Single Cell Analysis and Immunogenetics

Project Summary The projects proposed for this grant application seek to characterize response and resistance to treatments for chronic graft versus host disease (cGVHD) following hematopoietic stem cell transplantation (HCT). Core 1 will support the single cell- and immunogenomics-related goals of these projects by focusing on applying the latest experimental and computational tools to these studies. Bulk and single-cell transcriptome sequencing of immune and lung cell populations (Aim 1) will be used to identify relevant pathways related to response to treatment of cGVHD, to identify transcriptional aspects of the metabolic signature elucidated in mouse lung cGVHD models, and to characterize the lung pathogenesis and immune response related to Bronchiolitis Obliterans Syndrome (BOS) following HCT. Response of T cells to cGVHD treatments and to BOS will be further characterized by TCR repertoire analysis using targeted bulk and single-cell sequencing to assess T cell clonality (Aim 2). Core 1 will analyze whole exome sequencing data from donor and recipient DNA to identify polymorphic differences between donor and recipient, and use tissue expression databases to determine which of these variants are expressed in lung. Recently developed sophisticated algorithms will be implemented to use this information to predict personal HLA-binding peptides that comprise minor histocompatibility antigens (Aim 3). The paired alpha/beta TCR chain single-cell sequence information will be used to reconstruct cell lines expressing individual enriched TCRs (Aim 4) in order to functionally determine exactly which TCR interacts with which antigen. This analysis will directly assess if mHAg-directed T cell responses contribute to clinical responses to therapy.