Myelodysplastic Neoplasm (MDS) is an age-associated neoplasia characterized by frequent epigenetic abnormalities. Hypermethylation of gene promoter sites is common in MDS and increases in advanced stages of the disease, which may be related to a more rapid progression to Acute Myeloid Leukemia (AML).

We aimed to evaluate the methylation profile of XPA, XPC, XPG, CSA, CSB, ATM, BRCA1, BRCA2, LIG4, and RAD51 genes in MDS bone marrow cells among different stages of the disease (early and advanced stages) and during the progression to AML.

We used pyrosequencing, a sequencing-by-synthesis that can quantitatively measure DNA methylation levels at single CpG sites, to evaluate the methylation status of promoter sites of single and double-strand breaks DNA repair genes in 56 patients diagnosed with MDS.

Regarding the MDS subtypes, early MDS subtypes presented increased methylation of XPA (median 9.25 versus median 7.25; p < 0.0001) compared to advanced MDS. We observed increased methylation of ATM in patients who progressed to AML (median 4.97 versus median 2.45; p = 0.016). Regarding the other single and double-strand breaks DNA repair genes (XPC, XPG, CSA, CSB, BRCA1, BRCA2, LIG4, and RAD51), we found no significant difference in DNA methylation status.

MDS is a disorder commonly characterized by genomic instability with mutations in up to 94% of patients and chromosomal abnormalities in up to 50%. The DNA repair system is fundamental to protect against genomic instability which may lead to translocations, deletions, and monosomies. As hypermethylation of CPG islands has been associated with gene silencing, the higher methylation of XPA in early MDS patients may suggest an increase in genomic instability for these patients. XPA misfunction leads to the lack of single lesion repair, predisposing to double-strand breaks and possibly to chromosomal abnormalities. We intend to evaluate the methylation status of XPA for the same patients prospectively, trying to define its actual relation to MDS prognosis. The ATM is one of the DNA repair genes frequently hypermethylated in its promoter region in various cancers, and has a central role signalizing and recruiting BRCA1, BRCA2, and RAD51. ATM encodes a protein kinase mainly distributed in the nucleus of proliferating cells, regulating multiple cell cycle checkpoints by phosphorylating different targets at different cell cycle phases and also regulating apoptosis and oxidative stress besides DNA double-strand breaks. Patients with MDS who evolved into AML showed higher methylation of ATM than patients who did not progress to AML. Of utmost importance, three cases (3/5) were predominantly low-risk patients, and AML transformation was not expected.

Our study is the first to demonstrate the site promoter hypermethylation of XPA and ATM genes in Myelodysplastic Neoplasm, linking both genes to the pathogenesis and prognosis of MDS.