Natalie J. Serkova

Clinical Applications of Metabolomics in Oncology: A Review

Metabolomics, an omic science in systems biology, is the global quantitative assessment of endogenous metabolites within a biological system. Either individually or grouped as a metabolomic profile, detection of metabolites is carried out in cells, tissues, or biofluids by either nuclear magnetic resonance spectroscopy or mass spectrometry. There is potential for the metabolome to have a multitude of uses in oncology, including the early detection and diagnosis of cancer and as both a predictive and pharmacodynamic marker of drug effect. Despite this, there is lack of knowledge in the oncology community regarding metabolomics and confusion about its methodologic processes, technical challenges, and clinical applications. Metabolomics, when used as a translational research tool, can provide a link between the laboratory and clinic, particularly because metabolic and molecular imaging technologies, such as positron emission tomography and magnetic resonance spectroscopic imaging, enable the discrimination of metabolic markers noninvasively in vivo. Here, we review the current and potential applications of metabolomics, focusing on its use as a biomarker for cancer diagnosis, prognosis, and therapeutic evaluation.

Phase I Pharmacologic and Biologic Study of Ramucirumab (IMC-1121B), a Fully Human Immunoglobulin G1 Monoclonal Antibody Targeting the Vascular Endothelial Growth Factor Receptor-2

PURPOSE To evaluate the safety, maximum-tolerated dose (MTD), pharmacokinetics (PKs), pharmacodynamics, and preliminary anticancer activity of ramucirumab (IMC-1121B), a fully human immunoglobulin G(1) monoclonal antibody targeting the vascular endothelial growth factor receptor (VEGFR)-2. PATIENTS AND METHODS Patients with advanced solid malignancies were treated once weekly with escalating doses of ramucirumab. Blood was sampled for PK studies throughout treatment. The effects of ramucirumab on circulating vascular endothelial growth factor-A (VEGF-A), soluble VEGFR-1 and VEGFR-2, tumor perfusion, and vascularity using dynamic contrast-enhanced magnetic resonance imaging were assessed. Results Thirty-seven patients were treated with 2 to 16 mg/kg of ramucirumab. After one patient each developed dose-limiting hypertension and deep venous thrombosis at 16 mg/kg, the next lower dose (13 mg/kg) was considered the MTD. Nausea, vomiting, headache, fatigue, and proteinuria were also noted. Four (15%) of 27 patients with measurable disease had a partial response (PR), and 11 (30%) of 37 patients had either a PR or stable disease lasting at least 6 months. PKs were characterized by dose-dependent elimination and nonlinear exposure consistent with saturable clearance. Mean trough concentrations exceeded biologically relevant target levels throughout treatment at all dose levels. Serum VEGF-A increased 1.5 to 3.5 times above pretreatment values and remained in this range throughout treatment at all dose levels. Tumor perfusion and vascularity decreased in 69% of evaluable patients. CONCLUSION Objective antitumor activity and antiangiogenic effects were observed over a wide range of dose levels, suggesting that ramucirumab may have a favorable therapeutic index in treating malignancies amenable to VEGFR-2 inhibition.

Imatinib (STI571)-Mediated Changes in Glucose Metabolism in Human Leukemia BCR-ABL-Positive Cells

The therapeutic efficacy of imatinib mesylate (Gleevec) is based on its specific inhibition of the BCR-ABL oncogene protein, a widely expressed tyrosine kinase in chronic myelogenous leukemia (CML) cells. The goal of this study was to evaluate glucose metabolism in BCR-ABL-positive cells that are sensitive to imatinib exposure. Two human BCR-ABL-positive cell lines (CML-T1 and K562) and one BCR-ABL-negative cell line (HC-1) were incubated with different imatinib concentrations for 96 hours. Magnetic resonance spectroscopy on cell acid extracts was performed to evaluate [1-13C]glucose metabolism, energy state, and changes in endogenous metabolites after incubation with imatinib. Imatinib induced a concentration-dependent inhibition of cell proliferation in CML-T1 (IC50, 0.69 ± 0.06 μmol/L) and K562 cells (IC50, 0.47 ± 0.04 μmol/L), but not in HC-1 cells. There were no metabolic changes in imatinib-treated HC-1 cells. In BCR-ABL-positive cells, the relevant therapeutic concentrations of imatinib (0.1–1.0 μmol/L) decreased glucose uptake from the media by suppressing glycolitic cell activity (C3-lactate at 0.25 mmol/L, 65% for K562 and 77% for CML-T1 versus control). Additionally, the activity of the mitochondrial Krebs cycle was increased (C4-glutamate at 0.25 μmol/L, 147% for K562 and 170% for CML-T1). The improvement in mitochondrial glucose metabolism resulted in an increased energy state (nucleoside triphosphate/nucleoside diphosphate at 0.25 μmol/L, 130% for K562 and 125% for CML-T1). Apoptosis was observed at higher concentrations. Unlike standard chemotherapeutics, imatinib, without cytocidal activity, reverses the Warburg effect in BCR-ABL-positive cells by switching from glycolysis to mitochondrial glucose metabolism, resulting in decreased glucose uptake and higher energy state.

Automated, fast and sensitive quantification of drugs in blood by liquid chromatography–mass spectrometry with on-line extraction: immunosuppressants

We developed a universal LC-mass spectrometry assay with automated online extraction (LC/LC-MS) to quantify the immunosuppressants cyclosporine, tacrolimus, sirolimus and SDZ-RAD alone or in combination in whole blood. After protein precipitation, samples were loaded on a C18 extraction column, were washed and, after activation of the column-switching valve, were backflushed onto the C8 analytical column. [M+Na]+ ions were detected in the selected ion mode. For tacrolimus, sirolimus and SDZ-RAD, the assay was linear from 0.25 to 100 microg/l and for cyclosporine from 7.5 to 1250 microg/l (all r2>0.99). Analytical recovery was >85% and, in general, inter-day, intra-day variability for precision and accuracy were <10%.

Pattern recognition and biomarker validation using quantitative 1H-NMR-based metabolomics

The collection of global metabolic data and their interpretation (both spectral and biochemical) using modern spectroscopic techniques and appropriate statistical approaches, are known as ‘metabolic profiling’, ‘metabonomics’ or ‘metabolomics’. This review addresses 1H-nuclear magnetic resonance (NMR)-based metabolomic principles and their application in biomedical science, with special emphasis on their potential in translational research in transplantation, oncology, and drug toxicity or discovery. Various steps in metabolomics analysis are described in order to illustrate the types of biological samples, their respective handling and preparation for 1H-NMR analysis; provide a rationale for using pattern-recognition techniques (spectral database concept) versus quantitative 1H-NMR-based metabolomics (metabolite database concept); and identify necessary technological and logistical future developments that will allow 1H-NMR-based metabolomics to become an established tool in biomedical research and patient care.

Therapeutic targets and biomarkers identified in cancer choline phospholipid metabolism

Choline phospholipid metabolism is altered in a wide variety of cancers. The choline metabolite profile of tumors and cancer cells is characterized by an elevation of phosphocholine and total choline-containing compounds. Noninvasive magnetic resonance spectroscopy can be used to detect this elevation as an endogenous biomarker of cancer, or as a predictive biomarker for monitoring tumor response to novel targeted therapies. The enzymes directly causing this elevation, such as choline kinase, phospholipase C and phospholipase D may provide molecular targets for anticancer therapies. Signal transduction pathways that are activated in cancers, such as those mediated by the receptor tyrosine kinases breakpoint cluster region-abelson (Bcr-Abl), c-KIT or epidermal growth factor receptor (EGFR), correlate with the alterations in choline phospholipid metabolism of cancers, and also offer molecular targets for specific anticancer therapies. This review summarizes recently discovered molecular targets in choline phospholipid metabolism and signal transduction pathways, which may lead to novel anticancer therapies potentially being monitored by magnetic resonance spectroscopy techniques.

Toxicity of MRI and CT contrast agents

Anatomical and physiological imaging using CT and MRI are playing a critical role in patients’ diagnosis, disease characterization and treatment planning. CT- and MRI-based protocols increasingly require an injection of iodinated CT and gadolinium (Gd)-based MRI contrast media. Although routinely used in clinical practice, iodinated and to a less extent Gd-based contrast media possess side effects: life-threatening contrast-induced nephropathy (CIN) is associated with CT and nephrogenic systemic fibrosis (NSF) with MRI contrast agents. CIN is defined as an acute decline in renal functions (serum creatinine increase > 0.5 mg/dl) after administration of iodinated contrast media. Patients with moderate-to-severe chronic kidney disease are considered the highest risk group for development of CIN. CIN is more common with ionic high-osmolar contrast CT media. NSF is a rare condition characterized by the formation of connective tissue in the skin and systemically in the lung, liver, heart and kidney. Patients with end stage kidney disease, acute kidney injury and stage 4 – 5 chronic kidney disease are at a high risk for NSF. The nonionic linear Gd-chelates are associated with the highest risk of NSF. This review summarizes the incidence, symptoms, safety profile of various CT and MRI contrast agents based on their physiochemical properties.

