Cancer systems immunology

We are a computational biology group with expertise in immunology and single-cell transcriptomics. Our objective is to elucidate the landscape of T-cell states in homeostasis and cancer and their association with clinical outcomes in response to cancer immunotherapies. Our approach: data curation, integration and development of computational tools for its biological interpretation.

A meta-analysis of CD8 T-cell transcriptomic states in cancer

In recent years, single-cell RNA sequencing (scRNA-seq) technologies have enabled us to discover immune cell types and states at an unprecedented scale and resolution. Whereas the amount of scRNA-seq data is rapidly increasing, its biological interpretation remains a major bottleneck.

Thus, the objective of this project is to develop and use computational tools for the curation, integration and biological interpretation of high-throughput scRNA-seq data. In particular, we will focus on CD8 T-cells, which are the main effectors of adaptive immune response against intracellular pathogens and cancer.  We aim to elucidate the landscape of T-cell states in homeostasis and cancer, understanding how this landscape is modulated by cancer immunotherapies and to exploit this understanding to predict clinical responses. To this end, we follow a data-driven approach and collaborate with our experimental partners to generate new datasets and test hypotheses.

1. Martinez-Usatorre A, Sempere LF, Carmona SJ et al. MicroRNA-155 expression is enhanced by T-cell receptor stimulation strength and correlates with improved tumor control in melanoma Cancer Immunology Research 2019
2. Siddiqui I et al. Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy. Immunity 2019
3. Carmona SJ & Gfeller D. Deciphering the Evolution of Vertebrate Immune Cell Types with Single-Cell RNA-Seq. Origin and Evolution of Biodiversity 2018
4. Carmona SJ et al. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Research 2017
5. Carmona SJ et al. Towards high-throughput immunomics for infectious diseases: use of next-generation peptide microarrays for rapid discovery and mapping of antigenic determinants.Molecular & Cellular Proteomics 2015

• 2019-2023 Swiss National Science Foundation (SNSF) Ambizione Grant (#PZ00P3_180010)