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.
