Journal: bioRxiv

Article Title: The spatial landscape of infectious mononucleosis tonsils

doi: 10.1101/2025.10.09.681345

Figure Lengend Snippet: a. Schematic overview of the multiomic spatial single-cell workflow. b. OPAL mIF staining of developed and validated EBV-panel showing co-expression of EBV viral latent antigens EBNA1, EBNA2, LMP1 & LMP2A as well as lytic protein BZLF1. c. PhenoCycler-FUSION mIF staining of full-face IM tonsil tissue showing human CD20 (red), pan-cytokeratin (yellow), CD3e (blue), CD68 (green) and the EBV viral protein LMP1 (purple). d. Uniform manifold approximation and projection (UMAP) of all 51,895 cells captured by CosMx spatial transcriptomics (ST), coloured and labelled by the 9 populations identified from Louvain single-cell clustering. e. Dot plot showing the average gene expression of the top differentially expressed genes per cluster, canonical lineage markers as well as EBV genes for the CosMx ST annotated populations. f. UMAP of re-clustered epithelial cells from CosMx ST showing columnar (basal), polygonal (intermediate) and squamous (superficial) phenotypes. g. Differential gene expression analysis of EBV+ vs. EBV-epithelial cells highlighting EBV EBERs and IgG expression h. Representative images of EBV protein expression in the PF mIF data showing co-expression with pan-cytokeratin.

Article Snippet: & G.S.T. acquired the CosMx spatial transcriptomics data; C.I.L.

Techniques: Staining, Expressing, Gene Expression

Journal: bioRxiv

Article Title: Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

doi: 10.1101/2025.09.26.678707

Figure Lengend Snippet: a. Human kidney samples from healthy reference tissues (HRT), as well as disease tissues associated with AKI and CKD, were processed using one or more assays. The strategy included deep single cell and spatial phenotyping, validations with orthogonal technologies and using analytical methods to delineate spatial contexts of recovery and failed repair. This included pathological staining and assessment, 10X Genomics single nucleus / cell RNA-seq and Multiome (RNA + ATAC), 10X Genomics Visium, Slide-seq2, 10X Xenium, Nanostring CosMx and spatial metabolomics. The atlas demonstrates clinical impact and utility to inform on pathogenetic mechanisms, druggable targets, non-invasive markers that predict clinical outcomes from early injury signatures and the underlying regulatory networks that contribute to AKI progression. Abbreviations: Sex (M = male, F = Female, Unk = unknown); Race (W = white, B = Black, O = other); Age range associated with decade-binned age values per participant. Asterix (other reference tissues including Diabetes Mellitus – Resilient (DM-R) biopsies and reference samples with unknown clinical status. b. Pathways predicted for each disease group in each FTU were grouped into 14 whole cell functions, 8 of which are shown. Heatmaps show the sum of the -log10(p-values) of all pathways annotated to the same whole cell function. ATL/DTL: ascending/descending thin limb, CD: collecting duct, CNT: connecting tubule, DCT: distal convoluted tubule, EC: endothelial cell, FIB: fibroblast, PT: proximal tubule, S: segment, TAL: thick ascending limb, POD: podocyte, PEC: parietal epithelial cell. c. Map of novel druggable targets specific to cell states. Created in BioRender. Jain, S. (2025) https://BioRender.com/rfy8fos . Source data provided.

Article Snippet: CosMx spatial transcriptomics assay was performed on FFPE biopsy tissue sections (5 um) from patients with diabetic nephropathy (n = 3) on a CosMx SMI system under the technology access program by Nanostring technologies.

