Proteomics

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Authors

Acknowledgements and Disclosures

The COVID-19 Community Research Partnership gratefully acknowledges the commitment and dedication of the study participants. Programmatic, laboratory, and technical support was provided by Vysnova Partners, Inc., Javara, Inc., Oracle Corporation, LabCorp, Scanwell Health, and Neoteryx. This presentation was supported by the CARES Act of the U.S. Department of Health and Human Services (HHS) [Contract # NC DHHS GTS #49927] and the Centers for Disease Control and Prevention (CDC) [contract #75D30120C08405]. The findings and conclusions in this report are those of the authors. We are grateful to the entire COVID-19 Community Research Partnership Study Group.

Background

There remain important gaps in knowledge concerning the effects of SARS-CoV-2 infection or vaccination on the human blood proteome. Several studies exist which characterize the protein in severely ill COVID-19 patients, but do not examine mild infection.1,2 In this analysis we explore the changes in the proteome amongst those with mild COVID-19 disease and those who were vaccinated, but not infected.

Methods

The CCRP is a longitudinal, surveillance study with information on SARS-CoV-2 infections, vaccinations and associated humoral immune responses in over 37,000 individuals. We selected a sample of blood spots cards (n=510) from serum antibody studies obtained between October 2020 and April 2021 Mass spectrometry proteomics performed covering 540 unique plasma proteins. We analyzed the quantified protein differences based on dried blood based on samples obtained before and after infection or vaccination among previously non-infected individuals (immune naïve) The majority of infected individuals were minimally symptomatic. Statistical methods: Adjustments were performed for batch effects, age, sex, prior diagnosis of cancer, evidence of an autimmune disease, pulmonary, cardiovascular or autoimmune disease, or diabetes using HCUP definitions3 Moderated t-statistics were estimated using empirical bayes statistics for differential expression using the R package, limma. Differentially expressed proteins were considered significant with an FDR adjusted p-value of <0.05 and log2 fold change (L2FC) >0.2.

Results

We found 7 and 11 proteins differentially abundant proteins in the naïve/infected and naïve/vaccinated people respectively, of which 6 were shared (Figure 2). Hepatocyte growth factor receptor (HGF) was upregulated (L2FC 0.21; p < 0.001) only in those who were infected (Fig 1) Seven proteins in the vaccinated were downregulated only in the vaccinated samples include: Transferrin receptor protein 1 (L2FC -0.48; p<0.001) , Septin-2 (L2FC -0.36; p<0.001) , Fibrillarin (L2FC -0.28; p<0.001) and lambda-crystallin homolog (L2FC -0.29, p <0.001) (Fig 1). Elongation factor 2 (L2FC 0.23; p<0.001), Keratin (L2FC 0.20; p=0.003), and Serine/arginine repetitive matrix protein 2 (L2FC 0.20; p<0.001) were found to be upregulated only in the vaccinated samples (Fig 1). The remaining DE protein were associated with a wide array of functions including metabolic, cytostructural, extracellular matrix and DNA regulatory processes.

Discussion

We found changes in the proteome both from mild infection and vaccination; however, notably the proteome was relatively stable between timepoints with largest absolute observed fold change of 0.52. HGF, elevated in the infected, has been associated with endothelial inflammation, upregulation of pro-inflammatory cytokines to reduce lung fibrosis and is known to promote tissue repair. Prior studies have indicated elevated HGF is associated with progression to ICU care in those hospitalized with COVID-19.4 Fibrillarin, downregulated in the vaccinated, has been associated with higher rates of bacterial and viral clearance, inflammation reduction, and increased cell survival.5 Limitations include demographic representation and high rates of comorbidities limit generalizability of these results Heterogeneity in time since infection/vaccination limited ability to examine cytokines and other immune markers.

Conclusion

We found changes in the proteome both from infection and vaccination. These findings suggest detectable complex inflammation from mild to moderate infections. Further investigation is required to understand the mechanism of action and clinical implication of these findings.

References

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