A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

Abstract

Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans. Deficiencies in OXPHOS can arise from mutations in either mitochondrial or nuclear genomes and comprise the largest collection of inborn errors of metabolism. At present we lack a complete catalog of human genes and pathways essential for OXPHOS. Here we introduce a genome-wide CRISPR "death screen" that actively selects dying cells to reveal human genes required for OXPHOS, inspired by the classic observation that human cells deficient in OXPHOS survive in glucose but die in galactose. We report 191 high-confidence hits essential for OXPHOS, including 72 underlying known OXPHOS diseases. Our screen reveals a functional module consisting of NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 that regulates the mitochondrial 16S rRNA and intra-mitochondrial translation. Our work yields a rich catalog of genes required for OXPHOS and, more generally, demonstrates the power of death screening for functional genomic analysis.

Keywords: 16S RNA; CRISPR; Mitochondria; OXPHOS; death screen; mitochondrial ribosome; neugrin; pseudouridine; pseudouridylation; synthetic lethality.

Figure 1. A Genome-wide CRISPR Death Screen to Identify Genes Necessary for OXPHOS

(A) Cell death was measured by Annexin V staining and flow cytometry in K562 cells cultured in glucose- or galactose-containing medium with the RC inhibitors piericidin (10 nM), antimycin (100 nM), or oligomycin (10 nM) or DMSO vehicle control. Data are expressed as mean ± SEM (n = 3). *p < 0.05, ***p < 0.001, t test relative to DMSO treatment in the corresponding medium. (B) Schematic overview of the genome-wide CRISPR screen. K562 cells expressing Cas9 were infected with a lentiviral CRISPR sgRNA library, split into glucose-containing or galactose-containing medium, and cultured for 24 hr. Dead cells under each condition were purified using Annexin V, and the abundance of each sgRNA was compared with a reference sample of all cells from before the medium exchange (pre-swap). Red represents cells expressing an sgRNA for an OXPHOS disease gene. (C and D) The median-normalized read count of each sgRNA averaged across two infection replicates is compared between the pre-swap cells (x axis) and the Annexin V+ dead cells after growth in glucose (C) or galactose (D) (y axis). (E) Gene enrichment in Annexin V+ cells from glucose (top) and galactose medium (bottom) was scored using MAGeCK, and the fraction of known OXPHOS disease genes and all genes with a given FDR is shown. (F) Schematic representing the approach used to identify hits in the screen and the number of hits below each galactose FDR threshold. (G) The distribution of hits for each galactose FDR threshold between known OXPHOS disease genes (red), other mitochondrial genes as defined by MitoCarta2.0 (maroon), and non-mitochondrial genes (gray). See also Figure S1 and S2.

Figure 2. Known and Candidate OXPHOS Disease Genes Identified by the Glucose/Galactose Death Screen

The 300 hits with a galactose FDR < 30% and a glucose FDR ≥ 30% are shown in manually curated functional categories.

Figure 3. Mitochondrial Pathways Underlying the Glucose/Galactose Death Phenotype

(A) The MitoCarta2.0 genes targeted by the CRISPR library were partitioned into eight distinct functional categories, and the fraction of genes in each category that were hits below 30% FDR is shown for the glucose/galactose death phenotype (left) or growth defect phenotype (right). The fractions of all genes and all MitoCarta2.0 genes that were hits are shown at top (black bars). Dashed lines indicate the fraction of MitoCarta2.0 hits. (B) The distribution of hits below 30% FDR into the same eight MitoCarta2.0 categories and the non-MitoCarta2.0 category is shown. The distribution of all genes in the CRISPR library into those categories is shown for comparison.

Figure 4. Functional Validation of the Screening Results

(A) Annexin V staining and flow cytometry analysis of K562 cell lines expressing Cas9 and sgRNAs directed against the genes indicated and grown for 24 hr in glucose or galactose-containing medium. Data are shown as mean ± SEM (n = 3, n = 6 for control). *p < 0.05, **p < 0.01, ***p < 0.001, t test relative to control sgRNA-treated cells in the corresponding medium. (B) Basal whole-cell oxygen consumption was measured in the indicated K562 knockout cell lines. Data are shown as mean ± SEM (n = 4, n = 9 for control). *p < 0.05, **p < 0.01, ***p < 0.001, t test relative to control sgRNA-treated cells. (C) Protein immunoblot analysis of the indicated K562 cell lines using a multiplex antibody cocktail targeting a subunit of each respiratory complex (CI–CV). See also Figure S3.

Figure 5. Non-mitochondrial Pathways Identified in the Screen

(A) Gene ontology enrichment analysis of the non-mitochondrial hits. (B) Schematic representation of five proteins within the AMPK pathway that were hits in the screen, with pathway inhibition by Compound C indicated. (C) Phase-contrast microscopy of HeLa cells grown in glucose- or galactose-containing medium and treated for 16 hr with 2 μM Compound C.

Figure 6. A Protein Module Required for 16S rRNA Stability and Intra-mitochondrial Translation

(A) Confocal microscopy analysis of HeLa cells expressing pDsRed2-Mito (a mitochondrial marker) and NGRN-3xFLAG and immunolabeled with antibodies to FLAG. (B) Protein immunoblot analysis of a mitochondrion-rich fraction from K562 cells expressing sgRNAs targeting NGRN and/or an sgRNA-resistant version of human NGRN-3xFLAG cDNA. (C) Autoradiography after ³⁵S-methionine/cysteine labeling of mitochondrial translation on K562 cells expressing sgRNAs targeting NGRN and/or an sgRNA-resistant version of human NGRN-3xFLAG cDNA. All cells were treated with 200 μg/mL emetine. (D) qPCR analysis of the small (12S, mt-RNR1) or large (16S, mt-RNR2) mitochondrial rRNAs from K562 cells expressing sgRNAs targeting NGRN and/or an sgRNA-resistant version of human NGRN-3xFLAG. (E) qPCR analysis of the small (12S, mt-RNR1) or large (16S, mt-RNR2) mitochondrial rRNAs from NGRN-3xFLAG or WBSCR16-3xFLAG immunoprecipitations. (F) qPCR analysis of the 16S 5′ (Val-16S) and 3′ (16S-Leu) rRNA precursors from NGRN-3xFLAG or WBSCR16-3xFLAG immunoprecipitations. (G and H) Relative peptide abundance of two independent NGRN-3xFLAG or WBSCR16-3xFLAG immunoprecipitations, respectively, and analysis by mass spectrometry. Baits are underlined. Genes identified in our screen (Figure 2) are shown in red. (I) qPCR analysis of the small (12S, mt-RNR1) or large (16S, mt-RNR2) mitochondrial rRNAs from K562 cells expressing sgRNAs targeting the indicated genes. (J) Autoradiography after ³⁵S-methionine/cysteine labeling of mitochondrial translation on K562 cells expressing sgRNAs targeting the indicated genes. All cells were treated with 200 μg/mL emetine. (K) A functional module that regulates the 16S rRNA and mitochondrial translation, with lines indicating protein-protein interactions detected by co-immunoprecipitation. All bar plots (D–F and I) display mean ± SEM (n = 3) with asterisks indicating t test significance (*p < 0.05, **p < 0.01, ***p < 0.001). See also Figure S4.