HTR2A Gene Changes Found Only in Progressive MS May Be New Biomarker

Scientists have discovered epigenetic changes in a gene called HTR2A, found only in immune cells isolated from people with secondary progressive multiple sclerosis (SPMS), a study reported. 

These findings suggest that such changes — external modifications to DNA that turn genes “on” or “off” — may be a potential biomarker for progressive MS, the researchers said.

The details were published in the journal Nature Scientific Reports, in the study “Epigenetic differences at the HTR2A locus in progressive multiple sclerosis patients.” 

A combination of genetic predisposition and environmental factors is thought to trigger the immune system attack on the brain and spinal cord in people with MS, causing their symptoms.

Environmental factors can influence genetics via epigenetic mechanisms that control gene activity. In one such mechanism, enzymes add so-called methyl groups to DNA, without changing its sequence, to suppress gene activity. This process is known as DNA methylation.

Studies investigating DNA methylation in immune cells isolated from people with relapsing-remitting MS (RRMS) found significant changes in methylation patterns in genes that play a critical role in immune responses. In particular, the gene variant HLA-DRB1 15*01, associated with an increased risk of developing MS, had significantly lower DNA methylation, thus increasing gene activity.

However, understanding which factors drive MS progression, leading to further disability, is limited. Thus, an epigenetic analysis of cells from people with progressive MS may help find important biomarkers to measure the course of the disease as well as to identify potential therapeutic targets.

To this end, researchers based at the University of Newcastle, in Australia, collected blood samples from 23 female SPMS patients and 16 age-and gender-matched healthy people (controls) to analyze DNA methylation patterns in their immune CD4-positive T-cells, which are central to immune responses.

To validate the results, an independent group of 11 female SPMS participants, along with 12 matched healthy controls, also were included.

The team extracted DNA from the participants’ T-cells and identified 72 positions with methylation patterns that were different in patients compared with controls. These were called differentially methylated positions (DMPs). 

These DMPs were located in 34 genes and 23 non-coding regions along the DNA strand. A majority of these DMPs (74%) had more methylation (hypermethylated) in patients than in controls, whereas 26% showed less methylation (hypomethylated).

An analysis of the validation group found 65 DMPs, which mapped to 32 genes and 22 non-coding positions. Similarly, there were higher levels of hypermethylation (68%) in this group.

When the two lists of DMPs from each group were compared, the analysis revealed 12 common DMPs occurring in three genes — specifically, HTR2A, SLC17A9, and HDAC4 — as well as four non-coding positions. All common DMPs identified were consistently methylated between the two groups. 

Of note, HTR2A carries instructions for a serotonin (signaling hormone) receptor protein in the nervous system and is associated with the psychiatric disorder schizophrenia. SLC17A9 encodes a protein involved in transporting molecules across cell membranes, while HDAC4 carries the code for a protein critical to other epigenetic (externally modifying) mechanisms.

To identify differentially methylated regions (DMRs), the team focused on regions with two or more DMPs within 1,500 nucleotides — the building blocks of the DNA — in both the testing and validation groups.

Common DMRs were found in the same three genes (HTR2A, SLC17A9, and HDAC4), with hypermethylated and hypomethylated patterns being consistent across the two groups.

DNA methylation normally exerts an effect when present in regions that control gene activity, called the transcriptional start site. Looking at those regions in all three genes, the team found that the only DMR common in both groups was in the HTR2A control region, which contained eight positions with 5% or less methylation compared with controls.

This region also contained a point mutation, or a single nucleotide change, known as rs6313. This point mutation has been linked to other inflammatory and neurological disorders.

Notably, SPMS patients in this study were 5.3 times more likely to carry rs6313 than were healthy controls.

However, an examination of whether this DMR led to more gene activity found no differences between SPMS patients and control samples. Additionally, the differences in DNA methylation in progressive MS were found to be independent of the gene mutations.  

A final comparison of previous data collected from RRMS patients did not find these same methylation changes, suggesting they are specific to progressive MS, “making it a potential biomarker of progressive disease,” the researchers wrote. 

The team noted that there “are currently no biomarkers of progression, and progressive MS is diagnosed retrospectively.”

Although the connection between MS and HTR2A is unclear, the investigators point to evidence suggesting that platelets from MS patients fail to secrete serotonin, which is normally taken up in the gut and transported to the blood to help activate CD4-positive T-cells.