sirt3  (Cell Signaling Technology Inc)


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    Structured Review

    Cell Signaling Technology Inc sirt3
    Knocking down <t>SIRT3</t> caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .
    Sirt3, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival"

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    Journal: Blood Cancer Discovery

    doi: 10.1158/2643-3230.BCD-20-0183

    Knocking down SIRT3 caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .
    Figure Legend Snippet: Knocking down SIRT3 caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .

    Techniques Used: Inhibition, RNA Sequencing Assay, Transduction, Expressing, Chromatin Immunoprecipitation

    Knockdown SIRT3 caused ATF4 protein decrease via translation regulation. A, Western blots show ATF4 protein levels in different DLBCL cells with control or SIRT3 shRNAs. SIRT3 was blotted showing knockdown efficiency, and ACTB was used as reference protein control. B, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in OCI-LY1 cells. Samples were harvested at day 4 after viral transduction. Results were normalized to the mRNA levels in control shRNA–transduced cells. C, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in Karpas 422 cells. Samples were harvested at day 4 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. D, qPCR results show the relative levels of ATF4 mRNAs in different cell lines at different time points after shRNA transduction. Samples were harvested at days 2, 3, 4, and 7 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. E, Western blots show changes of phosphorylation of EIF2A and ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Total EIF2A and ACTB were blotted as loading controls. F, Western blots show GFP expression from the ATF4-5′UTR-GFP reporter and endogenous ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Tubulin and ACTB were blotted as loading controls. G, FCs of mean fluorescence intensity (MFI) of GFP expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal yellow fluorescent protein (YFP) expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. H, FCs of MFI of GFP expressed from the ATF4-5′UTR-GFP translation reporter in OCI-LY1 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal YFP expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: Knockdown SIRT3 caused ATF4 protein decrease via translation regulation. A, Western blots show ATF4 protein levels in different DLBCL cells with control or SIRT3 shRNAs. SIRT3 was blotted showing knockdown efficiency, and ACTB was used as reference protein control. B, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in OCI-LY1 cells. Samples were harvested at day 4 after viral transduction. Results were normalized to the mRNA levels in control shRNA–transduced cells. C, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in Karpas 422 cells. Samples were harvested at day 4 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. D, qPCR results show the relative levels of ATF4 mRNAs in different cell lines at different time points after shRNA transduction. Samples were harvested at days 2, 3, 4, and 7 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. E, Western blots show changes of phosphorylation of EIF2A and ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Total EIF2A and ACTB were blotted as loading controls. F, Western blots show GFP expression from the ATF4-5′UTR-GFP reporter and endogenous ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Tubulin and ACTB were blotted as loading controls. G, FCs of mean fluorescence intensity (MFI) of GFP expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal yellow fluorescent protein (YFP) expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. H, FCs of MFI of GFP expressed from the ATF4-5′UTR-GFP translation reporter in OCI-LY1 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal YFP expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Western Blot, Transduction, shRNA, Expressing, Fluorescence

    ATF4 is required in DLBCL cells and is partially responsible for SIRT3′s functions to promote DLBCL cell proliferation and survival. A, Effect of ATF4 knockdown on the proliferation of DLBCL cell lines. Each cell line was infected with lentivirus expressing control or ATF4 shRNAs and yellow fluorescent protein (YFP), and YFP + viable (DAPI − ) cells were monitored by flow cytometry for 8 days. B, FCs of cell numbers of HBL1 cells expressing control or SIRT3 shRNA with or without exogeneous ATF4. HBL1 cells were transduced with viral vectors containing shRNAs or genes as presented. Cell number changes were normalized to data of initial time point (day 3 after infection). C, Summarized results show the rescue effects of exogenous ATF4 to SIRT3 shRNA-induced cell proliferation inhibition in different DLBCL cells. The data were summarized from day 10 after infections and normalized to the cell numbers of their respective control shRNA–expressing cell. D, Effects of exogenous ATF4 on different DLBCL cells expressing control or SIRT3 shRNAs. Dead cells were stained with DAPI and quantified through flow cytometry. The relative cell death was calculated by normalizing the percentage of dead cells in control shRNA–expressing cells in respective cell lines. *, P < 0.05; **, P < 0.01. Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: ATF4 is required in DLBCL cells and is partially responsible for SIRT3′s functions to promote DLBCL cell proliferation and survival. A, Effect of ATF4 knockdown on the proliferation of DLBCL cell lines. Each cell line was infected with lentivirus expressing control or ATF4 shRNAs and yellow fluorescent protein (YFP), and YFP + viable (DAPI − ) cells were monitored by flow cytometry for 8 days. B, FCs of cell numbers of HBL1 cells expressing control or SIRT3 shRNA with or without exogeneous ATF4. HBL1 cells were transduced with viral vectors containing shRNAs or genes as presented. Cell number changes were normalized to data of initial time point (day 3 after infection). C, Summarized results show the rescue effects of exogenous ATF4 to SIRT3 shRNA-induced cell proliferation inhibition in different DLBCL cells. The data were summarized from day 10 after infections and normalized to the cell numbers of their respective control shRNA–expressing cell. D, Effects of exogenous ATF4 on different DLBCL cells expressing control or SIRT3 shRNAs. Dead cells were stained with DAPI and quantified through flow cytometry. The relative cell death was calculated by normalizing the percentage of dead cells in control shRNA–expressing cells in respective cell lines. *, P < 0.05; **, P < 0.01. Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Infection, Expressing, Flow Cytometry, shRNA, Transduction, Inhibition, Staining

    ATF4 protein level is decreased in vavP-Bcl2;Sirt3 −/− mice and associated with lymphoma progression. A, Western blot results show the protein levels of ATF4, LC3, EIF2A, ACTB, and SIRT3 in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results. B, Summarized results of ATF4 protein level normalized to ACTB in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. C, Correlation between levels of autophagy (LC3II/LC3I) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. D, Correlation between levels of phospho-EIF2A (p-EIF2A/EIF2A) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. E, Summarized results of phospho-EIF2A level normalized to total EIF2A in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. F, Correlation between splenomegaly phenotype (spleen/body weight) and levels of ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. ATF4 levels were quantified with densitometry results from Western blots. G, Western blot results show ATF4 levels from human DLBCL tumor samples or normal GC B cells from human tonsil. ACTB levels were used as loading control. H, GSEA shows the enrichment of ATF4 target genes in DLBCL tumors versus normal GC B cells. Gene expression data were from published microarray data . Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: ATF4 protein level is decreased in vavP-Bcl2;Sirt3 −/− mice and associated with lymphoma progression. A, Western blot results show the protein levels of ATF4, LC3, EIF2A, ACTB, and SIRT3 in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results. B, Summarized results of ATF4 protein level normalized to ACTB in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. C, Correlation between levels of autophagy (LC3II/LC3I) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. D, Correlation between levels of phospho-EIF2A (p-EIF2A/EIF2A) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. E, Summarized results of phospho-EIF2A level normalized to total EIF2A in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. F, Correlation between splenomegaly phenotype (spleen/body weight) and levels of ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. ATF4 levels were quantified with densitometry results from Western blots. G, Western blot results show ATF4 levels from human DLBCL tumor samples or normal GC B cells from human tonsil. ACTB levels were used as loading control. H, GSEA shows the enrichment of ATF4 target genes in DLBCL tumors versus normal GC B cells. Gene expression data were from published microarray data . Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Western Blot, Expressing, Microarray

    ATF4 protein level is regulated downstream of the SIRT3–GDH–TCA cycle–autophagy cascade. A, Western blots show the effects of ATF4 expression to autophagy activation induced by SIRT3 shRNA in Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. EV, empty vector. B, Western blots show the ATF4 protein level being rescued by exogenous GDH in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. C, Western blots show the ATF4 protein level being rescued by DMKG in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. D, Western blots show the ATF4 protein level being rescued by CQ (50 μmol/L) in SIRT3 knockdown Karpas 422 cells. CQ treatment was done in 16 to 18 hours, followed by immunoblot with the indicated antibodies. Densitometry values are shown for ATF4/ACTB and LC3II/LC3I ratios. Hypothetical cascade model is presented to the left. E, Western blots show the changes of ATF4 protein level control or ATG5 knockdown Karpas 422 cells with control or SIRT3 shRNAs. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. F, Summarized bar plot shows the NES ( y -axis) and FDRs (bar colors) of results from GSEA using published proteomic data . NES show the enrichment of ATF4 target genes (human and mouse) or ATF4 target genes from ChIP (mouse embryonic fibroblasts, MEF) in Atg5 knockout MEF cells in normal or starvation (5 hours) treatment condition. The experiments were done with stable isotope labeling by amino acids in cell culture (SILAC) coupled with off-gel fractionations (OG) and strong cation exchange chromatography (SCX) methods. HBSS, Hank's Balanced Salt Solution. G, Western blots show ATF4 protein levels under CHX and CQ treatment in Karpas 422 cells. Protein samples were collected at the indicated time points after treatment to monitor the kinetics of ATF4 degradation. SIRT3 and LC3 were blotted as controls. NT, not treated. H, EIF2A phosphorylation from Karpas 422 cells exposed to two different doses of CQ or DMSO, or to DMKG treatment. Proteins were blotted with the indicated antibodies, and the densitometry showed relative abundance of phospho-EIF2A over total EIF2A.
    Figure Legend Snippet: ATF4 protein level is regulated downstream of the SIRT3–GDH–TCA cycle–autophagy cascade. A, Western blots show the effects of ATF4 expression to autophagy activation induced by SIRT3 shRNA in Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. EV, empty vector. B, Western blots show the ATF4 protein level being rescued by exogenous GDH in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. C, Western blots show the ATF4 protein level being rescued by DMKG in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. D, Western blots show the ATF4 protein level being rescued by CQ (50 μmol/L) in SIRT3 knockdown Karpas 422 cells. CQ treatment was done in 16 to 18 hours, followed by immunoblot with the indicated antibodies. Densitometry values are shown for ATF4/ACTB and LC3II/LC3I ratios. Hypothetical cascade model is presented to the left. E, Western blots show the changes of ATF4 protein level control or ATG5 knockdown Karpas 422 cells with control or SIRT3 shRNAs. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. F, Summarized bar plot shows the NES ( y -axis) and FDRs (bar colors) of results from GSEA using published proteomic data . NES show the enrichment of ATF4 target genes (human and mouse) or ATF4 target genes from ChIP (mouse embryonic fibroblasts, MEF) in Atg5 knockout MEF cells in normal or starvation (5 hours) treatment condition. The experiments were done with stable isotope labeling by amino acids in cell culture (SILAC) coupled with off-gel fractionations (OG) and strong cation exchange chromatography (SCX) methods. HBSS, Hank's Balanced Salt Solution. G, Western blots show ATF4 protein levels under CHX and CQ treatment in Karpas 422 cells. Protein samples were collected at the indicated time points after treatment to monitor the kinetics of ATF4 degradation. SIRT3 and LC3 were blotted as controls. NT, not treated. H, EIF2A phosphorylation from Karpas 422 cells exposed to two different doses of CQ or DMSO, or to DMKG treatment. Proteins were blotted with the indicated antibodies, and the densitometry showed relative abundance of phospho-EIF2A over total EIF2A.

