Journal: Cell reports

Article Title: Interferon-γ induces combined pyroptotic angiopathy and APOL1 expression in human kidney disease

doi: 10.1016/j.celrep.2024.114310

Figure Lengend Snippet:

Article Snippet: BX795 (DMSO, 1 μM) , MedChemExpress , HY-10514.

Techniques: Plasmid Preparation, Recombinant, High Molecular Weight, Cell Culture, RNA sequencing, Derivative Assay, Modification, Software

Journal: Journal of Neuroinflammation

Article Title: Retinoic acid inducible gene-I mediated detection of bacterial nucleic acids in human microglial cells

doi: 10.1186/s12974-020-01817-1

Figure Lengend Snippet: Bacterial components stimulate RIG-I-dependent signaling in hμglia human microglial cells. Cells were untreated or treated with 1 μM BX795, an inhibitor of TBK1/IKKε, for 3 h prior to transfection with 0.1 μg/ml BDNA, 1 μg/ml 5′pppRNA, 0.5 μg/ml bacterial genomic DNA (gDNA), or 1 μg/ml bacterial RNA ( a , b ). Total cell lysates were collected at 3 h and analyzed for protein expression of phosphorylated IRF3 (pIRF3) and β-actin via immunoblot analysis ( a ). Relative phosphorylated IRF3 expression was normalized to β-actin and is displayed graphically below the representative immunoblot. Cell supernatants were collected 24 h post transfection. IFN-β and IL-6 levels were quantified with specific capture ELISAs ( b ). Microglial cells were treated with scrambled siRNA or siRNA targeting RIG-I (αRIG-I) at a final concentration of 5 nM for 24 h. Cells were placed in fresh media for 24 h prior to transfection with 0.1 μg/ml BDNA, 1 μg/ml 5′pppRNA, 0.5 μg/ml bacterial gDNA, 1 μg/ml bacterial RNA, or infection with S . aureus at a MOI of 50 ( c ). Microglial cells were treated with scrambled siRNA or siRNA targeting RNA polymerase III (αRP3) at a final concentration of 5 nM for 24 h, then placed in fresh media for 24 h, and then transfected with 0.1 μg/ml BDNA, 0.5 μg/ml bacterial gDNA, or 5 nM DNA/RNA triangles ( d ). Cell supernatants were collected at 24 h post transfection and IFN-β levels were quantified by specific capture ELISA. Data are expressed as mean ± SEM for a minimum of three independent experiments. Asterisks indicate statistical significance compared to untreated condition as determined by Student’s t test or two-way ANOVA ( p < 0.05)

Article Snippet: In some experiments, microglia were untreated or treated with 1 μM BX795 (Invivogen) in DMEM supplemented with 5% FBS and 100 U/ml penicillin–100 μg/ml streptomycin at 37 °C 5% CO 2 for 3 h prior to transfection with bacterial nucleic acids or nucleic acid nanoparticles as described above.

Techniques: Transfection, Expressing, Western Blot, Analysis, Concentration Assay, Infection, Enzyme-linked Immunosorbent Assay

Journal: Journal of Neuroinflammation

Article Title: Retinoic acid inducible gene-I mediated detection of bacterial nucleic acids in human microglial cells

doi: 10.1186/s12974-020-01817-1

Figure Lengend Snippet: RNA triangle nanoparticles stimulate RIG-I dependent responses in hμglia human microglial cells. DNA and RNA triangle formations assessed by atomic force microscopy (AFM) and ethidium bromide total staining native-PAGE ( a , b ). “L” corresponds to DNA low molecular weight ladder. Cells were untreated or treated with 1 μM BX795, an inhibitor for TBK1/IKKε, for 3 h prior to transfection with 0.1 μg/ml BDNA, 1 μg/ml 5′pppRNA, 5 nM DNA triangles, or 5 nM RNA triangles. Cell lysates collected at 1, 2, or 3 h were analyzed for protein expression of phosphorylated IRF3 (pIRF3) and the housekeeping gene β-actin via immunoblot analysis ( c , d ). Cell supernatants were collected 24 h post transfection and IFN-β levels were quantified by specific capture ELISA ( e ). Microglia were treated with scrambled control siRNA or siRNA targeted against RIG-I (αRIG-I) at a final concentration of 5 nM for 24 h. Cells were placed in fresh media for 24 h prior to transfection with 5 nM RNA triangles. Cell supernatants were collected 24 h post transfection and IFN-β levels were quantified by specific capture ELISA. Cell lysates were collected 24 h post transfection and analyzed for protein expression of RIG-I and the housekeeping gene, β-actin, via immunoblot analysis ( f ). Data are expressed as mean ± SEM for a minimum of three independent experiments. Asterisks indicate statistical significance compared to untreated condition as determined by Student’s t test or two-way ANOVA ( p < 0.05)

