Periodic Reporting for period 1 - SingCelCD (Single Cell approaches for the study of oncogenic processes during coeliac disease.)
Période du rapport: 2019-05-01 au 2021-04-30
In the present complementary project, we intended to: 1- to search for an anti-tumor T cell response in RCDII; and 2- to analyze the functional intra-clonal heterogeneity of RCDII IEL and the peri-tumor microenvironment (figure 1).
The results should provide further insight into the mechanisms, which control disease progression and will help us to assess therapeutic strategies. They will notably help to assess if the JAK1/STAT3 pathway is a pertinent therapeutic target.
Single-cell RNAseq data allowed us to identify an amplified tumor clone in the biopsy sharing characteristics of malignant RCDII IELs. Interestingly in 3 out of 6 RCDII donors, single cell V(D)J revealed a unique clonotype shared by malignant RCDII IELs expressing an α chain and no in-frame re-arrangement of the β chain. In parallel we used a graph-based clustering algorithm to define tumor heterogeneity. This method allowed us to pinpoint heterogeneity in the transcriptional profile of cells belonging to the cluster of malignant RCDII IELs. The next step will be to define functional signatures of key signaling pathways expressed in individual cells and thus to anticipate their possible contribution to disease progression and resistance to treatment by JAK inhibitors. Finally, to get better insight into the natural history of the malignant transformation induced by CD-associated chronic autoimmune-like activation, we analyzed samples from RCDI donors. Interestingly, in one patient, we found a strongly amplified clone of CD8+ T cells. Further investigations are needed to understand if these cells represent an amplified autoreactive clonotype or may be malignant T cells.
Unfortunately the Covid epidemics has considerably restricted digestive endoscopy causing major delays in the completion of the project. Collection and processing of additional healthy donor biopsies will be necessary to confirm our results and consider their publication.
In parallel, we identified a putative anti-tumoral T cell responses in RCDII. Interestingly, in the 8 patients so far studied, analysis of paired α and β V(D)J sequences at single-cell level allowed us to pinpoint oligoclonal expansion of CD8+ TCRab+ T cells find both in the biopsy and in the blood, with a transcriptomic profile of exhausted CD8+ T cells that is compatible with tumor infiltrating T cells. Altogether our data suggest that amplified T cells clones might be engaged in anti-tumor response.
The results should provide further insight into the mechanisms, which control disease progression and will help to assess therapeutic strategies. It will notably help to assess if the JAK1/STAT3 pathway is a pertinent therapeutic target and the possible interest of using check-point inhibitors.