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

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. Overall design: Heart tissue samples (20–30 mg) were cleared from pericardial fat, crushed with ceramic beads (CK14, diameter 1.4 mm, Bertin) in 350 µL of RLT lysis buffer supplemented with 3.5 µL of ß-mercapto-ethanol. Total RNA was extracted from biopsies using the RNeasy Mini Kit adapted with Trizol. RNA quantity and quality were measured with a 2100 BioAnalyzer (Agilent). Ribosomal RNAs were depleted and samples were prepared for sequencing according to the Illumina TruSeq RNA Preparation Kit and subjected to pairwise sequencing (2x150bp) with an Illumina HiSeq sequencer. Sequencer results were obtained as raw fastq file format.