Article Snippet: In some experiments, microglia were untreated or treated with 1 μM BX795 (Invivogen) in DMEM supplemented with 5% FBS and 100 U/ml penicillin–100 μg/ml streptomycin at 37 °C 5% CO 2 for 3 h prior to transfection with bacterial nucleic acids or nucleic acid nanoparticles as described above.

Techniques: Microscopy, Staining, Clear Native PAGE, Molecular Weight, Transfection, Expressing, Western Blot, Analysis, Enzyme-linked Immunosorbent Assay, Control, Concentration Assay

Journal: BMC Cancer

Article Title: IΚΚε cooperates with either MEK or non-canonical NF-kB driving growth of triple-negative breast cancer cells in different contexts

doi: 10.1186/s12885-018-4507-2

Figure Lengend Snippet: IKKε supports viability and MEK activation. a ) 30 μg of protein was analyzed in whole cell lysates of breast cancer cells grown to 70% confluence. Cells were treated with vehicle control (Ctl), 2 μM MEK inhibitor (MEKi), 2 μM IKKβ inhibitor (IKKβi), or 2 μM BX795 for inhibition of IKKε (IKKεi) for 6 h before lysate collection. b ) 30 μg of protein was analyzed in whole cell lysates of breast cancer cells grown to 70% confluence after siRNA mediated knockdown of IKBKE (siIKKε). Quantification of three independent replicates reveals increased non-canonical NF-κB proteins with IKBKE knockdown. c ) 30 μg of protein was analyzed in whole cell lysates of MDA MB 468 cells after 1 h exposure to 2 μM BX795 for IKKε inhibition. Quantification of three independent replicates confirms pharmacological inhibition of IKKε activity significantly increased non-canonical NF-κB protein levels. *significantly different from corresponding vehicle control P < 0.05, unpaired T-test ( b - c )

Article Snippet: MEK inhibitor, AZD6244, and a non-selective inhibitor of Ser/Thr kinases, BX795, that inhibits IKKε, among others were purchased from Selleck Chemicals (Houston, TX).

Techniques: Activation Assay, Control, Inhibition, Knockdown, Activity Assay

Journal: Nature Communications

Article Title: Targeting leucine-rich repeat kinase 2 overcomes resistance to oncolytic herpes simplex virus-based therapies in glioblastoma

doi: 10.1038/s41467-026-70132-9

Figure Lengend Snippet: a Anti-myc immunoprecipitates prepared from 293 T cells transfected with the indicated plasmids were subjected to SDS‒PAGE and blotted with the indicated antibodies. The samples derive from the same experiment but different gels for Myc and another for STAT1 were processed in parallel. b Endogenous LRRK2 and STAT1 complexes in U-118 MG cells were isolated by co-immunoprecipitation (co-IP) and detected using anti-LRRK2 antibodies. The samples derive from the same experiment but different gels for LRRK2 and another for STAT1 were processed in parallel. c The interactions between STAT1-Flag and Myc-LRRK2 mutants were detected by a co-IP assay. FL, full-length. The samples derive from the same experiment but different gels for Myc and another for Flag were processed in parallel. d , e The interactions between Myc-LRRK2 and STAT1-HA truncations were detected by a co-IP assay. The samples derive from the same experiment but different gels for Myc and another for HA were processed in parallel. f STAT1-His proteins were incubated with human FL LRRK2 proteins in the presence of ATP. The reaction products were analyzed with the indicated antibodies. CD300A proteins served as a negative control. The samples derive from the same experiment but different gels for Flag and another for His were processed in parallel. g , h 293 T cells were cotransfected with Flag-STAT1 and LRRK2 in the presence or absence of LRRK2-IN-1, and the phosphorylation of STAT1 was analyzed by western blot analysis. The samples derive from the same experiment but different gels for STAT1, another for p-STAT1 701 and another for p-STAT1 727 were processed in parallel. i 293 T cells were cotransfected with Flag-STAT1 and each LRRK2 mutant, either in the presence or absence of LRRK2-IN-1, and STAT1 phosphorylation was assessed via western blot analysis. The samples derive from the same experiment but different gels for STAT1, another for p-STAT1 701 and another for GAPDH were processed in parallel. j Western blotting was performed to assess and quantify phosphorylated STAT1 and HSV-derived GFP in U-87 MG cells treated with fludarabine (10 µM) for 4 h, either in the presence or absence of LRRK2-IN-1, followed by infection with oHSV-GFP (MOI = 1 PFU/cell). The samples derive from the same experiment but different gels for STAT1 and GFP, another for p-STAT1 701 and another for actin were processed in parallel. k Western blotting was performed to assess and quantify phosphorylated STAT1 and HSV-derived GFP in GBM-1 cells. Cells transfected with EV, LRRK2 or LRRK2 D1994A were infected with oHSV-GFP (MOI = 0.5 PFU/cell), with or without LRRK2-IN-1. The samples derive from the same experiment but different gels for STAT1 and GFP, another for p-STAT1 701 and another for actin were processed in parallel. l Western blotting was performed to assess and quantify phosphorylated TBK1, phosphorylated LRRK2, phosphorylated Rab10, and phosphorylated STAT1 in BX795 (10 µM)-treated U-87 cells following infection with oHSV-GFP (MOI = 0.5 PFU/cell). The samples derive from the same experiment but different gels for p-TBK1, another for p-LRRK2, another for LRRK2, another for p-Rab10 and p-STAT1, another for STAT1 and another for actin were processed in parallel. Western blot analyses were independently repeated twice for panels ( a – d and f )and three times for panels ( e , g and i – l ), with similar results. The data are presented as the mean ± SD from three independent experiments ( h – l ), and P values were calculated using an ordinary one-way ANOVA ( h – l ).

