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I tried to find some studies a few weeks ago and didn’t really see anything noteworthy besides this study. There was one methylation study I believe but no more ATAC-seq. I’d personally really be interested in ATAC-seq of tissue resident immune cells in ME, but logistically I think it would be...

It would be interesting to see if TPPP is downregulated in neurons as well, though that would probably require a post-mortem sample. My experience with ATAC-seq is that the findings are very rarely consistent between different cell types. In the context of “T cell exhaustion” I suppose it might...

That’s a wonderful bit of confluence. I was just thinking that calcium is exactly where the threads of synapses, metabolism, and immune function all converge both in the muscle and the brain.

Never too late :)

Fair enough, thanks for your insight. The NK thing has been niggling at me, I’ve been trying to find a way to make sense of it. If they were somehow an indirect marker of autoantibody presence in the first place, it would make sense why they would correlate with responders.

That’s a really good point, I haven’t even considered that. I sincerely hope they didn’t use the AI text mining data, gene2pubmed was already such a disappointment when I tried verifying the gene names that AI was pulling from abstracts alone. I can’t assume it’s much better on the protein side

This is the study I’m thinking of: https://pubmed.ncbi.nlm.nih.gov/39427243/ though I’m not well read on lupus so obviously this might not be a consistent finding. Just a thread I was running down to potentially explain the NK discrepancy in the Dara trial and how it might fit into some other...

Pulling this quote from another thread to avoid going off topic there. @Jonathan Edwards would you generally expect to see a higher level of NKs in response to autoantibodies, regardless of the specific autoantibody? I know it’s been observed in SLE but not sure how generalizable that is. In...

I agree with @forestglip ’s thoughts. HEAL2 seems to be better at picking out relevant pathways, whereas HEAL picks out relevant one-offs. In general, across -omics analyses, there’s a crisis of replication at the individual analyte level. There’s simply two much intra-group variation...

I will also put out there into the void: If you took a couple of us very motivated youngsters, put us in a room together and told us that we were all individually guaranteed funding for the next few years so we ought to work as a team as much as possible, that would be a very powerful thing….

Thank you for bringing it up again, yes that’s exactly what I had in mind. The way I see it, either those afferent neurons are properly sensing a dysregulated metabolic environment, or (to paraphrase some of the speculation of others on this thread) somehow there is an exaggerated transduction...

Agreed!

I suppose it's reaffirming that this basic process happens everywhere. It's how I got all my computational knowledge as well. Someone tells me I should start using a package for something, the documentation is absolutely nonsensical, but stick with it for a few weeks and suddenly I'm the lab's...

Please do! It's definitely way more possible than people think, it mainly just requires a lot of stubbornness. I can't emphasize enough that it took a long time before I felt like anything was falling into place when I first started. But looking back retroactively every few weeks, I could...

Thank you, that's very kind! I think much of it was a very slow process over long periods of time, and it was definitely unconventional learning since I had to work around the cognitive deficits. To describe the basic process, I have gotten extremely comfortable with diving headfirst into...

Just as a general response to the comments I’ve been tagged in (thank you all for the discussion): I want to reiterate that in principle, I'm not against the idea of some neural or neuro-immune circuit being important to the disease. What I'm hoping to push forward through my questions is a...

Ah thanks, I forgot SCENIC was used here. I have used SCENIC myself and ended up abandoning it because of less-than-ideal results. Unless they’ve changed things substantially since I used it, it uses a manually curated long-form list of transcription factors for humans or mice with all the...

Hi @hotblack! I’ll take a position bridging @Jonathan Edwards and @Trish—I certainly agree that spinning wheels like this can be useful (I spend more than enough time doing it myself), it just needs to be backed up by plausible mechanisms from the literature, or pinpoint an exact place where the...

@Hutan is your first quote from a paper? I just ask because the two PSMDs are definitely not transcription factors, though they may be involved in regulating them via the proteasome.

Oh wonderful, thanks for letting me know.