Trial Report Bulk RNA sequencing for analysis of post COVID-19 condition in adolescents and young adults, 2024, Sommen

[Dolphin]

Free fulltext:
https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-024-05117-7

• Research
• Open access
• Published: 26 March 2024

Bulk RNA sequencing for analysis of post COVID-19 condition in adolescents and young adults

• Silke Lauren Sommen,
• Zhi Zhao,
• Sunniva Segtnan,
• Tonje Stiansen-Sonerud,
• Joel Selvakumar,
• Lise Beier Havdal,
• Johannes Gjerstad,
• Vegard Bruun Bratholm Wyller &
• Lise Lund Berven

Journal of Translational Medicine volume 22, Article number: 312 (2024) Cite this article

Abstract
Background
Post COVID-19 condition (PCC) is a complication of SARS-COV-2 infection and can lead to long-term disability.

Methods
The present study was designed to analyse the gene expression patterns of PCC through bulk RNA sequencing of whole blood and to explore the potential molecular mechanisms of PCC. Whole blood was collected from 80 participants enrolled in a prospective cohort study following SARS-CoV-2 infected and non-infected individuals for 6 months after recruitment and was used for bulk RNA sequencing. Identification of differentially expressed genes (DEG), pathway enrichment and immune cell deconvolution was performed to explore potential biological pathways involved in PCC.

Results
We have found 13 differentially expressed genes associated with PCC. Enriched pathways were related to interferon-signalling and anti-viral immune processes.

Conclusion
The PCC transcriptome is characterized by a modest overexpression of interferon-stimulated genes, pointing to a subtle ongoing inflammatory response.

https://twitter.com/user/status/1773182136536715684

 

[Dolphin]

I noticed that biopsychosocial proponent Vegard Bruun Bratholm Wyller is one of the co-authors though in the least important position.

Another co-author is Joel Selvakumar.
That's not a name that is familiar to me but here is his Twitter profile:
Paediatrician. PhD student @UniOslo. ‘Long COVID’, child health, overdiagnosis. Father of

 

[Dolphin]

https://twitter.com/user/status/1773236374470045762

 

[SNT Gatchaman]

I noticed that biopsychosocial proponent Vegard Bruun Bratholm Wyller is one of the co-authors though in the least important position.

Another co-author is Joel Selvakumar.

Senior and lead authors of Prevalence and Characteristics Associated With Post–COVID-19 Condition Among Nonhospitalized Adolescents and Young Adults (2023, JAMA Network Open)

The thread for discussion on that paper's preprint is here.

 

[SNT Gatchaman]

Top 5 enriched transcription factors were —

STAT2
IRF1
STAT1
CUX1
GFI1B

 

[SNT Gatchaman]

In this study, we identified a PCC-related RNA expression pattern comprising 13 differentially expressed genes. To our knowledge, this is the first comparative analysis of whole blood transcriptomes in adolescents and young adults with PCC after a COVID-19 infection and several control groups including recovered infected, symptomatic uninfected and symptom-free uninfected participants.

The main result from the study was a PCC-related transcriptional upregulation in interferon signalling related genes. These genes were not upregulated in uninfected controls with fatigue symptoms or in recovered SARS-CoV-2 infected participants.

How immune perturbations contribute to PCCrelated symptoms remains largely unanswered.

Although causal conclusions cannot be made from our cross-sectional design, the present data suggests a positive association between differential gene expression and clinical symptoms, especially post-exertional malaise.

Earlier findings from our cohort show that PCC symptoms are associated to psychosocial factors (eg. loneliness) rather than the SARS-CoV-2 infection itself. Interestingly, this aligns with the “Conserved Transcriptional Response to Adversity (CTRA)”, a concept describing stress-induced changes in immune related gene expression. The biological factors in PCC, such as immune activation, might be the result of a conditioning mechanism by chronic stress in addition to the SARS-COV-2 infection.

 

[Eleanor]

"The biological factors in PCC, such as immune activation, might be the result of a conditioning mechanism by chronic stress"

... if we ignore all the cases in which there was no chronic stress. No need to even think about them. Just stick our fingers in our ears and sing la la la and they'll go away.

 

[Midnattsol]

I noticed that biopsychosocial proponent Vegard Bruun Bratholm Wyller is one of the co-authors though in the least important position.

