The genome of pancreatic ductal adenocarcinoma (PDAC) frequently contains deletions of tumour suppressor gene loci, most notably SMAD4, which is homozygously deleted in nearly one-third of cases1. As loss of neighbouring housekeeping genes can confer collateral lethality, we sought to determine whether loss of the metabolic gene malic enzyme 2 (ME2) in the SMAD4 locus would create cancer-specific metabolic vulnerability upon targeting of its paralogous isoform ME3. The mitochondrial malic enzymes (ME2 and ME3) are oxidative decarboxylases that catalyse the conversion of malate to pyruvate and are essential for NADPH regeneration and reactive oxygen species homeostasis2,3. Here we show that ME3 depletion selectively kills ME2-null PDAC cells in a manner consistent with an essential function for ME3 in ME2-null cancer cells. Mechanistically, integrated metabolomic and molecular investigation of cells deficient in mitochondrial malic enzymes revealed diminished NADPH production and consequent high levels of reactive oxygen species. These changes activate AMP activated protein kinase (AMPK), which in turn directly suppresses sterol regulatory element-binding protein 1 (SREBP1)-directed transcription of its direct targets including the BCAT2 branched-chain amino acid transaminase 2) gene. BCAT2 catalyses the transfer of the amino group from branched-chain amino acids to α-ketoglutarate (α-KG)4 thereby regenerating glutamate, which functions in part to support de novo nucleotide synthesis. Thus, mitochondrial malic enzyme deficiency, which results in impaired NADPH production, provides a prime ‘collateral lethality’ therapeutic strategy for the treatment of a substantial fraction of patients diagnosed with this intractable disease.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


Primary accessions

Gene Expression Omnibus


  1. 1.

    et al. Smad4 is dispensable for normal pancreas development yet critical in progression and tumor biology of pancreas cancer. Genes Dev. 20, 3130–3146 (2006)

  2. 2.

    , , & Cytosolic and mitochondrial malic enzyme isoforms differentially control insulin secretion. J. Biol. Chem. 282, 200–207 (2007)

  3. 3.

    , , , & Reciprocal regulation of p53 and malic enzymes modulates metabolism and senescence. Nature 493, 689–693 (2013)

  4. 4.

    , & Role of mitochondrial transamination in branched chain amino acid metabolism. J. Biol. Chem. 263, 3618–3625 (1988)

  5. 5.

    , & Collateral lethality: a new therapeutic strategy in oncology. Trends Cancer 1, 161–173 (2015)

  6. 6.

    et al. Passenger deletions generate therapeutic vulnerabilities in cancer. Nature 488, 337–342 (2012)

  7. 7.

    et al. Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets. Nat. Commun. 6, 6744 (2015)

  8. 8.

    et al. Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. Mol. Cell 55, 253–263 (2014)

  9. 9.

    et al. Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell 149, 656–670 (2012)

  10. 10.

    et al. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature 496, 101–105 (2013)

  11. 11.

    et al. Genetics and biology of pancreatic ductal adenocarcinoma. Genes Dev. 30, 355–385 (2016)

  12. 12.

    Relation between glutamine, branched-chain amino acids, and protein metabolism. Nutrition 18, 130–133 (2002)

  13. 13.

    et al. A molecular model of human branched-chain amino acid metabolism. Am. J. Clin. Nutr. 68, 72–81 (1998)

  14. 14.

    , & Branched-chain amino acid metabolism: implications for establishing safe intakes. J. Nutr. 135 (Suppl.), 1557S–1564S (2005)

  15. 15.

    The complex role of branched chain amino acids in diabetes and cancer. Metabolites 3, 931–945 (2013)

  16. 16.

    et al. Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development. Nat. Med. 20, 1193–1198 (2014)

  17. 17.

    , & Cancer cachexia: mediators, signaling, and metabolic pathways. Cell Metab. 16, 153–166 (2012)

  18. 18.

    & Cancer cachexia: malignant inflammation, tumorkines, and metabolic mayhem. Trends Endocrinol. Metab. 24, 174–183 (2013)

  19. 19.

    et al. Branched-chain amino acid catabolism: unique segregation of pathway enzymes in organ systems and peripheral nerves. Am. J. Physiol. Endocrinol. Metab. 286, E64–E76 (2004)

  20. 20.

    & Aspects of the regulation of the metabolism of branched-chain amino acids. Adv. Enzyme Regul. 15, 375–394 (1976)

  21. 21.

    , & Regulation of leucine and alpha-ketoisocaproate metabolism in skeletal muscle. J. Biol. Chem. 253, 8126–8133 (1978)

  22. 22.

    , , & In the regulation of cytochrome P450 genes, phenobarbital targets LKB1 for necessary activation of AMP-activated protein kinase. Proc. Natl Acad. Sci. USA 104, 1045–1050 (2007)

  23. 23.

    et al. Identification of phosphorylation sites in AMP-activated protein kinase (AMPK) for upstream AMPK kinases and study of their roles by site-directed mutagenesis. J. Biol. Chem. 278, 28434–28442 (2003)

  24. 24.

    et al. AMPK phosphorylates and inhibits SREBP activity to attenuate hepatic steatosis and atherosclerosis in diet-induced insulin-resistant mice. Cell Metab. 13, 376–388 (2011)

  25. 25.

    et al. SREBP activity is regulated by mTORC1 and contributes to Akt-dependent cell growth. Cell Metab. 8, 224–236 (2008)

  26. 26.

