DNA Methylation Dynamics in Blood after Hematopoietic Cell Transplant

Classically, epigenetic deregulation is considered a common hallmark of cancer. Nevertheless, recent publications have demonstrated its association with a large array of human diseases such as autoimmune disorders and environmental factors such as diet. Despite the increasing relevance of DNA methylation for the study of critical biological processes and for the development of novel biomarkers, DNA methylation analysis applied to the study of hematopoietic cell transplantation (HCT) has not yet been explored. Here, we analyzed global DNA methylation in blood samples by using a pyrosequencing based methylation assay of repetitive DNA elements (LINE1 and NBL2) in a cohort of 47 patients with allogenic HCT up to 12 months post-HCT. We observed that the recipients stably maintained the donor’s global methylation levels after transplant. Nonetheless, NBL2 methylation is affected by physiopathological events such as development of mixed chimerism. Microarray-based DNA methylation analysis of promoters revealed that methylation in more than 200 genes is altered 1 month post-HCT when compared with non-pathological methylation levels in the donor’s blood. Interestingly, this number dramatically decreased by 6 months post-HCT. Finally, based in the microarray data, we analyzed by pyrosequencing DNA methylation in IFN-γ, FASL, and IL-10 and found a statistically significant association between methylation in these immune genes and the severity of the acute graft-versus-host disease. In conclusion, our results provide strong evidence that DNA methylation changes in blood are linked to underlying physiological events and demonstrate that DNA methylation analysis is a viable strategy for the study of hematopoietic cell transplantation and for development of biomarkers. Bisulphite converted DNA from 6 blood samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2