Journal: bioRxiv

Article Title: Selective Immune Silencing by Targeted TGF-β Agonists

doi: 10.64898/2026.01.19.700410

Figure Lengend Snippet: Design and characterization of mouse T cell-targeted TGF- β agonists. a. Schematic of the plasmid construct encoding the MSA–TGM1-targeting-arm fusion protein. b. SDS–PAGE analysis showing the molecular weight and purity of the indicated recombinant proteins. c. SDS–PAGE analysis showing the molecular weight and purity of the indicated recombinant proteins. d. Representative flow cytometry plots showing mouse CD4 and CD8α expression in mouse CD4- or CD8α-transduced HEK293 cells. e. Dose-dependent curves showing GITR, IRF4, and T-bet expression levels in in vitro –cultured CD4 T cells treated with the indicated proteins on day 3. f. Dose-dependent curves showing GITR, IRF4, and T-bet expression levels in in vitro –cultured CD8 T cells treated with the indicated proteins on day 3. g. Dose-dependent curves showing percentages of IFN-γ– and TNF-α–producing cells among in vitro –cultured CD4 T cells treated with the indicated proteins on day 3. h. Dose-dependent curves showing percentages of IFN-γ– and TNF-α–producing cells among in vitro –cultured CD8 T cells treated with the indicated proteins on day 3. i. Dose-dependent curves showing Foxp3 cell percentages in in vitro -cultured CD4 T cells, and Granzyme B–producing cell percentages in in vitro -cultured CD8 T cells treated with the indicated proteins on day 3. Data are presented as mean ± s.e.m.

Article Snippet: The following antibodies were purchased from Miltenyi Biotec: human IgA (130-113-480) and IRF4 (130-100-909).

Techniques: Plasmid Preparation, Construct, SDS Page, Molecular Weight, Recombinant, Flow Cytometry, Expressing, In Vitro, Cell Culture

Journal: bioRxiv

Article Title: Selective Immune Silencing by Targeted TGF-β Agonists

doi: 10.64898/2026.01.19.700410

Figure Lengend Snippet: a. Frequencies of immune cell subsets. b. SCENIC prediction of IRF4 and Blimp1 transcription factor activity. c. Immunoglobulin gene expression. d. UMAP plots showing cell cycle gene signature scores. e. Quantification of cell cycle gene signature scores. f. Scaled signature scores for TGF-β–inducible genes, senescence genes, and apoptosis-related genes, aggregated by sample.

Article Snippet: The following antibodies were purchased from Miltenyi Biotec: human IgA (130-113-480) and IRF4 (130-100-909).

Techniques: Activity Assay, Gene Expression

Journal: Journal of the American Society of Nephrology : JASN

Article Title: Deletion of Myeloid Interferon Regulatory Factor 4 (Irf4) in Mouse Model Protects against Kidney Fibrosis after Ischemic Injury by Decreased Macrophage Recruitment and Activation

doi: 10.1681/ASN.2020071010

Figure Lengend Snippet: Renal myeloid IRF4 was efficiently deleted in LysM-Cre IRF4f/f mice. (A) Renal myeloid cell IRF4 mRNA levels were significantly reduced in LysM-Cre IRF4f/f (MΦ IRF4−/−) mice compared with IRF4f/f (WT) mice. ***P<0.001, n=6 in WT group and n=7 in MΦ IRF4−/− group. (B and C) Immunofluorescence staining demonstrated that most renal F4/80-positive cells (macrophages/dendritic cells) were also IRF4 positive in WT mouse kidneys at day 0 (B) and 5 days (C) after AKI, whereas only a small portion of F4/80-positive cells were IRF4 positive in MΦ IRF4−/− mouse kidneys, indicating effective IRF4 deletion in renal myeloid cells.

Article Snippet: Antibodies Rat anti-mouse F4/80 (MCA497R, a marker of macrophages) was purchased from AbD Serotec (now Bio-Rad), mouse anti–α-smooth muscle actin (α-SMA, a marker of myofibroblasts, A5228) was from Sigma; rabbit anti-murine collagen type I (600–401–103–0.1) and collage type IV (600–401–106–0.1) were from Rockland Immunochemicals; mouse anti–4-hydroxynonenal (4-HNE, a marker of oxidative stress, MAB3249), goat anti-CCL19 (AF880), goat anti-CCL21 (AF457) were from R&D; mouse anti-C/EBP homologous protein (2895), mouse anti–α-Tubulin (3873), rabbit anti–phospho-AKT (4060), rabbit anti-AKT (4691), rabbit anti–phospho-ERK (4370), rabbit anti-ERK (9102), rabbit anti–phospho-p38 (4511), rabbit anti-p38 (9212), rabbit anti–phospho-JNK (4668), rabbit anti-JNK (9252), and rabbit anti-PTEN (9552) were from Cell Signaling Technology; goat anti-human connective tissue growth factor (CTGF, SC-14939) was from Santa Cruz Biotechnology; rabbit anti-IRF4 was from St John’s Laboratory ( STJ93764 ); and rabbit anti-CX3CL1 (ab25088) and rabbit anti-CD68 (ab125212) were from Abcam.

