Anderson R. Frank

Oncocytic (Hürthle cell) carcinoma of the thyroid (OCT) is characterized by widespread loss of heterozygosity (LOH), mitochondrial accumulation, and recurrent mitochondrial DNA mutations leading to impairment of complex I. Here, we establish and characterize a novel OCT cell line, UT946, which displays severe mitochondrial electron transport chain dysfunction and a Warburg metabolic phenotype. Using a series of cytoplasmic hybrids, we establish that the complex I defect in UT946 stems from a nuclear-encoded loss-of-function mutation in the complex I subunit NDUFS1. To our surprise, the mutation in NDUFS1 was inherited as a recessive germline allele that underwent LOH in the tumor to expose functional loss of complex I. A reanalysis of 91 OCT tumor genomes revealed that LOH-driven exposure of recessive germline mutations in complex I subunits was a recurrent mechanism underlying complex I inactivation in OCT. These findings unveil a previously unidentified germline-driven mechanism of complex I loss and metabolic reprogramming in cancer and provide further evidence of the selective pressure for complex I impairment in OCT.

Supplementary Table S1 shows key mtDNA mutations identified through whole-exome sequencing and targeted mtDNA sequencing.

Supplementary Table S2 shows nuclear genome variants identified in NCI-237-R PDX through whole-exome sequencing.

Supplementary Figure S1 shows validation of key genetic features in NCI-237 and metabolic characterization of thyroid cancer cell lines. Supplementary Figure S2 shows growth curves and depletion/enrichment plots for pooled CRISPR-Cas9 screens. Supplementary Figure S3 shows validation of complex I impairment conferring sensitivity to LDH inhibition. Supplementary Figure S4 shows metabolic profiling of LDH inhibition in NCI-237 cells. Supplementary Figure S5 shows the validation of NADH-oxidizing enzymes and that NAD+ regeneration rescues LDH inhibition. Supplementary Figure S6 shows that LDH inhibition impairs NCI-237-R PDX proliferation.

Supplementary Table S3 shows the results of our genome-wide and targeted CRISPR-Cas9 screens.

A metabolic hallmark of cancer identified by Warburg is the increased consumption of glucose and secretion of lactate, even in the presence of oxygen. Although many tumors exhibit increased glycolytic activity, most forms of cancer rely on mitochondrial respiration for tumor growth. We report here that Hürthle cell carcinoma of the thyroid (HTC) models harboring mitochondrial DNA-encoded defects in complex I of the mitochondrial electron transport chain exhibit impaired respiration and alterations in glucose metabolism. CRISPR–Cas9 pooled screening identified glycolytic enzymes as selectively essential in complex I–mutant HTC cells. We demonstrate in cultured cells and a patient-derived xenograft model that small-molecule inhibitors of lactate dehydrogenase selectively induce an ATP crisis and cell death in HTC. This work demonstrates that complex I loss exposes fermentation as a therapeutic target in HTC and has implications for other tumors bearing mutations that irreversibly damage mitochondrial respiration.Significance:HTC is enriched in somatic mtDNA mutations predicted to affect complex I of the electron transport chain (ETC). We demonstrate that these mutations impair respiration and induce a therapeutically tractable reliance on aerobic fermentation for cell survival. This work provides a rationale for targeting fermentation in cancers harboring irreversible genetically encoded ETC defects.See related article by Gopal et al., p. 1904.This article is highlighted in the In This Issue feature, p. 1749

Oncocytic (Hurthle cell) carcinoma of the thyroid (OCT) is characterized by widespread loss of heterozygosity (LOH), mitochondrial accumulation and recurrent mitochondrial DNA mutations leading to impairment of complex I. Here, we establish and characterize a novel OCT cell line, UT946, which displays severe mitochondrial electron transport chain dysfunction and a Warburg metabolic phenotype. Using a series of cytoplasmic hybrids, we establish that the complex I defect in UT946 stems from a nuclear-encoded loss of function mutation in the complex I subunit NDUFS1. To our surprise, the mutation in NDUFS1 was inherited as a recessive germline allele that underwent LOH in the tumor to expose functional loss of complex I. A re-analysis of 91 OCT tumor genomes revealed that LOH-driven exposure of recessive germline mutations in complex I subunits was a recurrent mechanism underlying complex I inactivation in OCT. These findings unveil a new germline-driven mechanism of complex I loss and metabolic reprogramming in cancer, and provide further evidence of the strong selective pressure for complex I impairment in OCT.

Supplementary Table S1 shows key mtDNA mutations identified through whole-exome sequencing and targeted mtDNA sequencing.

Supplementary Table S2 shows nuclear genome variants identified in NCI-237-R PDX through whole-exome sequencing.

Supplementary Table S1 shows key mtDNA mutations identified through whole-exome sequencing and targeted mtDNA sequencing.