Identifying mis-splicing-derived antigens in spliceosomal mutant myelodysplasia and targeting via T-cell receptor therapeutics - Project Summary/Abstract Myelodysplastic syndromes (MDS) are clonal blood disorders, whose pathogenesis is driven by a class of oncogenic somatic mutations in RNA splicing factors (in the genes SRSF2, SF3B1, U2AF1, and ZRSR2) in up to 80% of cases. Efforts to target these mutations in MDS with splicing modulatory drugs have been largely unsuccessful, and there is a great need for improved therapy. To this end, our group previously demonstrated that mis-spliced mRNAs induced by splicing modulatory drugs can serve as rich sources of immunogenic tumor antigens. Based on this proof-of-concept work, we hypothesize that mis-spliced mRNA isoforms induced by spliceosomal gene mutations can also generate meaningful tumor antigens that can be targeted by cognate T-cell receptor (TCR) therapeutics. The long-term goal of this project is to develop novel antigen-based TCR therapeutics for MDS with spliceosomal mutations. Spliceosomal mutations are also prevalent in clonal hematopoiesis (CH) and associated with an increased risk of progression to MDS and acute myeloid leukemia, and the project also aspires to develop safe and effective immunization strategies for these genomic subtypes of CH. The immediate objectives of the project are to identify mis-splicing-derived tumor antigens induced by spliceosomal mutations as well as their cognate TCRs. In Aim 1, we will predict such tumor antigens by analyzing RNA-Seq datasets of myeloid leukemia patient samples and performing immunopeptidomics. We will then validate candidate peptides in vitro for their HLA binding affinity and ability to elicit CD8+ T cell responses. In Aim 2, we will identify antigen-specific CD8+ T cells in MDS patient peripheral blood and bone marrow and extract their TCR sequences using dextramer-based single-cell multiomics. We will validate the potency and specificity of the identified TCRs both in vitro and in vivo. Overall, the project will (1) corroborate our previously findings that mis-spliced mRNAs are viable immunotherapeutic targets and (2) inspire novel immunotherapies such as TCR therapeutics for MDS patients and vaccines for subjects with CH. Dr. Omar Abdel-Wahab, a clinician-scientist with expertise in spliceosomal mutations in MDS and passion for mentoring future clinician-scientists, will sponsor the project. Dr. David Scheinberg, also a clinician-scientist with expertise in TCR therapeutics as well as a track-record of training multiple MD-PhD students, will co-sponsor the project. The research efforts will take place at the Sloan Kettering Institute, where its researchers have made tremendous contributions to the understanding and clinical implementation of immunotherapies into cancer medicine. Direct mentorship from Dr. Abdel-Wahab and Dr. Scheinberg, combined with the guidance provided by the Tri-Institutional MD-PhD Program, will ensure the successful completion of the proposed project and prepare the applicant for the future career path as an independent investigator.
