Skip to main content

Deconstructing the Metabolic Networks of Oncogenic Signaling Using Targeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)

  • Protocol
  • First Online:
Kinase Signaling Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1636))

Abstract

Metabolic reprogramming is recognized as an emerging hallmark of oncogenic signaling and cancer development. Hence the need to identify novel quantitative analytical platforms for studying metabolism in vitro and in vivo has dramatically increased. Here, we describe the experimental workflow for a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach involving positive/negative ion switching to analyze >250 metabolites of central carbon metabolism, nucleotides, and amino acids.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Warburg O (1956) On the origin of cancer cells. Science 123(3191):309–314

    Article  CAS  PubMed  Google Scholar 

  2. Vander Heiden MG, Cantley LC, Thompson CB (2009) Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324(5930):1029–1033. doi:10.1126/science.1160809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Metallo CM, Gameiro PA, Bell EL, Mattaini KR, Yang J, Hiller K, Jewell CM, Johnson ZR, Irvine DJ, Guarente L, Kelleher JK, Vander Heiden MG, Iliopoulos O, Stephanopoulos G (2012) Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia. Nature 481(7381):380–384. doi:10.1038/nature10602

    CAS  Google Scholar 

  4. Mullen AR, Wheaton WW, Jin ES, Chen PH, Sullivan LB, Cheng T, Yang Y, Linehan WM, Chandel NS, DeBerardinis RJ (2012) Reductive carboxylation supports growth in tumour cells with defective mitochondria. Nature 481(7381):385–388. doi:10.1038/nature10642

    CAS  Google Scholar 

  5. Wise DR, Ward PS, Shay JE, Cross JR, Gruber JJ, Sachdeva UM, Platt JM, DeMatteo RG, Simon MC, Thompson CB (2011) Hypoxia promotes isocitrate dehydrogenase-dependent carboxylation of alpha-ketoglutarate to citrate to support cell growth and viability. Proc Natl Acad Sci U S A 108(49):19611–19616. doi:10.1073/pnas.1117773108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Yuneva MO, Fan TW, Allen TD, Higashi RM, Ferraris DV, Tsukamoto T, Mates JM, Alonso FJ, Wang C, Seo Y, Chen X, Bishop JM (2012) The metabolic profile of tumors depends on both the responsible genetic lesion and tissue type. Cell Metab 15(2):157–170. doi:10.1016/j.cmet.2011.12.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ying H, Kimmelman AC, Lyssiotis CA, Hua S, Chu GC, Fletcher-Sananikone E, Locasale JW, Son J, Zhang H, Coloff JL, Yan H, Wang W, Chen S, Viale A, Zheng H, Paik JH, Lim C, Guimaraes AR, Martin ES, Chang J, Hezel AF, Perry SR, Hu J, Gan B, Xiao Y, Asara JM, Weissleder R, Wang YA, Chin L, Cantley LC, DePinho RA (2012) Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell 149(3):656–670. doi:10.1016/j.cell.2012.01.058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kang HB, Fan J, Lin R, Elf S, Ji Q, Zhao L, Jin L, Seo JH, Shan C, Arbiser JL, Cohen C, Brat D, Miziorko HM, Kim E, Abdel-Wahab O, Merghoub T, Frohling S, Scholl C, Tamayo P, Barbie DA, Zhou L, Pollack BP, Fisher K, Kudchadkar RR, Lawson DH, Sica G, Rossi M, Lonial S, Khoury HJ, Khuri FR, Lee BH, Boggon TJ, He C, Kang S, Chen J (2015) Metabolic rewiring by oncogenic BRAF V600E links ketogenesis pathway to BRAF-MEK1 signaling. Mol Cell 59(3):345–358. doi:10.1016/j.molcel.2015.05.037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kohn AD, Summers SA, Birnbaum MJ, Roth RA (1996) Expression of a constitutively active Akt Ser/Thr kinase in 3T3-L1 adipocytes stimulates glucose uptake and glucose transporter 4 translocation. J Biol Chem 271(49):31372–31378

    Article  CAS  PubMed  Google Scholar 

  10. Deprez J, Vertommen D, Alessi DR, Hue L, Rider MH (1997) Phosphorylation and activation of heart 6-phosphofructo-2-kinase by protein kinase B and other protein kinases of the insulin signaling cascades. J Biol Chem 272(28):17269–17275

