to follow Echo EKG? How do we follow these patients on this new set of medications that we're creating for them? The molecular tumor board in this case also, is it very important that we have the bioinformatics team participating as they help us really look deeper into the genomics of each patients and the pathways and the biology? So it's team medicine, not just a single oncologist taking care of patients, but a larger group of specialists that can help guide individualized treatment plan for that patient.
Giselle Sholler, MD: [00:19:30] And during the molecular tumor board, we are able to take in considerations from the family. We do discuss that at the beginning of tumor board. The primary clinician presents the case and then we'll say if this is a patient that has relapsed multiple times and just wants to be home, does not want to be admitted, we can avoid IV medications that require admission and focus on oral or medication so that can be done in clinic. Or if it's a family that wants to be as aggressive as possible, maybe we'll lean more towards the IV. So it's very personalized towards that patient, that family, their situation as well as the genomics of the cancer. Then we try treatment and response. At the same time, a piece of the tumor also in this clinical trial and continuing goes comes to our lab for generation of tumor cell line of that patient as well as a patient derived xenograft. So we create little avatars of each patient by injecting tumor into the flank to be able to then use these models for future research. We can look at different drugs, high throughput drug screening to look at what medications, specifically this patient cells might respond to or not respond to, and then that gets correlated into a larger body of research, which I'll talk a little bit about in the future.
Giselle Sholler, MD: [00:20:44] And so just in terms of this initial trial, one of the endpoints was looking at feasibility and how long does it take to actually get this done. Can we do this in real time for patients, patients who are waiting and need treatment right away? Again, these were relapsed refractory patients. So biopsy was performed. Generally, the genomic sequencing was completed within ten days. Then the genomic sequencing needs to go under the BIOINFORMATIC analysis. Their bioinformatics team that took between 16 and 18 days. And then the molecular tumor board generally within three weeks was able to meet. In terms of when drugs start, we do need to get drug approval from insurance companies. And so, as we all know, that can take some time. The CNS that really the delay here was recovery from brain surgery as to why this was delayed a little bit more in terms of starting medication. And sometimes some of these patients would get radiation therapy prior to starting the medication post surgery. So that that was delayed for other reasons other than the fact that the medications were available earlier. And so just in terms of how we choose drugs for patients, we do have a drug algorithm that molecular tumor board does follow. There's first line evidence, second line evidence and third line evidence.
Giselle Sholler, MD: [00:22:01] So the first line evidence is, does the variant have a direct drug match? So what does that mean? We do look at the DNA first. So if there is a DNA mutation that has a definitive drug match, so an ALK mutation, and then we have an ALK inhibitor and we can target that, that gets top priority. Those get pulled up to the top of the discussion and are selected first. Then what do we choose second? Second is does the is there a DNA that infers a drug? So it's a drug that doesn't necessarily target that DNA, but there's a mutation in a gene involved in a pathway that that drug would target. So, again, DNA, again, is still brought up, even though it's an inferred match, not a direct match. Third is the RNA. So the RNA we do use as a third line, and that is looking at our expression. You look at what the expression of the gene is compared to normal, also compared to other children with the same cancer. And when that, for instance, ALK can be mutated, it can also be overexpressed. And we see ALK overexpression, we may select an inhibitor for that patient. And so those are the three ways we choose in this study. We would choose up to four different agents. We know from original from phase one trials that single agents in and of itself have a very poor response rates. Children who are treated with, for instance, in phase one studies, when there's a single agent, the response rate is usually about 10%.
Giselle Sholler, MD: [00:23:35] When there's two drugs, it's usually about 35%. So we know that when we combine drugs allowing or NOT allowing tumors to become resistant to a single agent by targeting that tumor with multiplied multiple different ways, we can get better responses. And so our goal on this study was to have four different medications available for that patient to try and get better responses. These are some of the drugs that were selected using RNA. So every patient on the study, about 20% of the patients did have a DNA match. And we're able to have a drug selected by DNA, but 100% had drugs selected by RNA as well. And again, here are the rare or the blue or the sarcomas over here. These are different drugs based on different pathways. And these are if the drug was chosen more than ten times, we pulled this up. So these are some of the common drugs that were selected on this trial. Again, it's multiple different ones, but some of these are Irinotecan, Temodar, that are commonly used in Ewing Sarcoma, combined with some drugs that we're seeing as maybe effective such as Palbociclib or vorinostat in Ewing's as well. So just in terms of how do these patients do this is change in tumor. So an increase here. We see tumors going, getting bigger here we see tumors getting smaller. So two thirds of the patients and again, these were relapsed refractory patients that had bypassed all standard of care and had most of them had been on multiple other relapse trials prior to coming onto this.
