Journal: Pathology, research and practice

Article Title: Spatial transcriptome analysis of lung squamous cell carcinoma arising from interstitial pneumonia provides insights into tumor heterogeneity.

doi: 10.1016/j.prp.2024.155805

Figure Lengend Snippet: Fig. 1. Spatial transcriptome analysis of lung squamous cell carcinoma (LUSC) tissue. (A) Schematic workflow of spatial transcriptome analysis. (B) Results of spatial transcriptome analysis of an LUSC tissue specimen from a patient with interstitial pneumonia. Hematoxylin and eosin staining (left), gene expression profiles of 2104 barcoded spots (middle), and Uniform Manifold Approximation and Projection (UMAP) visualization (right) are presented. Whole tissues were classified via graph-based clustering. (C) Histological image of cancerous areas, colored orange (left), and an image representing the two clusters identified as representative of LUSC (right). (D) The top seven upregulated pathways in cluster 2 compared to cluster 5 (left), and the top nine pathways upregulated in cluster 5 compared to cluster 2 (right). Only pathways where the false discovery rate (FDR) was < 1.0e-5 are presented.

Article Snippet: Among them, tissue from one patient was subjected to spatial transcriptome analysis (Visium; 10x Genomics, Pleasanton, CA, USA).

Techniques: Staining, Gene Expression

Journal: Pathology, research and practice

Article Title: Spatial transcriptome analysis of lung squamous cell carcinoma arising from interstitial pneumonia provides insights into tumor heterogeneity.

doi: 10.1016/j.prp.2024.155805

Figure Lengend Snippet: Fig. 6. Analysis of tumor-associated macrophages with spatial transcriptome data. (A) Clusters of LUSC (clusters 2, 5) and clusters histologically including inflammatory cells in the tumor microenvironment (clusters 3, 4, 7) in the transcriptome data. (B) Bubble heatmap showing the expression levels of the macrophage marker genes in clusters 3, 4, and 7. (C) Bubble heatmap showing the expression levels of the M2 macrophage marker genes in clusters 3, 4, and 7. (D) Bubble heatmap showing the expression levels of the vascular endothelial cell marker genes in clusters 3, 4, and 7.

Article Snippet: Among them, tissue from one patient was subjected to spatial transcriptome analysis (Visium; 10x Genomics, Pleasanton, CA, USA).

Techniques: Expressing, Marker

Journal: bioRxiv

Article Title: Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

doi: 10.1101/2025.09.09.675235

Figure Lengend Snippet: Healthy human skin scRNA-seq datasets were collected and curated. Datasets were divided into PSU-containing and PSU-free samples. PSU-containing datasets underwent standardized reanalysis and processing, and integration performance was benchmarked. The most suitable tool was used to integrate these datasets into the HSCA core, followed by cell type annotation. Through transfer learning, 21 additional PSU-free datasets were incorporated, resulting in the HSCA extended (160 subjects, 177 samples, 110 cell types, >800,000 cells). Gene marker signatures were validated and refined using Visium HD spatial transcriptomics. Downstream analyses included the identification of novel and rare cell types, functional enrichment, and cell–cell communication analysis.

Article Snippet: To validate the spatial organization of the PSU defined in our core atlas and to assess additional relevant cell types, we generated two 10X Visium HD spatial transcriptomics sections (8 μm spot diameter) derived from healthy facial skin of a 48-year-old White female donor ( ).

Techniques: Marker, Functional Assay

Journal: bioRxiv

Article Title: Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

doi: 10.1101/2025.09.09.675235

Figure Lengend Snippet: ( a , b ) Two 10X Genomics Visium HD spatial transcriptomic sections (8 µm spot diameter) derived from healthy facial skin of a 48-year-old White female donor (temporal region). Spots were annotated with marker gene expression, and the derived cell types are overlaid on the H&E sections. The bottom-right inset of each panel displays the number of detected genes per spot (maximum 3,683 in D1 and 3,199 in D2). Bar = 250 µm. Abbreviations: see Supplementary Table 3.

Article Snippet: To validate the spatial organization of the PSU defined in our core atlas and to assess additional relevant cell types, we generated two 10X Visium HD spatial transcriptomics sections (8 μm spot diameter) derived from healthy facial skin of a 48-year-old White female donor ( ).

Techniques: Derivative Assay, Marker, Gene Expression

Journal: bioRxiv

Article Title: Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

doi: 10.1101/2025.09.09.675235

Figure Lengend Snippet: (a) Illustrative schematic of hair bulb anatomy. (b) Visium HD spots corresponding to the hair bulb overlaid on the tissue section. ( c ) Spatial feature plot of Dermal papilla markers. ( d ) Dot plot showing marker gene expression across major bulb cell types. ( e ) Catagen hair follicle section (D2) highlighting cell clustering. ( f ) Violin plots of gene expression in the catagen follicle cluster, reflecting hair-cycle-specific transcriptional dynamics. ( g ) Heatmap of spatial ligand-receptor crosstalk between follicular compartments inferred by CellChat. Bar = 8 µm. Abbreviations: see Supplementary Table 3.

Article Snippet: To validate the spatial organization of the PSU defined in our core atlas and to assess additional relevant cell types, we generated two 10X Visium HD spatial transcriptomics sections (8 μm spot diameter) derived from healthy facial skin of a 48-year-old White female donor ( ).

Techniques: Marker, Gene Expression

Journal: bioRxiv

Article Title: Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

doi: 10.1101/2025.09.09.675235

Figure Lengend Snippet: ( a ) UMAP of the HSCA core restricted to 8,572 cells from lower follicular compartments. ( b ) RCTD deconvolution of Visium HD data (from ) using the HSCA core, showing concordant cell type gene signatures. ( c , d ) Violin plots of marker gene expression for the SHG in the HSCA core (c) and in Visium HD (d). ( e ) PHATE embedding of sebaceous gland cells illustrating differentiation trajectories. ( f ) Pie chart summarizing the relative abundance of sebocyte maturation stages in the HSCA core. ( g ) Pie chart showing dataset origin of sebaceous cells across maturation stages. ( h ) Violin plots of PTN and C1QTNF12 expression in sebaceous progenitors and the JZ in the HSCA core. ( i ) Independent spatial validation of PTN and C1QTNF12 expression in Visium HD sections. Abbreviations: see Supplementary Table 3.

Article Snippet: To validate the spatial organization of the PSU defined in our core atlas and to assess additional relevant cell types, we generated two 10X Visium HD spatial transcriptomics sections (8 μm spot diameter) derived from healthy facial skin of a 48-year-old White female donor ( ).

Techniques: Marker, Gene Expression, Expressing, Biomarker Discovery

Journal: bioRxiv

Article Title: Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

doi: 10.1101/2025.09.09.675235

Figure Lengend Snippet: (a) Feature plot of CCER2 expression highlighting the Merkel cell cluster in the HSCA core. (b) Gene signature of the cluster, including the characteristic KRT20 marker for Merkel cells. (c) Functional enrichment analysis of the Merkel cell gene signature, visualized as a dot plot. ( d , e ) Spatial visualization of CCER2 expression in the bulge region of hair follicles in Visium HD sections.

Article Snippet: To validate the spatial organization of the PSU defined in our core atlas and to assess additional relevant cell types, we generated two 10X Visium HD spatial transcriptomics sections (8 μm spot diameter) derived from healthy facial skin of a 48-year-old White female donor ( ).

Techniques: Expressing, Marker, Functional Assay