Metabolic Labeling of Cultured Mammalian Cells for Stable Isotope-Resolved Metabolomics: Practical Aspects of Tissue Culture and Sample Extraction

Stable isotope-resolved metabolomics (SIRM) methods are used increasingly by cancer researchers to probe metabolic pathways and identify vulnerabilities in cancer cells. Analytical and computational advances are being made constantly, but tissue culture and sample extraction procedures are often variable and not elaborated in the literature. This chapter discusses basic aspects of tissue culture practices as they relate to the use of stable isotope tracers and provides a detailed metabolic labeling and metabolite extraction procedure designed to maximize the amount of information that can be obtained from a single tracer experiment.

Quantification of Isotopologues of Amino Acids by Multiplexed Stable Isotope-Resolved Metabolomics Using Ultrahigh-Resolution Mass Spectrometry Coupled with Direct Infusion

Stable isotope-resolved metabolomics (SIRM) is increasingly used among researchers for metabolic studies including amino acid metabolism. However, the classical GC- or HPLC-based methods for amino acid quantification do not meet the needs for multiplexed stable isotope-enriched analysis by ultrahigh-resolution Fourier transform mass spectrometry (UHR-FTMS). This is due to insufficient acquisition time during chromatographic separations and large dynamic range in concentrations of analytes, which compromises detection and quantification of the numerous metabolite isotopologues present in crude extracts. This chapter discusses a modified ethyl chloroformate derivatization method to enable rapid quantitative analysis of stable isotope-enriched amino acids using direct infusion ion introduction coupled with UHR-FTMS.

NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism

There is considerable interest in defining metabolic reprogramming in human diseases, which is recognized as a hallmark of human cancer. Although radiotracers have a long history in specific metabolic studies, stable isotope-enriched precursors coupled with modern high resolution mass spectrometry and NMR spectroscopy have enabled systematic mapping of metabolic networks and fluxes in cells, tissues and living organisms including humans. These analytical platforms are high in information content, are complementary and cross-validating in terms of compound identification, quantification, and isotope labeling pattern analysis of a large number of metabolites simultaneously. Furthermore, new developments in chemoselective derivatization and in vivo spectroscopy enable tracking of labile/low abundance metabolites and metabolic kinetics in real-time. Here we review developments in Stable Isotope Resolved Metabolomics (SIRM) and recent applications in cancer metabolism using a wide variety of stable isotope tracers that probe both broad and specific aspects of cancer metabolism required for proliferation and survival.

New methods to identify high peak density artifacts in Fourier transform mass spectra and to mitigate their effects on high-throughput metabolomic data analysis

INTRODUCTION

Direct injection Fourier-transform mass spectrometry (FT-MS) allows for the high-throughput and high-resolution detection of thousands of metabolite-associated isotopologues. However, spectral artifacts can generate large numbers of spectral features (peaks) that do not correspond to known compounds. Misassignment of these artifactual features creates interpretive errors and limits our ability to discern the role of representative features within living systems.

OBJECTIVES

Our goal is to develop rigorous methods that identify and handle spectral artifacts within the context of high-throughput FT-MS-based metabolomics studies.

RESULTS

We observed three types of artifacts unique to FT-MS that we named high peak density (HPD) sites: fuzzy sites, ringing and partial ringing. While ringing artifacts are well-known, fuzzy sites and partial ringing have not been previously well-characterized in the literature. We developed new computational methods based on comparisons of peak density within a spectrum to identify regions of spectra with fuzzy sites. We used these methods to identify and eliminate fuzzy site artifacts in an example dataset of paired cancer and non-cancer lung tissue samples and evaluated the impact of these artifacts on classification accuracy and robustness.

CONCLUSION

Our methods robustly identified consistent fuzzy site artifacts in our FT-MS metabolomics spectral data. Without artifact identification and removal, 91.4% classification accuracy was achieved on an example lung cancer dataset; however, these classifiers rely heavily on artifactual features present in fuzzy sites. Proper removal of fuzzy site artifacts produces a more robust classifier based on non-artifactual features, with slightly improved accuracy of 92.4% in our example analysis.

Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS

The extensive range of chemical structures, wide range of abundances, and chemical instability of metabolites present in the metabolome pose major analytical challenges that are difficult to address with existing technologies. To address these issues, one approach is to target a subset of metabolites that share a functional group, such as ketones and aldehydes, using chemoselective tagging. Here we report a greatly improved chemoselective method for the quantitative analysis of hydrophilic and hydrophobic carbonyl-containing metabolites directly in biological samples. This method is based on direct tissue or cells extraction with simultaneous derivatization of stable and labile carbonylated metabolites using N-[2-(aminooxy)ethyl]-N,N-dimethyl-1-dodecylammonium (QDA) and ¹³CD₃ labeled QDA. We combined innovations of direct quenching of biological sample with frozen derivatization conditions under the catalyst N,N-dimethyl-p-phenylenediamine, which facilitated the formation of oxime stable-isotope ion pairs differing by m/z 4.02188 while minimizing metabolite degradation. The resulting oximes were extracted by HyperSep C8 tips to remove interfering compounds, and the products were detected using nano-electrospray ionization interfaced with a Thermo Fusion mass spectrometer. The quaternary ammonium tagging greatly increased electrospray MS detection sensitivity and the signature ions pairs enabled simple identification of carbonyl compounds. The improved method showed the lower limits of quantification for carbonyl standards to be in the range of 0.20-2 nM, with linearity of R² > 0.99 over 4 orders of magnitude. We have applied the method to assign 66 carbonyls in mouse tumor tissues, many of which could not be assigned solely by accurate mass and tandem MS. Fourteen of the metabolites were quantified using authentic standards. We also demonstrated the suitability of this method for determining ¹³C labeled isotopologues of carbonyl metabolites in ¹³C₆-glucose-based stable isotope-resolved metabolomic (SIRM) studies.

Acute loss of iron-sulfur clusters results in metabolic reprogramming and generation of lipid droplets in mammalian cells

Iron-sulfur (Fe-S) clusters are ancient cofactors in cells and participate in diverse biochemical functions, including electron transfer and enzymatic catalysis. Although cell lines derived from individuals carrying mutations in the Fe-S cluster biogenesis pathway or siRNA-mediated knockdown of the Fe-S assembly components provide excellent models for investigating Fe-S cluster formation in mammalian cells, these experimental strategies focus on the consequences of prolonged impairment of Fe-S assembly. Here, we constructed and expressed dominant-negative variants of the primary Fe-S biogenesis scaffold protein iron-sulfur cluster assembly enzyme 2 (ISCU2) in human HEK293 cells. This approach enabled us to study the early metabolic reprogramming associated with loss of Fe-S-containing proteins in several major cellular compartments. Using multiple metabolomics platforms, we observed a ∼12-fold increase in intracellular citrate content in Fe-S-deficient cells, a surge that was due to loss of aconitase activity. The excess citrate was generated from glucose-derived acetyl-CoA, and global analysis of cellular lipids revealed that fatty acid biosynthesis increased markedly relative to cellular proliferation rates in Fe-S-deficient cells. We also observed intracellular lipid droplet accumulation in both acutely Fe-S-deficient cells and iron-starved cells. We conclude that deficient Fe-S biogenesis and acute iron deficiency rapidly increase cellular citrate concentrations, leading to fatty acid synthesis and cytosolic lipid droplet formation. Our findings uncover a potential cause of cellular steatosis in nonadipose tissues.