Giselle Sholler, MD: [00:25:10] So this was a very experimental when we did this study, you can see progressive disease versus all the way down to CR and we had a two thirds of patients did have a decrease in their tumor size with the genomic guided therapy. When we pull out our 18 Ewing sarcoma patients in this group, this is some of the mutations. Again, the EWS-FLI1 one was seen in the majority. One EWS-ERG, as I said before, 90% are going to be this and then 10% will be a different fusion. These are some of the drugs that were selected for our Ewing's patients here. And we did have two patients going to have a CR. Four had stabilization of their disease. And just going back here, stabilization of the disease even here can be a decrease in size. It just has to be more than 30% decrease to upper. So we had six out of the 18 that did well on this study. So from that, we have now 17 Ewing cell lines established in our research laboratory here over the last year with funding from the Little Warrior and Sam Day Foundation, we really grown our Ewing Sarcoma research in our lab and Dr. Katie Smith is on the call as well. Who can help answer questions later if you want to hear more about the lab research that we're doing.
Giselle Sholler, MD: [00:26:31] But since over just in the last less than a year, since we've about a year now, since we started this collaboration, we have, as I said, 17 cell lines established in our laboratory for research. This is some of the RNA sequencing that we did. We performed RNA sequencing on 13 of our Ewing's patients. And we can see these are some of the genes that popped up across --again, red is overexpressed and blue is under expressed -- and so we can see JAK1 and there are JAK1 inhibitors available have the read most of these patients except for this last one are overexpressing JAK1, CDK4 as well. There's over and under and there are CDK4 inhibitors that we can look at. ALK, as I mentioned earlier, not a common gene that we think about in Ewing's, but we are seeing significant expression in some patients. And then HDAC, which is the histone deacetylase and there are histone deacetylase inhibitors such as vorinostat and panobinostat that are of interest. There are others as well that you can see on this list, but those are for that we thought were of interest.
Giselle Sholler, MD: [00:27:43] What's important to see in this is how different each patient is. Again, why we want to really personalize the treatment for children with Ewing Sarcoma and other pediatric cancer. But we can see this [Pixie38?] Is overexpressed in this one patient, but really not in the others very much. But this one patient might benefit by targeting that pathway.
Giselle Sholler, MD: [00:28:05] NRAS is another pathway that we sometimes have selected. Actually, one of the patients that had the CRs in our previous study was was treated with an NRAS inhibitor. You can see for these two patients, that drug might be really important and moderately important from some others, but not at all for this. And so that's why understanding your particular child and what's happening in their cancer at the moment when we're treating it again, we don't want to when a relapse happens, we need to re sequence at that moment in time, because especially the RNA may be very different than it was a year ago. And looking at that, so as I mentioned, but looking at these patients here we saw overexpression of these four genes that were of interest. So Katie who's Dr. Smith who's on the call, has tested I think 5 to 10 of these patients cell lines with each of these drugs. What we're seeing so far and again, that would be a whole discussion in itself for her to share all that lab research that she's done. But looking at HDAC, panibinostat is showing significant sensitivity across all patient cell lines that we've looked at that we shared before - and at a very low doses, doses are achievable in patients. What's been really interesting and this is just a bit of a teaser, but she's also compared share treated panibinostat with the upfront therapies. Again, as I mentioned at the very beginning of the talk, we really need to make a difference upfront for these kids, especially for the metastatic children. And so where we see VDC and IE being used as the standard chemo's, she was able to combine that with VDC, combine that with IE and it's showing in the laboratory that adding panibinostat to each of those chemotherapy regimens significantly improves the cytotoxicity of that regimen and shows a significant decrease in increase in cell death with those combinations across three patient cell lines that she's looked at so far. So we're really excited to move that forward in the lab and to move into animal models and ideally move that towards a clinical trial and even a pilot study looking at adding that to upfront treatment and seeing if we can make a difference, especially in the metastatic patient. So that's why I'm most excited about at the moment.
