Journal: The Journal of Biological Chemistry

Article Title: Disruption of sirtuin 7 in zebrafish facilitates hypoxia tolerance

doi: 10.1016/j.jbc.2023.105074

Figure Lengend Snippet: Zebrafish sirt7 is suppressed by hypoxia. A , quantitative real-time PCR analysis (qPCR) of sirt7 , as well as well-defined hypoxia-responsive genes, including cited2 , pai1 , phd3 , vegfaa , and epoa , in zebrafish larvae (3 dpf) under normoxia (Nor) and hypoxia (Hyp). B , qPCR analysis of sirt7 , as well as well-defined hypoxia-responsive genes, including phd3 , cited2 , ldha , and vegfaa , in ZFL cells under normoxia (Nor) and hypoxia (Hyp). C , qPCR analysis of sirt7 in ZFL cells transfected with empty vector control (Flag empty) or Flag- hif-1αa , or Flag- hif-1αb , or Flag- hif-2αa , or Flag- hif-2αb under normoxia. D , qPCR analysis of phd3 in ZFL cells transfected with empty vector control (Flag empty) or Flag- hif-1αa , or Flag- hif-1αb , or Flag- hif-2αa , or Flag- hif-2αb under normoxia. E , qPCR analysis of cited2 in ZFL cells transfected with empty vector control (Flag empty) or Flag- hif-1αa , or Flag- hif-1αb , or Flag- hif-2αa , or Flag- hif-2αb under normoxia. F , qPCR analysis of ldha in ZFL cells transfected with empty vector control (Flag empty) or Flag- hif-1αa , or Flag- hif-1αb , or Flag- hif-2αa , or Flag- hif-2αb under normoxia. G , qPCR analysis of vegfaa in ZFL cells transfected with empty vector control (Flag empty) or Flag- hif-1αa , or Flag- hif-1αb , or Flag- hif-2αa , or Flag- hif-2αb under normoxia. p Values were calculated by unpaired Student's t test ( A and B ) or two-way ANOVA analysis ( C – G ); ns, not significant, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001 and ∗∗∗∗ p < 0.0001; data based on one representative experiment performed in three biological replicates from at least three independent experiments (mean ± SD).

Article Snippet: Zebrafish liver (ZFL) cells (originally obtained from the American Type Culture Collection) were cultured in Ham’s F-12 medium (HyClone) supplemented with 10% fetal bovine serum (FBS) (Biological Industries).

Techniques: Real-time Polymerase Chain Reaction, Transfection, Plasmid Preparation, Control

Journal: The Journal of Biological Chemistry

Article Title: Disruption of sirtuin 7 in zebrafish facilitates hypoxia tolerance

doi: 10.1016/j.jbc.2023.105074

Figure Lengend Snippet: Zebrafish sirt7 suppresses hypoxia-responsive gene expression. A , Western blot analysis of indicated protein levels in EPC cells transfected empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 (Myc- sirt7 ). B , luciferase activity of hypoxia-responsive element (HRE)-luciferase reporter in EPC cells transfected with empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 (Myc- sirt7 ) under normoxia (Nor) or hypoxia (Hyp). C , Western blot analysis of indicated protein levels in ZFL cells transfected empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 (Myc- sirt7 ). D , quantitative real-time PCR (qPCR) analysis of phd3 in ZFL cells transfected with empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 (Myc- sirt7 ) under normoxia (Nor) or hypoxia (Hyp). E , qPCR analysis of vegfaa in ZFL cells transfected with empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 (Myc- sirt7 ) under normoxia (Nor) or hypoxia (Hyp). F , qPCR analysis of ldha in ZFL cells transfected with empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 (Myc- sirt7 ) under normoxia (Nor) or hypoxia (Hyp). G , qPCR analysis of cited2 in ZFL cells transfected with empty vector control (Myc empty) or Myc-tagged zebrafish sirt7 under normoxia (Nor) or hypoxia (Hyp). p Values were calculated by two-way ANOVA analysis ( B , D , E , F , and G ); ∗∗∗∗ p < 0.0001; data based on one representative experiment performed in three biological replicates from at least three independent experiments (mean ± SD).