    Article  CAS  PubMed  Google Scholar 

  11. Gottlob K, Majewski N, Kennedy S, Kandel E, Robey RB, Hay N (2001) Inhibition of early apoptotic events by Akt/PKB is dependent on the first committed step of glycolysis and mitochondrial hexokinase. Genes Dev 15(11):1406–1418. doi:10.1101/gad.889901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Rathmell JC, Fox CJ, Plas DR, Hammerman PS, Cinalli RM, Thompson CB (2003) Akt-directed glucose metabolism can prevent Bax conformation change and promote growth factor-independent survival. Mol Cell Biol 23(20):7315–7328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Berwick DC, Hers I, Heesom KJ, Moule SK, Tavare JM (2002) The identification of ATP-citrate lyase as a protein kinase B (Akt) substrate in primary adipocytes. J Biol Chem 277(37):33895–33900. doi:10.1074/jbc.M204681200

    Article  CAS  PubMed  Google Scholar 

  14. Porstmann T, Santos CR, Griffiths B, Cully M, Wu M, Leevers S, Griffiths JR, Chung YL, Schulze A (2008) SREBP activity is regulated by mTORC1 and contributes to Akt-dependent cell growth. Cell Metab 8(3):224–236. doi:10.1016/j.cmet.2008.07.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Yue S, Li J, Lee SY, Lee HJ, Shao T, Song B, Cheng L, Masterson TA, Liu X, Ratliff TL, Cheng JX (2014) Cholesteryl ester accumulation induced by PTEN loss and PI3K/AKT activation underlies human prostate cancer aggressiveness. Cell Metab 19(3):393–406. doi:10.1016/j.cmet.2014.01.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Yuan M, Breitkopf SB, Yang X, Asara JM (2012) A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc 7(5):872–881. doi:10.1038/nprot.2012.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Bennett BD, Yuan J, Kimball EH, Rabinowitz JD (2008) Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc 3(8):1299–1311. doi:10.1038/nprot.2008.107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Anastasiou D, Poulogiannis G, Asara JM, Boxer MB, Jiang JK, Shen M, Bellinger G, Sasaki AT, Locasale JW, Auld DS, Thomas CJ, Vander Heiden MG, Cantley LC (2011) Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses. Science 334(6060):1278–1283. doi:10.1126/science.1211485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kelly AD, Breitkopf SB, Yuan M, Goldsmith J, Spentzos D, Asara JM (2011) Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: application in sarcoma. PLoS One 6(10):e25357. doi:10.1371/journal.pone.0025357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Locasale JW, Grassian AR, Melman T, Lyssiotis CA, Mattaini KR, Bass AJ, Heffron G, Metallo CM, Muranen T, Sharfi H, Sasaki AT, Anastasiou D, Mullarky E, Vokes NI, Sasaki M, Beroukhim R, Stephanopoulos G, Ligon AH, Meyerson M, Richardson AL, Chin L, Wagner G, Asara JM, Brugge JS, Cantley LC, Vander Heiden MG (2011) Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nat Genet 43(9):869–874. doi:10.1038/ng.890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Vander Heiden MG, Locasale JW, Swanson KD, Sharfi H, Heffron GJ, Amador-Noguez D, Christofk HR, Wagner G, Rabinowitz JD, Asara JM, Cantley LC (2010) Evidence for an alternative glycolytic pathway in rapidly proliferating cells. Science 329(5998):1492–1499. doi:10.1126/science.1188015

    Article  CAS  PubMed  Google Scholar 

  22. Yi CH, Pan H, Seebacher J, Jang IH, Hyberts SG, Heffron GJ, Vander Heiden MG, Yang R, Li F, Locasale JW, Sharfi H, Zhai B, Rodriguez-Mias R, Luithardt H, Cantley LC, Daley GQ, Asara JM, Gygi SP, Wagner G, Liu CF, Yuan J (2011) Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival. Cell 146(4):607–620. doi:10.1016/j.cell.2011.06.050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Rabinowitz JD, Kimball E (2007) Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal Chem 79(16):6167–6173. doi:10.1021/ac070470c

    Article  CAS  PubMed  Google Scholar 

  24. Mackay GM, Zheng L, van den Broek NJ, Gottlieb E (2015) Analysis of cell metabolism using LC-MS and isotope tracers. Methods Enzymol 561:171–196. doi:10.1016/bs.mie.2015.05.016

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to George Poulogiannis .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Poulogiannis, G. (2017). Deconstructing the Metabolic Networks of Oncogenic Signaling Using Targeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). In: Tan, AC., Huang, P. (eds) Kinase Signaling Networks. Methods in Molecular Biology, vol 1636. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7154-1_26

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7154-1_26

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7152-7

  • Online ISBN: 978-1-4939-7154-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics