Please join us for next week’s Biostatistics & Medical Informatics seminar on Friday!
Time: Friday, October 29 2021 at 12:00-1:00pm
Zoom Link: https://uwmadison.zoom.us/j/92290714337?pwd=TGZ3b0VTd2liQm5DL1VNM3dHaVFoZz09
Title: Pattern detection for precision cancer immunotherapy from spatial profiling and single-cell data
Presenter: Dr. Elana Fertig, Department of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics, Johns Hopkins University
Abstract: Therapeutic response in cancer depends critically on the state of cancer cells and additional cells in the tumor microenvironment, both of which evolve over time. New single-cell and spatial molecular technologies enable unprecedented characterization of these states across molecular and cellular scales, but are challenging to interpret due to the high-dimensional nature of these data. New computational methodologies are essential to interpret these data. We demonstrate how the Bayesian non-negative matrix factorization method, CoGAPS, enables us to learn patterns associated with immunotherapy response and resistance from single cell data. Further applying transfer learning of patterns inferred from preclinical models to patient samples enables discovery of unanticipated NK cell activation associated with anti-CTLA4 response that is preserved cross-species. While cellular composition is important, the spatial distribution of cells in the tumor microenvironment further mediate response and resistance to therapies. Emerging spatial molecular technologies provide a powerful tool to model these interactions. We demonstrate how CoGAPS further models intra-tumor heterogeneity of the tumor microenvironment and tumor cells from Visium spatial transcriptomics data.