Clinical Aspects of Metabolomics
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.
KeywordsStable Isotope Metabolomics Study Kinetic Isotope Effect Patient Accrual Lung Cancer Study
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.
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.
Health Insurance Portability and Accountability Act (1996).
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.
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.
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.
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.
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).
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).
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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.
US Pharmacopeia produces standards for drug safety that are effectively ratified by the FDA.
- 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
- 12.Lindon JC, Nicholson JK, Everett JR. Annual reports on NMR spectroscopy, vol. 38. San Diego: Academic Press; 1999. p. 1–88.Google Scholar
- 25.Harrigan GG, Goodacre R, editors. Metabolic profiling: its role in biomarker discovery and gene function analysis. New York: Springer; 2003.Google Scholar
- 28.Rossner B. Fundamentals of biostatistics. 6th ed. Belmont: Thomson; 2006.Google Scholar
- 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.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
- 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.Edelman RJ, Gandara DR. Lung Cancer. In: Casciato DA, editor. Manual of clinical oncology. 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2004.Google Scholar