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pcdna p65 flag wt mouse addgene addgene  (Addgene inc)


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    Structured Review

    Addgene inc pcdna p65 flag wt mouse addgene addgene
    Pcdna P65 Flag Wt Mouse Addgene Addgene, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/p65/RelA+cFlag+pcDNA3+(Plasmid+%2320012)/pm42905514-230-215-216
    Average 93 stars, based on 62 article reviews
    pcdna p65 flag wt mouse addgene addgene - by Bioz Stars, 2026-11
    93/100 stars

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    Related Articles

    Functional Assay:

    Article Title: Potential of omega-3 and conjugated fatty acids to control microglia inflammatory imbalance elicited by obesogenic nutrients.
    Article Snippet: .. The measurement of the nuclear accumulation of the p65 subunit of NF-κB as a functional indicator of NF-κB activation was achieved by using the NF-κB GFP-tagged p65 (here defined and GFP-p65; addgene plasmid #23255) [82]. ..

    Activation Assay:

    Article Title: Potential of omega-3 and conjugated fatty acids to control microglia inflammatory imbalance elicited by obesogenic nutrients.
    Article Snippet: .. The measurement of the nuclear accumulation of the p65 subunit of NF-κB as a functional indicator of NF-κB activation was achieved by using the NF-κB GFP-tagged p65 (here defined and GFP-p65; addgene plasmid #23255) [82]. ..

    Plasmid Preparation:

    Article Title: Potential of omega-3 and conjugated fatty acids to control microglia inflammatory imbalance elicited by obesogenic nutrients.
    Article Snippet: .. The measurement of the nuclear accumulation of the p65 subunit of NF-κB as a functional indicator of NF-κB activation was achieved by using the NF-κB GFP-tagged p65 (here defined and GFP-p65; addgene plasmid #23255) [82]. ..

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..

    other:

    Article Title: Daily alcohol intake triggers aberrant synaptic pruning leading to synapse loss and anxiety-like behavior.
    Article Snippet: Plasmids used in this study were purchased from Addgene: NF-B GFP–tagged p65 (RRID:Addgene_23255), IB-miRFP703 (RRID:Addgene_80005), pLNCX chick src Y527F (RRID:Addgene_13660), pUSE-RapR-Src-myc (RRID:Addgene_25933), psPAX2 (RRID: Addgene_12260), pMD2.G (RRID:Addgene_12259), pUMVC (RRID:Addgene_8449), pMSCV (RRID:Addgene_24828), and pCherry-FRB (RRID:Addgene_25920).

    Control:

    Article Title: The NF-κB-HE4 axis: A novel regulator of HE4 secretion in ovarian cancer
    Article Snippet: Other materials were obtained from venders as follows; cytokines: TNFα (R&D Systems cat. No. 210-TA-020), IL-1β (BioLegend cat. No. 579402); chemicals: TPCA-1 (BioVision cat. No. 2431-5), BIRB-769 (APExBIO cat. No. A5639), JNK-IN-8 (APExBIO cat. No. A3520), CI-1040 (Selleckchem cat. No. S1020); siRNAs: Silencer Select siRNAs (ThermoFisher) for control (cat. No. 4390843) and HE4 (ID No. s20356). siGENOME siRNAs (horizon) for control (cat. No. D-001210-03-05), HE4 (cat. No. M-010564-02), and p65 (cat. No. M-003533-02). .. Santa Cruz Biotechnology siRNAs for control (cat. No. sc-37007) and HE4 (cat. No. sc-43826); Vectors: empty (addgene, cat. No. 24165), p65 (addgene, cat. No. 21966), IKK2-EE (addgene, cat. No.11105); antibodies: p53 (Santa Cruz Biotechnology cat. No. sc-126), HE4 (OriGene cat. No. UM870019), p50 (BioLegend cat. No. 603901), P-c-Jun (BioLegend cat. No. 605551). .. All other antibodies were purchased from Cell Signaling Technology: P-p38 (cat. No. 4511), p38 (cat. No. 9212), c-Jun (cat. No. 9165), P-p44/42 (cat. No. 4370), p44/42 (cat. No. 9102), Iκβα (cat. No. 4814), α-Tubulin (cat. No. 2144), p65 (cat. No. 8242), GAPDH (cat. No. 2118), Lamin A/C (cat. No. 4777), p21 (cat. No. 2947), Cyclin E1 (cat. No. 4129), α 4 -Integrin (cat. No. 8440), α 5 -Integrin (cat. No. 4705), β 1 -integrin (cat. No. 9699), β 4 -Integrin (cat. No. 14803), E-Cadherin (cat. No. 3195), COX2 (cat. No. 12282), ICAM-1 (cat. No. 67836).

