Issues with X chromosome inactivation as a reason for female predominance in ME/CFS

[Utsikt]

Split from United Kingdom: ME Research UK (MERUK) News

From MERUK at the link above:

A closer look at the X chromosome​

Chromosomes carry our genetic information and, typically, females have two X chromosomes while males have one X and one Y chromosome. In females, one of the X chromosomes is inactivated in each cell in order to avoid a double-dose of X-linked genes.

X chromosome inactivation (XCI) therefore needs to be maintained throughout life, and disruption of this can lead to developmental problems and diseases, including those affecting the immune system, such as systemic lupus erythematosus. There is also reason to suspect that dysregulation of XCI could affect the function of the mitochondria, the powerhouses of the cell.

Objectives​

Dr Manousaki’s research will test the idea that, in ME/CFS, XCI is not being maintained correctly. This could lead to abnormal levels of certain X-linked genes, disrupting immune balance and energy production in cells.

This mechanism could therefore explain the higher prevalence of ME/CFS in females than in males. Dr Manousaki plans to investigate this using super-resolution microscopy and gene expression analysis.

She will first assess whether XCI is dysregulated in women with ME/CFS, specifically looking at genetic factors which regulate XCI and may therefore have value as a diagnostic biomarker.

She will also investigate whether cells from men and women with ME/CFS struggle to generate and use energy efficiently, analysing mitochondrial structure and its interactions with associated endoplasmic reticulum contact sites which have been implicated in other diseases such as Alzheimer’s and Parkinson’s diseases.

Finally, linking these two areas, Dr Manousaki will test whether XCI disruption can directly cause mitochondrial dysfunction, linking the genetic findings with cellular energy problems and exploring whether these effects differ between men and women.

 

[Hutan]

Background reading

The Role of Genetic Sex and Mitochondria in Response to COVID-19 Infection, 2020
Looks like the sex chromosomes are very important for immunity. (I'm looking forward to the DecodeME results for these chromosomes.) I guess there might be something protective on the Y chromosome.

the human chromosome X consists of over 150 million DNA base pairs and contains more than 800 protein-coding genes, which include the highest number of the innate and adaptive immunity-related genes of the whole human genome, and several hundred non-coding genes.

The Y chromosome regulates many different immune-response functions, immune cell numbers, and immune cell phenotypes through the regulation of transcriptionally inert (heterochromatin) and active (euchromatin) status of X chromosome and autosomes.

Studies showed that Y chromosome can regulate the heterochromatin/euchromatin status of the autosomes and X chromosomes and, thus, affects silencing/expression of various genes, including the immune response genes, and regulate the tissue-/cell-specific alternative gene splicing

Although the mechanism by which the Y chromosome influences heterochromatin/euchromatin content and thus the transcription of the other genes is largely unknown, one of the hypotheses postulates that the Y chromosome sequesters heterochromatinization factors and another that it affects the architecture of cell nucleus, which makes specific genes inaccessible to the transcription factors

Mosaicism in females - some cells express one X chromosome, other cells can express the other X chromosome

Because in the female cells, the inactivation of one of the X chromosomes is random, the female body may contain different alleles of the same gene.

 

[Jonathan Edwards]

I don't understand the motive for this study. MECFS is almost certainly more common in women because they are women and have no Y chromosome. Not because they are rare cases where the normal female state has gone wrong. No man has MECFS because of X chromosomes going wrong, so it seems unlikely to be why women do.

 

[SNT Gatchaman]

No man has MECFS because of X chromosomes going wrong, so it seems unlikely to be why women do.

My experience is that the key to these diseases is finding the way in which the normal rules are broken, not in finding what is following the normal rules. We have done those diseases.

The normal rule here is that the "spare" X chromosome in females is silenced by XIST to compensate for dosage. In males, apart from normal spermatogenesis, this can occur in cancer cells Somatic XIST activation and features of X chromosome inactivation in male human cancers (2022, Cell Systems)

So could the rule be broken? Males and females both have X chromosomes and XIST is derived from the XIC (X-chromosome inactivation centre). What if XIST is inappropriately affecting the "good" X chromosome in females or the solitary X chromosome in males and reducing some gene product that's needed — rather than the normal rule of not over-producing some gene product that isn't wanted?

And then the rules might be further bent if there is any possibility it's able to adversely affect an autosome (with more chance in females because XIST is always active). This paper looks to suggest that possibility (in mice).

XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells (2024, Cell, PMC)

We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. […] Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

 

[ME/CFS Science Blog]

I noticed that SMCHD1 was one of the genes below the significance threshold that was associated with ME/CFS in DecodeME.

it seems to play a role in X-chromosome inactivation
SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation - PubMed

 

[Jonathan Edwards]

I noticed that SMCHD1 was one of the genes below the significance threshold that was associated with ME/CFS in DecodeME.

it seems to play a role in X-chromosome inactivation

That might be in line with a role for incomplete X inactivation being relevant to the sex ratio.

Maybe worth mentioning that the posts on this thread are out of date in the sense that we have had much more discussion of this topic since and I have completely changed my view on studying X inactivation. My initial concerns are still to some extent a worry but not knowing the detail of the research project I may have misunderstood its aims.

 

[forestglip]

This post is about X-chromosome dosage in general, not necessarily dysregulated X-inactivation in females. Not sure if it should be on a separate thread.

Quoting my post about this from the DecodeME thread:

Previous work has shown that men with Klinefleter’s syndrome (47,XXY) as well as women with 47,XXX are found in excess among SLE patients well as among Sjogren’s disease, systemic sclerosis and idiopathic inflammatory myositis.

