Figure 1.
OGDH is a bona fide genetic dependency across AML systems. (A) Schematic of the TCA cycle highlighting the αKG dehydrogenase complex. (B) Differential gene dependency in AML vs all non-AML (other) cancer types, based on difference of mean depletion or enrichment of sgRNAs targeting individual genes across available CRISPR screens. An y-axis value <0 indicates preferential dependency in AML and a value >0 indicates preferential dependency in other. Each data point represents an individual gene. Selected genes are labeled. (C) OGDH, DLST, and DLD gene effect across CRISPR screens for AML vs other cell lines included in the DepMap database. A lower gene effect indicates an increased likelihood of gene dependency, with 0 indicating nondependency and –1 representing the median of all pan-essential genes. Each data point represents an individual cell line, and the mean ± standard error are shown. P values indicated (Wilcoxon rank-sum test). (D) OGDH gene dependency ranking across CRISPR screens for AML vs other cell lines included in the DepMap database. Each data point represents an individual cell line, and the mean ± standard error are shown. P value is indicated (Wilcoxon rank-sum test). (E) For each indicated gene, the violin plot shows change in sgRNA abundance (measured as log2 fold change) in publicly available whole-genome CRISPR screens across multiple AML vs other cancer cell lines. P values are indicated (Wilcoxon rank-sum test). (F-G) Western blot analysis showing the expression of OGDH in AML cell lines transduced with the indicated shRNA after 3 days of doxycycline treatment. (F) NrasG12D; MLL-AF9 cells. (G) p53R172H cells. (H-I) Depletion of Ogdh shRNAs in the competition assay. (H) NrasG12D; MLL-AF9 murine leukemia cells were infected with retroviruses encoding the indicated doxycycline-inducible shRNAs linked to a GFP reporter and admixed with 20% uninfected (GFP–) cells. The relative percentages of GFP+ cells (normalized to day 1 for each shRNA) were counted on the indicated days after doxycycline treatment. P values of shOgdh vs shControl groups indicated (2-way analysis of variance [ANOVA] with Sidak multiple comparisons test). (I) p53R172H murine leukemia cells were infected with lentiviruses encoding reverse tetracycline-controlled transactivator and the indicated doxycycline-inducible shRNAs linked to a blue fluorescent protein (BFP) reporter on single backbone (LT3 BEPIR). Infected cells were admixed with 20% uninfected cells. The relative percentages of BFP+ cells (normalized to day 2 for each shRNA) were counted on the indicated days after doxycycline treatment. (J) Western blot analysis showing expression of OGDH in PDX1 AML cells 4 days after transduction with the indicated shRNAs. (K) Cell proliferation of PDX1 AML cells transduced with the indicated shRNAs (normalized to day 6 after infection for each shRNA). (L) Depletion of OGDH shRNAs in a competition assay in PDX2 cells. PDX2 AML cells were infected at day –7 with a lentivirus encoding shControl or shOGDH linked to a GFP reporter and a second lentivirus encoding shControl linked to a red fluorescent protein (RFP) reporter. The GFP:RFP ratio (normalized to day 0 for each shRNA pair) was measured on the indicated days. P value of shOGDH vs shControl group is indicated (2-way ANOVA). αKGDC, α-ketoglutarate dehydrogenase complex; ns, not significant; OAA, oxaloacetate.

OGDH is a bona fide genetic dependency across AML systems. (A) Schematic of the TCA cycle highlighting the αKG dehydrogenase complex. (B) Differential gene dependency in AML vs all non-AML (other) cancer types, based on difference of mean depletion or enrichment of sgRNAs targeting individual genes across available CRISPR screens. An y-axis value <0 indicates preferential dependency in AML and a value >0 indicates preferential dependency in other. Each data point represents an individual gene. Selected genes are labeled. (C) OGDH, DLST, and DLD gene effect across CRISPR screens for AML vs other cell lines included in the DepMap database. A lower gene effect indicates an increased likelihood of gene dependency, with 0 indicating nondependency and –1 representing the median of all pan-essential genes. Each data point represents an individual cell line, and the mean ± standard error are shown. P values indicated (Wilcoxon rank-sum test). (D) OGDH gene dependency ranking across CRISPR screens for AML vs other cell lines included in the DepMap database. Each data point represents an individual cell line, and the mean ± standard error are shown. P value is indicated (Wilcoxon rank-sum test). (E) For each indicated gene, the violin plot shows change in sgRNA abundance (measured as log2 fold change) in publicly available whole-genome CRISPR screens across multiple AML vs other cancer cell lines. P values are indicated (Wilcoxon rank-sum test). (F-G) Western blot analysis showing the expression of OGDH in AML cell lines transduced with the indicated shRNA after 3 days of doxycycline treatment. (F) NrasG12D; MLL-AF9 cells. (G) p53R172H cells. (H-I) Depletion of Ogdh shRNAs in the competition assay. (H) NrasG12D; MLL-AF9 murine leukemia cells were infected with retroviruses encoding the indicated doxycycline-inducible shRNAs linked to a GFP reporter and admixed with 20% uninfected (GFP–) cells. The relative percentages of GFP+ cells (normalized to day 1 for each shRNA) were counted on the indicated days after doxycycline treatment. P values of shOgdh vs shControl groups indicated (2-way analysis of variance [ANOVA] with Sidak multiple comparisons test). (I) p53R172H murine leukemia cells were infected with lentiviruses encoding reverse tetracycline-controlled transactivator and the indicated doxycycline-inducible shRNAs linked to a blue fluorescent protein (BFP) reporter on single backbone (LT3 BEPIR). Infected cells were admixed with 20% uninfected cells. The relative percentages of BFP+ cells (normalized to day 2 for each shRNA) were counted on the indicated days after doxycycline treatment. (J) Western blot analysis showing expression of OGDH in PDX1 AML cells 4 days after transduction with the indicated shRNAs. (K) Cell proliferation of PDX1 AML cells transduced with the indicated shRNAs (normalized to day 6 after infection for each shRNA). (L) Depletion of OGDH shRNAs in a competition assay in PDX2 cells. PDX2 AML cells were infected at day –7 with a lentivirus encoding shControl or shOGDH linked to a GFP reporter and a second lentivirus encoding shControl linked to a red fluorescent protein (RFP) reporter. The GFP:RFP ratio (normalized to day 0 for each shRNA pair) was measured on the indicated days. P value of shOGDH vs shControl group is indicated (2-way ANOVA). αKGDC, α-ketoglutarate dehydrogenase complex; ns, not significant; OAA, oxaloacetate.

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