    Techniques Used: Western Blot, Expressing, Activation Assay, shRNA, Plasmid Preparation, Knock-Out, Labeling, Cell Culture, Chromatography

    ATF4 translation and protein level respond to nutrient level and are regulated by autophagy. A, FCs of mean fluorescence intensity (MFI) of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells containing control or SIRT3 shRNAs under different culture conditions. Top, experiments were done as in the schema. Briefly, cells were cultured with fresh medium for 48 hours and then replenished with same volume of fresh medium or maintained without replenishment (as a control) for another 16 hours. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. B, FCs of MFI of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs under control or glutamine starvation or tunicamycin (10 μg/mL) treatment. Both starvation and tunicamycin treatment were maintained for 15 hours at day 4 after viral transduction. C, Western blot results show the GFP expression from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells from B . D, The heatmap shows that relative abundances of amino acids were detected by metabolic profiling from Karpas 422 cells transduced with SIRT3 or control shRNAs. The metabolite levels were mean value from five to six replicate samples obtained on day 6 after infection. E, Relative activities of the ATF4-5′UTR-GFP reporter in Karpas 422 were cultured for 48 hours, replenished with fresh media or with the indicated nutrients, and then assessed for ATF4 translation reporter activity 16 hours later. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. NT, not treated; Q, glutamine. F, Western blots show ATF4 protein levels from the indicated cell lines cultured as in A and E , and then replenished with NEAA or not replenished, after which immunoblots were performed for ATF4, with tubulin and actin as loading controls, in control or NEAA-added conditions. G, The heatmap shows the amino acid abundance measured with LC/MS from Karpas 422 cells transduced with SIRT3 or control shRNA and cultured with or without DMKG supplementation. The values show the average logFC from three replicates in amino acid abundance as compared with DSMO-treated control shRNA–transduced cells. H, Western blot results show ATF4 level changes in control or ATG5 knockdown Karpas 422 cells under glutamine starvation condition. Samples were collected at different time points, and protein level changes were quantified with densitometry results. I, Western blots show the ATF4 and autophagy changes in Karpas 422 cells treated with DMSO or YC8-02 (YC; 3 μmol/L) for 40 hours. Cell lysates were subjected to Western blot using the indicated antibodies. Protein levels were quantified with densitometry results. J, The barplot shows the relative cell viability after OCI-LY1 and Karpas 422 cells were treated with DMSO, YC8-02 (OCI-LY1: 6 μmol/L; Karpas 422: 2 μmol/L), GCN2IN6 (OCI-LY1: 7.5 μmol/L; Karpas 422: 10 μmol/L), and combinations for 72 hours. Cells were subject to flow cytometry for viability tests (DAPI staining) and counting. *, P < 0.05; **, P < 0.01. NS, not significant. Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: ATF4 translation and protein level respond to nutrient level and are regulated by autophagy. A, FCs of mean fluorescence intensity (MFI) of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells containing control or SIRT3 shRNAs under different culture conditions. Top, experiments were done as in the schema. Briefly, cells were cultured with fresh medium for 48 hours and then replenished with same volume of fresh medium or maintained without replenishment (as a control) for another 16 hours. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. B, FCs of MFI of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs under control or glutamine starvation or tunicamycin (10 μg/mL) treatment. Both starvation and tunicamycin treatment were maintained for 15 hours at day 4 after viral transduction. C, Western blot results show the GFP expression from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells from B . D, The heatmap shows that relative abundances of amino acids were detected by metabolic profiling from Karpas 422 cells transduced with SIRT3 or control shRNAs. The metabolite levels were mean value from five to six replicate samples obtained on day 6 after infection. E, Relative activities of the ATF4-5′UTR-GFP reporter in Karpas 422 were cultured for 48 hours, replenished with fresh media or with the indicated nutrients, and then assessed for ATF4 translation reporter activity 16 hours later. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. NT, not treated; Q, glutamine. F, Western blots show ATF4 protein levels from the indicated cell lines cultured as in A and E , and then replenished with NEAA or not replenished, after which immunoblots were performed for ATF4, with tubulin and actin as loading controls, in control or NEAA-added conditions. G, The heatmap shows the amino acid abundance measured with LC/MS from Karpas 422 cells transduced with SIRT3 or control shRNA and cultured with or without DMKG supplementation. The values show the average logFC from three replicates in amino acid abundance as compared with DSMO-treated control shRNA–transduced cells. H, Western blot results show ATF4 level changes in control or ATG5 knockdown Karpas 422 cells under glutamine starvation condition. Samples were collected at different time points, and protein level changes were quantified with densitometry results. I, Western blots show the ATF4 and autophagy changes in Karpas 422 cells treated with DMSO or YC8-02 (YC; 3 μmol/L) for 40 hours. Cell lysates were subjected to Western blot using the indicated antibodies. Protein levels were quantified with densitometry results. J, The barplot shows the relative cell viability after OCI-LY1 and Karpas 422 cells were treated with DMSO, YC8-02 (OCI-LY1: 6 μmol/L; Karpas 422: 2 μmol/L), GCN2IN6 (OCI-LY1: 7.5 μmol/L; Karpas 422: 10 μmol/L), and combinations for 72 hours. Cells were subject to flow cytometry for viability tests (DAPI staining) and counting. *, P < 0.05; **, P < 0.01. NS, not significant. Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Fluorescence, Cell Culture, Expressing, Flow Cytometry, Transduction, Western Blot, Infection, Activity Assay, Liquid Chromatography with Mass Spectroscopy, shRNA, Staining

    Graphical summary of SIRT3–ATF4 regulation in DLBCLs. Left, DLBCL cells depend on glutamine anaplerosis driven by SIRT3 and GDH to produce metabolic precursors from the TCA cycle for cell survival and proliferation, which also suppress autophagy and the downstream protein recycling in the lysosome. The active proliferation and high metabolic demand of DLBCL cells leads to a shortage of NEAAs and results in translational activation of ATF4, which can transcribe target genes for importation of extracellular nutrients to maintain the amino acid flux. Right, pharmaceutically inhibiting or knocking down SIRT3 suppresses the TCA cycle metabolism as a metabolic engine and decreases the consumption of amino acids (including NEAAs). The reduced TCA cycle metabolism in turn triggers activation of autophagy, which produces amino acids from lysosomal protein degradations to compensate the metabolic suppression. However, the increased amino acids cannot be used in the mitochondria of the defective TCA cycle, but instead block the translation of ATF4 and then shut down the nutrient importation. Together, these induce metabolic stress in DLBCL cells and lead to cell-cycle arrest and death. The larger, bold font indicates more activity or function of indicated proteins or biological activities. The thickness of lines and numbers of arrows indicate the impacts of upstream molecules/biological activities to downstream targets.
    Figure Legend Snippet: Graphical summary of SIRT3–ATF4 regulation in DLBCLs. Left, DLBCL cells depend on glutamine anaplerosis driven by SIRT3 and GDH to produce metabolic precursors from the TCA cycle for cell survival and proliferation, which also suppress autophagy and the downstream protein recycling in the lysosome. The active proliferation and high metabolic demand of DLBCL cells leads to a shortage of NEAAs and results in translational activation of ATF4, which can transcribe target genes for importation of extracellular nutrients to maintain the amino acid flux. Right, pharmaceutically inhibiting or knocking down SIRT3 suppresses the TCA cycle metabolism as a metabolic engine and decreases the consumption of amino acids (including NEAAs). The reduced TCA cycle metabolism in turn triggers activation of autophagy, which produces amino acids from lysosomal protein degradations to compensate the metabolic suppression. However, the increased amino acids cannot be used in the mitochondria of the defective TCA cycle, but instead block the translation of ATF4 and then shut down the nutrient importation. Together, these induce metabolic stress in DLBCL cells and lead to cell-cycle arrest and death. The larger, bold font indicates more activity or function of indicated proteins or biological activities. The thickness of lines and numbers of arrows indicate the impacts of upstream molecules/biological activities to downstream targets.

