Tumour Immunology Laboratory- Vincenzo Cerundolo
We are currently developing three complementary single cell research projects:
1. Analysis of the effect of melanoma genetic alterations on the expression of pro- and anti-inflammatory factors. We are currently stratifying melanoma patients according to genetic alterations of specific oncogenes and in particular according to the presence or absence of BRAF and NRAS mutations. By using 14 colours flow cytometric analysis and CYTOF analysis we will be assessing whether distinct genetic alterations in melanoma cells are linked to specific phenotypic and functional profiles of tumour infiltrated lymphoid and myeloid cell populations and cancer associated fibroblasts. The link between genetic alteration and expression of immune-modulatory genes in tumour cells will be assessed ex-vivo at the single cell level, performing targeted single cell DNA sequencing and gene expression analysis on selected oncogenes and inflammatory genes. This analysis will allow to investigate whether intra-tumour genetic heterogeneity normally present in melanomas results in the distinct expression of inflammatory genes as a function of different genetic mutations.
Collaboration: Mark Middleton
2. Understanding the immunogenic potential of BRCA1 loss-of-function in ovarian cancer. Ovarian cancer is a devastating disease due to the late presentation and resistance to chemotherapy. The urgent need for alternative therapies has encouraged clinical trials based on novel immunotherapeutic strategies, such as the use of immune check-point inhibitors. Recent reports indicate that patients with increased lymphocyte infiltration respond better to such therapies. Interestingly, higher lymphocyte infiltration correlates with mutations of BRCA1/2 genes, which contribute to an extreme genomic instability due to defects in the homologous recombination repair (HR) pathway. These results are consistent with the hypothesis that BRCA1/2-mutated ovarian cancers have a higher load of immunogenic mutations that can effectively prime anti-tumour T cell responses. In collaboration with Professor Ahmed Ahmed, we are characterizing the neo-antigen load of tumour samples at single cell level with or without BRCA1/2 mutations or with other alteration in the HR pathway, also associated to ovarian cancer. The results of these experiments will be important to develop personalized immunotherapies to ovarian cancer patients.
Collaboration: Ahmed Ahmed
3. Use of Mass Cytometry for the characterization of antigen specific T cell responses in a human model of Salmonella infection. To explore the potential for new vaccines against Salmonella the UK Medical Research Council funded an Experimental Medicine study aimed at defining the correlates of protective immunity to Salmonella Typhi and Paratyphi A in a human challenge model. This ongoing study involves challenge of numerous healthy volunteers (120) with live S. Typhi or S. Paratyphi followed, after 1 year, by either live S. Typhi or S. Paratyphi, with the ultimate aim of characterizing multiple immune parameters associated with protection, cross-protection or predisposition to development of enteric fever. Repeated blood samples, gut biopsies and tool specimen are being collected to study innate and adaptive immune responses and gut microbiota. We will take advantage of single-cell mass spectrometry (CyTOF) to probe large number of T cell antigen specificities in the same sample, while at the same time characterizing the phenotypic, TCR repertoire and functional features of these cells in depth.
Beside providing possible targets for the development of T cells vaccines capable to protect against S. Typhi and S. Paratyphi, this analysis will give the opportunity to investigate fundamental questions on the mechanism of adaptive and innate T cell immunity against intracellular pathogens, such as the impact of antigen localization (intracellular or secreted) and of the bacterial capsule on the functional phenotype of antigen specific T cells, and the mechanism of activation and expansion of non –classical T cell responses.
Collaboration: Andrew Pollard and Alison Simmons.