Display options
Cite
Varshavi D, Varshavi D, McCarthy N, et al. Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines. Metabolomics. 2021;17(12):104doi: 10.1007/s11306-021-01852-w.
Varshavi, D., Varshavi, D., McCarthy, N., Veselkov, K., Keun, H. C., & Everett, J. R. (2021). Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines. Metabolomics : Official journal of the Metabolomic Society, 17(12), 104. https://doi.org/10.1007/s11306-021-01852-w
Varshavi, Dorna, et al. "Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines." Metabolomics : Official journal of the Metabolomic Society vol. 17,12 (2021): 104. doi: https://doi.org/10.1007/s11306-021-01852-w
Varshavi D, Varshavi D, McCarthy N, Veselkov K, Keun HC, Everett JR. Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines. Metabolomics. 2021 Nov 25;17(12):104. doi: 10.1007/s11306-021-01852-w. PMID: 34822010; PMCID: PMC8616861.
Copy Download .nbib Format: NLM
Share it on

Metabolomics. 2021 Nov 25;17(12):104. doi: 10.1007/s11306-021-01852-w.

Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines.

Metabolomics : Official journal of the Metabolomic Society

Dorna Varshavi, Dorsa Varshavi, Nicola McCarthy, Kirill Veselkov, Hector C Keun, Jeremy R Everett

Affiliations

  1. Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK.
  2. Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada.
  3. Horizon Discovery Ltd., Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL, UK.
  4. Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
  5. Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK.
  6. Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 ONN, UK.
  7. Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK. [email protected].

PMID: 34822010 PMCID: PMC8616861 DOI: 10.1007/s11306-021-01852-w

Abstract

INTRODUCTION: KRAS was one of the earliest human oncogenes to be described and is one of the most commonly mutated genes in different human cancers, including colorectal cancer. Despite KRAS mutants being known driver mutations, KRAS has proved difficult to target therapeutically, necessitating a comprehensive understanding of the molecular mechanisms underlying KRAS-driven cellular transformation.

OBJECTIVES: To investigate the metabolic signatures associated with single copy mutant KRAS in isogenic human colorectal cancer cells and to determine what metabolic pathways are affected.

METHODS: Using NMR-based metabonomics, we compared wildtype (WT)-KRAS and mutant KRAS effects on cancer cell metabolism using metabolic profiling of the parental KRAS

RESULTS: Mutation in the KRAS oncogene leads to a general metabolic remodelling to sustain growth and counter stress, including alterations in the metabolism of amino acids and enhanced glutathione biosynthesis. Additionally, we show that KRAS

CONCLUSIONS: Our study showed the effect of a single point mutation in one KRAS allele and KRAS allele loss in an isogenic genetic background, hence avoiding confounding genetic factors. Metabolic differences among different KRAS mutations might play a role in their different responses to anticancer treatments and hence could be exploited as novel metabolic vulnerabilities to develop more effective therapies against oncogenic KRAS.

© 2021. The Author(s).

Keywords: Cells; Colorectal cancer; HCT116; KRAS; Metabolic profiling; Metabolomics; Metabonomics; Mutations; NMR

