Somatic mutations of activating signalling, transcription factor, and tumour suppressor are a precondition for leukaemia transformation in myelodysplastic syndromes.

The transformation biology of secondary acute myeloid leukaemia (AML) from myelodysplastic syndromes (MDSs) is still not fully understood. We performed paired self-controlled sequencing, including targeted, whole exome, and single-cell RNA sequencing, in a cohort of MDS patients to search for AML transformation-related mutations (TRMs). Thirty-nine target genes from paired samples from 72 patients with MDS who had undergone AML transformation were analysed. The targeted sequencing results showed that 64 of 72 (88.9%) patients presented TRMs involving signalling pathway activation, transcription factors, or tumour suppressors. Of the 64 patients, most of the TRMs (62.5%, 40 cases) emerged at the leukaemia transformation point. Paired whole exome sequencing showed some presumptive TRMs, which were not included in the reference targets in three patients. No patient developed AML only by acquiring mutations involved in epigenetic modulation or ribonucleic acid splicing. Single-cell sequencing indicated that the activating cell signalling route was related to TRMs in one paired sample. Targeted sequencing defined TRMs were limited to a small set of seven genes (in the order: NRAS/KRAS, CEBPA, TP53, FLT3, CBL, PTPN11, and RUNX1, accounting for nearly 90.0% of the TRMs). In conclusion, somatic mutations involved in signalling, transcription factors, or tumour suppressors appeared to be a precondition for AML transformation from MDS.