Advertisement

Clinical Aspects of Metabolomics

  • Michael BousamraII
  • Jamie Day
  • Teresa Whei-Mei Fan
  • Goetz Kloecker
  • Andrew N. LaneEmail author
  • Donald M. Miller
Protocol
Part of the Methods in Pharmacology and Toxicology book series (MIPT)

Abstract

Clinical metabolomics using stable isotope tracing represents an important new approach to obtaining metabolic parameters in human subjects in situ. In this chapter, the considerations for such clinical metabolomics are outlined and discussed. Descriptions include the essentials of patient accrual, permission, and institutional review approvals as well as specifics of treatments, tissue and biofluid collection, and curation. Although procedures vary among Institutes, the basic features for clinical research are common. Here, we illustrate the process from concept to analysis with an example from a recent study on non-small cell lung cancer metabolomics. This powerful new approach has already provided important new insights into metabolic adaptations in lung cancer cells.

Keywords

Stable Isotope Metabolomics Study Kinetic Isotope Effect Patient Accrual Lung Cancer Study 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Glossary

Buffy coat

It is the fraction of an anticoagulated blood sample after centrifugation that contains most of the white blood cells and platelets. It comprises the interstitial layer between the red cells and the plasma, and accounts for <1% of the total volume of the blood sample, and contains most of the white blood cells and platelets. It this contains the DNA component of (mammalian) blood.

CITI

Collaborative Institutional Training Initiative is an organization that provides a (subscription) service in ethics for researchers, and includes modules in patient privacy and biomedical research. Participating organizations require annual training and certification.

HIPAA

Health Insurance Portability and Accountability Act (1996).

IND

Investigational new drug. FDA approval for use of an agent in a manner different from its original designation, such as a New indication; Change in the approved route of administration or dosage level; Change in the approved patient population (e.g., pediatric) or a population at greater or increase of risk.

IBC

Institutional Biosafety Committee. All biological tissues and recombinant material must be approved by a biological safety committee that determines the level of risk from exposure. Human tissues require strict regulations for handling owing to the potential for disseminating disease, viruses, etc. Only authorized personnel may handle such specimens, and they must be provided with appropriate safety clothing, containment facilities and adequate sterilization procedures. This usually also requires undertaking additional biological safety training and blood borne pathogen training.

IRB

Institutional Review Boards. Ethical oversight committees for all biomedical experimentation. Ethical issues, statistical and basic science are all assessed for quality and legal requirements, and the committee can approve or deny any specific research project. This is designed to protect the subject as well as the institution and the researchers from ethicolegal breaches.

MRI/MRS

Magnetic resonance imaging/magnetic resonance spectroscopy. These are clinical manifestations of the NMR experiment (cf.  Chap. 6). The former uses pulsed field gradients to obtain spatial resolution of an intense signal intrinsic to the object (usually tissue water), and produces high-resolution anatomical images especially of soft tissue. Some biochemical information can be obtained using chemical shift imaging. MRS is explicitly a spectroscopic approach that can be combined with imaging (image guided spectroscopy) and provides direct information about spatial distribution and concentrations of certain abundant metabolites. Variants of the approach can be used to obtain very detailed metabolic information in situ in an alert subject.

NSCLC

Non small cell lung cancer is a class of lung carcinoma that involves a variety of cell types that are distinguishable from the small cell type. Small cell carcinoma is usually not treatable by surgery, and generally chemotherapeutic regimens differ from the NSCLC. NSCL cancers comprise squamous cell carcinoma, adenocarcinoma (the two most common varieties), bronchioalveolar carcinoma (BAC) which is a subset of adenocarcinoma, and large cell carcinomas (“other”) (36).

PET

Positron emission tomography is an imaging modality that detects the gamma photons emitted when a positron annihilates an electron. The positron is emitted from an unstable nuclide such as 18F (half-life ca. 110 min) that is incorporated into a marker metabolite for injection. A common compound is 18F-2-deoxyglucose, which is taken up by cells by the usual glucose transported, and phosphorylated by hexokinase. The resulting 6-phosphate is not further metabolized, so the radionuclide accumulates in cells that have active glucose transport, such as cancer cells (which also often have downregulated G6P phosphatase, thereby maintaining a high concentration of the labeled sugar).

PHI

Public health information covered under HIPAA rules regarding any health information of individuals.

Stable isotope

Isotopes are variants of an element that differ in the number of neutrons, but have the same number of protons (or atomic number). A stable isotope is one that does not decay into another elements or isotope. For example, there are three isotopes of hydrogen, containing 1 proton and 0 (protium, 1H 99.99%), 1 (deuterium, 2H 0.01%) or 2 (tritium, 3H) neutrons. Protium and deuterium are stable, whereas tritium is radioactive, and emits a low energy electron (beta particle) to decay to a form of 3He with a half-life of 12.32 years.

USP

US Pharmacopeia produces standards for drug safety that are effectively ratified by the FDA.

