Journal: Nature

Article Title: Netrin-1 blockade inhibits tumour growth and EMT features in endometrial cancer.

doi: 10.1038/s41586-023-06367-z

Figure Lengend Snippet: Fig. 4 | NP137 treatment inhibits EMT in patients with EC. a, Diagram showing EMT score calculated with Mak’s signature20 from RNA-seq of biopsies before (C1D1) and following two cycles of NP137 (C3D1) treatment (n = 12). Boxplots represent mean (25th–75th), whiskers range from minimum to maximum values and paired samples are identified on single-value representation; *P = 0.0161 by two-sided t-test. b, Swimmer plots showing individual evolution of EMT score for each patient; ΔEMT is the EMT score at C3D1 minus that at C1D1; ΔEMT < 0 means evolution towards epithelial phenotype (green) and >0 towards mesenchymal (red). c, Percentage of EpCAM high-expressing cells in C1D1 versus C3D1 biopsy samples as identified by IHC; *P = 0.0313 by Wilcoxon two-sided test (n = 6 patients). Boxplots represent mean (25th–75th), whiskers range from minimum to maximum values and paired samples are identified on single-value representation. d, Representative IHC of EpCAM in tumours in C1D1 and C3D1 for patient nos. 01-030, 01-035 and 01-040. Scale bar, 50 µm. e, Representative images of pancytokeratin (PanKRT) and vimentin (VIM) expression (colocalization of pancytokeratin (green) and vimentin (red) in the merged picture, right) in primary endometrial adenocarcinoma from patient no. 01-040 before and after NP137 treatment. Scale bars, 50 μm. Quantifications were performed on the full slides and similar results were observed for patient nos. 01-030 and 01-034. f, Analysis of tumour cell compartment in patient nos. 01-034 and 01-039 by Visium spatial gene expression. Violin plot of EMT UCell normalized enrichment score (NES) from tumoural histologically selected Visium spot between cells of C1D1 and C3D1 biopsy. ***P < 0.01 by Mann–Whitney two-sided test.

Article Snippet: Spatial transcriptomics using Visium FFPE technology FFPE tissue sections were placed on Visium slides and prepared according to the 10x Genomics protocols.

Techniques: RNA Sequencing, Expressing, Paraffin-embedded Immunohistochemistry, Gene Expression, MANN-WHITNEY

Journal: bioRxiv

Article Title: Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction

doi: 10.1101/2025.11.08.687255

Figure Lengend Snippet: A) Overview of iECM manufacturing, where porcine left ventricular myocardium is chopped into small pieces (1). The resulting ECM is washed with sodium dodecyl sulfate (SDS) (2) followed by rinsing, milled into a fine powder (3) and digested (4). High speed centrifugation is then performed to separate out large particulate matter (5) and is finally reconstituted for infusion for MI treatment (6). B) SDS-PAGE of iECM and collagen. C) Overall timeline for iECM bioactivity studies in acute MI. Simulated intracoronary infusion of iECM or saline was performed after MI and reperfusion. Hearts were harvested 1-, 3-, and 7-days post infusion. Samples were analyzed via single nucleus RNA sequencing (snRNAseq) and spatial transcriptomics.

Article Snippet: Odd slices were frozen in TissueTek OCT TM and sectioned into 10 μm thick slices and placed onto a 10X Visium Spatial Transcriptomics Slide or a regular histology slide.

Techniques: Centrifugation, SDS Page, Saline, RNA Sequencing

Journal: bioRxiv

Article Title: Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction

doi: 10.1101/2025.11.08.687255

Figure Lengend Snippet: A) 10X Visium sections indicate the spatial difference between iECM treated infarcts (red) to saline treated infarcts (cyan). B) Volcano plot displays differences between iECM and saline treated spatial transcriptomic sections at 1 day post infusion. C) Volcano plot displays differences between iECM and saline treated spatial transcriptomic sections at 3 days post infusion. D) Volcano plot displays differences between iECM and saline treated spatial transcriptomic sections at 7 days post infusion. E) Volcano plot displays differences between iECM at 1-day vs. 3-day post infusion. F) Volcano plot displays differences between iECM at 1-day vs. 7-day post infusion.

