UCSF specialists in cancer genomics and pediatric oncology describe the process of evaluating and determining treatment options for referred patients, with specifics on how care for certain childhood cancers – such as neuroblastoma, leukemia, brain tumors and hepatoblastoma – can be correlated to individual genetic testing results. The speakers detail the scope of the UCSF 500 Cancer Gene Panel and its real-life benefits – leading to targeted treatments and personalized monitoring – and depict how the UCSF Molecular Tumor Board experts collaboratively arrive at recommendations.
Welcome to our presentation this morning on the pediatric oncology precision Medicine program at UCSF. Benioff Children's hospitals. My name is Alejandro Sweet cordero. I'm a professor of pediatrics and the chief of pediatric oncology at UCSF. I'm joined today by my colleagues Dr Arun Ranga swami, also professor of pediatrics in the division of pediatric oncology at UCSF. Dr Jessica Vans Ifo, Associate clinical professor of pathology. Also molecular geneticist within the clinical cancer genomics laboratory in the department of pathology at UCSF. Um and Professor Dr James granite, who's a clinical professor of pathology. Also molecular pathologists in the department of pathology at UCSF. So our precision oncology program at UCSF really expands the wheel of discovery from clinical care to discovery. As shown on this slide, we begin with patients who come to us for evaluation for a psychologic problem. Those patients receive a sequencing essay using the U. C. S. F. 500 as we will describe in this presentation. This essay is discussed at a molecular tumor board where a group of clinicians and geneticists and by mathematicians and um other specialists will evaluate these results and provide a recommendation for the patient. That patient can then be followed clinically. We can evaluate whether there was a response based on the analysis and the recommendation that was made. That information is then put into a database that can be used to identify in the future other patients who have had similar alterations and who have either responded or not responded to the recommended therapy and therefore we can learn from prior patients in order to treat our future patients in this wheel of discovery and Clinical care. So our process begins with a referral from either a physician here at UCSF for an outside provider who has a patient with a cancer diagnosis who gets a biopsy um and needs to have that evaluated with our U. C. S. F. 500 S. A. Um We have a group of patient navigators who can help the clinicians as well as the patients enter our system and be evaluated in our molecular tumor board. As shown here. The molecular tumor board will then define the relevance of the findings found on the UCSF 500 for the care of the patient. That can either be a diagnostic recommendation based on the molecular findings sometimes that will lead to a change in diagnosis can also be recommendation in terms of targeted therapy. Or sometimes we also identify cancer predispositions that would entail that a patient should be referred to the cancer genetics clinic. That patient can then either enter into a clinical trial here at UCSF or go back to their home institution where the recommendations made by the molecular tumor board can be used to guide therapy in the future. So uh we have a very active early phase clinical program here at UCSF. We are one of 21 children's oncology group, early phase member institutions. We participate in this. The network shown here on the right on this map of other institutions that participate in these children's oncology group trials. We are also one of only four Alex's lemonade stand foundation centers of excellence in pediatric developmental therapeutics. So these two affiliations provide us with an opportunity to bring to our patients the most cutting edge clinical therapy clinical trials available, particularly those clinical trials that are informed by the molecular findings that we can determine using the UCSF 500. We are also part of a large number of consortia, including the C. O. G. Pepsi tiene, as I mentioned, also a consortium that are dedicated to treating specific uh types of cancer for example and and consortium which focuses on neuroblastoma. The peanut consortium which was initiated here out of UCSF which focuses on brain tumors. The taco consortium for leukemia lymphoma, the nacho consortium for history, acidic disorders as well as a large number of industry sponsored trials and perhaps most importantly investigator initiated trials. So these are trials that are um not available anywhere else because they were based on discoveries from our physician scientists um and other investigators here at UCSF um are Phase One program is led by DR Q. ArVO on the extra solid tumor side. Uh The immunotherapy um side of our Phase one program is led by Michelle Hermiston are leukemia trials are led by Eliot Stieglitz and the brain tumors. But Sabine Mueller we also have a large number of clinical trials that are really focused on what we call biomarker driven trials. So these are trials where you need to have a molecular alteration identified in an essay such as the U. C. S. F. 500. This includes the pediatric match trial which is the national effort to match pediatric cancer patients to targeted therapies. We also have a number of biomarker selective trials including uh contract fusion trial and I. D. H. One to trial and several other molecularly driven um uh clinical trials. And these include a wide range of investigational drug classes