Cancer systems immunology

santiago_carmona-7225.jpg (Santigo Carmona - DO CHUV Unil)

Santiago CARMONA
Group Leader, SNF Ambizione Fellow
Laboratory S. Carmona
(hosted by Laboratory G. Coukos)

Department of oncology UNIL CHUV
Ludwig Institute for Cancer Research Lausanne

Phone +41 21 692 58 92

Ludwig.jpg (Print)



Research interest

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.

Research group projects

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.



Selected publications

  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)

Group members

Ch. des Boveresses 155 - CH-1066 Epalinges
Tel. +41 21 692 59 92
Fax +41 21 692 59 95
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