Podcasts about mutational

#048 Rebroadcast New College-Style Sweatshirt! And the Ghost Halloween Design is Back! This week, Melissa and Jam dive into spiciness. What is it? Is it a flavor? Is it a feeling? Is it both? Is it more? Why can some people handle more than others? Does spiciness have any benefits? References from this episode https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/vanilloids Solomon's Organic Chemistry 11th edition Analogues of Capsaicin with Agonist Activity as Novel Analgesic agents; Structure-Activity Studies 2. The Amide Bond “B-Reigion” byWalpole et. al Similarities and Differences in the Structure−Activity Relationships of Capsaicin and Resiniferatoxin Analogues by Walpole et. al Detailed Analysis of the Binding Mode of Vanilloids to Transient Receptor Potential Vanilloid Type I (TRPV1) by a Mutational and Computational Study by Ohbuchi et. al The Art and Science of Organic andNatural Products Synthesis - by Nicolau et. al https://www.acs.org/content/acs/en/pressroom/reactions/videos/2015/why-are-hot-peppers-hot-and-how-milk-helps.html Find us on Instagram, Twitter, and Facebook @ChemForYourLife. Email us at chemforyourlife@gmail.com And check out our chill, simple little website at https://chemforyourlife.transistor.fm/   Thanks to our monthly supporters Scott B Jessie Reder Ciara Linville J0HNTR0Y Jeannette Napoleon Cullyn R Erica Bee Elizabeth P Sarah Moar Rachel Reina Letila Katrina Barnum-Huckins Suzanne Phillips Venus Rebholz Lyn Stubblefield Jacob Taber Brian Kimball Emerson Woodhall Kristina Gotfredsen Timothy Parker Steven Boyles Chris Skupien Chelsea B Bri McAllister Avishai Barnoy Hunter Reardon ★ Support this podcast on Patreon ★ ★ Buy Podcast Merch and Apparel ★ Check out our website at chemforyourlife.com Watch our episodes on YouTube Find us on Instagram, Twitter, and Facebook @ChemForYourLife  

CME credits: 1.25 Valid until: 16-08-2025 Claim your CME credit at https://reachmd.com/programs/cme/mutational-testing-to-guide-therapy-in-cll-why-and-when/26496/ Determining the optimal treatment regimen for patients with chronic lymphocytic leukemia (CLL) has been a clinical challenge, especially since most patients are older than 70 years, present with significant coexisting comorbidities, and exhibit one or more common chromosomal alterations. However, outcomes in CLL are improving with the availability of non-chemotherapy options with fewer toxicities. Fixed-duration therapy has emerged as an even more attractive approach for the frontline treatment of CLL and is associated with mild toxicities, improved treatment adherence and monitoring, and reduced financial burden. Embark on a journey through this educational series to achieve a better understanding of the rationale and supporting clinical data for fixed-duration therapy, monitoring strategies, the role of MRD-guided treatment selection, and approaches to overcome relapsed/refractory CLL.

Dr. Nikolaos Papadantonakis discusses cytogenetics and mutational testing in MDS with Dr. Hetty Carraway and Dr. Moshe Mittelman and how they utilize this information in the clinical setting.

In this week's episode we'll discuss the mutational and transcriptional landscape of pediatric BCP lymphoblastic leukemia; learn more about the role of platelet-derived TGF-β1 in immune thrombocytopenia; and discuss the findings from a phase 3 trial of mavorixafor in WHIM syndrome.Featured Articles:Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma Platelet-derived TGF-β1 induces functional reprogramming of myeloid-derived suppressor cells in immune thrombocytopenia Phase 3 randomized trial of mavorixafor, CXCR4 antagonist, in WHIM syndrome 

Asexual reproduction has its advantages, but organisms that depend too much on it also face potential extinction. In this classic episode of Stuff to Blow Your Mind, Robert and Joe discuss mutational meltdown and Muller's ratchet. (originally published 04/20/2023)See omnystudio.com/listener for privacy information.

What is mutation bias and how can scientists study it? How does changing a population's mutation bias influence its evolutionary trajectory? In this episode, we talk with Deepa Agashe, an Associate Professor at the National Centre for Biological Sciences in Bangalore, India. We first talk with Deepa about mutation bias and how she uses  E. coli to understand it. We then focus on a 2023 PNAS paper about the fitness effects of experimentally changing the mutation bias in E. coli. In this research, Deepa and her team used a strain (MutY) of bacteria containing a mutation that knocks out an important DNA repair enzyme. They then isolated subsequent single mutations produced within both MutY and wildtype lines and studied the fitness effects of those mutations. Surprisingly, more than a third of mutations in the mutant lines were beneficial, and often across several different environments. Zooming out, the big picture is that shifts in mutation bias seem to generate new kinds of mutations that weren't previously accessible to lineages, and a greater fraction of those may be beneficial in some circumstances. Art by Keating Shahmehri. Find a transcript of this episode on our website. --- Support this podcast: https://podcasters.spotify.com/pod/show/bigbiology/support

References FEMS Microbiol Rev.1998. Oct;22(4):255-75 Discoveries(Craiova). 2017 Jul-Sep; 5(3): e77. J Cell Mol Med. 2015 Jul; 19(7): 1427–1440. Oncogene. 2017 Mar 23; 36(12): 1607–1618. Bach, JS. 1742. Kunst der Fuge , BWV 1080; Marta Czech https://youtu.be/p1Sq1HOYglU?si=2GMF7kf3dLW4rr2O Lennon and MCartney.1968. "Martha my Dear" https://youtu.be/RXawa90YU2s?si=dUPDtTdm4UqrgWit --- Send in a voice message: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/message Support this podcast: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/support