    Activity Assay:

    Article Title: A red light-responsive photoswitch for deep tissue optogenetics.
    Article Snippet: All constructs encoding sgRNAs were cloned into the pSPgRNA vector (Addgene, 47108). cDNA encoding codon-optimized Streptococcus pyogenes Cas9 was amplified from pX330-U6-Chimeric_BB-CBh-hSpCas9 (Addgene, 42230). .. To eliminate the nuclease activity of Cas9, we introduced D10A and H840A mutations. cDNAs encoding the MS2 (N55K) mutant and p65–HSF1 were amplified from MS2-P65-HSF1_GFP (Addgene, 61423). .. The EGFP-Cre gene was amplified from pENN.AAV.hSyn.HI.eGFP-Cre.WPRE.SV40 (Addgene, 105540). cDNAs encoding PIF6CreN and PhyBΔCreC (CreLite) were amplified from pCS2+PIF6CreN (Addgene, 131780) and pCS2+PhyBΔCreC (Addgene, 131781), respectively. cDNAs encoding PhyBNT-CreN (Light-Cre1), PhyB-NLS-CreN (Light-Cre2) and PIF3-NLS-CreC (Light-Cre1 and Light-Cre2) were amplified from pLH_Scr15 (Addgene, 100537) and pLH_Scr16 (Addgene, 100538). cDNAs encoding iCre, DrBphP, RpBphP1, PpsR2, Zdk1, LDB-14 and LDB-3 were synthesized with optimized codons. cDNAs encoding VP16-NLS and tetR were amplified from tetR-VP16-NLS/pSV40, gifted from Wilfried Weber.

    Mutagenesis:

    Article Title: A red light-responsive photoswitch for deep tissue optogenetics.
    Article Snippet: All constructs encoding sgRNAs were cloned into the pSPgRNA vector (Addgene, 47108). cDNA encoding codon-optimized Streptococcus pyogenes Cas9 was amplified from pX330-U6-Chimeric_BB-CBh-hSpCas9 (Addgene, 42230). .. To eliminate the nuclease activity of Cas9, we introduced D10A and H840A mutations. cDNAs encoding the MS2 (N55K) mutant and p65–HSF1 were amplified from MS2-P65-HSF1_GFP (Addgene, 61423). .. The EGFP-Cre gene was amplified from pENN.AAV.hSyn.HI.eGFP-Cre.WPRE.SV40 (Addgene, 105540). cDNAs encoding PIF6CreN and PhyBΔCreC (CreLite) were amplified from pCS2+PIF6CreN (Addgene, 131780) and pCS2+PhyBΔCreC (Addgene, 131781), respectively. cDNAs encoding PhyBNT-CreN (Light-Cre1), PhyB-NLS-CreN (Light-Cre2) and PIF3-NLS-CreC (Light-Cre1 and Light-Cre2) were amplified from pLH_Scr15 (Addgene, 100537) and pLH_Scr16 (Addgene, 100538). cDNAs encoding iCre, DrBphP, RpBphP1, PpsR2, Zdk1, LDB-14 and LDB-3 were synthesized with optimized codons. cDNAs encoding VP16-NLS and tetR were amplified from tetR-VP16-NLS/pSV40, gifted from Wilfried Weber.

    Amplification:

    Article Title: A red light-responsive photoswitch for deep tissue optogenetics.
    Article Snippet: All constructs encoding sgRNAs were cloned into the pSPgRNA vector (Addgene, 47108). cDNA encoding codon-optimized Streptococcus pyogenes Cas9 was amplified from pX330-U6-Chimeric_BB-CBh-hSpCas9 (Addgene, 42230). .. To eliminate the nuclease activity of Cas9, we introduced D10A and H840A mutations. cDNAs encoding the MS2 (N55K) mutant and p65–HSF1 were amplified from MS2-P65-HSF1_GFP (Addgene, 61423). .. The EGFP-Cre gene was amplified from pENN.AAV.hSyn.HI.eGFP-Cre.WPRE.SV40 (Addgene, 105540). cDNAs encoding PIF6CreN and PhyBΔCreC (CreLite) were amplified from pCS2+PIF6CreN (Addgene, 131780) and pCS2+PhyBΔCreC (Addgene, 131781), respectively. cDNAs encoding PhyBNT-CreN (Light-Cre1), PhyB-NLS-CreN (Light-Cre2) and PIF3-NLS-CreC (Light-Cre1 and Light-Cre2) were amplified from pLH_Scr15 (Addgene, 100537) and pLH_Scr16 (Addgene, 100538). cDNAs encoding iCre, DrBphP, RpBphP1, PpsR2, Zdk1, LDB-14 and LDB-3 were synthesized with optimized codons. cDNAs encoding VP16-NLS and tetR were amplified from tetR-VP16-NLS/pSV40, gifted from Wilfried Weber.

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..

