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Locasale, Jason

Positions:

Assistant Professor of Pharmacology & Cancer Biology

Pharmacology & Cancer Biology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

B.A. 2003

B.A. — Rutgers University New Brunswick

Ph.D. 2008

Ph.D. — Massachusetts Institute of Technology

Grants:

Host pathways regulating Epstein-Barr virus-mediated B cell growth transformation

Administered By
Molecular Genetics and Microbiology
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
August 01, 2016
End Date
July 31, 2021

Regulatory principles of the Warburg Effect

Administered By
Pharmacology & Cancer Biology
AwardedBy
American Cancer Society, Inc.
Role
Principal Investigator
Start Date
July 01, 2017
End Date
December 31, 2020

Characterization of the SGOC Metabolic Network in Cancer Pathogenesis

Administered By
Pharmacology & Cancer Biology
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
August 14, 2015
End Date
July 31, 2020

Understanding metabolic flux and the control of mammalian cell growth

Administered By
Pharmacology & Cancer Biology
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
October 17, 2015
End Date
February 28, 2018

Metabolic Reprogramming of Colon Cancer Liver Metastasis

Administered By
Biomedical Engineering
AwardedBy
National Institutes of Health
Role
Co-Principal Investigator
Start Date
January 13, 2016
End Date
December 31, 2017

Exploiting metabolic vulnerabilities of CD4 T cell subsets to control inflammatory disease

Administered By
Pharmacology & Cancer Biology
AwardedBy
Vanderbilt University Medical Center
Role
Principal Investigator
Start Date
November 10, 2015
End Date
March 31, 2017

Functional optimization of CD8+ T cell metabolism for tumor control

Administered By
Pharmacology & Cancer Biology
AwardedBy
University of Virginia - Charlottesville
Role
Principal Investigator
Start Date
August 01, 2015
End Date
December 31, 2016
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Publications:

Metabolic interactions with cancer epigenetics.

Cancer cells have epigenetic alterations that are known to drive cancer progression. The reversibility of the epigenetic posttranslational modifications on chromatin and DNA renders targeting these modifications an attractive means for cancer therapy. Cellular epigenetic status interacts with cell metabolism, and we are now beginning to understand the nature of how this interaction occurs and the biological contexts that mediate its function. Given the tremendous interest in understanding and targeting metabolic reprogramming in cancer, this nexus also provides opportunities for exploring the liabilities of cancers. This review summarizes recent developments in our understanding of the interaction of cancer metabolism and epigenetics.

Authors
Gao, X; Reid, MA; Kong, M; Locasale, JW
MLA Citation
Gao, X, Reid, MA, Kong, M, and Locasale, JW. "Metabolic interactions with cancer epigenetics." Molecular aspects of medicine 54 (April 2017): 50-57. (Review)
PMID
27620316
Source
epmc
Published In
Molecular Aspects of Medicine
Volume
54
Publish Date
2017
Start Page
50
End Page
57
DOI
10.1016/j.mam.2016.09.001

Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis.

During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis. Changes were targeted to thousands of large chromatin domains across the genome that collectively specified malignant traits, including euchromatin and large organized chromatin histone H3 lysine 9 (H3K9)-modified (LOCK) heterochromatin. Remarkably, distant metastases co-evolved a dependence on the oxidative branch of the pentose phosphate pathway (oxPPP), and oxPPP inhibition selectively reversed reprogrammed chromatin, malignant gene expression programs, and tumorigenesis. These findings suggest a model whereby linked metabolic-epigenetic programs are selected for enhanced tumorigenic fitness during the evolution of distant metastasis.

Authors
McDonald, OG; Li, X; Saunders, T; Tryggvadottir, R; Mentch, SJ; Warmoes, MO; Word, AE; Carrer, A; Salz, TH; Natsume, S; Stauffer, KM; Makohon-Moore, A; Zhong, Y; Wu, H; Wellen, KE; Locasale, JW; Iacobuzio-Donahue, CA; Feinberg, AP
MLA Citation
McDonald, OG, Li, X, Saunders, T, Tryggvadottir, R, Mentch, SJ, Warmoes, MO, Word, AE, Carrer, A, Salz, TH, Natsume, S, Stauffer, KM, Makohon-Moore, A, Zhong, Y, Wu, H, Wellen, KE, Locasale, JW, Iacobuzio-Donahue, CA, and Feinberg, AP. "Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis." Nature genetics 49.3 (March 2017): 367-376.
PMID
28092686
Source
epmc
Published In
Nature Genetics
Volume
49
Issue
3
Publish Date
2017
Start Page
367
End Page
376
DOI
10.1038/ng.3753

Metabolomics: A Primer.