JCO PO author Dr. Amit Mahipal shares insights into his JCO PO article, “Tumor Mutational Burden in Real-world Patients with Pancreatic Cancer: Genomic Alterations and Predictive Value for Immune Checkpoint Inhibitor Effectiveness.” Host Dr. Rafeh Naqash and Dr Mahipal discuss real world evidence of immune checkpoint inhibitors in pancreatic ductal adenocarcinoma. TRANSCRIPT Dr. Rafeh Naqash: Welcome to JCO Precision Oncology Conversations, where we bring you engaging conversations with authors of clinically relevant and highly significant JCO PO articles. I'm your host, Dr. Rafeh Naqash, Social Media Editor for JCO Precision Oncology and Assistant Professor at the OU Health Stephenson Cancer Center, University of Oklahoma. Today we are joined by Dr. Amit Mahipal, Professor of Medicine and Director of GI Oncology at the Case Western Reserve University in Seidman Cancer Center. Dr. Mahipal is also the author of the JCO Precision Oncology article titled "Tumor Mutational Burden in Real World Patients with Pancreatic Cancer: Genomic Alterations and Predictive Value of Immune Checkpoint Inhibitor Effectiveness."  Our guest disclosures will be linked in the transcript. For the sake of this conversation, we will refer to each other using our first names. So Amit, welcome to our podcast and thank you for joining us today. Dr. Amit Mahipal: Thanks for having me here. Dr. Rafeh Naqash: Excellent. We came across your article in JCO Precision Oncology and it really aroused my interest because the topic and the audience that it caters to is very important in the current times. Because immunotherapy generally is considered- pancreas cancer the graveyard in immunotherapy in essence, based on what I have seen or what I have encountered. And now you're the expert here who sees people with pancreas cancer or has done a lot of work in pancreas cancer research side. So can you tell us the context of this work and why you wanted to look at immune checkpoint inhibitors in pancreas cancer? Dr. Amit Mahipal: Absolutely, Rafeh. As you mentioned, pancreatic cancer is considered a what we call "cold tumors." They don't typically respond to immunotherapy. And when we talk to our patients or patient advocates, as you know, patients are very excited about immunotherapy. Immunotherapy has transformed the treatment for a lot of different cancers and not only has increased survival, but the quality of life is so much different than with chemotherapy. This work came from based on the KEYNOTE-158 trial, which was a tumor-agnostic trial which accrued patients who had TMB high tumor. What that means is that tumor mutation had more than 10 mutations per megabase. And what happens is because of that trial, more than 200 patient trial, the FDA actually approved this immunotherapy or pembrolizumab as a single agent pembrolizumab for any patient with a solid tumor who has high TMB. Again, tumor mutation burden, more than 10 mut/Mb. This question comes in now. Does this apply to our pancreatic cancer patient groups? Especially as we know these are "cold tumors" that typically do not respond. There have been multiple trials looking at immunotherapy, single agent, dual immunotherapy agents, as well as combinations with chemotherapy, with somewhat very, very limited success. So that was kind of the basis. So we wanted to look at this retrospective kind of review of a big database to see how many patients we can find who have high TMB and see in that patient population is immunotherapy really active based on the FDA approval or is pancreatic cancer not a tumor where we should try immunotherapy unit as a selective group.    Dr. Rafeh Naqash: Thank you for that explanation. Taking a step back again, since you see these individuals with pancreatic cancer I imagine day in and day out in the space of drug development, what is the general current standard of care approach for individuals with pancreas cancer in your clinic? I'm talking about what are the most common approaches that you utilize that seem to be working or have FDA approvals in the pancreas cancer space. Dr. Amit Mahipal: As with any tumor, the first thing is obviously staging. So depending on whether we're dealing with early stage or advanced stage and what are the goals of treatment. At this point, the only thing that can cure pancreatic cancer patients that would be considered conventional therapy is surgical resection. So any patient who is a candidate for surgical resection is in a different bucket compared to advanced patients. For early stage patients, we try to do what we call neoadjuvant treatment or neoadjuvant chemotherapy. We shrink the tumor or at least maintain it, look at the biology of the disease, and then take them to surgery, which typically involves a Whipple procedure if it's a head of the pancreatic mass.   Moving on to advanced patients, that's where we know the goal of treatment is palliative to increase survival, but unfortunately, most of the times we cannot cure them. And there the standard of care options include systemic chemotherapy. We have two typical regimens that we use, one is called FOLFIRINOX, which is a three-drug regimen of 5-fluorouracil, leucovorin, oxaliplatin, and irinotecan. And another regimen is gemcitabine plus abraxane, which is a two-drug regimen of gemcitabine plus abraxane. These are considered the standard of care. Unfortunately, the median survival even with the best standard of care chemotherapy is only about a year, 12-13 months, depending on what trials we look at.  Dr. Rafeh Naqash: I still remember some of these regimens from my fellowship, where we had to decide which to give to each individual based on their performance status and clinical status, etc. But now I can see a lot of ongoing drug development in the space of pancreas cancer. I'm guessing that's why you wanted to assess both the molecular genomic landscape of pancreas cancer in this study and also look at the immune biomarker aspect. Could you tell us a little bit about the Foundation Medicine Clinical Genomic Database? How did you identify the patients, how many patients did you identify, what you narrowed down in the criteria, and the eventual sample size of what you were looking at?  Dr. Amit Mahipal: FoundationOne has a rich database. They have two or three things. One is a genomic database only. So in our clinical practice, I think it's some sort of next-generation sequencing or mutational testing for all patients with advanced solid tumors. All of these goes into their database. All of the samples that are sent to FoundationOne that goes into their database where they know the diagnosis of the patient and the know the sequencing results of these patients. In addition, they also have a clinical database called Flatiron. Basically, they collaborated with them. Flatiron has about 280 or so cancer clinics throughout the country, so a lot of community settings and some academic sites as well. They did not only have a genomic database, but they actually have a clinical database. They have demographics, clinical features, baseline clinical features, comorbidities, what kind of treatment they received, what would be the stage of the cancer, how many months of treatment they received, and their overall survival, and so on. So from that perspective, the FoundationOne has access to this partnership with Flatiron, clinical genomic database where they have both clinical data as well as genomic database for a lot of these patients.  In our study, we only focused on patients with advanced pancreatic cancer. We excluded a lot of patients who did not have sequencing results available, they cannot be performed due to lack of tissue. So the first we talked about the genomic database and we found about about 21,932 patients, so almost 22,000 patients and there we had the sequencing and we also had the data on TMB or tumor mutational burden. So here, we classified them into two groups: high TMB and low TMB. High TMB was seen in 1.3% of the patients, and about 98.3% of the patients had low TMB. Here we looked at the genomic alterations between the two groups. So these are like our genomic group, so to speak of about 22,000 patients. And among them, as mentioned, that the clinical data was available for about 3300 patients or 3279 patients to be exact.   After excluding some of those patients, we found about 51 patients who received immunotherapy. And when we say immunotherapy, it is single agent immuno checkpoint inhibitor like pembrolizumab or nivolumab. And then we classified them into high TMB versus low TMB and then we also looked at patients with high TMB and compared them to who received immunotherapy versus other therapies. Just to recap, we had about 22,000 patients where we have the genomic database and about 3300 or so patients who we have both genomic and clinical data for this patients. One of the key findings was that high TMB was present in only 1.3% of the patients, or about 293 patients out of 21,932.  Dr. Rafeh Naqash: Definitely an interesting sample size that you had utilizing this resource, which, of course, is more or less real-world. It is important to gather real-world outcomes that you did.   So, going to the TMB story of this paper, where you looked at immune checkpoint inhibitor use in these individuals, was there a reason why some of the individuals with low TMB were also given immune checkpoint inhibitors? From my understanding, I did see some checkpoint inhibitor use there. What could be the explanation for that? Dr. Amit Mahipal: So this data is from 2014 to 2022. So from the span of about eight or so years. And as you know, immune checkpoint inhibitors were approved in the last decade. And there were a lot of not only trials, but even in the non-trial setting, people had tried immune checkpoint inhibitors in, frankly, different tumor types because of the success in some of the common tumor types, like melanomas, lung cancer, and so on. So I agree, as of today, we probably would not use immune checkpoint inhibitors in patients with low TMB or MSS. But at that time, I think that information was not available. So people with low TMB and MSI-stable tumors also received immune checkpoint inhibitors. But those numbers are again low. So it's not very high numbers. Dr. Rafeh Naqash: Understandable. That makes it a little more clear.  Now, you looked at the TMB aspect. I'm guessing you also looked at the MSI aspect of PDAC. What is your understanding, or what was your understanding before this study, and how did it enhance your understanding of the MSI aspect of PDAC? And I'm again guessing, since TMB high individuals are on the lower side percentage, so MSI high is likely to be low as well. Did you see any interaction between those MSI highs and the TMB highs on the PDAC side?  Dr. Amit Mahipal: Yeah, absolutely. So we are very excited in general about MSI-high tumors for solid tumors because of their response to immunotherapy. Although I would do a caveat because we still don't know how MSI-high pancreatic cancer responds although there have been some real-world, very, very small series as well. In this study, one of the things is, is high TMB totally driven by MSI-high? That's a question that comes up, and TMB high may not matter. It's only the MSI-high that might matter. So definitely when we look at this patient population, we found that the patients who were 35-36% of patients who were TMB high also had MSI-high patients. So we do expect MSI-high patients to have a higher TMB compared to MSS patients. But there were about 66 or two-thirds of the patients who did not have MSI-high tumors and still had high TMB, as defined by, again, ten mutations per megabase. So we did see patients with MSI-stable tumors who had high TMB. And I think that was one of our biggest questions. I think MSI-high patients, we all tend to think that we would try immunotherapy even if it's in pancreatic cancer. I think what is not clear, at least from the real-world or any of the trial data, is if we were to give MSI-stable patients who have high TMB, if we give immunotherapy, are there any responses or any disease control that we see? And that was one of the reasons for this study.  Dr. Rafeh Naqash: Now, one of the things that comes to mind, and again, I think you based it on the FDA approval for TMB high, which is ten mutations per megabase, as you defined earlier. I do a lot of biomarker research, and oftentimes you come across this aspect of binary versus a linear biomarker, in this case being TMB, where about ten, less than ten. Do you think, in general, an approach where you maybe have tertiles or quartiles or a biomarker, or perhaps a better approach in trying to stratify individuals who may or may not benefit from immunotherapy? Dr. Amit Mahipal: That's a great point. I think when we use ten mutations per megabase as a biomarker, as a binary endpoint, do we apply it to all tumor types? I don't think that's a fair comparison, frankly speaking. We do know that high TMB, even in different tumor types, do tend to respond a little bit better to or do have better outcomes for patients treated with immune checkpoint inhibitors in different tumor types. But what that cutoff is not known in most of the tumor types. And also, one of the problems is how do you measure TMB and is it standard across different platforms? Like I'm just giving some names like FoundationOne, Tempus, Caris, and some obviously like MSKCC and some other university-owned panels as well. And frankly, I think if you look at different panels and if you send the same tumor tissue, you will get different measurements. So I think standardization is a problem as well.  In one of the studies involving cholangiocarcinoma, for example, we found that a TMB of 5 was enough to have an additive effect of immunotherapy, same with chemotherapy, so to speak. But again, this needs to be validated.  So you're absolutely correct. I don't know why we use the binary endpoint, but on the same token, the binary endpoint is easy to understand as a clinician. Like, “Hey, someone has this, do this, not this.” And when we look into a continuous range, I think the benefit obviously varies between high and low, different tertiles, and becomes somewhat challenging. How do you classify patients and what treatments to give? So I think in clinical decision-making, we like the cutoffs, but I think in reality, I don't know if the cutoff is a true representation. And maybe with the more use of AI or computing, we can just input some values, and then it can tell us what the best treatment option might be for the patient. But that's way in the future. Dr. Rafeh Naqash: That would definitely be the futuristic approach of incorporating AI, machine learning perhaps, or even digital pathology slides in these individuals to ascertain which individuals benefit.  Going back to your paper, could you highlight some of the most important results that you identified as far as which individual is better, whether it was immunotherapy, and you've also looked at some of the mutation co-mutation status. Could you highlight that for our listeners? Dr. Amit Mahipal: So the first thing we looked at was the genomic database of almost 22,000 patients, and then we classified them into high TMB and low TMB, with about 300 patients in the high TMB group and the rest in the low TMB group. And what we found was, talking about again in the genomic database, that patients who have high TMB actually have low KRAS mutation. So if we think about KRAS mutation, pancreatic cancer, almost 85% or so of patients have KRAS mutation who have pancreatic adenocarcinoma. So patients in this subgroup, so in the high TMB group, only about two-thirds of the patients had KRAS mutation, compared to 92% of the patients with low TMB who had KRAS mutation. So just giving that perspective. So KRAS mutation, which is the most common mutation in pancreatic cancer and is a driver mutation, their rates vary differ from the high TMB group versus the low TMB group.   And then in addition, in the high TMB group, we found higher rates of BRCA mutation, BRAF mutation, interestingly, and then obviously from the DNA damage repair genes like PALB2 mutation, MSH2 or MSH6, MLH1, and PMS2. So all these mismatch repair protein mutations were higher. As I mentioned before, one-third of the patients with high TMB also had MSI-high. So it's not a totally unexpected finding. I think the biggest finding was that we found more KRAS wild-type pancreatic adenocarcinoma in the high TMB group, almost a third. And those tend to have different targetable mutations like BRCA2, BRAF, and PALB2 mutations. So I think one of the interesting findings is that patients in the high TMB group actually tend to have KRAS wild-type or less KRAS mutations. So they're not necessarily KRAS-driven tumors, and they have a higher chance of having other targetable mutations like BRAF and so on, for which we have therapies for. So it's always something to keep in mind. Dr. Rafeh Naqash: Would you think that from a DDR perspective, the mutations that you did  identify that were more prevalent in individuals with high TMB, do you think that this is linked to perhaps more DNA damage, more replication stress, more neoantigens leaning toward more tumor mutation burden perhaps? Or is there a different explanation?  Dr. Amit Mahipal: For sure. As we said, MSI-high tumors have mutations in the DNA damage repair pathway and they definitely tend to have higher TMB. So I don't think that is very surprising that we found PALB2, or other MMR genes like MSH2, MSH6, MLH1, and PMS2 at much higher rates. I think the interesting finding is the fact that the KRAS wild-type and having BRAF alterations at least that's not suspected to definitely increase TMB. Although if we look at colorectal cancer, BRAF mutation and MSI are somewhat correlated to patients with BRAF mutations and to have high rates of MSI-high tumors. But that's not the case in pancreatic cancer. We also found an increase in BRCA2 mutations as well. So I agree that the DNA damage pathway repair gene alteration is not unexpected because they tend to increase TMB, but I think the other mutations were interesting. Dr. Rafeh Naqash: And I think one other aspect of this, which I'm pretty sure you would've thought about is the germline implications for some of these mutations where you could very well end up screening not only the individual patient, but also their family members and have measures in place that we're trying to enhance screening opportunities there. In your current practice, you are at an academic center but I'm talking about in general with your experience, how common is it to sequence broad sequencing panels in individuals with pancreas cancer? The reason I asked that is I do a lot with lung cancer and even now despite having all those targets in lung cancer which sort of paved the pathway for targeted therapy in many tumor types, we still don't see a full uptake for NGS Phase I drug development. And I get a lot of referrals from outside and I often see that it's a limited gene panel. So what is your experience with pancreatic cancer? Dr. Amit Mahipal: We kind of changed our practice. Similar to you, I'm involved in drug developments. I've been a big proponent of NGS for almost a decade now, when didn't even have targeted therapies but these companies first came in and they're like, “Okay. We're very very low chance.” But now obviously, we transformed the treatment for a lot of different cancers. Especially lung cancer, you don't sometimes even start treatment before you get an NGS panel like you said in situ. So what we're finding, at least for pancreatic cancer, as you know, the targetable mutations are there but they are somewhat not that common, I would say, in the 10-15% range. So many people would get dissuaded and then it's like, what's the point of doing it?   But I think for those 10% to 15% of the patients, firstly we can really change their treatment course and their prognosis. Secondly, if you don't do it and they cannot go in a different clinical trials, now we have trials targeting KRAS G12C, but not only that, KRAS G12D which is the most common mutation we see in pancreatic cancer and so on. So it's becoming very very important. One thing, at least with our practice we adopted last two or three years is sending liquid biopsies or liquid based NGS or blood-based NGS testing. Otherwise, what's happening I would send a solid tumor NGS from the tissue. And pancreatic cancer as you know has sometimes a very small amount of tissue obtained from FNA. And inevitably after four weeks, we'll get the result that there's not enough tumor to do NGS testing. And then the patient comes one or two months later and then we order the test, and that just delays everything.  So now we adopted a practice where we are trying to send both blood based NGS and solid tumor NGS at the same time the first time of diagnosis when we see the oncologist for the first time. And that has really increased the rate of NGS testing results for our patient population. And it's not 100%, even in blood-based NGS, sometimes they may not be able to find enough circulating tumor cells to do this blood-based NGS testing, but at least they're having these. But you're correct. I think we still see about one third of the patients who had not had NGS testing or referred for phase I clinical trial and have gone through more than two or three line of therapies which is unfortunate for our patients.  Dr. Rafeh Naqash: That's a very interesting perspective on how important it is to sequence these individuals. As you said, it may not be that all of them may benefit, but the ones that have those important alterations, especially BRCA, PALB, and KRAS could benefit from novel precision medicine-based approaches.  A question that came to my mind, I saw that you were trying to look at MYC and turmeric low tumors as well. So what is the role of MYC in the context of these individuals? Is there any drug development that's going on? Because I see small cell lung cancer. MYC is an important target there. These are two different tumors, but it looks like there was a hint of some correlation with respect to some of the findings that you showed. Is that something that you're currently looking at or planning to look at?  Dr. Amit Mahipal: I think that if we just talk about MYC in general, it is present at somewhat lower rate. I think we found MYC amplification in about 5% or so of TMB-low patients who had that and not really seen in the TMB-high patients. So right now, I am not aware of any trials targeting MYC in pancreatic cancer. But as you said, if it's successful in lung cancer, maybe that's when we can transform into the pancreatic cancer group. Dr. Rafeh Naqash: Of course we can all learn from each other's specialties.We learned a lot from melanoma with respect to therapy. Hopefully, other fields can also benefit from each other's experiences in the space of drug development.  Thank you so much for this interesting discussion. The last few questions are more or less about you as an individual researcher. So could you tell us briefly on your career trajectory and what led you into the space of GI oncology, pancreas cancer, even for that matter, drug development? And some of the advice that you may want to give to listeners who are trainees or early career individuals? Dr. Amit Mahipal: Sure. So I have gone through some different institutions. During my fellowship, that's when I really decided that I wanted to do GI oncology. Prior to that, I actually have a Masters in Public Health, where I learned about epidemiological research and how to design clinical trials, how to design cohort studies. My focus was on, actually there was somewhat a lot, but one of my mentors was working on colorectal cancer, and they had this huge database called the Iowa Women's Health Study Database of 100,000 patients. So that's where I started by clearly getting into colorectal cancer and GI cancer in general and how to learn from this database, how to mine these databases, how to do analyses, which seems easy but is actually quite complicated.  During my fellowship, I think the key to it is finding a good mentor during the fellowship. And I worked with one of the top GI oncologists in the country who's practicing. And I worked under her and learned a lot not only from the clinic side but also from the research perspective and how sometimes you'll come up with the ideas during the clinic itself.Like, “Hey, this patient had this and why aren't we looking into this.” And she would even do some of the therapies based on phase II trials and she was a part of a lot of these trials and learning from those experiences.  And following my fellowship, I joined Moffitt Cancer Center, where I led the phase I program there. So I was heavily involved in drug development programs, all training programs I've been to, NIH in Bethesda, an observership in the CTEP program, and also did the ASCO/AACR Vail workshop, where you really learned a lot in just like one week. So those are kind of opportunities present for fellows and even the early investigators and attendings as well in the first few years can go there, have your proposal. And really they are the world experts in trial design and they'll talk about how to design trials, how to add collaborators, improve your trial, and basically learn the whole protocol in a week so to speak.   And then I was at Moffitt Cancer Center for about five, six years. My home was GI so I did both GI oncology as well as phase I. And in terms of the GI oncology, my main focus was pancreatic cancer and liver tumors. Then I was at Mayo Clinic in Rochester for about seven or so years. I kind of did the same thing and solidified my career at GI oncology, looking at liver tumors, and pancreatic cancer and then being a part of the phase I division program. And now, most recently, about a year or so ago, I joined Case Western to lead the GI program here. Dr. Rafeh Naqash: Are the winters in Cleveland better than the winters in Minnesota? Dr. Amit Mahipal: For sure. I always say, you don't know cold until you go to Minnesota. It's a different kind of cold. I'm sure people in Dakota might say the same thing, but the cold in Minnesota is very brutal and different compared to any other place I've been to.  Dr. Rafeh Naqash: Well, it was great learning about you. Thank you so much for spending this time with us and for sharing your work with our journal. We hope you'll continue to do the same in the near future.  Thank you for listening to JCO Precision Oncology Conversations. Don't forget to give us a rating or review, and be sure to subscribe so you never miss an episode. You can find all ASCO shows at ascopubs.org/podcasts. Dr. Amit Mahipal: Thank you for having me here, Rafeh. Good luck. Take care. Dr. Rafeh Naqash: Thank you so much. The purpose of this podcast is to educate and inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions.   The guests on this podcast express their own opinions, experiences, and conclusions. Their statements do not necessarily express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.   Dr. Mahipal: Consulting or Advisory Role:QED TherapeuticsAstraZeneca/MedImmuneTaiho Oncology Speakers' Bureau:AstraZeneca Research Funding:Taiho Pharmaceutical"

