Thesis Investigation of an ME/CFS-associated Mutation in the Transmembrane PRR L-SIGN and Its Effect on Infection and Phagocytosis, 2024, Schwarz

[forestglip]

Investigation of an ME/CFS-associated Mutation in the Transmembrane PRR L-SIGN and Its Effect on Infection and Phagocytosis

Michael Schwarz

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystemic
disease that affects millions of people across the globe. It is characterized by a variety
of debilitating symptoms such as post-exertional malaise, brain fog, extreme fatigue, and many others that are shared by a variety of illnesses. In conjunction with the overlap in symptoms, a lack of consistency across studies and lack of unique diagnostic biomarkers has left ME/CFS poorly understood with a lack of detailed mechanistic studies.

A single nucleotide polymorphism, denoted rs479448, in the CLEC4M gene that encodes the C-type lectin L-SIGN has been associated with ME/CFS in a genome-wide association study (GWAS). The aim of the study described here was to test the hypothesis that the CLEC4M mutation causes cells to become more pro-inflammatory, more easily infected by pathogens recognized by L-SIGN, and, in the case of macrophages more efficient at phagocytosing pathogens. To this end, we used epifluorescence microscopy and live cell imaging to analyze cells transfected with both the mutant and wild-type variants of CLEC4M, with regard to their response to Candida albicans infection.

Our study establishes the groundwork for testing the phagocytosis efficiency of macrophages expressing the ME/CFS-associated variant of CLEC4M, which could lead to an exacerbation of the pro-inflammatory response. Additional work will need to be conducted in order to determine statistical significance of these findings, but the preliminary data proves promising.

Link (Thesis) [Paywall]

 

[Peter T]

Is it normal for a master’s thesis to be behind a paywall?

 

[Utsikt]

Is it normal for a master’s thesis to be behind a paywall?

No, mine is free and public (from Norway). His is from the US, so I guess everything goes there.

 

[Yann04]

A single nucleotide polymorphism, denoted rs479448, in the CLEC4M gene that encodes the C-type lectin L-SIGN has been associated with ME/CFS in a genome-wide association study (GWAS).

Anyone know what GWAS they are talking about?

 

[Utsikt]

Google gave me this:
https://www.s4me.info/threads/genom...bjects-with-me-cfs-2016-schlauch-et-al.42179/

 

[Jonathan Edwards]

This is the study with 40 ME/CFS cases I think - which seems unlikely to be reliable evidence for a link. The investigation of the mutation does not seem to have come to any great conclusion?

 

[Midnattsol]

Is it normal for a master’s thesis to be behind a paywall?

No, mine is free and public (from Norway). His is from the US, so I guess everything goes there.

One of mine, that used data from a clinical trial, is not even published on the university’s own library pages as the chief investigator who owns the data had not published their findings. For the other the thesis is available from the university, but the scientific article is behind paywall at the journal. The thesis was not available until the article was published.

 

[forestglip]

Google gave me this:
https://www.s4me.info/threads/genom...bjects-with-me-cfs-2016-schlauch-et-al.42179/

The study says this:

Twelve of the 442 candidate SNPs associated with the ME/CFS cohort were identified in the coding region (exon) of their respective gene: five of these were synonymous substitutions (rs16973831, rs2274515, rs3732196, rs7613828 and rs17722227), two were missense substitutions (rs2015035 and rs479448) and the remainder were within T-cell receptor or immunoglobulin loci.

The SNP in the coding region of the CLEC4M gene, which codes for the C-type lectin domain family 4, member M, results in a non-conservative substitution of the amino acid tyrosine (Y) to cysteine (C).

CLEC4M, also know as L-SIGN or CD299, is a mannose-binding C-type lectin receptor, a component of the innate immune system that recognizes a broad range of pathogens.

One missense substitution occurs in the CLEC4M gene, which codes for the C-Type Lectin Domain Family 4, Member M protein and leads to a substitution of the amino acid tyrosine (Y) to cysteine (C). The phenolic functionality of tyrosine is an important component in proteins that are part of signal transduction processes as well as acceptors of phosphate groups in kinase reactions. In contrast, cysteine, when present in pairs, can form disulfide bonds to give proteins stable secondary and tertiary structures and, individually, can serve as nucleophiles in enzymatic reactions. These two amino acids have distinct functional moieties, and therefore this polymorphism produces a non-conservative substitution and potentially may lead to decreased functionality of the receptor.

CLEC4M is a pattern recognition receptor capable of binding to a broad range of pathogens, including hepatitis C virus, human immunodeficiency virus and Mycobacterium tuberculosis. A dysregulation of CLEC4M may have significant consequences in the pathogenesis of infectious diseases. Although ME/CFS has been associated with numerous viral infections or reactivations, including Epstein Barr virus, Enterovirus and Parvovirus B19, a causative infectious agent has never been identified. Future studies will be required to determine whether a CLEC4M polymorphism may predispose subjects with ME/CFS to viral infection.