    Luciferase:

    Article Title: A Gain-of-Function Cleavage of TonEBP by Coronavirus NSP5 to Suppress IFN-β Expression
    Article Snippet: The plasmid encoding the N-terminal fragment of TonEBP generated by SARS-CoV-2 NSP5 cleavage was cloned into the pCMV-tag 2B vector (#211172, Agilent Technologies, Santa Clara, CA, USA) by amplification and standard restriction cloning. .. The IFN-β promoter luciferase reporter (#102597), as well as transient expression vectors for MDA5 (#52876), MAVS (#52135), TBK1 (#131792), IRF3 (#127663), and p65 (#111192), were obtained from Addgene. ..

    Article Title: A Gain-of-Function Cleavage of TonEBP by Coronavirus NSP5 to Suppress IFN-β Expression.
    Article Snippet: The plasmid encoding the N-terminal fragment of TonEBP generated by SARS-CoV-2 NSP5 cleavage was cloned into the pCMV-tag 2B vector (#211172, Agilent Technologies, Santa Clara, CA, USA) by amplification and standard restriction cloning. .. The IFN-β promoter luciferase reporter (#102597), as well as transient expression vectors for MDA5 (#52876), MAVS (#52135), TBK1 (#131792), IRF3 (#127663), and p65 (#111192), were obtained from Addgene. ..

    Expressing:

    Article Title: A Gain-of-Function Cleavage of TonEBP by Coronavirus NSP5 to Suppress IFN-β Expression
    Article Snippet: The plasmid encoding the N-terminal fragment of TonEBP generated by SARS-CoV-2 NSP5 cleavage was cloned into the pCMV-tag 2B vector (#211172, Agilent Technologies, Santa Clara, CA, USA) by amplification and standard restriction cloning. .. The IFN-β promoter luciferase reporter (#102597), as well as transient expression vectors for MDA5 (#52876), MAVS (#52135), TBK1 (#131792), IRF3 (#127663), and p65 (#111192), were obtained from Addgene. ..

    Article Title: A Gain-of-Function Cleavage of TonEBP by Coronavirus NSP5 to Suppress IFN-β Expression.
    Article Snippet: The plasmid encoding the N-terminal fragment of TonEBP generated by SARS-CoV-2 NSP5 cleavage was cloned into the pCMV-tag 2B vector (#211172, Agilent Technologies, Santa Clara, CA, USA) by amplification and standard restriction cloning. .. The IFN-β promoter luciferase reporter (#102597), as well as transient expression vectors for MDA5 (#52876), MAVS (#52135), TBK1 (#131792), IRF3 (#127663), and p65 (#111192), were obtained from Addgene. ..

    Construct:

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..

    Polymerase Chain Reaction:

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..

    Synthesized:

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..

    Clone Assay:

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..

    Sequencing:

    Article Title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo
    Article Snippet: .. Plasmid Construction 1) pHRdSV40-scFv-GCN4-sfGFP-VPR-GB1-NLS To construct the VPR system, the sequences VP64 (PCR amplified from the Addgene plasmid, # 60904), p65 (PCR amplified from the Addgene plasmid, # 61423) and truncated RTA (125-190 aa, chemically synthesized) separated by a short amino acid linker, were cloned to the plasmid (#60904) to replace VP64 sequence. ..



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    ( A ) KEGG enrichment analysis of down-regulated DEGs in Sik2 F/F ; LysM Cre cardiac macrophages on day 3 post-MI. The top 20 enriched pathways are listed. ( B ) DEGs (fold change ≥ 2 and P .adjust ≤ 0.05) overlapped in top 20 of enriched pathways. ( C ) Transcription factor prediction was performed using TRRUST databases. The top 10 transcription factors are listed. ( D ) Immunoblotting analysis and quantification of P65 in the cytoplasm and nucleus of WT and SIK2-knockout PMs and treated with TNF-α (20 ng/ml) or vehicle ( n = 4) for 1 hour. ( E ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression in WT and SIK2-knockout PMs stimulated with TNF-α for 24 hours ( n = 6). ( F ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression ( n = 6). PMs were pretreated with ARN3236 (3 μmol) and stimulated with TNF-α for 24 hours. ( G ) WikiPathways enrichment analysis of differentially phosphorylated proteins in PMs treated with ARN3236 (3 μmol) or control. The top 20 enriched pathways are listed. ( H ) Immunoblotting analysis and quantification of phosphorylated P65 (p-P65), P65, phosphorylated P38 (p-P38), and P38 expression in WT and SIK2-knockout PMs stimulated with TNF-α or vehicle ( n = 6). ( I and J ) Flow cytometry analysis of efferocytosis in WT or LeSik2 Raw264.7 cells [stimulated with SB 203580 (10 μmol) or not] treated with CFSE-prelabeled RBCs ( n = 6).

