Immunotherapy and Big Data

We study dynamics of immune cells in the tumor microenvironment, and how it changes in response to therapy. We develop new computational tools for synthesizing transcriptional and epigenetic profiles of millions of single cells into models of interacting cell ensembles in immune-compartments. We use such tissue-level models to decipher the mode of action of immuno-modulators, design biomarkers from a mechanistic viewpoint and push toward development of responsive and combinatorial immunotherapeutic approaches.

Immunotherapy, which has revolutionized cancer treatment, largely relies on the ability of cytotoxic T cells to specifically recognize malignant cells and mark them for elimination. The Samuels lab aims to elucidate the attributes that lead to this specific recognition. As one of the main features for this vital interaction is presentation of neopeptides, degradation products of altered proteins specific to cancer cells presented on their surface, the Samuels lab aims to comprehensively identify such cancer-specific antigens, which together constitute the cancer immunopeptidome. Seeing as cancer-specific antigens are uncurbed by immune tolerance, and their expression is restricted to the diseased tissue, they constitute attractive therapeutic targets, which enable the generation of personalized therapeutic cancer vaccines. Our research approach combines genetics, comprehensive quantitative immunopeptidomics, novel imaging and computational approaches, advanced functional assays and novel mouse models. Our project will provide a fresh view of melanoma-immune interactions, new research tools and pipelines and cancer-specific antigen targets for immunotherapy.

Amit lab is a world pioneer and leader in developing technologies for simultaneous profiling of immune cells in single-cell resolution. The lab developed technologies for detecting protein and gene expression in single cells, combining scRNA-seq with advanced CRISPR gene editing, spatial scRNA-seq, cell-to-cell interactions and intracellular protein expression. The lab uses single-cell technologies to dissect immunological aspects of cancer biology with the goal of developing more effective and precise immunotherapies, to understand how immune cells and mechanisms impact the brain in health and neurodegenerative pathologies, to decipher the aberrant immune responses characteristic of autoimmune diseases and much more.