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      Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool

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          Abstract

          Background

          Colorectal cancers (CRC) are associated with perturbations in cellular amino acids, nucleotides, pentose-phosphate pathway carbohydrates, and glycolytic, gluconeogenic, and tricarboxylic acid intermediates. A non-targeted global metabolome approach was utilized for exploring human CRC, adjacent mucosa, and stool. In this pilot study, we identified metabolite profile differences between CRC and adjacent mucosa from patients undergoing colonic resection. Metabolic pathway analyses further revealed relationships between complex networks of metabolites.

          Methods

          Seventeen CRC patients participated in this pilot study and provided CRC, adjacent mucosa ~10 cm proximal to the tumor, and stool. Metabolomes were analyzed by gas chromatography-mass spectrometry (GC/MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). All of the library standard identifications were confirmed and further analyzed via MetaboLync TM for metabolic network interactions.

          Results

          There were a total of 728 distinct metabolites identified from colonic tissue and stool matrices. Nineteen metabolites significantly distinguished CRC from adjacent mucosa in our patient-matched cohort. Glucose-6-phosphate and fructose-6-phosphate demonstrated 0.64-fold and 0.75-fold lower expression in CRC compared to mucosa, respectively, whereas isobar: betaine aldehyde, N-methyldiethanolamine, and adenylosuccinate had 2.68-fold and 1.88-fold higher relative abundance in CRC. Eleven of the 19 metabolites had not previously been reported for CRC relevance. Metabolic pathway analysis revealed significant perturbations of short-chain fatty acid metabolism, fructose, mannose, and galactose metabolism, and glycolytic, gluconeogenic, and pyruvate metabolism. In comparison to the 500 stool metabolites identified from human CRC patients, only 215 of those stool metabolites were also detected in tissue. This CRC and stool metabolome investigation identified novel metabolites that may serve as key small molecules in CRC pathogenesis, confirmed the results from previously reported CRC metabolome studies, and showed networks for metabolic pathway aberrations. In addition, we found differences between the CRC and stool metabolomes.

          Conclusions

          Stool metabolite profiles were limited for direct associations with CRC and adjacent mucosa, yet metabolic pathways were conserved across both matrices. Larger patient-matched CRC, adjacent non-cancerous colonic mucosa, and stool cohort studies for metabolite profiling are needed to validate these small molecule differences and metabolic pathway aberrations for clinical application to CRC control, treatment, and prevention.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s40170-016-0151-y) contains supplementary material, which is available to authorized users.

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          Most cited references30

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            The Warburg effect dictates the mechanism of butyrate-mediated histone acetylation and cell proliferation.

            Widespread changes in gene expression drive tumorigenesis, yet our knowledge of how aberrant epigenomic and transcriptome profiles arise in cancer cells is poorly understood. Here, we demonstrate that metabolic transformation plays an important role. Butyrate is the primary energy source of normal colonocytes and is metabolized to acetyl-CoA, which was shown to be important not only for energetics but also for HAT activity. Due to the Warburg effect, cancerous colonocytes rely on glucose as their primary energy source, so butyrate accumulated and functioned as an HDAC inhibitor. Although both mechanisms increased histone acetylation, different target genes were upregulated. Consequently, butyrate stimulated the proliferation of normal colonocytes and cancerous colonocytes when the Warburg effect was prevented from occurring, whereas it inhibited the proliferation of cancerous colonocytes undergoing the Warburg effect. These findings link a common metabolite to epigenetic mechanisms that are differentially utilized by normal and cancerous cells because of their inherent metabolic differences. Copyright © 2012 Elsevier Inc. All rights reserved.
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              Targeting glucose metabolism for cancer therapy