References

  1. Ahn, C. S., & Metallo, C. M. (2015). Mitochondria as biosynthetic factories for cancer proliferation. Cancer & Metabolism, 3(1), 1. - PubMed
  2. Amelio, I., Cutruzzolá, F., Antonov, A., Agostini, M., & Melino, G. (2014). Serine and glycine metabolism in cancer(). Trends in Biochemical Sciences, 39(4), 191–198. - PubMed
  3. Aquilano, K., Baldelli, S., & Ciriolo, M. R. (2014). Glutathione: New roles in redox signaling for an old antioxidant. Frontiers in Pharmacology, 5, 196. - PubMed
  4. Arrick, B. A., & Nathan, C. F. (1984). Glutathione metabolism as a determinant of therapeutic efficacy: A review. Cancer Research, 44(10), 4224. - PubMed
  5. Arrington, A. K., Heinrich, E. L., Lee, W., Duldulao, M., Patel, S., Sanchez, J., Garcia-Aguilar, J., & Kim, J. (2012). Prognostic and predictive roles of KRAS mutation in colorectal cancer. International Journal of Molecular Sciences, 13(10), 12153–12168. - PubMed
  6. Benjamini, Y. (2010). Discovering the false discovery rate. Journal of the Royal Statistical Society: Series B (statistical Methodology), 72(4), 405–416. - PubMed
  7. Calvert, P., Yao, K.-S., Hamilton, T. C., & O’Dwyer, P. J. (1998). Clinical studies of reversal of drug resistance based on glutathione. Chemico-Biological Interactions, 111, 213–224. - PubMed
  8. De Ingeniis, J., Ratnikov, B., Richardson, A. D., Scott, D. A., Aza-Blanc, P., De, S. K., Kazanov, M., Pellecchia, M., Ronai, Z. E., Osterman, A. L., & Smith, J. W. (2012). Functional specialization in proline biosynthesis of melanoma. PLoS ONE, 7(9), e45190. - PubMed
  9. Dettmer, K., Nürnberger, N., Kaspar, H., Gruber, M. A., Almstetter, M. F., & Oefner, P. J. (2011). Metabolite extraction from adherently growing mammalian cells for metabolomics studies: Optimization of harvesting and extraction protocols. Analytical and Bioanalytical Chemistry, 399(3), 1127–1139. - PubMed
  10. Dinu, D., Dobre, M., Panaitescu, E., Bîrlă, R., Iosif, C., Hoara, P., Caragui, A., Boeriu, M., Constantinoiu, S., & Ardeleanu, C. (2014). Prognostic significance of KRAS gene mutations in colorectal cancer—preliminary study. Journal of Medicine and Life, 7(4), 581–587. - PubMed
  11. Dona, A. C., Kyriakides, M., Scott, F., Shephard, E. A., Varshavi, D., Veselkov, K., & Everett, J. R. (2016). A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments. Computational and Structural Biotechnology Journal, 14, 135–153. - PubMed
  12. Ernst, T., Hergenhahn, M., Kenzelmann, M., Cohen, C. D., Bonrouhi, M., Weninger, A., Klaren, R., Grone, E. F., Wiesel, M., Gudemann, C., Kuster, J., Schott, W., Staehler, G., Kretzler, M., Hollstein, M., & Grone, H. J. (2002). Decrease and gain of gene expression are equally discriminatory markers for prostate carcinoma: A gene expression analysis on total and microdissected prostate tissue. American Journal of Pathology, 160(6), 2169–2180. - PubMed
  13. Estrela, J. M., Obrador, E., Navarro, J., De La Vega, M. C. L., & Pellicer, J. A. (1995). Elimination of Ehrlich tumours by ATP-induced growth inhibition, glutathione depletion and X-rays. Nature Medicine, 1(1), 84–88. - PubMed
  14. Estrela, J. M., Ortega, A., & Obrador, E. (2006). Glutathione in cancer biology and therapy. Critical Reviews in Clinical Laboratory Sciences, 43(2), 143–181. - PubMed
  15. Everett, J. R. (2015). A new paradigm for known metabolite identification in metabonomics/metabolomics: metabolite identification efficiency. Computational and Structural Biotechnology Journal, 13, 131–144. - PubMed
