Identifying clones in myelodysplastic syndromes by using single-cell RNA sequencing

We employed single-cell RNA sequencing to sequence hematopoietic stem cells (HSC) derived from bone marrow aspirations of seven patients with myelodysplastic syndrome (MDS) and four control subjects. Based on gene expression and pathway-enrichment analyses, we inferred chromosomal Y deletion and characterized the transcriptome of chromosome Y-deleted HSC in comparison to chromosomally intact HSC. Our results support the premise that chromosome Y deletion is not a benign aging phenomenon and highlight the importance of upregulation of the anti-apoptotic pathway in the pathogenesis of MDS. Overall design: Eleven subjects who were evaluated for MDS were recruited to the study. Fresh bone marrow aspirations were collected and sorted for HSC by using fluorescence-activated cell sorting (FACS). The Smart-Seq2 protocol was applied to sequence 1,150 HSC. Reads were mapped to the human genome, and gene expression levels were calculated. After application of quality control measures, the expression matrix included 1,101 cells and 26,199 genes.