Journal: bioRxiv

Article Title: A ML-framework for the discovery of next-generation IBD targets using a harmonized single-cell atlas of patient tissue

doi: 10.64898/2026.02.06.699999

Figure Lengend Snippet: A) Schematic overview of the atlas informed model system selection matching disease-relevant cell populations to transcriptionally matched MNP polarization conditions. B) Atlas informed MNP polarization condition selection for PTGIR KO. The left heatmap shows the average z-score normalized SystemMatch values of transcriptional similarity to disease-relevant myeloid subsets including lipid-macrophages and inflammatory macrophages. The right heatmap shows the logCPM normalized expression of PTGIR, genes associated with lipid macrophages, and IPR feature 1 genes. Human monocytes across 6 donors were differentiated under multiple polarization conditions. Results for 6 representative conditions are shown. For the functional validation of PTGIR KO, KO of PTGIR and F8 (negative control) was performed in MNPs monocytes (n=5-6 donors). Cells were then cultured with M-CSF for 5 days, polarized with M-CSF and IL-1 β for 2 days followed by stimulation with the PTGIR agonist Iloprost for 2 days (Ilo, 0.1nM, details in supplementary methods). C) Volcano Plot of differentially expressed genes in the PTGIR KO vs F8 KO contrast under iloprost stimulation. Top DEGs with |logFC|> 0.5 and adj_p < 0.1 are displayed. D) Left: Gene set enrichment analysis for PTGIR KO vs F8 KO contrast genes under iloprost stimulation. Right: Enrichment plot for Inflammation related genes and steroid refractory UC signatures . The logFC expression of the top leading-edge genes is shown for each replicate in the 6 individual donors. E) LogFC for secreted VEGF-A (top) and CCL7 (bottom) upon PTGIR KO when compared to F8 KO following stimulation with Iloprost. Representative boxplot from 2 replicate experiments with n=6 each are shown. F) Representative flow cytometry plot of the surface protein expression of CD36 and CD200R in PTGIR KO and F8 KO controls under Iloprost stimulation. G) For the ex vivo comparison of the MoA of PTGIR and anti-TNF targeting, MNPs monocytes (n=5-6) were cultured with G-MCSF + IFN γ + LPS for 6 days followed by treatment with a blocking anti-TNF antibody for 3 days (Infliximab, 1.25ug/mL before processing for multi-omic analysis (details in supplementary methods). Gene set enrichment analysis for the top pathways modulated by TNF blockade (anti-TNF vs unstimulated contrast) and/or PTGIR KO (PTGIR KO vs F8 KO contrast with Iloprost). Signatures are grouped as anti-TNF specific, PTGIR KO specific, or shared.

Article Snippet: Cellular phenotypes were assessed by multi-color spectral flow cytometry (Cytek Aurora), and secreted protein levels in supernatants were measured using a multiplexed analyte assay (Nomic Bio).

Techniques: Selection, Expressing, Functional Assay, Biomarker Discovery, Negative Control, Cell Culture, Flow Cytometry, Ex Vivo, Comparison, Blocking Assay