Journal: Materials Today Bio

Article Title: Spatial transcriptomic interrogation of the tumour-stroma boundary in a 3D engineered model of ameloblastoma

doi: 10.1016/j.mtbio.2023.100923

Figure Lengend Snippet: 3D model set-up for GeoMx DSP. (A) The 3D tumouroid set-up and (B) sectioning of the 3D tumouroids for GeoMx DSP. Diagrams were created using Smart Servier Medical Art.

Article Snippet: Individual genes were plotted using GraphPad Software (La Jolla, CA, USA) and their statistical tests were completed using the GeoMx Digital Spatial Profiler (DSP) Software.

Techniques:

Journal: Materials Today Bio

Article Title: Spatial transcriptomic interrogation of the tumour-stroma boundary in a 3D engineered model of ameloblastoma

doi: 10.1016/j.mtbio.2023.100923

Figure Lengend Snippet: Invasion of AM cells to different stroma. (A) Invasion of AM-1 cells within the 3D tumouorids shown from H&E-stained samples and GeoMx Profiler scanned samples, green = Pan Cytokeratin (PanCK), blue = DNA. scale bars = 250 μm and 1.5mm respectively. White lines = tumour mass and stroma boundary, orange lines = invasion of tumour cells to the surrounding stroma. (B) Invasion distance of AM-1 cells from the tumour mass to acellular, HGF, and hOB stroma at day 14. (C) Correlation heatmap of differentially expressed genes in invasion pathway in AM-1 tumouroids with acellular, HGF, and hOB. Heatmap presents log 2 change from Mean. T-test (non-paired), BH test correction, and tested by Factors. (D) Plot showing significant gene change. The inner ring represents the percentage of pathway genes significantly changed in the presence of each stroma type. The outer ring indicates the relative fold change in the gene expression observed for each gene in the subgroups. Gene counts of (E) MMP3, (F) BMP2, and (G) STAT3 in AM-1 tumouroids with acellular, HGF and hOB stroma. One-Way ANOVA, Dunnet's Post Hoc; p-values 0.05 < *, 0.005 < **, and 0.0005 < ***. Diagrams were created using Smart Servier Medical Art.

Article Snippet: Individual genes were plotted using GraphPad Software (La Jolla, CA, USA) and their statistical tests were completed using the GeoMx Digital Spatial Profiler (DSP) Software.

Techniques: Staining, Gene Expression

Journal: bioRxiv

Article Title: Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis

doi: 10.1101/2025.07.11.664335

Figure Lengend Snippet: (A) Proportional Venn diagram showing the overlap of DEGs between Visium (FindAllMarkers) and GeoMx datasets (all compartments). Fourteen DEGs were consistently differentially regulated in myocarditis relative to controls across both platforms. Corresponding fold changes for these overlapping genes are shown in the heatmap below. (B) Proportional Venn diagram comparing DEGs identified only in cardiomyocyte-stained segments (TNNI3⁺CD45⁻) and leukocyte depleted, cardiomyocyte-enriched genes (Visium), revealing ten shared DEGs between both datasets. Fold change values for these overlapping genes are shown in the heatmap. Color intensity in the heatmaps reflects the magnitude of absolute fold change values for each gene. Genes shown were filtered based on adjusted p-value of at least < 0.01 and exhibited consistent directionality of effect across platforms. Heatmap values for upregulated genes with FC higher than 4 were capped to this maximum value to aid visualization (see Supplementary Table 10 for values). (C) Chord plot illustrating inferred ligand– receptor interactions derived from differentially expressed genes in cardiomyocyte-enriched regions from both experimental techniques, focusing on overlapping antigen presentation–related genes, weighted by expression confidence. Arcs represent predicted interactions between ligands and immune receptors. Interactions were inferred using the OmniPath ligand–receptor database, and visualized using network-based filtering of curated, directional signaling interactions. Bolded genes represent overlapped genes present in OmniPath, between the two orthogonal experimental techniques.

Article Snippet: GeoMx Digital Spatial Profiling (DSP) was subsequently performed in the Spatial Cancer Research Immunobiology & Therapeutics (SCRIPT) Laboratory and the Johns Hopkins Experimental and Computational Genomics Core to validate transcriptional findings and enable spatially resolved whole-transcriptome gene expression profiling in cardiac tissue.

Techniques: Staining, Derivative Assay, Immunopeptidomics, Expressing

Journal: bioRxiv

Article Title: Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis

doi: 10.1101/2025.07.11.664335

Figure Lengend Snippet: (A) Representative immunohistochemical (IHC) micrograph of endomyocardial biopsy (EMBx) tissue highlighting cardiomyocytes (TNNI3⁺, yellow), leukocytes (CD45⁺, red), and nuclei (Syto83, green). (B) Representative segmentation overlay into three compartments: cardiomyocytes (TNNI3⁺CD45⁻, yellow), leukocytes (TNNI3⁻CD45⁺, red), and non-myocytes (TNNI3⁻CD45⁻, blue), for IHC-guided transcriptomics (GeoMx DSP). (C) Volcano plot showing all DEGs between controls and myocarditis in all segments, (D) TNNI3 + CD45 - cardiomyocytes, (E) TNNI3 - CD45 + leukocytes, and (F) TNNI3 - CD45 - non-myocytes/stromal cells. DEGs were computed using Q3 normalization followed by linear mixed-effects modeling with a FC threshold > 1.5 and an adjusted p < 0.05. For non-myocyte comparisons (F), unadjusted p -values were used due to lower segment counts and limited detection sensitivity.

Article Snippet: GeoMx Digital Spatial Profiling (DSP) was subsequently performed in the Spatial Cancer Research Immunobiology & Therapeutics (SCRIPT) Laboratory and the Johns Hopkins Experimental and Computational Genomics Core to validate transcriptional findings and enable spatially resolved whole-transcriptome gene expression profiling in cardiac tissue.

Techniques: Immunohistochemical staining