Perturbation of interactome through micro-RNA and methylome analysis in diabetes endophenotypes: the PIRAMIDE pathogenic clinical study design

Abstract

<p class="abstract"><strong>Background:</strong> The main challenge in type 2 diabetes (T2D) is to detect the regulators of pathogenic events during early stages of disease, as well as prevention and progression follow-up of cardiovascular (CV) complications. DNA methylation and micro-RNAs (miRNAs) are major components of the epigenome, which are involved in the diabetic interactome. This study protocol may contribute to advance our knowledge on molecular basis underlying T2D and its CV complications, as well as provide putative useful prognostic biomarkers.</p><p class="abstract"><strong>Methods:</strong> The perturbation of interactome through micro-RNA and methylome analysis in diabetes endophenotypes: the PIRAMIDE pathogenic clinical study protocol is a cross-sectional research program planned to combine big data and network-based analysis aimed to investigate whether DNA methylation and miRNAs may act as simultaneous regulators of the interactome in T2D patients. Clinical datasets will be aggregate to large-scale DNA methylation, mRNA-Seq, and miRNA-Seq analysis performed both on purified CD4<sup>+</sup> and CD8<sup>+ </sup>T cells isolated from 35 T2D patients and 35 sex and age-matched controls. DNA methylome data will be used as input for the weighted human DNA methylation PPI network (WMPN) algorithm. RNA sequencing data will be used as input data for the TargetScan algorithm. The primary endpoint will be to integrate both DNA methylation and miRNA networks to potentially capture which genes are simultaneously modulate by interactions between epigenetic changes. Then, statistical analysis will be performed to correlate these molecular modifications with development of T2D-related CV complications.</p><p class="abstract"><strong>Conclusions: </strong>PIRAMIDE pathogenic clinical study protocol will test the hypothesis that simultaneous interactions between DNA methylation and miRNAs may hit T2D-associated candidate genes and predict the development of T2D-related CV complications.</p><p class="abstract"><strong>Trial Registration:</strong> The ongoing PIRAMIDE pathogenic clinical study protocol has been registered on NIH website (NCT03792607).</p>

Early targeted DNA methylation profiling of CD04+/CD08+ T cells reveals pathogenic mechanisms in different stages of impaired glucose homeostasis Cardiovascular Diabetology

“…The strengths of our study are that we evaluated and compared the differential DNA methylation profiles of two T lymphocyte subpopulations, CD04 + and CD08 + T, which may contribute to early vascular damage in different stages of impaired glucose homeostasis. Recently, a DNA methylome analysis reported a predominant contribution from CD04+ and CD08+ T cells in regulating expression levels of IL6R, FASLG, and CCL18 genes in ACS patients vs HS suggesting a significant role in disease pathogenesis [26]. Since pathogenesis of ACS is related to vasculature damage and diabetes onset [27], we hypothesized that DNA methylation changes in both CD04 + and CD08 + T cells may reveal early molecular signals of CV dysfunction in Pre-Diab to T2D.…”

“…Our group has a longstanding experience in epigenetics and CV diseases [18][19][20][21][22][23][24][25]. This pilot study is part of the clinical trial (NCT03792607) aimed at investigating early epigenetic changes in different stages of impaired glucose [26]. We performed a very complex DNA methylome analysis on both CD04 + and CD08 + T cells isolated from healthy subjects (HS), Pre-Diab and T2D patients (Figure 1).…”

Differential epigenetic factors in the prediction of cardiovascular risk in diabetic patients

“…Recently, we have designed the ‘Perturbation of Interactome through micro-RNA and Methylome analysis In Diabetes Endophenotypes: the PIRAMIDE pathogenic clinical study design’ (NCT03792607). 60 This ongoing pilot study combines epigenetic interactions and network-based algorithms in order to provide useful biomarkers predicting the onset of macrovascular complications in T2D patients. 60 The similarity of our approach was present in two studies analysing the interaction of epigenetic mechanisms in diabetic patients complicated with CHD and their putative clinical role as biomarkers or drug targets.…”

“… 60 This ongoing pilot study combines epigenetic interactions and network-based algorithms in order to provide useful biomarkers predicting the onset of macrovascular complications in T2D patients. 60 The similarity of our approach was present in two studies analysing the interaction of epigenetic mechanisms in diabetic patients complicated with CHD and their putative clinical role as biomarkers or drug targets. 48 , 49 Moreover, it is crucial to investigate how epigenetic modifications may affect the individual response to pharmacological and non-pharmacological treatments, including lifestyle changes such as dietary modifications, exercise, avoiding stress, and minimizing alcohol consumption.…”