Journal: Nature Communications

Article Title: Multi-omics analysis identifies a microbiota–bile acid–TLR signaling axis driving bladder injury in interstitial cystitis

doi: 10.1038/s41467-025-68060-1

Figure Lengend Snippet: A Differentially expressed genes (DEGs) in full-thickness bladder tissues from HIC patients and controls identified via RNA sequencing (|log₂FC|≥2; adjusted p < 0.05, two-sided Wald test using DESeq2). Gene Ontology (GO) ( B ) and KEGG ( C ) enrichment analyses of DEGs (two-sided hypergeometric test with FDR correction). D UMAP visualization of single-cell transcriptomic landscape of urothelium, with urothelial cells (UCs) identified by KRT19 and UPK1A expression. GO ( E ) and KEGG ( F ) analyses of upregulated DEGs in UCs (two-sided hypergeometric test with FDR correction). GO ( G ) and KEGG ( H ) analyses of downregulated DEGs in UCs (two-sided hypergeometric test with FDR correction). I , J Gene Set Enrichment Analysis (GSEA) of altered pathways in UCs (two-sided permutation test with 1000 permutations, with multiple testing corrected using the FDR). The exact p value for TLR signaling of UCs in panel I is 0.0009. K Expression of Toll-like receptor (TLR) subtypes in UCs from HIC bladders. mRNA ( L ) and protein ( M ) expression levels of TLR3 in isolated urothelium from control and HIC patients ( n = 7 control vs. 10 HIC; data show median (IQR); two-sided Mann–Whitney U test; ns not significant; Bar for panel M: 1 cm). N Immunostaining showing the distribution of TLR3 protein in the urothelium of patients with HIC ( n = 7 control vs. 10 HIC; one section and field per patient; Bar: 100 μm). IHC immunohistochemistry, HL Hunner lesions, U urothelium, LP lamina propria (blue line), M muscularis. Source data are provided as a Source Data file.

Article Snippet: To explore the role of Toll-like receptor 3 (TLR3), TCDCA-pretreated HUCs were treated with either a TLR3 agonist (Poly(I:C) Sodium Salt, CST, Cat. 61401; 5 μg/mL) or TLR3 siRNA (Toll-like Receptor 3 siRNA I, CST, Cat. 6236; 100 nM).

Techniques: RNA Sequencing, Expressing, Isolation, Control, MANN-WHITNEY, Immunostaining, Immunohistochemistry

Journal: Nature Communications

Article Title: Multi-omics analysis identifies a microbiota–bile acid–TLR signaling axis driving bladder injury in interstitial cystitis

doi: 10.1038/s41467-025-68060-1

Figure Lengend Snippet: A Experimental workflow of E. avium colonization in antibiotic-pretreated mice (Abx-mice, n = 6 per group). Created in BioRender. Chen, J. (2025) https://BioRender.com/3lccwo1 . B Increased abundance of E. avium confirmed by metagenomic sequencing ( n = 6 per group). C Evaluation of voiding behavior following E. avium transplantation ( n = 6 per group; one measurement per mouse). D Measurement of mechanical pain threshold post-transplantation ( n = 6 per group). E Representative histological analysis of bladder tissues after E. avium transplantation ( n = 6 per group; one section and field per mouse). F , G Quantification of blood and urinary bile acids using comprehensive targeted bile acid profiling ( n = 6 per group). H Cell viability of human urothelial cells (HUCs) following TCDCA or TUDCA treatment ( n = 3 independent experiments). I Expression of ZO-1, TNF-α, and TLR3 following TCDCA (200 µM) exposure ( n = 3 independent experiments). J Experimental workflow of intravesical instillation of TCDCA in rats ( n = 5 per group). Created in BioRender. Chen, J. (2025) https://BioRender.com/3lccwo1 . K Evaluation of voiding function after TCDCA instillation ( n = 5 per group; each rate measured once). L Assessment of mechanical pain threshold following TCDCA exposure ( n = 5 per group). M Representative histology of bladder tissues post-instillation ( n = 5 per group; one section per rat, one field quantified per section). For panels ( B – H , K , L ): data are presented as median (IQR). Statistical analysis was performed using the two-sided Mann–Whitney U test. IHC immunohistochemistry, Red arrow: urothelial thinning, detachment, and exposure, Blue line: LP lamina propria, U urothelium, M muscularis. Source data are provided as a Source Data file.