    , , & ADD1: a novel helix-loop-helix transcription factor associated with adipocyte determination and differentiation. Mol. Cell. Biol. 13, 4753–4759 (1993)

  27. 27.

    , & Biochemistry 7th edn (, 2012)

  28. 28.

    et al. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat. Biotechnol. 32, 1262–1267 (2014)

  29. 29.

    et al. Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing. Nat. Biotechnol. 32, 941–946 (2014)

  30. 30.

    , & Estrogen receptor β upregulates FOXO3a and causes induction of apoptosis through PUMA in prostate cancer. Oncogene 33, 4213–4225 (2014)

  31. 31.

    et al. Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer. Cell 158, 185–197 (2014)

  32. 32.

    et al. Telomere dysfunction induces metabolic and mitochondrial compromise. Nature 470, 359–365 (2011)

  33. 33.

    et al. FoxOs cooperatively regulate diverse pathways governing neural stem cell homeostasis. Cell Stem Cell 5, 540–553 (2009)

  34. 34.

    & Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012)

  35. 35.

    et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protocols 7, 562–578 (2012)

  36. 36.

    et al. Simultaneous single-sample determination of NMNAT isozyme activities in mouse tissues. PLoS One 7, e53271 (2012)

Download references


We thank T. Tieu for vector cloning; the MD Anderson core facilities, including K. Dunner Jr for High Resolution Electron Microscopy Facility, Sequencing and Microarray Facility (SMF), Flow Cytometry and Cellular Imaging Core Facility; S. Jiang and Z. Xu for assistance in maintenance of mouse colonies; Z. Lu for discussion; and D. Spring for editing. This study was supported by NCI P01 CA117969 grant (R.A.D.); UT Star award (R.A.D.); CPRIT grant RP140612 (R.A.D.); DOD Postdoctoral research fellowship W81XWH-14-1-0429 (P.D.); MD Anderson Bridge Fund (R.A.D.); St. Louis Ovarian Cancer Awareness Research Grant (D.N.) and Odyssey Fellowships at MD Anderson (D.Z., T.G.). The MD Anderson core facilities are supported by NIH P30 CA16672.

Author information

Author notes

    • Prasenjit Dey
    •  & Joelle Baddour

    These authors contributed equally to this work.


  1. Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Prasenjit Dey
    • , Wen-Ting Liao
    • , Zangdao Lan
    • , Alina Chen
    • , Di Zhao
    • , Y. Alan Wang
    •  & Ronald A. DePinho
  2. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Prasenjit Dey
    • , Chia Chin Wu
    • , Tony Gutschner
    • , Edward Chang
    • , Giannicola Genovese
    • , Andrea Viale
    • , Giulio Draetta
    •  & Y. Alan Wang
  3. Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, USA

    • Joelle Baddour
    • , Abhinav Achreja
    • , Lifeng Yang
    • , Jiyoon Lee
    •  & Deepak Nagrath
  4. Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Florian Muller
    •  & Nikunj Satani
  5. Department of Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Huamin Wang
  6. Department of Surgical Oncology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Yaan Kang
    •  & Jason Fleming
  7. Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Edward Chang
    •  & Giulio Draetta
  8. Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Haoqiang Ying
    •  & Giulio Draetta
  9. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Anirban Maitra
  10. Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA

    • Anirban Maitra


  1. Search for Prasenjit Dey in:

  2. Search for Joelle Baddour in:

  3. Search for Florian Muller in:

  4. Search for Chia Chin Wu in:

  5. Search for Huamin Wang in:

  6. Search for Wen-Ting Liao in:

  7. Search for Zangdao Lan in:

  8. Search for Alina Chen in:

  9. Search for Tony Gutschner in:

  10. Search for Yaan Kang in:

  11. Search for Jason Fleming in:

  12. Search for Nikunj Satani in:

  13. Search for Di Zhao in:

  14. Search for Abhinav Achreja in:

  15. Search for Lifeng Yang in:

  16. Search for Jiyoon Lee in:

  17. Search for Edward Chang in:

  18. Search for Giannicola Genovese in:

  19. Search for Andrea Viale in:

  20. Search for Haoqiang Ying in:

  21. Search for Giulio Draetta in:

  22. Search for Anirban Maitra in:

  23. Search for Y. Alan Wang in:

  24. Search for Deepak Nagrath in:

  25. Search for Ronald A. DePinho in:


P.D., Y.A.W., D.N. and R.A.D. designed the studies, interpreted the data and wrote the manuscript; P.D. performed all experiments; J.B. performed experiments and analysis of metabolite isotope tracing, Seahorse and UPLC; A.A. and L.Y. conducted metabolomics data analysis; C.C.W. performed bioinformatics analysis; W.-T.L. and H.W. conducted tissue microarray analysis; Z.L. conducted ChIP analysis; T.G. was responsible for ME2 CRISPR design and cloning; Y.K., J.F. and A.V. contributed essential reagents and resources; F.M., G.G., H.Y., G.D. and A.M. provided intellectual input; A.C., N.S., D.Z., Y.K., J.L. and E.C. provided technical support.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Y. Alan Wang or Deepak Nagrath or Ronald A. DePinho.

Reviewer Information Nature thanks C. Van Dang, A. Trumpp and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figures

    This file contains the raw data for the Figures and Extended Data Figures (see Contents for details) and additional references.

Excel files

  1. 1.

    Supplementary Table

    This table contains the tumor progression data.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.