including Amtrak inhibitors, part inhibitors, rap map kinase inhibitors, a TR inhibitors and P. D. HFR. And this list changes all the time since we have a very active um Phase one program where we are always trying to bring to UCSF the most cutting edge um trials that will drive new therapies for our patients. So now I'm going to talk a little bit about the U. C. S. F 500 NGS panel. I'm going to pass this on to my colleague dr Jessica Evans if oh who will explain the how the the UCSF 500 was designed um and how we utilize it to identify molecular alterations in in our pediatric cancer patients. Dr fanciful. Yeah. Thank you. So RUCSF 500 cancer gene panel is a custom pan cancer panel. It does include 529 cancer genes and 72 n tronic regions of these genes. Um and the design of this panel was initiated and developed through interaction with UCSF providers including our pediatric oncologists who provided input into the gene list and continued to provide input as we evolve the panel. So this panel is able to detect the common um or identified variant types seen in cancer. This includes single nucleotide variants or S. N. V. S. Which are the most common mutation type that's seen that affect coding regions or splice site changes. Often they're known hotspot alterations. It also detects in Dell's which are insertion or deletion variants. Often these lead to frame shifts. Sometimes they are in frame and can be hot spot regions also in known genes or known pathways. The essay also has um the ability to detect copy number variants including gene specific amplifications or deletions as well as chromosomal copy number changes such as whole chromosome or arm level gains or losses. In addition, the inclusion of the N. Tronic regions from those 72 genes allows us to identify some structural variants or gene fusion events. These can result from trans locations or tandem duplications, inversions or other in del alterations within the genome. We do offer this test as both as a tumor normal analysis as well as tumor only and when we perform normal analysis, this allows us to distinguish between somatic alterations which are required in the tumor versus germline alterations which are present in the constitutional genome. In addition, our essay identifies tumor mutation burden as well as micro satellite instability and tumor mutation burden That's high as well as a micro satellite instability. That's high is associated with immunotherapy and so can have therapeutic implications. The U. C. S. F. 500 S. A. Is a capture based next generation sequencing assay. And if we are doing a paired tumor normal analysis versus a tumor only analysis, the first step is to identify appropriate tumor for sequencing which we recommend is at least 25% neo plastic cell content. We then isolate high quality d. n. a. from these samples and separately prepare libraries which are then captured or enriched for the regions of interest in our sequencing. And that's those 529 cancer genes and the select introns that I just described. The libraries are then sequenced on Illumina sequencers and our minimum quality threshold is 500 x coverage to make sure we have sufficient sequencing to allow for high quality variant calling. We do run an in house bioinformatics pipeline Um to allow for this variant calling. And we do report those variants that I just described on the previous slide with a median turnaround time from sample receipt to release of the results of 14 days Over the past several years. We have seen a large increase in our case volume in the number of orders that we receive. Um and we have now over 10,000 cases reported. Um we do see the significant growth year over year and we do see really a large breadth of cancer types referred for testing at UCSF. We do have a strong neuro oncology and neuropathology program that have been very early and strong adopters. And so we do see an emphasis on neuro cases submitted but you can also appreciate a broad diversity of cancer types that are referred for our testing within pediatric cancers because of the strong neuro oncology component as well. We do see a high percentage of cns cases referred but you can also appreciate on the left um that we do see a diversity of different cancer types in our pediatric population and many of these cases are referred for tumor normal testing in the pediatric population. The reason that that's important is that germline findings of significance are identified in almost 20% of pediatric cases sent for sequencing and so this is a significant consideration and of importance in these pediatric cancer cases. In addition, over 30% of our cases have clinically actionable finding and that includes FADA approved therapies or other potentially actionable findings identified by the sequencing assay. Our increased volume is seen both locally at UCSF but also has been seen across the state of California and beyond that we have seen increased adoption of our assay for referrals from many other states across the United States beyond the United States. We also have seen increased referrals internationally, many from our closest neighbors of Canada and Mexico but also you can appreciate that. We do have international orders from across the globe. And with that I'd like to introduce my colleague Dr Rango swami, who will present pediatric cancer genetics at UCSF. Thank you. Doctor Fanciful as Dr Fanciful highlighted one of the unique aspects of the UCSF 100 is its ability to identify a germline variants in Children. An estimated 15% of Children with cancer have a familial or genetic previous position to