hdac3 f f mice  (Jackson Laboratory)

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: Representative images of retina flatmount immunolabeling ( A ) at 14 days post-injury and quantitative analyses ( B ) demonstrate decreased neurodegeneration indicated by the neuronal marker NeuN and a reduction in microglia/ macrophage numbers, marked by Iba-1 ( C ) in the M-HDAC3 −/− retinas ( N = 5) compared to control HDAC3 f/f retinas ( N = 7). FOV = Field of view, * p < 0.05, *** p < 0.005, **** p < 0.001.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Immunolabeling, Marker, Control

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: A , B Representative N1, P1, and N2 waveforms in the retinas of HDAC3 f/f and M-HDAC3 −/− sham and injured mice, conducted on day 7 post-ONC injury. Quantification and comparison of the ONC groups reveal improved waveform amplitudes in M-HDAC3 −/− retinas with statistical significance achieved in N2 and P1-N2 amplitudes compared to HDAC3 f/f retinas at 7 days post-ONC injury (HDAC3 f/f , N = 6 ; M-HDAC3 −/− , N = 7 )( C – F ), with no effect on the wave latencies ( G – I ). Similarly, N2 and P1-N2 amplitudes were significantly improved ( J – N ), but not their latencies ( O – Q ) at 14 days post-ONC injury (HDAC3 f/f , N = 5; M-HDAC3 −/− , N = 6). * p < 0.05, ** p < 0.01, **** p < 0.001, ns not statistically significant.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Comparison

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: M-HDAC3 −/− and HDAC3 f/f mice were subjected to ONC, and retinas were collected at days 5 (HDAC3 f/f , N = 8; M-HDAC3 −/− , N = 15), 7, and 14 days (HDAC3 f/f , N = 4; M-HDAC3 −/− , N = 5) post-injury. A Representative Z-Stack confocal images of retina flatmounts at day 5 post-ONC injury display colocalization of TUNEL + apoptotic cells (red) and Iba-1 + microglia/macrophages (green). Arrows indicate free TUNEL + apoptotic cells, while arrowheads denote Iba-1-associated apoptotic cells. B Magnification of the crosshair area from the orthogonal view and 3D rendering showing a myeloid cell wrapping its processes around an apoptotic cell. C The ratio of engulfed apoptotic cells by microglia/macrophages (Iba-1 + TUNEL + ) to free apoptotic cells was markedly increased in injured retinas of M-HDAC3 −/− mice compared to HDAC3 f/f mice, indicating improved efferocytosis on day 5 after ONC. * p < 0.05.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: TUNEL Assay

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: A Representative confocal images of optic nerve sections from M-HDAC3 −/− and HDAC3 f/f mice immunolabeled with Iba-1 (myeloid cell marker, green), CD68 (phagocytic cell marker, red), and DAPI (nuclei marker, blue) demonstrate an increase in phagocytic myeloid cells, indicated by arrows, in M-HDAC3 −/− mice compared to HDAC3 f/f on day 7 after ONC. B Representative confocal images of axonal growth and nerve fiber sprouting in the axons distal to the crush site by anterograde tracing with cholera toxin B (CTB) on day 14 post-ONC. C The quantification of the sprouting axons demonstrated significant improvement in axonal growth in M-HDAC3 −/− compared to HDAC3 f/f retinas, indicated by fluorescence intensity at distances of 200, 400, and 600 μm beyond the crush site (HDAC3 f/f , N = 5; M-HDAC3 −/− , N = 7). * p < 0.05, ** p < 0.01, *** p < 0.005.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Immunolabeling, Marker, Anterograde Tracing, Fluorescence

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: A Experimental setup using myelin debris from the optic nerve labeled with Dil-red dye (top) and unlabeled debris stained with Oil Red O (ORO, bottom). B Representative images show the internalization of DiI-labeled myelin (arrows) by bone-marrow-derived macrophages derived from HDAC3 f/f and M-HDAC3 −/− mice. C Quantification of uptake of DiI-labeled myelin, expressed as mean fluorescence intensity (MFI), demonstrates significant improvement in the phagocytic activity of M-HDAC3 −/− macrophages compared to HDAC3 f/f macrophages. D ORO staining confirmed the improved uptake of myelin debris (arrows) by M-HDAC3 −/− macrophages compared to HDAC3 f/f macrophages. E Representative confocal images of Iba-1+ myeloid cells (red) and myelin basic protein (MBP, green) in optic nerve sections 7 days after ONC show a considerable increase in myelin clearance by myeloid cells in M-HDAC3 −/− optic nerves compared to HDAC3 f/f injured controls, as evidenced by increased Iba-1/MBP colocalization. N = 3 per group, **** p < 0.001.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Labeling, Staining, Derivative Assay, Fluorescence, Activity Assay