    Techniques Used: Activation Assay, Blocking Assay, Activity Assay

    antibodies against piwil2  (Cell Signaling Technology Inc)


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    Structured Review

    Cell Signaling Technology Inc antibodies against piwil2
    piR-54265 interacts with <t>PIWIL2,</t> facilitating PIWIL2/STAT3/p-SRC formation. (A) RNA immunoprecipitation assays showed specific bind of piR-54265 to PIWIL2. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (B) Biotin-labeled piR-54265 RNA pulldown coupled with western blot analysis revealed interaction of piR-54265 with PIWIL2, STAT3 and p-SRC. (C) Schematic of the domain structure of PIWIL2 protein. (D) Biotin-labeled piR-54265 RNA pulldown from lysates containing FLAG-tagged full-length or truncated PIWIL2 protein coupled with Western blot analysis revealed the interaction of piR-54265 with PIWIL2 via the PIWI domain in PIWIL2. (E) Co-immunoprecipitation assays revealed the interaction of STAT3 with PIWIL2 via the PAZ domain in PIWIL2. (F) RNA immunoprecipitation assays showed specific association of piR-54265 with STAT3 and p-SRC in CRC cells. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (G) Reciprocal immunoprecipitation assays showed that the interaction among PIWIL2, STAT3 and SRC in CRC cells was affected by piR-54265 expression. (H) Effects of overexpression or knockdown of piR-54265 on the expression levels of STAT3 and SRC and their phosphorylated forms detected by western blot.
    Antibodies Against Piwil2, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    antibodies against piwil2 - by Bioz Stars, 2023-03
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    1) Product Images from "PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma"

    Article Title: PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma

    Journal: Theranostics

    doi: 10.7150/thno.28001

    piR-54265 interacts with PIWIL2, facilitating PIWIL2/STAT3/p-SRC formation. (A) RNA immunoprecipitation assays showed specific bind of piR-54265 to PIWIL2. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (B) Biotin-labeled piR-54265 RNA pulldown coupled with western blot analysis revealed interaction of piR-54265 with PIWIL2, STAT3 and p-SRC. (C) Schematic of the domain structure of PIWIL2 protein. (D) Biotin-labeled piR-54265 RNA pulldown from lysates containing FLAG-tagged full-length or truncated PIWIL2 protein coupled with Western blot analysis revealed the interaction of piR-54265 with PIWIL2 via the PIWI domain in PIWIL2. (E) Co-immunoprecipitation assays revealed the interaction of STAT3 with PIWIL2 via the PAZ domain in PIWIL2. (F) RNA immunoprecipitation assays showed specific association of piR-54265 with STAT3 and p-SRC in CRC cells. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (G) Reciprocal immunoprecipitation assays showed that the interaction among PIWIL2, STAT3 and SRC in CRC cells was affected by piR-54265 expression. (H) Effects of overexpression or knockdown of piR-54265 on the expression levels of STAT3 and SRC and their phosphorylated forms detected by western blot.
    Figure Legend Snippet: piR-54265 interacts with PIWIL2, facilitating PIWIL2/STAT3/p-SRC formation. (A) RNA immunoprecipitation assays showed specific bind of piR-54265 to PIWIL2. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (B) Biotin-labeled piR-54265 RNA pulldown coupled with western blot analysis revealed interaction of piR-54265 with PIWIL2, STAT3 and p-SRC. (C) Schematic of the domain structure of PIWIL2 protein. (D) Biotin-labeled piR-54265 RNA pulldown from lysates containing FLAG-tagged full-length or truncated PIWIL2 protein coupled with Western blot analysis revealed the interaction of piR-54265 with PIWIL2 via the PIWI domain in PIWIL2. (E) Co-immunoprecipitation assays revealed the interaction of STAT3 with PIWIL2 via the PAZ domain in PIWIL2. (F) RNA immunoprecipitation assays showed specific association of piR-54265 with STAT3 and p-SRC in CRC cells. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (G) Reciprocal immunoprecipitation assays showed that the interaction among PIWIL2, STAT3 and SRC in CRC cells was affected by piR-54265 expression. (H) Effects of overexpression or knockdown of piR-54265 on the expression levels of STAT3 and SRC and their phosphorylated forms detected by western blot.

    Techniques Used: Immunoprecipitation, Labeling, Western Blot, Expressing, Over Expression

    piR-54265 enhances oncogenic STAT3 signaling. (A) Effects of piR-54265 on expression and/or activation of proliferation and metastasis-related STAT3 downstream modules in CRC cells detected by western blot. (B-C) Immunohistochemical (IHC) staining of proliferation- and metastasis-related STAT3 downstream modules in mouse xenograft tumors of CRC cells with overexpression or knockdown of piR-54265. IHC staining of proliferation-related molecules (B) and metastasis-related molecules (C). 200×; scale bars, 50 μm. (D) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell proliferation (each point in the curve represents mean ± SEM; N=6; **, P <0.01; ***, P <0.001). (E) Knockdown of PIWIL2 or STAT3 affects the piR-54265-induced migration ( upper panel ) and invasion ( lower panel ) abilities of CRC cells (mean ± SEM; N=6. ***, P <0.001; ****, P <0.0001). See also Figure B . (F) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell apoptosis (mean ± SEM; N=3; ***, P <0.001). See also Figure C . OE: overexpression; KD: knockdown.
    Figure Legend Snippet: piR-54265 enhances oncogenic STAT3 signaling. (A) Effects of piR-54265 on expression and/or activation of proliferation and metastasis-related STAT3 downstream modules in CRC cells detected by western blot. (B-C) Immunohistochemical (IHC) staining of proliferation- and metastasis-related STAT3 downstream modules in mouse xenograft tumors of CRC cells with overexpression or knockdown of piR-54265. IHC staining of proliferation-related molecules (B) and metastasis-related molecules (C). 200×; scale bars, 50 μm. (D) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell proliferation (each point in the curve represents mean ± SEM; N=6; **, P <0.01; ***, P <0.001). (E) Knockdown of PIWIL2 or STAT3 affects the piR-54265-induced migration ( upper panel ) and invasion ( lower panel ) abilities of CRC cells (mean ± SEM; N=6. ***, P <0.001; ****, P <0.0001). See also Figure B . (F) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell apoptosis (mean ± SEM; N=3; ***, P <0.001). See also Figure C . OE: overexpression; KD: knockdown.

    Techniques Used: Expressing, Activation Assay, Western Blot, Immunohistochemical staining, Immunohistochemistry, Over Expression, Migration

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    Structured Review

    Cell Signaling Technology Inc sirt3
    Knocking down <t>SIRT3</t> caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .
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    Images

    1) Product Images from "Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival"

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    Journal: Blood Cancer Discovery

    doi: 10.1158/2643-3230.BCD-20-0183

    Knocking down SIRT3 caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .
    Figure Legend Snippet: Knocking down SIRT3 caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .

    Techniques Used: Inhibition, RNA Sequencing Assay, Transduction, Expressing, Chromatin Immunoprecipitation

    Knockdown SIRT3 caused ATF4 protein decrease via translation regulation. A, Western blots show ATF4 protein levels in different DLBCL cells with control or SIRT3 shRNAs. SIRT3 was blotted showing knockdown efficiency, and ACTB was used as reference protein control. B, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in OCI-LY1 cells. Samples were harvested at day 4 after viral transduction. Results were normalized to the mRNA levels in control shRNA–transduced cells. C, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in Karpas 422 cells. Samples were harvested at day 4 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. D, qPCR results show the relative levels of ATF4 mRNAs in different cell lines at different time points after shRNA transduction. Samples were harvested at days 2, 3, 4, and 7 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. E, Western blots show changes of phosphorylation of EIF2A and ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Total EIF2A and ACTB were blotted as loading controls. F, Western blots show GFP expression from the ATF4-5′UTR-GFP reporter and endogenous ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Tubulin and ACTB were blotted as loading controls. G, FCs of mean fluorescence intensity (MFI) of GFP expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal yellow fluorescent protein (YFP) expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. H, FCs of MFI of GFP expressed from the ATF4-5′UTR-GFP translation reporter in OCI-LY1 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal YFP expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: Knockdown SIRT3 caused ATF4 protein decrease via translation regulation. A, Western blots show ATF4 protein levels in different DLBCL cells with control or SIRT3 shRNAs. SIRT3 was blotted showing knockdown efficiency, and ACTB was used as reference protein control. B, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in OCI-LY1 cells. Samples were harvested at day 4 after viral transduction. Results were normalized to the mRNA levels in control shRNA–transduced cells. C, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in Karpas 422 cells. Samples were harvested at day 4 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. D, qPCR results show the relative levels of ATF4 mRNAs in different cell lines at different time points after shRNA transduction. Samples were harvested at days 2, 3, 4, and 7 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. E, Western blots show changes of phosphorylation of EIF2A and ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Total EIF2A and ACTB were blotted as loading controls. F, Western blots show GFP expression from the ATF4-5′UTR-GFP reporter and endogenous ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Tubulin and ACTB were blotted as loading controls. G, FCs of mean fluorescence intensity (MFI) of GFP expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal yellow fluorescent protein (YFP) expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. H, FCs of MFI of GFP expressed from the ATF4-5′UTR-GFP translation reporter in OCI-LY1 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal YFP expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Western Blot, Transduction, shRNA, Expressing, Fluorescence

    ATF4 is required in DLBCL cells and is partially responsible for SIRT3′s functions to promote DLBCL cell proliferation and survival. A, Effect of ATF4 knockdown on the proliferation of DLBCL cell lines. Each cell line was infected with lentivirus expressing control or ATF4 shRNAs and yellow fluorescent protein (YFP), and YFP + viable (DAPI − ) cells were monitored by flow cytometry for 8 days. B, FCs of cell numbers of HBL1 cells expressing control or SIRT3 shRNA with or without exogeneous ATF4. HBL1 cells were transduced with viral vectors containing shRNAs or genes as presented. Cell number changes were normalized to data of initial time point (day 3 after infection). C, Summarized results show the rescue effects of exogenous ATF4 to SIRT3 shRNA-induced cell proliferation inhibition in different DLBCL cells. The data were summarized from day 10 after infections and normalized to the cell numbers of their respective control shRNA–expressing cell. D, Effects of exogenous ATF4 on different DLBCL cells expressing control or SIRT3 shRNAs. Dead cells were stained with DAPI and quantified through flow cytometry. The relative cell death was calculated by normalizing the percentage of dead cells in control shRNA–expressing cells in respective cell lines. *, P < 0.05; **, P < 0.01. Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: ATF4 is required in DLBCL cells and is partially responsible for SIRT3′s functions to promote DLBCL cell proliferation and survival. A, Effect of ATF4 knockdown on the proliferation of DLBCL cell lines. Each cell line was infected with lentivirus expressing control or ATF4 shRNAs and yellow fluorescent protein (YFP), and YFP + viable (DAPI − ) cells were monitored by flow cytometry for 8 days. B, FCs of cell numbers of HBL1 cells expressing control or SIRT3 shRNA with or without exogeneous ATF4. HBL1 cells were transduced with viral vectors containing shRNAs or genes as presented. Cell number changes were normalized to data of initial time point (day 3 after infection). C, Summarized results show the rescue effects of exogenous ATF4 to SIRT3 shRNA-induced cell proliferation inhibition in different DLBCL cells. The data were summarized from day 10 after infections and normalized to the cell numbers of their respective control shRNA–expressing cell. D, Effects of exogenous ATF4 on different DLBCL cells expressing control or SIRT3 shRNAs. Dead cells were stained with DAPI and quantified through flow cytometry. The relative cell death was calculated by normalizing the percentage of dead cells in control shRNA–expressing cells in respective cell lines. *, P < 0.05; **, P < 0.01. Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Infection, Expressing, Flow Cytometry, shRNA, Transduction, Inhibition, Staining

