Journal: bioRxiv

Article Title: Cellular and Immune Adaptations at the Maternal–Fetal Interface in Bats

doi: 10.1101/2025.05.15.654282

Figure Lengend Snippet: (A) Left, DotPlot of canonical trophoblast marker expression across TO-derived clusters. Right, FeaturePlots of GATA3 (top) and KRT7 (bottom) expression in TOs. Scales at right. (B) Confocal immunofluorescence staining for GATA3 (top, green) and KRT7(bottom, green) with actin (red), confirming widespread trophoblast marker expression throughout organoids. Nuclei are counterstained with DAPI (blue); right panels show individual grayscale channels. Scale bar, 50 μm. (C) UMAP showing final cell type annotations based on trajectory and root cluster analysis, including mononuclear trophoblasts (mTB), invasive trophoblasts (iTB1, iTB2), syncytiotrophoblasts (sTB1, sTB2), proliferative progenitors (TB-p1–3), and transitional populations (tTB1–3). Key at right. (D) Dot plots of canonical trophoblast markers (e.g., TEAD4 , MSX2 , KRT18 , MAL2 , HOPX ), validating cell type assignments. Scale at right. (E) Bar plot showing the number of differentially expressed genes (DEGs) following poly I:C treatment in human and Jfb TOs, using DESeq2 (log2FC > 1, adjusted p < 0.05). Upregulated genes are shown in red and downregulated are shown in blue. (F) Volcano plots of DEGs in human (left) and bat (right) TOs after poly I:C exposure. Significantly upregulated interferon-stimulated genes (ISGs) are labeled in red in human TOs, while Jfb TOs show minimal transcriptional changes. Non-ISG DEGs are shown in light blue and non-significant genes are shown in grey. (G) Lollipop plot showing poly I:C–induced log2 fold changes in selected interferon-stimulated genes (ISGs) and interferon lambda ( IFNL ) genes in human (red) and Jfb (yellow) TOs. The plot highlights consistently higher induction of antiviral genes in human cells compared to bat cells following stimulation. (H) Heatmap of top poly I:C–responsive genes (ranked by log2FC) showing markedly higher induction in human compared to Jfb TOs. Red indicates high indiction and grey/white indicates no or low induction. Scale at right. (I) Heatmap showing scaled average expression (Z-score) of ISGs and IFN genes expressed in mock and poly I:C-treated TOs, grouped by species. Bat TOs exhibit limited upregulation following stimulation. Scale at right. (J) Boxplot comparing ISG scores in human and Jfb TOs under mock and poly I:C-treated conditions. Jfb TOs show elevated ISG expression at baseline (mock), whereas human TOs exhibit a greater dynamic induction following poly I:C treatment. (K) Boxplots showing expression of representative ISGs ( IRF35 , IFIT3 ) across species and conditions. (L) Heatmap showing scaled average expression (Z-score) of key innate immune signaling genes including Toll-like receptors (TLRs), RIG-I–like receptors (RLRs), NOD-like receptors (NLRs), adaptor proteins, inflammasome components, and downstream transcription factors across mock-treated Jfb and human TOs. Genes are grouped by functional category, with color-coded annotations at right. Expression values were derived from gene reads. (M) Boxplots comparing baseline and induced expression of select PRRs ( TLR3 , TLR2 , NOD1 ), further supporting attenuated innate immune sensing in bat TOs.

Article Snippet: The following primary antibodies were used: KRT18 (1:100; Abcam, ab668), pan-KRT (1:100; Abcam, ab308262), KRT7 (1:200; Abcam, ab181598), GATA3 (CST, 5852), E-cadherin (CDH1, Invitrogen, PA5-85088).

Techniques: Marker, Expressing, Derivative Assay, Immunofluorescence, Staining, Labeling, Functional Assay

Journal: Cell Genomics

Article Title: Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model

doi: 10.1016/j.xgen.2025.100821

Figure Lengend Snippet:

Article Snippet: Rabbit monoclonal anti-GATA3 , Cell Signaling , 5852T.

Techniques: Immunofluorescence, Recombinant, Ligation, Gel Extraction, Polymerase Chain Reaction, Hybridization, Cloning, Luciferase, CRISPR, Plasmid Preparation, Software, Sonication, Microscopy