Characterization of Serous Cell-Free DNA in Myelodysplastic Syndromes

Myelodysplastic syndromes (MDS) are a group of malignant clonal diseases presenting abnormal development of acquired hematopoietic progenitor/stem cell myeloid differentiation. MDS have been clinically divided into different types. There is a lack of clear gold standard, which makes the diagnosis of MDS with clinical signs and laboratory examination difficult. Cell-free DNA (cfDNA) is a resource of DNA fragments from apoptotic or necrotic cells, and has been considered as a measurement with ample sensitive, specific, and effective traits for auxiliary diagnosis. In this study, we collected 25 cases of relatively high-risk MDS (HRM), 22 cases of low-risk MDS (LRM), and 15 cases of benign blood diseases (control) and conducted reduced representation bisulfite sequencing (RRBS) to investigate the variants and DNA methylation of cfDNA in serum of three cases of each group. We observed increased single-nucleotide polymorphisms (SNPs) particularly distributed in intergenic and intronic regions in HRM compared with LRM and control. Moreover, HRM presented more nonsynonymous and harmful variants that would affect amino acid sequence. Meanwhile, we also observed that global DNA methylation on non-CpG sites (CHG and CHH) in HRM was obviously higher than that in LRM and control. Finally, we picked up the candidate genes with specific variants and abnormal methylation at the promoter in HRM and LRM, and combined to examine the specificity and sensitivity of HRM and LRM diagnosis in our collection. We found that FANCM with T49G mutation at first exon and promoter hypermethylation (-835 to transcription start site [TSS]) was indicated as the most confident factor with the highest area under curve (AUC) value (0.9271) for HRM. Similarly, ICAM1 with C1211T mutation at sixth exon and promoter hypermethylation (-282 to TSS) was suggested to identify LRM (AUC = 0.9338). Taken together, our study characterized the variants and methylation pattern of cfDNA in MDS, and provided the potential biomarkers for HRM and LRM identification.