Patients with BCR-ABL negative myeloproliferative neoplasms (MPNs) are at risk of progressing to accelerated-phase or blast-phase disease (MPN-AP/BP). Several mutations, including... The post Accelerated-phase MPNs: mutational landscape, challenges, and novel treatment strategies being explored appeared first on VJHemOnc.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.06.28.546756v1?rss=1 Authors: Jakkamsetti, V., Ma, Q., Angulo, G., Scudder, W., Beutler, B., Pascual, J. M. Abstract: Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1,408 normal mice for reference. 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least 3 mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included preferentially histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the rest of mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behavior influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Bang H. Hoang, MD, is a board-certified orthopedic surgeon specializing in musculoskeletal tumor surgery. Dr. Hoang is an expert in benign and malignant tumors, metastatic bone disease, pathologic fractures, complex bone and joint reconstruction with large-segment prosthesis and allograft, tumors of the pelvis and sacrum, and investigational therapy for bone and soft tissue sarcoma. He is the Co-Director of the Orthopaedic Oncology Division at Montefiore and Professor of Orthopaedic Surgery at Albert Einstein College of Medicine. -- What We Do at MIB Agents: PROGRAMS: End-of-Life MISSIONS Gamer Agents Agent Writers Prayer Agents Healing Hearts - Bereaved Parent and Sibling Support Ambassador Agents - Peer Support Warrior Mail Young Adult Survivorship Support Group EDUCATION for physicians, researchers and families: OsteoBites, weekly webinar & podcast with thought leaders and innovators in Osteosarcoma MIB Book: Osteosarcoma: From our Families to Yours RESEARCH: Annual MIB FACTOR Research Conference Funding multiple $100,000 and $50,000 grants annually for OS research MIB Testing & Research Directory The Osteosarcoma Project partner with Broad Institute of MIT and Harvard ... Kids are still dying with 40+ year old treatments. Help us MakeItBetter. https://www.mibagents.org​ Help support MIB Agents, Donate here https://give-usa.keela.co/embed/YAipuSaWxHPJP7RCJ SUBSCRIBE for all the Osteosarcoma Intel

Asexual reproduction has its advantages, but organisms that depend too much on it also face potential extinction. In this episode of Stuff to Blow Your Mind, Robert and Joe discuss mutational meltdown and Muller's ratchet.See omnystudio.com/listener for privacy information.

In this episode of the IJGC podcast, Editor-in-Chief, Dr. Pedro Ramirez, is joined by Dr. Giuseppe Caruso and Prof. Nicoletta Colombo to discuss updates on PARPi in ovarian cancer. Dr. Caruso is a fifth-year resident in Obstetrics and Gynecology and a first-year fellow of the PhD in “Network Oncology and Precision Medicine” at the Sapienza University of Rome in Italy. Over the past year, he has been attending the Department of Gynecologic Oncology at the European Institution of Oncology (Milan) and had the huge opportunity to follow the clinical, surgical and research activities of an international center of excellence, under the mentorship of Prof. Nicoletta Colombo and Prof. Giovanni D. Aletti. His main interest areas are gynecologic oncology, personalized oncology, clinical research, and medical writing. Prof. Nicoletta Colombo is Chair of Gynecology Program and Director of the Ovarian Cancer Centre at the European Institute of Oncology in Milan. Principal investigators of several international clinical trials and author of several publications, she was President of ESGO and Chair of the ESMO-ESGO-ESTRO Consensus Conference in endometrial cancer (2015) and the ESMO-ESGO Consensus Conference in ovarian Cancer (2018). In 2020, Prof. Colombo received the IGCS Lifetime Achievement Award in recognition of her work in gynecological oncology. Highlights: - PARPi should be preferred in the upfront setting for both efficacy and safety reasons. - Mutational status and platinum response are key factors for personalizing the maintenance treatment. - Identifying better predictors of resistance to platinum and PARPi is an unmet need. - PARPi combinations could become a strategy for overcoming PARPi resistance. - The best treatment algorithm after PARPi progression needs prospective validation.

In this episode of the IJGC podcast, Editor-in-Chief, Dr. Pedro Ramirez, is joined by Dr. Giuseppe Caruso and Prof. Nicoletta Colombo to discuss updates on PARPi in ovarian cancer. Dr. Caruso is a fifth-year resident in Obstetrics and Gynecology and a first-year fellow of the PhD in “Network Oncology and Precision Medicine” at the Sapienza University of Rome in Italy. Over the past year, he has been attending the Department of Gynecologic Oncology at the European Institution of Oncology (Milan) and had the huge opportunity to follow the clinical, surgical and research activities of an international center of excellence, under the mentorship of Prof. Nicoletta Colombo and Prof. Giovanni D. Aletti. His main interest areas are gynecologic oncology, personalized oncology, clinical research, and medical writing. Prof. Nicoletta Colombo is Chair of Gynecology Program and Director of the Ovarian Cancer Centre at the European Institute of Oncology in Milan. Principal investigators of several international clinical trials and author of several publications, she was President of ESGO and Chair of the ESMO-ESGO-ESTRO Consensus Conference in endometrial cancer (2015) and the ESMO-ESGO Consensus Conference in ovarian Cancer (2018). In 2020, Prof. Colombo received the IGCS Lifetime Achievement Award in recognition of her work in gynecological oncology. Highlights: - PARPi should be preferred in the upfront setting for both efficacy and safety reasons. - Mutational status and platinum response are key factors for personalizing the maintenance treatment. - Identifying better predictors of resistance to platinum and PARPi is an unmet need. - PARPi combinations could become a strategy for overcoming PARPi resistance. - The best treatment algorithm after PARPi progression needs prospective validation.