              Tumor cells exhibit high levels of glycolysis despite the presence of ample oxygen, a phenomenon termed aerobic glycolysis. This observation was first published by Warburg et al. (1924); it has since been supported by multiple studies in a variety of tumor types, and is now exploited in the clinic for diagnostic purposes. Positron emission tomography using 2-deoxy-2(18F)-fluoro-D-glucose, a glucose analogue, demonstrates a significant increase in glucose uptake in tumors compared with adjacent normal tissue (Gambhir, 2002). Warburg’s initial observations led him to hypothesize that cancer is caused by mitochondrial injury, followed by an increase in glycolysis that converts differentiated cells into proliferating cancer cells (Warburg, 1956). However, primary defects in mitochondrial enzymes or complexes within the electron transport chain are not frequently observed in cancer (Frezza and Gottlieb, 2009). Recent studies indicate that the activation of protooncogenes (e.g., Myc), signaling pathways (e.g., PI3K), and transcription factors (e.g., HIF-1), as well as the inactivation of tumor suppressors (e.g., p53), induce the Warburg effect in cancer cells (Vander Heiden et al., 2009) Glycolysis generates ATP with lower efficiency, but at a faster rate, than oxidative phosphorylation (Pfeiffer et al., 2001). This enhanced rate of ATP generation has been postulated to be beneficial for rapidly proliferating cells. However, this is probably not the main reason why proliferating cells engage in high levels of aerobic glycolysis, as multiple studies have suggested that mitochondria are the major source of cellular ATP in most cancer cell lines and tissues (Zu and Guppy, 2004). Furthermore, it was recognized >30 yr ago that galactose or fructose, which are preferentially shunted into glycolytic subsidiary pathways and do not generate substantial amounts of glycolytic ATP, allow cancer cells to proliferate in the absence of glucose (Reitzer et al., 1979). Thus, high glycolytic rates likely benefit proliferating cells through the production of glycolytic intermediates, which are shunted into subsidiary pathways to fuel metabolic pathways that generate de novo nucleotides, lipids, amino acids, and NADPH (Lunt and Vander Heiden, 2011). Meeting the biosynthesis needs of proliferating cells Glycolytic intermediates fuel several biosynthetic pathways that are essential for duplication of biomass during cellular proliferation (Fig. 1). After cellular uptake through glucose transporters (GLUTs), glucose is phosphorylated by hexokinases (HKs), which produces glucose-6-phosphate. Glucose-6-phosphate can either proceed into glycolysis through conversion into fructose-6-phosphate by glucose-6-phosphate isomerase, or it can be shunted into the oxidative branch of the pentose phosphate pathway (PPP) by glucose-6-phosphate dehydrogenase. The oxidative branch of the PPP generates NADPH, which is used for the reduction of cellular glutathione pools to promote redox homeostasis and acts as a reducing agent for lipid, nucleotide, and amino acid biosynthesis. The nonoxidative branch of the PPP generates ribose-5-phosphate, which is used in the biosynthesis of nucleic acids. Back in glycolysis, phosphofructokinase-1 (PFK-1) irreversibly converts fructose-6-phosphate to fructose-1,6-bisphosphate. Fructose-1,6-bisphosphate is converted into glyceraldehyde-3-phosphate or dihydroxyacetone phosphate. The latter is a precursor to glycerol-3-phosphate, which is crucial for the biosynthesis of the phospholipids and triacylglycerols required for generation of cell membranes. Fructose-6-phosphate and glyceraldehyde-3-phosphate can also combine to generate ribose-5-phosphate through transketolases and transaldolases. Further down the glycolytic pathway, 3-phosphoglycerate can undergo oxidation to generate serine and NADH. Serine can be used to generate two critical amino acids, cysteine and glycine, and to generate important signaling molecules such as ceramide. Figure 1. Potential targets for cancer therapy found within metabolic pathways involved in glucose metabolism. The PPP is shaded in blue, and glycolysis is shaded in yellow. Red text is used to denote potential therapeutic targets. The green arrow indicates positive regulation of PFK1. Mechanisms maintaining high glycolytic flux Cellular glycolytic rates are subject to several negative feedback mechanisms, which proliferating cells must overcome to maintain biosynthesis. PFK-1 is a critical driver of glycolytic flux and is allosterically inhibited by high ATP levels. Proliferating cells up-regulate the expression of PFK-2, which generates fructose-2,6-bisphospate, a potent allosteric activator of PFK-1, thus maintaining high glycolytic flux in the presence of high ATP (Vora et al., 1985; Colombo et al., 2010). High glycolytic flux is also maintained by the overexpression of lactate dehydrogenase (LDH), a transcriptional target of Myc (Shim et al., 1997). LDH generates NAD+ from NADH while reducing pyruvate to lactate. NAD+ regeneration is necessary for continued flux through glycolysis, as NAD+ is required for conversion of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate. The overexpression of LDH is sufficient to increase glycolytic flux (Shim et al., 1997). Although NAD+ can also be regenerated by mitochondria, this requires the transport of NADH into the mitochondria through various shuttles that are likely too slow to meet the high demands of the cytosolic NAD+ required to maintain glycolysis (Locasale and Cantley, 2011). Emerging studies indicate that pyruvate kinase (PK) plays an essential role in regulating the balance between glycolytic ATP generation and biosynthetic needs for proliferating cells (Christofk et al., 2008b). PK catalyzes the rate-limiting and ATP-producing step