  16. Everett, J. R., Holmes, E., Veselkov, K. A., Lindon, J. C., & Nicholson, J. K. (2019). A unified conceptual framework for metabolic phenotyping in diagnosis and prognosis. Trends in Pharmacological Sciences, 40(10), 763–773. - PubMed
  17. Franco, R., Sánchez-Olea, R., Reyes-Reyes, E. M., & Panayiotidis, M. I. (2009). Environmental toxicity, oxidative stress and apoptosis: Ménage à Trois. Mutation Research/genetic Toxicology and Environmental Mutagenesis, 674(1–2), 3–22. - PubMed
  18. Hartman, D. J., Davison, J. M., Foxwell, T. J., Nikiforova, M. N., & Chiosea, S. I. (2012). Mutant allele-specific imbalance modulates prognostic impact of KRAS mutations in colorectal adenocarcinoma and is associated with worse overall survival. International Journal of Cancer, 131(8), 1810–1817. - PubMed
  19. Jain, M., Nilsson, R., Sharma, S., Madhusudhan, N., Kitami, T., Souza, A. L., Kafri, R., Kirschner, M. W., Clish, C. B., & Mootha, V. K. (2012). Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science, 336(6084), 1040–1044. - PubMed
  20. Kamphorst, J. J., Chung, M. K., Fan, J., & Rabinowitz, J. D. (2014). Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate. Cancer & Metabolism, 2(1), 23. - PubMed
  21. Kerr, E., Gaude, E., Turrell, F., Frezza, C., & Martins, C. P. (2016). Mutant Kras copy number defines metabolic reprogramming and therapeutic susceptibilities. Nature, 531(7592), 110–113. - PubMed
  22. Kim, J.-W., Tchernyshyov, I., Semenza, G. L., & Dang, C. V. (2006). HIF-1-mediated expression of pyruvate dehydrogenase kinase: A metabolic switch required for cellular adaptation to hypoxia. Cell Metabolism, 3(3), 177–185. - PubMed
  23. Labuschagne, C. F., van den Broek, N. J. F., Mackay, G. M., Vousden, K. H., & Maddocks, O. D. K. (2014). Serine, but not glycine, supports one-carbon metabolism and proliferation of cancer cells. Cell Reports, 7(4), 1248–1258. - PubMed
  24. Lindon, J., Nicholson, J., Holmes, E., & Everett, J. (2000). Metabonomics: Metabolic processes studied by NMR spectroscopy of biofluids. Concepts in Magnetic Resonance, 12(5), 289–320. - PubMed
  25. Liu, W., Le, A., Hancock, C., Lane, A. N., Dang, C. V., Fan, T. W. M., & Phang, J. M. (2012). Reprogramming of proline and glutamine metabolism contributes to the proliferative and metabolic responses regulated by oncogenic transcription factor c-MYC. Proceedings of the National Academy of Sciences, 109(23), 8983–8988. - PubMed
  26. Luo, F., Poulogiannis, G., Ye, H., Hamoudi, R., Dong, G., Zhang, W., Ibrahim, A. E. K., & Arends, M. J. (2014). Wild-type K-ras has a tumour suppressor effect on carcinogen-induced murine colorectal adenoma formation. International Journal of Experimental Pathology, 95(1), 8–15. - PubMed
  27. Lyssiotis, C. A., Son, J., Cantley, L. C., & Kimmelman, A. C. (2013). Pancreatic cancers rely on a novel glutamine metabolism pathway to maintain redox balance. Cell Cycle, 12(13), 1987–1988. - PubMed
  28. Maddocks, O. D. K., Berkers, C. R., Mason, S. M., Zheng, L., Blyth, K., Gottlieb, E., & Vousden, K. H. (2013). Serine starvation induces stress and p53-dependent metabolic remodelling in cancer cells. Nature, 493(7433), 542–546. - PubMed
  29. Mayers, J. R., Torrence, M. E., Danai, L. V., Papagiannakopoulos, T., Davidson, S. M., Bauer, M. R., Lau, A. N., Ji, B. W., Dixit, P. D., Hosios, A. M., Muir, A., Chin, C. R., Freinkman, E., Jacks, T., Wolpin, B. M., Vitkup, D., & Vander Heiden, M. G. (2016). Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Science, 353(6304), 1161–1165. - PubMed