Metabolomics generates a profile of small molecules that are derived from cellular metabolism and can directly reflect the outcome of complex networks of biochemical reactions, thus providing insights into multiple aspects of cellular physiology. Technological advances have enabled rapid and increasingly expansive data acquisition with samples as small as single cells; however, substantial challenges in the field remain. In this primer we provide an overview of metabolomics, especially mass spectrometry (MS)-based metabolomics, which uses liquid chromatography (LC) for separation, and discuss its utilities and limitations. We identify and discuss several areas at the frontier of metabolomics. Our goal is to give the reader a sense of what might be accomplished when conducting a metabolomics experiment, now and in the near future.

Authors
Liu, X; Locasale, JW
MLA Citation
Liu, X, and Locasale, JW. "Metabolomics: A Primer." Trends in biochemical sciences (February 11, 2017). (Review)
PMID
28196646
Source
epmc
Published In
Trends in Biochemical Sciences
Publish Date
2017
DOI
10.1016/j.tibs.2017.01.004

Short term methionine restriction increases hepatic global DNA methylation in adult but not young male C57BL/6J mice.

Despite well-documented evidence for lifespan extension by methionine restriction (MR), underlying mechanisms remain unknown. As methionine can alter S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), the substrate and product of DNA methyltransferase-1 (DNMT1), we hypothesized that MR diet alters DNA methylation. Young (8-week-old) and adult (1-year-old) male C57BL/6J mice were fed diets with different levels of methionine (0.12%-MR, 0.84%-CD) for 12weeks. Functional indicators of DNA methylation, including global methylation (GM), gene-specific methylation (GSM) and LINE-1 methylation; and biochemical factors affecting DNA methylation, SAH, SAM, and DNMT1 were assessed in different tissues. MR altered DNA methylation depending on the age of intervention. While MR had no effect on hepatic GM in young animals, it increased GM by 27% over CD in adults (p<0.01). In comparison with young animals, hepatic GM levels were 17% lower in CD adults (p<0.05), but not different in MR adults. The MR-induced increase in hepatic GM was associated with a 38% decrease in SAH levels in adults (p<0.001), with SAH and GM levels being negatively correlated (r2=0.33, p<0.001). No changes were observed in DNMT protein levels in liver. In adipose tissue, MR caused a 6% decline in GM in adults (p<0.05), a corresponding 2-fold increase in SAH (p<0.05), and a 2-fold decrease in DNMT1 (p<0.01). MR caused both increases and decreases in GSM of liver and adipose. No changes were observed in LINE-1. Together, these findings provide evidence for protective effects of MR diet on hepatic DNA hypomethylation in adults, apparently mediated by SAH. These findings also indicate that altered DNA methylation might be playing a role in benefits conferred by MR diet.

Authors
Mattocks, DAL; Mentch, SJ; Shneyder, J; Ables, GP; Sun, D; Richie, JP; Locasale, JW; Nichenametla, SN
MLA Citation
Mattocks, DAL, Mentch, SJ, Shneyder, J, Ables, GP, Sun, D, Richie, JP, Locasale, JW, and Nichenametla, SN. "Short term methionine restriction increases hepatic global DNA methylation in adult but not young male C57BL/6J mice." Experimental gerontology 88 (February 2017): 1-8.
PMID
27940170
Source
epmc
Published In
Experimental Gerontology
Volume
88
Publish Date
2017
Start Page
1
End Page
8
DOI
10.1016/j.exger.2016.12.003

Glutamine Metabolism in Cancer: Understanding the Heterogeneity

© 2017 Elsevier Ltd.Reliance on glutamine has long been considered to be a hallmark of cancer cell metabolism. However, some recent studies have challenged this notion in vivo, prompting a need for further clarification of the role of glutamine metabolism in cancer. We find that there is ample evidence of an essential role for glutamine in tumors, and that a variety of factors, including tissue type, the underlying cancer genetics, the tumor microenvironment, and other variables such as diet and host physiology collectively influence the role of glutamine in cancer. Thus the requirements for glutamine in cancer are overall highly heterogeneous. In this review we discuss the implications both for basic science and for targeting glutamine metabolism in cancer therapy. The role of glutamine in cancer metabolism is more complex than previously appreciated.Glutaminase inhibition effectiveness in vivo is highly dependent on tumor cell origin and tumor microenvironment.Animal studies and anchorage-independent cell culture studies can greatly complement monolayer cell culture studies and may reveal unique metabolic patterns.The synthesis or uptake, and the utilization, of glutamine in cancer cells is highly flexible and is dependent on cell origin, oncogenic drivers, and the tumor microenvironment.Some tumor types rely on catabolism of exogenous glutamine, and might be effectively targeted by therapeutic regimes involving glutaminase inhibition.Different metabolic pathways, including glutamine catabolism, can achieve TCA cycle anaplerosis.