Article Snippet: Zebrafish liver (ZFL) cells (originally obtained from the American Type Culture Collection) were cultured in Ham’s F-12 medium (HyClone) supplemented with 10% fetal bovine serum (FBS) (Biological Industries).

Techniques: Gene Expression, Western Blot, Transfection, Plasmid Preparation, Control, Luciferase, Activity Assay, Real-time Polymerase Chain Reaction

Journal: The Journal of Biological Chemistry

Article Title: Disruption of sirtuin 7 in zebrafish facilitates hypoxia tolerance

doi: 10.1016/j.jbc.2023.105074

Figure Lengend Snippet: Zebrafish sirt7 attenuates hypoxia signaling independent of its deacetylase activity. A , Western blot analysis of indicated protein levels in EPC cells transfected with empty vector, wildtype sirt7 , or the enzyme-deficient mutants sirt 7 -S115A and sirt 7 -H191Y. B , luciferase activity of HRE-luciferase reporter in EPC cells transfected with empty vector, wildtype sirt7 , or the enzyme-deficient mutants sirt 7 -S115A and sirt 7 -H191Y under normoxia (Nor) or hypoxia (Hyp). C , Western blot analysis of indicated protein levels in ZFL cells transfected with empty vector, wildtype sirt7 , or the enzyme-deficient mutants sirt 7 -S115A and sirt 7 -H191Y. D , quantitative real-time PCR (qPCR) analysis of phd3 in ZFL cells transfected with empty vector, wildtype sirt7 , or the enzyme-deficient mutants sirt 7 -S115A and sirt 7 -H191Y under normoxia (Nor) or hypoxia (Hyp). E , qPCR analysis of cited2 in ZFL cells transfected with empty vector, wildtype sirt7 , or the enzyme-deficient mutants sirt 7 -S115A and sirt 7 -H191Y under normoxia (Nor) or hypoxia (Hyp). F , qPCR analysis of ldha in ZFL cells transfected with empty vector, wildtype sirt7 , or the enzyme-deficient mutants sirt 7 -S115A and sirt 7 -H191Y under normoxia (Nor) or hypoxia (Hyp). p Values were calculated by two-way ANOVA analysis ( B , D , E , and F ); ∗∗ p < 0.01, ∗∗∗ p < 0.001 and ∗∗∗∗ p < 0.0001; data based on one representative experiment performed in three biological replicates from at least three independent experiments (mean ± SD).

Article Snippet: Zebrafish liver (ZFL) cells (originally obtained from the American Type Culture Collection) were cultured in Ham’s F-12 medium (HyClone) supplemented with 10% fetal bovine serum (FBS) (Biological Industries).

Techniques: Histone Deacetylase Assay, Activity Assay, Western Blot, Transfection, Plasmid Preparation, Luciferase, Real-time Polymerase Chain Reaction

Journal: Nature Genetics

Article Title: Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers

doi: 10.1038/s41588-025-02221-2

Figure Lengend Snippet: a , Method for phenotyping cancer cell lines that are Δ CDS2 lethal and CDS1 -low compared to those that are Δ CDS2 nonlethal and CDS1 -high (DepMap) (illustrative). b , Genome-wide calculated Pearson correlations using the method depicted in a (DepMap). Representative genes enriched on either side are marked. Bonferroni-corrected P values from Pearson correlation tests were used to determine the significance cut-off. n = 913 cancer cell lines. c , Plot depicting CDS1 RNA expression on ZEB1 CRISPR perturbation as measured by qPCR analysis. The dashed line indicates the baseline of no change (1-fold change). Two-way ANOVA followed by Dunnett’s test was used for each cancer cell line. n = 4 replicates for 2 cancer cell lines in 2 independent experiments with each 2 sg ZEB1 and 1 sgControl. d , For each cancer lineage, the percentage of ZEB1 -high cancer cell lines (DepMap) was plotted against the percentage of CDS1- high or CDH1 -high cancer cell lines. A linear regression, the associated Pearson correlation and associated P values were added. n = 906 cancer cell lines. e , Diagram depicting the characteristics of cancer cell lines with and without the CDS1–CDS2 SLI. CDH1 and VIM are representative epithelial and mesenchymal markers, respectively. f , Diagram depicting the core CDS pathway. The lethality on perturbation (color) and lineage-specific expression patterns (gray boxes on the left) of each enzyme in the pathway are indicated (DepMap). Gene dependency is represented by CERES. n = 913 cancer cell lines. g , Correlation between Δ CDS2 lethality and Δ CDIPT lethality, Δ PIK3CA lethality, PIK3CA inhibitor lethality (alpelisib) or the pan-PI3K inhibitor lethality (copanlisib) in solid cancer cell lines (DepMap). Bonferroni-corrected P values from Pearson correlation tests were used. n (cancer cell lines) = 865 ( CDIPT and PIK3CA ), 428 (copanlisib) and 441 (alpelisib). h , Rescue of synthetic lethality on supplementation with PI or phosphatidylcholine (PC, control). The method to quantify synthetic lethality was introduced in Fig. . PI and PC were complexed with lipid-free bovine serum albumin (BSA). Treatment was with 0.25 mM lipid for 7 d, started 7 d after transduction. Two-way ANOVA followed by Dunnett’s test was used. n = 3 replicates for 2 cancer cell lines. In c , d , g and h : *** P < 0.01, *** P < 0.001.