Selenium toxicity to survival and reproduction of Collembola and Enchytraeids in a sandy loam soil

We investigated the toxicity of selenium (Se) to the soil invertebrates Folsomia candida (Collembola) and Enchytraeus crypticus (potworm). Studies were designed to generate ecotoxicological benchmarks for developing ecological soil screening levels (Eco-SSLs) for risk assessments of contaminated soils. For the present studies, we selected Sassafras sandy loam, an aerobic upland soil with soil characteristics (low levels of clay and organic matter, soil pH adjusted from 5.2 to 7.1) that support high relative bioavailability of the anionic Se species that is typically found in aerobic soil. The Se was amended into soil as sodium selenate, subjected to weathering and aging using 21 d of alternating cycles of air-drying/rehydration to 60% of the water-holding capacity of the Sassafras sandy loam soil, under ambient greenhouse conditions. Effective concentrations at 20 and 50% (EC20 and EC50) levels for production of juveniles (reproduction) were 4.7 and 10.9 mg of Se/kg of soil (dry mass basis), respectively, for Collembola, and 4.4 and 6.2 mg/kg, respectively, for the potworms. The data enabled the derivation of toxicity benchmarks, contributing to the development of a soil invertebrate-based Eco-SSL of 4.1 mg/kg for Se. Environ Toxicol Chem 2018;37:846-853. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

Correction: Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS

Correction for 'Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS' by Pan Deng, et al., Analyst, 2018, 143, 311-322.

Probing the metabolic phenotype of breast cancer cells by multiple tracer stable isotope resolved metabolomics

Breast cancers vary by their origin and specific set of genetic lesions, which gives rise to distinct phenotypes and differential response to targeted and untargeted chemotherapies. To explore the functional differences of different breast cell types, we performed Stable Isotope Resolved Metabolomics (SIRM) studies of one primary breast (HMEC) and three breast cancer cells (MCF-7, MDAMB-231, and ZR75-1) having distinct genotypes and growth characteristics, using 13C6-glucose, 13C-1+2-glucose, 13C5,15N2-Gln, 13C3-glycerol, and 13C8-octanoate as tracers. These tracers were designed to probe the central energy producing and anabolic pathways (glycolysis, pentose phosphate pathway, Krebs Cycle, glutaminolysis, nucleotide synthesis and lipid turnover). We found that glycolysis was not associated with the rate of breast cancer cell proliferation, glutaminolysis did not support lipid synthesis in primary breast or breast cancer cells, but was a major contributor to pyrimidine ring synthesis in all cell types; anaplerotic pyruvate carboxylation was activated in breast cancer versus primary cells. We also found that glucose metabolism in individual breast cancer cell lines differed between in vitro cultures and tumor xenografts, but not the metabolic distinctions between cell lines, which may reflect the influence of tumor architecture/microenvironment.

Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM)

Metabolic reprogramming is a hallmark of cancer. The changes in metabolism are adaptive to permit proliferation, survival, and eventually metastasis in a harsh environment. Stable isotope-resolved metabolomics (SIRM) is an approach that uses advanced approaches of NMR and mass spectrometry to analyze the fate of individual atoms from stable isotope-enriched precursors to products to deduce metabolic pathways and networks. The approach can be applied to a wide range of biological systems, including human subjects. This review focuses on the applications of SIRM to cancer metabolism and its use in understanding drug actions.

Abstract 2502: Liquid diet introduction of tracers into mice for stable isotope-resolved metabolomics (SIRM) investigations

Tracer-based mapping of metabolic networks in vivo is a powerful approach for revealing metabolic reprogramming in human cancer. However, current in vivo labeling techniques for model animals face important challenges including insufficient depth of pathway coverage (e.g. inability to detect labeled nucleotides, proteins, and lipids) and stress-related artifacts. Here, we report stress-free administration of 13C6-glucose via liquid diet into mice. 13C enrichment was observed in metabolites of glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleobases, UDP-sugars, as well as macromolecules glycogen, lipids, and proteins from major organs in NSG mice. We have applied the liquid diet method to map the glucose metabolic networks in NSCLC tumors in a patient-derived xenograft (PDX) model. We observed a high enrichment in the metabolites of glycolysis, Krebs cycle, and PPP as well as de novo synthesized nucleotides and amino acids by IC-UHR-FTMS analysis. Lung PDX displayed unexpected metabolic complexity, such as the use of pyruvate to fuel anaplerosis as well as gluconeogenesis. We also found high 13C enrichment in both tumor and plasma glutamine, which implies that glutamine in the PDX tumors largely came from other organs via the blood rather than being synthesized in situ. Our data showed that liquid diet is an effective and noninvasive means for comprehensive analysis of glucose-associated metabolic networks in human tumor xenografts, which can also be extended to SIRM studies with other fuel sources.