    Journal: Science Advances

    Article Title: SIK2 antagonizes postinfarction cardiac repair by driving macrophage proinflammatory and impairing efferocytosis

    doi: 10.1126/sciadv.adw6624

    Figure Lengend Snippet: ( A ) KEGG enrichment analysis of down-regulated DEGs in Sik2 F/F ; LysM Cre cardiac macrophages on day 3 post-MI. The top 20 enriched pathways are listed. ( B ) DEGs (fold change ≥ 2 and P .adjust ≤ 0.05) overlapped in top 20 of enriched pathways. ( C ) Transcription factor prediction was performed using TRRUST databases. The top 10 transcription factors are listed. ( D ) Immunoblotting analysis and quantification of P65 in the cytoplasm and nucleus of WT and SIK2-knockout PMs and treated with TNF-α (20 ng/ml) or vehicle ( n = 4) for 1 hour. ( E ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression in WT and SIK2-knockout PMs stimulated with TNF-α for 24 hours ( n = 6). ( F ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression ( n = 6). PMs were pretreated with ARN3236 (3 μmol) and stimulated with TNF-α for 24 hours. ( G ) WikiPathways enrichment analysis of differentially phosphorylated proteins in PMs treated with ARN3236 (3 μmol) or control. The top 20 enriched pathways are listed. ( H ) Immunoblotting analysis and quantification of phosphorylated P65 (p-P65), P65, phosphorylated P38 (p-P38), and P38 expression in WT and SIK2-knockout PMs stimulated with TNF-α or vehicle ( n = 6). ( I and J ) Flow cytometry analysis of efferocytosis in WT or LeSik2 Raw264.7 cells [stimulated with SB 203580 (10 μmol) or not] treated with CFSE-prelabeled RBCs ( n = 6).

    Article Snippet: Primary antibodies used to specifically detect the proteins of interest were as follows: SIK2 (6919s, CST), GAPDH (G9545, Sigma-Aldrich), α-SMA (A5228, Sigma-Aldrich), Collagen I (AB765P, Sigma-Aldrich), Collagen III (AB7778, Abcam), CD31 (3528s, CST), Phospho-NF-κB P65 (Ser 536 ) (3033s, CST), NF-κB P65 (8242s, CST), Phospho-P38 MAPK (Thr 180 /Tyr 182 ) (4511s, CST), P38 MAPK (8690s, CST), α-Tubulin (66031-1, Proteintech), Histone H3 (68345-1, Proteintech), NOS2 (13120s, CST), FLAG-Tag (14793s, CST), HA-Tag (3724s, CST), TRAF1 (4710s, CST), TRAF2 (4724s, CST), TRAF4 (18527s, CST), TRAF6 (67591s, CST), His-Tag (12698s, CST), and Myc-Tag (2276s, CST).

    Techniques: Analysis, Western Blot, Knock-Out, Expressing, Control, Flow Cytometry, Significance Assay

    ( A ) Venn diagram delineating the intersection of SIK2-binding protein candidates in the top enriched pathways identified in , that is, NF-κB signaling pathway and MAPK signaling pathway. LC-MS/MS, liquid chromatography–tandem mass spectrometry. ( B ) Top proteins interacting with SIK2 identified through mass spectrometry analysis of peptides pulled down using anti-Flag antibody in HEK293T cells transfected with Flag-Sik2. ( C ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 using anti-Flag antibody, followed by immunoblotting with corresponding antibodies. HA, hemagglutinin. ( D and E ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 and HA-Traf2 using anti-Flag (D) or anti-HA (E) antibody, followed by immunoblotting with corresponding antibodies. FL, full length. ( F ) Immunoprecipitation (IP) in HEK293T cells cotransfected with HA-Traf2 and truncated Flag-Sik2 using an anti-HA antibody, followed by immunoblotting (IB) with corresponding antibodies. ( G ) Immunoprecipitation in HEK293T cells cotransfected with Flag-Sik2 and truncated HA-Traf2 using an anti-HA antibody, followed by immunoblotting with corresponding antibodies. ( H ) Western blotting analysis and quantification of SIK2, TRAF2, p-P38, P38, p-P65, and P65 expression in HEK293T cells transfected with SIK2 and si-TRAF2 or control ( n = 4). ( I ) Coimmunoprecipitation (Co-IP) analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and His-Ub, along with Flag-Sik2 or Flag-Sik2 T175A mutant. ( J ) Co-IP analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and Flag-Sik2, along with Myc-K48-Ub or Myc-K63-Ub. ( K ) Co-IP analysis of TRAF2 phosphate serine (p-Ser) and phosphate threonine (p-Thr) in HEK293T cells transfected with HA-Traf2, along with Flag-Sik2 or Flag-Sik2 T175A mutant.