Article Snippet: The following chemicals and recombinant proteins were used: Bioactive Compound Library (MedChemExpress, HY-L001), LRRK2-IN-1 (MedChemExpress, HY-10875), DCLK1-IN-1 (MedChemExpress, HY-135985), MLi-2 (MedChemExpress, HY-100411), Fludarabine (MedChemExpress, HY-B0069), PFE-360 (MedChemExpress, HY-120085), BX795 (TopScience, T1830), Phosphatase inhibitor cocktail III (TopScience, C0004), Protease inhibitor cocktail (MedChemExpress, HY-K0011), and RIPA lysis buffer (Beyotime, P0013C).

Techniques: Transfection, Isolation, Immunoprecipitation, Co-Immunoprecipitation Assay, Incubation, Negative Control, Phospho-proteomics, Western Blot, Mutagenesis, Derivative Assay, Infection

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Enhanced IFN Sensing by Aggressive Chronic Lymphocytic Leukemia Cells.

doi: 10.4049/jimmunol.2200199

Figure Lengend Snippet: FIGURE 1. IFN production and response of CLL cells in vitro. Purified CLL cells with U-CLL (n 5 26) or M-CLL (n 5 27) IGHV loci were cultured in AIM V media (A). CLL cells from nine additional patients were stimulated with the TLR7 agonist resiquimod (S28; 1 mg/ml) in the presence or absence of ibrutinib (400 nM) (B). After 24 h, IFN-a levels in the supernatants were measured as described in the Materials and Methods. Freshly purified CLL cells were stimulated with the supernatant of a 7-d-old culture from an unrelated sample for 30 min (C) or with S28 for 24 h (D) in the presence or absence of ani- frolumab (ANI). p-STAT2 levels were then measured by immunoblotting and densitometry using b-actin as a loading control. CLL cells in AIM V were cul- tured with inhibitors of TBK1 (BX795 [1 mM] and GSK8612 [5 mM]) or STING (H151 [1 mM]) for 24 h (E). Other samples were cultured with the TBK1 inhibitors or the IRAK4 inhibitor (1 mM) for 24 h and stimulated with S28 for another 24 h (F). p-STAT2, -IRF3, and -IRF7 levels were then measured by immunoblotting and quantified by densitometry using b-actin as a loading control. Representative immunoblots are shown. Averages and SEs are indicated in the graphs with the dots and lines representing different patient samples. p values were calculated with one-way ANOVA with multiple comparisons, paired and unpaired Student t tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.

Article Snippet: The TBK1 inhibitor BX795 and PTPN2 inhibitor SF1670 were from Tocris Bioscience (Toronto, ON, Canada).