Acknowledgements: This work was supported in part by grants: 1R01ES022191-01 (to TWMF and RMH), 1P01CA163223-01A1 (to ANL and TWMF), and 1U24DK097215-01A1 (to RMH, TWMF, and ANL)

R.C. Sun was supported by a T32 training grant to M. Vore (5T32ES007266-25)

Citation Format: Ramon C. Sun, Marc O. Warmoes, Ye Yang, Pan Deng, Qiushi Sun, Andrew N. Lane, Richard M. Higashi, Teresa W-M Fan. Liquid diet introduction of tracers into mice for stable isotope-resolved metabolomics (SIRM) investigations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2502. doi:10.1158/1538-7445.AM2017-2502

Chloroformate derivatization for tracing the fate of Amino acids in cells and tissues by multiple stable isotope resolved metabolomics (mSIRM)

Amino acids have crucial roles in central metabolism, both anabolic and catabolic. To elucidate these roles, steady-state concentrations of amino acids alone are insufficient, as each amino acid participates in multiple pathways and functions in a complex network, which can also be compartmentalized. Stable Isotope-Resolved Metabolomics (SIRM) is an approach that uses atom-resolved tracking of metabolites through biochemical transformations in cells, tissues, or whole organisms. Using different elemental stable isotopes to label multiple metabolite precursors makes it possible to resolve simultaneously the utilization of these precursors in a single experiment. Conversely, a single precursor labeled with two (or more) different elemental isotopes can trace the allocation of e.g. C and N atoms through the network. Such dual-label experiments however challenge the resolution of conventional mass spectrometers, which must distinguish the neutron mass differences among different elemental isotopes. This requires ultrahigh resolution Fourier transform mass spectrometry (UHR-FTMS). When combined with direct infusion nano-electrospray ion source (nano-ESI), UHR-FTMS can provide rapid, global, and quantitative analysis of all possible mass isotopologues of metabolites. Unfortunately, very low mass polar metabolites such as amino acids can be difficult to analyze by current models of UHR-FTMS, plus the high salt content present in typical cell or tissue polar extracts may cause unacceptable ion suppression for sources such as nano-ESI. Here we describe a modified method of ethyl chloroformate (ECF) derivatization of amino acids to enable rapid quantitative analysis of stable isotope labeled amino acids using nano-ESI UHR-FTMS. This method showed excellent linearity with quantifiable limits in the low nanomolar range represented in microgram quantities of biological specimens, which results in extracts with total analyte abundances in the low to sub-femtomole range. We have applied this method to profile amino acids and their labeling patterns in ¹³C and ²H doubly labeled PC9 cell extracts, cancerous and non-cancerous tissue extracts from a lung cancer patient and their protein hydrolysates as well as plasma extracts from mice fed with a liquid diet containing ¹³C₆-glucose (Glc). The multi-element isotopologue distributions provided key insights into amino acid metabolism and intracellular pools in human lung cancer tissues in high detail. The ¹³C labeling of Asp and Glu revealed de novo synthesis of these amino acids from ¹³C₆-Glc via the Krebs cycle, specifically the elevated level of ¹³C₃-labeled Asp and Glu in cancerous versus non-cancerous lung tissues was consistent with enhanced pyruvate carboxylation. In addition, tracking the fate of double tracers, (¹³C₆-Glc + ²H₂-Gly or ¹³C₆-Glc + ²H₃-Ser) in PC9 cells clearly resolved pools of Ser and Gly synthesized de novo from ¹³C₆-Glc (¹³C₃-Ser and ¹³C₂-Gly) versus Ser and Gly derived from external sources (²H₃-Ser, ²H₂-Gly). Moreover the complex ²H labeling patterns of the latter were results of Ser and Gly exchange through active Ser-Gly one-carbon metabolic pathway in PC9 cells.

NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry

Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.