Article Snippet: Stock solutions of 500 μM were generated by incubating phospholipid with 2.5% fatty-acid free BSA from Sigma-Aldrich (cat. no. A8806) in DMEM at 37 °C for 1 h. Liver phosphatidylcholine (PC; cat. no. 840055P-25MG) or PI (cat. no. 840042P-25MG) from Avanti Polar Lipids was used.

Techniques: Genome Wide, RNA Expression, CRISPR, Expressing, Control, Transduction

Journal: Nature Genetics

Article Title: Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers

doi: 10.1038/s41588-025-02221-2

Figure Lengend Snippet: a , Δ CDS2 lipid changes, presented in alphabetic order. Only lipid classes detected in all samples were plotted. Stars indicate number of CDS1 -negative cancer cell lines with at least two-star significant lipid alterations compared to the CDS1 -high cancer cell line. For abbreviations see bottom of figure description. Two-way ANOVA followed up by Šidák’s test was used. n = 4 replicates for 5 cancer cell lines. b , CDS2 pathway with Δ CDS2 -changed lipid classes in CDS1 -negative cancer cell lines marked with arrows. For abbreviations see bottom of figure description. Included enzymes are annotated on UniProt. c , Graphs depicting sg CDS2 lipid changes in a second independent experiment for SK-MEL-2 ( y axis). Key lipids from Fig. were plotted. Data is plotted against the Fig. data ( x axis). All plotted changes were significant. Two-way ANOVA followed up by Šidák’s test was used. n = 4 replicates for 1 cancer cell line in 2 independent experiments. In a : Significance was indicated by one * for each cell line with P < 0.01. Lipids: CE = cholesterol esters, Cerd18:0 = ceramide d18:0, Cerd18:1 = ceramide d18:1, DAG = diacylglycerol, FFA = free fatty acids, HexCER = hexosylceramides, LPC = lysophosphatidylcholine, LPE = lysophosphatidylethanolamine, PA = phosphatidic acid, PC = phosphatidylcholine, PE = phosphatidylethanolamine, PG = phosphatidylglycerol, PI = phosphatidylinositol, PS = phosphatidylserine, SM = sphingomyelin, TAG = triglycerides. Enzymes: PEMT = phosphatidylethanolamine n-methyltransferase, CEPT1 = choline/ethanolamine phosphotransferase 1, DGATs = diacylglycerol o-acyltransferases, DGKs = diacylglycerol kinases, CDS = cytidine diphosphate diacylglycerol synthase, TAM41 = mitochondrial phosphatidate cytidylyltransferase, CDIPT = cytidine diphosphate diacylglycerol synthase inositol-3-phosphatidyltransferase, PGS1 = phosphatidylglycerophosphate synthase 1, PTPMT1 = protein tyrosine phosphatase mitochondrial 1.

Article Snippet: Stock solutions of 500 μM were generated by incubating phospholipid with 2.5% fatty-acid free BSA from Sigma-Aldrich (cat. no. A8806) in DMEM at 37 °C for 1 h. Liver phosphatidylcholine (PC; cat. no. 840055P-25MG) or PI (cat. no. 840042P-25MG) from Avanti Polar Lipids was used.

Techniques: