Upcoming Programs and Events

The Herbert and Florence Irving Institute for Cancer Dynamics will continue its seminar series on the topic of mathematical sciences underpinning cancer research. The monthly seminars take place on the second Wednesday of the month, 2:00-3:00 PM EST. The presentations are open to the Columbia community (in person and online) and to researchers outside Columbia (via Zoom). On Wednesday, December 10th (2:00 PM ET), IICD welcomes Dr. Sanjay Srivatsan from Fred Hutch Cancer Center. Seminar hosted by Dr. José L. McFaline-Figueroa. The seminar will take place in person in Schermerhorn Hall 603 (Morningside Heights campus). If you wish to attend the seminar remotely, please register using the following link: https://columbiauniversity.zoom.us/meeting/register/VtQKKrCYTkiEJNoGDx41SQ Title: Capsule-Based Genome Sequencing and Lineage Tracing Abstract: As cells divide and age they acquire mutations at a rate of 1-2 mutations per cell division. These mutations, which are stably inherited across generations, could serve as time-calibrated lineage marks; however, detecting these mutations has lagged severely due to their sparsity and a lack of methods for cloning whole genomes en masse. To address these problems we developed a novel semi-permeable capsule (SPC) formulation, capable of isolating single cells and their contents while facilitating biomolecular exchange based on size-selectivity. We demonstrate that SPCs facilitate the simultaneous, clonal expansion of over 200,000 cellular colonies, unbiased nucleic acid amplification, and develop a combinatorial indexing-based single-cell whole genome sequencing (CapWGS) protocol. Using CapWGS we profile cells harboring an ultramutator polymerase ε allele (POLE P286R), which increases the mutation rate per cell division by three orders of magnitude. Sequencing 1000 single-cell genomes from POLE P286R harboring cells, facilitates the recovery of distributed lineage marks, enables the reconstruction of time-calibrated cellular genealogies and reveals a rapid, recurrent and adaptive response to ultramutation through whole genome amplification. These capsule-based approaches establish a framework for the detection and reconstruction of time-calibrated lineages through the cloning and sequencing of ultramutated cells from culture or organisms. Bio: Sanjay Srivatsan is an Assistant Professor in the Basic Sciences Division of the Fred Hutch Cancer Center. He received his undergraduate training at the University of California, Berkeley in Bioengineering, followed by training in the labs of Cole Trapnell, Jay Shendure and David Baker. He now runs a genomics lab where he builds tools to measure, model and write genomes. If you would like to meet one-on-one (possibly via Zoom) or attend the lunch or dinner with the speaker, please contact the event organizer.

Enhance your literature reviews with forward and backward citation tracking and AI-powered tools in Web of Science and Scite. Learn how to uncover foundational studies, trace emerging research, map scholarly connections, and define the scope of your research domain with greater clarity and confidence. Click here to register!

This trainee talk features trainees who are engaged in mentored cancer research. The in-person location is Conference Room 117, First Floor, Irving Cancer Research Center, 1130 St Nicholas Ave New York, NY 10032.   We will have food so be sure to register here to ensure we provide the appropriate amount of food! This month the following trainees will present: A novel approach for pancreas acinar cell multiomics reveals the chromatin and gene expression landscape in acinar to ductal metaplasia Noriyuki Nishiwaki Postdoctoral Research Scientist Herbert Irving Comprehensive Cancer Center Mentor: Dr. Anil K Rustgi   Tissue resident memory T cells in the human colon and their functionality during homeostasis and in colorectal cancer Claudia Aiello MD PhD Candidate Cellular, Molecular and Biomedical Studies Mentor: Dr. Donna Farber

The Herbert and Florence Irving Institute for Cancer Dynamics will continue its seminar series on the topic of mathematical sciences underpinning cancer research. The monthly seminars take place on the second Wednesday of the month, 2:00-3:00 PM EST. The presentations are open to the Columbia community (in person and online) and to researchers outside Columbia (via Zoom). On Wednesday, January 14th (2:00 PM ET), IICD welcomes Dr. Matthew G. Jones from MIT. Seminar hosted by Dr. Jellert Gaublomme. The seminar will take place in person in Schermerhorn Hall 603 (Morningside Heights campus). If you wish to attend the seminar remotely, please register using the following link: https://columbiauniversity.zoom.us/meeting/register/8BKD8L-xQZWOaZlQ6Kz6qQ Title: Quantitatively Profiling Tumor Evolution Beyond Chromosomes Abstract: Oncogene amplification on extrachromosomal DNA (ecDNA) is a common driver of tumor progression, where it is associated with acquired drug resistance and poor patient survival. While whole genome sequencing (WGS) studies have revealed the landscape of genes amplified on ecDNA in tumors, it has remained challenging to study the dynamics and phenotypic consequences of ecDNA on tumors. In this seminar, I will present our recent work integrating high-resolution genomic technologies and computational tools to dissect the single-cell dynamics of ecDNA. These studies have given new insight into the complex copy-number dynamics of ecDNA over time (including in drug resistant disease) and the molecular consequences of ecDNA in patient tumors. Together, we hope these findings and tools will broadly enable several studies - both retrospective and prospective - that dissect critical questions of how ecDNA affect cancer cells and the tumors in which they reside. Bio: Matt Jones is an Assistant Professor at MIT in the Department of Biology and core member of the Koch Institute for Integrative Cancer Research and the Institute for Medical Science & Engineering. Previously, Matt earned his PhD at UCSF, where he developed computational approaches for single-cell lineage-tracing technologies and evolutionary approaches to study cancer dynamics. He then performed postdoctoral work at Stanford University, where he pursued fundamental studies on extrachromosomal DNA — circular, megabase-scale DNA amplifications found across cancers and associated with poor patient survival, drug resistance, and metastasis. Currently, his lab aims to develop innovative computational and technological approaches to uncover mechanisms of tumor evolution, identify new therapeutic targets, and create predictive models to monitor tumor initiation and progression. They integrate computation with multiomic approaches, lineage tracing, and high-resolution imaging to investigate the spatiotemporal dynamics of copy-number alterations, particularly extrachromosomal DNA, and elucidate the principles by which tumors are organized over time. You can read more about his lab here. If you would like to meet one-on-one (possibly via Zoom) or attend the lunch or dinner with the speaker, please contact the event organizer.