Another co-author is Joel Selvakumar.
That's not a name that is familiar to me but here is his Twitter profile:
Paediatrician. PhD student @UniOslo. ‘Long COVID’, child health, overdiagnosis. Father of

Selvkuumar has multiple times on twitter defended the notion that children have symptoms of long covid due to "long lockdown" and being scared. Explaining what stress can to do the body to the children (and their parents) they will feel empowered and complaints will reduce.

 

[rvallee]

Selvkuumar has multiple times on twitter defended the notion that children have symptoms of long covid due to "long lockdown" and being scared. Explaining what stress can to do the body to the children (and their parents) they will feel empowered and complaints will reduce.

Given this, how does it even make sense to do RNA analysis? What possible relevance could this possibly have in a "long lockdown" model?

Or I guess the philosopher's stone of psychosomatic ideologues everywhere is finding evidence of psychology influencing biology, nevermind that in all cases they are overlooking the actual biological cause. In the sense that it's just a myth and they'll never find it. But it still seems obvious that this person's biases make them useless contributors to this kind of research at best.

 

[Midnattsol]

Given this, how does it even make sense to do RNA analysis? What possible relevance could this possibly have in a "long lockdown" model?

Not the first time BPS throws in som biomedical stuff they can then point to and say "see, we look at that too".

 

[Hutan]

So
SARS+F+: 20 participants SARS-CoV-2 positive; high fatigue (numerical CFQ>=21); meeting WHO PCC and Fukuda criteria
SARS+F-: 20 participants SARS-CoV-2 positive; low fatigue (numerical CFQ<=11); not meeting WHO PCC and Fukuda criteria
SARS-F+: 20 participants SARS-CoV-2 negative; high fatigue (bimodal CFQ>=4)
SARS-F-: 20 participants SARS-CoV-2 negative; low fatigue ('not reporting fatigue'), not meeting WHO PCC and Fukuda criteria

That's already looking a bit odd - they used a different method to identify SARS-CoV-2-negative participants with high fatigue. Figure 1 shows that the SARS-F+ group did not all meet WHO PCC and did not all meet Fukuda criteria

They don't say how they selected the 20 participants for each group from the larger numbers qualifying.
All participants female.

 

[Hutan]

However, 13 genes were returned as differentially expressed in the SARS + /F + group versus SARS + /F- group after adjustment using the gene expression data from the SARS-/F + and SARS-/F- groups as control data. These DEGs were retained for further analysis. Interestingly, these 13 genes only showed differential expression for participants that reported both fatigue symptoms and a prior SARS-COV-2 infection. The comparisons of SARS + /F- versus SARS-/F- groups and SARS-/F + versus SARS-/F- groups did not show any differentially expressed genes after multiple testing correction.

The 13 differentially expressed genes are between the SARS+F+ group and the SARS+F- group. That's good. Although 20 people is not a big sample.

 

[Hutan]

PCA analysis

Whole blood derived transcriptome sequencing resulted in 58 735 profiled features. A global overview of the data through principal components analysis (PCA) did not reveal distinct clustering among the four experimental groups (Fig. 2).

The PCA is in Figure 2 - there's no separation of any of the groups, despite the axes accounting for a lot of the variation in gene expression. I guess there's just so much individual variation.

Performing PCA when the sample size is less than the number of variables can lead to spurious results and should be done with caution .

I guess PCA probably isn't appropriate with such a small number of samples relative to the massive number of gene expression features.

Maybe the blood sample needs to be stratified, to get smaller samples of features, to zero in on what is different? Or there could be prior decisions to only look at certain gene expressions, such as those for viral defense genes.

 

[Hutan]

Top differentially expressed genes



Fig 4 looks a bit more exciting. The heat map is the difference between each group versus the mean of the other three groups. They say that the only significant differences were the 13 gene expressions different between the SARS+F+ and the rest.

And the upregulated gene expressions do tell a pretty coherent story about an immune response to viral infection.

We just have to remember that these are the most different gene expressions found out of about 59,000. And also , it looks as though about 4 individuals in the 20 people in the SARS+F+ group are doing the heavy lifting in terms of the upregulation. Most of the others look quite a lot like the rest of the people in the other groups. (Each individual is represented by a column in the heat map - see the red coloured columns.)