Genome-wide CRISPR/Cas9 deletion screen defines mitochondrial gene essentiality and identifies routes for tumour cell viability in hypoxia

Luke W Thomas,Lucas A Maddalena,Stacey Price,Margaret Ashcroft,Ultan Mcdermott,Jamie Young,Steven P Williams,Rachel E Morgan,Cinzia Esposito

doi:10.1038/s42003-021-02098-x

Luke W Thomas, Lucas A Maddalena + Show 7 more

Open Access

https://doi.org/10.1038/s42003-021-02098-x

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Abstract

Mitochondria are typically essential for the viability of eukaryotic cells, and utilize oxygen and nutrients (e.g. glucose) to perform key metabolic functions that maintain energetic homeostasis and support proliferation. Here we provide a comprehensive functional annotation of mitochondrial genes that are essential for the viability of a large panel (625) of tumour cell lines. We perform genome-wide CRISPR/Cas9 deletion screening in normoxia-glucose, hypoxia-glucose and normoxia-galactose conditions, and identify both unique and overlapping genes whose loss influences tumour cell viability under these different metabolic conditions. We discover that loss of certain oxidative phosphorylation (OXPHOS) genes (e.g. SDHC) improves tumour cell growth in hypoxia-glucose, but reduces growth in normoxia, indicating a metabolic switch in OXPHOS gene function. Moreover, compared to normoxia-glucose, loss of genes involved in energy-consuming processes that are energetically demanding, such as translation and actin polymerization, improve cell viability under both hypoxia-glucose and normoxia-galactose. Collectively, our study defines mitochondrial gene essentiality in tumour cells, highlighting that essentiality is dependent on the metabolic environment, and identifies routes for regulating tumour cell viability in hypoxia.

Highlights

Mitochondria are typically essential for the viability of eukaryotic cells, and utilize oxygen and nutrients to perform key metabolic functions that maintain energetic homeostasis and support proliferation
Our study provides a comprehensive survey of mitochondrial gene essentiality in tumour cells, which shows that gene essentiality depends on the metabolic context, and highlights routes for tumour cell viability in hypoxia
A greater proportion of mitochondrial genes (23.2%) were common essential genes, as compared to the proportion of common essential genes in the genome as a whole (11.5%, Fig. 1b, Supplementary Data 1), in line with other studies of this kind[14]. This analysis identified that the largest groups of common essential mitochondrial genes are involved in respiration, mitochondrial gene expression and mitochondrial functions that are well characterised as being required for the survival and proliferation of tumour cells including mitochondrial import and sorting (e.g. CHCHD43,21–23) (Fig. 1c)

Summary

Introduction

Mitochondria are typically essential for the viability of eukaryotic cells, and utilize oxygen and nutrients (e.g. glucose) to perform key metabolic functions that maintain energetic homeostasis and support proliferation. 1234567890():,; Altered mitochondrial metabolism and function contribute to several pathologies, including cancer Tumour microenvironmental conditions, such as hypoxia, and changes in nutrient availability can profoundly impact mitochondrial activity, providing metabolic adaptive responses that enable tumour cell survival and promote metastasis[1]. We performed genome-wide CRISPR/Cas[9] deletion screening under different environmental conditions (normoxia-glucose, hypoxia-glucose, and normoxiagalactose) to interrogate the dependency of tumour cells on nuclear-encoded mitochondrial genes (referred to as mitochondrial genes) and non-mitochondrial genes for their survival when oxygen or glucose is abundant or limited. Our study provides a comprehensive survey of mitochondrial gene essentiality in tumour cells, which shows that gene essentiality depends on the metabolic context, and highlights routes for tumour cell viability in hypoxia

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