GoT-Splice: unraveling cell-type-specific impact of splicing factor mutations

RNA splicing factors are recurrently mutated in blood diseases, but their impact on hematopoiesis remains unclear. The study of splicing factor mutations has been technologically challenging. To overcome such limitations, we integrated genotyping of transcriptomes (GoT) with long-read single-cell transcriptomics and proteo-genomics for single-cell profiling of transcriptomes, surface proteins, somatic mutations, and RNA splicing (GoT-Splice). We applied GoT-Splice to hematopoietic progenitors from myelodysplastic syndrome (MDS) patients with mutations in the core splicing factor SF3B1 as well as clonal hematopoiesis samples (CH). In both conditions, we observed an erythroid bias and cell-type-specific cryptic 3′ splice site usage in SF3B1 mutant cells. Collectively, our work demonstrated the conserved mechanisms of mutational impact profiled directly in human samples.