In the ALK patient cell lines, she tested against two ALK inhibitors that we use currently very frequently in neuroblastoma. So Ceritinib and erlotinib. Erlotinib is actually the newer ALK inhibitor. What we're seeing in the lab is that the Ewing Sarcoma cell lines are the ones that are sensitive, are sensitive to ceritinib, but they're not. None of the Ewing circumcisions are sensitive to erlotinib, so even selecting the right drug within a class may be really important and something we need to study further.
That might be important in the JAK inhibitors, we have tested ruxolitinib with JAK inhibitor and we're not seeing any response to that. We have a newer JAK inhibitor coming into the lab to start testing. But but looking at that, I mean this overexpression of JAK1 is, is significant. So we would expect, but we're not seeing that with the JAK, this current JAK inhibitor.
Giselle Sholler, MD: [00:31:26] And CDK4 as I mentioned earlier, this is something that we see sometimes mutated in the DNA but also overexpressed in the RNA. Palbociclib as well as Ribociclib and others are CDK4 six inhibitors and palbociclib is showing significant sensitivity across all cell lines. So these may be --for patients that have overexpression of these -- maybe important drugs. And one of the important questions that Katie is also answering is, does RNA expression correlate with drug sensitivity? And so just because you have overexpression of a gene, does it mean that those cells will be more sensitive? And what we're seeing here is, based on the x axis here is expression of the gene. We can see here with HDAK expression, a higher expression... and then this is the dose of the drug here -panibinostat -- so the higher expression, the lower the dose that you need to kill the cells. So and it's the trend is across for all three the higher ALK expression, the more sensitive the cells are to ceritonib, the higher CDK4 expression, the more sensitive they are to palbociclib.So it does correlate that with higher expression of the gene, those cells are going to be more sensitive to that drug.
Giselle Sholler, MD: [00:32:46] So our program vision in the IN:Formation Project is to take this from being purely research, to be able to apply this to our patients. And that's what we have been doing over the last year. Our goal has been to all children with cancer will have complete genomic sequencing and analysis of their tumor, both at diagnosis and at relapse. We piloted the study here at Levine Children's Hospital over the last year and have sequenced 170 pediatric cancers. And that was great to see the entire hospital -- and that requires collaboration from the surgeons, from the neurosurgeons, from all the research department, from the the nurses pathology, really to be able to obtain these tumors at the time they're having their surgery, flash freeze them, send them for genomic sequencing, get the data back and such. But we have shown that it is possible to do here and now are expanding this out to all of our hospitals because we believe the information can help us understand each child and their cancer to better improve outcomes. And not just for that one trial, but the more information we collect, the more we can learn how to better interpret this information as we're doing in the lab. Better interpretation and understanding better which drugs and use this information.
Giselle Sholler, MD: [00:34:05] So we're working and collaborating with SEMA4 genomics to create a database.That will put all the sequencing information and combine all of this, not only the genomic information and the genes, but the patient's de-identified clinical data, their data, their outcome data and the lab research to be able to be usable and searchable by all our investigators so that we can work together and analyze this data in lots of different ways to improve outcomes for children. So here is kind of the the whole process that I outlined before. We are collecting the patient information into the database. The sequencing DNA and RNA TRANSCRIPTOME is being done both at diagnosis and relapses, bioinformatic analysis again, we'll look at the different pathways and what's driving that patient's cancer. Molecular tumor boards are occurring. They're going on right now. Every other Monday, we're discussing somewhere between two and four patients. In our lab, we are creating cell lines, xenograft modelsfor tumors that are collected. And then we are collaborating and sharing data and sharing tumor tissues. So cell lines. We have sent cell lines to UMass in Massachusetts, San Diego. We are sending quite a few cell lines now to Hershey at Penn State. And we want to really be able to share more and more information and stimulate more and more research happening for our patients.
