Journal: Nature Communications

Article Title: NF-κB activation in astrocytes impairs wound healing after traumatic brain injury in male mice

doi: 10.1038/s41467-026-70304-7

Figure Lengend Snippet: a Heat map (log 2 normalization) of genes encoding inflammasome components expressed in GoF ACSA-2+ astrocytes at day 3 post-TBI compared to TBI controls. b Immunoblot analysis and corresponding quantification of c ASC, d NLRP3 and e AIM2 inflammasome components. Expression was normalized to eIF2 loading control. f Immunoblot analyses and the corresponding quantification of protein expression of g TGM1, h NRF2, i IBA1, j HO-1, k MAC2, l OPN and m LCN2 in the ipsilateral insult region (ip) and in the contralateral uninjured (co) cortical brain tissue from control ( n = 3) and IKK2-CA GFAP ( n = 3) animals. Tissue was isolated at day 3 post-TBI. n Ratio of normalized OPN and LCN2. For quantification, protein levels were normalized to β-actin loading control. Bars indicate mean ± SEM. Statistical comparison by ordinary one-way ANOVA with Tukey’s multiple comparisons test. Exact significances indicated in graphs. Protein expression presented in arbitrary units (arb. units). Protein data are presented as biological replicates. Blue: control ipsi, white: control contra, red: IKK2-CA GFAP ipsi, black: IKK2-CA GFAP contra. OPN: Osteopontin (Spp1), HO-1: Heme oxygenase 1 (Hmox1), MAC2: Galectin-3 (Lgals3). Source data are provided as a file.

Article Snippet: The following antibodies were used for immunoblot stainings: Anti-TGM1 rabbit pAb (1:500, Abcam #ab103814), anti-Lipocalin-2 goat pAb (1:2000, R&D Systems #AF1857), anti-Osteopontin goat pAb (1:1000, R&D Systems #AF808), anti-Heme Oxygenase 1 rabbit pAb (1:2000, Abcam #ab13243), anti-NRF2 mouse mAb (1:1000, SantaCruz Biotechnology #sc-365949), anti-Galectin-3 rabbit pAb (SantaCruz Biotechnology #sc-20157), anti-IBA1 rabbit pAb (1:2000, FUJIFILM Wako #019-19741), anti-IKKβ rabbit mAb (1:1000, Cell Signaling Technology #8943), β-Actin rabbit mAb (1:500, Cell Signaling Technology #8457), HRP-linked anti-rabbit IgG (1:2000, Cell Signaling Technology #7074), anti-EAAT1 rabbit mAb (1:1000, Cell Signaling Technology #56845).