    ATF4 protein level is decreased in vavP-Bcl2;Sirt3 −/− mice and associated with lymphoma progression. A, Western blot results show the protein levels of ATF4, LC3, EIF2A, ACTB, and SIRT3 in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results. B, Summarized results of ATF4 protein level normalized to ACTB in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. C, Correlation between levels of autophagy (LC3II/LC3I) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. D, Correlation between levels of phospho-EIF2A (p-EIF2A/EIF2A) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. E, Summarized results of phospho-EIF2A level normalized to total EIF2A in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. F, Correlation between splenomegaly phenotype (spleen/body weight) and levels of ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. ATF4 levels were quantified with densitometry results from Western blots. G, Western blot results show ATF4 levels from human DLBCL tumor samples or normal GC B cells from human tonsil. ACTB levels were used as loading control. H, GSEA shows the enrichment of ATF4 target genes in DLBCL tumors versus normal GC B cells. Gene expression data were from published microarray data . Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: ATF4 protein level is decreased in vavP-Bcl2;Sirt3 −/− mice and associated with lymphoma progression. A, Western blot results show the protein levels of ATF4, LC3, EIF2A, ACTB, and SIRT3 in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results. B, Summarized results of ATF4 protein level normalized to ACTB in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. C, Correlation between levels of autophagy (LC3II/LC3I) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. D, Correlation between levels of phospho-EIF2A (p-EIF2A/EIF2A) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. E, Summarized results of phospho-EIF2A level normalized to total EIF2A in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. F, Correlation between splenomegaly phenotype (spleen/body weight) and levels of ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. ATF4 levels were quantified with densitometry results from Western blots. G, Western blot results show ATF4 levels from human DLBCL tumor samples or normal GC B cells from human tonsil. ACTB levels were used as loading control. H, GSEA shows the enrichment of ATF4 target genes in DLBCL tumors versus normal GC B cells. Gene expression data were from published microarray data . Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Western Blot, Expressing, Microarray

    ATF4 protein level is regulated downstream of the SIRT3–GDH–TCA cycle–autophagy cascade. A, Western blots show the effects of ATF4 expression to autophagy activation induced by SIRT3 shRNA in Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. EV, empty vector. B, Western blots show the ATF4 protein level being rescued by exogenous GDH in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. C, Western blots show the ATF4 protein level being rescued by DMKG in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. D, Western blots show the ATF4 protein level being rescued by CQ (50 μmol/L) in SIRT3 knockdown Karpas 422 cells. CQ treatment was done in 16 to 18 hours, followed by immunoblot with the indicated antibodies. Densitometry values are shown for ATF4/ACTB and LC3II/LC3I ratios. Hypothetical cascade model is presented to the left. E, Western blots show the changes of ATF4 protein level control or ATG5 knockdown Karpas 422 cells with control or SIRT3 shRNAs. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. F, Summarized bar plot shows the NES ( y -axis) and FDRs (bar colors) of results from GSEA using published proteomic data . NES show the enrichment of ATF4 target genes (human and mouse) or ATF4 target genes from ChIP (mouse embryonic fibroblasts, MEF) in Atg5 knockout MEF cells in normal or starvation (5 hours) treatment condition. The experiments were done with stable isotope labeling by amino acids in cell culture (SILAC) coupled with off-gel fractionations (OG) and strong cation exchange chromatography (SCX) methods. HBSS, Hank's Balanced Salt Solution. G, Western blots show ATF4 protein levels under CHX and CQ treatment in Karpas 422 cells. Protein samples were collected at the indicated time points after treatment to monitor the kinetics of ATF4 degradation. SIRT3 and LC3 were blotted as controls. NT, not treated. H, EIF2A phosphorylation from Karpas 422 cells exposed to two different doses of CQ or DMSO, or to DMKG treatment. Proteins were blotted with the indicated antibodies, and the densitometry showed relative abundance of phospho-EIF2A over total EIF2A.
    Figure Legend Snippet: ATF4 protein level is regulated downstream of the SIRT3–GDH–TCA cycle–autophagy cascade. A, Western blots show the effects of ATF4 expression to autophagy activation induced by SIRT3 shRNA in Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. EV, empty vector. B, Western blots show the ATF4 protein level being rescued by exogenous GDH in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. C, Western blots show the ATF4 protein level being rescued by DMKG in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. D, Western blots show the ATF4 protein level being rescued by CQ (50 μmol/L) in SIRT3 knockdown Karpas 422 cells. CQ treatment was done in 16 to 18 hours, followed by immunoblot with the indicated antibodies. Densitometry values are shown for ATF4/ACTB and LC3II/LC3I ratios. Hypothetical cascade model is presented to the left. E, Western blots show the changes of ATF4 protein level control or ATG5 knockdown Karpas 422 cells with control or SIRT3 shRNAs. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. F, Summarized bar plot shows the NES ( y -axis) and FDRs (bar colors) of results from GSEA using published proteomic data . NES show the enrichment of ATF4 target genes (human and mouse) or ATF4 target genes from ChIP (mouse embryonic fibroblasts, MEF) in Atg5 knockout MEF cells in normal or starvation (5 hours) treatment condition. The experiments were done with stable isotope labeling by amino acids in cell culture (SILAC) coupled with off-gel fractionations (OG) and strong cation exchange chromatography (SCX) methods. HBSS, Hank's Balanced Salt Solution. G, Western blots show ATF4 protein levels under CHX and CQ treatment in Karpas 422 cells. Protein samples were collected at the indicated time points after treatment to monitor the kinetics of ATF4 degradation. SIRT3 and LC3 were blotted as controls. NT, not treated. H, EIF2A phosphorylation from Karpas 422 cells exposed to two different doses of CQ or DMSO, or to DMKG treatment. Proteins were blotted with the indicated antibodies, and the densitometry showed relative abundance of phospho-EIF2A over total EIF2A.

    Techniques Used: Western Blot, Expressing, Activation Assay, shRNA, Plasmid Preparation, Knock-Out, Labeling, Cell Culture, Chromatography

    ATF4 translation and protein level respond to nutrient level and are regulated by autophagy. A, FCs of mean fluorescence intensity (MFI) of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells containing control or SIRT3 shRNAs under different culture conditions. Top, experiments were done as in the schema. Briefly, cells were cultured with fresh medium for 48 hours and then replenished with same volume of fresh medium or maintained without replenishment (as a control) for another 16 hours. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. B, FCs of MFI of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs under control or glutamine starvation or tunicamycin (10 μg/mL) treatment. Both starvation and tunicamycin treatment were maintained for 15 hours at day 4 after viral transduction. C, Western blot results show the GFP expression from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells from B . D, The heatmap shows that relative abundances of amino acids were detected by metabolic profiling from Karpas 422 cells transduced with SIRT3 or control shRNAs. The metabolite levels were mean value from five to six replicate samples obtained on day 6 after infection. E, Relative activities of the ATF4-5′UTR-GFP reporter in Karpas 422 were cultured for 48 hours, replenished with fresh media or with the indicated nutrients, and then assessed for ATF4 translation reporter activity 16 hours later. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. NT, not treated; Q, glutamine. F, Western blots show ATF4 protein levels from the indicated cell lines cultured as in A and E , and then replenished with NEAA or not replenished, after which immunoblots were performed for ATF4, with tubulin and actin as loading controls, in control or NEAA-added conditions. G, The heatmap shows the amino acid abundance measured with LC/MS from Karpas 422 cells transduced with SIRT3 or control shRNA and cultured with or without DMKG supplementation. The values show the average logFC from three replicates in amino acid abundance as compared with DSMO-treated control shRNA–transduced cells. H, Western blot results show ATF4 level changes in control or ATG5 knockdown Karpas 422 cells under glutamine starvation condition. Samples were collected at different time points, and protein level changes were quantified with densitometry results. I, Western blots show the ATF4 and autophagy changes in Karpas 422 cells treated with DMSO or YC8-02 (YC; 3 μmol/L) for 40 hours. Cell lysates were subjected to Western blot using the indicated antibodies. Protein levels were quantified with densitometry results. J, The barplot shows the relative cell viability after OCI-LY1 and Karpas 422 cells were treated with DMSO, YC8-02 (OCI-LY1: 6 μmol/L; Karpas 422: 2 μmol/L), GCN2IN6 (OCI-LY1: 7.5 μmol/L; Karpas 422: 10 μmol/L), and combinations for 72 hours. Cells were subject to flow cytometry for viability tests (DAPI staining) and counting. *, P < 0.05; **, P < 0.01. NS, not significant. Error bars represent the mean ± SD of three or more replicates.
    Figure Legend Snippet: ATF4 translation and protein level respond to nutrient level and are regulated by autophagy. A, FCs of mean fluorescence intensity (MFI) of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells containing control or SIRT3 shRNAs under different culture conditions. Top, experiments were done as in the schema. Briefly, cells were cultured with fresh medium for 48 hours and then replenished with same volume of fresh medium or maintained without replenishment (as a control) for another 16 hours. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. B, FCs of MFI of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs under control or glutamine starvation or tunicamycin (10 μg/mL) treatment. Both starvation and tunicamycin treatment were maintained for 15 hours at day 4 after viral transduction. C, Western blot results show the GFP expression from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells from B . D, The heatmap shows that relative abundances of amino acids were detected by metabolic profiling from Karpas 422 cells transduced with SIRT3 or control shRNAs. The metabolite levels were mean value from five to six replicate samples obtained on day 6 after infection. E, Relative activities of the ATF4-5′UTR-GFP reporter in Karpas 422 were cultured for 48 hours, replenished with fresh media or with the indicated nutrients, and then assessed for ATF4 translation reporter activity 16 hours later. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. NT, not treated; Q, glutamine. F, Western blots show ATF4 protein levels from the indicated cell lines cultured as in A and E , and then replenished with NEAA or not replenished, after which immunoblots were performed for ATF4, with tubulin and actin as loading controls, in control or NEAA-added conditions. G, The heatmap shows the amino acid abundance measured with LC/MS from Karpas 422 cells transduced with SIRT3 or control shRNA and cultured with or without DMKG supplementation. The values show the average logFC from three replicates in amino acid abundance as compared with DSMO-treated control shRNA–transduced cells. H, Western blot results show ATF4 level changes in control or ATG5 knockdown Karpas 422 cells under glutamine starvation condition. Samples were collected at different time points, and protein level changes were quantified with densitometry results. I, Western blots show the ATF4 and autophagy changes in Karpas 422 cells treated with DMSO or YC8-02 (YC; 3 μmol/L) for 40 hours. Cell lysates were subjected to Western blot using the indicated antibodies. Protein levels were quantified with densitometry results. J, The barplot shows the relative cell viability after OCI-LY1 and Karpas 422 cells were treated with DMSO, YC8-02 (OCI-LY1: 6 μmol/L; Karpas 422: 2 μmol/L), GCN2IN6 (OCI-LY1: 7.5 μmol/L; Karpas 422: 10 μmol/L), and combinations for 72 hours. Cells were subject to flow cytometry for viability tests (DAPI staining) and counting. *, P < 0.05; **, P < 0.01. NS, not significant. Error bars represent the mean ± SD of three or more replicates.