Authors
Cluntun, AA; Lukey, MJ; Cerione, RA; Locasale, JW
MLA Citation
Cluntun, AA, Lukey, MJ, Cerione, RA, and Locasale, JW. "Glutamine Metabolism in Cancer: Understanding the Heterogeneity (Accepted)." Trends in Cancer (January 1, 2017).
Source
scopus
Published In
Trends in cancer
Publish Date
2017
DOI
10.1016/j.trecan.2017.01.005

Rational Design of Selective Allosteric Inhibitors of PHGDH and Serine Synthesis with Anti-tumor Activity.

Metabolic reprogramming in cancer cells facilitates growth and proliferation. Increased activity of the serine biosynthetic pathway through the enzyme phosphoglycerate dehydrogenase (PHGDH) contributes to tumorigenesis. With a small substrate and a weak binding cofactor, (NAD+), inhibitor development for PHGDH remains challenging. Instead of targeting the PHGDH active site, we computationally identified two potential allosteric sites and virtually screened compounds that can bind to these sites. With subsequent characterization, we successfully identified PHGDH non-NAD+-competing allosteric inhibitors that attenuate its enzyme activity, selectively inhibit de novo serine synthesis in cancer cells, and reduce tumor growth in vivo. Our study not only identifies novel allosteric inhibitors for PHGDH to probe its function and potential as a therapeutic target, but also provides a general strategy for the rational design of small-molecule modulators of metabolic enzyme function.

Authors
Wang, Q; Liberti, MV; Liu, P; Deng, X; Liu, Y; Locasale, JW; Lai, L
MLA Citation
Wang, Q, Liberti, MV, Liu, P, Deng, X, Liu, Y, Locasale, JW, and Lai, L. "Rational Design of Selective Allosteric Inhibitors of PHGDH and Serine Synthesis with Anti-tumor Activity." Cell chemical biology 24.1 (January 2017): 55-65.
PMID
28042046
Source
epmc
Published In
Cell chemical biology
Volume
24
Issue
1
Publish Date
2017
Start Page
55
End Page
65
DOI
10.1016/j.chembiol.2016.11.013

Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism.

Altered DNA methylation is common in cancer and often considered an early event in tumorigenesis. However, the sources of heterogeneity of DNA methylation among tumours remain poorly defined. Here we capitalize on the availability of multi-platform data on thousands of human tumours to build integrative models of DNA methylation. We quantify the contribution of clinical and molecular factors in explaining intertumoral variability in DNA methylation. We show that the levels of a set of metabolic genes involved in the methionine cycle is predictive of several features of DNA methylation in tumours, including the methylation of cancer genes. Finally, we demonstrate that patients whose DNA methylation can be predicted from the methionine cycle exhibited improved survival over cases where this regulation is disrupted. This study represents a comprehensive analysis of the determinants of methylation and demonstrates the surprisingly large interaction between metabolism and DNA methylation variation. Together, our results quantify links between tumour metabolism and epigenetics and outline clinical implications.

Authors
Mehrmohamadi, M; Mentch, LK; Clark, AG; Locasale, JW
MLA Citation
Mehrmohamadi, M, Mentch, LK, Clark, AG, and Locasale, JW. "Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism." Nature communications 7 (December 14, 2016): 13666-.
PMID
27966532
Source
epmc
Published In
Nature Communications
Volume
7
Publish Date
2016
Start Page
13666
DOI
10.1038/ncomms13666

Foxp3 and Toll-like receptor signaling balance Treg cell anabolic metabolism for suppression.

CD4+ effector T cells (Teff cells) and regulatory T cells (Treg cells) undergo metabolic reprogramming to support proliferation and immunological function. Although signaling via the lipid kinase PI(3)K (phosphatidylinositol-3-OH kinase), the serine-threonine kinase Akt and the metabolic checkpoint kinase complex mTORC1 induces both expression of the glucose transporter Glut1 and aerobic glycolysis for Teff cell proliferation and inflammatory function, the mechanisms that regulate Treg cell metabolism and function remain unclear. We found that Toll-like receptor (TLR) signals that promote Treg cell proliferation increased PI(3)K-Akt-mTORC1 signaling, glycolysis and expression of Glut1. However, TLR-induced mTORC1 signaling also impaired Treg cell suppressive capacity. Conversely, the transcription factor Foxp3 opposed PI(3)K-Akt-mTORC1 signaling to diminish glycolysis and anabolic metabolism while increasing oxidative and catabolic metabolism. Notably, Glut1 expression was sufficient to increase the number of Treg cells, but it reduced their suppressive capacity and Foxp3 expression. Thus, inflammatory signals and Foxp3 balance mTORC1 signaling and glucose metabolism to control the proliferation and suppressive function of Treg cells.

