Changes in DNA methylation profiles of [ME/CFS] patients reflect systemic dysfunctions (Helliwell et al. 2020)

Pyrrhus

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A new scientific publication on epigenetics from Warren Tate's group:
https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-020-00960-z

Epigenetics:
The field of epigenetics looks at types of modifications that a cell makes to its DNA, without changing the coding for genes. Such modifications may increase the translation of certain genes or may inhibit the translations of certain genes, changing the programming of a cell. One of these types of modifications is called DNA methylation.

DNA Methylation:
The chemical process of methylation simply refers to the addition of a "methyl group" to a given molecule, such as DNA. A "methyl group" contains one carbon atom and three hydrogen atoms. In the methylation of DNA, a methyl group is added to a specific location on the DNA, which generally inhibits the translation of that section of DNA into RNA. When a gene's translation is inhibited, there will be fewer copies of that gene's RNA found in the cell.

Excerpt:
Helliwell et al 2020 said:
Background
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a lifelong debilitating disease with a complex pathology not yet clearly defined. Susceptibility to ME/CFS involves genetic predisposition and exposure to environmental factors, suggesting an epigenetic association. Epigenetic studies with other ME/CFS cohorts have used array-based technology to identify differentially methylated individual sites. Changes in RNA quantities and protein abundance have been documented in our previous investigations with the same ME/CFS cohort used for this study.

Results
DNA from a well-characterised New Zealand cohort of 10 ME/CFS patients and 10 age-/sex-matched healthy controls was isolated from peripheral blood mononuclear (PBMC) cells
, and used to generate reduced genome-scale DNA methylation maps using reduced representation bisulphite sequencing (RRBS). The sequencing data were analysed utilising the DMAP analysis pipeline to identify differentially methylated fragments, and the MethylKit pipeline was used to quantify methylation differences at individual CpG sites. DMAP identified 76 differentially methylated fragments and Methylkit identified 394 differentially methylated cytosines that included both hyper- and hypo-methylation. Four clusters were identified where differentially methylated DNA fragments overlapped with or were within close proximity to multiple differentially methylated individual cytosines. These clusters identified regulatory regions for 17 protein encoding genes related to metabolic and immune activity. Analysis of differentially methylated gene bodies (exons/introns) identified 122 unique genes. Comparison with other studies on PBMCs from ME/CFS patients and controls with array technology showed 59% of the genes identified in this study were also found in one or more of these studies. Functional pathway enrichment analysis identified 30 associated pathways. These included immune, metabolic and neurological-related functions differentially regulated in ME/CFS patients compared to the matched healthy controls.

Conclusions
Major differences were identified in the DNA methylation patterns of ME/CFS patients that clearly distinguished them from the healthy controls.
Over half found in gene bodies with RRBS in this study had been identified in other ME/CFS studies using the same cells but with array technology. Within the enriched functional immune, metabolic and neurological pathways, a number of enriched neurotransmitter and neuropeptide reactome pathways highlighted a disturbed neurological pathophysiology within the patient group.
(emphasis added)
 
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sometexan84

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I have been leaning towards virus-induced epigenetic dysregulation via DNA methylation alterations for a little while now. And the deeper I dig, the more it all makes sense.

Virus(es) >>> DNA Methylation changes (and/or histone modifications) >>> Epigenetic changes >>> gene modifications that EFF US UP!!!

For added "Significance" - This is the first ME/CFS study regarding DNA methylation using this newer technology - "reduced representation bisulphite sequencing (RRBS)". Though, this study says there have only been 5 previous ME/CFS studies on their methylation states. All were using "lesser" technology.

Complex V

It's nice to see that this study corresponds with the Mitochondria dysfunction found via Complex V from earlier this year.

"The results from this study also support a model of deficient ATP production in ME/CFS, compensated for by upregulation of pathways immediately upstream of Complex V that would suggest an elevation of oxidative stress. Missailidis et al. [5] concluded the activity of mitochondrial complex V involved in the actual synthesis of ATP is impaired resulting in up-regulation of remaining complexes and in particular complex 1 resulting in an inability to compensate for energy need during activity and stress"
"...implicates an attempt to compensate for impaired energy production in these cohorts of ME/CFS patients"

Associations of Genes mentioned in study....

IRF4

They mention differential methylation found in the gene IRF4. IRF4 is associated with EBV re-activation, as well as some other stuff about EBV proteins regulating cell genes.

GNG7

Another mention in the study. This gene is actually targeted by EBV miRNA (in response to lactic acid), promoting EBV growth.

GABRB3

Association w/ Coxsackie virus

UCP2

Association w/ Coxsackie 3

NDUFA11

Association w/ HSV
 
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I am in the middle of a crash and do not currently have the mental stamina to read these studies in detail. Does anyone foresee something actionable from these findings?
In my personal case, I experienced abrupt onset in March 2007. EBV numbers were very high. Several times in '07, the CFS turned off just as suddenly and I was back to normal. However, an event such as dental work or stress at work brought the CFS back after a couple weeks. And it settled in for good. The only reason I mention that, is somewhere there is a way for the human body to correct to a balanced state. Unfortunately, I have no idea what that is.
 

sometexan84

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Does anyone foresee something actionable from these findings?
Short answer is yes. There are treatment options to address some of this. But it's complicated.

Long answer...
There are treatments that involve promoting and/or inhibiting genes, transcriptional factors, and DNA methylation.

Any major changes to your system by a virus needs to be addressed for symptom relief. For instance, a virus can cause changes that persist even after viral clearance. Maybe it modified genes that regulate interferon, or mitochondria function, or apoptosis. If that virus is gone, and the gene(s) is still hypo or hyper methylated or something, then that would need to be remedied as well.

The way I see it, we all need to treat ALL of the following....
  1. Infections
  2. Epigenetic alterations caused by infections
  3. Conditions caused by infections
  4. Symptoms and damage from infections
It's challenging to treat this though. There aren't enough studies. And you could get it wrong, and end up making things much worse. But I'm working on it.
 

Pyrrhus

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How they tried to assess significance, from the Discussion section of the paper:
Helliwell et al 2020 said:
Multiple statistical approaches were taken in order to detect as many meaningful changes as possible. In order to detect broad changes in DNA methylation likely linked to functional changes, the fragment-based DMAP analysis was utilised. To both support and build upon this initial approach, individual cytosine methylation was also interrogated utilising MethylKit. As would be expected both showed similar overall distributions of differential methylation (Fig. 2) in addition to a small number of shared features identified in the most differentially methylated DMFs and individual cytosines. However, there were also many differences in the outputs between the two analyses of the promoter region and of the gene bodies (exons/introns), and consequent enrichment analysis highlighting the divergence of results that can occur when utilising different statistical approaches.

This is especially relevant for making comparisons among the studies that have investigated DNA methylation changes in ME/CFS cohorts where varying results were obtained [6,7,8,9,10]. Among them there are differences in study design with consideration of (1) clinical case definition used for diagnosis, (2) methodology, (3) study population and (4) statistical analysis.

[...]

Our study demonstrates how DNA methylation has provided an imprint of multiple systemic changes in ME/CFS with links to disease pathophysiology. Comparisons with previous relevant publications have provided compelling support that the genes identified in this work are reflecting changes specific to an ME/CFS state. Many of the specific targets highlighted can now become the focus of validation and stimulation of further work to ameliorate the devastating effects of ME/CFS on those affected by the disease.
 

Marylib

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Inara

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Again, @pattismith, thanks for tagging. It led me into the DNA methylation, DNA silencing and epigenetics field, which opened a new door of understanding. Quite interesting! It may be trivial to some, but I never took a closer look.