Distinctly perturbed metabolic networks underlie differential tumor tissue damages induced by immune modulator β-glucan in a two-case ex vivo non-small-cell lung cancer study

Cancer and stromal cell metabolism is important for understanding tumor development, which highly depends on the tumor microenvironment (TME). Cell or animal models cannot recapitulate the human TME. We have developed an ex vivo paired cancerous (CA) and noncancerous (NC) human lung tissue approach to explore cancer and stromal cell metabolism in the native human TME. This approach enabled full control of experimental parameters and acquisition of individual patient's target tissue response to therapeutic agents while eliminating interferences from genetic and physiological variations. In this two-case study of non-small-cell lung cancer, we performed stable isotope-resolved metabolomic (SIRM) experiments on paired CA and NC lung tissues treated with a macrophage activator β-glucan and (13)C6-glucose, followed by ion chromatography-Fourier transform mass spectrometry (IC-FTMS) and nuclear magnetic resonance (NMR) analyses of (13)C-labeling patterns of metabolites. We demonstrated that CA lung tissue slices were metabolically more active than their NC counterparts, which recapitulated the metabolic reprogramming in CA lung tissues observed in vivo. We showed β-glucan-enhanced glycolysis, Krebs cycle, pentose phosphate pathway, antioxidant production, and itaconate buildup in patient UK021 with chronic obstructive pulmonary disease (COPD) and an abundance of tumor-associated macrophages (TAMs) but not in UK049 with no COPD and much less macrophage infiltration. This metabolic response of UK021 tissues was accompanied by reduced mitotic index, increased necrosis, and enhaced inducible nitric oxide synthase (iNOS) expression. We surmise that the reprogrammed networks could reflect β-glucan M1 polarization of human macrophages. This case study presents a unique opportunity for investigating metabolic responses of human macrophages to immune modulators in their native microenvironment on an individual patient basis.

Abstract 4271: Beta-glucan activates macrophages in human NSCLC demonstrated by Stable Isotope Resolved Metabolomics (SIRM)

Introduction: We use SIRM to evaluate metabolic reprogramming of lung cancer cells in monoculture, in mouse xenograft/explant models, and in NSCLC patients in situ (1,2). We have now extended the range of models to fresh human tissue slices, which retain the original tissue architecture and heterogeneity with a paired benign versus cancer tissue design under defined cell culture conditions. β-glucan is a polysaccharide that repolarizes tumor-associated macrophages (TAMs) from the M2 to the M1 phenotype in mice (3). Here we report the activation of TAMs in human NSCLC tissue slices.

Experimental: Freshly resected paired tissue slices from individual patients (approx. 1 mm or less thick and 5-40 mg wet weight) were incubated ± particulate β-glucan in standard cell culture conditions, with gentle rocking to enable efficient gas, nutrient, and waste product exchange. Tissue slices could be maintained metabolically viable for at least 48 h of incubation. The metabolic activity was determined by measuring the uptake and transformation of 13C and/or 15N-enriched common nutrient tracers such as glucose and glutamine, using high resolution mass spectrometry, GC-MS, and NMR after a period of incubation (2).

Findings: Time-course analysis of the slices by NMR, MS, and histology revealed that NSCLC tissue slices, both benign and tumorous, retained their architecture and a broad spectrum of metabolic activities. Glucose and glutamine metabolism was reprogrammed in the tumor relative to the paired benign tissues ex vivo, as the in vivo case. The paired tissues from different patients showed significantly different metabolic responses to β-glucan, as expected

Conclusions: This platform offers a human tissue model for preclinical studies on metabolic reprogramming of human cancer and stromal cells in their tissue context, and response to drug treatment (4). As the microenvironment of the target human tissue is maintained, including the resident immune cells, individualized response to immune-active agents can be determined in a clinically relevant setting.

Supported by NCI P01CA163223-01 and NIEHS 1R01ES022191-01

1. Lane, A.N., Fan, T.W.-M., Bousamra II, M., et al. (2011) Clinical Applications of Stable Isotope-Resolved Metabolomics (SIRM) in Non-Small Cell Lung Cancer. Omics, 15, 173-182.

