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Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

Nature volume 477, pages 225–228 (2011)Cite this article

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Abstract

Fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle (TCA cycle) that catalyses the hydration of fumarate into malate. Germline mutations of FH are responsible for hereditary leiomyomatosis and renal-cell cancer (HLRCC)1. It has previously been demonstrated that the absence of FH leads to the accumulation of fumarate, which activates hypoxia-inducible factors (HIFs) at normal oxygen tensions2,3,4. However, so far no mechanism that explains the ability of cells to survive without a functional TCA cycle has been provided. Here we use newly characterized genetically modified kidney mouse cells in which Fh1 has been deleted, and apply a newly developed computer model of the metabolism of these cells to predict and experimentally validate a linear metabolic pathway beginning with glutamine uptake and ending with bilirubin excretion from Fh1-deficient cells. This pathway, which involves the biosynthesis and degradation of haem, enables Fh1-deficient cells to use the accumulated TCA cycle metabolites and permits partial mitochondrial NADH production. We predicted and confirmed that targeting this pathway would render Fh1-deficient cells non-viable, while sparing wild-type Fh1-containing cells. This work goes beyond identifying a metabolic pathway that is induced in Fh1-deficient cells to demonstrate that inhibition of haem oxygenation is synthetically lethal when combined with Fh1 deficiency, providing a new potential target for treating HLRCC patients.

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Figure 1: Characterization of Fh1 -deficient cells.
Figure 2: Metabolic analyses of Fh1 −/− cells.
Figure 3: The haem pathway is predicted to be synthetically lethal with Fh1.
Figure 4: Targeting the haem degradation pathway is lethal for Fh1 -deficient cells.

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Data deposits

Microarray data are deposited at the website http://bioinformatics.picr.man.ac.uk/vice/Welcome.vice, accession reference GE_EG(2).

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Acknowledgements

This work was supported by Cancer Research UK. We would like to acknowledge the Patterson Institute for Cancer Research for the Exon Array analysis. C.F. is supported by an EMBO long term fellowship (ALTF330). P.J.P. is in receipt of a Beit Memorial Fellowship funded by the Wellcome Trust (WT091112MA). D.G.W. and L.Z. would like to acknowledge SULSA (Scottish Universities Life Science Alliance). R.J.D. and K.N.R. are supported by the NIH (DK072565-05) and the Cancer Prevention and Research Institute of Texas (HIRP100437-01). O.F., T.S. and E.R. are supported by the Israel Science Foundation (ISF) and the Israel Cancer Research Foundation. L.J. is supported by the Edmond J. Safra Bioinformatics program at TAU. We thank UOB Tumor Cell Line Repository and W. Marston Linehan for providing us with the UOK262 cell lines, and A. King for editorial work.

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Author notes

  1. Tomer Shlomi and Eytan Ruppin: These authors contributed equally to this work.

Authors and Affiliations

  1. Cancer Research UK, Beatson Institute for Cancer Research, Switchback Road, Glasgow G61 1BD, UK

    Christian Frezza, Liang Zheng, Elaine D. MacKenzie, Barbara Chaneton, Ann Hedley, Gabriela Kalna & Eyal Gottlieb

  2. The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

    Ori Folger, Livnat Jerby & Eytan Ruppin

  3. Department of Pediatrics and McDermott Center for Human Growth and Development, University of Texas–Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, 75390-9063, Texas, USA

    Kartik N. Rajagopalan & Ralph J. Deberardinis

  4. The University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane, Queensland 4072, Australia

    Massimo Micaroni

  5. Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

    Julie Adam & Patrick J. Pollard

  6. Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK

    Ian P. M. Tomlinson

  7. Strathclyde Institute of Pharmaceutical and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, UK

    Dave G. Watson

  8. Computer Science Department, Technion, Israel Institute of Technology, Haifa, 32000, Israel

    Tomer Shlomi

  9. The Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

    Eytan Ruppin

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  1. Christian Frezza
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Contributions

C.F. and E.G. conceived the project, analysed the data and wrote the manuscript. C.F. and. E.D.M. generated the kidney cell lines. O.F., L.J., T.S. and E.R. built the metabolic network of the cells and predicted the synthetic lethal genes. J.A., I.P.M.T. and P.J.P. provided the Fh1fl/fl mice, generated the UOKpFH cell line and provided genotyping tools. G.K. and A.H. performed the bioinformatics and statistical analysis. L.Z. and D.G.W. performed the LC–MS analysis. K.N.R. and R.J.D. performed GC–MS and the BioProfile metabolic analyses. C.F. performed all other experiments with the help of B.C. M.M. performed the electron microscopy. All the authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Eyal Gottlieb.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-6 with legends, Supplementary Tables 5 and 6, Supplementary Text and additional references. (PDF 1467 kb)

Supplementary Table 1

This table contains the reconstructed metabolic network models for the Fh1fl/fl and Fh1-deficient cell lines. (XLS 389 kb)

Supplementary Table 2

This table contains the definition of cellular growth medium and metabolite uptake for both Fh1fl/fl and Fh1-deficient cell lines. (XLS 10 kb)

Supplementary Table 3

This table shows the reactions whose deletion is predicted to be synthetic lethal with FH. (XLS 11 kb)

Supplementary Table 4

This table contains the definition of essential biomass constituents and their relative concentration. (XLS 18 kb)

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Frezza, C., Zheng, L., Folger, O. et al. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature 477, 225–228 (2011). https://doi.org/10.1038/nature10363

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