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.