JCO PO author Dr. Shilpa Gupta, MD, Associate Professor of Medicine at the Cleveland Clinic and GU Medical Oncology Director, shares analysis on outcomes in real-world settings for metastatic urothelial carcinoma (mUC) patients. Host Dr. Rafeh Naqash and Dr. Gupta discuss the utility of tumor mutational burden (TMB) to determine treatment, and mUC patient response from immune checkpoint inhibitors (ICPI) as compared with carboplatin. Click here to read the article!   TRANSCRIPT Dr. Rafeh Naqash: Hello and welcome to JCO Precision Oncology Conversations. I am Dr. Rafeh Naqash, assistant professor of medicine at OU Stephenson Cancer Center. You're listening to the JCO Precision Oncology Conversations podcast.   Today I'll be talking with Dr. Shilpa Gupta, who is an associate professor of medicine at the Cleveland Clinic and also the GU Medical Oncology Director. And we'll be talking about their group's recent paper, ‘Tumor Mutational Burden as a Predictor of First-Line Immune Checkpoint Inhibitor Versus Carboplatin Benefit in Cisplatin-Unfit Patients With Urothelial Carcinoma'.   Full disclosures for our guest can be found on the article's publication page.   Hello and welcome to the podcast, Dr. Gupta. It's nice to have you here. For the sake of this podcast, we'll be referring to each other using our first names. So welcome and thanks for joining us today.   Dr. Shilpa Gupta: It's my pleasure to be here, Rafeh, I'm really excited about chatting about this paper with you. Thank you for the opportunity.   Dr. Rafeh Naqash: Thank you so much. So today we'll be discussing this interesting publication of yours, talking about biomarkers. And I often refer to biomarkers as the Pandora's Box for immune checkpoint inhibitors because definitely one size does not fit all. And reading through your paper, I saw a lot of interesting findings that you have defined in this publication. But for starters, what was the premise and background of why you wanted to study this question of tumor mutational burden as a biomarker in this patient population?   Dr. Shilpa Gupta: Yeah, that's a great question, Rafeh. The treatment paradigm for urothelial cancer patients has really evolved over the last many years. For example, patients who are eligible to receive cisplatin-based chemotherapy, that's the treatment of choice. And for patients who are not eligible to receive cisplatin due to a variety of reasons like chronic kidney disease, heart failure, peripheral neuropathy, poor performance status, or hearing loss, in the past, we used to treat them with gemcitabine and carboplatin, but outcomes were quite dismal with median overall survival less than six months or so. And then in 2017, the approval of pembrolizumab and atezolizumab as single agents was welcome news because these patients had more durable responses and survival was longer than historically with gemcitabine-carboplatin. And this is what became the standard of care based on the FDA expedited approval.   However, in 2018, the FDA restricted the use of immunotherapy only to those patients whose tumors had high PD-L1 or who were not eligible to receive carboplatin, based on the interim analysis from the phase three trials IMvigor130, which compared atezolizumab to gemcitabine-carboplatin, one of the cohorts for cis-ineligible patients, and KEYNOTE-361, which compared pembrolizumab to gemcitabine-carboplatin in the cis-ineligible cohort. And furthermore, recently, the FDA actually further restricted the label for pembrolizumab, because in the phase 3 study, even in high PD-L1 subgroups, pembrolizumab did worse than gemcitabine-carboplatin, regardless of their PD-L1 status. There were early deaths, lower response rates, and in the IMvigor130 study, we recently saw that atezolizumab was actually withdrawn for this indication altogether.   So there has been this attraction for PD-L1 for a long time, but now multiple studies in urothelial cancer have shown that PD-L1 is not a durable biomarker. And we wanted to see if there's other biomarkers which can be accessible at the point of care. And we wanted to study how tumor mutational burden can or cannot pan out as a treatment selection or complementary to clinical criteria. Right now, there's no biomarkers to guide treatment for patients in urothelial cancer for carboplatin or immunotherapy use. And that was the premise for the study.   Dr. Rafeh Naqash: Excellent. Thank you so much for that detailed understanding of why you decided to pursue this.   Now, from the listener standpoint when you define cisplatin-ineligible patients, in your practice, what is the percentage of patients that you see who are technically cisplatin-ineligible? Does comorbidity play an important role in determining which patients, or does it depend on your discussion with the patient? What are those factors that you would describe to define what cisplatin-ineligibility would constitute?   Dr. Shilpa Gupta: So historically, Matt Galsky and colleagues described cisplatin-ineligibility as patients with a creatinine clearance less than 60 mLs per minute, hearing loss greater than grade two, poor ECOG performance status two or higher, peripheral neuropathy, which is significant or significant heart failure. Now, those all make patients ineligible for cisplatin. Now, more recently, we know that we can safely give cisplatin as long as creatinine clearance is above 50. So for the real world, 50 is a threshold where we can use split dose cisplatin. And I'll say, given that bladder cancer or urothelial cancer is a disease of the elderly, median age being 71 years, a lot of our patients have these comorbidities, chronic kidney disease, diabetes, and whatnot, which precludes us from using cisplatin. So in the real world, I would say that around 50% of patients are ineligible to receive cisplatin.   Dr. Rafeh Naqash: Interesting. And that goes back to the point where not everything that resulted from clinical trials, or the data that we get, may not be exactly applicable to the real world patient population, as you have pointed out in this interesting paper. So going back to the manuscript now from a methodology perspective, what kind of data did you include to get to the results that we'll talk about next? What was the inclusion and what was the patient population in this analysis?   Dr. Shilpa Gupta: So the patient population basically were patients who had a confirmed diagnosis of metastatic urothelial cancer. And the databases we used were the US-wide Flatiron Foundation Medicine Clinical Genomic Database, which has patients who were listed as metastatic urothelial cancer. But in addition, they also had genomic testing performed from their tumors, and results were available. And we accessed the database between 2011 until April 2021. And all these patients had had genomic testing using Foundation Medicine assay. And this de-identified data was basically US-wide across 280 cancer clinics and that's around 800 sites of care. And there's a whole range of retrospective longitudinal clinical data that was available, derived from the electronic health records comprising patient-level structured and unstructured data and also their genomic information from the tumors. And there was clinical data including demographics, lab values, performance status, timing of treatment, exposure, as well as time of progression and survival.   We decided to include patients if they received a frontline single agent immunotherapy, no matter what it was, whether pembrolizumab, atezolizumab, Nivolumab, durvalumab or avelumab, or a carboplatin-based chemotherapy. And just for the readers, this is a retrospective review. So we just used these selected patients who got in these therapies. We also required that these patients had tumor mutational burden information available through the tissue biopsy and patients who received chemotherapy and immunotherapy together were excluded and details are present in the manuscript, but this was pretty much the broad selection criteria.   Dr. Rafeh Naqash: Thank you so much. And definitely a very representative patient population from a real world setting with different therapy and different other clinical variables that are relevant in the real world setting.   So from an analysis standpoint, you, from what I read, define both a predictive and a prognostic aspect to tumor mutational burden. Could you tell us more about those results and highlight some of the interesting findings from that perspective?   Dr. Shilpa Gupta: Yes, absolutely. So as you know, tumor mutation burden cut off of ten mutations per megabase is currently utilized by the FDA, whereby approval of pembrolizumab for tumor agnostic condition was made. So that's what we considered high versus low. And we found that in this, after propensity weighing in, the tumor mutational burden less than ten group, basically those patients did not benefit from checkpoint inhibitor single agent as compared to tumor mutational burden of ten or greater. And so basically, we found that patients who had tumor mutational burden ten or higher overall had more favorable progression-free survival time to next treatment, as well as overall survival when they got a single agent immune checkpoint inhibitor, as opposed to those who got carboplatin, and also when compared to those who had tumor mutational burden less than ten. So we also looked at PD-L1 information available from the genomic database, but it was only available for around 35% of patients and still we were able to see that PD-L1 did not correlate with any of these outcomes as we show in the paper.   Dr. Rafeh Naqash: I see. And as you mentioned, you show both time to treatment failure PFS being better in TMB high patients defined as ten mutations per megabase. I didn't specifically see results related to TMB high versus low in a carboplatin specific cohort. Is that analysis something that was looked at and trying to understand whether neoantigens in a platinum-based setting specifically make a difference whether high TMB is predictive there in the carboplatin setting. Was that looked at?   Dr. Shilpa Gupta: So yes, we looked at, in the Figure 4, for the comparison of the TMB and which we were looking at the checkpoint inhibitor versus chemo. So for TMB low the chemotherapy cohort had more favorable results. Is this what you were getting at?   Dr. Rafeh Naqash: Yeah, I think what I was specifically trying to look at, like you have shown in the paper, is TMB is predictive of benefit with checkpoint inhibitors and is also prognostic in the checkpoint inhibitor setting. So my question was more whether it had a prognostic implication in a carboplatin specific cohort. So meaning high TMB, whether it correlated with better outcomes with carboplatin therapy versus low TMB. So if that was looked at.   Dr. Shilpa Gupta: We didn't look at that specifically, we only compared whether high TMB did better with the immunotherapy or chemotherapy.   Dr. Rafeh Naqash: And some of the correlation of this in my mind comes from some data that people have looked at in the lung cancer setting, whether high TMB makes a difference and for example, resected lung cancer patients, which usually gets platinum-based adjuvant therapies. So that's why I was wondering if there's any correlation there. But this is definitely interesting.   Now, my next question was going to be in your manuscript you mentioned around 30% of patients had tumor mutational burden more than or equal to ten. Did you identify any other unique characteristics from any other mutational standpoint or a PD-L1 standpoint in the high TMB cohort?   Dr. Shilpa Gupta: Yes. So PD-L1 didn't really stand out to be a very steady biomarker in our experience. And this is also what was reflected in the phase three trials like DANUBE where they looked at the durvalumab and tremelimumab, IMvigor130 or KEYNOTE-361. So that was pretty consistent that these studies also showed TMB to be more useful in exploratory analysis. Of course, these patients were not stratified based on that. And we also looked at other emerging biomarkers, for example, F-TBRS and angiogenesis gene expression signatures as well as tGE3. And we need to evaluate them in a separate study to see what pans out.   But for now, I think as far as in the real world, we are looking at a lot of genomic testing being done and right now we really don't know how to use that for making treatment decisions, right? PD-L1 has really phased out as of any utility whatsoever. And using TMB; I think in addition to the clinical characteristics, like when possible, we should be offering patients carboplatin. There's no doubt about that for cisplatin ineligible patients. But there's those patients who, if they're refusing chemotherapy and we really can't make a case for giving them single agent immunotherapy, I think TMB can come in handy to justify and make sure that we're not doing them a disservice by not giving carboplatin. And I think future trials need to use this biomarker in a prospective setting to further establish its utility.   Dr. Rafeh Naqash: Definitely, I agree it's a case-by-case situation from a patient standpoint to determine what therapy is appropriate for the patient and what is most realistic, what is the expectation that the patient has, from that treatment.   Now, from a TMB standpoint, one of the ongoing debates is if it is a binary cut off or whether it could be tertiles for a certain tumor type or quartiles. Was there any subanalysis or any subsequent study that your team would be looking at from a TMB cut off standpoint? Maybe a higher cut off would mean a better outcome and maybe lesser duration of therapy in those patients. Is that somewhat of a consideration?   Dr. Shilpa Gupta: Yeah, that's a great question, Rafeh. And I think the reason we stuck to it as a binary end point is because that's the FDA definition, so people don't try to extrapolate based on anything higher or lower. But yeah, that's a great question. And I know in lung cancer they're looking at different ranges. As far as urothelial cancer, we just stuck to the ten mutations per megabase for now.   Dr. Rafeh Naqash: Of course. And one of the other interesting things I really like to see in the paper is your figure specifically on the ECOG performance status and how clinical trials sometimes do not include patients on the higher ECOG performance status spectrum. And your study obviously had a good representation on that standpoint. What were some of the findings from the ECOG standpoint that were somewhat different in your cohort than what you would see in clinical trials in general?   Dr. Shilpa Gupta: Yes, as we've shown in Figure 5, the ECOG in real world, it was quite an eye opener to see that there was a considerable number of patients who were documented as ECOG performance status three. And if you see the ECOG performance status two bar was around 50% and ECOG performance status one was also lower than what has traditionally been included in the phase three trials. And in the phase three trials, there's hardly any patients with ECOG performance status two compared to what we saw in the real world. And very few patients, in fact, hardly any had ECOG performance status zero in our real world analysis. So clearly the trials need to be more inclusive, as has been the ASCO message all along. And it's always very surprising to see the big gap between the real world and the clinical trial patient population.   Dr. Rafeh Naqash: Definitely, I think more and more, especially cooperative group trials that you and many others are leading, are trying to be as inclusive as possible, which is important to get a better understanding of how these therapies do in different patient populations. And one of the questions I wanted to ask you, and I've seen this a few times in different checkpoint therapy treated tumors, is this initial rapid progression in some patients where the chemotherapy arm does better, but the immunotherapy arm kind of falls rapidly and then starts plateauing. In your clinical experience, have you seen that? And if yes, what are the features of some of those patients that have this rapid progression from a clinical and both from a biomarker standpoint?   Dr. Shilpa Gupta: That's a great question, Rafeh, and we do see that every now and then, and especially in my experience, we've seen that in women in particular who have bone metastases are really challenging to treat with immunotherapy. And sometimes we find that the disease just rapidly blows through immunotherapy and we really need to do more biomarker work to understand what determines these biomarkers of hyper-progression, so to speak. I know there's a lot of work going on in the field and we are also trying to understand these by serially collecting blood and circulating tumor DNA from our patients during their treatment journey.   Dr. Rafeh Naqash: Exactly. Definitely work in progress and another unique patient population where more needs to be done to understand what are the events that lead to these hyper-progression aspects, whether it's in the bone or brain or any other compartment in the body.   Well, this has been exciting and interesting, but before we end, we try to know a little bit more about the investigator, the author. So, Shilpa, can you tell us a little bit about your journey in oncology and your journey as a trainee, your journey as faculty, as a clinical trialist, as a successful clinical trialist? And any advice for junior investigators listening to this conversation?   Dr. Shilpa Gupta: Yeah, thank you for asking. I think oncology always struck me as a very exciting field back in my residency days, 2005, 2006. And at the time, so much was going on, like just drugs like bevasizumab were just coming around for colorectal cancer and in lung cancer drugs like EGFR inhibitors were coming around. And that kind of really excited me. And talking with my mentor at the time, who was a really well-renowned transplanter, he said to me that if he had to do it all over again, he would love to get into solid tumor oncology with all the excitement that's going on. I was drawn to oncology also because of, not only it's a learning experience every day, but it can be very gratifying to see amazing responses and patients living longer despite having advanced disease, and also provides a lot of challenges every day when every patient is not the same. So I think that was the reason why I was drawn to oncology and provides us an opportunity to really develop new therapies as opposed to some of the other specialties because of how challenging the patient population is.   And as far as my journey, you know, I've now been in the US for almost 18 years and have been in a variety of places, and I think it's been a very rewarding journey despite multiple bumps along the way. And I'm really glad to be doing what I'm doing and trying to advance the field, clinical trials, and learning from people around me.   Dr. Rafeh Naqash: Thank you so much for giving us a little glimpse into your journey and your experiences. And it's always inspiring to listen to successful investigators and also try to emulate in some ways what you have done and what you've achieved. And thank you again for coming on this podcast. And thank you for choosing JCO Precision Oncology as a destination for your manuscript, and hopefully we'll see more of the same from you and your group in the subsequent years to come and more in this field of biomarkers.   Thank you for listening to JCO Precision Oncology Conversations. You can find all our shows, including this one, at ASCO.org/podcasts or wherever you get your podcasts. To stay up to date, be sure to follow and share JCO PO content on Twitter @JCOPO_ASCO. All JCO PO articles and series can be found at ascopubs.org/journal/PO.     The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions.   Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.     Guest Bio Shilpa Gupta, MD, is Associate Professor of Medicine at the Cleveland Clinic and GU Medical Oncology Director.   Guest disclosures Stock and Other Ownership Interests: Nektar, Moderna Therapeutics Honoraria: Bristol Myers Squibb Consulting or Advisory Role: Gilead Sciences, Guardant Health, AVEO, EMD Serono, Pfizer, Merck, Loxo/Lilly Speakers' Bureau: Bristol Myers Squib

BUFFALO, NY-April 25, 2022 – A new research paper, entitled, “Real-world survival analysis by tumor mutational burden in non-small cell lung cancer: a multisite U.S. study,” was published in Oncotarget on January 31, 2022, by researchers from University of Utah, University of Minnesota Duluth, Huntsman Cancer Institute, H. Lee Moffitt Cancer Center and Research Institute, Baptist Health Medical Group, MetroHealth Medical Center, Rutgers Cancer Institute of New Jersey, University of Southern California, Saint Luke's Cancer Institute, University of Kentucky, and Bristol Myers Squibb. This multidisciplinary research team analyzed tumor mutational burden (TMB) among a large cohort of patients who had been diagnosed with stage IV non-small cell lung cancer (NSCLC). The cohort included 667 patients recruited from nine different academic and community cancer centers across the United States. “The purpose of this study is to evaluate clinical outcomes by TMB among NSCLC patients treated with immunotherapy containing regimens in the first-line setting.” (Source, 2022) While having a high TMB may sound unfavorable, a higher TMB has been associated with a higher number of neoantigens. The presence of a greater number of neoantigens may potentiate a stronger immune response. Thus, TMB may be a viable biomarker of tumor response to immuno-oncology agents. “Based on the results in this study and prior research, TMB along with other biomarkers, such as PD-L1, may help identify patients more likely to benefit from first-line immunotherapy.” (Source, 2022) Results of the study confirmed the association between a higher TMB and smoking history. However, the study did not show an association between TMB and sex, age or tumor histology. The team found that, among patients treated with first-line immunotherapy, TMB levels greater than or equal to 10 mutations per megabase were significantly associated with improved overall survival and progression-free survival. DOI: https://doi.org/10.18632/oncotarget.28178 Corresponding author: Connor Willis – Connor.Willis@pharm.utah.edu Video: https://youtu.be/Q5JI4L6Moq0 Sign up for free Altmetric alerts about this article: https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28178 About Oncotarget: Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science. To learn more about Oncotarget, visit Oncotarget.com and connect with us on social media: Twitter – https://twitter.com/Oncotarget Facebook – https://www.facebook.com/Oncotarget YouTube – www.youtube.com/c/OncotargetYouTube Instagram – https://www.instagram.com/oncotargetjrnl/ LinkedIn – https://www.linkedin.com/company/oncotarget/ Pinterest – https://www.pinterest.com/oncotarget/ LabTube – https://www.labtube.tv/channel/MTY5OA SoundCloud – https://soundcloud.com/oncotarget For media inquiries, please contact media@impactjournals.com.