    Journal: Science Advances

    Article Title: SIK2 antagonizes postinfarction cardiac repair by driving macrophage proinflammatory and impairing efferocytosis

    doi: 10.1126/sciadv.adw6624

    Figure Lengend Snippet: ( A ) Venn diagram delineating the intersection of SIK2-binding protein candidates in the top enriched pathways identified in , that is, NF-κB signaling pathway and MAPK signaling pathway. LC-MS/MS, liquid chromatography–tandem mass spectrometry. ( B ) Top proteins interacting with SIK2 identified through mass spectrometry analysis of peptides pulled down using anti-Flag antibody in HEK293T cells transfected with Flag-Sik2. ( C ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 using anti-Flag antibody, followed by immunoblotting with corresponding antibodies. HA, hemagglutinin. ( D and E ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 and HA-Traf2 using anti-Flag (D) or anti-HA (E) antibody, followed by immunoblotting with corresponding antibodies. FL, full length. ( F ) Immunoprecipitation (IP) in HEK293T cells cotransfected with HA-Traf2 and truncated Flag-Sik2 using an anti-HA antibody, followed by immunoblotting (IB) with corresponding antibodies. ( G ) Immunoprecipitation in HEK293T cells cotransfected with Flag-Sik2 and truncated HA-Traf2 using an anti-HA antibody, followed by immunoblotting with corresponding antibodies. ( H ) Western blotting analysis and quantification of SIK2, TRAF2, p-P38, P38, p-P65, and P65 expression in HEK293T cells transfected with SIK2 and si-TRAF2 or control ( n = 4). ( I ) Coimmunoprecipitation (Co-IP) analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and His-Ub, along with Flag-Sik2 or Flag-Sik2 T175A mutant. ( J ) Co-IP analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and Flag-Sik2, along with Myc-K48-Ub or Myc-K63-Ub. ( K ) Co-IP analysis of TRAF2 phosphate serine (p-Ser) and phosphate threonine (p-Thr) in HEK293T cells transfected with HA-Traf2, along with Flag-Sik2 or Flag-Sik2 T175A mutant.

    Article Snippet: Primary antibodies used to specifically detect the proteins of interest were as follows: SIK2 (6919s, CST), GAPDH (G9545, Sigma-Aldrich), α-SMA (A5228, Sigma-Aldrich), Collagen I (AB765P, Sigma-Aldrich), Collagen III (AB7778, Abcam), CD31 (3528s, CST), Phospho-NF-κB P65 (Ser 536 ) (3033s, CST), NF-κB P65 (8242s, CST), Phospho-P38 MAPK (Thr 180 /Tyr 182 ) (4511s, CST), P38 MAPK (8690s, CST), α-Tubulin (66031-1, Proteintech), Histone H3 (68345-1, Proteintech), NOS2 (13120s, CST), FLAG-Tag (14793s, CST), HA-Tag (3724s, CST), TRAF1 (4710s, CST), TRAF2 (4724s, CST), TRAF4 (18527s, CST), TRAF6 (67591s, CST), His-Tag (12698s, CST), and Myc-Tag (2276s, CST).

    Techniques: Binding Assay, Liquid Chromatography with Mass Spectroscopy, Liquid Chromatography, Mass Spectrometry, Analysis, Transfection, Immunoprecipitation, Western Blot, Expressing, Control, Co-Immunoprecipitation Assay, Ubiquitin Proteomics, Mutagenesis, Tandem Mass Spectroscopy

    CRISPRa-mediated activation of endogenous UMOD enables functional testing of knockdown strategies. ( A ) Schematic of the synergistic activation mediator (SAM) system for CRISPR-mediated transcriptional activation. MS2-containing sgRNAs target the proximal UMOD promoter and recruit dCas9-VP64 together with the MS2-p65-HSF1 (MPH) helper complex. ( B ) Positions of the ten sgRNAs (act_sgRNA1–10) targeting the proximal UMOD promoter. Guides target both strands (arrows) within −20 to −239 bp upstream of the transcription start site (TSS), located within exon 1. ( C ) UMOD expression quantified by ΔΔCt qRT-PCR in CRISPRa-competent HEK293T cells (HEK293T/ dCas9-VP64 + MPH) after transfection with each individual sgRNA, with a combination of all sgRNAs (act_all) or with a combination of the three best-performing guides (act_sgRNA mix). CTL, mock transfection with non-targeting sgRNAs. Data are shown as mean ± SD from n = 3 replicates; experiment was independently repeated (n=2). ( D ) Left: schematic of hUREC isolation from human urine. Right: western blot of hUREC lysates after transfection with act_sgRNA mix or non-targeting sgRNAs, from three activated samples. Recombinant Uromodulin (0.25, 1 and 2.5 fmol) was loaded on the same blot for quantitative reference. β-actin served as loading control. ( E ) Deglycosylation analysis of CRISPRa-activated hURECs. Lysates were mock-treated or digested with Endo H or PNGase F. β-actin served as loading control. ( F ) Schematic of the experimental workflow: 1. base editing for splice-site disruption or stop codon introduction, 2. FACS enrichment of edited cells, 3. CRISPRa activation, and 4. analysis by qRT-PCR or western blot. (G) UMOD mRNA levels quantified by qRT-PCR in CRISPRa-activated HEK293T cells following splice-site disruption with seven sgRNA–base editor combinations (SSD_sgRNA1, 2, 4, 5, 6, 7 and 8 with ABE8.20m or BE4max), compared with base editor-only (no_sgRNA_CTL) controls (n = 4 biological replicates). ( H ) Left: Western blot of uromodulin in CRISPRa-activated HEK293T cells following stop codon introduction with STOP_sgRNA1, 3 and 4 and TadCBEd-V106W, compared with base editor-only transfected controls. Right: quantification of uromodulin protein levels (n = 3 biological replicates). β-actin served as loading control. ( G, H ) Data are shown as mean ± SD. Statistical significance was determined using ordinary one-way ANOVA followed by multiple comparisons testing. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; ns, not significant.

