Journal: bioRxiv
Article Title: Persistent SARS-CoV-2 Spike is Associated with Localized Immune Dysregulation in Long COVID Gut Biopsies
doi: 10.64898/2026.03.09.707564
Figure Lengend Snippet: (A) Representative staining images of the left colon and terminal ileum between healthy and Long COVID participants used for ROI collection. Tissue sections were stained with SYTO-13 (Blue), anti-SARS-CoV-2 Spike ( CR3022 ) (Yellow), anti-PanCK (Green), and anti -CD19 (CB19) (red) and visualized using the GeoMx DSP (Long COVID = 8; Healthy = 3). (B) SARS-COV-2 Spike protein positive cell detection based on a QuPath pipeline comparing condition and tissue type between tissue compartments. Cell detection was performed using an adapted StarDist script followed by cell classification based on a supervised ML model. Kruskal-Wallis with multiple comparisons was performed ( p ≤ 0.05 (*), p ≤ 0.01 (**), p ≤ 0.001 (***)). (D) ROI selection and differential expression strategies comparing detected Spike protein positive ROI’s in colon tissue between Long COVID and healthy participants. (D) Differential analysis was performed using the limma-voom pipeline, correcting for replicate samples and variation in the frequency of detected SARS-CoV-2 Spike by ROI. 18,582 transcript targets were plotted. The main volcano plot highlights 26 and 31 genes that are upregulated and downregulated, respectively, at an unadjusted p -value threshold of 0.05 and an absolute log 2 FC > 1. Points with a triangular shape passed the adjusted p-value threshold based on a Benjamini-Hochberg correction. Smaller volcano plots show differentially expressed genes belonging to GeneOntology (GO) panels (GO:0002376 & GO:0006954) at an unadjusted p -value threshold of 0.05 and a Fold-Change value of 1.5. (E) Gene-Set Enrichment Analysis was performed on a ranked list of log 2 FC values with GeneOntology and KEGG ( 54 and 38 statistically significant pathways, respectively ) . Representative categories were selected, and pathways/ gene sets were plotted using the normalized enrichment score (NES) alongside the ratio of genes in the leading edge to total genes in the gene set (GeneRatio) and the adjusted p-value. (F) Spatial deconvolution was performed using a safeTME reference expression profile. Statistical significance was assessed using the propeller framework, a moderated two-tailed Mann-Whitney U test with BH FDR correction ( FDR ≤ 0.05 (*), FDR ≤ 0.01 (**), FDR ≤ 0.001 (***)).
Article Snippet: NBP2-90980AF532), anti-PanCK (Novus; Ca.
Techniques: Staining, Selection, Quantitative Proteomics, Expressing, Two Tailed Test, MANN-WHITNEY
Proteintech is a verified supplier 