of glycolysis in which phosphoenolpyruvate (PEP) is converted to pyruvate. Cancer cells express higher levels of M2 isoform (PKM2) over the more catalytically active M1 isoform (PKM1), and cancer cells engineered to express PKM1 instead of PKM2 exhibit reduced tumor-forming ability (Christofk et al., 2008a; Bluemlein et al., 2011). PKM2 alternates between a dimer that exhibits low catalytic activity and a highly active tetramer that is driven by allosteric binding of fructose-1,6-bisphosphate (Spoden et al., 2009). PKM2 is phosphorylated on tyrosine 105 downstream of growth factor signaling, disrupting tetramer assembly required for PKM2 activity (Hitosugi et al., 2009). Furthermore, high glucose consumption triggers acetylation of PKM2 at lysine 305 to further reduce its activity (Lv et al., 2011). This inhibition of PKM2 allows diversion of glycolytic intermediates upstream of pyruvate into biosynthetic pathways. Under these conditions, PEP can be converted to pyruvate through alternative, non–ATP-producing pathways, allowing for lactate and NAD+ generation (Vander Heiden et al., 2010). Targets for cancer therapy Targeting metabolic pathways for cancer therapy seems appealing at first glance, as enzymes are attractive molecular targets. However, to be an attractive candidate for cancer therapy, there must be a significant difference in the requirement for a given enzyme’s activity between cancer cells and normal proliferating cells. A few potential candidates that are overexpressed in certain cancer types include GLUT1, HKII, phosphoglycerate dehydrogenase (PHGDH), and LDH-A (Fig. 1). GLUT1 is overexpressed in many cancer types, including renal cell carcinomas (RCCs) that exhibit loss of the von Hippel-Lindau (VHL) tumor suppressor gene (Younes et al., 1996; Chan et al., 2011). A recent study identified a series of small molecules that inhibit GLUT1 and selectively kill VHL-deficient RCCs (Chan et al., 2011). HKs catalyze the first step of glycolysis and are another potentially attractive target. There are four mammalian HKs (HKI–IV). HKI is the ubiquitously expressed isoform, whereas HKII is expressed in insulin-sensitive tissues such as muscle and adipose (Robey and Hay, 2006). Many tumor cells overexpress HKII, and preclinical studies demonstrate that HKII inhibition could be an effective cancer therapy (Jae et al., 2009). PHGDH converts 3-phosphoglycerate into 3-phosphohydroxypyruvate, a rate-limiting step in the conversion of 3-phosphoglycerate into serine. Two recent studies reported that subsets of human melanoma and breast cancers have high levels of PHGDH, and these cancer cells are dependent on these enzymes for growth (Locasale et al., 2011; Possemato et al., 2011). LDH-A was the first metabolic target demonstrated to be directly regulated by an oncogene (MYC), and genetic or pharmacologic inhibition of LDH-A diminishes MYC-dependent tumors (Shim et al., 1997; Le et al., 2010). Although these are promising preliminary studies, GLUT1, HKII, PHGDH, and LDH-A are expressed in normal tissues, and it remains to be seen whether inhibition of these enzymes will be effective in diminishing tumors without imparting significant toxicity to normal tissues. The finding that PKM2 expression provides a proliferative advantage for cancer cells raised the possibility that PKM2 could be an attractive target for cancer therapy. Tumors express higher levels of PKM2 than normal control tissues (Bluemlein et al., 2011); however, inhibiting PKM2 could also allow glycolytic intermediates to accumulate and feed biosynthetic pathways, resulting in tumor promotion. Remarkably, there is data to suggest that either inhibiting or activating PKM2 in cancer cells diminishes tumor growth. Anastasiou et al. (2011) have recently demonstrated that PKM2 is regulated by cellular oxidative stress. PKM2 is specifically oxidized on cysteine 358, inhibiting its activity and promoting diversion of glycolytic intermediates into the PPP, producing NADPH and promoting redox balance. Expression of a nonoxidizable PKM2 mutant reduced flux through the PPP, increased oxidative stress, and inhibited tumor growth (Anastasiou et al., 2011). These results indicate that PKM2 activators could be viable cancer therapeutics, especially when used in conjunction with radiation or chemotherapeutic agents known to promote oxidative stress. Paradoxically, in this issue Goldberg and Sharp have demonstrated that inhibition of PKM2 activity using small interfereing RNA (siRNA) increases apoptosis in cell culture, and can also inhibit tumor cell growth. Work by this group demonstrates that in vivo delivery of siRNA molecules targeting PKM2 causes tumor regression in mouse xenograft models. This is potentially promising, as recent advances in nanotechnology are attempting to target siRNA delivery specifically to tumor cells in vivo. Although seemingly irreconcilable with the data from Anastasiou et al., 2011, these disparate results may be explained by cellular responses to varying degrees of hypoxia. Moderate hypoxia (1.5% O2) promotes mitochondrial generation of hydrogen peroxide (H2O2), which activates signaling pathways critical for the cellular response to hypoxia. Under these conditions, PKM2 becomes oxidized, which inhibits its activity, promotes flux through the PPP, and promotes redox balance (Anastasiou et al., 2011). This prevents accumulation of aberrantly high levels of cellular H2O2 and oxidative cellular damage. Under severe hypoxia (<0.5% O2), however, oxygen becomes limiting for the mitochondrial electron transport chain and production of mitochondrial ATP and H2O2 ceases. Under these conditions, cells become dependent on PK activity for ATP production. Thus, PKM2 inhibitors and activators could both be therapeutically beneficial for different reasons. PKM2 