Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

Gatto, Francesco,1987Chalmers tekniska högskola,Chalmers University of Technology (author)

Flux balance analysis is the only modelling approach that is capable of producing genome-wide predictions of gene essentiality that may aid to unveil metabolic liabilities in cancer. Nevertheless, a systemic validation of gene essentiality predictions by flux balance analysis is currently missing. Here, we critically evaluated the accuracy of flux balance analysis in two cancer types, clear cell renal cell carcinoma (ccRCC) and prostate adenocarcinoma, by comparison with large-scale experiments of gene essentiality in vitro. We found that in ccRCC, but not in prostate adenocarcinoma, flux balance analysis could predict essential metabolic genes beyond random expectation. Five of the identified metabolic genes, AGPAT6, GALT, GCLC, GSS, and RRM2B, were predicted to be dispensable in normal cell metabolism. Hence, targeting these genes may selectively prevent ccRCC growth. Based on our analysis, we discuss the benefits and limitations of flux balance analysis for gene essentiality predictions in cancer metabolism, and its use for exposing metabolic liabilities in ccRCC, whose emergent metabolic network enforces outstanding anabolic requirements for cellular proliferation.

Miess, H.Cancer Research UK (author)
Schulze, A.Julius-Maximilians Universität Würzburg,University of Würzburg,Cancer Research UK,Comprehensive Cancer Center Mainfranken (author)
Nielsen, Jens B,1962Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)nielsenj (author)
Chalmers tekniska högskolaCancer Research UK (creator_code:org_t)

In:Scientific Reports: Springer Science and Business Media LLC5, s. Art. no. 10738-2045-23222045-2322

By the author/editor: Gatto, Francesco ...; Miess, H.; Schulze, A.; Nielsen, Jens B, ...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

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