    Techniques Used: Fluorescence, Cell Culture, Expressing, Flow Cytometry, Transduction, Western Blot, Infection, Activity Assay, Liquid Chromatography with Mass Spectroscopy, shRNA, Staining

    Graphical summary of SIRT3–ATF4 regulation in DLBCLs. Left, DLBCL cells depend on glutamine anaplerosis driven by SIRT3 and GDH to produce metabolic precursors from the TCA cycle for cell survival and proliferation, which also suppress autophagy and the downstream protein recycling in the lysosome. The active proliferation and high metabolic demand of DLBCL cells leads to a shortage of NEAAs and results in translational activation of ATF4, which can transcribe target genes for importation of extracellular nutrients to maintain the amino acid flux. Right, pharmaceutically inhibiting or knocking down SIRT3 suppresses the TCA cycle metabolism as a metabolic engine and decreases the consumption of amino acids (including NEAAs). The reduced TCA cycle metabolism in turn triggers activation of autophagy, which produces amino acids from lysosomal protein degradations to compensate the metabolic suppression. However, the increased amino acids cannot be used in the mitochondria of the defective TCA cycle, but instead block the translation of ATF4 and then shut down the nutrient importation. Together, these induce metabolic stress in DLBCL cells and lead to cell-cycle arrest and death. The larger, bold font indicates more activity or function of indicated proteins or biological activities. The thickness of lines and numbers of arrows indicate the impacts of upstream molecules/biological activities to downstream targets.
    Figure Legend Snippet: Graphical summary of SIRT3–ATF4 regulation in DLBCLs. Left, DLBCL cells depend on glutamine anaplerosis driven by SIRT3 and GDH to produce metabolic precursors from the TCA cycle for cell survival and proliferation, which also suppress autophagy and the downstream protein recycling in the lysosome. The active proliferation and high metabolic demand of DLBCL cells leads to a shortage of NEAAs and results in translational activation of ATF4, which can transcribe target genes for importation of extracellular nutrients to maintain the amino acid flux. Right, pharmaceutically inhibiting or knocking down SIRT3 suppresses the TCA cycle metabolism as a metabolic engine and decreases the consumption of amino acids (including NEAAs). The reduced TCA cycle metabolism in turn triggers activation of autophagy, which produces amino acids from lysosomal protein degradations to compensate the metabolic suppression. However, the increased amino acids cannot be used in the mitochondria of the defective TCA cycle, but instead block the translation of ATF4 and then shut down the nutrient importation. Together, these induce metabolic stress in DLBCL cells and lead to cell-cycle arrest and death. The larger, bold font indicates more activity or function of indicated proteins or biological activities. The thickness of lines and numbers of arrows indicate the impacts of upstream molecules/biological activities to downstream targets.

    Techniques Used: Activation Assay, Blocking Assay, Activity Assay

    anti mili  (Cell Signaling Technology Inc)


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    mili  (Cell Signaling Technology Inc)


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    anti mili antibody  (Cell Signaling Technology Inc)


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    sirt3 antibody  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc sirt3 antibody
    (A) Effect of <t>SIRT3</t> shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).
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    1) Product Images from "Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis"

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    Journal: Cancer cell

    doi: 10.1016/j.ccell.2019.05.002

    (A) Effect of SIRT3 shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).
    Figure Legend Snippet: (A) Effect of SIRT3 shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).

    Techniques Used: Infection, Expressing, shRNA, Flow Cytometry, Transduction

    (A) Growth curves of DLBCL cell lines with SIRT3 or control shRNAs. Relative cell growth represents the fold increase of cell numbers normalized to that from first time point (the third day post transduction).
    Figure Legend Snippet: (A) Growth curves of DLBCL cell lines with SIRT3 or control shRNAs. Relative cell growth represents the fold increase of cell numbers normalized to that from first time point (the third day post transduction).

    Techniques Used: Transduction

    (A) PNA (top), B220 (middle) and hematoxylin and Eosin (FI&E) (bottom) staining of spleen sections derived from Sirt3+/+ and Sirt3−/− mice.
    Figure Legend Snippet: (A) PNA (top), B220 (middle) and hematoxylin and Eosin (FI&E) (bottom) staining of spleen sections derived from Sirt3+/+ and Sirt3−/− mice.

    Techniques Used: Staining, Derivative Assay

    (A) Unsupervised hierarchical clustering of metabolomic profiles performed in SIRT3 or control shRNA transduced Karpas 422 at day 10 post-infection.
    Figure Legend Snippet: (A) Unsupervised hierarchical clustering of metabolomic profiles performed in SIRT3 or control shRNA transduced Karpas 422 at day 10 post-infection.

    Techniques Used: shRNA, Infection

    (A) Autophagy levels by detecting the ratio of LC3II/LC3I and p62 level in DLBCL cell lines with SIRT3 or control shRNAs. LC3II/LC3I ratios were quantified by densitometry and normalized to control shRNA (shCtr).
    Figure Legend Snippet: (A) Autophagy levels by detecting the ratio of LC3II/LC3I and p62 level in DLBCL cell lines with SIRT3 or control shRNAs. LC3II/LC3I ratios were quantified by densitometry and normalized to control shRNA (shCtr).

    Techniques Used: shRNA

    (A) Karpas 422 cells were transduced with SIRT3 or control shRNA followed by exposure to [U-13C5] glutamine. Color green indicates reduction and black indicates no change/detection. Carbon atom (13C in grey and 12C in white circles) transitions and tracers were used to detect glutamine metabolism.
    Figure Legend Snippet: (A) Karpas 422 cells were transduced with SIRT3 or control shRNA followed by exposure to [U-13C5] glutamine. Color green indicates reduction and black indicates no change/detection. Carbon atom (13C in grey and 12C in white circles) transitions and tracers were used to detect glutamine metabolism.

    Techniques Used: Transduction, shRNA

    (A) Representative images of spleens from control C57B6/J(B6) mouse or recipient mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells at 110 days post bone marrow transplantation (top) and comparison of spleen/body weight ratios from mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells (bottom).
    Figure Legend Snippet: (A) Representative images of spleens from control C57B6/J(B6) mouse or recipient mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells at 110 days post bone marrow transplantation (top) and comparison of spleen/body weight ratios from mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells (bottom).

    Techniques Used: Transplantation Assay

    TABLE WITH EXAMPLES FOR AUTHOR REFERENCE
    Figure Legend Snippet: TABLE WITH EXAMPLES FOR AUTHOR REFERENCE

    Techniques Used: Plasmid Preparation, Recombinant, In Vitro, BrdU Staining, Activity Assay, Isolation, Cell Viability Assay, Expressing, Software

    piwil2  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc sirt3
    Knocking down <t>SIRT3</t> caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .
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    (A) Effect of <t>SIRT3</t> shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).
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    (A) Effect of <t>SIRT3</t> shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).
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    Image Search Results


    Knocking down SIRT3 caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: Knocking down SIRT3 caused ATF4 signaling inhibition but not HIF1a. A, Dendrograms from hierarchical clustering of RNA-seq data from three DLBCL cells lines transduced with lentiviruses containing control (scramble) or two SIRT3 shRNAs. B, Heatmap showing differential expression in SIRT3 knockdown cells versus control (FC > 1.5, q < 0.05). C, Heatmap showing enrichment of SIRT3 knockdown signatures within key pathways. CHIP, chromatin immunoprecipitation; CHOP, C/EBP homologous protein; dn, down; KEGG, Kyoto Encyclopedia of Genes and Genomes; MEF, mouse embryonic fibroblast; TM, tunicamycin. D, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh1 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . ATF4 target genes were summarized from previous publications . E, GSEA showing the enrichment of ATF4 target genes in SIRT3-downregulated genes in Karpas 422, OCI-LY1, and HBL1 cells with SIRT3 sh2 versus control scramble shRNAs. The rank lists were from RNA-seq analysis from B . The same ATF4 target gene list was used here as in D .

