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: Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis

doi: 10.1101/2022.11.14.516398

Figure Lengend Snippet: (A) Representative mIHC images of P + CoV19 CHI cases highlighting extent of fibrin deposition (left panel) and immune cell composition and location (right panel). (B) tSNE plot showing cell metaclusters identified by quantification of multiplex immunohistochemistry (mIHC) images of placentas from infected mothers and controls. (C and D) Principal Component Analysis (PCA) of cellular abundance of mIHC data (C) and bulk RNAseq transcriptomic reads (D). (E) Combined and normalised PCA loadings of combined mIHC and bulk RNAseq showing relative contribution of immunological and molecular features to P + CoV19 CHI disease uniqueness. (F) Epithelial cell abundance and fibrin deposition quantification across disease entities. (G) Immune cell abundance in COVID-19 placentitis, control CHI/VUE cases and normal placenta. (H) Functional marker expression on CD4+ T cells (top heatmap) and CD8+ T cells (bottom heatmap) across disease states. See also Figure S3.

Article Snippet: Next, we unbiasedly clustered the GeoMx transcriptomic data from trophoblast ROIs of all CHI cases arising in SARS-CoV-2 infected mothers, regardless of virus status (P +/ - Cov19 CHI ; ).

Techniques: Multiplex Assay, Immunohistochemistry, Infection, Control, Functional Assay, Marker, Expressing

Journal: bioRxiv

Article Title: Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis

doi: 10.1101/2022.11.14.516398

Figure Lengend Snippet: (A) Gene Set Enrichment Analysis (GSEA) with hallmark gene sets of bulk RNAseq P + CoV19 CHI vs. rest. (B) Heatmap showing expression of interferon signature genes (type I & II) by bulk RNAseq of placental tissue across all disease states. (C) Bulk RNAseq analysis showing genes differentially expressed between virus positive and negative placentas with CHI pathology from SARS-CoV-2 infected mothers. (D) SARS-CoV-2 viral restriction factor gene set expression by bulk RNAseq across disease states. (E) Interferon Alpha response gene set expression across disease states by bulk RNAseq (left panel) and by villous stroma (VS) NanoString GeoMx DSP compartment with split in P+CoV19CHI cases into VS compartments adjacent to (Virus Hi ) and not adjacent to (Virus Lo ) SARS-CoV-2 infected trophoblasts (right panel). (F) Illustration of relationship between virus infection and interferon expression. See also Figure S5.

Article Snippet: Next, we unbiasedly clustered the GeoMx transcriptomic data from trophoblast ROIs of all CHI cases arising in SARS-CoV-2 infected mothers, regardless of virus status (P +/ - Cov19 CHI ; ).

Techniques: Expressing, Virus, Infection

Journal: bioRxiv

Article Title: Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis

doi: 10.1101/2022.11.14.516398

Figure Lengend Snippet: (A) Normalised abundance of various cell types with increasing distance from SARS-CoV-2 infected trophoblasts. (B) Schematic of virus microenvironment calculation. (C) Representative mIHC images highlighting PDL1 expression in virus high and absence in virus low regions of a SARS-CoV-2 infected placenta. (D) Differential gene expression analysis of SARS-CoV-2 positive vs. negative GeoMx trophoblast compartments. (E) Unbiased clustering and PCA visualisation of trophoblast regions from P+CoV19CHI placentas. (F) Illustration of immune evasion mechanisms operating in SARS-CoV-2 infected placentas. See also Figure S6.

Article Snippet: Next, we unbiasedly clustered the GeoMx transcriptomic data from trophoblast ROIs of all CHI cases arising in SARS-CoV-2 infected mothers, regardless of virus status (P +/ - Cov19 CHI ; ).

Techniques: Infection, Virus, Expressing, Gene Expression

Journal: Nature Communications

Article Title: Isotope-encoded spatial biology identifies plaque-age-dependent maturation and synaptic loss in an Alzheimer’s disease mouse model