    Journal: bioRxiv

    Article Title: Base Editing as a Therapeutic Strategy for Autosomal Dominant Tubulointerstitial Kidney Disease caused by Pathogenic UMOD Variants

    doi: 10.64898/2026.10.15.758759

    Figure Lengend Snippet: CRISPRa-mediated activation of endogenous UMOD enables functional testing of knockdown strategies. ( A ) Schematic of the synergistic activation mediator (SAM) system for CRISPR-mediated transcriptional activation. MS2-containing sgRNAs target the proximal UMOD promoter and recruit dCas9-VP64 together with the MS2-p65-HSF1 (MPH) helper complex. ( B ) Positions of the ten sgRNAs (act_sgRNA1–10) targeting the proximal UMOD promoter. Guides target both strands (arrows) within −20 to −239 bp upstream of the transcription start site (TSS), located within exon 1. ( C ) UMOD expression quantified by ΔΔCt qRT-PCR in CRISPRa-competent HEK293T cells (HEK293T/ dCas9-VP64 + MPH) after transfection with each individual sgRNA, with a combination of all sgRNAs (act_all) or with a combination of the three best-performing guides (act_sgRNA mix). CTL, mock transfection with non-targeting sgRNAs. Data are shown as mean ± SD from n = 3 replicates; experiment was independently repeated (n=2). ( D ) Left: schematic of hUREC isolation from human urine. Right: western blot of hUREC lysates after transfection with act_sgRNA mix or non-targeting sgRNAs, from three activated samples. Recombinant Uromodulin (0.25, 1 and 2.5 fmol) was loaded on the same blot for quantitative reference. β-actin served as loading control. ( E ) Deglycosylation analysis of CRISPRa-activated hURECs. Lysates were mock-treated or digested with Endo H or PNGase F. β-actin served as loading control. ( F ) Schematic of the experimental workflow: 1. base editing for splice-site disruption or stop codon introduction, 2. FACS enrichment of edited cells, 3. CRISPRa activation, and 4. analysis by qRT-PCR or western blot. (G) UMOD mRNA levels quantified by qRT-PCR in CRISPRa-activated HEK293T cells following splice-site disruption with seven sgRNA–base editor combinations (SSD_sgRNA1, 2, 4, 5, 6, 7 and 8 with ABE8.20m or BE4max), compared with base editor-only (no_sgRNA_CTL) controls (n = 4 biological replicates). ( H ) Left: Western blot of uromodulin in CRISPRa-activated HEK293T cells following stop codon introduction with STOP_sgRNA1, 3 and 4 and TadCBEd-V106W, compared with base editor-only transfected controls. Right: quantification of uromodulin protein levels (n = 3 biological replicates). β-actin served as loading control. ( G, H ) Data are shown as mean ± SD. Statistical significance was determined using ordinary one-way ANOVA followed by multiple comparisons testing. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; ns, not significant.

    Article Snippet: A total of 5 × 10 5 cells were electroporated per sample with 5μg plasmid DNA comprising dCas9-VP64 (Addgene plasmid #61422), MS2-p65-HSF1 (Addgene plasmid #61423), and the act_sgRNA mix at a 1:1:1 mass ratio.