This is really interesting. Looking at the number of patients that have an extra X chromosome helped nail down that the X chromosome was a risk factor for SLE. Here are the two papers it cites for the above:

Klinefelter's syndrome (47,XXY) in male systemic lupus erythematosus patients: Support for the notion of a gene-dose effect from the X chromosome (2008)

Spoiler: Abstract

Objective
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that predominantly affects women. Despite isolated reports of patients with coexisting Klinefelter's syndrome (47,XXY) and SLE, no association of Klinefelter's syndrome with SLE or any other autoimmune disease has been established. The present study was undertaken to investigate the prevalence of Klinefelter's syndrome in a large population of patients with SLE.

Methods
Sex chromosome genotyping was performed in 981 SLE patients, of whom 213 were men. A first group of 844 SLE patients from 378 multiplex families and a second group of 137 men with nonfamilial SLE were evaluated. In selected cases, chromosomes were enumerated by fluorescence in situ hybridization (FISH) and karyotyping in transformed B cell lines.

Results
Of 213 men with SLE, 5 had Klinefelter's syndrome (1 in 43). Four of them were heterozygous at X markers, and Klinefelter's syndrome was confirmed by FISH and karyotyping in the fifth. An overall rate of 47,XXY of 235 per 10,000 male SLE patients was found (95% confidence interval 77–539), a dramatic increase over the known prevalence of Klinefelter's syndrome in an unselected population (17 per 10,000 live male births). Asking men with SLE about fertility was highly sensitive (100%) for Klinefelter's syndrome. All 768 women with SLE were heterozygous at X.

Conclusion
The frequency of Klinefelter's syndrome (47,XXY), often subclinical, is increased in men with SLE by ∼14-fold compared with its prevalence in men without SLE. Diagnostic vigilance for 47,XXY in male patients with SLE is warranted. These data are the first to show an association of Klinefelter's syndrome with an autoimmune disease found predominantly in women. The risk of SLE in men with Klinefelter's syndrome is predicted to be similar to the risk in normal women with 46,XX and ∼14-fold higher than in men with 46,XY, consistent with the notion that SLE susceptibility is partly explained by an X chromosome gene-dose effect.

Web | Arthritis and Rheumatology | Paywall

X Chromosome Dose and Sex Bias in Autoimmune Diseases: Increased Prevalence of 47,XXX in Systemic Lupus Erythematosus and Sjögren's Syndrome (2015)

Spoiler: Abstract

Objective
More than 80% of autoimmune disease predominantly affects females, but the mechanism for this female bias is poorly understood. We suspected that an X chromosome dose effect accounts for this, and we undertook this study to test our hypothesis that trisomy X (47,XXX; occurring in ∼1 in 1,000 live female births) would be increased in patients with female-predominant diseases (systemic lupus erythematosus [SLE], primary Sjögren's syndrome [SS], primary biliary cirrhosis, and rheumatoid arthritis [RA]) compared to patients with diseases without female predominance (sarcoidosis) and compared to controls.

Methods
All subjects in this study were female. We identified subjects with 47,XXX using aggregate data from single-nucleotide polymorphism arrays, and, when possible, we confirmed the presence of 47,XXX using fluorescence in situ hybridization or quantitative polymerase chain reaction.

Results
We found 47,XXX in 7 of 2,826 SLE patients and in 3 of 1,033 SS patients, but in only 2 of 7,074 controls (odds ratio in the SLE and primary SS groups 8.78 [95% confidence interval 1.67–86.79], P = 0.003 and odds ratio 10.29 [95% confidence interval 1.18–123.47], P = 0.02, respectively). One in 404 women with SLE and 1 in 344 women with SS had 47,XXX. There was an excess of 47,XXX among SLE and SS patients.

Conclusion
The estimated prevalence of SLE and SS in women with 47,XXX was ∼2.5 and ∼2.9 times higher, respectively, than that in women with 46,XX and ∼25 and ∼41 times higher, respectively, than that in men with 46,XY. No statistically significant increase of 47,XXX was observed in other female-biased diseases (primary biliary cirrhosis or RA), supporting the idea of multiple pathways to sex bias in autoimmunity.

Web | American College of Rheumatology | Paywall

Notably, they were able to find an excess of SLE patients that have extra X chromosomes with only 213 males and 2826 females. DecodeME has far more cases than this, so if the X chromosome is similarly involved in ME/CFS, maybe people with extra X chromosomes would be over-represented in the cohort.

This seems like a straightforward way to test the X-chromosome dosage hypothesis. I'm not sure if the data collected in DecodeME allows for testing this.

There is also a preprint about mice that provides some support for post-infectious symptoms being linked to X-dosage:

Mechanisms of sex differences in acute and long COVID sequelae in mice, 2025, Liu et al.

With a focus on neurocognition and memory at 42 dpi [days post infection], infected mice with two ChrX, regardless of ChrY (XXF and XXYM), displayed greater spatial working memory impairments as compared with mice that had a single ChrX (XYM, X0F; Fig. 7M). There was no effect of sex chromosome complement on working memory in mock-infected mice (Extended Data Fig. 10G-H). Infected mice with two ChrX also failed to display NOR [novel object recognition], whereas mice with one ChrX displayed intact NOR (Fig. 5N) that was consistent with mock-infected mice (Extended Data Fig. 10I).

 

[Jonathan Edwards]

This seems like a straightforward way to test the X-chromosome dosage hypothesis. I'm not sure if the data collected in DecodeME allows for testing this.

There might be bias in recruitment of Klinefelter or Turner subjects. The prevalence rates are around 1/1000 and 1/2500 so there will not be many but there might be 3-4 of each. The situation may be easier for lupus because the sex ratio is bigger (9:1).