Listen to a blog summary of a trending research paper published by Oncotarget in Volume 13, entitled, "Real-world survival analysis by tumor mutational burden in non-small cell lung cancer: a multisite U.S. study." ___________________________________ While a high tumor mutational burden (TMB) may seem unfavorable in the midst of battling non-small cell lung cancer (NSCLC), a higher TMB has been associated with a higher number of neoantigens. The presence of more neoantigens can potentially elicit a stronger immune response. Therefore, TMB may be a viable biomarker of tumor response to immunotherapeutic agents. However, the definitions, parameters and units used to measure high- and low-TMB have been inconsistent over the years. Today, the consensus unit for reporting TMB has shifted to mutations per megabase (mut/Mb). The common cut-off for high- vs. low-TMB from tissue samples is >10 mut/Mb in NSCLC. “Despite inconsistencies with TMB definition and reporting over time, high TMB has consistently been associated with improved clinical benefit among patients receiving immunotherapy for NSCLC [22].” Researchers—from University of Utah, University of Minnesota Duluth, Huntsman Cancer Institute, H. Lee Moffitt Cancer Center and Research Institute, Baptist Health Medical Group, MetroHealth Medical Center, Rutgers Cancer Institute of New Jersey, University of Southern California, Saint Luke's Cancer Institute, University of Kentucky, and Bristol Myers Squibb—used the newest consensus unit and common cut-off parameters for TMB expression to measure TMB's relationship to treatment response and survival outcomes among metastatic NSCLC patients. Their trending research paper was published in Oncotarget's Volume 13 on January 31, 2022, and entitled, “Real-world survival analysis by tumor mutational burden in non-small cell lung cancer: a multisite U.S. study.” “The purpose of this study is to evaluate clinical outcomes by TMB among NSCLC patients treated with immunotherapy containing regimens in the first-line setting.” Full blog - https://www.oncotarget.org/2022/04/21/trending-with-impact-analysis-of-mutational-burden-in-nsclc/ DOI - https://doi.org/10.18632/oncotarget.28178 Correspondence to - Connor Willis - Connor.Willis@pharm.utah.edu Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28178 Press release - https://www.oncotarget.com/news/pr/oncotarget-mutational-burden-in-lung-cancer-studied-in-multisite-cohort/ Keywords - lung neoplasma, tumor biomarkers, immunotherapy About Oncotarget Oncotarget is a peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/OncotargetYouTube LinkedIn - https://www.linkedin.com/company/oncotarget Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget/ Oncotarget is published by Impact Journals, LLC: https://www.ImpactJournals.com Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

An expert panel discusses the latest data for the treatment of advanced gastrointestinal stromal tumor (GIST). Credit available for this activity expires: 7/20/2022 Earn Credit / Learning Objectives & Disclosures: https://www.medscape.org/viewarticle/954995?src=mkm_podcast_addon_954995

In this Podcast, I interview Robin, who is a fighter of a rare Polygenic Disease, "Polygenic Mutational Syndrome of Methylations." Learn about this rare condition, and hear her story! --- Support this podcast: https://anchor.fm/theraredisorderpodcast/support

Dr. Matthew Gubens joins GRACE to discuss Tumor Mutational Burden in NSCLC.

Today we interview Dr. Luc Morris of Memorial Sloan Kettering Cancer Center on his new paper out now in JAMA Oncology titled "Response Rates to Anti-PD-1 Immunotherapy in Microsatellite-Stable Solid Tumors With 10 or More Mutations per Megabase". Response Rates: doi.org/10.1001/jamaoncol.2020.7684 Back us on Patreon! www.patreon.com/plenarysession Check out our YouTube channel: www.youtube.com/channel/UCUibd0E2kdF9N9e-EmIbUew

Listen to short summaries of the latest oncology-focused research literature published in this week's issue of Oncotarget Volume 12, Issue 5. Click here for the complete issue: https://www.oncotarget.com/archive/v12/i5/ Oncotarget Volume 12, Issue 5 features: Cover Paper: "The cancer testis antigens CABYR-a/b and CABYR-c are expressed in a subset of colorectal cancers and hold promise as targets for specific immunotherapy." https://doi.org/10.18632/oncotarget.27897 Research Perspective: "Tumor mutational burden as a predictor of immunotherapy response in breast cancer." https://doi.org/10.18632/oncotarget.27877 Research Paper: "STAT3 induces the expression of GLI1 in chronic lymphocytic leukemia cells." https://doi.org/10.18632/oncotarget.27884 Research Paper: "Multi-modal effects of 1B3, a novel synthetic miR-193a-3p mimic, support strong potential for therapeutic intervention in oncology." https://doi.org/10.18632/oncotarget.27894 Research Paper: "Mutational profile of skin lesions in hepatocellular carcinoma patients under tyrosine kinase inhibition: a repercussion of a wide-spectrum activity." https://doi.org/10.18632/oncotarget.27891 Research Paper: "Development of a ghrelin receptor inverse agonist for positron emission tomography." https://doi.org/10.18632/oncotarget.27895 Research Paper: "Global DNA hypermethylation pattern and unique gene expression signature in liver cancer from patients with Indigenous American ancestry." https://doi.org/10.18632/oncotarget.27890 Research Paper: "Fine–mapping of two differentiated thyroid carcinoma susceptibility loci at 2q35 and 8p12 in Europeans, Melanesians and Polynesians." https://doi.org/10.18632/oncotarget.27888 Research Paper: "Quantitative proteome profiling stratifies fibroepithelial lesions of the breast." https://doi.org/10.18632/oncotarget.27889 About Oncotarget: Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit www.oncotarget.com or follow us: SoundCloud - @oncotarget Facebook - www.facebook.com/Oncotarget/ Twitter - twitter.com/oncotarget LinkedIn - www.linkedin.com/company/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/OncotargetYouTube Pinterest - www.pinterest.com/oncotarget/ Reddit - www.reddit.com/user/Oncotarget/ Oncotarget is published by Impact Journals, LLC please visit www.ImpactJournals.com or connect with @ImpactJrnls Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957x105

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Hans Clevers, MD, PhD presents his paper as published in the February 27, 2020 issue of Nature. Series: "Stem Cell Channel" [Health and Medicine] [Science] [Show ID: 36177]

