Journal: bioRxiv

Article Title: Scalable longitudinal imaging and transcriptomics of cells in dynamic enclosures

doi: 10.64898/2026.05.05.723030

Figure Lengend Snippet: A: UMAP based on transcriptomic data from primary human preadipocytes differentiated for seven days on a fibronectin-coated flow cell. The colors correspond to different clusters based on transcriptomic analysis. B: Transcriptomic UMAP colored by the lipid accumulation score, defined as the ratio between the BODIPY stain and the nuclear stain in each CCE. The insets show examples of cells that are very close in gene expression space but differ in their lipid content. C: violin plots depicting the distribution of lipid accumulation scores (y axis) across the transcriptomic clusters (x axis). D: actual (x axis) vs predicted (y axis) lipid accumulation scores from the elastic net model. The plot is for the held-out test set (20% of the total data). E: Euler diagram showing the overlap between top-20 differentially expressed genes between transcriptomic clusters (blue) and model-selected predictors of lipid accumulation (pink). F: average Log2 fold-change between clusters (x axis) vs absolute model coefficient (y axis) for the genes selected by the model. The red color indicates genes that are among the top-20 differentially expressed genes between transcriptomic clusters. G: Gene expression UMAP colored by the top-3 positive predictors identified by the model, showing that the expression values of these genes are uniformly distributed across the UMAP based on global transcriptomic differences. H: UMAP based on transcriptomic data for BV2 mouse microglial cells. The colors correspond to different clusters based on transcriptomic analysis. I: transcriptomic UMAP colored by phagocytic activity as measured by pHrodo™ intensity after four hours. J: UMAP based on DINOv2 features, colored by phagocytic activity showing a greater degree of separation between high vs low phagocytic scores, compared to the transcriptomic UMAP in panel H. K: violin plots depicting the distribution of phagocytic scores (y axis) across the transcriptomic clusters (x axis). L: R 2 performance of elastic net models trained on expression-only features, DINOv2-only features or a combination of the two (x axis). The data refers to the held-out test set (20% of the total data). M: actual (x axis) vs predicted (y axis) phagocytic scores from the elastic net model using the combined expression and DINOv2 features. The plot is for the held-out test set (20% of the total data). N: Euler plot showing the overlap between top-20 differentially expressed genes between transcriptomic clusters (blue) and model-selected predictors of phagocytic activity (pink). O: average Log2 fold-change between clusters (x axis) vs absolute models coefficient (y axis) for the genes selected by the expression-only model. The red color indicates genes that are among the top-20 differentially expressed genes between transcriptomic clusters. P: ridge plots displaying the expression level (x axis) of Gpnmb and Clec4e across transcriptomic clusters (x axis). These two genes are among the top positive predictors for the gene expression-based model and have clear mechanistic evidence linking them to the phagocytosis process. However, their expression is very similar across all the transcriptomic clusters.

Article Snippet: Adipogenesis was induced using Adipocytes Differentiation Toolkit for Adipose Derived MSCs and Preadipocytes (ATCC, # PCS-500-050).

Techniques: Staining, Gene Expression, Expressing, Activity Assay

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Critical role of SRF in regulating actin cytoskeletal gene expression in adipocytes in vitro . (A) Motif identified by MEME that is enriched in H3K27ac peaks within the HFD-associated super-enhancer regions. (B) Alignment of the SRF binding motif identified de novo from SRF ChIP-Seq in TGFβ1-treated 3T3L1 adipocytes, compared to the canonical SRF motif from the HOMER database. (C) Pathway analysis of genes associated with SRF ChIP-seq peaks. (D) Genomic tracks showing SRF and H3K27ac ChIP-seq signals at the Acta2 locus, highlighting SRF binding induced by TGFβ1 treatment (indicated by a black arrow) within an adipocyte super-enhancer region. (E–G) In vitro loss- and gain-of function experiments in 3T3-L1 adipocytes. Gene expression analysis of cytoskeletal genes following (E) Srf knockdown ( shSrf , n = 3 per condition, total N = 6) and (F) overexpression ( Srf OE, n = 3 per condition, total N = 6). (G) Western blot analysis of SRF and ACTA2 protein levels upon Srf overexpression ( Srf OE, n = 2 per condition, total N = 4). A two-tailed Student’s t -test was used for statistical analysis. * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: For generation of SRF knockout mice specific to beige and brown adipocytes (SRF-BKO), Srf -flox mice were crossed with Ucp1 -Cre mice (Jackson Laboratory, 024670).