Article Snippet: To explore the role of Toll-like receptor 3 (TLR3), TCDCA-pretreated HUCs were treated with either a TLR3 agonist (Poly(I:C) Sodium Salt, CST, Cat. 61401; 5 μg/mL) or TLR3 siRNA (Toll-like Receptor 3 siRNA I, CST, Cat. 6236; 100 nM).

Techniques: Sequencing, Transplantation Assay, Expressing, MANN-WHITNEY, Immunohistochemistry

Journal: Nature Communications

Article Title: Multi-omics analysis identifies a microbiota–bile acid–TLR signaling axis driving bladder injury in interstitial cystitis

doi: 10.1038/s41467-025-68060-1

Figure Lengend Snippet: A , B Expression of tight junction protein ZO-1 and inflammatory marker TNF-α after TLR3 intervention in TCDCA-pretreated human urothelial cells (HUCs) ( n = 3 independent experiments). C Transepithelial resistance (TER) changes following TLR3 intervention in TCDCA-pretreated HUCs ( n = 3 independent experiments). D , E Expression of ZO-1 and TNF-α after pentosan polysulfate sodium (PPS) administration in TCDCA-pretreated HUCs ( n = 3 independent experiments). F TER changes following PPS intervention in TCDCA-pretreated HUCs ( n = 3 independent experiments). G Experimental workflow showing TLR3 inhibitor and PPS administration to rats following intravesical TCDCA instillation ( n = 5 per group). Created in BioRender. Chen, J. (2025) https://BioRender.com/3lccwo1 . H Assessment of voiding function (one measurement per rat) and pain threshold after TLR3 inhibition ( n = 5 per group). I Representative histological images of bladder tissues post-TLR3 inhibition ( n = 5 per group; one section and field per rat). For panels ( B , C , E , F , H ): data are presented as median (IQR). Statistical analysis was performed using the Kruskal–Wallis test. ns not significant, IHC immunohistochemistry, Red arrow: urothelial thinning, detachment, and exposure, Blue line: LP lamina propria, U urothelium, M muscularis. Source data are provided as a Source Data file.

Article Snippet: To explore the role of Toll-like receptor 3 (TLR3), TCDCA-pretreated HUCs were treated with either a TLR3 agonist (Poly(I:C) Sodium Salt, CST, Cat. 61401; 5 μg/mL) or TLR3 siRNA (Toll-like Receptor 3 siRNA I, CST, Cat. 6236; 100 nM).

Techniques: Expressing, Marker, Inhibition, Immunohistochemistry

Journal: bioRxiv

Article Title: Viral Microglia Reprogramming Clears Oligomeric Neurotoxic Debris

doi: 10.64898/2026.04.06.716590

Figure Lengend Snippet: Microglia phagocytic activity and antigen cross presentation triggered by treatment with mock, poly(I:C), recombinant IFN γ , and PVSRIPO. The phagocytosis/cross presentation assay template with microglia exposure to B16 OVA , described in , was repeated with juxtaposing PVSRIPO to mock, (transfected) poly(I:C), and recombinant IFNγ. Phagocytosis of CD11b + -bead-isolated, hCD155 -tg mouse microglia was determined by flow cytometry analyses of CT-label (A , C) ; antigen cross presentation was tested by flow cytometry for H2Kb:SIINFEKL complexes (B , C) ; cells were tested 0h, 24h, 48h and 72h post treatment; flow cytometry histograms for phagocytosis/cross presentation at 48h and 72h post treatment are shown (C) . (A , B) Data were analyzed by Shapiro-Wilk test and 2-way ANOVA with multiple comparisons.

Article Snippet: Microglia were plated at 70% confluency and infected with PVSRIPO (MOI 10) or mock (DMEM), recombinant mouse IFNγ (200 U/ml; R&D Systems, #485-MI), or poly(I:C) (10 μg/ml; Invivogen, high molecular weight polyinosine:polycytidylic acid; LyoVec TM complexed, #tlrl-piclv) and incubated with 200,000 UV-irradiated cells for the duration of the intervals shown in the figures.

Techniques: Activity Assay, Recombinant, Transfection, Isolation, Flow Cytometry