Specific methylation marks in promoter regions are associated to the pathogenic process of Chronic Chagas disease Cardiomyopathy by modifying transcription factor binding patterns [methylation]

Chagas disease, caused by Trypanosoma cruzi, is an endemic parasitical disease of Latin America, affecting 7 million people. Although most patients are asymptomatic, 30% develop complications, including Chronic Chagasic Cardiomyopathy (CCC), which ranges from moderate to severe stages depending on the cardiac ejection fraction. The pathogenic process remains poorly understood, although genetic and epigenetic factors have already been proposed. Based on bulk RNA-seq and EPIC methylation data, we investigated the genetic and epigenetic deregulations present in the moderate and severe stages of CCC. We identified 4 main biological processes associated with the pathology development, including immune response, ion transport, cardiac muscle processes and nervous system. An in-depth study of the transcription factors binding sites in the differentially methylated regions corroborated the importance of these processes. We also conducted a methylation study on blood to identify potential biomarkers for CCC. Our data revealed 198 differentially methylated positions (DMPs) that could serve as biomarkers of the disease, of which 61 are associated with disease severity. DNAs, extracted from whole tissue of 14 samples, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California). Blood (5 to 15 ml of blood) from 144 samples was collected in EDTA tubes. Genomic DNA was isolated on a silica-membrane according to the manufacturer’s protocol (QIAamp DNA Blood Max Kit, Qiagen, Hilden, Germany). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).