2. Sellers, K., Fox, M.P., Bousamra, M., II, et al. (2015) Pyruvate carboxylase is critical for non-small-cell lung cancer proliferation. Journal of Clinical Investigation, 125, 687-698.

3. Liu, M., Luo, F., Ding, C., et al. (2015) Particulate β-Glucan Converts Immunosuppressive Macrophages into M1 Phenotype Through Dectin-1-induced Syk-Card9-Erk Pathway and Raf-1-c-Maf Pathway. J. Immunol., 195, 5055-5065.

4. Xie, H., Hanai, J., Ren, et al. (2014) Targeting lactate dehydrogenase-A (LDH-A) inhibits tumorigenesis and tumor progression in mouse models of lung cancer and impacts tumor initiating cells. Cell Metabolism 19, 795-809

Citation Format: Teresa W-M Fan, Andrew N. Lane, Jun Yan, Richard M. Higashi, Jeremiah T. Martin, Michael Bousamra. Beta-glucan activates macrophages in human NSCLC demonstrated by Stable Isotope Resolved Metabolomics (SIRM). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4271.

Preclinical models for interrogating drug action in human cancers using Stable Isotope Resolved Metabolomics (SIRM)

AIMS

In this review we compare the advantages and disadvantages of different model biological systems for determining the metabolic functions of cells in complex environments, how they may change in different disease states, and respond to therapeutic interventions.

BACKGROUND

All preclinical drug-testing models have advantages and drawbacks. We compare and contrast established cell, organoid and animal models with ex vivo organ or tissue culture and in vivo human experiments in the context of metabolic readout of drug efficacy. As metabolism reports directly on the biochemical state of cells and tissues, it can be very sensitive to drugs and/or other environmental changes. This is especially so when metabolic activities are probed by stable isotope tracing methods, which can also provide detailed mechanistic information on drug action. We have developed and been applying Stable Isotope-Resolved Metabolomics (SIRM) to examine metabolic reprogramming of human lung cancer cells in monoculture, in mouse xenograft/explant models, and in lung cancer patients in situ (Lane et al. 2011; T. W. Fan et al. 2011; T. W-M. Fan et al. 2012; T. W. Fan et al. 2012; Xie et al. 2014b; Ren et al. 2014a; Sellers et al. 2015b). We are able to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by O. Warburg (Warburg 1923), which retain the native tissue architecture and heterogeneity with a paired benign versus cancer design under defined cell culture conditions. This platform offers an unprecedented human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (Xie et al. 2014a). As the microenvironment of the target human tissue is retained and individual patient's response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments.

CONCLUSIONS AND FUTURE WORK

Development of ex vivo human tissue and animal models with humanized organs including bone marrow and liver show considerable promise for analyzing drug responses that are more relevant to humans. Similarly using stable isotope tracer methods with these improved models in advanced stages of the drug development pipeline, in conjunction with tissue biopsy is expected significantly to reduce the high failure rate of experimental drugs in Phase II and III clinical trials.

An obligatory role for neurotensin in high-fat-diet-induced obesity

Obesity and its associated comorbidities (for example, diabetes mellitus and hepatic steatosis) contribute to approximately 2.5 million deaths annually and are among the most prevalent and challenging conditions confronting the medical profession. Neurotensin (NT; also known as NTS), a 13-amino-acid peptide predominantly localized in specialized enteroendocrine cells of the small intestine and released by fat ingestion, facilitates fatty acid translocation in rat intestine, and stimulates the growth of various cancers. The effects of NT are mediated through three known NT receptors (NTR1, 2 and 3; also known as NTSR1, 2, and NTSR3, respectively). Increased fasting plasma levels of pro-NT (a stable NT precursor fragment produced in equimolar amounts relative to NT) are associated with increased risk of diabetes, cardiovascular disease and mortality; however, a role for NT as a causative factor in these diseases is unknown. Here we show that NT-deficient mice demonstrate significantly reduced intestinal fat absorption and are protected from obesity, hepatic steatosis and insulin resistance associated with high fat consumption. We further demonstrate that NT attenuates the activation of AMP-activated protein kinase (AMPK) and stimulates fatty acid absorption in mice and in cultured intestinal cells, and that this occurs through a mechanism involving NTR1 and NTR3 (also known as sortilin). Consistent with the findings in mice, expression of NT in Drosophila midgut enteroendocrine cells results in increased lipid accumulation in the midgut, fat body, and oenocytes (specialized hepatocyte-like cells) and decreased AMPK activation. Remarkably, in humans, we show that both obese and insulin-resistant subjects have elevated plasma concentrations of pro-NT, and in longitudinal studies among non-obese subjects, high levels of pro-NT denote a doubling of the risk of developing obesity later in life. Our findings directly link NT with increased fat absorption and obesity and suggest that NT may provide a prognostic marker of future obesity and a potential target for prevention and treatment.