Techniques: In Vitro, Purification, Cell Culture, Western Blot, Control

Journal: iScience

Article Title: Heme regulates protein interactions and phosphorylation of BACH2 intrinsically disordered region in humoral response

doi: 10.1016/j.isci.2024.111529

Figure Lengend Snippet: Identification of Tbk1 gene as a direct target of BACH2 (A) The ChIP-seq binding profiles for BACH2 in Ebf1 KO pre-pro-B cell line (GSE87503) and those of histone H3 lysine 27 acetylation (H3K27Ac) and histone H3 lysine 4 trimethylation (H3K4me3) in mouse primary B cell (GSM1441280 and GSM1441328 in GSE60103 ). The ChIP-seq data were visualized using Integrative Genomics Viewer (IGV v2.11.1 ). Two BACH2-binding sites were found in the promoter (#1) and intron (#2) regions of the Tbk1 gene. Blue arrow indicates the transcription start site (TSS) of the Tbk1 gene. (B) The binding of BACH2 to sites #1 and #2 was demonstrated by ChIP-qPCR in the BAL17 mature B cell line. The results are shown as enrichment relative to samples immunoprecipitated by NRS. (C) The electrophoretic mobility shift assay showing the binding of BACH2 to the MERE-like sequences found in BACH2-binding sites #1 (left) and #2 (right). The 32 P-labeled probes were mixed with the BACH2 and MAFK proteins without any additive (lane 2) or in the presence of an anti-BACH2 antibody (lane 3, anti-BACH2), a normal rabbit serum (lane 4, NRS) or an anti-MafK antiserum (lane 5, anti-MafK). Competition assays using the unlabeled wild-type or mutant probes as competitors were also shown (lanes 6 and 7, no competitor, lane 8, wild-type competitor and lane 9, Mut competitor). The results shown here are representative of those from three experiments. (D) The RT-qPCR analysis of the TBK1 mRNA expression in wild-type and BACH2 KO mouse splenic B cell stimulated with LPS (20 μg/mL) for 1 or 2 days. (E) The western blotting results of wild-type and BACH2 KO mouse splenic B cell. BACH2 was revealed with an anti-BACH2 antibody. TBK1 was revealed with an anti-TBK1 antibody. GAPDH served as an internal control. (F) The effect of BX795 on the TBK1 mRNA expression in wild-type and BACH2 KO splenic B cell stimulated with LPS (20 μg/mL) in the presence or absence of 1 μM BX795 for 1 or 2 days. (G) HEK293T cells were transfected with the indicated reporter and effector plasmids. The amounts of plasmids were as follows: pGL4-4.28- Slc48a1 MARE luciferase reporter (2.0 μg), pEF seapansy (10 ng), pCMV BACH2 (200 ng), and pcDNA FLAG 3.1 TBK1 (200 ng).

Article Snippet: BX795 , CEM , CS-0259.

Techniques: ChIP-sequencing, Binding Assay, ChIP-qPCR, Immunoprecipitation, Electrophoretic Mobility Shift Assay, Labeling, Mutagenesis, Quantitative RT-PCR, Expressing, Western Blot, Control, Transfection, Luciferase

Journal: iScience

Article Title: Heme regulates protein interactions and phosphorylation of BACH2 intrinsically disordered region in humoral response

