Organ and cell-specific biomarkers of Long-COVID identified with targeted proteomics and machine learning, 2023, Patel et al

A good start to the paper:

Selection of the cohorts looks fine. An Ontario, Canada study. 22 people in each cohort.


PEA: Proximity Extension Assay - done using thawed plasma. Basically I think, if markers of a specific protein occurred near each other, that resulted in multiplication of the marker, providing a way to measure the amount of protein in a sample. Pretty much what the method name says: Proximity Extension Assay.

Measured 2925 unique proteins. Some effort made to account for the large number of variables:

The details of some of the analysis done is beyond me, but so far this is looking like a solid study. The only thing is that 22 people in a cohort is a little small.

 

Ah, damn, there is no 'recovered from Covid with no ongoing symptoms' cohort. That limits the usefulness of this study. The proteins might just identify people who have had a recent infection. The blood draw was taken from the acute Covid patients upon hospital admission; the blood draw from the Long Covid patients was taken when they turned up at the Long covid outpatient clinic.

Also worth noting the median age of the cohorts - I guess that was necessary to match with the ICU cohort, but the whole study is of older people.

 

Here are the 9 differentiating proteins that made it into their model:
CXCL5, AP3S2, MAX, PDLIM7, EDAR, LTA4H, CRACR2A, CXCL3, FRZB
All were elevated, except for FRZB which was lowered.

I think we have seen something about some of these immune cell receptors before:

In the limitations, the authors don't acknowledge the problem caused by not having a 'post-Covid, now healthy' cohort. Yet, it is that issue that makes the results of much less value than they would otherwise have been. I'm sure that among the 119 proteins that were found to be different to pre-covid healthy controls there are some clues, but those clues are buried in post-illness noise. Comparing the 119 protein list with the findings from other studies with a 'recovered healthy' cohort might unearth something.

I hope the authors will now make the same measurements on larger cohorts of people with Long Covid and healthy people who have recovered from Covid.

 

I note that cd69, one of the immune cell receptors found to be upregulated in the Long Covid cohort compared to the healthy controls, is one of the proteins found to be possibly affected by long term freezing*. The healthy control serum had been stored frozen for some time.

* Impact of Long-Term Cryopreservation on Blood Immune Cell Markers in ME/CFS: Implications for Biomarker Discovery Gomez-Mora et al 2020

It would be good to see researchers replicating studies like this with fresh, never frozen serum. I understand that introduces different variability - analyses undertaken on different days by different lab workers - but the possibility that findings are just the result of storage differences should be investigated.

 

So this set of patients was used to set up the model, then surely they need to verify it with a different set of patients before claiming that it differentiates accurately.

 

Figure 2 does possibly show that. I can't quite understand the charts, they say that the green shaded area is the 5-95% range for healthy controls, but for most charts the healthy controls are mostly just represented by a single line (the mean?) with the Long Covid individual points plotted relative to that. The x axis is days from infection onset.






Supplementary Table 1 is more clear I think:
Here's an excerpt. The corrected p values indicate big differences.


I'll try to make the uploaded images better.

I think surely, studies looking for proteins in plasma have a good chance of finding some differences. We just need them to get cohort selection right and make sure that technical difficulties are excluded. I guess there isn't the capacity to test for every protein, so even though 2000-odd proteins sounds a lot, they may not test for crucial ones.

 

Listing all of the 119 proteins found to be different from Supplementary Table 1, so the search engine will pick them up:
(Again, I'm so disappointed that the comparator isn't post-Covid healthy people. This could have been a treasure-trove of clues.)

 

Yes, one of my synapses was pinged about Serpina5 also. Googling some of those on the list, there are interesting possibilities.

edit - only problem is, in this study, Serpina5 in LC was 4 times the mean of the healthy controls and acute /covid combined (not sure why the authors did that) i.e. the levels were 4 times higher. In that other study, Serpina 5 was lower.