Authors
Gerriets, VA; Kishton, RJ; Johnson, MO; Cohen, S; Siska, PJ; Nichols, AG; Warmoes, MO; de Cubas, AA; MacIver, NJ; Locasale, JW; Turka, LA; Wells, AD; Rathmell, JC
MLA Citation
Gerriets, VA, Kishton, RJ, Johnson, MO, Cohen, S, Siska, PJ, Nichols, AG, Warmoes, MO, de Cubas, AA, MacIver, NJ, Locasale, JW, Turka, LA, Wells, AD, and Rathmell, JC. "Foxp3 and Toll-like receptor signaling balance Treg cell anabolic metabolism for suppression." Nature immunology 17.12 (December 2016): 1459-1466.
PMID
27695003
Source
epmc
Published In
Nature Immunology
Volume
17
Issue
12
Publish Date
2016
Start Page
1459
End Page
1466
DOI
10.1038/ni.3577

Serine Metabolism Links Tumor Suppression to the Epigenetic Landscape.

Intermediary metabolism provides substrates that shape epigenetic status, but whether this interaction can be responsible for oncogenesis is largely unknown. In a recent issue of Nature, Kottakis et al. (2016) now show that the common tumor suppressor gene LKB1 can function by mediating this connection through an LKB1/AMPK/mTOR signaling axis.

Authors
Gao, X; Locasale, JW
MLA Citation
Gao, X, and Locasale, JW. "Serine Metabolism Links Tumor Suppression to the Epigenetic Landscape." Cell metabolism 24.6 (December 2016): 777-779.
PMID
27974177
Source
epmc
Published In
Cell Metabolism
Volume
24
Issue
6
Publish Date
2016
Start Page
777
End Page
779
DOI
10.1016/j.cmet.2016.11.012

Metformin Targets Central Carbon Metabolism and Reveals Mitochondrial Requirements in Human Cancers.

Repurposing metformin for cancer therapy is attractive due to its safety profile, epidemiological evidence, and encouraging data from human clinical trials. Although it is known to systemically affect glucose metabolism in liver, muscle, gut, and other tissues, the molecular determinants that predict a patient response in cancer remain unknown. Here, we carry out an integrative metabolomics analysis of metformin action in ovarian cancer. Metformin accumulated in patient biopsies, and pathways involving nucleotide metabolism, redox, and energy status, all related to mitochondrial metabolism, were affected in treated tumors. Strikingly, a metabolic signature obtained from a patient with an exceptional clinical outcome mirrored that of a responsive animal tumor. Mechanistically, we demonstrate with stable isotope tracing that these metabolic signatures are due to an inability to adapt nutrient utilization in the mitochondria. This analysis provides new insights into mitochondrial metabolism and may lead to more precise indications of metformin in cancer.

Authors
Liu, X; Romero, IL; Litchfield, LM; Lengyel, E; Locasale, JW
MLA Citation
Liu, X, Romero, IL, Litchfield, LM, Lengyel, E, and Locasale, JW. "Metformin Targets Central Carbon Metabolism and Reveals Mitochondrial Requirements in Human Cancers." Cell metabolism 24.5 (November 2016): 728-739.
PMID
27746051
Source
epmc
Published In
Cell Metabolism
Volume
24
Issue
5
Publish Date
2016
Start Page
728
End Page
739
DOI
10.1016/j.cmet.2016.09.005

Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation.

Poorly organized tumour vasculature often results in areas of limited nutrient supply and hypoxia. Despite our understanding of solid tumour responses to hypoxia, how nutrient deprivation regionally affects tumour growth and therapeutic response is poorly understood. Here, we show that the core region of solid tumours displayed glutamine deficiency compared with other amino acids. Low glutamine in tumour core regions led to dramatic histone hypermethylation due to decreased α-ketoglutarate levels, a key cofactor for the Jumonji-domain-containing histone demethylases. Using patient-derived (V600E)BRAF melanoma cells, we found that low-glutamine-induced histone hypermethylation resulted in cancer cell dedifferentiation and resistance to BRAF inhibitor treatment, which was largely mediated by methylation on H3K27, as knockdown of the H3K27-specific demethylase KDM6B and the methyltransferase EZH2 respectively reproduced and attenuated the low-glutamine effects in vitro and in vivo. Thus, intratumoral regional variation in the nutritional microenvironment contributes to tumour heterogeneity and therapeutic response.

