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: 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: 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.

Techniques: Control

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: 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