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Inhibition, RNA Sequencing Assay, Transduction, Expressing, Chromatin Immunoprecipitation

    Knockdown SIRT3 caused ATF4 protein decrease via translation regulation. A, Western blots show ATF4 protein levels in different DLBCL cells with control or SIRT3 shRNAs. SIRT3 was blotted showing knockdown efficiency, and ACTB was used as reference protein control. B, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in OCI-LY1 cells. Samples were harvested at day 4 after viral transduction. Results were normalized to the mRNA levels in control shRNA–transduced cells. C, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in Karpas 422 cells. Samples were harvested at day 4 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. D, qPCR results show the relative levels of ATF4 mRNAs in different cell lines at different time points after shRNA transduction. Samples were harvested at days 2, 3, 4, and 7 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. E, Western blots show changes of phosphorylation of EIF2A and ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Total EIF2A and ACTB were blotted as loading controls. F, Western blots show GFP expression from the ATF4-5′UTR-GFP reporter and endogenous ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Tubulin and ACTB were blotted as loading controls. G, FCs of mean fluorescence intensity (MFI) of GFP expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal yellow fluorescent protein (YFP) expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. H, FCs of MFI of GFP expressed from the ATF4-5′UTR-GFP translation reporter in OCI-LY1 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal YFP expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. Error bars represent the mean ± SD of three or more replicates.

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: Knockdown SIRT3 caused ATF4 protein decrease via translation regulation. A, Western blots show ATF4 protein levels in different DLBCL cells with control or SIRT3 shRNAs. SIRT3 was blotted showing knockdown efficiency, and ACTB was used as reference protein control. B, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in OCI-LY1 cells. Samples were harvested at day 4 after viral transduction. Results were normalized to the mRNA levels in control shRNA–transduced cells. C, qPCR results reflect the mRNA levels of ATF4 and PSAT1 in Karpas 422 cells. Samples were harvested at day 4 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. D, qPCR results show the relative levels of ATF4 mRNAs in different cell lines at different time points after shRNA transduction. Samples were harvested at days 2, 3, 4, and 7 after viral transduction. Actin mRNA was used as reference, and results were normalized to the mRNA levels in control shRNA–transduced cells. E, Western blots show changes of phosphorylation of EIF2A and ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Total EIF2A and ACTB were blotted as loading controls. F, Western blots show GFP expression from the ATF4-5′UTR-GFP reporter and endogenous ATF4 protein levels in Karpas 422 cells with control or SIRT3 shRNAs. Tubulin and ACTB were blotted as loading controls. G, FCs of mean fluorescence intensity (MFI) of GFP expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal yellow fluorescent protein (YFP) expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. H, FCs of MFI of GFP expressed from the ATF4-5′UTR-GFP translation reporter in OCI-LY1 cells with control or SIRT3 shRNAs. The data were collected from days 4 and 7 after viral transduction. MFI of normal YFP expression in control or SIRT3 knockdown cells were used for normalization to avoid background translation variations. Error bars represent the mean ± SD of three or more replicates.

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Western Blot, Transduction, shRNA, Expressing, Fluorescence

    ATF4 is required in DLBCL cells and is partially responsible for SIRT3′s functions to promote DLBCL cell proliferation and survival. A, Effect of ATF4 knockdown on the proliferation of DLBCL cell lines. Each cell line was infected with lentivirus expressing control or ATF4 shRNAs and yellow fluorescent protein (YFP), and YFP + viable (DAPI − ) cells were monitored by flow cytometry for 8 days. B, FCs of cell numbers of HBL1 cells expressing control or SIRT3 shRNA with or without exogeneous ATF4. HBL1 cells were transduced with viral vectors containing shRNAs or genes as presented. Cell number changes were normalized to data of initial time point (day 3 after infection). C, Summarized results show the rescue effects of exogenous ATF4 to SIRT3 shRNA-induced cell proliferation inhibition in different DLBCL cells. The data were summarized from day 10 after infections and normalized to the cell numbers of their respective control shRNA–expressing cell. D, Effects of exogenous ATF4 on different DLBCL cells expressing control or SIRT3 shRNAs. Dead cells were stained with DAPI and quantified through flow cytometry. The relative cell death was calculated by normalizing the percentage of dead cells in control shRNA–expressing cells in respective cell lines. *, P < 0.05; **, P < 0.01. Error bars represent the mean ± SD of three or more replicates.

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: ATF4 is required in DLBCL cells and is partially responsible for SIRT3′s functions to promote DLBCL cell proliferation and survival. A, Effect of ATF4 knockdown on the proliferation of DLBCL cell lines. Each cell line was infected with lentivirus expressing control or ATF4 shRNAs and yellow fluorescent protein (YFP), and YFP + viable (DAPI − ) cells were monitored by flow cytometry for 8 days. B, FCs of cell numbers of HBL1 cells expressing control or SIRT3 shRNA with or without exogeneous ATF4. HBL1 cells were transduced with viral vectors containing shRNAs or genes as presented. Cell number changes were normalized to data of initial time point (day 3 after infection). C, Summarized results show the rescue effects of exogenous ATF4 to SIRT3 shRNA-induced cell proliferation inhibition in different DLBCL cells. The data were summarized from day 10 after infections and normalized to the cell numbers of their respective control shRNA–expressing cell. D, Effects of exogenous ATF4 on different DLBCL cells expressing control or SIRT3 shRNAs. Dead cells were stained with DAPI and quantified through flow cytometry. The relative cell death was calculated by normalizing the percentage of dead cells in control shRNA–expressing cells in respective cell lines. *, P < 0.05; **, P < 0.01. Error bars represent the mean ± SD of three or more replicates.

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Infection, Expressing, Flow Cytometry, shRNA, Transduction, Inhibition, Staining

    ATF4 protein level is decreased in vavP-Bcl2;Sirt3 −/− mice and associated with lymphoma progression. A, Western blot results show the protein levels of ATF4, LC3, EIF2A, ACTB, and SIRT3 in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results. B, Summarized results of ATF4 protein level normalized to ACTB in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. C, Correlation between levels of autophagy (LC3II/LC3I) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. D, Correlation between levels of phospho-EIF2A (p-EIF2A/EIF2A) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. E, Summarized results of phospho-EIF2A level normalized to total EIF2A in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. F, Correlation between splenomegaly phenotype (spleen/body weight) and levels of ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. ATF4 levels were quantified with densitometry results from Western blots. G, Western blot results show ATF4 levels from human DLBCL tumor samples or normal GC B cells from human tonsil. ACTB levels were used as loading control. H, GSEA shows the enrichment of ATF4 target genes in DLBCL tumors versus normal GC B cells. Gene expression data were from published microarray data . Error bars represent the mean ± SD of three or more replicates.

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: ATF4 protein level is decreased in vavP-Bcl2;Sirt3 −/− mice and associated with lymphoma progression. A, Western blot results show the protein levels of ATF4, LC3, EIF2A, ACTB, and SIRT3 in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results. B, Summarized results of ATF4 protein level normalized to ACTB in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. C, Correlation between levels of autophagy (LC3II/LC3I) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. D, Correlation between levels of phospho-EIF2A (p-EIF2A/EIF2A) and ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The data for correlation study were obtained with densitometry results from Western blots. E, Summarized results of phospho-EIF2A level normalized to total EIF2A in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. The protein amounts were quantified with densitometry results from Western blots. F, Correlation between splenomegaly phenotype (spleen/body weight) and levels of ATF4 (ATF4/ACTB) in splenocytes from vavP-Bcl2;Sirt3 +/+ and vavP-Bcl2;Sirt3 −/− mice. ATF4 levels were quantified with densitometry results from Western blots. G, Western blot results show ATF4 levels from human DLBCL tumor samples or normal GC B cells from human tonsil. ACTB levels were used as loading control. H, GSEA shows the enrichment of ATF4 target genes in DLBCL tumors versus normal GC B cells. Gene expression data were from published microarray data . Error bars represent the mean ± SD of three or more replicates.

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Western Blot, Expressing, Microarray

    ATF4 protein level is regulated downstream of the SIRT3–GDH–TCA cycle–autophagy cascade. A, Western blots show the effects of ATF4 expression to autophagy activation induced by SIRT3 shRNA in Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. EV, empty vector. B, Western blots show the ATF4 protein level being rescued by exogenous GDH in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. C, Western blots show the ATF4 protein level being rescued by DMKG in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. D, Western blots show the ATF4 protein level being rescued by CQ (50 μmol/L) in SIRT3 knockdown Karpas 422 cells. CQ treatment was done in 16 to 18 hours, followed by immunoblot with the indicated antibodies. Densitometry values are shown for ATF4/ACTB and LC3II/LC3I ratios. Hypothetical cascade model is presented to the left. E, Western blots show the changes of ATF4 protein level control or ATG5 knockdown Karpas 422 cells with control or SIRT3 shRNAs. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. F, Summarized bar plot shows the NES ( y -axis) and FDRs (bar colors) of results from GSEA using published proteomic data . NES show the enrichment of ATF4 target genes (human and mouse) or ATF4 target genes from ChIP (mouse embryonic fibroblasts, MEF) in Atg5 knockout MEF cells in normal or starvation (5 hours) treatment condition. The experiments were done with stable isotope labeling by amino acids in cell culture (SILAC) coupled with off-gel fractionations (OG) and strong cation exchange chromatography (SCX) methods. HBSS, Hank's Balanced Salt Solution. G, Western blots show ATF4 protein levels under CHX and CQ treatment in Karpas 422 cells. Protein samples were collected at the indicated time points after treatment to monitor the kinetics of ATF4 degradation. SIRT3 and LC3 were blotted as controls. NT, not treated. H, EIF2A phosphorylation from Karpas 422 cells exposed to two different doses of CQ or DMSO, or to DMKG treatment. Proteins were blotted with the indicated antibodies, and the densitometry showed relative abundance of phospho-EIF2A over total EIF2A.

