Journal: Journal of Nanobiotechnology

Article Title: PEGylated black-phosphorus nanosheet–alginate hydrogels enable local PRRX1 delivery to drive fibroblast reprogramming in intestinal fibrosis

doi: 10.1186/s12951-025-03896-9

Figure Lengend Snippet: Single-cell and fibroblast DEGs prioritise PRRX1 as a key regulator of intestinal fibrosis. ( A ) Volcano plot of differentially expressed genes (DEGs) in in silico–isolated fibroblasts comparing fibrotic versus non-fibrotic samples. Transcription factors (TFs) among the upregulated DEGs are highlighted. ( B ) Gene Ontology (GO) biological process enrichment analysis of fibroblast DEGs. ( C ) KEGG pathway enrichment analysis of fibroblast DEGs presented as a bubble plot with similar annotation. ( D ) Gene set enrichment analysis (GSEA) demonstrating positive enrichment of TGF-β signaling, Wnt signaling, and ECM–receptor interaction pathways in fibrotic fibroblasts. ( E ) Venn diagram intersecting upregulated TFs, high-stringency DEGs, and qPCR-screened candidates. ( F ) Immunoblot validation of GATA6 and PRRX1 protein abundance in independent human ileal specimens; GAPDH is used as a loading control. ( G ) qPCR validation of GATA6 and PRRX1 mRNA levels; bars show mean ± SD; two-sided unpaired Student’s t-test. ( H ) UMAP and feature plots showing the spatial distribution of GATA6 and PRRX1 expression across fibroblast populations. ( I ) Violin plots comparing GATA6 and PRRX1 expression between fibrotic and non-fibrotic fibroblasts at the single-cell level. Two-sided Wilcoxon tests with multiple-testing correction were used

Article Snippet: Complementary DNA (cDNA) synthesis was carried out from 1 μg of total RNA using a reverse transcription kit, yielding templates for subsequent qPCR analysis.Quantitative gene expression was performed on a LightCycler 480 system (Roche Diagnostics, Indianapolis, IN, USA).

Techniques: In Silico, Isolation, Western Blot, Biomarker Discovery, Quantitative Proteomics, Control, Expressing

Journal: Journal of Nanobiotechnology

Article Title: PEGylated black-phosphorus nanosheet–alginate hydrogels enable local PRRX1 delivery to drive fibroblast reprogramming in intestinal fibrosis

doi: 10.1186/s12951-025-03896-9

Figure Lengend Snippet: PRRX1 directly targets the FAP locus and activates profibrotic transcription in intestinal fibroblasts. ( A ) Venn diagram illustrating the intersection of three datasets in human intestinal fibroblasts: differentially expressed genes (DEGs) from PRRX1 overexpression (OE), DEGs from PRRX1 knockdown (KD), and genes associated with PRRX1 ChIP–seq peaks. ( B ) KEGG pathway enrichment analysis of PRRX1 ChIP–seq peak–associated genes. ( C ) Genome browser tracks showing PRRX1 ChIP–seq signal at the FAP and FN1 loci, demonstrating promoter-proximal occupancy. ( D ) ChIP–qPCR validation of PRRX1 binding at the FAP promoter. Bars show mean ± SD; two-sided unpaired Student’s t-test; P < 0.05. ( E ) Dual-luciferase reporter assays using wild-type (WT) and motif-disrupting mutant (Mut) FAP promoter constructs in fibroblasts transduced with either non-targeting (sgCon) or PRRX1-targeting sgRNAs (sgPRRX1). Bars show mean ± SD; two-sided unpaired Student’s t-test; P < 0.05. ( F ) UMAP feature plots of single-cell RNA-seq data showing increased FAP expression in fibroblasts from fibrotic compared to non-fibrotic ileal tissue

Article Snippet: Complementary DNA (cDNA) synthesis was carried out from 1 μg of total RNA using a reverse transcription kit, yielding templates for subsequent qPCR analysis.Quantitative gene expression was performed on a LightCycler 480 system (Roche Diagnostics, Indianapolis, IN, USA).

Techniques: Over Expression, Knockdown, ChIP-sequencing, ChIP-qPCR, Biomarker Discovery, Binding Assay, Luciferase, Mutagenesis, Construct, Transduction, RNA Sequencing, Expressing