doi: 10.1038/s41467-025-63328-y

Figure Lengend Snippet: A PULSE-CHASE iSILK paradigm. Experimental Design 1: PULSE period ( 15 N diet) between 6-10 months of age. Experimental Design 2: PULSE period between 6-10 months of age, CHASE period ( 14 N diet) between 10–18 months of age. Resulting Aβ1-42 MALDI MS isotopologue pattern that is right-shifted (Δm) due to increasing 15 N incorporation. B Representative images of plaque load from GeoMx whole slide scans, repeated on four independent whole-brain slices at 18-months and three at 10-months. C MALDI MSI single ion image of Aβ1-42 in cortex section. D Schematic overview of the correlative hyperspectral imaging and MALDI MSI experiment. 15 N enrichment (nitrogen index) was calculated as the AUC ratio of the 4th to 3rd peak in the Aβ1-42 isotopologue pattern. Higher values indicate greater 15 N incorporation. E Schematic overview of the correlative spatial transcriptomics (GeoMx) and MALDI MSI experiment. Stable 15 N enrichments (nitrogen index) corresponding to plaque age was calculated by extracting the FWHM of the Aβ1-42 peak, where a broader peak indicates increased 15 N incorporation and higher age. F Schematic overview of the validation experiment. Plaque morphology was evaluated by LCO hyperspectral imaging. IHC of selected proteins were correlated with plaque age, as evaluated by hyperspectral imaging. G Representative spectra from MALDI MSI showing the 14 N and 15 N-enriched Aβ1-42 m/z peak. H Aβ1-42 mass analysis comparing the plaque center (Cen) vs. the periphery (Peri) in 10-month-old mice ( p = 0.00017), ( I ) in 18-month-old mice ( p = 0.00000077), and ( J ) differences between cortex and hippocampus ( p = 0.022). H , I Linear Mixed Model accounting for across animals and repeated measures, point color indicates animal, 15 replicates over n = 3 m mice and 22 replicates over n = 4 m mice, respectively. J Two-sided Paired t-test, 22 replicates over n = 4 m mice, data presented as mean ± SEM. K Representative MALDI MSI image of 15 N and 14 N enriched Aβ1-42 distribution in plaques in 18-month-old mice. Parts of the figure created in BioRender. Szadziewska, A. ( https://BioRender.com/4qpojxz ) Image in ( E ) provided by Bruker Spatial Biology. Significance levels: *** P < 0.001, ** P < 0.01; * P < 0.05. Source data are provided as a Source Data file. FWHM full width at half maximum, RP reflector mode, LP linear mode.

Article Snippet: The spatial transcriptomics platform GeoMx® Digital Spatial Profiler was selected over other sequencing techniques due to its ability to target plaque-specific gene expression changes, offering a more spatially resolved technique for AD pathology-associated alterations compared to the more commonly used RNA sequencing methods .

Techniques: Pulse Chase, Imaging, Biomarker Discovery

Journal: bioRxiv

Article Title: CHCHD2 mutant mice display mitochondrial protein accumulation and disrupted energy metabolism

doi: 10.1101/2024.08.30.610586

Figure Lengend Snippet: (A) Transcriptomic levels of CHCHD2 and CHCHD10 in DA neurons of SND (dorsal tier of substantia nigra, orange) and SNV (ventral, blue) measured with GeoMx WTA show significant downregulation of CHCHD2 in the SNV of ILB and ePD cases. Data represent mean ± SEM. Brown-Forsythe and Welch ANOVA tests were applied for data covariates with age, sex, and post-mortem delay. *** P < 0.001. NC, normalized counts; Ct, control; ILBD, incidental Lewy body disease; ePD, PD with early Braak stage pathology; lPD, PD with late Braak stage pathology. (B) Moderate positive linear associations were revealed between expression levels of either CHCHD2 or CHCHD10 with SNCA in the SN by Spearman correlation. (C) CHCHD2 localization in control and PD SN DA neurons and (E) orthogonal views of the relative location of CHCHD2 in different staged αSyn aggregations. (D) CHCHD10 localization in control and PD SN DA neurons, and (F) orthogonal views of the relative location of CHCHD10 in different staged αSyn aggregations. Scale bars represent 50 μm in (C, D), and 20 μm in (E, F). (G) Representative images and quantification of TH (green) and either total α-synuclein (Syn1) or phosphorylated synuclein, P-syn (PS129, red) immunoreactivity in SN and VTA at 63X magnification in midbrain sections of WT, HET and HOM mice at 16 months. Syn1 and P-syn immunoreactivities increased in midbrain DA neurons of HOM mice by two-way ANOVA with Tukey’s post hoc test. Data represent mean ± SEM. * P < 0.05. N = 4 sections/mouse, 4 mice/genotype. Scale bar indicates 10 μm. (H) Representative images and quantifications of Syn1 (top) and P-syn (PS129, bottom), immunoreactivity in striatal sections of mice at 16 months. Syn1 and P-Syn areas in dorsal and ventral striatum are indicated with dotted lines. Significant increases in both Syn1 and p-Syn immunoreactivity were observed in HOM mice compared with WT by two-way ANOVA with Tukey’s post hoc test. Data represent mean ± SEM. * P < 0.05, ** P < 0.01. N = 4 sections/mouse, 4 mice/genotype. Scale bar indicates 300 μm.

Article Snippet: Sections were mounted on Fisher Scientific (12-550-15) for GeoMx Human Whole Transcriptome Atlas (WTA, nanostring) according to the manufacturer’s instruction or on Series 2 adhesive microscope slides (Trajan Scientific Medical, AU) for immunofluorescence.

Techniques: Control, Expressing