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma 1H-nuclear magnetic resonance quantitative metabolomics and computational analysis

Metabolomics is an emerging component of systems biology that may be a viable strategy for the identification and validation of physiologically relevant biomarkers. Nuclear magnetic resonance (NMR) spectroscopy allows for establishing quantitative data sets for multiple endogenous metabolites without preconception. Sepsis-induced acute lung injury (ALI) is a complex and serious illness associated with high morbidity and mortality for which there is presently no effective pharmacotherapy. The goal of this study was to apply ¹H-NMR based quantitative metabolomics with subsequent computational analysis to begin working towards elucidating the plasma metabolic changes associated with sepsis-induced ALI. To this end, this pilot study generated quantitative data sets that revealed differences between patients with ALI and healthy subjects in the level of the following metabolites: total glutathione, adenosine, phosphatidylserine, and sphingomyelin. Moreover, myoinositol levels were associated with acute physiology scores (APS) (ρ = -0.53, P = 0.05, q = 0.25) and ventilator-free days (ρ = -0.73, P = 0.005, q = 0.01). There was also an association between total glutathione and APS (ρ = 0.56, P = 0.04, q = 0.25). Computational network analysis revealed a distinct metabolic pathway for each metabolite. In summary, this pilot study demonstrated the feasibility of plasma ¹H-NMR quantitative metabolomics because it yielded a physiologically relevant metabolite data set that distinguished sepsis-induced ALI from health. In addition, it justifies the continued study of this approach to determine whether sepsis-induced ALI has a distinct metabolic phenotype and whether there are predictive biomarkers of severity and outcome in these patients.

The Metabolites Citrate, Myo-Inositol, and Spermine Are Potential Age-Independent Markers of Prostate Cancer in Human Expressed Prostatic Secretions

Due to specific physiological functions, prostatic tissues and fluids have unique metabolic profiles. In this study, proton nuclear magnetic resonance spectroscopy (1H‐NMRS) is used to assess potential metabolic markers of prostate cancer (PCa) in human expressed prostatic secretions (EPS).

Sirolimus, but not the structurally related RAD (everolimus), enhances the negative effects of cyclosporine on mitochondrial metabolism in the rat brain

Clinical studies have shown enhancement of cyclosporine toxicity when co‐administered with the immunosuppressant sirolimus. We evaluated the biochemical mechanisms underlying the sirolimus/cyclosporine interaction on rat brain metabolism using magnetic resonance spectroscopy (MRS) and compared the effects of sirolimus with those of the structurally related RAD. Two‐week‐old rats (25 g) were allocated to the following treatment groups (all n=6): I. control, II. cyclosporine (10 mg kg−1 d−1), III. sirolimus (3 mg kg−1 d−1), IV. RAD (3 mg kg−1 d−1), V. cyclosporine+sirolimus and VI. cyclosporine+RAD. Drugs were administered by oral gavage for 6 days. Twelve hours after the last dose, metabolic changes were assessed in brain tissue extracts using multinuclear MRS. Cyclosporine significantly inhibited mitochondrial glucose metabolism (glutamate: 78±6% of control; GABA: 67±12%; NAD+: 76±3%; P<0.05), but increased lactate production. Sirolimus and RAD inhibited cytosolic glucose metabolism via lactate production (sirolimus: 81±3% of control, RAD: 69±2%; P<0.02). Sirolimus enhanced cyclosporine‐induced inhibition of mitochondrial glucose metabolism (glutamate: 60±4%; GABA: 59±8%; NAD+: 45±5%; P<0.02 versus cyclosporine alone). Lactate production was significantly reduced. In contrast, RAD antagonized the effects of cyclosporine (glutamate, GABA, and NAD+, not significantly different from controls). The results can partially be explained by pharmacokinetic interactions: co‐administration increased the distribution of cyclosporine and sirolimus into brain tissue, while co‐administration with RAD decreased cyclosporine brain tissue concentrations. In addition RAD, but not sirolimus, distributed into brain mitochondria. The combination of cyclosporine/RAD compares favourably to cyclosporine/sirolimus in regards to their effects on brain high‐energy metabolism and tissue distribution in the rat.