Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Molecular and Chromatin Accessibility Programs Underlying Epithelial Injury and Impaired Regeneration in Neonatal Necrotizing Enterocolitis

doi: 10.1016/j.jcmgh.2026.101730

Figure Lengend Snippet: MERFISH spatial maps illustrate the alteration of intestinal epithelial cells. ( A ) Schematic plot of MERFISH data processing. ( B ) Typical regions of anatomical annotation and predicted cell types from snRNA-seq. Gene expression was shown with marker genes measured by MERFISH and imputed by the iSpatial algorithm. ( C ) Barplot showing the cell proportions in the crypt and villus regions in MERFISH datasets. ( D ) GO enrichment analysis of genes upregulated and downregulated in NEC in the crypt and villus regions. ( E ) Spatial mapping of crypt-villus domains showing centroid positions and cell numbers in control and NEC. ( F ) Subtype proximity analysis comparing lineage relationships between control and NEC.

Article Snippet: MERFISH images were segmented using Vizgen’s post-processing tool (VPT) and with a deep learning algorithm, CellPose 2.0.

Techniques: Gene Expression, Marker, Control

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Molecular and Chromatin Accessibility Programs Underlying Epithelial Injury and Impaired Regeneration in Neonatal Necrotizing Enterocolitis

doi: 10.1016/j.jcmgh.2026.101730

Figure Lengend Snippet: Spatial transcriptomic profiling reveals disrupted tissue architecture and communication changes in NEC. ( A ) Volcano plots showing DEGs that are upregulated and downregulated in NEC within the crypt and ( B ) villus regions based on MERFISH datasets. ( C ) Spatial gradient comparison between control and NEC conditions. Scatter plot displaying gradient strength (deviance explained from GAMs) for each gene in control (x-axis) vs NEC (y-axis). Points above the diagonal ( dashed line ) indicate genes with stronger spatial gradients in NEC, whereas points below indicate weakened gradients. Genes are colored by category: gray (not significant), orange (disrupted in NEC), red (top 10 magnitude changes), and blue (marker genes of interest). Key genes are labeled, including differentiation markers (Vil1, Lgr4, Hnf4a, Rnf43), the stem cell marker Lgr6, proliferation markers (Birc5, Stmn1), Paneth cell marker (Spink4), and metabolic/transport genes showing the largest gradient changes (Dpyd, Immp2l, Pcsk5, Gm20275, Pard3b, Epb41l3, Ghr, Abcc2, Chka, Cubn). ( D ) Regional specificity of NEC transcriptional effects. Scatter plot comparing log2 FC (NEC vs control) in crypt (x-axis) vs villus (y-axis) compartments for all differentially expressed genes. Points are colored by significance category: red (significant in both regions; FDR <0.05), orange (crypt-specific), blue (villus-specific), and gray (not significant in either region). The diagonal dashed line indicates equal effects in both compartments. Points along the diagonal represent genes with concordant responses across tissue compartments, whereas off-diagonal points indicate region-specific or divergent responses. Top genes from each category are labeled. ( E ) Spatial expression patterns of top SVGs showing altered crypt-villus polarity. Representative genes are grouped by functional category: Vil1 (villin, enterocyte brush border marker), Lgr4 (differentiation/Wnt signaling), Spink4 (Paneth cell marker), Hnf4a (hepatocyte nuclear factor, master regulator of enterocyte differentiation), and Dpyd (dihydropyrimidine dehydrogenase, pyrimidine metabolism). Each panel shows expression in control ( top row ) and NEC ( bottom row ) tissue, with color intensity representing normalized expression level. ( F ) Spatial expression patterns of top region-specific DEGs. Sipa1l2 (signal-induced proliferation-associated 1 like 2) represents a villus-specific differentially expressed gene, whereas Trim30d (tripartite motif-containing 30D) represents a crypt-specific differentially expressed gene. ( G-I ) Cell–cell communication analysis by Cellchat illustrating differences in ( G ) secreted signaling, ( H ) ECM–receptor interactions, and ( I ) direct contact pathways between Control and NEC.

Article Snippet: MERFISH images were segmented using Vizgen’s post-processing tool (VPT) and with a deep learning algorithm, CellPose 2.0.

Techniques: Comparison, Control, Marker, Labeling, Expressing, Functional Assay