High-throughput targeted proteomics from serum
Serum samples (4 COVID-MDR, 3 MDR, 5 DRESS, 5 HC) were analyzed using
the inflammation panel of a proteomic multiplex assay by proximity
extension assay (OLINK, Uppsala, Sweden),. The proteomic multiplex assay
by OLINK is a proximity extension assay with oligonucleotide-labeled
antibody probe pairs that bind to their respective
targets23-25. It
measures proteins via an antibody-mediated detection system linked to
synthetic DNA for quantification by a real-time polymerase chain
reaction platform24.
RNA-seq and proximity
extension assay data analysis
A detailed description of the analysis is found in the Supplementary
Materials and Methods. Genes with a p-value of less than 0.01 and log2
fold change of greater than 0.5 or less than -0.5
(|L2FC|>0.5) were included in this study
(Table S1-S2).
All RNA-seq data performed in this paper can be found on the NCBI Gene
Expression Omnibus (GEO) under accession number GSE161225. Enrichr, a
gene list enrichment analysis tool, was utilized to search for enriched
Gene ontology biological processes (GO BP). The data of a proteomic
multiplex assay in Normalized protein expression (NPX) format were
imported, processed by Olink-R Package
(https://github.com/ge11232002/OlinkR). The statistical comparison of
protein levels between groups was performed as previously
described26. The fold
change and p- values were estimated by fitting a linear model for
each protein. The statistically differentiated proteins were
characterized for each sample (|L2FC| >
1, p-value < 0.05), depicted as venn diagrams, and mapped to
the search tool for retrieval of interacting genes (STRING) to acquire
protein–protein interaction networks.