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: ATF4 protein level is regulated downstream of the SIRT3–GDH–TCA cycle–autophagy cascade. A, Western blots show the effects of ATF4 expression to autophagy activation induced by SIRT3 shRNA in Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. EV, empty vector. B, Western blots show the ATF4 protein level being rescued by exogenous GDH in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. C, Western blots show the ATF4 protein level being rescued by DMKG in SIRT3 knockdown Karpas 422 cells. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. D, Western blots show the ATF4 protein level being rescued by CQ (50 μmol/L) in SIRT3 knockdown Karpas 422 cells. CQ treatment was done in 16 to 18 hours, followed by immunoblot with the indicated antibodies. Densitometry values are shown for ATF4/ACTB and LC3II/LC3I ratios. Hypothetical cascade model is presented to the left. E, Western blots show the changes of ATF4 protein level control or ATG5 knockdown Karpas 422 cells with control or SIRT3 shRNAs. Protein level changes were quantified with densitometry results. Hypothetical cascade model is presented to the left. F, Summarized bar plot shows the NES ( y -axis) and FDRs (bar colors) of results from GSEA using published proteomic data . NES show the enrichment of ATF4 target genes (human and mouse) or ATF4 target genes from ChIP (mouse embryonic fibroblasts, MEF) in Atg5 knockout MEF cells in normal or starvation (5 hours) treatment condition. The experiments were done with stable isotope labeling by amino acids in cell culture (SILAC) coupled with off-gel fractionations (OG) and strong cation exchange chromatography (SCX) methods. HBSS, Hank's Balanced Salt Solution. G, Western blots show ATF4 protein levels under CHX and CQ treatment in Karpas 422 cells. Protein samples were collected at the indicated time points after treatment to monitor the kinetics of ATF4 degradation. SIRT3 and LC3 were blotted as controls. NT, not treated. H, EIF2A phosphorylation from Karpas 422 cells exposed to two different doses of CQ or DMSO, or to DMKG treatment. Proteins were blotted with the indicated antibodies, and the densitometry showed relative abundance of phospho-EIF2A over total EIF2A.

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Western Blot, Expressing, Activation Assay, shRNA, Plasmid Preparation, Knock-Out, Labeling, Cell Culture, Chromatography

    ATF4 translation and protein level respond to nutrient level and are regulated by autophagy. A, FCs of mean fluorescence intensity (MFI) of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells containing control or SIRT3 shRNAs under different culture conditions. Top, experiments were done as in the schema. Briefly, cells were cultured with fresh medium for 48 hours and then replenished with same volume of fresh medium or maintained without replenishment (as a control) for another 16 hours. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. B, FCs of MFI of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs under control or glutamine starvation or tunicamycin (10 μg/mL) treatment. Both starvation and tunicamycin treatment were maintained for 15 hours at day 4 after viral transduction. C, Western blot results show the GFP expression from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells from B . D, The heatmap shows that relative abundances of amino acids were detected by metabolic profiling from Karpas 422 cells transduced with SIRT3 or control shRNAs. The metabolite levels were mean value from five to six replicate samples obtained on day 6 after infection. E, Relative activities of the ATF4-5′UTR-GFP reporter in Karpas 422 were cultured for 48 hours, replenished with fresh media or with the indicated nutrients, and then assessed for ATF4 translation reporter activity 16 hours later. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. NT, not treated; Q, glutamine. F, Western blots show ATF4 protein levels from the indicated cell lines cultured as in A and E , and then replenished with NEAA or not replenished, after which immunoblots were performed for ATF4, with tubulin and actin as loading controls, in control or NEAA-added conditions. G, The heatmap shows the amino acid abundance measured with LC/MS from Karpas 422 cells transduced with SIRT3 or control shRNA and cultured with or without DMKG supplementation. The values show the average logFC from three replicates in amino acid abundance as compared with DSMO-treated control shRNA–transduced cells. H, Western blot results show ATF4 level changes in control or ATG5 knockdown Karpas 422 cells under glutamine starvation condition. Samples were collected at different time points, and protein level changes were quantified with densitometry results. I, Western blots show the ATF4 and autophagy changes in Karpas 422 cells treated with DMSO or YC8-02 (YC; 3 μmol/L) for 40 hours. Cell lysates were subjected to Western blot using the indicated antibodies. Protein levels were quantified with densitometry results. J, The barplot shows the relative cell viability after OCI-LY1 and Karpas 422 cells were treated with DMSO, YC8-02 (OCI-LY1: 6 μmol/L; Karpas 422: 2 μmol/L), GCN2IN6 (OCI-LY1: 7.5 μmol/L; Karpas 422: 10 μmol/L), and combinations for 72 hours. Cells were subject to flow cytometry for viability tests (DAPI staining) and counting. *, P < 0.05; **, P < 0.01. NS, not significant. Error bars represent the mean ± SD of three or more replicates.

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: ATF4 translation and protein level respond to nutrient level and are regulated by autophagy. A, FCs of mean fluorescence intensity (MFI) of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells containing control or SIRT3 shRNAs under different culture conditions. Top, experiments were done as in the schema. Briefly, cells were cultured with fresh medium for 48 hours and then replenished with same volume of fresh medium or maintained without replenishment (as a control) for another 16 hours. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. B, FCs of MFI of the GFP reporter expressed from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells with control or SIRT3 shRNAs under control or glutamine starvation or tunicamycin (10 μg/mL) treatment. Both starvation and tunicamycin treatment were maintained for 15 hours at day 4 after viral transduction. C, Western blot results show the GFP expression from the ATF4-5′UTR-GFP translation reporter in Karpas 422 cells from B . D, The heatmap shows that relative abundances of amino acids were detected by metabolic profiling from Karpas 422 cells transduced with SIRT3 or control shRNAs. The metabolite levels were mean value from five to six replicate samples obtained on day 6 after infection. E, Relative activities of the ATF4-5′UTR-GFP reporter in Karpas 422 were cultured for 48 hours, replenished with fresh media or with the indicated nutrients, and then assessed for ATF4 translation reporter activity 16 hours later. The y -axis denotes GFP signal intensity relative to control cells without expression of reporter, determined with MFI of GFP signals from flow cytometer. NT, not treated; Q, glutamine. F, Western blots show ATF4 protein levels from the indicated cell lines cultured as in A and E , and then replenished with NEAA or not replenished, after which immunoblots were performed for ATF4, with tubulin and actin as loading controls, in control or NEAA-added conditions. G, The heatmap shows the amino acid abundance measured with LC/MS from Karpas 422 cells transduced with SIRT3 or control shRNA and cultured with or without DMKG supplementation. The values show the average logFC from three replicates in amino acid abundance as compared with DSMO-treated control shRNA–transduced cells. H, Western blot results show ATF4 level changes in control or ATG5 knockdown Karpas 422 cells under glutamine starvation condition. Samples were collected at different time points, and protein level changes were quantified with densitometry results. I, Western blots show the ATF4 and autophagy changes in Karpas 422 cells treated with DMSO or YC8-02 (YC; 3 μmol/L) for 40 hours. Cell lysates were subjected to Western blot using the indicated antibodies. Protein levels were quantified with densitometry results. J, The barplot shows the relative cell viability after OCI-LY1 and Karpas 422 cells were treated with DMSO, YC8-02 (OCI-LY1: 6 μmol/L; Karpas 422: 2 μmol/L), GCN2IN6 (OCI-LY1: 7.5 μmol/L; Karpas 422: 10 μmol/L), and combinations for 72 hours. Cells were subject to flow cytometry for viability tests (DAPI staining) and counting. *, P < 0.05; **, P < 0.01. NS, not significant. Error bars represent the mean ± SD of three or more replicates.

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Fluorescence, Cell Culture, Expressing, Flow Cytometry, Transduction, Western Blot, Infection, Activity Assay, Liquid Chromatography with Mass Spectroscopy, shRNA, Staining

    Graphical summary of SIRT3–ATF4 regulation in DLBCLs. Left, DLBCL cells depend on glutamine anaplerosis driven by SIRT3 and GDH to produce metabolic precursors from the TCA cycle for cell survival and proliferation, which also suppress autophagy and the downstream protein recycling in the lysosome. The active proliferation and high metabolic demand of DLBCL cells leads to a shortage of NEAAs and results in translational activation of ATF4, which can transcribe target genes for importation of extracellular nutrients to maintain the amino acid flux. Right, pharmaceutically inhibiting or knocking down SIRT3 suppresses the TCA cycle metabolism as a metabolic engine and decreases the consumption of amino acids (including NEAAs). The reduced TCA cycle metabolism in turn triggers activation of autophagy, which produces amino acids from lysosomal protein degradations to compensate the metabolic suppression. However, the increased amino acids cannot be used in the mitochondria of the defective TCA cycle, but instead block the translation of ATF4 and then shut down the nutrient importation. Together, these induce metabolic stress in DLBCL cells and lead to cell-cycle arrest and death. The larger, bold font indicates more activity or function of indicated proteins or biological activities. The thickness of lines and numbers of arrows indicate the impacts of upstream molecules/biological activities to downstream targets.

    Journal: Blood Cancer Discovery

    Article Title: Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival

    doi: 10.1158/2643-3230.BCD-20-0183

    Figure Lengend Snippet: Graphical summary of SIRT3–ATF4 regulation in DLBCLs. Left, DLBCL cells depend on glutamine anaplerosis driven by SIRT3 and GDH to produce metabolic precursors from the TCA cycle for cell survival and proliferation, which also suppress autophagy and the downstream protein recycling in the lysosome. The active proliferation and high metabolic demand of DLBCL cells leads to a shortage of NEAAs and results in translational activation of ATF4, which can transcribe target genes for importation of extracellular nutrients to maintain the amino acid flux. Right, pharmaceutically inhibiting or knocking down SIRT3 suppresses the TCA cycle metabolism as a metabolic engine and decreases the consumption of amino acids (including NEAAs). The reduced TCA cycle metabolism in turn triggers activation of autophagy, which produces amino acids from lysosomal protein degradations to compensate the metabolic suppression. However, the increased amino acids cannot be used in the mitochondria of the defective TCA cycle, but instead block the translation of ATF4 and then shut down the nutrient importation. Together, these induce metabolic stress in DLBCL cells and lead to cell-cycle arrest and death. The larger, bold font indicates more activity or function of indicated proteins or biological activities. The thickness of lines and numbers of arrows indicate the impacts of upstream molecules/biological activities to downstream targets.