  30. Meister, A. (1991). Glutathione deficiency produced by inhibition of its synthesis, and its reversal; applications in research and therapy. Pharmacology & Therapeutics, 51(2), 155–194. - PubMed
  31. Mitchell, J. B., & Russo, A. (1987). The role of glutathione in radiation and drug induced cytotoxicity. The British Journal of Cancer. Supplement, 8, 96–104. - PubMed
  32. Obrador, E., Carretero, J., Ortega, A., Medina, I., Rodilla, V., Pellicer, J. A., & Estrela, J. M. (2002). γ-Glutamyl transpeptidase overexpression increases metastatic growth of B16 melanoma cells in the mouse liver. Hepatology, 35(1), 74–81. - PubMed
  33. Ortega, Á. L., Mena, S., & Estrela, J. M. (2010). Oxidative and nitrosative stress in the metastatic microenvironment. Cancers, 2(2), 274–304. - PubMed
  34. Papandreou, I., Cairns, R. A., Fontana, L., Lim, A. L., & Denko, N. C. (2006). HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption. Cell Metabolism, 3, 187–197. - PubMed
  35. Possemato, R., Marks, K. M., Shaul, Y. D., Pacold, M. E., Kim, D., Birsoy, K., Sethumadhavan, S., Woo, H.-K., Jang, H. G., Jha, A. K., Chen, W. W., Barrett, F. G., Stransky, N., Tsun, Z.-Y., Cowley, G. S., Barretina, J., Kalaany, N. Y., Hsu, P. P., Ottina, K., … Sabatini, D. M. (2011). Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature, 476(7360), 346–350. - PubMed
  36. Schug, Z. T., Peck, B., Jones, D. T., Zhang, Q., Grosskurth, S., Alam, I. S., Goodwin, L. M., Smethurst, E., Mason, S., Blyth, K., McGarry, L., James, D., Shanks, E., Kalna, G., Saunders, R. E., Jiang, M., Howell, M., Lassailly, F., Thin, M. Z., … Gottlieb, E. (2015). Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress. Cancer Cell, 27(1), 57–71. - PubMed
  37. Schulze, A., & Harris, A. L. (2012). How cancer metabolism is tuned for proliferation and vulnerable to disruption. Nature, 491(7424), 364–373. - PubMed
  38. Scopelliti, A. J., Font, J., Vandenberg, R. J., Boudker, O., & Ryan, R. M. (2018). Structural characterisation reveals insights into substrate recognition by the glutamine transporter ASCT2/SLC1A5. Nature Communications, 9, 38. - PubMed
  39. Selak, M. A., Armour, S. M., MacKenzie, E. D., Boulahbel, H., Watson, D. G., Mansfield, K. D., Pan, Y., Simon, M. C., Thompson, C. B., & Gottlieb, E. (2005). Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-α prolyl hydroxylase. Cancer Cell, 7(1), 77–85. - PubMed
  40. Son, J., Lyssiotis, C. A., Ying, H., Wang, X., Hua, S., & Ligorio, M. (2013a). Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature, 496, 101–105. - PubMed
  41. Son, J., Lyssiotis, C. A., Ying, H., Wang, X., Hua, S., Ligorio, M., Perera, R. M., Ferrone, C. R., Mullarky, E., Shyh-Chang, N., Kang, Y. A., Fleming, J. B., Bardeesy, N., Asara, J. M., Haigis, M. C., DePinho, R. A., Cantley, L. C., & Kimmelman, A. C. (2013b). Glutamine supports pancreatic cancer growth through a Kras-regulated metabolic pathway. Nature, 496(7443), 101–105. - PubMed
  42. Spratlin, J. L., Serkova, N. J., & Eckhardt, S. G. (2009). Clinical applications of metabolomics in oncology: A review. Clinical Cancer Research, 15(2), 431–440. - PubMed
  43. Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W. M., Fiehn, O., Goodacre, R., Griffin, J. L., Hankemeier, T., Hardy, N., Harnly, J., Higashi, R., Kopka, J., Lane, A. N., Lindon, J. C., Marriott, P., Nicholls, A. W., … Viant, M. R. (2007). Proposed minimum reporting standards for chemical analysis. Metabolomics, 3(3), 211–221. - PubMed
  44. Tavares, L. C., Jarak, I., Nogueira, F. N., Oliveira, P. J., & Carvalho, R. A. (2015). Metabolic evaluations of cancer metabolism by NMR-based stable isotope tracer methodologies. European Journal of Clinical Investigation, 45, 37–43. - PubMed
  45. To, M. D., Del Rosario, R., Westcott, P. M. K., Banta, K. L., & Balmain, A. (2013). Interactions between wildtype and mutant ras genes in lung and skin carcinogenesis. Oncogene, 32(34), 4028–4033. - PubMed
  46. Toda, K., Kawada, K., Iwamoto, M., Inamoto, S., Sasazuki, T., Shirasawa, S., Hasegawa, S., & Sakai, Y. (2016). Metabolic alterations caused by KRAS mutations in colorectal cancer contribute to cell adaptation to glutamine depletion by upregulation of asparagine synthetase()(). Neoplasia, 18(11), 654–665. - PubMed
  47. Tsuchida, N., Murugan, A. K., & Grieco, M. (2016). Kirsten Ras oncogene: significance of its discovery in human cancer research. Oncotarget, 7(29), 46717–46733. - PubMed
  48. Tsun, Z.-Y., & Possemato, R. (2015). Amino acid management in cancer. Seminars in Cell & Developmental Biology, 43, 22–32. - PubMed
  49. Varshavi, D., McCarthy, N., Veselkov, K., Keun, H. C., & Everett, J. R. (2020). Metabolic characterization of colorectal cancer cells harbouring different KRAS mutations in codon 12, 13, 61 and 146 using human SW48 isogenic cell lines. Metabolomics, 16(4), 51. - PubMed
  50. Varshavi, D., Scott, F. H., Varshavi, D., Veeravalli, S., Phillips, I. R., Veselkov, K., Strittmatter, N., Takats, Z., Shephard, E. A., & Everett, J. R. (2018). Metabolic biomarkers of ageing in C57BL/6J wild-type and Flavin-containing monooxygenase 5 (FMO5)-knockout mice. Frontiers in Molecular Biosciences, 5, 28. - PubMed
  51. Vartanian, S., Bentley, C., Brauer, M. J., Li, L., Shirasawa, S., Sasazuki, T., Kim, J.-S., Haverty, P., Stawiski, E., Modrusan, Z., Waldman, T., & Stokoe, D. (2013). Identification of mutant K-Ras-dependent phenotypes using a panel of isogenic cell lines. The Journal of Biological Chemistry, 288(4), 2403–2413. - PubMed
  52. Vermeersch, K. A., & Styczynski, M. P. (2013). Applications of metabolomics in cancer research. J Carcinog, 12, 9. - PubMed
  53. Veselkov, K. A., Mirnezami, R., Strittmatter, N., Goldin, R. D., Kinross, J., Speller, A. V. M., Abramov, T., Jones, E. A., Darzi, A., Holmes, E., Nicholson, J. K., & Takats, Z. (2014). Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer. Proceedings of the National Academy of Sciences, 111(3), 1216–1221. - PubMed
  54. Yang, C., Ko, B., Hensley, C. T., Jiang, L., Wasti, A. T., Kim, J., Sudderth, J., Calvaruso, M. A., Lumata, L., Mitsche, M., Rutter, J., Merritt, M. E., & DeBerardinis, R. J. (2014). Glutamine oxidation maintains the TCA cycle and cell survival during impaired mitochondrial pyruvate transport. Molecular Cell, 56(3), 414–424. - PubMed
  55. Yang, M., & Vousden, K. H. (2016). Serine and one-carbon metabolism in cancer. Nature Reviews Cancer, 16(10), 650–662. - PubMed
  56. Zhang, J., Fan, J., Venneti, S., Cross, J. R., Takagi, T., & Bhinder, B. (2014). Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion. Molecular Cell, 56, 205–218. - PubMed
  57. Zhang, Z., Wang, Y., Vikis, H. G., Johnson, L., Liu, G., Li, J., Anderson, M. W., Sills, R. C., Hong, H. L., Devereux, T. R., Jacks, T., Guan, K.-L., & You, M. (2001). Wildtype Kras2 can inhibit lung carcinogenesis in mice. Nature Genetics, 29(1), 25–33. - PubMed
  58. Zhao, D., Li, F.-L., Cheng, Z.-L., & Lei, Q.-Y. (2014). Impact of acetylation on tumor metabolism. Molecular & Cellular Oncology, 1(3), e963452. - PubMed

Publication Types