Journal: Scientific reports

Article Title: Cystic fibrosis-related diabetes is associated with reduced islet protein expression of GLP-1 receptor and perturbation of cell-specific transcriptional programs.

doi: 10.1038/s41598-024-76722-1

Figure Lengend Snippet: Figure 4. Spatial transcriptomics analysis of pancreas specimens from subjects in Cohort 2. (A) Representative images of islets immunostained for glucagon and insulin that were imaged on the GeoMx Digital Spatial Profiler. (B) Principal component analysis for the entire transcriptome of 7 (green) and 5 (pink) glucagon- positive regions of interest in control and CFRD pancreas respectively, and 7 (blue) and 9 (orange) insulin- positive regions of interest in control and CFRD pancreas respectively. Up- (red) and down- (blue) regulated genes in glucagon- (C) and insulin- (D) positive regions of interest in CFRD vs. control pancreas.

Article Snippet: Spatial transcriptomics analysis of pancreas specimens from subjects in Cohort 2. (A) Representative images of islets immunostained for glucagon and insulin that were imaged on the GeoMx Digital Spatial Profiler. (B) Principal component analysis for the entire transcriptome of 7 (green) and 5 (pink) glucagonpositive regions of interest in control and CFRD pancreas respectively, and 7 (blue) and 9 (orange) insulinpositive regions of interest in control and CFRD pancreas respectively.

Techniques: Control

Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial transcriptomics using GeoMx® DSP: slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .

Article Snippet: Spatial Transcriptomics GeoMx® DSP and CosMxTM SMI analyses of human coronary arteries with different stages of atherosclerosis progression provide state-of-the-art datasets to interrogate immune pathways involved in disease establishment and progression.

Techniques: Staining, Selection, cDNA Library Assay, Next-Generation Sequencing, Sequencing, Imaging, Marker

Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) In situ expression of ANXA2 in a representative severe lesion in GeoMx® (top panel) and CosMx ™ (bottom panel). Higher magnification boxes show ANXA2 expression in an ATLO. Figure was reused to create this panel. ( B ) NanoString-provided workflow for spatial deconvolution of GeoMx® data. ( C ) Proposed workflow for spatial deconvolution utilising a CosMx-generated single cell matrix (from the same tissue) to inform cell estimates. .

Article Snippet: Spatial Transcriptomics GeoMx® DSP and CosMxTM SMI analyses of human coronary arteries with different stages of atherosclerosis progression provide state-of-the-art datasets to interrogate immune pathways involved in disease establishment and progression.

Techniques: In Situ, Expressing, Generated

Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) Heatmap of spatial deconvolution estimates using the inbuilt GeoMx® reference matrix 'safeTME'. Scaled abundances are shown as a ratio to the maximum value are displayed across five tissue localisations (adventitia, plaque, negative control, muscle and infiltrated muscle layer). 'Subsets' correspond to ROIs segmented on the GeoMx® platform and are highlighted. Cell types present in the safeTME matrix are indicated as rows. ( B ) Heatmap of the CosMx™-derived cell signature matrix. Census-annotated cell populations from the CosMx™ are represented as columns with rows representing genes on the CosMx™ platform. Genes are scaled from red to white, with red indicating a higher expression. ( C ) Heatmap of the genes present in the GeoMx® dataset from the CosMx™-derived cell signature matrix. ( D ) Heatmap of spatial deconvolution estimates using the CosMx™-derived matrix. Cell types present in the CosMx™-matrix are indicated as rows.

Article Snippet: Spatial Transcriptomics GeoMx® DSP and CosMxTM SMI analyses of human coronary arteries with different stages of atherosclerosis progression provide state-of-the-art datasets to interrogate immune pathways involved in disease establishment and progression.

Techniques: Negative Control, Derivative Assay, 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) 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