Giselle Sholler, MD: [00:35:32] So to participate in this study, the genomic testing requires paired tumor and normal. So we really need the following. The tumor is preferred flash frozen. That has the least effect on the RNA. We can use paraffin embedded tumor blocks, but that does sometimes affect the RNA. But we can do that now. We can do this from if a patient has a bone marrow biopsy and tumor is in the bone marrow, we can use that as well. As long as there's tumor and greater than 20% present, we can use that. We also need a normal because as we all know, nobody's perfect. And so our own DNA does have alterations in it, most of which have no consequence whatsoever. But what we need to do is sequence the patient's normal genome and then we sequenced tumor. And we want to look at what changed to cause the tumor. So that's why we need the normal to see what are just normal DNA changes that are present, that aren't really actually causing the tumor. We can subtract those out. The bioinformatics team can check those out, not me. And so for that, we need either a blood sample or a saliva sample or just a buckle swab, which is the swab inside the cheek. And then we also need pathology reports and then consent for genomic sequencing. And those are clinical consents like you would consent to have a surgery done. The testing is then sent to SEMA4 our genomics and that's Connecticut that they do all of our genomic sequencing, the whole exome and RNA transcriptome is completed and then they generate a clinical report that will become part of the child's medical record and shared with their oncology team.
Giselle Sholler, MD: [00:37:14] We also do involve invite home oncologists to participate in molecular tumor board for their patients. So while if we do want the tumor to come to the research lab, then patients do need to enroll on the information project because the piece that's happening in the lab is still research. While the clinical care and the sequencing is clinical, the having the tumor come to the lab and grow the cells, etc. is research so there's no cost to participation. But patients must be seen at one of our enrolling sites to enroll in that, and we do need to have that enroll prior to the biopsy because we do need to collect the cells alive to be able to come to the lab. So from the biopsy, some one piece gets frozen a little bit, other goes into a tumor tissue storage solution that comes to the lab so we can grow the cells. This can be done at diagnosis or at any relapse or multiple times for patients. And so again, the goal of the information project is to have DNA, RNA transcriptome for all our pediatric patients being done at diagnosis relapse to provide as much information for the clinical team to best take care of patients, to create a searchable database of clinical information, including therapies, responses, event free survival, overall survival along with genomic information so that we can learn if certain number of patients with a certain genomic mutation all do well, why? Or a certain number of patients with a genomic mutation treated with drug x do well.Then we should get drug next to all those kids that have that mutation. That's the power of having the numbers.
Giselle Sholler, MD: [00:38:53] And again, our goal is we were able to do 170 just at one institution we have I'll show you the list of institutions that are opening soon. And our goal is that we have six currently open. So we can multiply that by six just this year. Here we go. These are the sites that are currently open and we have 14 are planning to open summer of 2022. So these are all in process of opening. So we'll have 20 sites so we can multiply that by 20. Our goal is to have 1000 each year being sequenced, and that's really what's going to give power to the economic analysis and the research we can to really try and find that. So again, we want to create cell lines and xenogafts for all patient samples so that we can collaborate and share data and share tumor tissue with researchers across the country that want to help us to find answers for Ewing Sarcoma. And we'll continue to host molecular tumor boards for any sites that are participating in the genomic sequencing for their patients to get. Again, it's it's really clinical care that it's hard to do. Just as a single oncologist, we really need a team of people looking deeply at the genomic information and have a pharmacist who is experienced in genomic sequencing and in combining drugs together for a particular patient.
Giselle Sholler, MD: [00:40:13] I think that's everything. And I, I didn't go too far over, but we're really excited to have this project kick off over the last year and see how successful it's been just in the one year that it's been open and the interest in hospitals across the country to participate and to make this available to patients locally for their kids. So all stuff. Now, I did want to mention that we do have more members of my team that are on. And Dr. Thomas Russell is one of our Beat Childhood Cancer physicians from Wake Forest who is an expert in Ewing Sarcoma and helping us with this project. So Dr. Thomas Russell is is on the call to help me with the questions as well. Dr. Katie Smith, who is our PhD in our research lab, who is really focused on Ewing Sarcoma and doing all of the laboratory research. And Abby Moore is our Beat Childhood Cancer Research Consortium manager who is helping us to run this entire project and getting all the sites open and helping to connect patients with hospitals that might be close to them to be able to participate. So they're all on the call as well. And I think I'll hand it back over to the Spadas to talk about questions.