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: Macrophages from HDAC3 f/f and M-HDAC3 −/− mice were co-incubated with K-562 apoptotic cells (apop) in an in vitro efferocytosis assay. Controls included either co-incubation of macrophages with K-562 non-apoptotic cells (non-apop) or no treatment (no ttt). A – C Quantification of mRNA levels of ODC, MerTK, and the anti-inflammatory cytokine IL-10 demonstrated significant upregulation in M-HDAC3 −/− macrophages as compared to HDAC3 f/f macrophages incubated with apoptotic cells. D – F Western blotting shows significant upregulation of MerTK and ODC in M-HDAC3 −/− macrophages co-cultured with K-562 cells compared to untreated M-HDAC3 −/− macrophages, but not in the HDAC3 f/f control co-cultures. β-actin was used as a loading control. G Representative confocal images of Iba-1 + myeloid cells (green) and MerTK (red) in retinal sections 7 days after ONC show a considerable increase in MerTK expression by myeloid cells in M-HDAC3 −/− retinas compared to HDAC3 f/f controls, as evidenced by increased Iba-1/MerTK colocalization. H Similarly, MerTK expression by myeloid cells is increased in injured optic nerve sections, with arrowheads pointing to Iba-1 + MerTK + myeloid cells. GCl ganglion cell layer, INL inner nuclear layer, ONL outer nuclear layer. N = 4 per group. * p < 0.05, *** p < 0.005, **** p < 0.001.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Incubation, In Vitro, Western Blot, Cell Culture, Control, Expressing

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: A Representative images illustrate the internalization of DiI-labeled myelin debris (red), derived from optic nerve axons, by CFDA-labeled macrophages (green) obtained from HDAC3 f/f and M-HDAC3 −/− mice ( N = 5 per group). These cells were pretreated with 0.8 nM of the MertK inhibitor (UNC2025) or vehicle for 1 h in vitro. B Quantification of DiI-labeled myelin debris uptake, expressed as mean fluorescence intensity (MFI), demonstrates a significant reduction in myelin uptake in the UNC2025 pretreatment groups, with UNC2025 abolishing the enhanced myelin uptake observed in vehicle-treated M-HDAC3 −/− macrophages, indicating that myeloid HDAC3 deletion promotes myelin uptake at least in part via MerTK. C Representative images of immunolabeling for neurons, marked by NeuN (green), and microglia/macrophages, marked by Iba-1 (red), of adult M-HDAC3 −/− and HDAC3 f/f mice retinas that were explanted for 24 h and treated with UNC2025 or vehicle (HDAC3 f/f , N = 3, 4; M-HDAC3 −/− , N = 5) for another 24 h. D , E Quantification of NeuN and Iba-1 shows that UNC2025 treatments had no significant effect on neuronal preservation in retinal explants of both treated groups, while it significantly increased myeloid cell number in M-HDAC3 −/− compared to flox retina explants. F , G Representative images of Iba-1 (red) labeling and quantification of optic nerve explants treated with UNC2025 show no effect of the treatment on myeloid cell count between M-HDAC3 −/− and HDAC3 f/f derived optic nerves ( N = 3 per group). * p < 0.05, **** p < 0.001; ns, not statistically significant; FOV, field of view.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Labeling, Derivative Assay, In Vitro, Fluorescence, Immunolabeling, Preserving, Cell Characterization

Journal: Cell Death Discovery

Article Title: Myeloid HDAC3 deletion protects against traumatic optic injury

doi: 10.1038/s41420-026-03030-0

Figure Lengend Snippet: A Representative retina flatmount images from microglia-specific HDAC3 KO (im-HDAC3 −/− ) and HDAC3 f/f controls immunolabeled for NeuN (neuronal marker, green) and Iba-1 (microglia/macrophages marker, red) at 14 days after ONC. B , C Quantitative analyses reveal significant neurodegeneration, indicated by a decrease in the neuronal marker NeuN and increase in Iba-1 + cell count in injured im-HDAC3 −/− ( N = 5) and HDAC3 f/f ( N = 6) mice compared to shams ( N = 3 for im-HDAC3 −/− , and N = 4 for HDAC3 f/f ). However, no differences were observed between the injured groups. D , E Representative images and Iba-1 quantification at the optic nerve injury site of im-HDAC3 −/− ( N = 5) and HDAC3 f/f ( N = 4) mice 14 days post-ONC injury show a robust presence of activated microglia and macrophages, with no differences observed between the injured groups. *** p < 0.005, **** p < 0.001; ns, not statistically significant; FOV, field of view.