References

  1. 1.
    Kaddurah-Daouk R, Kristal BS, Weinshilboum RM. Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol. 2008;48:23.21–32.31.CrossRefGoogle Scholar
  2. 2.
    Fan TW-M, Lane AN, Higashi RM. The promise of metabolomics in cancer molecular therapeutics. Curr Opin Mol Ther. 2004;6:584–92.PubMedGoogle Scholar
  3. 3.
    Serkova NJ, Spratlin JL, Eckhardt SG. NMR-based metabolomics: translational application and treatment of cancer. Curr Opin Mol Ther. 2007;9:572–85.PubMedGoogle Scholar
  4. 4.
    Di Buono M, Jones PJH, Beaumier L, Wykes LJ. Comparison of deuterium incorporation and mass isotopomer distribution analysis for measurement of human cholesterol biosynthesis. J Lipid Res. 2000;41:1516–23.PubMedGoogle Scholar
  5. 5.
    Mason GF, Petersen KF, de Graaf RA, Kanamatsu T, Otsuki T, Rothman DL. A comparison of C-13 NMR measurements of the rates of glutamine synthesis and the tricarboxylic acid cycle during oral and intravenous administration of 1-C-13 glucose. Brain Res Protoc. 2002;10:181–90.CrossRefGoogle Scholar
  6. 6.
    Patel AB, de Graaf RA, Mason GF, Rothman DL, Shulman RG, Behar KL. The contribution of GABA to glutamate/glutamine cycling and energy metabolism in the rat cortex in vivo. Proc Natl Acad Sci USA. 2005;102:5588–93.PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Fan TW, Lane AN. Structure-based profiling of metabolites and isotopomers by NMR. Prog NMR Spectrosc. 2008;52:69–117.CrossRefGoogle Scholar
  8. 8.
    Mayes PD, Bender DA. In: Murray RK, Granner DK, Mayes PA, Rodwell VW, editors. Harper’s illustrated biochemistry. 26th ed. McGraw-Hill: New York; 2003.Google Scholar
  9. 9.
    Lane AN, Fan TW-M, Higashi RM. Stable isotope assisted metabolomics in cancer research. IUBMB Life. 2008;60:124–9.PubMedCrossRefGoogle Scholar
  10. 10.
    Lindon JC, Holmes E, Nicholson JK. Toxicological applications of magnetic resonance. Prog Nucl Magn Reson Spectrosc. 2004; 45:109–43.CrossRefGoogle Scholar
  11. 11.
    Bollard ME, Stanley EG, Lindon JC, Nicholson JK, Holmes E. NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition. NMR Biomed. 2005;18:143–62.PubMedCrossRefGoogle Scholar
  12. 12.
    Lindon JC, Nicholson JK, Everett JR. Annual reports on NMR spectroscopy, vol. 38. San Diego: Academic Press; 1999. p. 1–88.Google Scholar
  13. 13.
    Fan TWM, Lane AN, Higashi RM. The promise of metabolomics in cancer molecular therapeutics. Curr Opin Mol Ther. 2004;6:584–92.PubMedGoogle Scholar
  14. 14.
    Griffin JL, Kauppinen RA. Tumour metabolomics in animal models of human cancer. J Proteome Res. 2007;6:498–505.PubMedCrossRefGoogle Scholar
  15. 15.
    Ippolito JE, Xu J, Jain SJ, Moulder K, Mennerick S, Crowley JR, Townsend RR, Gordon JI. An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers. Proc Natl Acad Sci U S A. 2005;102:9901–6.PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Zimmermann D, Hartmann M, Moyer MP, Nolte J, Baumbach JI. Determination of volatile products of human colon cell line metabolism by GC/MS analysis. Metabolomics. 2007;3:13–7.CrossRefGoogle Scholar
  17. 17.
    Kind T, Tolstikov V, Fiehn O, Weiss RH. A comprehensive urinary metabolomic approach for identifying kidney cancer. Anal Biochem. 2007;363:185–95.PubMedCrossRefGoogle Scholar
  18. 18.
    Beger RD, Schnackenberg LK, Holland RD, Li DH, Dragan Y. Metabonomic models of human pancreatic cancer using 1D proton NMR spectra of lipids in plasma. Metabolomics. 2006;2:125–34.CrossRefGoogle Scholar
  19. 19.
    Hoffmeister KN, Falet H, Toker A, Barkalow KL, StosselDagger TP, Hartwig JH. Mechanisms of cold-induced platelet actin assembly. J Biol Chem. 2001;276:24751–9.PubMedCrossRefGoogle Scholar
  20. 20.
    Tablin F, Oliver AE, Walker NJ, Crowe LM, Crowe JH. Membrane phase transition of intact human platelets: correlation with cold-induced activation. J Cell Physiol. 1996;168:305–13.PubMedCrossRefGoogle Scholar
  21. 21.
    Saude EJ, Sykes BD. Urine stability for metabolomic studies: effects of preparation and storage. Metabolomics. 2007;3:19–27.CrossRefGoogle Scholar
  22. 22.
    Saude EJ, Adamko D, Rowe BH, Marrie T, Sykes BD. Variation of metabolites in normal human urine. Metabolomics. 2007;3:439–51.CrossRefGoogle Scholar
  23. 23.
