1. The change of T cell quality during the disease progression (using HIV infected patient as a human model)In our current study, we found the expression of different inhibitory receptors bearing Tyrosine-based Inhibitory Motifs (ITIM) on T cell clones with identical T Cell Receptors (TCR) determines the antigen sensitivity of different T cell clones. Several tissue homing receptors were also differentially expressed by the same T cell clones, sharing identical TCR. We are in the processing of sorting HIV specific T cells from donor patient to be assessed ex-vivo at the single cell level, performing targeted single cell DNA sequencing and gene expression analysis on selected genes of interest identified above using samples collected in same patient before and after disease progression.
Collaborator: Andrew McMichael, Adam Mead and Neil Ashley
2. Analysis of the effect of HBV infection on the expression of pro- and anti-inflammatory factors in liver tissueAccess to a large cohort of HCC patients allows us to stratify HCC patients according to the presence or absence of infection by HBV. By using 17 colours flow cytometric analysis, we will assess whether the presence or absence of HBV infection is linked to specific phenotypic and functional profiles of HCC infiltrated lymphoid and myeloid cell populations. These experiments will be further extended by analysing the expression profiles of pro and anti-inflammatory genes in FACS sorted immune cell populations. The link between the presence or absence of infection by HBV and expression of immune-modulatory genes in tumour cells will also 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 identified above (200-500), using the dedicated single-cell facility in the WIMM. This analysis will help to unravel heterogeneity of candidate gene expression in mixed cell populations, further helping to clarify whether the presence or absence of infection by HBV present in HCC results in the distinct expression of inflammatory genes in distinct populations of immune cells.
Collaborator: Vincenzo Cerundolo, Adam Mead and Neil Ashley