Techniques: Gene Expression, In Vitro, Binding Assay, ChIP-sequencing, Knockdown, Over Expression, Western Blot, Two Tailed Test

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Role of SRF in actin filament structure and cellular expansion in adipocytes in vivo during obesity. (A) Body weight trajectories of wild-type (WT, n = 11) and tamoxifen-inducible, adipocyte-specific Srf KO (SRF-AKO, n = 9) male mice during HFD feeding. Total N = 20. (B) Heatmap showing the relative expression of cytoskeletal and collagen genes in eWAT from WT ( n = 6) and SRF-AKO male mice ( n = 5). Total N = 11. (C) Phalloidin staining of actin filaments in isolated adipocytes from WT and SRF-AKO male mice (scale bar: 20 μm). (D–E) Co-staining of isolated adipocytes with phalloidin (red) and PLIN1 (green) from both eWAT and iWAT of female mice. Scale bar: 100 μm, with quantification of phalloidin signal intensity. (F–G) Representative H&E-stained adipose tissue sections from (F) eWAT and (G) iWAT of WT and SRF-AKO male mice, with quantification of average adipocyte size. Scale bar: 100 μm. A two-tailed Student’s t -test was used for statistical analysis. ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: For generation of SRF knockout mice specific to beige and brown adipocytes (SRF-BKO), Srf -flox mice were crossed with Ucp1 -Cre mice (Jackson Laboratory, 024670).

Techniques: In Vivo, Expressing, Staining, Isolation, Two Tailed Test

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Compromised structural integrity and increased cellular fragility in SRF-deficient adipocytes. (A) Basal and isoproterenol (ISO)-stimulated lipolysis, measured by glycerol release from 4-h eWAT and iWAT explants from WT and SRF-AKO male mice ( n = 3 per condition, total N = 12). (B) Representative transmission electron microscopy (TEM) images of eWAT from WT and SRF-AKO female mice, showing ruptured adipocyte membranes (indicated by black arrows). Scale bar: 5 μm. (C) Quantification of apoptotic cells in eWAT and iWAT from WT (eWAT, n = 3; iWAT, n = 5) and SRF-AKO (eWAT, n = 3; iWAT, n = 3) male mice by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. (D) BODIPY staining of eWAT and iWAT from WT and SRF-AKO male mice following 1.5-h of compression. Scale bar: 100 μm. A two-tailed Student’s t -test was used for statistical analysis. * P < 0.05, ** P < 0.01.

Article Snippet: For generation of SRF knockout mice specific to beige and brown adipocytes (SRF-BKO), Srf -flox mice were crossed with Ucp1 -Cre mice (Jackson Laboratory, 024670).

Techniques: Transmission Assay, Electron Microscopy, TUNEL Assay, Staining, Two Tailed Test

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Impaired vascular integrity and altered cell-cell communication in adipose tissue driven by loss of SRF in adipocytes. (A) UMAP visualization of 34,457 single nuclei isolated from eWAT and iWAT of WT and SRF-AKO male mice (total N = 4), with annotated cell types. (B) Violin plots of cell type-specific marker gene expression across all identified cell types. (C) Relative proportions of each cell type in eWAT and iWAT from WT and SRF-AKO male mice. (D–E) Whole-mount staining of eWAT from WT and SRF-AKO mice with Hoechst (blue), BODIPY (green), and either F4/80 (red, D) or PECAM1 (red, E). Scale bar: 100 μm. (F) Circle plots from CellChat analysis showing altered cell-cell communication in eWAT of SRF-AKO male mouse compared to WT. Increases in interaction number (left) and strength (right) are shown in red; decreases are shown in blue.

Article Snippet: For generation of SRF knockout mice specific to beige and brown adipocytes (SRF-BKO), Srf -flox mice were crossed with Ucp1 -Cre mice (Jackson Laboratory, 024670).

Techniques: Isolation, Marker, Gene Expression, Staining

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Role of SRF in actin filament structure and cellular expansion in adipocytes in vivo during obesity. (A) Body weight trajectories of wild-type (WT, n = 11) and tamoxifen-inducible, adipocyte-specific Srf KO (SRF-AKO, n = 9) male mice during HFD feeding. Total N = 20. (B) Heatmap showing the relative expression of cytoskeletal and collagen genes in eWAT from WT ( n = 6) and SRF-AKO male mice ( n = 5). Total N = 11. (C) Phalloidin staining of actin filaments in isolated adipocytes from WT and SRF-AKO male mice (scale bar: 20 μm). (D–E) Co-staining of isolated adipocytes with phalloidin (red) and PLIN1 (green) from both eWAT and iWAT of female mice. Scale bar: 100 μm, with quantification of phalloidin signal intensity. (F–G) Representative H&E-stained adipose tissue sections from (F) eWAT and (G) iWAT of WT and SRF-AKO male mice, with quantification of average adipocyte size. Scale bar: 100 μm. A two-tailed Student’s t -test was used for statistical analysis. ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: To generate inducible adipocyte-specific SRF knockout (SRF-AKO) mice, Srf -flox mice (Jackson Laboratory, 006658) were crossed with Adipoq -CreERT2 mice (Jackson Laboratory, 024671).