    Viant MR, Ludwig C, Rhodes S, Günther UL, Allaway D. Validation of a urine metabolome fingerprint in dog for phenotypic classification. Metabolomics. 2007;3:453–63.CrossRefGoogle Scholar
  24. 24.
    Wilson JF. Health Insurance Portability and Accountability Act Privacy Rule causes ongoing concerns among clinicians and researchers. Ann Intern Med. 2006;145:313–6.PubMedCrossRefGoogle Scholar
  25. 25.
    Harrigan GG, Goodacre R, editors. Metabolic profiling: its role in biomarker discovery and gene function analysis. New York: Springer; 2003.Google Scholar
  26. 26.
    Trygg J, Holmes E, Lundstedt T. Chemometrics in metabonomics. J Proteome Res. 2007;6:469–79.PubMedCrossRefGoogle Scholar
  27. 27.
    Kettaneh N, Berglund A, Wold S. PCA and PLS with very large data sets. Comput Stat Data Anal. 2005;48:69–85.CrossRefGoogle Scholar
  28. 28.
    Rossner B. Fundamentals of biostatistics. 6th ed. Belmont: Thomson; 2006.Google Scholar
  29. 29.
    Fan TWM. Recent advances in profiling plant metabolites by multinuclear and multidimensional NMR. In: Shachar-Hill Y, Pfeffer PE, editors. Nuclear magnetic resonance in plant biology, Vol 16. American Society of Plant Physiologists, Rockville; 1996. p. 181–254.Google Scholar
  30. 30.
    Fan TWM. Metabolite profiling by one- and two-dimensional NMR analysis of complex mixtures. Prog Nucl Magn Reson Spectrosc. 1996;28:161–219.Google Scholar
  31. 31.
    Lane AN, Fan TW. Quantification and identification of isotopomer distributions of metabolites in crude cell extracts using 1H TOCSY. Metabolomics. 2007;3:79–86.CrossRefGoogle Scholar
  32. 32.
    Fan TW, Lane AN, Higashi RM, Farag MA, Gao H, Bousamra M, Miller DM. Altered regulation of metabolic pathways in human lung cancer discerned by 13C stable isotope-resolved metabolomics (SIRM). Mol Cancer. 2009;8:41.PubMedCentralPubMedCrossRefGoogle Scholar
  33. 33.
    Lane AN, Fan TW, Higashi RM, Tan J, Bousamra M, Miller DM. Prospects for clinical cancer metabolomics using stable isotope tracers. J Exp Mol Pathol. 2009;86:165–73.CrossRefGoogle Scholar
  34. 34.
    Fan TW-M, Lane AN, Higashi M, Bousamra M, Kloecker G, Miller DM. Erlotinib-sensitive and resistant lung tumors show radically different metabolic profiles. Exp Mol Pathol. 2009;87:83–6.PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Lane AN, Fan TW-M, Bousamra II M, Higashi RM, Yan J, Miller DM. Clinical applications of stable isotope-resolved metabolomics (SIRM) in non-small cell lung cancer. Omics. 2011;15:173–182.Google Scholar
  36. 36.
    Edelman RJ, Gandara DR. Lung Cancer. In: Casciato DA, editor. Manual of clinical oncology. 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2004.Google Scholar
  37. 37.
    Griffin JL, Nicholls AW, Daykin CA, Heald S, Keun HC, Schuppe-Koistinen I, Griffiths JR, Cheng LL, Rocca-Serra P, Rubtsov DV, et al. Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments. Metabolomics. 2007;3:179–88.CrossRefGoogle Scholar
  38. 38.
    Goodacre R, Broadhurst D, Smilde AK, Kristal BS, Baker JD, Beger R, Bessant C, Connor S, Calmani G, Craig A, et al. Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics. 2007;3:231–41.CrossRefGoogle Scholar
  39. 39.
    Boros LG. Metabolic targeted therapy of cancer: current tracer technologies and future drug design strategies in the old metabolic network. Metabolomics. 2005;1:11–5.CrossRefGoogle Scholar
  40. 40.
    Harrigan GG, Brackett DJ, Boros LG. Medicinal chemistry, metabolic profiling and drug target discovery: a role for metabolic profiling in reverse pharmacology and chemical genetics. Mini Rev Med Chem. 2005;5:13–20.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Michael BousamraII
    • 1
  • Jamie Day
    • 2
  • Teresa Whei-Mei Fan
    • 3
  • Goetz Kloecker
    • 4
  • Andrew N. Lane
    • 5
    Email author
  • Donald M. Miller
    • 6
  1. 1.Department of SurgeryUniversity of LouisvilleLouisvilleUSA
  2. 2.James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA
  3. 3.Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA
  4. 4.Department of Medicine and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA
  5. 5.Departments of Medicine and Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA
  6. 6.Department of Medicine, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA

Personalised recommendations