Techniques: Staining, RNA Sequencing, Cell Function Assay

Journal: bioRxiv

Article Title: Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

doi: 10.1101/2025.09.26.678707

Figure Lengend Snippet: a . Slide-seq2 cell types grouped by structure and spatially localized along the cortico-medullary axis. b . Left, a single Slide-seq HRT puck showing renal corpuscle associated cell types. Right, enlarged area of that shown in the left panel for the same cell types and highlighting correct spatial localization of rare MD and REN cells. Tissue pucks are 3mm in diameter. c . Slide-seq2 tissue pucks (halved) associated with HRT (left) and CKD (right), showing enriched mapping for adaptive state epithelial cells (aPT, aTAL, failed repair PT and TAL epithelial cells or frEpi) as well as general fibroblast, lymphoid and myeloid cells in the diseased tissue. d . CosMx cell types grouped by structure and spatially localized to different cortico-medullary fields of view (FOV) for three different diabetic kidney disease (DKD) biopsies. e . Cortical FOV indicated in (d) showing spatial mapping of cell type specific transcripts. Renal corpuscles (RC) are indicated. f . Same FOV as in ( e ) showing protein immunofluorescent staining for epithelial pan cytokeratin (panCK) that highlighted collecting ducts, lymphoid CD45 and T-cell CD3 antibodies. Minimal staining of the latter two is consistent with the low immune cell infiltration found within this FOV. g . Medullary FOV indicated in ( d ) showing spatial mapping of cell type specific transcripts. h . Immunofluorescence staining as in ( f ) and highlighting medullary collecting ducts. i . Enlarged area shown in ( d ) highlighting RC cell types. j . Enlarged area shown in ( d ) highlighting medullary cell types.

Article Snippet: CosMx spatial transcriptomics assay was performed on FFPE biopsy tissue sections (5 um) from patients with diabetic nephropathy (n = 3) on a CosMx SMI system under the technology access program by Nanostring technologies.

Techniques: Staining, Immunofluorescence

Journal: bioRxiv

Article Title: Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

doi: 10.1101/2025.09.26.678707

Figure Lengend Snippet: a-e . CosMx cortical FOV indicated in . a . Spatial mapping of specific cell types and structures. Renal corpuscles (RC) are indicated. b . Protein immunofluorescent staining for epithelial pan cytokeratin (panCK) highlighted collecting ducts and distal tubules, lymphoid CD45 and T-cell CD3. c . Spatial mapping of fibroblast subtypes. d . Spatial mapping of immune subtypes. e . Corresponding histology image. f . Slide-seq2 subset region of tissue in Figure 2e showing TF GRN target gene set expression scores within the associated broad cell types. g . Slide-seq2 tissue sub-region of that found in Figure 2ed showing TF GRN target gene set expression scores within macrophage cell types. h. Heatmap of enrichment scores for fibroblast subtype neighbors (Slide-seq2 cortical or cortico-medullary tissues) that show significant (p < 0.01) difference in enrichment scores between HRT and diseased (CKD/AKI) tissues. i. Visium ST characterization of pvFIB niches with cell type distribution, transcription factor network activities, and association with clinical status, with log odds ratio and confidence interval. j. Example of pvMYOF niche 2 mapped to FFPE histology. Source data provided.

Article Snippet: CosMx spatial transcriptomics assay was performed on FFPE biopsy tissue sections (5 um) from patients with diabetic nephropathy (n = 3) on a CosMx SMI system under the technology access program by Nanostring technologies.

Techniques: Staining, Expressing

Journal: bioRxiv

Article Title: Comparative Analysis of Neonatal Hypomyelination Models Using Spatial Transcriptomics

doi: 10.1101/2025.06.23.661209

Figure Lengend Snippet: Macromolecular proton fraction (MPF) maps in control (A) , intermittent hypoxia (B) and hypoxia-ischemia (C) mouse pups at P20. Red arrows indicate internal capsule ipsi-and contralateral to H-I lesion. Pseudo color bar indicates MPF values in %. Scale bar 1 mm. Presence and extent of H-I injury was evaluated by hyperintensity on T2-weighted image ( D , black arrow) at P12 pups, 72 hours after H-I. E . Paraffin sections from the corresponding MPF maps with selected regions of interest for special transcriptomics analysis. F . Decrease of MPF in both hypoxia models at P20, one-way ANOVA with post-hoc pairwise comparisons, *- p<0.06, **-p<0.01.

Article Snippet: Leveraging the power of single-cell spatial transcriptomics (CosMx technology), this study investigated interactions between neuroinflammatory cells (astrocytes and microglia), excitatory and inhibitory neurons, and oligodendrocyte populations.

Techniques: Control