High information throughput analysis of nucleotides and their isotopically enriched isotopologues by direct-infusion FTICR-MS

Lorkiewicz, Pawel; Higashi, Richard M.; Lane, Andrew N.; Fan, Teresa W.‐M.

doi:10.1007/s11306-011-0388-y

Cited by 57 publications

(64 citation statements)

References 34 publications

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“…A549 cells transduced with shPC55 or shEV were incubated with 13 C 6 -glucose or 13 C 5 -glutamine for 24 hours. Fractional enrichment of UTP and CTP isotopologs from FT-ICR-MS analysis of polar cell extracts showed reduced enrichment of 13 C 6 -glucose-derived 13 C 5 -ribose (the "5" isotopolog) and 13 C 6 -glucose-or 13 C 5 -glutamine-derived 13 C 1-3 -pyrimidine rings (the "6-8" or "1-3" isotopologs, highlighted by dashed green rectangles; for the "6-8" isotopologs, 5 13 Cs arose from ribose and 1-3 13 Cs from the ring) (10,45). These data suggest that PC knockdown inhibits de novo pyrimidine biosynthesis from both glucose and glutamine.…”

Section: Resultsmentioning

confidence: 99%

Pyruvate carboxylase is critical for non–small-cell lung cancer proliferation

Sellers¹,

Fox²,

Bousamra³

et al. 2015

J. Clin. Invest.

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445

483

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Section: Resultsmentioning

confidence: 99%

Pyruvate carboxylase is critical for non–small-cell lung cancer proliferation

Sellers¹,

Fox²,

Bousamra³

et al. 2015

J. Clin. Invest.

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445

483

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“…Gas and liquid chromatography (GC and LC) methods have been developed to resolve large numbers of metabolites, which are often used orthogonally with MS detection. Ultra-high-resolution MS, defined here as m/z mass-resolving power of Ն350,000 (m/z 400), of which all current models are Fourier-transform MS (UHR-FTMS), can resolve all non-isomeric metabolites without chromatography (10,14). At the sufficiently high resolution of UHR-FTMS, the neutron m/z differences for metabolites containing 13 C, 15 N, or 2 H can all be distinguished, allowing for multiplexed labeling experiments.…”

Section: Analytical Tools For Sirmmentioning

confidence: 99%

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

Bruntz

Lane

Higashi

et al. 2017

Journal of Biological Chemistry

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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.Metabolism is the collection of predominantly enzyme-catalyzed biochemical transformations that meet the growth and survival demands of an organism. For nearly a century, scientists have documented profound metabolic changes that occur in tumors (1, 2). One of the earliest insights into cancer metabolism came when Otto Warburg noted increased uptake and fermentation of glucose (Glc) 3 to lactate in tumors relative to surrounding tissue, even in the presence of ample oxygen (2). Clinical cancer diagnosis exploits this "Warburg effect" by measuring uptake of the Glc analogue 18 F-deoxyglucose using positron emission tomography (PET), as the metabolic demands of differentiated, non-proliferating tissues generally require far less Glc than tumors (3).Oncoproteins and tumor suppressors are well-established regulators of metabolism, and mutations or dysregulated expression can lead to the altered metabolic phenotypes observed in many cancers (4, 5). Inactivating mutations in enzymes such as fumarate hydratase (FH) or succinate dehydrogenase (SDH) induce pathophysiological accumulation of substrates that inhibit other critical enzyme functions, whereas less common gain-of-function mutations such as in isocitrate dehydrogenases (IDH) produce metabolites that directly deregulate cellular processes (6). Additionally, cancer cells frequently express fetal isoforms of metabolic enzymes that are subject to different regulatory mechanisms to provide growth advantages (7). Gaining a systematic understanding of the metabolic changes that occur during carcinogenesis can thus be exploited for therapeutic and diagnostic purposes.Stable isotope-resolved metabolomics (SIRM) is a powerful approach developed by others and by us where isotopically enriched precursors such as [ 13 C 6 ]Glc are administered to a biological system, and the ensuing metabolic transformations are determined using appropriate analytic techniques to enable robust reconstruction of metabolic pathways (8 -11). Stable isotopes are non-radioactive and in SIRM practice are identical chemically and functionally to the most abundant isotope of that element. Incorporating stable isotopes such as 2 H, 13 C, or 15 N into biological precursors has long been used to trace their metabolism in living systems (12). SIRM is thus distinct from non-tracer-based metabolomics profiling for statistical models. Here, we review SIRM applications and demonstrate h...

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“…Nucleotides are considered of great interest, as these molecules are involved in nucleic acid synthesis, energy production, protein modification, and antisense oligonucleotide synthesis (57,58). The effect of THF exposure on the nucleotide concentration in strain YYL was slightly greater during growth in TY than during growth in CY.…”

Section: Discussionmentioning

confidence: 99%

Dynamic Metabolic and Transcriptional Profiling of Rhodococcus sp. Strain YYL during the Degradation of Tetrahydrofuran

Yao

Lü

et al. 2014

Appl Environ Microbiol

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cAlthough tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD ؉ , and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through 1 H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms.

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High information throughput analysis of nucleotides and their isotopically enriched isotopologues by direct-infusion FTICR-MS

Cited by 57 publications

References 34 publications

Pyruvate carboxylase is critical for non–small-cell lung cancer proliferation

Pyruvate carboxylase is critical for non–small-cell lung cancer proliferation

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

Dynamic Metabolic and Transcriptional Profiling of Rhodococcus sp. Strain YYL during the Degradation of Tetrahydrofuran

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