The supplementary table says:
36 controls and 20 ME/CFS have TT
2 controls and 22 ME/CFS have CT

 

[Yann04]

The supplementary table says:
36 controls and 20 ME/CFS have TT
2 controls and 22 ME/CFS have CT

That’s interesting, so if this study was well done it’s present in ~50% of pwME but just ~5% of controls.

 

[Jonathan Edwards]

That’s interesting, so if this study was well done it’s present in ~50% of pwME but just ~5% of controls.

Yes, but they rolled the dice a million times.

 

[Yann04]

Yes, but they rolled the dice a million times.

Is there a way we can cross check it with healthy controls in another study to see if the percentages are similar?
I know that doesn’t discount random error making the share of pwME having the mutation seem large, but it does potentially make the found proportion of HC with it more or less reliable if replicated.

 

[forestglip]

Is there a way we can cross check it with healthy controls in another study to see if the percentages are similar?
I know that doesn’t discount random error making the share of pwME having the mutation seem large, but it does potentially make the found proportion of HC with it more or less reliable if replicated.

Someone please correct me if I'm misunderstanding something.

The paper gives the alleles on the negative strand. The corresponding alleles on the positive strand, which dbSNP uses, are T->A and C->G.

According to dbSNP, globally, G (C on the negative strand above) is rare.

A=0.991286 G=0.008714 (n=231456)

African ancestry looks a bit higher at about 15% for the G allele.

 

[Utsikt]

This seems relevant here:
https://xkcd.com/882/

 

[Jonathan Edwards]

Is there a way we can cross check it with healthy controls in another study to see if the percentages are similar?

I may have misremembered but I think we had looked at this study and somebody did try to check it with another cohort and it didn't pan out.

 

[forestglip]

I may have misremembered but I think we had looked at this study and somebody did try to check it with another cohort and it didn't pan out.

I don't see any search results in the forum other than this thread for "CLEC4M", "L-SIGN" (had to use Google for this one because the minus sign messes up results), "CD299", or "rs479448".

This thread might be what you're remembering, though I don't think this SNP was one that was cross-referenced with the UK Biobank. I don't get any results for the thread's SNP.

Here is more evidence that the Schlauch et al 2016 paper is wrong. I searched for all the hugely significant variants in table 1 of that paper in the UK Biobank GWAS tool and selected data for chronic fatigue syndrome that has data for 2017 cases and 450247 controls, slighty more than Schlauch 42 CFS and 38 controls.

http://geneatlas.roslin.ed.ac.uk/se...010471+rs6757577+rs8029503+rs7849492+rs948440

View attachment 11610
It can be seen that for variant ID's that have matches there are no significant datapoints - nothing approaching a pv or p value of 10-8 that is usually used as a decision gate in this UK biobank GWAS study.

Sorry @Michiel Tack for taking things of track.

EDIT : Just a little rant about researchers. They like to fill their papers with big words and sound important with this and that correlation used, but sometimes they just forget to use common sense when evaluating and reporting the data.

 

[forestglip]

Just wondering why studies don't do something like this to increase statistical power:

It seems in a genetic study, for controls, you could use numbers from the huge GWAS studies that have been done on the general population. While some of the "controls" will be ME/CFS, you could estimate the prevalence to get the extreme possibilities for what non-ME/CFS was for the SNP.

So say you want to use a large GWAS as the controls for a given SNP. The GWAS says 99% of people have TT and 1% have CT.

You use an estimate for ME/CFS in the studied population, maybe 0.5%. (A range could also be used for prevalence.) You consider the two extreme possibilities as the range for SNP prevalence:

• 100% of the 1% of people who have CT were non-ME/CFS.
  • So if 99.5% of the population are non-ME/CFS, that means 98.5/99.5=98.99% of non-ME/CFS have TT and the rest, 1.01% have CT.
• All those with ME/CFS have CT.
  • That leaves 0.5% of the non-ME/CFS with CT. 99/99.5=99.5% of non-ME/CFS have TT and the rest, 0.5% have CT.

So instead of a control group of 38 people, you'd have a control group with 200,000 people, where you can test the significance using the most extreme scenario where 1.01% of people without ME/CFS have CT.

Some people in the GWAS will be CC which will complicate things, but I'm sure that could also be incorporated in the range.

There's less of a need to perfectly match the two groups for environment in a genetic study. They could make an attempt to use similar ancestry, though.

 

[Jonathan Edwards]

It seems in a genetic study, for controls, you could use numbers from the huge GWAS studies that have been done on the general population.

I think that is what was done with the Leeds UK Biobank data, with 2000 ME/CFS cases and probably 20,000 controls. If I remember rightly it did not confirm any prior suggested links, although that may not have been specifically published. DecodeME was set up on the basis that even with 2000 probands no very obvious gene linkages were found. That makes it hard to see why nothing further has been said about this 2016 study if the results are robust.

I am pretty sure somebody else knows more about this than I do. @Andy?

 

[forestglip]

DecodeME was set up on the basis that even with 2000 probands no very obvious gene linkages were found. That makes it hard to see why nothing further has been said about this 2016 study if the results are robust.

I don't know what the first sentence means so maybe you could explain if it's relevant for this SNP. But it seems like this SNP wasn't tested in the BioBank since it's not coming up in the results.