develop that cancer identifying these predisposition syndromes is critical not only for the treatment of the current diagnosis, but to prevent other cancers later in life. There are treatment implications which include avoiding toxicity, as in the case of lee from me syndrome where we try to avoid ionizing radiation exposure. There also implications for surveillance of patients in order to identify new cancers at an early stage. Their implications for lifestyle choices and prevention um as well as potential surgical and medical interventions and finally, implications for family planning. The Kaplan Meier curve on the right, which was published by the sick Children's Cancer genetics group highlights the importance of surveillance of patients with lee from any syndrome, as you can see on the upper graph. Uh the outcomes for patients who have surveillance instituted are significantly better with respect to overall survival than those who do not undergo a surveillance protocol. So, at um U. C. S. F. We have a pediatric predatory cancer clinic which identifies and follows Children who are born with a genetic mutation that places them at an increased risk for developing cancer. We see more than 40 different predisposition syndromes. Um And each of these has its own specific set of surveillance guidelines um that our clinic helps to coordinate our genetic counselors work very closely with families to help them understand the implications of being told that their child's at risk for developing cancer and also in addressing the significant psychosocial and emotional impact of a family who has a child with a predisposition syndrome. And I would like to um turn the presentation over to my colleague, Dr Sweet cordero will discuss the molecular tumor board. So molecular tumor board at UCSF is a multidisciplinary tumor board that consists of a number of experts and discussing shown on the right of this slide. Um We have experts in um targeted therapies such as Dr Beth winger as well as experts in adult on call gee and the precision oncology. Dr Mark Morris, our doctor eric collison and as well as several other experts here who have domain expertise in various areas that are important for discussion in the molecular tumor war depending on the patient and the diagnosis. Our tumor board meets every other week either on the second monday or the first thursday of the month. A requesting oncologist will provide a clinical history um that will and also a reason for why they would like this case to be discussed at molecular tumor board. That case will then be presented by the domain specific expert. Um and then we will have a very lively discussion that is intended to provide the clinician with information relevant to the care of the patient. For example the molecular findings in terms of whether it's likely to be as a sub called variant or whether it's likely to be a call variant, whether this is a alteration for which there is a known drug that targets that alteration as well as a number of other findings that may be relevant to the patient. As you will see in the next slides within a week. We then deliver a recommendation to the clinician. Yeah and we are always available for any follow up questions or discussion. So I'm going to now pass it back to Dr Ramaswamy Dr Granite who will discuss a specific patient who was referred to us with a diagnosis of glioblastoma with treatment effect of mixed type. Thank you Dr Sweet cordero. The case that I'm going to discuss today is a 36 month old child with recurrent glioblastoma who underwent resection at an outside institution and was receiving salvage chemotherapy. He was diagnosed in August of 2021 with a locally advanced pretext three annotation factor negative. Have had a blast oma after presenting with two days of abdominal pain fever and irritability. His initial alpha feta protein which is a sensitive biomarker for him to blast oMA was elevated at 110,476 and a liver biopsy was performed demonstrated to blast the mixed epithelial and mesenchymal histology. He was enrolled on the Children's oncology group frontline trial 15 31 and received two cycles of cis platinum monotherapy with minimal response by both resist and alpha feta protein criteria. He then received one cycle of docks Robison trans arterial chemo embolization with tumor and alpha feta protein measured progression. He was deemed un respectable at his local institution and was referred to a second outside institution for consideration for Ortho topic liver transplantation there. He underwent a resection in november of 2021. However, unfortunately his alpha feta protein following the resection was actually increased and he returned to his home institution for continued treatment as per the A. F 15 31 trial with continued cis platinum monotherapy. However, due to continued elevation of his alpha feta protein, we recommended re imaging which demonstrated recurrence at his resection margin and and in his right hepatic lobe. So molecular profiling was recommended at the outside institution. Uh their platform demonstrated no pathogenic variants. However we recommended sending the UCSF 500 on the resection sample for analysis of prognostic markers and potential therapeutic targets. So we performed UCSF 500 on this more recent specimen. And the first alteration I want to point out is an Exxon three deletion in the C. T. N. And B. One gene. So this gene codes for nicotine in which is a very important driver in both pediatric and adult liver tumors and exon three is an important regulatory domain of that protein. And deletion of exon