Proteomic Analysis of ARID1A-Deficient Ovarian Clear Cell Carcinoma Cells Reveals Differential Mitochondria ETC Subunit Abundances and Targetable Mitochondrial Pathways

Abstract

ARID1A-deficient ovarian clear cell carcinoma is a highly lethal gynecologic cancer that depends heavily on mitochondrial respiration. Our biochemical and proteomic analyses reveal that ARID1A knockout cells exhibit marked upregulation of specific subunits within mitochondrial electron transport chain (ETC) Complexes I, III, and IV. However, this upregulation does not directly translate into increased sensitivity to broad-spectrum inhibitors targeting these complexes. These findings suggest that broad-spectrum mitochondrial inhibitors may not be effective therapeutic options for ARID1A-deficient cancers. Instead, the selective inhibition of specific ETC subunits may offer a more promising approach to exploit the metabolic vulnerabilities of ARID1A-deficient cells.

Keywords: ARID1A; electron transport chain; mitochondria; ovarian clear cell carcinoma; proteomics.

Figure 1

ARID1A KO cells have a higher mitochondrial potential compared to WT cells. (A) Representative merged images of WT and D9 clones stained with DAPI (blue) and Mitotracker Deep Red FM (red). Cells were maintained at low cell density to prevent confluence. Scale bar is 10 µm. (B) Quantification of Mitotracker Deep Red FM fluorescence intensity per condition expressed as arbitrary fluorescence units (AFU). n = number of cells evaluated per condition. Error bars indicate mean ± S.D. Student’s t-test.

Figure 2

Gene Ontology Biological Process enrichment of proteins with increased relative abundance following ARID1A KO.

Figure 3

Differential expression of mitochondrial ETC components at the level of individual proteins vs. entire complexes. (A) Relative abundance of mitochondrial ETC proteins in the ARID1A WT vs. KO cells. * p < 0.05 (Welch’s t-test). Created in BioRender.com. (B) Estimation plots indicating the magnitude of differences in relative abundance between the ETC proteins. ETC proteins with significant differences in relative abundance between the ARID1A WT vs. KO cells are listed in purple font and are the same as those indicated in panel (A). The dashed horizontal lines indicate the lower and upper values of the 95% confidence interval. Differences between the mean protein abundance of each complex are plotted to the right of the solid vertical line. * p < 0.05.

Figure 4

ARID1A KO selectively increases sensitivity to ETC complex I and V inhibitors. Dose-dependent sensitivity of OCCC-derived RMG1 ARID1A WT and ARID1A D9 clone to a panel of mitochondrial ETC CI-CV inhibitors. Results are expressed as residual cell viability as compared to control. Drug treatment was conducted over a period of 48 h. n = 3 replicates.