Techniques: Western Blot, Expressing, Control, Isolation, Comparison

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Gene set enrichment analysis (GSEA) plots derived from RNA-Seq analysis of Cas9-expressing HepG2 cells transduced with sgRNA targeting KEAP1 (sg KEAP1 ) versus cells transduced with sgRNA targeting the safe harbour locus AAVS1 (sgAAVS1), n=4. HNF4A signature, Gene Set SUMI_HNF4A_TARGETS; Cholangiocyte signature, Gene set AIZARANI_LIVER_C39_EPCAM_POS_BILE_DUCT_CELLS_4. (B) Representative immunoblot analysis of sgAAVS1 and sg KEAP1 HepG2 cells. (C) GSEA plot derived from RNA-Seq analysis of HepG2 cells harbouring inducible expression of EGFP (Control) versus cells harbouring inducible expression of NRF2 T80K (TO:NRF2 T80K ) after 4 days of DOX-treatment, n=3. NRF2 pathway signature corresponds to Gene Set WP_NRF2_PATHWAY. (D) Volcano plot of differentially expressed genes (DEGs) identified by RNA-Seq analysis of TO:NRF2 T80K versus Control HepG2 cells after 4 days of DOX treatment, n=3. Significant DEGs are highlighted in pink. Select canonical NRF2 target genes are highlighted in blue. Cholangiocyte markers are highlighted in green. (E) GSEA plots derived from RNA-Seq analysis of Control versus TO:NRF2 T80K HepG2 cells, n=3. HNF4A signature, Gene Set SUMI_HNF4A_TARGETS; Cholangiocyte signature, Gene set AIZARANI_LIVER_C39_EPCAM_POS_BILE_DUCT_CELLS_4. (F) Representative immunoblot analysis of Control and TO:NRF2 T80K HepG2 cells after 4 days of DOX treatment. (G) Representative confocal images of hepatocyte membrane ( lf :CFP-CAAX, cyan), cholangiocytes ( anxa4 :mScarlet3, red), and a 3D-rendered mask of the cholangiocyte network derived from TO:NRF2 T80K ; anxa4 :mScarlet3 zebrafish larvae treated with DMSO or DOX from 5 to 10 days post-fertilisation (dpf). White scale bars represent 50 µm. (H) Quantification of mScarlet3 (cholangiocyte) area normalized to CFP (liver) area, n=8. (I) Magnification of liver sections denoted by hashed lines in (G). White arrows indicate cells expressing hepatocyte (cyan) and cholangiocyte (red) markers. Scale bars represent 10 µm.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: Derivative Assay, RNA Sequencing, Expressing, Transduction, Western Blot, Control, Membrane

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Quantitative PCR (qPCR) analysis of GCLM expression in Control and TO:NRF2 T80K HepG2 cells treated with DOX for 4 days, and sgAAVS1 and sg KEAP1 HepG2 cells, n=3. (B) Representative immunoblot analysis of nuclear fractions from Control and TO:NRF2 T80K HepG2 cells treated with 200 ng/mL DOX for 4 days and sgAAVS1 and sg KEAP1 HepG2 cells. (C) Representative confocal images of CFP (hepatocyte, cyan) and EGFP (NRF2 target gene expression, green) from TO:NRF2 T80K ; gstp1: EGFP zebrafish larvae treated with DMSO or DOX from 5 to 6 dpf. Scale bars represent 50 µm. (D) Schematic of the approach employed to generate the TgKI(mScarlet3-P2A-anxa4) transgenic zebrafish line. (E) Representative confocal images of mScarlet3 (cholangiocyte) from anxa4 :mScarlet3 zebrafish larvae at treated with DMSO or DOX from 5 to 10 dpf. Scale bars represent 50 µm. (F) Immunofluorescent staining of Anxa4 (cholangiocyte) in liver sections from WT and keap1a/b crispants at 14 dpf. Scale bars represent 25 µm.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: Real-time Polymerase Chain Reaction, Expressing, Control, Western Blot, Targeted Gene Expression, Transgenic Assay, Staining

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Representative H&E and immunofluorescent staining of CFP (hepatocyte, magenta) and Anxa4 (cholangiocyte, yellow) in liver sections from adult TO:NRF2 T80K zebrafish after 4 weeks treatment with DMSO or DOX. Scale bars represent 50 µm. (B) Magnification of liver sections denoted by hashed lines in (A). White arrows indicate cells that express CFP (hepatocyte, magenta) and Anxa4 (cholangiocyte, yellow) markers. Scale bars represent 10 µm. (C) Heatmap of hepatocyte and cholangiocyte gene expression in livers from adult TO:NRF2 T80K zebrafish after 4 weeks treatment with DMSO or DOX as determined by bulk RNA-Seq analysis, n=3. (D) Uniform Manifold Approximation and Projection (UMAP) visualization of scRNA-Seq data obtained from livers from adult TO:NRF2 T80K zebrafish after 3 weeks treatment with DMSO or DOX. (E) UMAP visualization from the joint clustering of scRNA-Seq data obtained from livers from adult TO:NRF2 T80K zebrafish after 3 weeks treatment with DMSO or DOX. Chol: cholangiocytes; ECs: Endothelial cells; Ery: Erythrocytes; Hep: Hepatocytes; HS_Cells: Hepatic stellate cells; Lymph: Lymphocytes; Mac: Macrophages; Nrf2_trans: Transdifferentiating cells; GB_Cells: Gall bladder cells. (F) Stacked bar chart showing the relative proportions of the major cell types in livers from adult TO:NRF2 T80K zebrafish treated with DMSO or DOX for 3 weeks. (G) UMAP visualization of fabp10a (hepatocyte) and anxa4 (cholangiocyte) expression in livers from adult TO:NRF2 T80K zebrafish treated with DMSO or DOX for 3 weeks. Hashed boxes outline cells expressing both markers.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: Staining, Gene Expression, RNA Sequencing, Expressing

