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.

Discover the Carmona Lab bioinformatics tools. 

1. Santiago J. Carmona*, Imran Siddiqui, Mariia Bilous, Werner Held, David Gfeller*. Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. OncoImmunology (2020) 9:1
2. Amaia Martinez-Usatorre, Santiago J. Carmona, Céline Godfroid, Céline Yacoub Maroun, Sara Labiano and Pedro Romero. Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells. Frontiers in Immunology (2020) 11:340
3. Amaia Martinez-Usatorre, Lorenzo Sempere, Santiago J Carmona, Laura Carretero-Iglesia, Gwennaëlle Monnot, Daniel Speiser, Nathalie Rufer, Alena Donda, Dietmar Zehn, Camilla Jandus, and Pedro Romero. MicroRNA-155 expression is enhanced by T-cell receptor stimulation strength and correlates with improved tumor control in melanoma. Cancer Immunology Research (2019)
4. Santiago J Carmona, Sarah A Teichmann, Lauren Ferreira, Iain C Macaulay, Michael J.T. Stubbington, Ana Cvejic, David Gfeller. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.Genome Research (2017) 27 (3), 451-461
5. Santiago J. Carmona, Morten Nielsen, Claus Schafer-Nielsen, Juan Mucci, Jaime Altcheh, Virginia Balouz, Valeria Tekiel, Alberto C. Frasch, Oscar Campetella, Carlos A. Buscaglia and Fernán Agüero. 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) 14(7): 1871–1884

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