We are grateful to the Super Sam Foundation for supporting Noah as the first Super Sam Fellow. Learn about Sam here. Noah will present the logistics of his work online at this blog – please bookmark it and visit weekly! Here’s Noah: see also the video about Noah’s work at https://www.facebook.com/SuperSamFoundation/videos/1913393832243243/ 08/08/2017: Hi everyone! First edition of the cancer math blog. First, a huge thank you to Cassie Santhuff everyone at the Super Sam Foundation, and everyone who supports the amazing work they do to push the world of children’s cancer treatment forward. Without the support of the Super Sam foundation, we wouldn’t be able to do what we do, and I cannot ever thank all of you enough.
Now, to the science. I’m currently working with a stellar team of interns from Oregon State University to develop a pipeline rapid, high-throughput analysis of sequencing data from pediatric cancers. It’s a privilege to mentor them, and their knowledge expands daily. Excellent taste in coffee, too. This pipeline will reduce the time commitment from a knowledgeable bioinformaticist required to generate standard analysis data, i.e. 40 hours of work per week of active data management will be reduced to a few hours. And that means my work on cancer math continues, as I’m working every day to develop the next iteration of algorithms. I’m excited to engage my colleagues with some of the new capabilities of cancer math, including a standardized approach to disease-wide cancer math modeling, which we will be using as soon as it’s ready.
More to come on cancer math, and this approach to picking the best treatment for an individual, or a group of individuals in need of a relapsed therapy recommendation! 08/30/2017: It’s been a busy couple of weeks. We at cc-TDI had the true privilege of hosting families touched by pediatric cancer and diseases at the 2017 Pediatric Cancer Nanocourse. We welcomed people affected by myriad different diseases; Alveolar Rhabdomyosarcoma, Epithelioid Sarcoma, Bloom’s Syndrome, and Embryonal Tumours with Multilayered Rosettes (ETMR) to name a few. This event occurs every year and the disease focus changes, but the emotional impact is always profound… this chance to connect with parents and families always hits hard, and always strengthens our resolve as individual scientists and as a lab. It’s sometimes hard to believe that I can be a part of something bigger than myself, but spending time with families reminds me that my work in cancer math, and everyone’s work at cc-TDI, offers the promise of new treatments for children’s cancer. On a lighter note, I’m also happy to report that our SciClone Liquid Handling Robot (a recent major equipment acquisition for cc-TDI) is up and running thanks to the efforts of my parent-turned-scientist/mentee Andy. Here’s us giving a demonstration of this powerful new research tool during the nanocourse to build drug screens on-the-fly in a matter of seconds, a task that previously took hours! I’ll probably brag about Andy a few more times, because mentoring him and working with him is one of my favorite parts of my life at cc-TDI. 09/14/2017: Stress-testing project building code for the Cancer Math GUI. One of the key aspects of developing software is to make it accessible to everyone. Developing this front-end GUI to enable the whole lab to access Cancer Math algorithms quickly and easily. One of the most important features is the ability to develop disease-wide combination therapies; the more well-characterized samples we have to work with, the better combinations Cancer Math can develop. It just so happens we have dozens of characterized mouse models of sarcoma ready for Cancer Math modeling… more to come!
09/27/2017: Last week was a busy week indeed! Aside from progressing on several scientific and programming projects, I also had the opportunity to visit our veterinary collaborators at the CSU Flint Animal Cancer Center in Fort Collins, Colorado. Dr. Bernard Seguin has been a wonderful collaborator over the past few years, and this was my first opportunity to present Cancer Math to the scientists and clinicians there. it’s exciting to lay out our vision for the future of personalized cancer treatment. You may be wondering what children’s cancer and animal cancer have in common… well, it turns out that dogs spontaneously develop the same sorts of tumors often seen in children, especially sarcomas. And since humans and dogs live side by side, we have long considered that dog cancer patients might be a great way to explore new treatments that can be translated to children’s cancer treatment. This presents a great way to test personalized cancer therapy built by cancer math… by testing it in dogs with cancer who also need new treatment options built for their biology. With a few successful tests in dogs, it will be that much easier for oncologists to explore using cancer math to help treat children’s cancer. See you soon, Super Sam foundation!
10/23/2017: Lots to report on since my last post! Biggest of all is my trip to the Super Sam Foundation Hope Gala. It was an unbelievable privilege to visit Matt, Cassie, Ava, and all the wonderful people who made the Hope Gala happen. It was great working alongside all of you on the last minute preparations to what proved to be a fun, fantastic, and heartfelt event. Sam’s story is powerful, and experiencing the emotion in the room firsthand is always a source of motivation for a researcher in the trenches. A big thanks to Ava for the lovely introduction, for all in attendance who listened to my presentation on my years of research, and for the support of everyone at the Hope Gala for supporting my work in changing the way children’s cancer is treated. (Full disclosure: this is probably the only picture I ended up with after the Hope Gala. I took quite a few Snapchats of the gorgeous venue for my friends, but I was a little too focused on my upcoming presentation to remember to keep any pictures for myself!). On the science front, a lot of work has gone into wrapping up the manuscript that will be critical to the next stage of moving Cancer Math to clinical utility. Concomitantly, we have been planning strategies to bring Cancer Math into the clinic to meet the needs of those cancer patients seeking new options to continue their fight against cancer (and those patients with diseases lacking defined clinical treatments from the outset). Manuscript writing is always a time-consuming process, but alongside that has been working with our new scientist (Cora) on computational modeling of patient stratification for rhabdomyosarcoma, supporting the research on Osteopontin in rhabdomyosarcoma with Naren and Ali, and statistical analysis of in vivo experiments with Megan, and submitting two letters of intent for research projects ready for further development. I’m proud to work with and support my friends and colleagues. And coming up, we have some important experiments to determine if cell cultures we have developed are cancerous in behavior. More to come!
