Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation (Almenar-Pérez 2019)

Pechius

Senior Member (Voting Rights)
EloyAlmenar-PérezMSc TamaraOvejeroPhD TeresaSánchez-FitoMSc José A.EspejoBSc LubovNathansonPhD ElisaOltraPhD

Abstract:
Purpose

Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease.

Methods

A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool.

Findings

Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection.

Implications

Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences (“junk repetitive DNA”), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.

FULL: https://sci-hub.tw/10.1016/j.clinthera.2019.02.012
https://www.sciencedirect.com/science/article/abs/pii/S0149291819300724
 
I am very grateful to Elisa Oltra :heart: for her commitment with ME patients and also to “Universidad Católica de Valencia” for the research grant.

Unfortunately this paper is too technical for me. I would love if anyone could summarize for us the conclusions in plain words if posible.
 
Transposons are bits of DNA that contain coding sequences that allow themselves to be cut out and then inserted into the genome at a different spot.

Transposons can be a source of genetic diversity, and it can also cause disease or other problems. It seems like they can also have a positive effect. They're found in all organisms.

Because a lot of lengths of DNA are used not to code protein by themselves, but to regulate how and when other sequences will be used, snipping bits of DNA out and putting them somewhere else can change DNA expression (what things get made in the cell and when). Also some of the transposons are complete regulatory sequences.

Methylation is a system of packing and tagging genetic information to regulate how and when it will be used. There's evidently methylation systems that affect transposons, too.

I am not clear on how they found transposon information from a literature review, but I didn't read the full paper.

Epigenetics is stuff that is not DNA itself but associated to DNA ("upon" is the literal meaning of the prefix epi-), and regulates how and when the DNA is used (including by how it's packed--DNA in a long strand would reach from here to the moon and back, many times over, and it has to be packed and organized in order to fit into and be used by the cell, but it can be more or less tightly packed in order to be more or less available). So methylation and I forgot what else.

A model for the disease emerged involving transcriptional induction of endogenous dormant transposons

They're saying maybe something turns on a transposon that had previously been inactive (something that's known to occur in some well-studied transposons).

and structured cellular RNA interactions

Sounds like they could be saying RNA (maybe miRNA?) could be involved in the epigenetics of this.

triggering the activation of the innate immune system without a concomitant active infection.

So without there being an infection, they figure the innate immune system is activated.

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I am not sure how much evidence there is for innate immune activity in ME.

The transposon stuff is super interesting but as they said in the abstract, one would need a very large genetic study to have any good evidence for or against something like this.
 
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I think @WillowJ has done a very good lay persons summary. My summary of the summary would be that

- the authors did a systematic literature review of genetic / epigenetic ME related findings in other published papers

- they came up with a hypothesis that some of the changes to genes and gene expression could activate the innate immune system without needing an infection to activate it.

- lots more research would be needed to test this hypothesis.
 
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