Techniques: Immunofluorescence, Staining

Journal: Journal of the American Society of Nephrology : JASN

Article Title: Deletion of Myeloid Interferon Regulatory Factor 4 (Irf4) in Mouse Model Protects against Kidney Fibrosis after Ischemic Injury by Decreased Macrophage Recruitment and Activation

doi: 10.1681/ASN.2020071010

Figure Lengend Snippet: Myeloid IRF4 deletion led to attenuated renal macrophage response to early acute ischemic injury. Male IRF4f/f (WT) and LysM-Cre IRF4f/f (MΦ IRF4−/−) mice underwent AKI and were sacrificed at indicated times. (A) WT and MΦ IRF4−/− mice had similar BUN at all early time points after AKI (n=9). (B) Then 1 day after ischemic injury, the mRNA levels of anti-inflammatory Th2/M2 cytokines (YM-1, IL-10, and FIZZ1) were markedly lower in renal myeloid cells from MΦ IRF4−/− mice than WT mice. ***P<0.001, n=9 in WT group and n=7 in MΦ IRF4−/− group. (C) The mRNA levels of proinflammatory Th1/M1 cytokines/chemokines, including iNOS, TNF-α, IL-1α, IL-1β, IL-6, and IL-23, were significantly lower in renal myeloid cells from MΦ IRF4−/− mice than WT mice 1 day after ischemic injury. ***P<0.001, n=9 in WT group and n=7 in MΦ IRF4−/− group. (D) Flow cytometric analysis showed the number of renal macrophages was similar at baseline between MΦ IRF4−/− mice and WT mice, but less increased at days 1 and 2 after ischemic injury in MΦ IRF4−/− mice. Similarly, increased renal neutrophils seen in WT mice day 1 after ischemic injury were attenuated in MΦ IRF4−/− mice. **P<0.01, n=4. (E) CD68 immunofluorescence staining indicated the increased renal macrophages seen in WT mice were markedly attenuated in MΦ IRF4−/− mice from day 1 until day 28. **P<0.01, ***P<0.001, n=4.

Article Snippet: Antibodies Rat anti-mouse F4/80 (MCA497R, a marker of macrophages) was purchased from AbD Serotec (now Bio-Rad), mouse anti–α-smooth muscle actin (α-SMA, a marker of myofibroblasts, A5228) was from Sigma; rabbit anti-murine collagen type I (600–401–103–0.1) and collage type IV (600–401–106–0.1) were from Rockland Immunochemicals; mouse anti–4-hydroxynonenal (4-HNE, a marker of oxidative stress, MAB3249), goat anti-CCL19 (AF880), goat anti-CCL21 (AF457) were from R&D; mouse anti-C/EBP homologous protein (2895), mouse anti–α-Tubulin (3873), rabbit anti–phospho-AKT (4060), rabbit anti-AKT (4691), rabbit anti–phospho-ERK (4370), rabbit anti-ERK (9102), rabbit anti–phospho-p38 (4511), rabbit anti-p38 (9212), rabbit anti–phospho-JNK (4668), rabbit anti-JNK (9252), and rabbit anti-PTEN (9552) were from Cell Signaling Technology; goat anti-human connective tissue growth factor (CTGF, SC-14939) was from Santa Cruz Biotechnology; rabbit anti-IRF4 was from St John’s Laboratory ( STJ93764 ); and rabbit anti-CX3CL1 (ab25088) and rabbit anti-CD68 (ab125212) were from Abcam.