Harmit Malik, PhD (Professor and Associate Director of the Basic Sciences Division at the Fred Hutchinson Cancer Research Center) joins host Lauren Richardson to discuss the results and implications of the article "Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races", by Jeannette L Tenthorey, Candice Young, Afeez Sodeinde, Michael Emerman, and Harmit S Malik,  published in eLife.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392878v1?rss=1 Authors: Wojtowicz, D., Hoinka, J., Amgalan, B., Kim, Y.-A., Przytycka, T. M. Abstract: Many mutagenic processes leave characteristic imprints on cancer genomes known as mutational signatures. These signatures have been of recent interest regarding their applicability in studying processes shaping the mutational landscape of cancer. In particular, pinpointing the presence of altered DNA repair pathways can have important therapeutic implications. However, mutational signatures of DNA repair deficiencies are often hard to infer. This challenge emerges as a result of deficient DNA repair processes acting by modifying the outcome of other mutagens. Thus, they exhibit non-additive effects that are not depicted by the current paradigm for modeling mutational processes as independent signatures. To close this gap, we present RepairSig, a method that accounts for interactions between DNA damage and repair and is able to uncover unbiased signatures of deficient DNA repair processes. In particular, RepairSig was able to replace three MMR deficiency signatures previously proposed to be active in breast cancer, with just one signature strikingly similar to the experimentally derived signature. As the first method to model interactions between mutagenic processes, RepairSig is an important step towards biologically more realistic modeling of mutational processes in cancer. The source code for RepairSig is publicly available at https://github.com/ncbi/RepairSig. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.385864v1?rss=1 Authors: Chevalier, A., Yang, S., Yajima, M., Campbell, J. D. Abstract: Mutational signatures are patterns of somatic alterations in the genome that cause carcinogenic exposures or aberrant cellular processes. We created the musicatk package to provide a comprehensive workflow for preprocessing, analysis, and visualization of mutational signatures. The musicatk package enables users to select different schemas for counting mutation types and easily combine count tables from different schemas. Several methods can be used to discover new signatures or infer the exposures for given a pre-existing set of signatures. Several visualizations are provided to facilitate exploratory analysis of signatures and exposures. These include comparison of discovered signatures to those in the COSMIC database, using UMAP to embed tumors in two dimensions, and plotting of exposure distributions across user-defined annotations. Overall, musicatk can be used to gain novel insights into the patterns of mutational signature observed in cancer. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.25.353946v1?rss=1 Authors: Gelman, S., Romero, P. A., Gitter, A. Abstract: The mapping from protein sequence to function is highly complex, making it challenging to predict how sequence changes will affect a protein's behavior and properties. We present a supervised deep learning framework to learn the sequence-function mapping from deep mutational scanning data and make predictions for new, uncharacterized sequence variants. We test multiple neural network architectures, including a graph convolutional network that incorporates protein structure, to explore how a network's internal representation affects its ability to learn the sequence-function mapping. Our supervised learning approach displays superior performance over physics-based and unsupervised prediction methods. We find networks that capture nonlinear interactions and share parameters across sequence positions are important for learning the relationship between sequence and function. Further analysis of the trained models reveals the networks' ability to learn biologically meaningful information about protein structure and mechanism. Our software is available from https://github.com/gitter-lab/nn4dms. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.14.338756v1?rss=1 Authors: Heyne, M., Shirian, J., Cohen, I., Peleg, Y., Radisky, E. S., Papo, N., Shifman, J. M. Abstract: Each protein-protein interaction (PPI) has evolved to possess binding affinity that is compatible with its cellular function. As such, cognate enzyme/inhibitor interactions frequently exhibit very high binding affinities, while structurally similar non-cognate PPIs possess substantially weaker binding affinities. To understand how slight differences in sequence and structure could lead to drastic changes in PPI binding free energy ({Delta}{Delta}Gbind), we study three homologous PPIs that span nine orders of magnitude in binding affinity and involve a serine protease interacting with an inhibitor BPTI. Using state-of-the-art methodology that combines protein randomization and affinity sorting coupled to next-generation sequencing and data normalization, we report quantitative binding landscapes consisting of {Delta}{Delta}Gbind values for the three PPIs, gleaned from tens of thousands of single and double mutations in the BPTI binding interface. We demonstrate that the three homologous PPIs possess drastically different binding landscapes and lie at different points in respect to the landscape maximum. Furthermore, the three PPIs demonstrate distinct patterns of coupling energies between two simultaneous mutations that depend not only on positions involved but also on the nature of the mutation. Interestingly, we find that in all three PPIs positive epistasis is frequently observed at hot-spot positions where mutations lead to loss of high affinity, while conversely negative epistasis is observed at cold-spot positions, where mutations lead to affinity enhancement. The new insights on PPI evolution revealed in this study will be invaluable in understanding evolution of other biological complexes and can greatly facilitate design of novel high-affinity protein inhibitors. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.12.336404v1?rss=1 Authors: Candia, J. Abstract: Summary: mutSigMapper aims to resolve a critical shortcoming of existing software for mutational signature analysis, namely that of finding parsimonious and biologically plausible exposures. By implementing a shot-noise-based model to generate spectral ensembles, this package addresses this gap and provides a quantitative, non-parametric assessment of statistical significance for the association between mutational signatures and observed spectra. Availability and implementation: The mutSigMapper R package is available under GPLv3 license at https://github.com/juliancandia/mutSigMapper. Its documentation provides additional details and demonstrates applications to biological datasets. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.17.301614v1?rss=1 Authors: Rahman, S. A., Singh, J., Singh, H., Hasnain, S. E. Abstract: We are in the midst of the third severe coronavirus outbreak caused by SARS-CoV-2 with unprecedented health and socio-economic consequences due to the COVID-19. Globally, the major thrust of scientific efforts has shifted to the design of potent vaccine and anti-viral candidates. Earlier genome analyses have shown global dominance of some mutations purportedly indicative of similar infectivity and transmissibility of SARS-CoV-2 worldwide. Using high-quality large dataset of 25k whole-genome sequences, we show emergence of new cluster of mutations as result of geographic evolution of SARS-CoV-2 in local population ({greater than or equal to}10%) of different nations. Using statistical analysis, we observe that these mutations have either significantly co-occurred in globally dominant strains or have shown mutual exclusivity in other cases. These mutations potentially modulate structural stability of proteins, some of which forms part of SARS-CoV-2-human interactome. The high confidence druggable host proteins are also up-regulated during SARS-CoV-2 infection. Mutations occurring in potential hot-spot regions within likely T-cell and B-cell epitopes or in proteins as part of host-viral interactome, could hamper vaccine or drug efficacy in local population. Overall, our study provides comprehensive view of emerging geo-clonal mutations which would aid researchers to understand and develop effective countermeasures in the current crisis. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.14.296129v1?rss=1 Authors: Voegele, A., Sadi, M., O'Brien, D. P., Gehan, P., Raoux-Barbot, D., Davi, M., Hoss, S., Brule, S., Raynal, B., Weber, P., Mechaly, A., Haouz, A., Rodriguez, N., Vachette, P., Durand, D., Brier, S., Ladant, D., Chenal, A. Abstract: The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells have thus far remained elusive. The adenylate cyclase (CyaA) toxin from Bordetella pertussis displays a unique intoxication pathway in which its catalytic domain is directly translocated across target cell membranes. We have previously identified a translocation region in CyaA that contains a segment, P454 (residues 454-484), exhibiting membrane-active properties related to antimicrobial peptides. Herein, we show that this peptide is able to translocate across membranes and interact with calmodulin. Structural and biophysical analyses have revealed the key residues of P454 involved in membrane destabilization and calmodulin binding. Mutational analysis demonstrated that these residues play a crucial role in CyaA translocation into target cells. We have also shown that calmidazolium, a calmodulin inhibitor, efficiently blocks CyaA internalization. We propose that after CyaA binding to target cells, the P454 segment destabilizes the plasma membrane, translocates across the lipid bilayer and binds calmodulin. Trapping of the CyaA polypeptide chain by the CaM:P454 interaction in the cytosol may assist the entry of the N-terminal catalytic domain by converting the stochastic process of protein translocation into an efficient vectorial chain transfer into host cells. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.24.265827v1?rss=1 Authors: Prasad, P., Prakash, S., Sahu, K., Singh, B., Shukla, S., Mishra, H., Khan, D. N., Prakash, O., Bhatt, M., Barik, S., Asif, M. H., Sawant, S. V., Jain, A., Bag, S. K. Abstract: COVID-19 leads to a global emergency that causes more than 7 million causalities until mid-August throughout the world. In India alone, 2 million confirmed cases were reported that increased abruptly day by day with the lowest fatality rate. The availability of a large number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV2) genome in the public domain provides a great opportunity to study mutational changes in COVID-19 genomes in Indian populations. In this study, we sequenced the genomes of SARS-CoV2 viruses isolated from 47 individuals from 13 districts of Uttar Pradesh (UP), the largest state of India using Third Generation Sequencing Technology. We further did the phylogenetic clustering of UP state of Indian SARS-CoV2 genomes revealed a perceivable point that no UP samples were aligned on the USA defined clade where the fatality rate is high. We also identified 56 distinctive Single Nucleotide Polymorphism variations in UP state that majorly clustered into two groups which shows the deleterious effects on the genome. Additionally, we conducted the mutation analysis of the 2323 SARS-CoV2 genome of different states of India from the Global Initiative on Sharing All Influenza Data (GISAID) where we find ~80% unique mutations rate in each sample of the Indian population. Thus, this is the first extensive mutational study of the largest state of Indian populations in which we report the novel deleterious SNPs in virus genome along with the other states which access the less infectious form of SARS-CoV2 genome through synonymous to nonsynonymous mutation variation. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.18.255570v1?rss=1 Authors: Banerjee, R., Basak, K., Ghosh, A., Rajachandran, V., Sureka, K., Ganguly, D., Chattopadhyay, S. Abstract: The dire need of effective preventive measures and treatment approaches against SARS CoV 2 virus, causing COVID 19 pandemic, calls for an in-depth understanding of its evolutionary dynamics with attention to specific geographic locations, since lockdown and social distancing to prevent the virus spread could lead to distinct localized dynamics of virus evolution within and between countries owing to different environmental and host specific selection pressures. To decipher any correlation between SARS CoV 2 evolution and its epidemiology in India, we studied the mutational diversity of spike glycoprotein, the key player for the attachment, fusion and entry of virus to the host cell. For this, we analyzed the sequences of 630 Indian isolates as available in GISAID database till June 07, 2020, and detected the spike protein variants to emerge from two major ancestors, Wuhan-Hu-1/2019 and its D614G variant. Average stability of the docked spike protein host receptor (SR) complexes for these variants correlated strongly (R2=0.96) with the fatality rates across Indian states. However, while more than half of the variants were found unique to India, 67% of all variants showed lower stability of SR complex than the respective ancestral variants, indicating a possible fitness loss in recently emerged variants, despite a continuous increase in mutation rate. These results conform to the sharply declining fatality rate countrywide (>7 fold during April 11 and June 28, 2020). Altogether, while we propose the potential of SR complex stability to track disease severity, we urge an immediate need to explore if SARS CoV 2 is approaching mutational meltdown in India. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.237206v1?rss=1 Authors: Anaya, J., Sidhom, J.-W., Cummings, C. A., Baras, A. S., The AACR Project GENIE Consortium Abstract: Deep learning has the ability to extract meaningful features from data given enough training examples. Large scale genomic data are well suited for this class of machine learning algorithms; however, for many of these data the labels are at the level of the sample instead of at the level of the individual genomic measures. To leverage the power of deep learning for these types of data we turn to a multiple instance learning framework, and present an easily extensible tool built with TensorFlow and Keras. We show how this tool can be applied to somatic variants (featurizing genomic position and sequence context), and accurately classify samples according to whether they contain a specific variant (hotspot or tumor suppressor) or whether they contain a type of variant (microsatellite instability). We then apply our model to the calibration of tumor mutational burden (TMB), an increasingly important metric in the field of immunotherapy, across a variety of commonly used gene panels. Regardless of the panel, we observed improvements in regression to the gold standard whole exome derived value for this metric, with additional performance benefits as more data were provided to the model (such as noncoding variants from panel assays). Our results suggest this framework could lead to improvements in a range of tasks where the sample level metric is determined by the aggregation of a set of genomic measures, such as somatic mutations that we focused on in this study. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.31.231472v1?rss=1 Authors: Tomaszewski, T., DeVries, R. S., Dong, M., Bhatia, G., Norsworthy, M. D., Zheng, X., Caetano-Anolles, G. Abstract: The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15,342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP 12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major beta-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.31.230987v1?rss=1 Authors: Patro, L. P. P., Sathyaseelan, C., Uttamrao, P. P., Rathinavelan, T. Abstract: To accelerate the drug and vaccine development against the severe acute respiratory syndrome virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F-NSP6, P323L-NSP12, D614G-spike, Q57H-ORF3a, G251V-ORF3a, L84S-ORF8, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring mutations and P323L-NSP12 and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85-NSP1 deletion, D268-NSP2 deletion, 112 amino acids deletion in ORF8, a phenylalanine insertion amidst F34-F36 (NSP6) and several co-existing substitution/deletion (I559V & P585S in NSP2, P504L & Y541C in NSP13, G82 & H83 deletions in NSP1 and K141, S142 & F143 deletions in NSP2) mutations. P323L-NSP12, D614G-spike, L37F-NSP6, L84S-ORF8 and the sequences deficient of the high significant mutations has led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations has evolved in the first phase and has already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid protein, ORF3a, ORF8, RNA dependent RNA polymerase and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9, NSP10, NSP8, the envelope protein and NSP4 are highly resistant to mutations and can be exploited for drug/vaccine development. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.29.225037v1?rss=1 Authors: Waneka, G., Vasquez, Y. M., Bennett, G. M., Sloan, D. B. Abstract: Compared to free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to partition the effects of mutation vs. selection. For example, the ancestor of auchenorrhynchan insects contained two obligate endosymbionts, Sulcia and a betaproteobacterium (BetaSymb; called Nasuia in leafhoppers) that exhibit divergent rates of sequence evolution and different propensities for loss and replacement in the ensuing ~300 Ma. Here, we use the auchenorrhynchan leafhopper Macrosteles sp. nr. severini, which retains both of the ancestral endosymbionts, to test the hypothesis that differences in evolutionary rate are driven by differential mutagenesis. We used a high-fidelity technique known as duplex sequencing to measure and compare low-frequency variants in each endosymbiont. Our direct detection of de novo mutations reveals that the rapidly evolving endosymbiont (Nasuia) has a much higher frequency of single-nucleotide variants than the more stable endosymbiont (Sulcia) and a mutation spectrum that is even more AT-biased than implied by the 83.1% AT content of its genome. We show that indels are common in both endosymbionts but differ substantially in length and distribution around repetitive regions. Our results suggest that differences in long-term rates of sequence evolution in Sulcia vs. BetaSymb, and perhaps the contrasting degrees of stability of their relationships with the host, are driven by differences in mutagenesis. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.23.217083v1?rss=1 Authors: Victor, M., Das, R., Ghosh, T. Abstract: SARS-CoV-2 has caused a global pandemic that has costed enormous human lives in the recent past. The present study is an investigation of the viral codon adaptation, ORF's stability and tRNA co-adaptation with humans. We observed that for the codon usage bias in viral ssRNA, ORFs have near values of folding free energies and codon adaptation index with mRNAs of the human housekeeping CDS. However, the correlation between the stability of the ORFs in ssRNA and CAI is stronger than the mRNA stability and CAI of HKG, suggesting a greater expression capacity of SARS-CoV-2. Mutational analysis reflects polymorphism in the virus for ORF1ab, surface glycoprotein and nucleocapsid phosphoprotein ORFs. Non-synonymous mutations have shown non-polar substitutions. Out of the twelve mutations nine are for a higher t-RNA copy number. Viruses in general have high mutation rates. To understand the chances of survival for the mutated SARS-CoV-2 we did simulation for synonymous mutations. It resulted in 50% ORFs with higher stability than their native equivalents. Thus, considering only the synonymous mutations the virus can exhibit a lot of polymorphism. Collectively our data provides new insights for SARS-CoV-2 mutations and the human t-RNA compatibility. Copy rights belong to original authors. Visit the link for more info

This podcast reviews the results of the whole genome sequencing study by Samur and colleagues that identified a genomic signature associated with superior survival in patients with newly diagnosed multiple myeloma. Disclosures: SAH has served on advisory boards or as a consultant for Adaptive Biotechnologies, Amgen, Celgene, Genentech, GSK, Oncopeptides, Sorrento; Takeda; has received research funding from Oncopeptides.     This JCO Podcast provides observations and commentary on the JCO article “Genome-Wide Somatic Alterations in Multiple Myeloma Reveals a Superior Outcome Group” by Samur et al. My name is Sarah Holstein, and I am an Associate Professor at the University of Nebraska Medical Center in Omaha, Nebraska in the United States. My oncologic specialty is plasma cell dyscrasias. I do not have any relationships to disclose related to these studies. The clinical heterogeneity of myeloma has long been appreciated as it is clear there is a broad range of disease behavior, with some patients having indolent disease and others having very aggressive disease. As a result, there has been significant interest in developing risk stratification systems that classify patients into different risk groups, thus providing some information about prognosis and potentially inform treatment decisions. Historically, staging systems were based on factors related to tumor burden. However, it is increasingly evident that the underlying disease biology is a key modulator of risk. Our ability to detect disturbances in the myeloma genome has changed dramatically over time. Metaphase karyotyping represents our lowest “power of magnification”. These studies led to the recognition that in general, hyperdiploidy involving odd-numbered chromosomes is associated with lower-risk disease while high-risk disease can involve translocations of chromosome 14, monosomy 13 and monosomy 17. Use of fluorescent in-situ hybridization (FISH) allowed for a higher power of magnification and identification of more subtle chromosomal abnormalities. Next, gene expression profiling studies utilizing small panels of genes, enabled classification of patients into different risk categories, although there was little concordance between the panels used in the various studies. The advent of deep whole genome sequencing technology has facilitated a much more “high-powered” view of the myeloma genome. In the article that accompanies this podcast, diagnostic bone marrow specimens were obtained from 183 patients enrolled in the IFM/DFCI 2009 study. This phase 3 study enrolled newly diagnosed transplant-eligible patients (up to age 65). All patients received three cycles of lenalidomide, bortezomib, dexamethasone (RVD) induction, underwent stem cell collection and then received consolidation with either 5 cycles of RVD or a single autologous stem cell transplant followed by 2 cycles of RVD. Of note, in the French portion of this study, all patients subsequently received one year of lenalidomide maintenance, while in the US portion, all patients received lenalidomide until progression. The French portion has already been published and showed a 14 month PFS benefit for the transplant arm compared to the non-transplant arm. Results from the US portion have not yet been released, but I would speculate that the PFS and OS for both arms will be superior to the French counterparts, given the existing data supporting the benefit of prolonged lenalidomide maintenance. Deep whole genome sequencing, with a median tumor depth of 75X, was used to interrogate the myeloma genome. Mutational signatures were based on identified single nucleotide variants, small insertions and deletions. The genomic scar score (GSS) was calculated based on allele-specific copy number alterations. A GSS of 5 or less was the cut-off for inclusion in the low GSS group. The goals of the study were to describe mutational loads and processes in order to establish genomically-defined subgroups, gain insight into patterns of evolution from clonal to subclonal mutations, and correlate these findings with clinical outcomes and more traditional risk factors. There were several key findings. First, mutational load varied amongst myeloma subgroups, with hyperdiploid myeloma having the lowest mutational load and t(14;16) having the highest mutational load. Second, analysis of mutational patterns led to identification of five separate mutational processes that contributed to eight mutational signatures. These five processes included: 1) an age-related process, 2) an AID/APOBEC process, 3) somatic hypermutation, 4) DNA repair, and 5) processes with unidentified etiology including the clock-like signature. Samur et al., found that these various processes contributed to different myeloma subgroups in different ways. For example, the age-related process was high in hyperdiploid myeloma, the APOBEC-related process was high in t(14;16) myeloma, the clock-like signature was high in t(4;14) myeloma and the DNA repair process was high in del(17p) and t(11;14) myeloma. Furthermore, analysis of these mutational patterns from a clonal vs subclonal perspective enabled insight into mutational development patterns of different subgroups of myeloma. Next, the GSS was correlated with mutational signature and clinical outcome data. The authors found that the frequency of a low GSS was higher in t(11;14) myeloma and lower in del17p, gain1q21, del1p and del13 subgroups. Patients in the low GSS group had a trend towards a longer median PFS and a statistically significant longer 4-year OS rate than other patients. In particular, patients with both low GSS and gain of chromosome 9 had a superior outcome compared to all other subgroups, with an OS probability of 100%. Patients with either low GSS and no gain(9) or with high GSS and gain(9) had intermediate outcome while those with high GSS and t(4;14), gain(1q) or no gain(9) had the worst OS. Although the numbers are quite small, an interesting finding was that for patients in the low-risk group (low GSS + gain(9)), there was a significantly superior PFS in favor of those patients in the transplant arm compared to the non-transplant arm. Overall, no statistically significant differences were found between the four subgroups and factors such as ISS stage, response, or achievement of MRD negativity.  The numbers in each subgroup were quite small though. Finally, the authors demonstrated that the low GSS could separate hyperdiploid myeloma into low-risk and high-risk subgroups. Overall, these studies are interesting because they provide insight into the mutational processes that drive different subgroups of myeloma and offer a potential method by which to differentiate low-risk hyperdiploid myeloma from high-risk hyperdiploid myeloma. The finding that there was a difference in PFS for patients who underwent transplant vs no transplant in the low-risk group (low GSS, gain(9)) is very intriguing. There has been much discussion centered around whether low-risk patients really “need” to go through a stem cell transplant since in general their outcomes are good. The present study, aside from highlighting the fact that our traditional methods of identifying low-risk disease are likely inadequate, raises the hypothesis that patients with low-risk disease may benefit even more from transplant than other risk groups. However, it is noted that this subgroup consisted of only 28 patients. In addition, it is not clear from the manuscript whether patients were in the US vs French portion of the study, thus differences in study design (i.e., lenalidomide maintenance duration) could impact PFS findings. Clearly, this type of whole genome sequencing analysis will need to be applied to additional prospective studies in order to validate the novel risk stratification system. For now, these results are not practice-changing. However, they provide a potential glimpse into the future, where whole genome sequencing analysis is performed as readily as FISH analysis, and where enrichment strategies using genomic markers are used to design clinical trials. Aside from studies evaluating the use of venetoclax in t(11;14)-positive myeloma and other studies focused on high-risk disease that encompass a variety of high-risk chromosomal abnormalities, the field of myeloma has not yet moved into an era of precision medicine. Whether whole genome sequencing can finally usher us into that era remains to be determined. While this plasma cell-centric analysis is certainly revealing, it is likely that in order to maximally target myeloma, the genomics analysis must be coupled with an equally in-depth understanding of the host’s immune system. This concludes this JCO Podcast. Thank you for listening.