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Volcano plot of DEGs identified by bulk RNA-Seq analysis of livers from adult TO:NRF2 T80K zebrafish treated with DOX versus DMSO for 4 weeks, n=3. Significant DEGs are highlighted in pink. Select canonical NRF2 target genes are highlighted in blue. (B) UMAP visualization of gstp1 expression in livers from adult TO:NRF2 T80K zebrafish treated with DMSO or DOX for 3 weeks. (C) Masson’s trichome stained histological sections from livers isolated from adult TO:NRF2 T80K zebrafish after 4 weeks treatment with DMSO or DOX. Scale bars represent 50 µm. (D) TUNEL- and DAPI-stained histological sections from livers isolated from adult TO:NRF2 T80K zebrafish after 4 weeks treatment with DMSO or DOX. DNase I treatment was employed as a positive control. Scale bars represent 50 µm.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: RNA Sequencing, Expressing, Staining, Isolation, TUNEL Assay, Positive Control

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Schematic of DMSO/DOX pulse-chase experiments in adult TO:NRF2 T80K zebrafish. (B) Representative H&E-staining in liver sections from adult TO:NRF2 T80K zebrafish after 7- or 14-days treatment with either DMSO or DOX, followed by 7- or 28-days withdrawal of DMSO or DOX. Scale bars represent 50 µm. (C) Representative immunofluorescent staining of CFP (hepatocyte, magenta) and Anxa4 (cholangiocyte, yellow) in liver sections from adult TO:NRF2 T80K zebrafish after 7- or 14-days treatment with either DMSO or DOX, followed by 7- or 28-days withdrawal of DMSO or DOX. Scale bars represent 50 µm. (D) Multidimensional scaling (MDS) plot of bulk RNA-Seq data obtained from livers isolated from adult TO:NRF2 T80K zebrafish after 14 days treatment with either DMSO or DOX, followed by 28-days withdrawal of DMSO or DOX, n=3. (E) Heatmap of hepatocyte and cholangiocyte gene expression in livers isolated from adult TO:NRF2 T80K zebrafish after 7- or 14-days treatment with either DMSO or DOX, followed by 7- or 28-days withdrawal of DMSO or DOX, as determined by bulk RNA-Seq analysis, n=3. (F) Volcano plot of DEGs identified by bulk RNA-Seq analysis of livers isolated from adult TO:NRF2 T80K zebrafish treated with DOX versus DMSO for 14 days (left), followed by withdrawal of DOX versus DMSO for 28 days (right), n=3. Significant DEGs are highlighted in pink. Hepatocyte markers are highlighted in blue. Cholangiocyte markers are highlighted in green. (G) Volcano plot of DEGs identified by RNA-Seq analysis of TO:NRF2 T80K versus Control HepG2 cells after 4 days of DOX treatment (left), followed by withdrawal of DOX for 4 days (right). Significant DEGs are highlighted in pink. Hepatocyte markers are highlighted in blue. Cholangiocyte markers are highlighted in green.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: Pulse Chase, Staining, RNA Sequencing, Isolation, Gene Expression, Control