    Techniques: Activation Assay, Functional Assay, Knockdown, CRISPR, Expressing, Quantitative RT-PCR, Transfection, Isolation, Western Blot, Recombinant, Control, Analysis, Disruption, FACS

    ( A ) KEGG enrichment analysis of down-regulated DEGs in Sik2 F/F ; LysM Cre cardiac macrophages on day 3 post-MI. The top 20 enriched pathways are listed. ( B ) DEGs (fold change ≥ 2 and P .adjust ≤ 0.05) overlapped in top 20 of enriched pathways. ( C ) Transcription factor prediction was performed using TRRUST databases. The top 10 transcription factors are listed. ( D ) Immunoblotting analysis and quantification of P65 in the cytoplasm and nucleus of WT and SIK2-knockout PMs and treated with TNF-α (20 ng/ml) or vehicle ( n = 4) for 1 hour. ( E ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression in WT and SIK2-knockout PMs stimulated with TNF-α for 24 hours ( n = 6). ( F ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression ( n = 6). PMs were pretreated with ARN3236 (3 μmol) and stimulated with TNF-α for 24 hours. ( G ) WikiPathways enrichment analysis of differentially phosphorylated proteins in PMs treated with ARN3236 (3 μmol) or control. The top 20 enriched pathways are listed. ( H ) Immunoblotting analysis and quantification of phosphorylated P65 (p-P65), P65, phosphorylated P38 (p-P38), and P38 expression in WT and SIK2-knockout PMs stimulated with TNF-α or vehicle ( n = 6). ( I and J ) Flow cytometry analysis of efferocytosis in WT or LeSik2 Raw264.7 cells [stimulated with SB 203580 (10 μmol) or not] treated with CFSE-prelabeled RBCs ( n = 6).

    Journal: Science Advances

    Article Title: SIK2 antagonizes postinfarction cardiac repair by driving macrophage proinflammatory and impairing efferocytosis

    doi: 10.1126/sciadv.adw6624

    Figure Lengend Snippet: ( A ) KEGG enrichment analysis of down-regulated DEGs in Sik2 F/F ; LysM Cre cardiac macrophages on day 3 post-MI. The top 20 enriched pathways are listed. ( B ) DEGs (fold change ≥ 2 and P .adjust ≤ 0.05) overlapped in top 20 of enriched pathways. ( C ) Transcription factor prediction was performed using TRRUST databases. The top 10 transcription factors are listed. ( D ) Immunoblotting analysis and quantification of P65 in the cytoplasm and nucleus of WT and SIK2-knockout PMs and treated with TNF-α (20 ng/ml) or vehicle ( n = 4) for 1 hour. ( E ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression in WT and SIK2-knockout PMs stimulated with TNF-α for 24 hours ( n = 6). ( F ) qPCR analysis of Il-1β , Il-6 , Nos2 , Cxcl-1 , and Mmp-9 mRNA expression ( n = 6). PMs were pretreated with ARN3236 (3 μmol) and stimulated with TNF-α for 24 hours. ( G ) WikiPathways enrichment analysis of differentially phosphorylated proteins in PMs treated with ARN3236 (3 μmol) or control. The top 20 enriched pathways are listed. ( H ) Immunoblotting analysis and quantification of phosphorylated P65 (p-P65), P65, phosphorylated P38 (p-P38), and P38 expression in WT and SIK2-knockout PMs stimulated with TNF-α or vehicle ( n = 6). ( I and J ) Flow cytometry analysis of efferocytosis in WT or LeSik2 Raw264.7 cells [stimulated with SB 203580 (10 μmol) or not] treated with CFSE-prelabeled RBCs ( n = 6).

    Article Snippet: Primary antibodies used to specifically detect the proteins of interest were as follows: SIK2 (6919s, CST), GAPDH (G9545, Sigma-Aldrich), α-SMA (A5228, Sigma-Aldrich), Collagen I (AB765P, Sigma-Aldrich), Collagen III (AB7778, Abcam), CD31 (3528s, CST), Phospho-NF-κB P65 (Ser 536 ) (3033s, CST), NF-κB P65 (8242s, CST), Phospho-P38 MAPK (Thr 180 /Tyr 182 ) (4511s, CST), P38 MAPK (8690s, CST), α-Tubulin (66031-1, Proteintech), Histone H3 (68345-1, Proteintech), NOS2 (13120s, CST), FLAG-Tag (14793s, CST), HA-Tag (3724s, CST), TRAF1 (4710s, CST), TRAF2 (4724s, CST), TRAF4 (18527s, CST), TRAF6 (67591s, CST), His-Tag (12698s, CST), and Myc-Tag (2276s, CST).

    Techniques: Analysis, Western Blot, Knock-Out, Expressing, Control, Flow Cytometry, Significance Assay

