Journal: bioRxiv

Article Title: The Immunoregulatory Architecture of the Adult Oral Cavity

doi: 10.1101/2024.12.01.626279

Figure Lengend Snippet: (a) The common coordinate framework of integrated niches in the oral cavity analyzed, comprehending 13 macroniches in the oral cavity. ( b) Publicly available studies (blue) and newly generated single-cell RNA sequencing (scRNAseq) data (red) were integrated into the study. ( c) A niche-matched FFPE collection was curated for spatial evaluation, representing each niche in hematoxylin & eosin staining. ( d) Integration of multi-modal data to construct a harmonized cell atlas for spatial multiomics and single-cell transcriptomics analysis. The scRNAseq Atlas (gray) integrates both publicly available datasets and newly generated data. The Multiplex IF Atlas (red) employs a 40-antibody panel to capture cell types and neighborhood architectures, while the Multiplexed ISH Atlas (green) applies a 300-plex panel to map cell types and cell-cell communication networks within tissues. Integrated analyses (blue) focus on cell-cell communication. ( e) Tiered annotation across scRNAseq data: Tier (T) 1: structural cell types and immune cell types and T1: structural cells are categorized into epithelial, stromal, vascular, lymphatic, muscle, and neural crest; immune cells are characterized as myeloid and lymphoid. ( f) Sex distribution (male, female, N/a), age groups (18-39, 40-49, 50-59, 60-69), and race/ethnicity (White, Asian, Black, Indian, Latino/a, N/a) of patients included in the scRNAseq Atlas. ( g) The integrated OCF Atlas (Tier 1), with UMAP plots depicting cell clustering. The top UMAP plot illustrates clusters based on cell types, the bottom plot shows clustering according to niche. The dataset includes 246,102 cells from 70 samples, spanning 14 studies and representing 13 distinct niches (available at CELLxGENE). The color-coded legend indicates the different tissue types: glands (pink), mucosa (green), and pulp (blue). ( h) The heterogeneity of T1 annotated cell types across samples, each bar representing a different patient/sample. The samples are grouped by tissue niches, including anatomical regions such as the salivary glands, mucosa, and dental pulp. Each color in the stacked bars represents distinct cell types, categorized using the tiered annotation framework. (i) Receptor-ligand analysis using CellPhoneDB , showing communication between structural cells and immune cells. The heatmap highlights interaction, with the strongest communication indicated by (+). Notably, the highest interaction is observed from and between vascular cells and fibroblasts. ( j) Chord plot showing the receptor-ligand statistical differences in the top 50 interactions across all niches, where communication was inferred between structural and immune cell types. (k,l) Pathway analysis validated the observed trends for both outgoing (ligands) and incoming signaling patterns (receptors) using CellChat , showing the statistical differences between receptors and ligands. Abbreviations: FFPE = formalin-fixed paraffin embedded, OCF = Oral and Craniofacial, T1 = Tier one. Scale bars: Glands: 100 µm Mucosal 250 µm; pulp 50 µm (c).

Article Snippet: OCT blocks were cut into 10 mm sections and stained with hematoxylin and eosin (H&E, Morphisto) after PFA fixation.

Techniques: Generated, RNA Sequencing, Staining, Construct, Single-cell Transcriptomics, Multiplex Assay, Formalin-fixed Paraffin-Embedded