doi: 10.1016/j.isci.2024.111529

Figure Lengend Snippet: TBK1 promotes plasma cell differentiation by inactivating BACH2 (A) Upper left: a schematic representation of the experimental design. Lower left and right panels: BX795 repressed the Blimp-1 gene expression in mouse splenic B cells. Lower left: The expression of the Blimp-1 -EGFP reporter gene determined by a FACS analysis. B220-positive cells from the wild-type Blimp-1 -EGFP mice were stimulated with 20 μg/mL LPS in the presence or absence of 1 μM BX795 on day 1 or day 2. Each gate shows the percentage of EGFP-positive cells. Representative results of a triplication are shown in right panel. The experiment was performed with N = 3. Right: the percentage of EGFP-positive cells cultured with LPS+BX795 or LPS alone in wild-type B cells. The data are presented as the means ± SD of triplicate determinations. The statistical analyses were performed by the use of the Student’s t test. The experiment was performed with N = 3. (B) The binding of BACH2 to the Prdm1 promoter (left panel) and Prdm1 intron5 (right panel) regions was demonstrated by ChIP-qPCR in the BAL17 mature B cell line. BAL17 cells were treated with BX795 for 3 h. Results are shown as enrichment relative to sample immunoprecipitated by a normal rabbit serum (NRS). The experiment was performed with N = 3. (C) The precursor mRNA expression of Prdm1 in wild-type and BACH2 KO splenic B cells treated with BX795 for 3 h was quantified by RT-qPCR. After the stimulation by LPS, the cells were cultured for 12 h before the treatment. The quantities of Prdm1 were normalized to the β-actin mRNA. The data are mean ± SD of three independent experiments. The experiment was performed with N = 3. (D) The mammalian two-hybrid (M2H) assay showing the inhibitory effect of TBK1 and TBK1-S172A on the interaction of BACH2 with NCoR1 (left). The inhibition of the interaction by TBK1 was diminished by a TBK1 inhibitor (right). HEK293T cells were co-transfected with the pGL4.35-9×GAL4UAS-Luc reporter (Promega) vector, pFN26A-hBACH2 GAL4-DBD fusion expression vector and pFN10A-hNCOR1 VP-16 AD expression vector together with either pCAG-hTBK1 or pCAG hTBK1(S172A). After 24 h of incubation, the cells were treated with the TBK1 inhibitor MRT67307 at the indicated concentrations of 0–3.0 μM for 6 h. After that, the cells were lysed, and luciferase activity was measured. The results are shown as fold induction compared to the negative control (pGL4.35-9×GAL4UAS-Luc alone) and represent the mean of triplicates from a representative experiment, with error bars showing the standard deviation.

Article Snippet: BX795 , CEM , CS-0259.

Techniques: Clinical Proteomics, Cell Differentiation, Gene Expression, Expressing, Cell Culture, Binding Assay, ChIP-qPCR, Immunoprecipitation, Quantitative RT-PCR, Inhibition, Transfection, Plasmid Preparation, Incubation, Luciferase, Activity Assay, Negative Control, Standard Deviation

Journal: iScience

Article Title: Heme regulates protein interactions and phosphorylation of BACH2 intrinsically disordered region in humoral response

doi: 10.1016/j.isci.2024.111529

Figure Lengend Snippet: The localization of BACH2 is regulated by TBK1 (A) Immunocytochemistry for the BACH2 protein in the presence of BX795 in M1 cells. The subcellular localization of BACH2 was evaluated by classification of 120 cells for each condition into two classes: cytoplasm dominant (N < C) and nucleus dominant (N > C). Blue represents nuclei stained by Hoechst, green represents BACH2 and red represents lamin B1. Scale bar represents 10 μm. (B) The subcellular localization of BACH2 in mouse splenic B cells cultured in the presence of BX795. Cells were cultured in the presence of LPS (20 μg/mL) for 12 h and then were treated with 1 or 5 μM BX795 for 3 h. BACH2 was revealed with an anti-BACH2 antibody (SE, short exposer; LE, long exposer). TBK1 was revealed with an anti-TBK1 antibody. p70S6K and p-p70S6K were revealed with anti-p70S6K and anti-p-p70S6K antibodies. Lamin B1 served as a control for the nuclear fraction and GAPDH was used as a control for the cytoplasmic fraction. W, whole-cell extract; C, cytoplasm; N, nucleus. (C) The dose-dependent effect of BX795 on the nuclear accumulation of BACH2 in mouse splenic B cells. Cells were cultured in the presence of LPS (20 μg/mL) for 20 h and then were treated with 1, 3 or 5 μM BX795 for 3 h. BACH2 was revealed with an anti-BACH2 antibody and lamin B1 served as a control for the nuclear fraction. (D) The western blotting results of the BACH2 protein before and after a CIAP-treatment of the whole-cell extracts from M1 cells. β-actin served as an internal control. (E) Namalwa cells were treated with the TBK1 inhibitors (2 μM) for the indicated periods, and BACH2 and actin were detected by western blotting.

Article Snippet: BX795 , CEM , CS-0259.

Techniques: Immunocytochemistry, Staining, Cell Culture, Control, Western Blot

Journal: iScience

Article Title: Heme regulates protein interactions and phosphorylation of BACH2 intrinsically disordered region in humoral response

doi: 10.1016/j.isci.2024.111529

Figure Lengend Snippet:

Article Snippet: BX795 , CEM , CS-0259.

Techniques: Virus, Recombinant, Protease Inhibitor, Transfection, Multiplex sample analysis, Protein Purification, Reporter Assay, Luciferase, Cell Isolation, Plasmid Preparation, Reverse Transcription, SYBR Green Assay, ChIP-qPCR, Sequencing, Negative Control, Software