New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA.
Cell Stem Cell. 2023 Sep 7;30(9):1262-1281.e8. doi: 10.1016/j.stem.2023.07.012. Epub 2023 Aug 14.
RNA splicing factors are recurrently mutated in clonal blood disorders, but the impact of dysregulated splicing in hematopoiesis remains unclear. To overcome technical limitations, we integrated genotyping of transcriptomes (GoT) with long-read single-cell transcriptomics and proteogenomics 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. SF3B1 cells were enriched in the megakaryocytic-erythroid lineage, with expansion of SF3B1 erythroid progenitor cells. We uncovered distinct cryptic 3' splice site usage in different progenitor populations and stage-specific aberrant splicing during erythroid differentiation. Profiling SF3B1-mutated clonal hematopoiesis samples revealed that erythroid bias and cell-type-specific cryptic 3' splice site usage in SF3B1 cells precede overt MDS. Collectively, GoT-Splice defines the cell-type-specific impact of somatic mutations on RNA splicing, from early clonal outgrowths to overt neoplasia, directly in human samples.
RNA 剪接因子在克隆性血液疾病中经常发生突变，但剪接失调对造血的影响尚不清楚。为了克服技术限制，我们将转录组基因分型（GoT）与长读长单细胞转录组学和蛋白质基因组学相结合，用于单细胞转录组、表面蛋白、体细胞突变和 RNA 剪接（GoT-Splice）的分析。我们将 GoT-Splice 应用于骨髓增生异常综合征（MDS）患者的造血祖细胞，这些患者的核心剪接因子 SF3B1 存在突变。SF3B1 细胞在巨核细胞-红细胞谱系中富集，SF3B1 红细胞祖细胞扩增。我们在不同祖细胞群体中发现了不同的隐蔽 3' 剪接位点的使用，以及红细胞分化过程中特定阶段的异常剪接。对 SF3B1 突变的克隆性造血样本进行分析表明，红细胞偏向性和 SF3B1 细胞中特定细胞类型的隐蔽 3' 剪接位点的使用先于明显的 MDS。总的来说，GoT-Splice 直接在人类样本中定义了体细胞突变对 RNA 剪接的特定细胞类型的影响，从早期的克隆生长到明显的肿瘤。
