Mitochondria-localised ZNFX1 functions as a dsRNA sensor to initiate antiviral responses through MAVS, 2019, Wang et al

[jnmaciuch]

Mitochondria-localised ZNFX1 functions as a dsRNA sensor to initiate antiviral responses through MAVS

Spoiler: Authors

Wang, Yao; Yuan, Shaochun; Jia, Xin; Ge, Yong; Ling, Tao; Nie, Meng; Lan, Xihong; Chen, Shangwu; Xu, Anlong

Abstract
In the past two decades, emerging studies have suggested that DExD/H box helicases belonging to helicase superfamily 2 (SF2) play essential roles in antiviral innate immunity. However, the antiviral functions of helicase SF1, which shares a conserved helicase core with SF2, are little understood. Here we demonstrate that zinc finger NFX1-type containing 1 (ZNFX1), a helicase SF1, is an interferon (IFN)-stimulated, mitochondrial-localised dsRNA sensor that specifically restricts the replication of RNA viruses. Upon virus infection, ZNFX1 immediately recognizes viral RNA through its Armadillo-type fold and P-loop domain and then interacts with mitochondrial antiviral signalling protein to initiate the type I IFN response without depending on retinoic acid-inducible gene I-like receptors (RLRs). In short, as is the case with interferon-stimulated genes (ISGs) alone, ZNFX1 can induce IFN and ISG expression at an early stage of RNA virus infection to form a positively regulated loop of the well-known RLR signalling. This provides another layer of understanding of the complexity of antiviral immunity.

Web | DOI | PDF | Nature Cell Biology

 

[jnmaciuch]

Reason for posting:

ZNFX1 is a decodeME candidate with eQTL data supporting its levels are increased in ME/CFS.

Also might be worth saying the eQTL data specifically points to increased expression in brain cortex and pancreas, not really much on anywhere else. So where NLRP3 is concerned could point to microglia.

An alternative way that ZNFX1 could be directly relevant to immune signaling in the brain, one that might make more sense with potentially increased expression in DecodeME pwME with that SNP

[Edit: realizing belatedly that this is a connection that was already made by DecodeME in the candidate gene list, we just didn't have a thread yet]

 

[jnmaciuch]

I think the PDF link should be paywall-free but if anyone wants to read this paper and has trouble accessing it, feel free to message me

 

[jnmaciuch]

Potentially interesting connection to some other thoughts about how cells could maintain a portion of the interferon response long term:

Further analyses of transcription factor binding sites revealed that the promoter of Znfx1 contains STAT1, STAT2, IRF1 and IRF9 binding motifs in a relatively concentrated and overlapped region

STAT1+STAT2+IRF9 form the ISGF3 complex, which has been found to be transcriptionally active and upregulated long term in several cell lines and tissue samples here (https://www.s4me.info/threads/unpho...ainst-viral-infections-wang-et-al-2017.45690/)

So ZNFX1 is something that triggers the interferon response when it detects "foreign" cytosolic RNA (which can come from a virus or potentially from mitochondria), and the interferon response then upregulates ZNFX1

 

[ME/CFS Science Blog]

interesting, thanks.

 

[jnmaciuch]

Explain like I'm brain-foggy:

ZNFX1 is a gene that was known to be important in the response of tissue cells to viral infection, but we didn't know exactly what it does in that context.

By knocking out the gene in a cell type, it was confirmed that cells without ZNFX1 produce much less interferon in response to a viral challenge (VSV)
Fig 3b:


They hypothesized that ZNFX1 might belong to a class of viral sensor proteins, which exist in the cytoplasm of cells and detect the presence of non-nuclear (e.g. foreign) DNA/RNA. It's the first line of defense against viral infection in tissue cells

Fig 5b:

This method is called co-immunoprecipitation, where you can detect how much of your protein of interest is physically bound to another molecule that you specifically "flag". RIG-I and MDA5 are two other proteins that are known to directly bind to viral RNA. This plot is basically showing that ZNFX1 directly binds to viral (VSV) RNA, similarly to two other proteins that are known to do this (IgG is their negative control)

The next question is after ZNFX1 detects viral RNA, how does it trigger the cell to produce interferon? There are a couple known options that are used by other RNA/DNA sensor proteins (those options are TRIF, MyD88, MAVS, and STING). Each of those proteins sets of a cascade that leads to interferon production, so they did another experiment where they checked whether ZNFX1 binds to any of them. The only one with detectable binding was MAVS (to interpret this figure, the important thing to know is that the one that binds to ZNFX1 would end up with a band in that first row)

Fig. 6d:


There's a lot of findings that I glossed over but these are the main important ones. So long story short: they determined that ZNFX1 is a protein that detects foreign RNA and sets off a cascade that leads to interferon production (a cellular response that tries to counteract a virus by making nearby tissue cells less suitable hosts). The intermediate that it uses to set off that interferon response is MAVS.

 

[V.R.T.]

It really seems like there is a solid theoretical basis for your hypothesis. obviously I am a layman but it seems that there are many ways it could fit with the evidence we have - can you share anything about how your hunt for muscle samples is going?

 

[jnmaciuch]

It really seems like there is a solid theoretical basis for your hypothesis. obviously I am a layman but it seems that there are many ways it could fit with the evidence we have

Thanks I am trying to be mindful of just always seeing connections to the thing I'm interested in whether it's real or not, but as far as hypotheses go this is the best one could hope for in terms of something strongly hinted at by the genetics data. I should note that TRIM38, another tier 1 candidate gene, directly prevents the degradation of cGAS (cGAS is basically the DNA-sensing cousin to ZNFX1/RIG-I/MDA5).

can you share anything about how your hunt for muscle samples is going?

Still no leads, unfortunately. I took some time over the holidays to regroup and came up with a different pilot study idea where I could feasibly handle the sample collection myself. It'll take a while for that to happen (I would need training on a couple things first, plus I will be doing every part of the study on my own) but it seemed worthwhile to pivot since it might lead to faster results anyways. Will still try to find muscle samples in the mean time