inhibitors would prevent ATP production in severely hypoxic cells, whereas PKM2 activators would promote oxidative damage in moderately hypoxic cells. As most tumors exhibit a range of oxygen concentrations depending on tumor size and vascularization, whether PKM2 activation or inhibition is most therapeutically effective may be tumor-dependent. It is important to note that insufficient inhibition of PKM2 activity, which allows for glycolytic ATP production during severe hypoxia, would promote flux through biosynthetic pathways and possibly accelerate tumor growth. It will also be important to study the effects of PKM2 modulation in relatively well-oxygenated tissues, such as the lung. Another mechanism by which PKM2 inhibition by siRNA could potentially diminish tumor growth is by inhibiting other nonglycolytic functions of PKM2. Goldberg and Sharp (2012) posit that PKM2 inhibition by siRNA selectively induces caspase-dependent cell death, suggesting that PKM2 might regulate apoptosis through yet to be defined mechanisms. Interestingly, PKM2 has recently been shown to bind to and enhance the transcriptional activity of the hypoxia-inducible factor-1 (HIF-1; Luo et al., 2011). HIF-1 is a critical mediator of cellular adaptation to hypoxic stress through transcription of diverse targets including GLUTs and glycolytic enzymes such as HKII and LDH-A. It will be important to determine whether pharmacological inhibition of PKM2 can inhibit HIF-1 transcriptional activity or whether inhibition of PKM2 expression is required. Similarly, PKM2 has been show to associate with OCT4 and β-catenin, two transcription factors associated with tumor progression (Lee et al., 2008; Yang et al., 2011). Going forward, it will be important to decipher whether PKM2 inhibition or activation affects nonglycolytic functions of PKM2, and whether PKM2 interaction with nonglycolytic proteins is important for tumorigenesis. Conclusions and future directions The genetic revolution brought with it the discovery of genes and signaling pathways that promote or repress cellular transformation, and a genetic basis for understanding tumorigenesis. More recent work has focused on deciphering interactions between these proliferative pathways and cellular metabolic pathways. Currently, there are three major issues that need to be addressed to determine whether targeting glucose metabolism is a viable strategy for cancer therapy. First, to date, the genetic or pharmacologic interventions performed have primarily been done using human cancer cells injected subcutaneously into nude mice. It will be important for future experiments to make use of genetically engineered mouse cancer models or orthotopic models with human cancer cells to assess whether glucose-dependent pathways are promising targets for cancer therapy. Second, the toxic effects of inhibiting metabolic enzymes in normal cells need to be deciphered. Aside from cancer cells, immune cells and stem cells also display aerobic glycolysis. Unless antimetabolic therapies can distinguish between malignant and nonmalignant cells with self-renewal capacity, then therapeutically targeting metabolism could be complicated by the same types of toxicity that plague conventional cytotoxic chemotherapeutic regimens. Third, cancer cells display metabolic plasticity. Thus, it is conceivable that cancer cells could develop resistance to inhibition of a particular metabolic pathway through expression of alternate isoforms or up-regulation of alternate pathways, such as gluconeogenesis. Adjacent cells such as adipocytes may also provide precursors for the biosynthetic needs of tumor cells (Nieman et al., 2011). Still, these are exciting times for the metabolism field as the links between gene expression, epigenetics, cell proliferation, differentiation, and metabolic pathways are being uncovered.
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                Author and article information

                Contributors
                970-491-1536 , 970-491-7569 , E.P.Ryan@colostate.edu
                Journal
                Cancer Metab
                Cancer Metab
                Cancer & Metabolism
                BioMed Central (London )
                2049-3002
                6 June 2016
                6 June 2016
                2016
                : 4
                : 11
                Affiliations
                [ ]Department of Environmental and Radiological Health Sciences, Colorado State University, 200 West Lake Street, 1680 Campus Delivery, Fort Collins, CO 80523 USA
                [ ]Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523 USA
                [ ]Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO 80523 USA
                [ ]University of Colorado Health-North, Fort Collins, CO 80522 USA
                [ ]Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO 80045 USA
                Article
                151
                10.1186/s40170-016-0151-y
                4893840
                27275383
                e0b06a8c-4baa-4939-b2ed-6ef68e15debf
                © The Author(s). 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 26 January 2016
                : 16 May 2016
                Funding
                Funded by: University of Colorado Cancer Center Control and Prevention Program
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: RO3CA150070-2
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/http://dx.doi.org/10.13039/100007235, Colorado State University;
                Categories
                Research
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                © The Author(s) 2016

                metabolomics,colorectal,cancer,stool,metabolites,tumor,colon mucosa,metabolic pathways

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