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

Journal: bioRxiv

Article Title: Developmental Plasticity and Stromal Co-option Shape a Pituitary Neuroendocrine Tumor Transcriptional Continuum

doi: 10.1101/2025.06.18.659743

Figure Lengend Snippet: ( a ) transcriptomic expression of DEGs of stromal nuclei in PitNETs relative to their counterpart nuclei in normal pituitary controls. ( b-l ) Volcano plots of all DEGs associated with each stromal cell identity, plotting the expression level of each gene in tumor stroma relative to normal pituitary stroma. ( m ) workflow of spatial transcriptomic analysis of tumor samples. Frozen pituitary adenomas from multiple patients were embedded into a single paraffin block after thawing and fixation, then mounted on a slide for GeoMx spatial transcriptomics. ( n ) Differential expression analysis comparing areas with high vascularization against those with low or no vascularization highlight 15 DEGs positively enriched for in vascularized areas. ( o ) An example of a tumor with four of the GeoMx ROI’s, represented as white circles. αSMA is stained for in red with Hoechst 33342 in teal and CD68 in green. P) The top ROI in panel C representing an area of low vascularization with and without the GeoMx segmentation for tumor segments. The tumor segment (grey) excludes αSMA positive pixels and CD68 positive pixels. Q) The ROI second from the top in panel C, representing an area of high vascularization with and without the GeoMx segmentation. The collected transcripts analyzed here are only from the tumor component, excluding the αSMA segment, which is highlighted in green. DEG: differentially expressed gene; NS: not significant; FC: fold-change.

Article Snippet: Deparaffinized slides underwent spatial whole-transcriptome profiling on the GeoMx Digital Spatial Profiler (DSP)(Bruker NanoStrings).

Techniques: Expressing, Blocking Assay, Quantitative Proteomics, Staining