Single cell profiling of the T cell response elicited by immune modulatory antibodies in cancer patients – DropTrep

The immune system plays a dual role in cancer: it can both promote and suppress tumor growth. In fully immune competent cancer patients the tumours eventually escape the anti-cancer function of the immune system. In many individuals this tumour-induced immunosuppression is mediated through cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and programmed death-1 (PD-1) proteins expressed on the anti-tumour T cells and thereby blocking the response. The emergence and development of monoclonal antibodies targeting these proteins, called anti-checkpoint antibodies, have offered the potential to intervene with this process by boosting the anti-tumour response, which resulted in improved patient survival in different types of cancer, including melanoma and lung cancers. In melanoma cancer patients treated with the best-responding dose level of anti-CTLA4 and anti-PD1 checkpoint antibodies, the 2-year survival rate was impressive at 88%, compared to a 2-year survival rate of about 15% for patients treated with conventional chemotherapy. However, these treatments remain ineffective in a large fraction of the patients and many other tumour types. Detailed characterization of the anti-tumour immune responses at the molecular and cellular levels before and during treatment is urgently needed to better stratify patients, to obtain optimal clinical treatment strategies and to guide the development of novel immune modulatory drugs. We will apply single T cell profiling of both the T cell receptor and a selected set of mRNAs that define T cell functions (including cytokines, chemokines, memory markers and transcription factors) to characterize immune responses at the clonal level during cancer therapy by anti-checkpoint antibodies. Our application will take advantage of the high-throughput droplet-based microfluidic technology for single-cell RNA sequencing developed by Partners 1 and 2. Partners 3 and 4 have extensive expertise in the analysis of T cell responses. Together, we will develop the molecular biology, microfluidics, immunologic and bioinformatics tools required to provide a detailed, high throughput, functional characterization of patient derived tumour reactive T cells at the clonal level.
Combining clonal and functional analysis of T cell responses is currently impossible for more than a few hundred cells. Our technology will provide a unique view of the functional organization of human immune responses for several hundred thousand cells in a single experiment. Single T cell analysis in metastatic uveal melanoma operated for liver metastasis and in advanced lung cancer patients before and after anti-PD-1 treatment will help to understand the therapeutic mechanisms involved, predict clinical responses and improve therapeutic strategies. In the mid-term, the technology will have major applications in the fields of vaccination, infectious disease, autoimmunity and inflammatory disease.