Piero Spada: [00:41:33] Dr. Sholler, that was amazing. We have so many questions in the chat here, so I'm going to do my best to kind of filter through this. There's lots of people thanking you for what you're doing, and they're asking the question "How if they don't see their local hospital listed, how can they help to have them become part of the Childhood Cancer Consortium?"
Giselle Sholler, MD: [00:41:54] Yeah. They can ask their oncologist to reach out to me directly and or to Abby, and we'd be happy to work with them to help get them to be part of the group.
Piero Spada: [00:42:05] Okay. And just as a follow up to that, we're going to be linking to a one page document that has a point of contact for everybody that's interested in this and that will be sent via email. So some of the practical questions will be done via follow up. All right. So here we go with questions. Is there an upper age? Is this just purely for Pediatrics or is this for Pediatric and adults? What are your thoughts there?
Giselle Sholler, MD: [00:42:28] Um. So technically there's no upper age. Our hospital here primarily sees patients up to age 21, although we do work with a lot with the Ewing Sarcoma adult team. Dr. Russell, How, what would you say in terms of upper age?
Dr. Russell: [00:42:48] Yeah. Yeah, I think I think the reality is, is we live in a world where there are some natural challenges between kind of a pediatric oncology and adult oncology. And I definitely think that is something we have to acknowledge and understand how to best do that. But as you guys well know, this is the disease that predominantly has a peak in kind of adolescent young adults. And in fact, in many centers, people defer to the pediatric oncologist. And in terms of treatment, because really we have a lot more expertise in terms of how to best treat this disease despite age. But of course, there are some natural limitations. I can treat your child or sorry, your young adult. That's 23, 24, 25. The challenge is, is how do I care for them in a system where I don't have access to an ICU or or some of those resources? So and I agree. I urge you as parents and as part of this congregation to really help us think about ways to systematically approach the disease in its full complement, rather than just thinking of it as a pediatric disease or an adult disease.
Giselle Sholler, MD: [00:43:56] Yeah, I would say for and I think that's the main question is the admissions and ICU, we have treated I've treated a neuroblastoma at age 35 outpatient. And so I think it differs in, you know, we can sequence and we can make recommendations. And if we're doing outpatient treatment, that's one thing. If it comes in-patient or can we work with your oncologists I guess would be make it more of a team approach for the adult or older ages.
Piero Spada: [00:44:26] Thanks for that follow up. So there's two patients that actually on here that have FUS-ERG mutations. Believe it or not, it seems like two separate patient families. Then one question is, do you have that cell line currently in the databank? And then the second question is, do you envision a day where we're actually treating the fusions differently based on the driving fusion gene?
Giselle Sholler, MD: [00:44:53] Yes. I don't know off the top of my head if that's one of the ones that grew. I don't know if Dr. Smith, if you know, but I can find that out. We can look and see if that is one of the ones that is growing in the lab. It's definitely came to the lab. So about when cells come to the lab for a patient's tumor, about 75 to 80% will grow a cell lines, not every patient's tumor -- and that's pretty much consistent across labs across the country. We don't know why not every tumor will grow, but I can find that out to you and I can let you know. Piero can pass it on.
Piero Spada: [00:45:31] And it seems like we have several European attendees as well. Is there anything they can do over there with regards to submitting tissue sample to this program? Is there European collaborators that you're thinking of bringing on board? Can you speak to that at all?
Giselle Sholler, MD: [00:45:48] Yes, so we can and Abby can talk to more about that. We are working to be able to do consents over virtual like this, basically virtual consent in families and having families that we are currently receiving samples from international patients as well. But there are terrific teams in Europe at the in Amsterdam or Princess Maxima Centre in the Netherlands and Gustave Roussy in Paris. There are teams there that are doing genomic sequencing as well that I would encourage kind of reaching out to them as well. But if you would like to participate with us and we can do a lot of it virtually.
Piero Spada: [00:46:30] And then there's a several questions revolving around maintenance during remission. Is this type of genetic sequencing and maybe this is the path you're headed down, do you foresee this as being part of the maintenance program that we're doing this kind of deep dive into the genetics, the RNA sequencing, etc., to make sure we're monitoring for relapse?