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Periodic Acid-Schiff (PAS)-stained histological sections from livers isolated from adult TO:NRF2 T80K zebrafish after 7- or 14-days treatment with DMSO or DOX, followed by 7- or 28-days withdrawal of DMSO or DOX. Scale bars represent 50 µm. (B) Heatmap of NRF2 target gene expression in livers isolated from adult TO:NRF2 T80K zebrafish after 7- or 14-days treatment with DMSO or DOX, followed by 7- or 28-days withdrawal of DMSO or DOX as determined by bulk RNA-Seq analysis, n=3. (C) MDS Plot of RNA-Seq data from Control and TO:NRF2 T80K HepG2 cells after 4 days of DOX treatment, followed by withdrawal of DOX for 4 days.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: Staining, Isolation, Targeted Gene Expression, RNA Sequencing, Control

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Schematic of the epigenetic-focused small molecule inhibitor screen. (B) Heatmap of NRF2 target gene expression in livers isolated from adult TO:NRF2 T80K zebrafish treated with DMSO or DOX in the absence or presence of 250 nM FHD-286 for 14 days as determined by bulk RNA-Seq analysis, n=3. (C) Volcano plot of DEGs identified by bulk RNA-Seq of livers isolated from adult TO:NRF2 T80K zebrafish treated with DOX versus DMSO both in the presence of 250 nM FHD-286 for 14 days as determined by bulk RNA-Seq analysis, n=3. Significant DEGs are highlighted in pink. Select canonical NRF2 target genes are highlighted in blue.

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: Targeted Gene Expression, Isolation, RNA Sequencing

Journal: bioRxiv

Article Title: NRF2 co-opts the SWI/SNF complex to drive liver cell plasticity

doi: 10.64898/2026.02.09.704724

Figure Lengend Snippet: (A) Quantification of cholangiocyte area (mScarlet3), as a ratio of liver area (CFP) area, from an in vivo chemical suppressor screen using an epigenetic-focused library of small molecule inhibitors. The blue dashed line indicates the mean of the DMSO-treated group, whereas the red dashed line indicates the mean of the DOX-treated group. (B) Representative confocal images of CFP (hepatocyte, cyan), mScarlet3 (cholangiocyte, red), and a 3D-rendered mask of the cholangiocyte network from TO:NRF2 T80K ; anxa4 :mScarlet3 zebrafish larvae with DMSO or DOX in the absence or presence of 100 nM FHD-286 from 5 to 10 dpf. White scale bars represent 50 µm. (C) Quantification of mScarlet3 (cholangiocyte) area normalized to CFP (liver) area, n=11. (D) Representative H&E and immunofluorescent staining of CFP (hepatocyte, magenta) and Anxa4 (cholangiocyte, yellow) in liver sections from adult TO:NRF2 T80K zebrafish treated with DMSO or DOX in the absence or presence of 250 nM FHD-286 for 14 days. (E) Quantification of Anxa4 (cholangiocyte) area normalized to CFP (liver) area, n=6. (F) Volcano plot of DEGs identified by bulk RNA-Seq analysis of livers isolated from adult TO:NRF2 T80K zebrafish treated with DOX (left) or DMSO (right) in the presence versus absence of 250 nM FHD-286 for 14 days. Significant DEGs are highlighted in pink. Hepatocyte markers are highlighted in blue. Cholangiocyte markers are highlighted in green. (G) Gene essentiality scores for SMARCA4 (left) and SMARCA2 (right) in KEAP1 (WT) and KEAP1 (Mutant) samples from TCGA DEPMAP .

Article Snippet: Membranes were incubated with anti-HNF4α (C11F12) Rabbit mAb (Cell Signaling Technology, 3113), anti-β-Actin (8H10D10) Mouse mAb (Cell Signaling Technology, 3700), anti-NRF2 (E5F1A) Rabbit mAb (Cell Signaling Technology, 20733), or anti-Histone H3 Rabbit pAb (Abcam, ab1791) primary antibodies prior to incubation with IRDye secondary antibodies (LI-COR) and imaged using the Odyssey DLx imaging system (LI-COR).

Techniques: In Vivo, Staining, RNA Sequencing, Isolation, Mutagenesis