Techniques: Immunofluorescence, Staining

Journal: Journal of the American Society of Nephrology : JASN

Article Title: Deletion of Myeloid Interferon Regulatory Factor 4 (Irf4) in Mouse Model Protects against Kidney Fibrosis after Ischemic Injury by Decreased Macrophage Recruitment and Activation

doi: 10.1681/ASN.2020071010

Figure Lengend Snippet: Myeloid IRF4 deletion led to relatively better kidney function and decreased renal fibrosis 4 weeks after AKI. Male IRF4f/f (WT) and LysM-Cre IRF4f/f (MΦ IRF4−/−) mice underwent AKI and were sacrificed 4 weeks later. (A and B) MΦ IRF4−/− mice had lower serum creatinine and albuminuria (A) and less tubular injury (B). *P<0.05, **P<0.01, ***P<0.001, n=9 in (A) and n=4 in (B). (C) MΦ IRF4−/− mice had less renal fibrosis as indicated by Sirius red staining. Original magnification ×160. ***P<0.001, n=6. (D) Quantitative PCR analysis showed decreases in renal mRNA levels of profibrotic and fibrotic components, including TGF-β1, TGF-β2, α-SMA, CTGF, collagen I (col I), col III, col IV, and fibronectin (FN) in MΦ IRF4−/− mice. **P<0.01, ***P<0.001; n=7 in WT group and n=8 in MΦ IRF4−/− group. (E) Immunoblotting showed decreased renal protein levels of α-SMA and CTGF in MΦ IRF4−/− mice. **P<0.01, n=4 in WT group and n=5 in MΦ IRF4−/− group. (F) Immunostaining showed that MΦ IRF4−/− mice had decreased renal expression of profibrotic and fibrotic components, including col I, col IV, α-SMA (marker of myofibroblasts), and CTGF. Original magnification ×160 for all. *P<0.05, **P<0.01, ***P<0.001, n=4 for all.

Article Snippet: Antibodies Rat anti-mouse F4/80 (MCA497R, a marker of macrophages) was purchased from AbD Serotec (now Bio-Rad), mouse anti–α-smooth muscle actin (α-SMA, a marker of myofibroblasts, A5228) was from Sigma; rabbit anti-murine collagen type I (600–401–103–0.1) and collage type IV (600–401–106–0.1) were from Rockland Immunochemicals; mouse anti–4-hydroxynonenal (4-HNE, a marker of oxidative stress, MAB3249), goat anti-CCL19 (AF880), goat anti-CCL21 (AF457) were from R&D; mouse anti-C/EBP homologous protein (2895), mouse anti–α-Tubulin (3873), rabbit anti–phospho-AKT (4060), rabbit anti-AKT (4691), rabbit anti–phospho-ERK (4370), rabbit anti-ERK (9102), rabbit anti–phospho-p38 (4511), rabbit anti-p38 (9212), rabbit anti–phospho-JNK (4668), rabbit anti-JNK (9252), and rabbit anti-PTEN (9552) were from Cell Signaling Technology; goat anti-human connective tissue growth factor (CTGF, SC-14939) was from Santa Cruz Biotechnology; rabbit anti-IRF4 was from St John’s Laboratory ( STJ93764 ); and rabbit anti-CX3CL1 (ab25088) and rabbit anti-CD68 (ab125212) were from Abcam.

Techniques: Staining, Real-time Polymerase Chain Reaction, Western Blot, Immunostaining, Expressing, Marker

Journal: Journal of the American Society of Nephrology : JASN

Article Title: Deletion of Myeloid Interferon Regulatory Factor 4 (Irf4) in Mouse Model Protects against Kidney Fibrosis after Ischemic Injury by Decreased Macrophage Recruitment and Activation

doi: 10.1681/ASN.2020071010

Figure Lengend Snippet: Myeloid IRF4 deficiency protected against renal fibrosis in UUO. Male IRF4f/f (WT) and LysM-Cre IRF4f/f (MΦ IRF4−/−) mice underwent UUO for 7 days. (A) Quantitative PCR analysis showed lower renal mRNA levels of profibrotic and fibrotic components, including α-SMA, CTGF, TGF-β1, TGF-β2, collagen I (col I), col III, col IV, and fibronectin (FN) in MΦ IRF4−/− mice. **P<0.01, ***P<0.001; n=8. (B) Sirius red staining showed less renal fibrosis in MΦ IRF4−/− mice. ***P<0.001, n=4.