three would be expected to increase beta cuttin and activation and subsequent wind pathway signaling. I also want to point out another gene found to have an alteration here is a red one. A. This was a nonsense mutation which results in a stop code on and truncation of the protein. A red one A. Is involved in chrome aton regulation and through that gene transcription and is an important suppressor across many cancer types. And finally there's a frame shift mutation in D. X. Three X. So frame shift mutations uh end up resulting in premature truncation and activation of proteins. DDX three X. Is an RNA Healy case that's involved in many different um functions of RNA including its transcription translation stability. And so it's a very important regulator of RNA in the cell. Our informatics pipelines did not show any evidence of micro satellite instability and they found that the tumor mutation burden was low. Thank you. Dr Brenner So as dr mentioned by nicotine in uh or the C. T. N. N. B. One gene codes for the protein by nicotine in which is a key signaling component of the wind signaling pathway which is illustrated here on the right side. So when ben nicotine in is um is activated through the singling access shown here. That leads to increase in transcription of a number of genes which normally during development or involved in um patterning um and various aspects of development. But it's well known that this pathway can be hijacked in several cancers including lung cancer. So the Exxon three um of this um gene encodes the seventh green phosphor relation site for the protein GSK three beta, which is involved in degradation of beta Cotino. So loss of this exon leads to lack of degradation and therefore increase the nuclear activity. Um There are approximately 50% of the power blast trauma cases that have been reported and the genie database have continued mutations. So the genie beta database is a data sharing effort with which UCSF participates that includes the data fabric cancer institute, the Memorial Sloan Kettering as well as several international partners. And depositing our data in this database allows us to have access to a much larger group of patients that can then be evaluated and compared to the cases that we see here at UCSF. Uh there have been several efforts to target the one pathway given its importance in in cancer therapy. So there are the drug PR I 7 24 has been tested in Phase one dose escalation study um in combination with this genocide, a bean. Um and there's been some evidence of stable disease in patients. There are several other clinical trials, such as the one shown here in adults which aim to target the beta carotene in pathway at various levels. And one of the important aspects of the molecular tumor board is because we have a very deep expertise and these molecular pathways, it helps us to for example, determine based on where where the the alteration is in the signaling pathway, whether it's drug is likely to work. So obviously, if the alteration as in this case, isn't the nicotine in trying to target the pathway higher up would not be likely to be effective in this case. So it's very important to have this kind of expertise to be able to truly um provide the clinicians with the best evidence. So, uh in in pediatric patients is also another clinical trial with a uh inhibitor called take of event uh which uh would also be potentially active in this patient. So that brings up another aspect of the importance of the molecular tumor board is that we can also determine whether there's likely to be a drug that will be available for pediatric patients. So not not all adult trials are for drugs that have been made available for pediatric patients. So, given the importance of the wind pathway in a variety of cancers, it's perhaps not surprising that this has been a major focus of the efforts to target cancer. There have been a number of companies who have evaluated various ways to target the one pathway is shown here on the right starting with the receptor on the cell surface down to the mechanisms of regulation of beta carotene in in the cytoplasm as well as the activated beta cuttin in uh in the nucleus. So for example, P. R. I 7 24 has been tested in a Phase one B dose escalation study in combination with jim side. I mean there's been some uh signal for stable disease. S. M 08502 is currently being evaluated in a Phase one trial. Um there's also a drug called Tega Vivint, which also target the one pathway and has been um and is currently being evaluated for use in pediatric patients. One important aspect of the molecule to our board is because of the deep expertise of the people who participate. We are able to give our clinicians advice regarding the most appropriate targeted therapy based on the alteration in the individual patient. So, for example, in this patient who has a mutation and nicotine in it would not be appropriate to select the drug the targets to win pathway higher up. For example, at the level of the cell surface because that would be unlikely to work when the alteration causes chronic activation of the nicotine in which is already in the nucleus. So in this case you would want a mechanism of action of a drug that would lead to blockade of beta carotene in um at the side of transcription. Another alteration that was found in his patient was in the gene a red one, a red one a codes for a protein which is a A. T rich interaction domain protein part of the solution if croatoan remodeling complex and a well described tumor suppressor protein, A Red one. A because it's part of