Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer

• Published in: NPJ systems biology and applications Vol. 10; no. 1; pp. 96 - 12
• Main Authors: Meeson, Kate E., Schwartz, Jean-Marc
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.08.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/553/2695; 631/67; Bioinformatics; Biomedical and Life Sciences; Cell Line, Tumor; Chemoresistance; Chemotherapy; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; CRISPR; Disease resistance; Female; Genomes; Genomic analysis; Growth rate; Humans; Life Sciences; Literature reviews; Metabolic flux; Metabolic Networks and Pathways - genetics; Metabolism; Models, Biological; Ovarian cancer; Ovarian Neoplasms - genetics; Ovarian Neoplasms - metabolism; Pentose phosphate pathway; Phenotypes; Systems Biology; Transcriptomics; Tumor cell lines
• ISSN: 2056-7189; 2056-7189
• DOI: 10.1038/s41540-024-00418-5

Ovarian cancer is an aggressive, heterogeneous disease, burdened with late diagnosis and resistance to chemotherapy. Clinical features of ovarian cancer could be explained by investigating its metabolism, and how the regulation of specific pathways links to individual phenotypes. Ovarian cancer is of particular interest for metabolic research due to its heterogeneous nature, with five distinct subtypes having been identified, each of which may display a unique metabolic signature. To elucidate metabolic differences, constraint-based modelling (CBM) represents a powerful technology, inviting the integration of ‘omics’ data, such as transcriptomics. However, many CBM methods have not prioritised accurate growth rate predictions, and there are very few ovarian cancer genome-scale studies. Here, a novel method for CBM has been developed, employing the genome-scale model Human1 and flux balance analysis, enabling the integration of in vitro growth rates, transcriptomics data and media conditions to predict the metabolic behaviour of cells. Using low- and high-grade ovarian cancer, subtype-specific metabolic differences have been predicted, which have been supported by publicly available CRISPR-Cas9 data from the Cancer Cell Line Encyclopaedia and an extensive literature review. Metabolic drivers of aggressive, invasive phenotypes, as well as pathways responsible for increased chemoresistance in low-grade cell lines have been suggested. Experimental gene dependency data has been used to validate areas of the pentose phosphate pathway as essential for low-grade cellular growth, highlighting potential vulnerabilities for this ovarian cancer subtype.