The latest episode of Lung Cancer Considered focuses on a recent publication in IASLC's Journal of Thoracic Oncology that features new guidelines on Tumor Mutational Burden as well as the effects of COVID-19. This episode features a conversation between host Dr. Marty Edelman; Dr. Lynette Scholl an associate professor of Pathology at Harvard Medical School and an associate pathologist, Pathology at Brigham And Women's Hospital; and Dr. John Longshore director of Molecular Pathology at Carolinas Pathology Group, Atrium Health, Carolinas HealthCare System.

The world is currently gripped by COVID-19, but could an often overlooked population genetic theory hold one of the keys to defeating it? In this episode we speak to Prof. Michael Lynch (Arizona State University) about a recent Comment he penned with Prof. Jeffrey Jensen, where they consider mutational meltdown as a potential SARS-CoV-2 treatment strategy. See acast.com/privacy for privacy and opt-out information.

Dr. Jack West recently had the privilege to spend time with Drs. Millie Das and Matthew Gubens for a series of case-based discussions regarding unresectable NSCLC . Dr. Millie Das specializes in the treatment of thoracic malignancies. She sees and treats patients both at the Stanford Cancer Center and at the Palo Alto VA Hospital. She is Chief of Oncology at the Palo Alto VA and also leads the VA thoracic tumor board on a biweekly basis.Dr. Matthew Gubens is a thoracic oncologist who treats patients with lung cancer, mesothelioma and other thoracic malignancies, including thymoma and thymic carcinoma, which are rare tumors of the mediastinum. He is an Assistant Clinical Professor of Medicine at UCSF.Recently the doctors sat down to discuss a series of case-based scenarios. In this video, the doctors discuss Tumor Mutational Burden (TMB) and it's value in testing. For more, please visit http://cancerGRACE.org/. To join the conversation, visit https://cancergrace.org/forum.

Dr. Charu Aggarwal from University of Pennsylvania Abramson Cancer Center joins Dr. Jack West to discuss new data on plasma-based testing for tumor mutational burden (TMB) & the current state of liquid biopsies, TMB, & immunotherapy-based options today.

The latest space mission to the Sun is due to launch on Sunday. SolO, the European Space Agency's Solar Orbiter, will loop around our star in an elliptical orbit, sling-shotting around Venus. Professor Richard Harrison at the Rutherford Appleton Laboratory has been on the mission from its conception, he details the instruments and what they're hoping to discover about the Sun and its impact on space weather back here on Earth. If chemicals in cigarette smoke or exposure to UV light played a role in causing a cancerous tumour, we can now see this evidence in the DNA. These and other causes of cancer are being catalogued by a huge international study revealing the genetic fingerprints of DNA-damaging processes that drive cancer development. Professor Mike Stratton, is director of the Wellcome Sanger Institute and author of one of many papers released in Nature and associated journals this week that detail the results of the Pan-Cancer of Whole Genomes Consortium. Cancer is not a modern disease. Evidence in bones and remains reveal our ancient ancestors also suffered. Dr. Kate Hunt is a paleo-pathologist studying paleo-oncology, a very specific, very recent branch of archaeology, looking through ancient burial sites, artefacts and literature for signs of cancer. Presenter - Marnie Chesterton Producer - Fiona Roberts

In this episode, Victor Weigman, Director of Translational Genomics at Q Squared Solutions and Mark Stewart, Vice President of Science Policy at Friends of Cancer Research (FOCR) joined to talk about standardization of TMB measurements by alignment to reference standards. TMB differs from other biomarkers such as PDL1 in that: "...we're leveraging next generation sequencing to generate a composite score from tens of thousands or in some cases millions of bases of sequence. So really you're summarizing this collection of mutations in a singular value versus a more qualitative range of expression levels done by looking at proteins in a microscope. - Victor Weigman One challenge is that as treatments are being developed, the thresholds for the diagnostics are out of sync. Friends of Cancer Research understands the difficulty of harmonizing assays to a standard after FDA approval. For that reason, there is strong interest in harmonizing the results of different assays to a standard reference set.    

Nels and Vincent analyze the genomes of canine transmissible tumors to provide insight into the worldwide spread of the disease from its origin in a single dog 4000-8500 years ago, and its diversity, mutation, and evolution. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Evolution and mutation of canine transmissible cancer (Science) Clam cancers (TWiEVO 17) Sixth modality of infectious disease (PLoS Path) Time stamps by Jolene. Thanks! Science Picks Nels - Vasa Museum in Stockholm Vincent - Nobel Museum in Stockholm Listener Pick Irene - @EndlessFormsand #PlantScienceFascinatesMe #plantsday Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Dr. Mark Stewart discusses the role of the tumor mutational burden (TMB) in cancer research and the need for harmonization throughout the process. For more information, please visit https://www.triconference.com/Companion-Diagnostics

In the first episode of our new series, Jack is joined by PhD student Bernadeta Dadonaite from the University of Oxford to hear about how the flu virus arranges its genome inside the virus particle. Bernadeta studied the flu genome structure by using a technique called 'SHAPE-Map', which stands for: Selective 2'-hydroxyl acylation analyzed by primer extension - Mutational profiling. This is essentially a tool to figure out how a molecule like RNA folds. You can find Bernadeta’s blogs at theartfulgene.tumblr.com and questiongene.com, or read her paper https://www.biorxiv.org/content/early/2017/12/21/236620. We also have bunch more content about flu over at our website, cvrblog.myportfolio.com. Music: The Zeppelin by Blue Dot Sessions (http://freemusicarchive.org/music/Blue_Dot_Sessions/Aeronaut/The_Zeppelin_1908)

Dr. Jack West reviews new findings highlighting the utility of using the biomarker tumor mutation burden (TMB) to predict which patients with small cell lung cancer (SCLC) will benefit from nivolumab or the combination of nivolumab with ipilimumab.

Dr Nicholas McGranahan talks with ecancertv at AACR 2016 about tumour heterogeneity and mutational markers for immunotherapy. Within tumours, mutations can give rise to varying gene expression that in turn effects the potential efficacy of a targeted treatment. However, each mutation may in turn give rise to a presented peptide that could be recognised by a patients innate immunity. Rather than the specific mutational drivers of cancer, Dr McGranahan reports on the targeting of these neoantigens as non-self markers, a highly personalised target for potential therapies.

Prof McArthur speaks with ecancer at WCCS 2016 about targetted medicine to reduce melanoma mutational burden, with specific focus on the BRIM trials of cobimetinib and vemurafinib. He outlines the expansion of personalised therapy and genotyping for improved duration and depth of response, considering the push from other quarters towards sequencing for all patients, and his hopes for the future of cancer vaccines. However, Prof McArthur notes that these results do not indicate clinical readiness, and highlights brain metastases in melanoma as an area in need of further research.

Dr Lavrov speaks with ecancertv at the IFHNOS 2016 session in Moscow about molecular genetics aiding in diagnosis and treatment of thyroid cancer. He outlines the processes by which mutational aberrations can be detected, and how to cope with the wealth of data rendered by next-generation sequencing.

Prof Loibl speaks with ecancer at IMPAKT 2017 about the differing genetic backgrounds and susceptibilities of breast cancer in patients who are pregnant. She describes results from next-generation sequencing of samples, compared to data in The Cancer Genome Atlas, noting that the samples assessed were taken from much younger women. Among the differences in gene expression, Prof Loibl highlights difference in PI3K and p53 mutation levels. Prof Loibl summarises treatment schedules for pregnant breast cancer patients, cautioning against under-treatment of aggressive tumours and over-treatment of HR2 patients.

Dr Montalban-Bravo speaks with ecancer at EHA 2017 about genomic sequencing of over 200 patients at diagnosis, identifying mutational markers which may predict response to hypomethylating agents He describes that mutations in TET family proteins and p53 were among the most common aberrations, and discusses how treatment pathways can be uncovered through sequencing analysis.

Dr Alexandrov speaks with ecancertv at EACR 2016 about the signatures and processes exhibited by genetic mutations which result in cancer. He outlines a number of processes that can contribute to disease states, including the time-bound 'clocklike' processes and socio-environmental contributors. Dr Alexandrov considers the potential impact of bioinformatics on cancer research, and discusses how his Young Investigator award will shape his future research.

Dr. Greg Riely from Memorial Sloan-Kettering Cancer Center reviews the limited data that help clarify the probability of benefit from new immunotherapy agents among patients with advanced NSCLC and an identified driver mutation.

Dr. Greg Riely from Memorial Sloan-Kettering Cancer Center reviews the limited data that help clarify the probability of benefit from new immunotherapy agents among patients with advanced NSCLC and an identified driver mutation.

Dr. Greg Riely from Memorial Sloan-Kettering Cancer Center reviews the limited data that help clarify the probability of benefit from new immunotherapy agents among patients with advanced NSCLC and an identified driver mutation.

Membrane remodeling is a dynamic process that occurs in bacterial cells to facilitate substrate transport and to provide protection to bacteria during environmental stress. In eukaryotic cells, membrane remodeling is carried out by dynamin-like proteins (DLPs). These proteins are involved in diverse membrane-associated functions such as cargo transport via vesicles, cytokinesis, division of cell organelles and resistance to pathogens. DLPs are also conserved in bacterial species; however, their function is still not clearly understood. The genome of B. subtilis contains a gene dynA (ypbR), which encodes a large DLP (136 KDa),DynA, that can tether membranes and induce membrane fusion in vitro. Deletion of dynA in B. subtilis strain 168 fails to produce any observable growth phenotype under standard laboratory conditions. B. subtilis is a soil bacterium and prey to several environmental stress factors to which laboratory strains are normally not exposed. Hence, it was conceivable that DynA might be required when bacteria are exposed to stress. To address this hypothesis, the behavior of DynA was examined under conditions causing membrane-stress, such as exposure to antibiotics and phage infection. A strain lacking dynA showed impaired growth in the presence of sublethal amounts of antibiotics that target the cell membrane and was more sensitive to phage infection compared to wild-type strains. Time-lapse microscopy and fluorescence loss in photobleaching (FLIP) experiments showed that ΔdynA cells have compromised membrane remodeling compared to wild-type strain. In conclusion, all results propose DynA to play a role in protecting the cell membrane under stress conditions. Also, for the first time, it is shown that a bacterial DLP contributes to innate immunity of bacteria. DynA not only has a unique membrane protection function but also distinctive structural features. A single DynA polypeptide contains two dynamin-like subunits, each consisting of a GTPase domain and a dynamin-like stalk region. Both subunits, D1 and D2, share strong intra-molecular cooperativity to facilitate GTPase activity. Here, a combination of mutational analysis and subsequent in vivo and in vitro investigation was applied to further characterise structural assembly and biochemical properties of DynA. Size-exclusion chromatography elucidated that DynA dimerisation requires C-terminal amino acids 591-620. In addition, in vivo localisation, in vitro lipid-binding and GTPase analysis revealed arginine at position 512 of DynA to be a key regulator of GTP hydrolysis as well as lipid-binding. Furthermore, in vivo localisation and bacterial two-hybrid experiments were employed to confirm interaction of DynA with putative interaction partners (YneK, YwpG and YmdA). YneK was found to interact with D1 and YwpG with D1 and D2 individually, whereas YmdA required a full-length DynA (D1+D2) for interaction. Taken together, the results presented here greatly expand on current knowledge regarding functional, biochemical and structural properties of a bacterial dynamin-like protein (BDLP). This thesis not only demonstrates the preserved membrane remodeling function of DLPs in bacteria but also explain their conservation from bacteria to higher-organisms.