the switch sniff complex has multiple facts as shown here on the left. Um but most importantly it regulates the chroma tin to lead to changes in gene expression of a variety of genes. I heard one name like nicotine is much less frequently mutated in the blast oma. In our review of the Genie database, we found that it was mutated in 6% of 49 cases of blast oma. So unfortunately the loss of a red one, A like many other tumor suppressors is not directly target herbal. However, it is increasingly recognized that loss of tumor suppressors can in some cases make tumors um susceptible to what is known as a synthetic vulnerability. So, loss of a gene can make jeans susceptible to treatment within another pathway that can sometimes cooperate with the pathway that has been lost in the patient. So for example, it's known that a lost in carcinoma leads to up regulation of a protein called edge to which may in some pre clinical studies suggest be susceptible to treatment with a receptor targeting chinese inhibitor called sarafina. Similarly, everybody lost in a very clear cell carcinomas is known to lead to sensitivity to inhibition with easy H2 inhibitor, which is an epigenetic therapy that is currently in preclinical studies and as well also in clinical trials as shown here um in some experiments uh and some data also suggests that in ovarian cancer at least are when a loss is associated with a so called mediator phenotype which leads to a higher tumor mutation burden and potentially sensitivity to checkpoint blockade. This points out the importance of not only looking at the genetic mutations but also the the specific context. As in this patient with a power blast oma, we did not see an elevated to a mutation burden, suggesting that perhaps this finding is specific to ovarian cancer. And lastly, this patient also demonstrated a very interesting alteration in another gene called DDX three X. Which is an A. T. P. Dependent or in a healer case. Uh The the process involved as shown here on the right. So RNA healer cases are important in regulating the structure of an RNA as suggested by the by the name. Uh These proteins have been found to be over expressed in a number of cancers including glioma, glioblastoma, apples, carcinoma and others. Um And lots of DDX three X. Has been suggested to lead to a Transit type one interferon response. Um and an increased infiltration with tea and dendritic cells. Um And that's uh in the reference from here. So interestingly DDX three X alterations are quite uncommon in oblast oma. So this side shows the prevalence of DDX three X alterations in the portal. We actually could not find evidence of any other patient that had ever been described with DDX three X. Alteration. DX mutations are commonly seen in a variety of other cancers as shown here on the right but but not previously demonstrated in a powerful blast oma. So on, careful review of the literature our discussions noticed that DDX three X has been recently associated with CISplatin resistance in oral squamous cell carcinoma. So this is a figure from a paper published recently where the authors used a variety of molecular techniques to demonstrate that loss of D. D. X reacts leads to resistance to CISplatin. This graph demonstrates our patients alpha feta protein response. Um The initial data point is that his initial diagnosis um following that we have his alpha feta protein following four cycles of cis platinum and taste chemotherapy with his M. R. I. Showing progression. And then following his reception, the rise in his alpha feta protein until upon based upon the UCSF 500 results, we recommended a change in chemotherapy to the agents when Christine and following the switch in his chemotherapy regimen, he had a very rapid decline in his alpha feta protein as well as in his imaging study. Um And following two cycles of V. I. Um he underwent an Ortho topic liver transplantation and these are representative slides showing an M. R. I. Scan that was performed prior and after institution of Vis I chemotherapy. One can see in the image on the left that he has a large tumor with multiple nodules and on the image on the right these nodules have shrunk significantly and that was immediately prior to his more definitive surgical procedure. Our patient received an Ortho topic liver transplant in february of this year. He had a second UCSF 500 analysis performed on the X planted liver that demonstrated absence of the DDX three X. And a red one a variance with persistent of the C. T. N. N. B. One variant. This suggests the effectiveness of switching from his sister platinum based regimen, Christine and unity can with subsequent eradication of the two clones above. He then completed a total of six cycles of V. I. Chemotherapy in july of 2022 remains in a continuous complete remission five months from the end of treatment with normal alpha feta protein levels and negative imaging studies. Of course beyond the science is our desire to impact patient care. And this is a quotation from the family with respect to how the U. C. S. F. 500 helped them and held. And I think the most important takeaway from here is the line today. He is cancer free. We are incredibly grateful she would like to refer a patient to UCSF for U. C. S. F. 100. Testing. The ordering information is shown here on the left. If you would like to refer a patient to UCSF, please call 877. You see child. There's also additional information about our Pediatric Oncology Precision Medicine program on our website. You can also contact us by email at Cancer Medicine at UCSF dot e d. U. Thank you.