Article Snippet: Two myeloid HDAC3 KO lines were used (genotyping is included in Supplementary Fig. ): A constitutive macrophage and microglia cell-specific HDAC3 KO (LysM Cre/+ ; HDAC3 f/f or M-HDAC3 −/− ) mice generated by crossing the HDAC3 f/f mice with LysM Cre/+ mice (Jackson laboratory Stock # 004781).

Techniques: Immunolabeling, Marker, Cell Characterization

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: Elevated expression of cathepsins in HDAC3 deficient macrophages. A Western blot analysis of HDAC3 in Vector and Hdac3 −/ − RAW264.7 cells. B Volcano plot for genes significantly changed (≥ 2 fold change, P < 0.05) after HDAC3 knockout. C , D Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for genes significantly changed (≥ 2 fold change, P < 0.05) after HDAC3 knockout. E Heat map of relative lysosome related mRNA expression. F PCR analysis of Ctsa , Ctsb , Ctsc , Ctsd , Ctse , Ctsf , Ctsg , Ctsh , Ctsk , Ctsl , Ctso , Ctss , Ctsw , Ctsz in Vector and Hdac3 −/ − RAW264.7 cells. Data are representative of three independent experiments and showed as mean ± SEM. ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Expressing, Western Blot, Plasmid Preparation, Knock-Out

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deficient macrophages have elevated expression of Ctsb . A , B Western blot analysis of CTSB in control and HDAC3 deficient RAW264.7. C , D Confocal micrographs of RAW264.7 cells stained with DAPI (blue, DNA) and antibodies against CTSB (AF488). Scale bar: 100/10 μm. E PCR analysis of Ctsb in Lysm Cre and Lysm Cre Hdac3 f/f BMDMs. F , G Western blot analysis of CTSB in Lysm Cre and Lysm Cre Hdac3 f/f BMDMs. H PCR analysis of Ctsb in Vector, Hdac1 −/− , Hdac2 −/− , Hdac3 −/− , Hdac8 −/− RAW264.7 cells. I , J Western blot analysis of HDAC1, HDAC2, HDAC3, HDAC8 and CTSB in Vector, Hdac1 −/− , Hdac2 −/− , Hdac3 −/− , Hdac8 −/− RAW264.7 cells. Data are representative of three independent experiments and showed as mean ± SEM. * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Expressing, Western Blot, Control, Staining, Plasmid Preparation

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deacetylases the histones on the promoters of cathepsins. A Heat map representation of correlation between each biological replicates of Vector and Hdac3 −/− RAW264.7 cells for H3K27ac. B Distribution of H3K27ac-binding loci relative to transcriptional start site (TSS). C H3K27ac signals in Vector and Hdac3 −/− RAW264.7 at TSS. D Genome-wide distribution of H3K27ac ChIP-seq peaks in RAW264.7 cells. E – J The Integrative Genomics Viewers (IGVs) for H3K27ac occupied on the promoter of Ctsa , Ctsb , Ctsd , Ctsl , Ctss and Ctsz . Each CHIPseq data of histone marks were merged from three individual replicates

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Plasmid Preparation, Binding Assay, Genome Wide, ChIP-sequencing

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: Reduced protein level of RIP1 is observed in HDAC3 deficient macrophage. A – C Western blot analysis of RIP1 in Neuro-2a cells transfected with CTSB. D – G Western blot analysis of RIP1 in control and HDAC3 deificient RAW264.7 and BMDMs. H – M Western blot analysis of RIP1 in Vector and Hdac3 −/− RAW264.7 stimulated with Leupeptin (25 μM), CA-074 (10 μM) or MG132 (10 μM) for 12 h. N – Q Western blot analysis of RIP1 in Lysm Cre and Lysm Cre Hdac3 f/f BMDMs stimulated with Leupeptin (100 μM) or CA-074 (40 μM) for 12 h. R , S Western blot analysis of RIP1 in Vector, Hdac1 −/− , Hdac2 −/− , Hdac3 −/− , Hdac8 −/− RAW264.7 cells. Data are representative of three independent experiments and showed as mean ± SEM. * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Western Blot, Transfection, Control, Plasmid Preparation