    Article Snippet: Antibodies of SIRT3 (5940S), ATF4 (11815S), ATG5 (12994S), LC3I/II (12741S), EIF2A (5324P), phospho-EIF2A (3398S), Grp75 (3593S), p62 (5114S), and acetylated histone 3 (8848S) were purchased from Cell Signaling Technology.

    Techniques: Activation Assay, Blocking Assay, Activity Assay

    piR-54265 interacts with PIWIL2, facilitating PIWIL2/STAT3/p-SRC formation. (A) RNA immunoprecipitation assays showed specific bind of piR-54265 to PIWIL2. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (B) Biotin-labeled piR-54265 RNA pulldown coupled with western blot analysis revealed interaction of piR-54265 with PIWIL2, STAT3 and p-SRC. (C) Schematic of the domain structure of PIWIL2 protein. (D) Biotin-labeled piR-54265 RNA pulldown from lysates containing FLAG-tagged full-length or truncated PIWIL2 protein coupled with Western blot analysis revealed the interaction of piR-54265 with PIWIL2 via the PIWI domain in PIWIL2. (E) Co-immunoprecipitation assays revealed the interaction of STAT3 with PIWIL2 via the PAZ domain in PIWIL2. (F) RNA immunoprecipitation assays showed specific association of piR-54265 with STAT3 and p-SRC in CRC cells. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (G) Reciprocal immunoprecipitation assays showed that the interaction among PIWIL2, STAT3 and SRC in CRC cells was affected by piR-54265 expression. (H) Effects of overexpression or knockdown of piR-54265 on the expression levels of STAT3 and SRC and their phosphorylated forms detected by western blot.

    Journal: Theranostics

    Article Title: PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma

    doi: 10.7150/thno.28001

    Figure Lengend Snippet: piR-54265 interacts with PIWIL2, facilitating PIWIL2/STAT3/p-SRC formation. (A) RNA immunoprecipitation assays showed specific bind of piR-54265 to PIWIL2. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (B) Biotin-labeled piR-54265 RNA pulldown coupled with western blot analysis revealed interaction of piR-54265 with PIWIL2, STAT3 and p-SRC. (C) Schematic of the domain structure of PIWIL2 protein. (D) Biotin-labeled piR-54265 RNA pulldown from lysates containing FLAG-tagged full-length or truncated PIWIL2 protein coupled with Western blot analysis revealed the interaction of piR-54265 with PIWIL2 via the PIWI domain in PIWIL2. (E) Co-immunoprecipitation assays revealed the interaction of STAT3 with PIWIL2 via the PAZ domain in PIWIL2. (F) RNA immunoprecipitation assays showed specific association of piR-54265 with STAT3 and p-SRC in CRC cells. Results are mean ± SEM of piR-54265 enrichment relative to input from three independent experiments. (G) Reciprocal immunoprecipitation assays showed that the interaction among PIWIL2, STAT3 and SRC in CRC cells was affected by piR-54265 expression. (H) Effects of overexpression or knockdown of piR-54265 on the expression levels of STAT3 and SRC and their phosphorylated forms detected by western blot.

    Article Snippet: Antibodies against PIWIL2 (sc-67502) or p-SRC (p-Tyr416, D4964) were from Santa Cruz or Cell Signaling Technology, respectively.

    Techniques: Immunoprecipitation, Labeling, Western Blot, Expressing, Over Expression

    piR-54265 enhances oncogenic STAT3 signaling. (A) Effects of piR-54265 on expression and/or activation of proliferation and metastasis-related STAT3 downstream modules in CRC cells detected by western blot. (B-C) Immunohistochemical (IHC) staining of proliferation- and metastasis-related STAT3 downstream modules in mouse xenograft tumors of CRC cells with overexpression or knockdown of piR-54265. IHC staining of proliferation-related molecules (B) and metastasis-related molecules (C). 200×; scale bars, 50 μm. (D) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell proliferation (each point in the curve represents mean ± SEM; N=6; **, P <0.01; ***, P <0.001). (E) Knockdown of PIWIL2 or STAT3 affects the piR-54265-induced migration ( upper panel ) and invasion ( lower panel ) abilities of CRC cells (mean ± SEM; N=6. ***, P <0.001; ****, P <0.0001). See also Figure B . (F) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell apoptosis (mean ± SEM; N=3; ***, P <0.001). See also Figure C . OE: overexpression; KD: knockdown.

    Journal: Theranostics

    Article Title: PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma

    doi: 10.7150/thno.28001

    Figure Lengend Snippet: piR-54265 enhances oncogenic STAT3 signaling. (A) Effects of piR-54265 on expression and/or activation of proliferation and metastasis-related STAT3 downstream modules in CRC cells detected by western blot. (B-C) Immunohistochemical (IHC) staining of proliferation- and metastasis-related STAT3 downstream modules in mouse xenograft tumors of CRC cells with overexpression or knockdown of piR-54265. IHC staining of proliferation-related molecules (B) and metastasis-related molecules (C). 200×; scale bars, 50 μm. (D) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell proliferation (each point in the curve represents mean ± SEM; N=6; **, P <0.01; ***, P <0.001). (E) Knockdown of PIWIL2 or STAT3 affects the piR-54265-induced migration ( upper panel ) and invasion ( lower panel ) abilities of CRC cells (mean ± SEM; N=6. ***, P <0.001; ****, P <0.0001). See also Figure B . (F) Knockdown of PIWIL2 or STAT3 affects piR-54265-induced CRC cell apoptosis (mean ± SEM; N=3; ***, P <0.001). See also Figure C . OE: overexpression; KD: knockdown.

    Article Snippet: Antibodies against PIWIL2 (sc-67502) or p-SRC (p-Tyr416, D4964) were from Santa Cruz or Cell Signaling Technology, respectively.

    Techniques: Expressing, Activation Assay, Western Blot, Immunohistochemical staining, Immunohistochemistry, Over Expression, Migration

    (A) Effect of SIRT3 shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) Effect of SIRT3 shRNAs on the proliferation of DLBCL and non-DLBCL cell lines. Each cell line was infected with lentivirus expressing control or SIRT3 shRNA and YFP. YFP+ viable (DAPI−) cells were monitored by flow-cytometry for 6 days. Data were normalized to cells transduced with control shRNA (dashed line).

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: Infection, Expressing, shRNA, Flow Cytometry, Transduction

    (A) Growth curves of DLBCL cell lines with SIRT3 or control shRNAs. Relative cell growth represents the fold increase of cell numbers normalized to that from first time point (the third day post transduction).

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) Growth curves of DLBCL cell lines with SIRT3 or control shRNAs. Relative cell growth represents the fold increase of cell numbers normalized to that from first time point (the third day post transduction).

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: Transduction

    (A) PNA (top), B220 (middle) and hematoxylin and Eosin (FI&E) (bottom) staining of spleen sections derived from Sirt3+/+ and Sirt3−/− mice.

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) PNA (top), B220 (middle) and hematoxylin and Eosin (FI&E) (bottom) staining of spleen sections derived from Sirt3+/+ and Sirt3−/− mice.

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: Staining, Derivative Assay

    (A) Unsupervised hierarchical clustering of metabolomic profiles performed in SIRT3 or control shRNA transduced Karpas 422 at day 10 post-infection.

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) Unsupervised hierarchical clustering of metabolomic profiles performed in SIRT3 or control shRNA transduced Karpas 422 at day 10 post-infection.

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: shRNA, Infection

    (A) Autophagy levels by detecting the ratio of LC3II/LC3I and p62 level in DLBCL cell lines with SIRT3 or control shRNAs. LC3II/LC3I ratios were quantified by densitometry and normalized to control shRNA (shCtr).

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) Autophagy levels by detecting the ratio of LC3II/LC3I and p62 level in DLBCL cell lines with SIRT3 or control shRNAs. LC3II/LC3I ratios were quantified by densitometry and normalized to control shRNA (shCtr).

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: shRNA

    (A) Karpas 422 cells were transduced with SIRT3 or control shRNA followed by exposure to [U-13C5] glutamine. Color green indicates reduction and black indicates no change/detection. Carbon atom (13C in grey and 12C in white circles) transitions and tracers were used to detect glutamine metabolism.

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) Karpas 422 cells were transduced with SIRT3 or control shRNA followed by exposure to [U-13C5] glutamine. Color green indicates reduction and black indicates no change/detection. Carbon atom (13C in grey and 12C in white circles) transitions and tracers were used to detect glutamine metabolism.

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: Transduction, shRNA

    (A) Representative images of spleens from control C57B6/J(B6) mouse or recipient mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells at 110 days post bone marrow transplantation (top) and comparison of spleen/body weight ratios from mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells (bottom).

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: (A) Representative images of spleens from control C57B6/J(B6) mouse or recipient mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells at 110 days post bone marrow transplantation (top) and comparison of spleen/body weight ratios from mice with VavP-Bcl2;Sirt3+/+ or VavP-Bcl2;Sirt3−/− bone marrow cells (bottom).

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: Transplantation Assay

    TABLE WITH EXAMPLES FOR AUTHOR REFERENCE

    Journal: Cancer cell

    Article Title: Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis

    doi: 10.1016/j.ccell.2019.05.002

    Figure Lengend Snippet: TABLE WITH EXAMPLES FOR AUTHOR REFERENCE

    Article Snippet: SIRT3 antibody , Cell Signaling Technology , Cat#5940S.

    Techniques: Plasmid Preparation, Recombinant, In Vitro, BrdU Staining, Activity Assay, Isolation, Cell Viability Assay, Expressing, Software