Article Snippet: Antibodies Rat anti-mouse F4/80 (MCA497R, a marker of macrophages) was purchased from AbD Serotec (now Bio-Rad), mouse anti–α-smooth muscle actin (α-SMA, a marker of myofibroblasts, A5228) was from Sigma; rabbit anti-murine collagen type I (600–401–103–0.1) and collage type IV (600–401–106–0.1) were from Rockland Immunochemicals; mouse anti–4-hydroxynonenal (4-HNE, a marker of oxidative stress, MAB3249), goat anti-CCL19 (AF880), goat anti-CCL21 (AF457) were from R&D; mouse anti-C/EBP homologous protein (2895), mouse anti–α-Tubulin (3873), rabbit anti–phospho-AKT (4060), rabbit anti-AKT (4691), rabbit anti–phospho-ERK (4370), rabbit anti-ERK (9102), rabbit anti–phospho-p38 (4511), rabbit anti-p38 (9212), rabbit anti–phospho-JNK (4668), rabbit anti-JNK (9252), and rabbit anti-PTEN (9552) were from Cell Signaling Technology; goat anti-human connective tissue growth factor (CTGF, SC-14939) was from Santa Cruz Biotechnology; rabbit anti-IRF4 was from St John’s Laboratory ( STJ93764 ); and rabbit anti-CX3CL1 (ab25088) and rabbit anti-CD68 (ab125212) were from Abcam.

Techniques: Real-time Polymerase Chain Reaction, Staining

Journal: Journal of the American Society of Nephrology : JASN

Article Title: Deletion of Myeloid Interferon Regulatory Factor 4 (Irf4) in Mouse Model Protects against Kidney Fibrosis after Ischemic Injury by Decreased Macrophage Recruitment and Activation

doi: 10.1681/ASN.2020071010

Figure Lengend Snippet: IRF4 deletion led to impaired BMDM migration in vitro. BMDMs were isolated from IRF4f/f (WT) and LysM-Cre IRF4f/f (MΦ IRF4−/−) mice, and were immediately used for in vitro Transwell migration assays. (A) Chemotactic responses to 10% FBS, fMLP, and CX3CL1 were markedly lower for IRF4−/− BMDMs than WT BMDMs. ***P<0.001, n=4–6. (B) Chemotactic responses to CCL19 and CCL21 were also significantly lower for IRF4−/− BMDMs than WT BMDMs. ***P<0.001, n=5.

Article Snippet: Antibodies Rat anti-mouse F4/80 (MCA497R, a marker of macrophages) was purchased from AbD Serotec (now Bio-Rad), mouse anti–α-smooth muscle actin (α-SMA, a marker of myofibroblasts, A5228) was from Sigma; rabbit anti-murine collagen type I (600–401–103–0.1) and collage type IV (600–401–106–0.1) were from Rockland Immunochemicals; mouse anti–4-hydroxynonenal (4-HNE, a marker of oxidative stress, MAB3249), goat anti-CCL19 (AF880), goat anti-CCL21 (AF457) were from R&D; mouse anti-C/EBP homologous protein (2895), mouse anti–α-Tubulin (3873), rabbit anti–phospho-AKT (4060), rabbit anti-AKT (4691), rabbit anti–phospho-ERK (4370), rabbit anti-ERK (9102), rabbit anti–phospho-p38 (4511), rabbit anti-p38 (9212), rabbit anti–phospho-JNK (4668), rabbit anti-JNK (9252), and rabbit anti-PTEN (9552) were from Cell Signaling Technology; goat anti-human connective tissue growth factor (CTGF, SC-14939) was from Santa Cruz Biotechnology; rabbit anti-IRF4 was from St John’s Laboratory ( STJ93764 ); and rabbit anti-CX3CL1 (ab25088) and rabbit anti-CD68 (ab125212) were from Abcam.

Techniques: Migration, In Vitro, Isolation

Journal: Journal of the American Society of Nephrology : JASN

Article Title: Deletion of Myeloid Interferon Regulatory Factor 4 (Irf4) in Mouse Model Protects against Kidney Fibrosis after Ischemic Injury by Decreased Macrophage Recruitment and Activation

doi: 10.1681/ASN.2020071010

Figure Lengend Snippet: Myeloid IRF4 deletion led to attenuated macrophage infiltration in vivo. BMDMs were isolated from WT and MΦ IRF4−/− mice, labeled with the monocyte tracking dye PKH26 and injected into WT mice that would undergo AKI 16 hours later, and labeled cells in the kidney were evaluated 3 days after ischemic injury. (A) The number of renal-infiltrated, PKH26, and F4/80 double-positive cells were significantly lower in mice receiving IRF4−/− monocytes than in mice receiving WT monocytes. ***P<0.001, n=4. (B) Flow cytometric analysis determined that F4/80 and PKH26 double-positive cell numbers were significantly lower in mice receiving IRF4−/− monocytes than in mice receiving WT monocytes. ***P<0.001, n=8.