11/06/2017: This week we welcomed a new potential collaborator into the fold, Dr. Stephen Ramsay at Oregon State University. Like me, he’s an electrical engineer working on cancer biology, and like cc-TDI, he’s working on sarcoma! In his case, it’s feline-origin cancer which makes a nice partner to our data on human and canine sarcoma. Seems there are some common biological signals amongst the three species, and it happens to be a biological pathway we’re currently exploring. There could be some interesting joint work going forward, and after a great couple of summer interns (Nick and Chandler) we’re excited by the coming possibilities of future collaborations with OSU. On the cancer math and cc-TDI front, the cancer math manuscript is going through final revisions before resubmission! This manuscript is critical to the continued development of Cancer Math. We’re almost almost there. The DIPG manuscript is also in the final stages as well. We’re counting on the Tech Transfer office at Hospital for Sick Children in Toronto to come through for us quickly. It was also a productive week on the grant front! Grants are one essential mechanism that helps support our research, and this past couple of weeks I submitted two letters of intent for promising research projects! It will be a busy grant cycle the next few months, so that means late nights in my favorite coffee shop. It’s ok, they know me (and Stormy!) there. Final thoughts, I’m starting a new project on the biology side. I’ll be transforming a mutant plasmid via E. coli to build up a large enough plasmid vector population to transfect into sarcoma cells and normal cells. Basically… giving sarcoma cells a rare mutation that will enable us to study how this rare mutation changes the behavior of the cancer. It’s a small but important project, and like most things in the lab, it’s motivated by a child struggling with a rare disease. picture credit: BioCat.com (https://www.biocat.com/cdna-clones/clones/RC403308-OR)
11/22/2017:Thanksgiving is fast approaching, which always means everything in the scientific world slows down. Not really the case here at cc-TDI! This past week I’ve been focused on concluding the two key manuscripts and working on a few key Cancer Math grants, the most recent draft was sent for review today! Our associates at Beijing Genomics Institute, the organization to which we contract all of our physical sequencing work, provided us with a few critical data sets today, including those necessary for the final piece of the Cancer Math manuscript. I’m moving them to the servers where I will begin computational analysis via analysis pipelines on our high-performance computing servers. Results should be available tomorrow… which is indeed another workday for me (maybe half workday, I have a vegan Thanksgiving to attend). On the biology front, we’re starting xenograft (human tissue into mice) experiments to attempt to develop important cancer models for alveolar soft part sarcoma (ASPS) and Ewing’s Sarcoma. We should know in the next month or two whether the mice are able to grow tumors. Additionally, the RET in rhabdo project should be expanding in the near future, which will require educating myself in the particulars of lentivirus-based genome altering (using modified HIV virus to stably change the genome of human cells) in order to add a mutant gene into several models of human and mouse cancer cells. Finally, there are some exciting steps forward for supporting the continued development of Cancer Math. Nothing I can report on at present, but there should be some exciting news in the next few months!Have a great Thanksgiving holiday, everyone!
12/22/2017: The past few weeks have been a rush at cc-TDI. One of them a rush of a different sort, as I took a week’s vacation/journey to Scotland and Iceland. It was deeply needed after two years of no personal travel. Even in the middle of winter, the European North is a sight to behold. Please enjoy a couple pictures from my travels! On the research side, the big announcement this week is resubmission of the Cancer Math manuscript! It’s been a long (but necessary) time coming. With the support of my friends and colleagues at cc-TDI, and all of my collaborators on the manuscript, the revised manuscript is in the hands of the editors and should soon be out for a review. If everything goes well, the manuscript will be published soon after the new year. At the same time, our DIPG manuscript should be published in short order, which will lead into a great new research project on a promising new target (or target combination!) for the treatment of DIPG. We have received positive responses to letter of intent submissions, so we’ll be submitting to a couple grant opportunities coming up. Meanwhile, several xenograft mice are growing to establish tumors for model development and experimentation. Everything is wrapping up as the year comes to a close, and everything is happily well timed. The new year will start fresh with several new projects and hopefully some further coding with Chandler and Nick, the summer interns! We are close to concluding our easy-to-use software pipeline. With my plate mostly clear, it’s time to delve deep into analysis and programming to push Cancer Math modeling forward, and resume my role as support to everyone at cc-TDI. Cancer Math’s next big role: helping Andy integrate newly generated sequencing data to identify promising drug combinations for classical and anaplastic Wilms’ Tumor! Happy holidays, everyone!
03/05/18: Last week at cc-TDI was filled with interesting visitors! Our first of the week was a molecular biology expert with years of experience working in pharma. His depth of experience in non-cellular biology is impressive and interesting to see. Our second visitor hails from Australia, and shared his work in machine learning approaches to challenges in clinical care. It’s fascinating work, and while I can’t share the details of unpublished work, it nicely serves a need before Cancer Math would come into play. I will keep an eye on upcoming publications, as I think there’s the potential for collaborations to bring computation to the clinic.
The cancer math manuscript will be resubmitted this week, just waiting on final overview from Charles!
Similarly, last week’s DIPG grant to St. Baldrick’s is mostly written and in local peer review. I’ll be submitting it shortly with plenty of time to spare. Everything should be coming to fruition soon.
Much of this past week was spent on working with sequencing data for my colleagues, finishing papers, finishing grants, and pushing forward on the GEAR project. Happily, the first round of GEAR experiments will begin this week, and Cora will soon be finalizing the eRMS dendrogram. Soon we’ll have some promising data-driven hypotheses to explore!
Thank you as always, SuperSam supporters, and please stay tuned!