Giselle Sholler, MD: [00:46:51] Absolutely. So a few of our first molecular tumor boards in Ewing, so we've had five now for Ewing Sarcoma patients and a few of them have been for patients who were metastatic at diagnosis. And for those patients we know the outcome is not great. And so two of them, the decision was to continue. Both patients I think are getting the Vincristine or [irinotecan / temodar] VOIT with targeted agents. And I believe palbociclib was one that was chosen for those. But yes, we think for those patients, it's really going to help us decide what the best maintenance therapy is, because we know that maintenance is we've seen it in other cancers become really, really important, obviously, in leukemia and then in neuroblastoma. And why aren't we doing this in Ewings? Tom, do you want to address.
Dr. Russell: [00:47:35] Yeah, I so appreciate that question because it's a paradigm that I think sarcoma has certainly been behind the ball, not with with bad intention, but just the realization of it. I think if you look at our history, we have gotten really good at using really aggressive medications in a cytotoxic fashion to eliminate the great majority, 99% of your cancer. The problem is it's the 1% that's left that comes back and harms your children. And that is the thing that keeps us up at night. And so but it's interesting is, is when we start thinking about stem and progenitor cells that really are the origins of cancer, often... We know these are cells that probably don't need high dose medications to actually harm them. They just need to be exposed to med on a continuous basis. And when they try to pop in a cell cycle, we can smash them. And that's been very clear in the literature with leukemia, where we now know there's probably about a three fold increased risk of relapse in patients that cannot tolerate or cannot comply with maintenance. We now see an intermediate risk rhabdomyosarcoma, a population I care deeply about. We also see that there's a survival advantage with maintenance. And so you're right. I would also suggest, though, I am not interested in waiting to maintenance to initiate molecular based treatments. And so it's we've got a lot to learn. But you're absolutely right, we have to think through this in a very scientific fashion because we are not one drug away from destroying Ewing Sarcoma. And so this is why this kind of work is so paramount in terms of how we advance the future.
Piero Spada: [00:49:26] Thank you for that response. This is a practical question. One participant is wondering why the need for blood test or saliva test along with the tumor biopsy. So could you answer that, please?
Giselle Sholler, MD: [00:49:37] Yeah. So that's great. And so the reason for the blood test is to sequence the normal your normal genome. So everyone's DNA has mutations in it that are just just they're kind of hanging out that don't actually cause any. Cancer or any illness whatsoever. But we just so but when we want to sequence the tumor DNA, we want to know which mutations are present normally in your in your blood, but they're not causing any problems so that we can kind of subtract those out if if X and Y mutation are just normally present in your blood and then we sequence your tumor, we see X and Y, but those don't matter. So we want to know. Those are just ones that were already present in your normal. We want to know what changed from your normal to cause cancer. So what happened? What changed in your DNA that was there originally to new mutations that happen that are only in your cancer and your cancer cells because those are the ones we want to look at. And so that's why we need the normal and the the tumor. Otherwise we can just sequence the tumor, but we might be looking at red herrings.
Piero Spada: [00:50:45] Okay. Thanks for that. And along the same lines with discussing somatic versus germline mutations, there's one question here that says, do we think the translocations are hereditary? And the concern being that the sibling might have the similar translocation.
Giselle Sholler, MD: [00:51:02] No. The EWS-FLI? No. We would learn that by sequencing the normal if we if we do find. So for instance in 10% of patients, we might find, for instance, a TP53 mutation that could be hereditary. If we do find there are certain mutations we'll look for in the normal. If there's anything abnormal in the normal, we will share that with the family, along with the genetic counselor to talk about, then sequencing the rest of the children or the rest of the family. And that does occur in some patients. We've seen BRCA2 mutations that can have prognostic importance for the rest of your family. And so that's another reason to look at the normal, to see is there something that's hereditary that's causing this cancer that could then be important for the other members of the family?
Emily McFadden: [00:51:52] There's a great question here about about safety. And once a target and a drug has been identified, how do you determine the safe and effective dose?
