Research outline
Cancer immunogenomics lab focuses on understanding the genomic basis of tumorigenesis and its interplay with the immune system. Our approach relies on performing large-scale tumor genomic analyses matched with a comprehensive profiling of the tumor’s immune microenvironment to better understand the tumor immune system interaction. Our final goal is to leverage this knowledge to improve the clinical development of tailored immunotherapies.
Our aims
1. Improve our understanding of the interplay between the immune system and tumor evolution across cancer types
2. Harness this knowledge to develop improved biomarkers of response and resitance to immunotherapies as well as develop in-silico tools to optimize tailored immunotherapies.
Our approach
Our approach relies on appliying state-of-the-art analytical and machine learning learning models to a variety of tumor-omics . Specifically we rely on the integration of the genomic portrait of tumors (based on whole-exome/genome sequencing), which includes identification of simple and complex tumor specific alterations, rationalized prioritization of the tumor neoantigens, and characterization of the tumor HLA-I status and other immune escape alterations; combined with a quantitative portrayal of tumor immune’s microenvironment (using both bulk transcriptomics/proteomics immune deconvolution, single cell and geospatial immune profiling, and TCR-sequencing).
As an example of this approach, we have recently performed a large-scale analysis of the prevalence and impact of genetic immune escape alterations across >6,000 primary and metastatic tumors (F. Martinez-Jiménez, Peter Priestley et al. Nat. Genetics 2023).