SDHB-Deficient Cancers: The Role of Mutations That Impair Iron Sulfur Cluster Delivery

BACKGROUND

Mutations in the Fe-S cluster-containing SDHB subunit of succinate dehydrogenase cause familial cancer syndromes. Recently the tripeptide motif L(I)YR was identified in the Fe-S recipient protein SDHB, to which the cochaperone HSC20 binds.

METHODS

In order to characterize the metabolic basis of SDH-deficient cancers we performed stable isotope-resolved metabolomics in a novel SDHB-deficient renal cell carcinoma cell line and conducted bioinformatics and biochemical screening to analyze Fe-S cluster acquisition and assembly of SDH in the presence of other cancer-causing SDHB mutations.

RESULTS

We found that the SDHBR46Q mutation in UOK269 cells disrupted binding of HSC20, causing rapid degradation of SDHB. In the absence of SDHB, respiration was undetectable in UOK269 cells, succinate was elevated to 351.4 ± 63.2 nmol/mg cellular protein, and glutamine became the main source of TCA cycle metabolites through reductive carboxylation.Furthermore, HIF1α, but not HIF2α, increased markedly and the cells showed a strong DNA CpG island methylatorphenotype (CIMP). Biochemical and bioinformatic screening revealed that 37% of disease-causing missense mutations in SDHB were located in either the L(I)YR Fe-S transfer motifs or in the 11 Fe-S cluster-ligating cysteines.

CONCLUSIONS

These findings provide a conceptual framework for understanding how particular mutations disproportionately cause the loss of SDH activity, resulting in accumulation of succinate and metabolic remodeling in SDHB cancer syndromes.

Applications of NMR spectroscopy to systems biochemistry

The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.

Stable Isotope Resolved Metabolomics Studies in Ex Vivo TIssue Slices

An important component of this methodology is to assess the role of the tumor microenvironment on tumor growth and survival. To tackle this problem, we have adapted the original approach of Warburg ¹, by combining thin tissue slices with Stable Isotope Resolved Metabolomics (SIRM) to determine detailed metabolic activity of human tissues. SIRM enables the tracing of metabolic transformations of source molecules such as glucose or glutamine over defined time periods, and is a requirement for detailed pathway tracing and flux analysis. In our approach, we maintain freshly resected tissue slices (both cancerous and non- cancerous from the same organ of the same subject) in cell culture media, and treat with appropriate stable isotope-enriched nutrients, e.g.¹³C₆-glucose or ¹³C₅, ¹⁵N₂ -glutamine. These slices are viable for at least 24 h, and make it possible to eliminate systemic influence on the target tissue metabolism while maintaining the original 3D cellular architecture. It is therefore an excellent pre-clinical platform for assessing the effect of therapeutic agents on target tissue metabolism and their therapeutic efficacy on individual patients ^2,3.

