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Abstract

Metabolic reprogramming by oncogenic signals promotes cancer initiation and progression. The oncogene KRAS and tumour suppressor STK11, which encodes the kinase LKB1, regulate metabolism and are frequently mutated in non-small-cell lung cancer (NSCLC). Concurrent occurrence of oncogenic KRAS and loss of LKB1 (KL) in cells specifies aggressive oncological behaviour1,2. Here we show that human KL cells and tumours share metabolomic signatures of perturbed nitrogen handling. KL cells express the urea cycle enzyme carbamoyl phosphate synthetase-1 (CPS1), which produces carbamoyl phosphate in the mitochondria from ammonia and bicarbonate, initiating nitrogen disposal. Transcription of CPS1 is suppressed by LKB1 through AMPK, and CPS1 expression correlates inversely with LKB1 in human NSCLC. Silencing CPS1 in KL cells induces cell death and reduces tumour growth. Notably, cell death results from pyrimidine depletion rather than ammonia toxicity, as CPS1 enables an unconventional pathway of nitrogen flow from ammonia into pyrimidines. CPS1 loss reduces the pyrimidine to purine ratio, compromises S-phase progression and induces DNA-polymerase stalling and DNA damage. Exogenous pyrimidines reverse DNA damage and rescue growth. The data indicate that the KL oncological genotype imposes a metabolic vulnerability related to a dependence on a cross-compartmental pathway of pyrimidine metabolism in an aggressive subset of NSCLC.

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Change history

  • 01 May 2019

    Further analysis has revealed that the signal reported in Extended Data Fig. 1c of this Letter is attributed to phosphorylethanolamine, not carbamoyl phosphate. A newly developed derivatization method revealed that the level of carbamoyl phosphate in these NSCLC extracts is below the detection threshold of approximately 10 nanomoles. These findings do not alter the overall conclusions of the Letter; see associated Amendment for full details. The Letter has not been corrected online.

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Acknowledgements

We thank A. Jaffe and members of the DeBerardinis laboratory for critiquing the manuscript and J. Kozlitina for statistical expertise. R.J.D. is supported by grants from the NIH (R01CA157996), Cancer Prevention and Research Institute of Texas (CPRIT RP130272), Robert A. Welch Foundation (I1733) and H.H.M.I. (Faculty Scholars Program). J.K. is supported by an American Lung Association Senior Research Training Fellowship (RT-306212). D.H.C. is supported by NIH grant (1R01CA196912). J.D.M., J.R.C., P.V. and I.W. are supported by the University of Texas Lung Specialized Programs of Research Excellence (SPORE) grant (P50CA70907). J.D.M. is also supported by NIH grant CA176284 and CPRIT grants RP120732 and RP110708.

Author information

Author notes

    • Christopher G. Peña

    Present address: University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA.

Affiliations

  1. Children’s Medical Center Research Institute, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Jiyeon Kim
    • , Zeping Hu
    • , Ling Cai
    • , Kailong Li
    • , Brandon Faubert
    • , Divya Bezwada
    • , Min Ni
    • , Jian Xu
    •  & Ralph J. DeBerardinis
  2. Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Eunhee Choi
  3. Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, Texas 77030, USA

    • Jaime Rodriguez-Canales
    • , Pamela Villalobos
    •  & Ignacio Wistuba
  4. Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Yu-Fen Lin
    •  & Benjamin P. C. Chen
  5. Hamon Center for Therapeutic Oncology, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Kenneth E. Huffman
    • , Luc Girard
    •  & John D. Minna
  6. Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, Texas 77030, USA

    • Lauren A. Byers
    •  & John V. Heymach
  7. Oncology Research Unit, Pfizer, 401 North Middletown Road, Pearl River, New York 10965, USA

    • Keziban Unsal-Kacmaz
  8. Department of Pathology, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Christopher G. Peña
    •  & Diego H. Castrillon
  9. Respiratory Division, University of Gasthuisberg, KU Leuven, Herestraat 49, 3000 Leuven, Belgium

    • Els Wauters
    •  & Johan Vansteenkiste
  10. Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, O&N 4 Herestraat 49 – box 912, 3000 Leuven, Belgium

    • Diether Lambrechts
  11. VIB Center for Cancer Biology, KU Leuven, O&N 4 Herestraat 49 – box 912, 3000 Leuven, Belgium

    • Diether Lambrechts
  12. Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Ralph J. DeBerardinis
  13. McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Ralph J. DeBerardinis

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Contributions

J.K. and R.J.D. designed the study and wrote the paper. Z.H. performed the metabolomics. L.C. and M.N. provided biostatistics expertise. E.C. provided advice about replication-fork stalling. K.L. and J.X. performed ChIP–qPCR and provided advice on epigenetics. E.W., J.V. and D.L. provided human NSCLC samples for metabolomics. K.U.-K. and L.G. provided expertise in metabolomics and transcript analysis. C.G.P., D.H.C., P.V., J.R.-C. and I.W. performed tumour microarrays. Y.-F.L. and B.P.C.C. performed DNA fibre assays. B.F. provided expertise on AMPK. D.B. performed transient gene silencing. L.A.B. and J.V.H. provided reverse-phase proteomics and patient survival data. K.E.H. and J.D.M. provided cell lines, gene expression data and intellectual input regarding molecular lung cancer subtypes.

Competing interests

R.J.D. is on the advisory board of Agios Pharmaceuticals.

Corresponding author

Correspondence to Ralph J. DeBerardinis.

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Extended data

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    Supplementary Information

    This file contains the Supplementary Discussion, Supplementary References, the uncropped gels and full legends for Supplementary Tables 1-10.

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https://doi.org/10.1038/nature22359

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