This podcast will use the study reported by Bejar and colleagues to review the role of screening for TET2, DNMT3A, and particularly TP53, mutations in deciding whether to recommend allogeneic hematopoietic cell transplant for patients with myelodysplastic syndromes.

Background: Sengers syndrome is an autosomal recessive condition characterized by congenital cataract, hypertrophic cardiomyopathy, skeletal myopathy and lactic acidosis. Mutations in the acylglycerol kinase (AGK) gene have been recently described as the cause of Sengers syndrome in nine families. Methods: We investigated the clinical and molecular features of Sengers syndrome in seven new families; five families with the severe and two with the milder form. Results: Sequence analysis of AGK revealed compound heterozygous or homozygous predicted loss-of-function mutations in all affected individuals. A total of eight different disease alleles were identified, of which six were novel, homozygous c.523_524delAT (p.Ile175Tyrfs}2), c.424-1G > A (splice site), c.409C > T (p.Arg137*)and c.877 + 3G > T (splice site), and compound heterozygous c.871C > T (p.Gln291*)and c.1035dup (p.Ile346Tyrf*39). All patients displayed perinatal or early-onset cardiomyopathy and cataract, clinical features pathognomonic for Sengers syndrome. Other common findings included blood lactic acidosis and tachydyspnoea while nystagmus, eosinophilia and cervical meningocele were documented in only either one or two cases. Deficiency of the adenine nucleotide translocator was found in heart and skeletal muscle biopsies from two patients associated with respiratory chain complex I deficiency. In contrast to previous findings, mitochondrial DNA content was normal in both tissues. Conclusion: We compare our findings to those in 21 previously reported AGK mutation-positive Sengers patients, confirming that Sengers syndrome is a clinically recognisable disorder of mitochondrial energy metabolism.

Die Bakteriophagen Integrase PhiC31 stellt ein viel versprechendes Werkzeug zur Integration genetischen Materials im nicht viral-basierten Gentransfer dar. Die PhiC31 Integrase vermittelt die Rekombination von spezifische Erkennungssequenz attB enthaltenden Plasmiden mit natürlich vorkommenden attP Erkennungssequenzen innerhalb des Zielgenoms mit unterschiedlicher Integrationsfrequenz und -spezifität. Nebeneffekte der Integration in Form von insertioneller Mutagenese, wie z.B. große Deletionen und chromosomale Veränderungen im Genom der Zielzelle konnten beobachtet werden. Ziel dieser Dissertation war, die PhiC31 vermittelte Effizienz zu verbessern und die Spezifität zu adressieren. Als Ansatz wurde die Mutagenese der DNA-Bindungsdomäne der Integrase basierend auf Punktmutanten zur verbesserten Integrationseffizienz gewählt. Integrationsassays wurden in verschiedenen humanen Zelllinien durchgeführt. Etablierung von Doppelmutanten, sowie Dosisoptimierung des Integrase kodierenden Plasmids verbesserten die Integrationseffizienz mehr als dreifach, verglichen mit der Wildtypintegrase in den Zelllinien HeLa und HCT. Weitere Assays verglichen die Exzisionsaktivität der Integrasemutanten mit dem Wildtyp. Bei fünf Mutanten wurde eine etwa zweifach erhöhte Exzision gefunden. Die Beurteilung der Spezifität der Integrasemutanten erfolgte durch Substitution der Wildtyp-attP Sequenz mit drei Pseudo attP Erkennungssequenzen des Reporterplasmids, deren erhöhte Spezifität bereits dokumentiert war. Einzelne Mutanten zeigten eine zweifach erhöhte Exzisionsaktivität. Die Rekombinationsaktivität von Integrasemutanten wurde im Kontext chromosomaler DNA mittels einer stabil GFP-exprimierenden Reporterzelllinie, in der die eGFP Expression mittels Integrase-vermittelter „Raus-Rekombination“ eines polyA Stoppsignals angeschaltet wird, untersucht. Auf chromosomaler Ebene wurde keine verbesserte Ausschneidungsaktivität erreicht. Zur Evaluierung der in vivo Effizienz zweier ausgewählter PhiC31 Integrasemutanten, die in vitro erhöhte Integrationsaktivität aufwiesen, wurden zwei Plasmide am C57BL/6 Mausmodell getestet. Reportergen war ein für den humanen Koagulationsfaktor IX kodierendes Gen. In Abhängigkeit von der Integrationseffizienz der Mutanten und des Wildtyps, wurden im Zeitraum von einhundert Tagen ähnliche Expressionslevel gefunden. Die Mutanten zeigten keine Verbesserung der Langzeitexpression von humanem Faktor IX. Die hier durchgeführten Studien zur Mutationsanalyse der Phagenintegrase PhiC31 zeigten einen wirksamen Ansatz zur Verbesserung der PhiC31 Integrase-vermittelten Integrationseffizienz in vitro.

Ulrich Hübscher, Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Zürich, SWITZERLAND speaks on "Oxygen as a friend and enemy: how to combat the mutational potential of 8-oxo-guanine". This seminar has been recorded by ICGEB Trieste

TGR5, the G protein-coupled bile acid receptor 1 (GPBAR1), has been linked to inflammatory pathways as well as bile homeostasis, and could therefore be involved in primary sclerosing cholangitis (PSC) a chronic inflammatory bile duct disease. We aimed to extensively investigate TGR5 sequence variation in PSC, as well as functionally characterize detected variants. Complete resequencing of TGR5 was performed in 267 PSC patients and 274 healthy controls. Six nonsynonymous mutations were identified in addition to 16 other novel single-nucleotide polymorphisms. To investigate the impact from the nonsynonymous variants on TGR5, we created a receptor model, and introduced mutated TGR5 constructs into human epithelial cell lines. By using confocal microscopy, flow cytometry and a cAMP-sensitive luciferase assay, five of the nonsynonymous mutations (W83R, V178M, A217P, S272G and Q296X) were found to reduce or abolish TGR5 function. Fine-mapping of the previously reported PSC and UC associated locus at chromosome 2q35 in large patient panels revealed an overall association between the TGR5 single-nucleotide polymorphism rs11554825 and PSC (odds ratio = 1.14, 95% confidence interval: 1.03-1.26, p = 0.010) and UC (odds ratio = 1.19, 95% confidence interval 1.11-1.27, p = 8.5 x 10(-7)), but strong linkage disequilibrium precluded demarcation of TGR5 from neighboring genes. Resequencing of TGR5 along with functional investigations of novel variants provided unique insight into an important candidate gene for several inflammatory and metabolic conditions. While significant TGR5 associations were detected in both UC and PSC, further studies are needed to conclusively define the role of TGR5 variation in these diseases.

Various stimuli like thrombin induce endothelial cell shape change and stress fiber formation via Rho/Rho-kinase-mediated reorganization of the actin cytoskeleton. LIM-kinases regulate actin cytoskeletal reorganization through phosphorylation of cofilin at Ser3. The LIMK family kinases possess characteristic structural features, consisting of two LIM domains, a PDZ domain and a C-terminal kinase domain. In cell transfection studies it has been shown that LIMK2 is phosphorylated at Thr505 by Rho-kinase thereby activating the enzyme. Recently it has been reported that nuclear LIMKs suppress cyclin D1 expression in a manner independent of cofilin phosphorylation and actin polymerization. In this study, we found that endothelial cells express both LIMK1 and LIMK2. By using live cell imaging, we confirm previous findings that thrombin induces stress fiber formation, ruffle formation and cell contraction. Furthermore, the cell-cell contacts were disrupted and F-actin fibers connecting two cells were broken. Thrombin induced a rapid and sustained Rho-kinase activation and subsequent phosphorylation of LIM-kinase and cofilin. Pretreatment of endothelial cells with the specific Rho-kinase inhibitor Y27632 inhibited MYPT1 phosphorylation, LIM-kinase and cofilin phosphorylation and blocked stress fiber formation in thrombin-stimulated cells. Notably, thrombin induced actin stress fiber formation was abolished in cells transfected with dominant negative LIMK2. LIMK2 was mainly localized in the cytoplasm. By using Leptomycin B (a specific inhibitor of CRM-1 dependent nuclear export) and FRAP and FLIP analysis, we demonstrate that LIMK2 in resting endothelial cells shuttles between the nucleus and cytoplasm. The LIM domains of LIMK2, but not of LIMK1 inhibited its nuclear import thereby keeping LIMK2 mainly in the cytoplasm. Mutational analysis of the unique basic amino acid-rich motif (amino acids 480-503) indicated that this motif regulates the nuclear and nucleolar localization of LIMK2. Activation of PKC in PMA-stimulated endothelial cells stimulated the phosphorylation of LIMK2 at Ser283 and the translocation of LIMK2 and the PDZ-kinase construct of LIMK2 from the nucleus to the cytoplasm. Of the various PKC isoforms, PKC- and PKC- were found to be mainly responsible for Ser283 phosphorylation and the regulation of translocation of LIMK2. Mutational analysis indicated that LIMK2 phosphorylation at Ser283 and Thr494 play a role in the regulation of nucleocytoplasmic shuttling of LIMK2 by PKC. These results show that LIM-kinase activation is mediated by Rho-kinase in stimulated endothelial cells, and that LIM-kinase-mediated cofilin phosphorylation plays an essential role in thrombin-induced stress fiber formation. LIMK2 shuttles between nucleus and cytoplasm in resting endothelial cells. Phosphorylation of LIMK2 at Ser283 and Thr494 by PKC regulates nucleocytoplasmic shuttling and suggests that LIMK2 might also have a function in the nucleus such as the suppression of cyclin D1 expression.

Sat, 1 Jan 1994 12:00:00 +0100 http://epub.ub.uni-muenchen.de/5137/ http://epub.ub.uni-muenchen.de/5137/1/5137.pdf Gabriel, Wilfried; Bürger, Reinhard Gabriel, Wilfried und Bürger, Reinhard (1994): Extinction risk by mutational meltdown. Synergistic effects between population regulation and genetic drift. In: Loeschcke, Volker (Hrsg.), Conservation genetics. Birkhäuser: Basel [u.a.], pp. 69-84. Biologie

Sat, 1 Jan 1994 12:00:00 +0100 http://epub.ub.uni-muenchen.de/5139/ http://epub.ub.uni-muenchen.de/5139/1/5139.pdf Gabriel, Wilfried Gabriel, Wilfried (1994): "Mutational Meltdown": Aussterberisiko durch Anhäufung schädlicher Mutationen. In: Zeitschrift für Ökologie und Naturschutz, Vol. 3: pp. 161-165.

Fri, 1 Jan 1993 12:00:00 +0100 http://epub.ub.uni-muenchen.de/5135/ http://epub.ub.uni-muenchen.de/5135/1/Gabriel_wilfried_5135.pdf Gabriel, Wilfried; Lynch, Michael; Bürger, Reinhard Gabriel, Wilfried; Lynch, Michael und Bürger, Reinhard (1993): Muller's ratchet and mutational meltdowns. In: Evolution, Vol. 47: pp. 1744-1757. Biologie

Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown, and provides a powerful explanation for the rarity of obligate asexuality. We give an overview of the theory of the mutational meltdown, showing how the process depends on the demographic properties of a population, the properties of mutations, and the relationship between fitness and number of mutations incurred.

Mon, 1 Jan 1990 12:00:00 +0100 http://epub.ub.uni-muenchen.de/5072/ http://epub.ub.uni-muenchen.de/5072/1/5072.pdf Gabriel, Wilfried; Bürger, Reinhard; Lynch, Michael Gabriel, Wilfried; Bürger, Reinhard und Lynch, Michael (1990): Population extinction by mutational load and demographic stochasticity. In: Seitz, Alfred und Loeschcke, V. (Hrsg.), Species Conservation. A population-biological approach. Birkhäuser: Basel ; Boston ; Berlin, pp. 49-59. Biologie