Methylation Profile of CD4+ T Cells in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis

Abstract

Objective: Methylation is known to regulate biological processes and alterations in methylation patterns have been associated with a variety of diseases. Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) is an unexplained disorder associated with immunological and molecular changes. CD4 + T cells specifically, regulatory T cells (Tregs) have been implicated in CFS/ME patients where significant increases in Tregs have been observed in these patients. Therefore the objective of this study was to examine methylation in CD4 + T cells from CFS/ME patients. Methods: The study comprised twenty-five CFS/ME participants and eighteen controls aged between 25-60 years. A volume of 20 ml whole blood was collected from each participant and peripheral blood mononuclear cells were isolated via density gradient centrifugation. A negative isolation kit was used to isolate the CD4 + T cells from the peripheral blood samples. Genome wide methylation studies were performed on isolated CD4 + T cells using the Illumina Infinium 450 K Human methylation array system. Data analysis was performed using Genome studio and Partek Enrichment software. Results: 120 CpGs were observed to be differentially methylated in the CFS/ME patients in comparison to the controls. Of these 70 were associated with known genes. The majority of the differential methylated regions in the CFS/ME patients were hypomethylated. Additionally, most of the genes with differentially methylated regions in the CFS/ME patients were responsible for apoptosis, cell development, cell function and metabolic activity. Conclusion: The present study demonstrates that epigenetic changes in CD4 + T cells may have a potential role in the immunological changes observed in CFS/ME patients.

Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts

“…This could be important given the large number of upregulated and even larger number of downregulated transcripts in the ME/CFS lymphoblast transcriptomes. Multiple studies examining DNA methylation in ME/CFS patients have taken place in recent years [78][79][80][81][82]. These studies examining differential methylation status have been recently reviewed, with the proportions of differentially hypoor hypermethylated sites in ME/CFS being inconsistent across studies [83].…”

Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

“…While previous epigenetic studies have utilised primarily array based methods, prior studies involving the same method of RRBS and analysis platforms described here have been performed successfully previously (21,22). Indeed, our recent study (16) with this method with ME/CFS patients gave methylation changes that significantly overlapped with the other similar studies of this disease that used the array technology (11)(12)(13)(14)(15) Utilising RRBS technology a large number of changes were identified that differentiated ME/CFS patients from controls. The use of RRBS here has followed extensive in house development and experience with the platform used (21)(22)(23).…”

“…Previous studies (11)(12)(13)(14)(15), including our own study that described the first RRBS methylome of ME patients (16) have established ME/CFS patients display an altered DNA methylome in comparison to matched controls. This current study is the first of its kind to analyse the DNA methylome of ME/CFS in individual patients across a longitudinal timeline to investigate a change in health status.…”

“…Table 1 Fragments associated with the relapse condition for P1. Fragments with a Pearson's correlation coefficient of at least 0.9 and a mean methylation difference between the "relapse" and "recovery" time points Whereas the ME-iVMFs that associated with the relapse condition of P1 were all hypomethylated (see Table 1), for P2, while the majority of the fragments 1-11 were also hypomethylated, three (12)(13)(14) by contrast were hypermethylated (shown in italics in Table 2) in the relapse condition (P2-C) compared to the recovery conditions.…”

“…A study in 2008 examining expression levels of transcripts classified 7 subtypes, through mean relative transcript quantities 88 transcripts that corresponded with clinical severity (10). In recent years DNA methylation has been applied to investigate the disease status of ME/CFS patients, and a number of studies have found important differences separating the patients from controls (11)(12)(13)(14)(15)(16). A recent publication with this technology has identified four subtypes utilising DNA methylation and symptom severity (17), with key differentially methylated genes between subtypes having primarily immune and metabolic functions.…”