    ( A ) Venn diagram delineating the intersection of SIK2-binding protein candidates in the top enriched pathways identified in , that is, NF-κB signaling pathway and MAPK signaling pathway. LC-MS/MS, liquid chromatography–tandem mass spectrometry. ( B ) Top proteins interacting with SIK2 identified through mass spectrometry analysis of peptides pulled down using anti-Flag antibody in HEK293T cells transfected with Flag-Sik2. ( C ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 using anti-Flag antibody, followed by immunoblotting with corresponding antibodies. HA, hemagglutinin. ( D and E ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 and HA-Traf2 using anti-Flag (D) or anti-HA (E) antibody, followed by immunoblotting with corresponding antibodies. FL, full length. ( F ) Immunoprecipitation (IP) in HEK293T cells cotransfected with HA-Traf2 and truncated Flag-Sik2 using an anti-HA antibody, followed by immunoblotting (IB) with corresponding antibodies. ( G ) Immunoprecipitation in HEK293T cells cotransfected with Flag-Sik2 and truncated HA-Traf2 using an anti-HA antibody, followed by immunoblotting with corresponding antibodies. ( H ) Western blotting analysis and quantification of SIK2, TRAF2, p-P38, P38, p-P65, and P65 expression in HEK293T cells transfected with SIK2 and si-TRAF2 or control ( n = 4). ( I ) Coimmunoprecipitation (Co-IP) analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and His-Ub, along with Flag-Sik2 or Flag-Sik2 T175A mutant. ( J ) Co-IP analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and Flag-Sik2, along with Myc-K48-Ub or Myc-K63-Ub. ( K ) Co-IP analysis of TRAF2 phosphate serine (p-Ser) and phosphate threonine (p-Thr) in HEK293T cells transfected with HA-Traf2, along with Flag-Sik2 or Flag-Sik2 T175A mutant.

    Journal: Science Advances

    Article Title: SIK2 antagonizes postinfarction cardiac repair by driving macrophage proinflammatory and impairing efferocytosis

    doi: 10.1126/sciadv.adw6624

    Figure Lengend Snippet: ( A ) Venn diagram delineating the intersection of SIK2-binding protein candidates in the top enriched pathways identified in , that is, NF-κB signaling pathway and MAPK signaling pathway. LC-MS/MS, liquid chromatography–tandem mass spectrometry. ( B ) Top proteins interacting with SIK2 identified through mass spectrometry analysis of peptides pulled down using anti-Flag antibody in HEK293T cells transfected with Flag-Sik2. ( C ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 using anti-Flag antibody, followed by immunoblotting with corresponding antibodies. HA, hemagglutinin. ( D and E ) Immunoprecipitation in HEK293T cells transfected with Flag-Sik2 and HA-Traf2 using anti-Flag (D) or anti-HA (E) antibody, followed by immunoblotting with corresponding antibodies. FL, full length. ( F ) Immunoprecipitation (IP) in HEK293T cells cotransfected with HA-Traf2 and truncated Flag-Sik2 using an anti-HA antibody, followed by immunoblotting (IB) with corresponding antibodies. ( G ) Immunoprecipitation in HEK293T cells cotransfected with Flag-Sik2 and truncated HA-Traf2 using an anti-HA antibody, followed by immunoblotting with corresponding antibodies. ( H ) Western blotting analysis and quantification of SIK2, TRAF2, p-P38, P38, p-P65, and P65 expression in HEK293T cells transfected with SIK2 and si-TRAF2 or control ( n = 4). ( I ) Coimmunoprecipitation (Co-IP) analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and His-Ub, along with Flag-Sik2 or Flag-Sik2 T175A mutant. ( J ) Co-IP analysis of TRAF2 ubiquitination in HEK293T cells cotransfected with HA-Traf2 and Flag-Sik2, along with Myc-K48-Ub or Myc-K63-Ub. ( K ) Co-IP analysis of TRAF2 phosphate serine (p-Ser) and phosphate threonine (p-Thr) in HEK293T cells transfected with HA-Traf2, along with Flag-Sik2 or Flag-Sik2 T175A mutant.

    Article Snippet: Primary antibodies used to specifically detect the proteins of interest were as follows: SIK2 (6919s, CST), GAPDH (G9545, Sigma-Aldrich), α-SMA (A5228, Sigma-Aldrich), Collagen I (AB765P, Sigma-Aldrich), Collagen III (AB7778, Abcam), CD31 (3528s, CST), Phospho-NF-κB P65 (Ser 536 ) (3033s, CST), NF-κB P65 (8242s, CST), Phospho-P38 MAPK (Thr 180 /Tyr 182 ) (4511s, CST), P38 MAPK (8690s, CST), α-Tubulin (66031-1, Proteintech), Histone H3 (68345-1, Proteintech), NOS2 (13120s, CST), FLAG-Tag (14793s, CST), HA-Tag (3724s, CST), TRAF1 (4710s, CST), TRAF2 (4724s, CST), TRAF4 (18527s, CST), TRAF6 (67591s, CST), His-Tag (12698s, CST), and Myc-Tag (2276s, CST).

    Techniques: Binding Assay, Liquid Chromatography with Mass Spectroscopy, Liquid Chromatography, Mass Spectrometry, Analysis, Transfection, Immunoprecipitation, Western Blot, Expressing, Control, Co-Immunoprecipitation Assay, Ubiquitin Proteomics, Mutagenesis, Tandem Mass Spectroscopy