Article Snippet: Odd slices were frozen in TissueTek OCT TM and sectioned into 10 μm thick slices and placed onto a 10X Visium Spatial Transcriptomics Slide or a regular histology slide.

Techniques: Saline

Journal: Frontiers in Allergy

Article Title: MRGPRX2-expressing mast cells are increased in the GI tract of individuals with active inflammatory bowel disease and hereditary α-tryptasemia

doi: 10.3389/falgy.2025.1726096

Figure Lengend Snippet: Mast cells from IBD patients with HαT demonstrate increased MRGPRX2 expression. Spatial transcriptomics (10x Xenium) was performed on 8 descending colon biopsies from the University of Pennsylvania IBD biobank (4 HαT, 4 non-HαT; balanced UC/CD). (A) UMAP embedding showing major cellular populations. (B) Mast cells (MCs), defined as TPSAB1 + MS4A2 + KIT + , are more abundant in HαT samples. (C) Feature map of isolated MCs demonstrating increased MRGPRX2 transcript levels in HαT. (D) Digital droplet PCR (ddPCR) of representative tissues from the same cohort confirms upregulated MRGPRX2 expression in HαT vs. non-HαT. (E) Spatial transcriptomics images showing increased MRGPRX2 transcripts (red dots) in HαT-positive IBD tissue compared with non-HαT tissue. (F) ddPCR validation on matched samples (HαT: n = 4; non-HαT: n = 4) showing elevated MRGPRX2 mRNA. (G) Pseudobulk differential expression demonstrates significantly increased MRGPRX2 in HαT samples. For transcriptomic analyses, differential expression was calculated using DESeq2 with Benjamini–Hochberg FDR correction (FDR < 0.05). Effect sizes are shown as log₂ fold-change with 95% CIs. For ddPCR comparisons, Welch's t -test was used with Cohen's d reported.

Article Snippet: Spatial transcriptomics cohort , 8 , 4 , 4 , Severe IBD: UC ( n = 4), CD ( n = 4)—balanced across HαT and non-HαT , Descending colon , 10x Visium Spatial Transcriptomics + scRNA-binning , Selected from genotyped cohort; used to evaluate MC abundance and MRGPRX2 expression patterns..

Techniques: Expressing, Isolation, Biomarker Discovery, Quantitative Proteomics

Journal: Frontiers in Allergy

Article Title: MRGPRX2-expressing mast cells are increased in the GI tract of individuals with active inflammatory bowel disease and hereditary α-tryptasemia

doi: 10.3389/falgy.2025.1726096

Figure Lengend Snippet: Individuals with IBD and HαT exhibit increased SIGLEC8 expression in colon tissue. Spatial transcriptomics and pseudobulk analysis were performed on 8 representative descending colon samples (4 HαT, 4 non-HαT; balanced UC/CD). (A) Pseudobulk counts aggregated by sample show higher SIGLEC8 expression in the HαT group (Wilcoxon test; Cohen's d and 95% CI reported). (B) Volcano plot of DESeq2 pseudobulk differential expression analysis contrasting non-HαT (blue) and HαT (red) samples. Genes surpassing FDR < 0.05 (Benjamini–Hochberg correction) are highlighted. SIGLEC8 is prominently upregulated in HαT, consistent with findings from CyTOF and ddPCR validation.

Article Snippet: Spatial transcriptomics cohort , 8 , 4 , 4 , Severe IBD: UC ( n = 4), CD ( n = 4)—balanced across HαT and non-HαT , Descending colon , 10x Visium Spatial Transcriptomics + scRNA-binning , Selected from genotyped cohort; used to evaluate MC abundance and MRGPRX2 expression patterns..

Techniques: Expressing, Quantitative Proteomics, Biomarker Discovery