Giselle Sholler, MD: [00:52:04] So all the drugs that we look at are FDA approved drugs that have pediatric dosing. So we don't recommend kind of investigational agents unless if we see something that might be really important and there's a clinical trial, we would refer that patient to the clinical trial for an investigation, but we wouldn't prescribe any investigational agents. So these are drugs that we know the safe dosing, that's been studied in pediatrics. We do know all drugs have side effects. So we do go over the side effect profile for each medication. But in terms of selecting dosing, that's what the pharmacist is really there for and important. So if we are going to combine two drugs that might both have liver toxicity, then we would likely go down in the dose to a 75% dose versus giving 100% of each drug. The pharmacists are trained and experience to do that. For instance, they would do that in a similar way that if you had a heart condition and need to be on a heart medication and you had a seizure disorder and needed to be on a seizure medication, you need both medications. But the pharmacists are trained how to combine those two medications together before that may not have normally be combined together. And that's what we look at here. That's the methods that our pharmacists use for different databases. So as we're combining different drugs, again, we know what the pediatric safe dose is, but we do do a deeper dive. And we also look, let's say the patient is on another medication for nausea or something. They look at all the medications that the patients are on. They also look at any naturopathic medications patients may be on. A lot of our patients might be taking curcumin or fish oils and things like that. That's okay. We just want to make sure that it's safe and again. Then we will have monitoring CBCs liver function tests, things like that to monitor for safety. If we need to make any adjustments, we would. Yeah, that's kind of big picture.
Piero Spada: [00:53:55] Thank you, Dr. Sholler. This seems to be a question from one of your colleagues, wondering if the data set that you're collecting at BCC will be shared with the NCI Childhood Cancer Molecular Characterization Initiative to reach even more researchers and drug developers?
Giselle Sholler, MD: [00:54:09] Yes. So the publication that we hope that I showed on the first that those 200 and fifties have all been patients have all been deposited into the NCI DB Gap database for sharing. And yes, the goal is that all of it will go into the NCI database, the DB Gap to share with researchers.
Piero Spada: [00:54:28] Excellent. All right. And the event of a relapse --and I'm sorry we're firing from all different angles here, but this is how the questions are -- in the event of a recurrence. Are you finding with your data set that there's commonalities there or is it completely different across the board?
Giselle Sholler, MD: [00:54:44] So we have done a look in, especially in neuroblastoma of upfront versus relapse, and we definitely see that relapse. Patients do have more mutations, more chromosome abnormalities and findings than upfront. So that's one of the biggest differences from upfront to relapse patients is as the tumor has become more and more resistance, we do see more and more changes happening. Some of it is from, as I said earlier, with the temozolomide from chemotherapy itself causing damage to the cells and then causing if the cells can survive the temadar, they become more resistant. But we haven't we don't have enough Ewing Sarcoma patients to pull out that data yet.
Piero Spada: [00:55:26] Okay. And then with your data set, too, there's a question about developing therapeutics. Do you have any collaborations or plans to work with companies on developing new therapies for Ewing's?
Giselle Sholler, MD: [00:55:37] So we are not developing them as per se, although that would be a goal in the future. But for instance, this afternoon I had a call with Lilly. They have a new CDK4/6 inhibitor that they're very interested in, in moving it forward and Ewing Sarcoma and their current trial [irinotecan / temodar]. And I talked to them about well why not the standard treatment for Ewing's right now in relapse is that in Vincristine [irinotecan / temodar] or why not add it to that combination where there's really good data and historical control? And so we're kind of talking about that and bringing that drug into the lab and starting to do some more testing. So yeah, we and we've worked with Novartis in the past. So we while we're not necessarily creating new drugs, we are interested in working with pharma companies to test those drugs into lab, to get them into clinical trials quickly for patients that are novel agents that are being researched and available.
Piero Spada: [00:56:33] Awesome. Okay. We got five more minutes here, so we'll just try to squeeze in a couple more questions, if that's all right. There's a direct question here about TKIs. And are you testing those as standalone agents or using them in combination with chemo? And just wondering, how about that line of work?
Giselle Sholler, MD: [00:56:49] Yeah. So the tyrosine kinase inhibitors such as ALK and the other inhibitors that we are using in the lab. So Katie is testing them primarily in and of themselves first to see if there is an effect and then in combination. And the combinations she's using right now are the two up front combinations, as well as in vincristine and [irinotecan / temodar] as a relapse. So we're looking at she's doing testing both with upfront combinations in our standard relapse combination. Okay.