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deficiency in macrophages results in impaired RIP1-dependent NF-κB signaling activity. A , B Western blot analysis of phosphorylated and total RIP1 in Vector and Hdac3 −/− RAW264.7 stimulated with TNFα (20 ng/ml) for indicated time. C , D Western blot analysis of phosphorylated and total P65 in control and HDAC3 deficient RAW264.7 stimulated with TNFα (20 ng/ml) for indicated time. E , F Confocal micrographs of RAW264.7 stimulated or unstimulated with TNFα (20 ng/ml) for 15 min stained with DAPI (blue, DNA) and antibodies against P65 (AF488). The nuclear P65 positive cells were calculated. Scale bar: 100/10 μm. Ctl, Control. G PCR analysis of Il1β , Mcp1 , Mip2 and Cox2 in Vector and Hdac3 −/− RAW264.7 stimulated with TNFα (20 ng/ml) for 1 h. Data are representative of three independent experiments and showed as mean ± SEM; * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Activity Assay, Western Blot, Plasmid Preparation, Control, Staining

Journal: Cell & Bioscience

Article Title: Histone deacetylase 3 facilitates TNFα-mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection

doi: 10.1186/s13578-022-00814-6

Figure Lengend Snippet: HDAC3 deficiency in macrophages aggravates pseudomonas aeruginosa induced acute lung injury due to impaired inflammatory response. A , B ELISA analysis of IL-6 and TNFα in BALF of Lysm Cre and Lysm Cre Hdac3 f/f mice uninstilled or intratracheally instilled with LPS (5 mg/kg) (12 h). C Survival curve of 8-week-olds Lysm Cre and Lysm Cre Hdac3 f/f mice intratracheally received with pseudomonas aeruginosa [Colony forming unit (CFU) = 2 × 10 7 ]. PA, Pseudomonas aeruginosa . D Temperature of Lysm Cre and Lysm Cre Hdac3 f/f mice intratracheally received with pseudomonas aeruginosa (CFU = 2 × 10 7 ) monitored for 36 h. E CFU of pseudomonas aeruginosa in BALF of Lysm Cre and Lysm Cre Hdac3 f/f mice uninstilled or intratracheally instilled with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h was calculated. F , G H&E staining of Lysm Cre and Lysm Cre Hdac3 f/f mice intratracheal unreceived or received with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h and the lung injury score was calculated. Scale bar: 50 μm. H Pulmonary hemorrhage of Lysm Cre and Lysm Cre Hdac3 f/f mice received with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h was judged by the color of BALF. I ELISA analysis of HMGB1 in the BALF of Lysm Cre and Lysm Cre Hdac3 f/f mice uninstilled or intratracheally instilled with pseudomonas aeruginosa (CFU = 2 × 10 7 ) for 36 h. J Schematic diagram of how HDAC3 regulates RIP1 mediated inflammatory response of macrophages. Data are showed as mean ± SEM; n = 4–9 mice per group; * P < 0.05 and ** P < 0.01

Article Snippet: Hdac3 f/f mice on a C57BL/6 J background were bought from the Jackson Lab (Stock number: 024119).

Techniques: Enzyme-linked Immunosorbent Assay, Staining

Journal: Cell metabolism

Article Title: Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP

doi: 10.1016/j.cmet.2016.10.012

Figure Lengend Snippet: (A) Heat map of ChIP-seq peaks in mouse liver. C57Bl/6 mice (2–3 months old) were tail-vein injected with either AAV8:GFP or AAV8:HA-nSREBP1c and sacrificed 10 days later at ZT10. All ChIPs were performed in parallel. High-confidence peaks were clustered into 3 groups: common peaks where HA-nSREBP1c and HDAC3 peaks overlapped (purple), nSREBP1c-specfic peaks (red), and HDAC3-specific peaks (blue).

Article Snippet: Analysis at Jackson Labs indicated that the Hdac3 f/f / Scap f/f mice were 88% 6J.

Techniques: ChIP-sequencing, Injection