Techniques: In Vivo, Expressing, Staining, Isolation, Two Tailed Test

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Impaired systemic glucose homeostasis and partial lipodystrophy phenotype in SRF-AKO mice during obesity. (A–C) Defective glucose homeostasis in SRF-AKO ( n = 9) compared to WT ( n = 11) male mice during obesity (total N = 20), assessed by (A) glucose tolerance test (GTT, 1 g/kg body weight glucose), (B) insulin tolerance test (ITT, 1 U/kg body weight insulin), and (C) fasting insulin levels (ng/mL) relative to body weight. (D) Tissue weight (% of body weight) of eWAT, iWAT, and BAT, and liver in WT ( n = 11) and SRF-AKO ( n = 9) male mice. Total N = 20. (E–F) Representative H&E-stained sections of (E) BAT and (F) liver from WT and SRF-AKO male mice. Scale bar: 100 μm. A two-tailed Student’s t -test was used for statistical analysis. * P < 0.05, ** P < 0.01.

Article Snippet: To generate inducible adipocyte-specific SRF knockout (SRF-AKO) mice, Srf -flox mice (Jackson Laboratory, 006658) were crossed with Adipoq -CreERT2 mice (Jackson Laboratory, 024671).

Techniques: Staining, Two Tailed Test

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Compromised structural integrity and increased cellular fragility in SRF-deficient adipocytes. (A) Basal and isoproterenol (ISO)-stimulated lipolysis, measured by glycerol release from 4-h eWAT and iWAT explants from WT and SRF-AKO male mice ( n = 3 per condition, total N = 12). (B) Representative transmission electron microscopy (TEM) images of eWAT from WT and SRF-AKO female mice, showing ruptured adipocyte membranes (indicated by black arrows). Scale bar: 5 μm. (C) Quantification of apoptotic cells in eWAT and iWAT from WT (eWAT, n = 3; iWAT, n = 5) and SRF-AKO (eWAT, n = 3; iWAT, n = 3) male mice by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. (D) BODIPY staining of eWAT and iWAT from WT and SRF-AKO male mice following 1.5-h of compression. Scale bar: 100 μm. A two-tailed Student’s t -test was used for statistical analysis. * P < 0.05, ** P < 0.01.

Article Snippet: To generate inducible adipocyte-specific SRF knockout (SRF-AKO) mice, Srf -flox mice (Jackson Laboratory, 006658) were crossed with Adipoq -CreERT2 mice (Jackson Laboratory, 024671).

Techniques: Transmission Assay, Electron Microscopy, TUNEL Assay, Staining, Two Tailed Test

Journal: Metabolism: clinical and experimental

Article Title: Serum Response Factor (SRF) promotes actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity in mice

doi: 10.1016/j.metabol.2026.156548

Figure Lengend Snippet: Impaired vascular integrity and altered cell-cell communication in adipose tissue driven by loss of SRF in adipocytes. (A) UMAP visualization of 34,457 single nuclei isolated from eWAT and iWAT of WT and SRF-AKO male mice (total N = 4), with annotated cell types. (B) Violin plots of cell type-specific marker gene expression across all identified cell types. (C) Relative proportions of each cell type in eWAT and iWAT from WT and SRF-AKO male mice. (D–E) Whole-mount staining of eWAT from WT and SRF-AKO mice with Hoechst (blue), BODIPY (green), and either F4/80 (red, D) or PECAM1 (red, E). Scale bar: 100 μm. (F) Circle plots from CellChat analysis showing altered cell-cell communication in eWAT of SRF-AKO male mouse compared to WT. Increases in interaction number (left) and strength (right) are shown in red; decreases are shown in blue.

Article Snippet: To generate inducible adipocyte-specific SRF knockout (SRF-AKO) mice, Srf -flox mice (Jackson Laboratory, 006658) were crossed with Adipoq -CreERT2 mice (Jackson Laboratory, 024671).

Techniques: Isolation, Marker, Gene Expression, Staining