Emily McFadden: [00:57:18] We are getting more questions about participation, getting hospitals to participate, but also options to participate. Participate remotely as a patient. Is there an option for a remote second opinion or does a patient have to travel to one of these sites?
Giselle Sholler, MD: [00:57:39] Abby, do you want to take that one?
Abigail Moore: [00:57:42] Yeah. I think that the guy that they were speaking of sending around to the rest of the group really does speak to how to get how to get involved or to go for more information. A remote second opinion is an option for families who don't want to travel to a BCC site. Basically, you would send all your records. And set up a call with our physicians to review the samples set up and then send out for the testing. And then we would come together, do a molecular tour board, and then meet back up at a remote second opinion in order to determine next steps and how we can work with home hospitals in that process. Okay.
Piero Spada: [00:58:30] All right, last question for Dr. Sholler. And this is going to be kind of open ended, so feel free to answer any way you feel like is necessary and any level that you think, whether it's with regards to your practice overall or within this program. But what gives you the greatest hope?
Giselle Sholler, MD: [00:58:46] The greatest hope. That's a great question. I think seeing so many people come together with the same passion to make a difference and to find the answers, because I think together we will. And it was really encouraging -- in March, we had our consortium come together in person. After two years, we usually do an annual meeting and it's been a few years and we had so much participate 80 people in person, 80 people virtually so much participation and excitement and just seeing everyone coming together. It's not just one person that's going to find the answer or on their own do it. It takes the researchers, the physicians, the research nurses and coordinators and the parents and the advocates and the fundraisers all coming together. And that just I have to say, that day just gave me so much hope that we're going to find the answer.
Piero Spada: [00:59:42] Indeed. It was a great day. I think I'm going to have Maggie wrap things up for us. Thank you so much, Dr. Sholler.
Giselle Sholler, MD: [00:59:47] Yeah.
Maggie Spada: [00:59:47] That was actually a timely question. So I thought about all that we've learned about Dr. Sholler over the last. This has been a just so everyone has some hope here. This is all really occurred with respect to Ewing Sarcoma as a focus really in the last 12 months, 14 months. I mean, this is this team is working at an incredible pace. And I was thinking about there's a quote that we love at Little Warrior Foundation. It's on our website, and it's by none other than Mother Theresa. And she says, "I used to think that prayer changes things, but now I know that prayer changes us and we change things." I think everybody on this call has been affected by Ewing Sarcoma in one way or another, and we all know what it is like or what it was like to just be clinging to hope. But what we love about Dr. Sholler and Dr. Russell and the entire team is that they bring tremendous hustle and that is really needed. It's the hustle and the collaboration with the family and the patient. Family is the foundations that can actually transform that hope into a reality. So we are really eternally grateful to you guys and all that you've been doing. And we we just you are brave to try new things, to flip the model on its head, to use those enormous brains. You are so brilliant as you're talking... we're just jaws around the floor and the comments coming in are just very grateful for all that you do.
Maggie Spada: [01:01:18] So thank you guys for all attending our first ever Ewing's U. I didn't like we didn't totally screw it up, so I'm going to call it a success. One thing to be aware of is that we do have another one scheduled. So. Oh, see, I said I wasn't going to screw up and now I'm totally botching this. But over here on the left, you can see my screen share. So we have our next one scheduled for Thursday, June 9th, 2 p.m. Central. Some of you might recognize Dr. Anderson, known to many of us as Dr. Pete, he is going to be talking on a patient level about how to understand and interpret labs, pathology reports and scans. So please do join us next month. Everybody who attended or registered is going to be receiving a follow up email from us and we are going to attach the PDF with a lot of the cue Q&A or fax rather to some of the things that were brought up today. And I believe Abbie's information will be on there if you have further questions. So with that, we have a phrase here at Little Warrior that we love. We feel it embodies our fight. So in honor of and in memory of too many patients, that's how we're going to sign off today. So swords up, everybody. Thanks for attending.
Dr. Russell: [01:02:39] Swords Up!