Dectin-1 Activation by a Natural Product β-Glucan Converts Immunosuppressive Macrophages into an M1-like Phenotype

Tumor-associated macrophages (TAM) with an alternatively activated phenotype have been linked to tumor-elicited inflammation, immunosuppression, and resistance to chemotherapies in cancer, thus representing an attractive target for an effective cancer immunotherapy. In this study, we demonstrate that particulate yeast-derived β-glucan, a natural polysaccharide compound, converts polarized alternatively activated macrophages or immunosuppressive TAM into a classically activated phenotype with potent immunostimulating activity. This process is associated with macrophage metabolic reprograming with enhanced glycolysis, Krebs cycle, and glutamine utilization. In addition, particulate β-glucan converts immunosuppressive TAM via the C-type lectin receptor dectin-1-induced spleen tyrosine kinase-Card9-Erk pathway. Further in vivo studies show that oral particulate β-glucan treatment significantly delays tumor growth, which is associated with in vivo TAM phenotype conversion and enhanced effector T cell activation. Mice injected with particulate β-glucan-treated TAM mixed with tumor cells have significantly reduced tumor burden with less blood vascular vessels compared with those with TAM plus tumor cell injection. In addition, macrophage depletion significantly reduced the therapeutic efficacy of particulate β-glucan in tumor-bearing mice. These findings have established a new paradigm for macrophage polarization and immunosuppressive TAM conversion and shed light on the action mode of β-glucan treatment in cancer.

Abstract 3199: Stable isotope resolved metabolomics (SIRM) on fresh human tissues as a preclinical drug testing platform

Introduction: All preclinical drug testing models have advantages and drawbacks. We have been using SIRM to evaluate metabolic reprogramming of lung cancer cells in monoculture, in mouse xenograft/explant models, and in NSCLC patients in situ (1), and to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by Warburg (2), which retain the original tissue architecture and heterogeneity with a paired benign versus cancer design under controlled cell culture conditions.

Experimental: Freshly resected tissue slices from individuals (ca. 1 mm or less thick and 5-40 mg wet weight) were incubated in standard cell culture conditions with gentle rocking for efficient gas, nutrient and waste product exchange. The metabolic activity was determined by measuring the uptake and transformation of 13C and/or 15N-enriched nutrient tracers such as glucose and glutamine, using high-resolution MS, GC-MS, and NMR after a period of incubation. Acute metabolic and histologic response to inhibitors or drugs was readily detected in treated tissue slices.

Findings: Analysis at different time points by NMR, MS and histology shows that the NSCLC tissue slices, both benign and tumorous, retained their architecture and remained metabolically viable for at least 48 h of incubation. Glucose and glutamine metabolism was reprogrammed in the tumor relative to the paired benign tissues. The paired tissue also showed very different responses to Se-containing compounds when incubated at the IC50 established for cell lines. After 24 h of incubation, large scale necrosis was evident in the tumor, but not in the benign slices, which was accompanied by large changes in metabolic activities observed by SIRM analysis.

Conclusions: This platform offers a human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (3). As the microenvironment of the target human tissue is retained and individualized response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments.

Supported by NCI P01CA163223-01A1 and NIEHS 1R01ES022191-01

1. Lane, A.N., Fan, T.W.-M., Bousamra II, M., Higashi, R.M., Yan, J. and Miller, D.M. (2011) Clinical Applications of Stable Isotope-Resolved Metabolomics (SIRM) in Non-Small Cell Lung Cancer. Omics, 15, 173-182.

2. Warburg, O. (1923) Versuche an überlebendem Carcinomgewebe (Methoden). Biochem. Zeitschr., 142, 317-333.

3. Xie, H., Hanai, J., Ren, J.-G., Kats, L., Burgess, K., Bhargava, P., Signoretti, S., Billiard, J., Duffy, K.J., Grant, A. et al. (2014) Targeting lactate dehydrogenase-A (LDH-A) inhibits tumorigenesis and tumor progression in mouse models of lung cancer and impacts tumor initiating cells. Cell Metabolism 19, 795-809.

Citation Format: Andrew N. Lane, Teresa W-M Fan, Alexander C. Belshoff, Richard M. Higashi, Jeremiah Martin, Michael Bousamra. Stable isotope resolved metabolomics (SIRM) on fresh human tissues as a preclinical drug testing platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3199. doi:10.1158/1538-7445.AM2015-3199