Article Snippet: Antibodies Rat anti-mouse F4/80 (MCA497R, a marker of macrophages) was purchased from AbD Serotec (now Bio-Rad), mouse anti–α-smooth muscle actin (α-SMA, a marker of myofibroblasts, A5228) was from Sigma; rabbit anti-murine collagen type I (600–401–103–0.1) and collage type IV (600–401–106–0.1) were from Rockland Immunochemicals; mouse anti–4-hydroxynonenal (4-HNE, a marker of oxidative stress, MAB3249), goat anti-CCL19 (AF880), goat anti-CCL21 (AF457) were from R&D; mouse anti-C/EBP homologous protein (2895), mouse anti–α-Tubulin (3873), rabbit anti–phospho-AKT (4060), rabbit anti-AKT (4691), rabbit anti–phospho-ERK (4370), rabbit anti-ERK (9102), rabbit anti–phospho-p38 (4511), rabbit anti-p38 (9212), rabbit anti–phospho-JNK (4668), rabbit anti-JNK (9252), and rabbit anti-PTEN (9552) were from Cell Signaling Technology; goat anti-human connective tissue growth factor (CTGF, SC-14939) was from Santa Cruz Biotechnology; rabbit anti-IRF4 was from St John’s Laboratory ( STJ93764 ); and rabbit anti-CX3CL1 (ab25088) and rabbit anti-CD68 (ab125212) were from Abcam.

Techniques: In Vivo, Isolation, Labeling, Injection

Journal: PLoS ONE

Article Title: Gene Expression Profiles in Paired Gingival Biopsies from Periodontitis-Affected and Healthy Tissues Revealed by Massively Parallel Sequencing

doi: 10.1371/journal.pone.0046440

Figure Lengend Snippet: Top 50 upregulated genes in periodontitis-affected tissue with Unigene entry.

Article Snippet: The expression of CD3, IRF4 and CCL18 was investigated using CD3 polyclonal rabbit antibody (1 μg/ml, PBS-Saponin) from Dako Sweden AB (Stockholm, Sweden), IRF4 polyclonal rabbit antibody (0.5 μg/ml, PBS-Saponin) from Atlas antibodies (Stockholm, Sweden) and CCL18 polyclonal rabbit anti-human antibody (0.5 μg/ml, PBS-Saponin) from Sigma-Aldrich (St. Louis, MO, USA).

Techniques: Binding Assay, Sequencing, Membrane, Activation Assay

Journal: PLoS ONE

Article Title: Gene Expression Profiles in Paired Gingival Biopsies from Periodontitis-Affected and Healthy Tissues Revealed by Massively Parallel Sequencing

doi: 10.1371/journal.pone.0046440

Figure Lengend Snippet: Selected upregulated genes identified in periodontitis and involved in other chronic inflammatory diseases.

Article Snippet: The expression of CD3, IRF4 and CCL18 was investigated using CD3 polyclonal rabbit antibody (1 μg/ml, PBS-Saponin) from Dako Sweden AB (Stockholm, Sweden), IRF4 polyclonal rabbit antibody (0.5 μg/ml, PBS-Saponin) from Atlas antibodies (Stockholm, Sweden) and CCL18 polyclonal rabbit anti-human antibody (0.5 μg/ml, PBS-Saponin) from Sigma-Aldrich (St. Louis, MO, USA).

Techniques: Activation Assay

Journal: PLoS ONE

Article Title: Gene Expression Profiles in Paired Gingival Biopsies from Periodontitis-Affected and Healthy Tissues Revealed by Massively Parallel Sequencing

doi: 10.1371/journal.pone.0046440

Figure Lengend Snippet: A. Immunohistochemical staining of IRF4. B. Immunohistochemical staining of CCL18.

Article Snippet: The expression of CD3, IRF4 and CCL18 was investigated using CD3 polyclonal rabbit antibody (1 μg/ml, PBS-Saponin) from Dako Sweden AB (Stockholm, Sweden), IRF4 polyclonal rabbit antibody (0.5 μg/ml, PBS-Saponin) from Atlas antibodies (Stockholm, Sweden) and CCL18 polyclonal rabbit anti-human antibody (0.5 μg/ml, PBS-Saponin) from Sigma-Aldrich (St. Louis, MO, USA).

Techniques: Immunohistochemical staining, Staining