Single-nucleus RNA sequencing resolves microenvironmental dynamics in brown/beige adipose tissue after bariatric surgery

Figures

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  Fig. 1. Single-nucleus atlas uncovers postoperative cellular dynamics in adipose tissue. (A) UMAP projection of nuclei, with colors representing different samples (Je, n = 10111; Ji, n = 10027; Se, n = 8838; Si, n = 5796); (B) UMAP projection of nuclei, with colors representing different cell types (AP, n = 10363; B, n = 2303; mDC, n = 204; EC, n = 4833; FB, n = 4018; MP, n = 3550; Mono, n = 110; muscle, n = 265; NK, n = 472; FBO, n = 4858; SMC, n = 835; T, n = 1930; Unknown, n = 1030); (C) Bubble plot visualization of cell type-specific marker gene expression. Darker shades denote higher average expression levels within each annotated cell type, while bubble size reflects the percentage of cells in that subtype expressing the given marker gene; (D) Stacked-bar comparison of cell-type proportions across samples, with colors coding for the annotated cell types; (E) Brown adipose tissue pathway activity. Top 5 |logFC| pathways are shown; dot size = fraction of cells with high activity, color intensity = mean activity level; (F) Beige adipose tissue pathway activity. Top 5 |logFC| pathways are shown

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  Fig. 2. Adipocyte-centric interactions after surgery (A, B) Differential signaling networks centred on AP cells. Left: AP as the signaling cell; right: AP as the target cell. Red edges = up-regulated interactions in Se vs. Je; blue edges = down-regulated interactions in Se vs. Je; edge width = magnitude of change, Brown adipose tissue (A), Beige adipose tissue (B); (C, D) Top-ranked receptor–ligand pairs identified by cell communication analysis. Brown adipose tissue (C), Beige adipose tissue (D)

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  Fig. 3. Postoperative rewiring of IGF/VEGF signaling heat-maps of pathway-activity scores (Je vs Se) for (A) Brown-adipose FBO, (B) Beige-adipose FBO, (C) Brown-adipose EC, and (D) Beige-adipose EC. Red = higher average activity; blue = lower activity

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  Fig. 4. Pseudotemporal reconstruction of the AP-to-FBO transition in brown adipose tissue (A) UMAP of AP and FBO cells colored by sample origin; (B) Same embedding colored by subcluster; (C) Subcluster identity annotation for (B); (D) Monocle2 trajectory branching across different conditions with pseudotime progression from AP (root) to FBO (terminus); (E) Trajectory plot colored by cell type illustrating the continuum of transition

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  Fig. 5. Pseudotemporal ordering of ap subcluster transitions (A) Monocle2 trajectory of brown-adipose ap cells colored by subcluster; node 3 marks the root; (B) Branch-specific gene modules. Pre-branch: cells mapping from node 3 toward pseudotime 0 (AP0, AP3, AP4, AP5, AP7). Fate 1: cells extending from node 3 to lower-ID branches (AP1, AP2). Fate 2: cells extending from node 3 to higher-ID branches (AP6). (AP0, n = 1907; AP1, n = 1039; AP2, n = 1015; AP3, n = 561; AP4, n = 91; AP5, n = 57; AP6, n = 45; AP7, n = 42)

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  Fig. 6. Nucb2 as a potential AP-to-FBO transition gene (A) Volcano plot of genes differentially expressed in AP6 versus all other ap subclusters (brown adipose tissue); (B) Candidate transition genes enriched in AP6; (C) Nucb2 expression distribution across AP subclusters; (D) Relative abundance of FBO subsets defined by Nucb2/Igf1r co-expression: Nucb2+ Igf1r−, Nucb2+ Igf1r+, Nucb2− Igf1r−, Nucb2− Igf1r+; (E) Same as (D) for EC populations; (F) Correlation between Nucb2 and Igf1r gene levels within FBO; (G) Correlation between Nucb2 and vegfa gene levels within ec

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  Fig. 7. Cross-species validation of FBO/EC markers and pathway activity after weight-loss surgery. (A, B) immunofluorescence staining of brown adipose tissue before and after surgery: NUCB2 and IGF1R co-localization in FBO (A); EMCN and IGF1R co-localization in EC (B); (C–H) human adipose tissue snRNA-seq: UMAP of nuclei colored by major cell type (c); ADIPOQ expression overlaid on the UMAP (D); VEGF-pathway activity scores: obese vs weight-loss (E); NUCB2 expression: obese vs weight-loss (F); UMAP of adipocyte subclusters (G); NUCB2 levels across adipocyte subclusters: obese vs weight-loss (H). ****p < 0.0001 using the two-tailed unpaired t-test