Authors
Pan, M; Reid, MA; Lowman, XH; Kulkarni, RP; Tran, TQ; Liu, X; Yang, Y; Hernandez-Davies, JE; Rosales, KK; Li, H; Hugo, W; Song, C; Xu, X; Schones, DE; Ann, DK; Gradinaru, V; Lo, RS; Locasale, JW; Kong, M
MLA Citation
Pan, M, Reid, MA, Lowman, XH, Kulkarni, RP, Tran, TQ, Liu, X, Yang, Y, Hernandez-Davies, JE, Rosales, KK, Li, H, Hugo, W, Song, C, Xu, X, Schones, DE, Ann, DK, Gradinaru, V, Lo, RS, Locasale, JW, and Kong, M. "Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation." Nature cell biology 18.10 (October 2016): 1090-1101.
PMID
27617932
Source
epmc
Published In
Nature Cell Biology
Volume
18
Issue
10
Publish Date
2016
Start Page
1090
End Page
1101
DOI
10.1038/ncb3410

Understanding metabolism with flux analysis: From theory to application.

Quantitative and qualitative knowledge of metabolic rates (i.e. fluxes) over a metabolic network and in specific cellular compartments gives insights into the regulation of metabolism and helps to understand the contribution of metabolic alterations to pathology. In this review we introduce methodology to resolve metabolic fluxes from stable isotope labeling and relevant techniques in model development, model simplification, flux uncertainty analysis and experimental design that together is termed metabolic flux analysis. Finally we discuss applications using metabolic flux analysis to elucidate mechanisms pertinent to tumor cell metabolism. We hope that this review gives the readers a brief introduction of how flux analysis is conducted, how technical issues related to it are addressed, and how its application has contributed to our knowledge of tumor cell metabolism.

Authors
Dai, Z; Locasale, JW
MLA Citation
Dai, Z, and Locasale, JW. "Understanding metabolism with flux analysis: From theory to application." Metabolic engineering (September 22, 2016).
PMID
27667771
Source
epmc
Published In
Metabolic Engineering
Publish Date
2016
DOI
10.1016/j.ymben.2016.09.005

mTORC1 and mTORC2 Kinase Signaling and Glucose Metabolism Drive Follicular Helper T Cell Differentiation.

Follicular helper T (Tfh) cells are crucial for germinal center (GC) formation and humoral adaptive immunity. Mechanisms underlying Tfh cell differentiation in peripheral and mucosal lymphoid organs are incompletely understood. We report here that mTOR kinase complexes 1 and 2 (mTORC1 and mTORC2) are essential for Tfh cell differentiation and GC reaction under steady state and after antigen immunization and viral infection. Loss of mTORC1 and mTORC2 in T cells exerted distinct effects on Tfh cell signature gene expression, whereas increased mTOR activity promoted Tfh responses. Deficiency of mTORC2 impaired CD4(+) T cell accumulation and immunoglobulin A production and aberrantly induced the transcription factor Foxo1. Mechanistically, the costimulatory molecule ICOS activated mTORC1 and mTORC2 to drive glycolysis and lipogenesis, and glucose transporter 1-mediated glucose metabolism promoted Tfh cell responses. Altogether, mTOR acts as a central node in Tfh cells by linking immune signals to anabolic metabolism and transcriptional activity.

Authors
Zeng, H; Cohen, S; Guy, C; Shrestha, S; Neale, G; Brown, SA; Cloer, C; Kishton, RJ; Gao, X; Youngblood, B; Do, M; Li, MO; Locasale, JW; Rathmell, JC; Chi, H
MLA Citation
Zeng, H, Cohen, S, Guy, C, Shrestha, S, Neale, G, Brown, SA, Cloer, C, Kishton, RJ, Gao, X, Youngblood, B, Do, M, Li, MO, Locasale, JW, Rathmell, JC, and Chi, H. "mTORC1 and mTORC2 Kinase Signaling and Glucose Metabolism Drive Follicular Helper T Cell Differentiation." Immunity 45.3 (September 7, 2016): 540-554.
PMID
27637146
Source
epmc
Published In
Immunity
Volume
45
Issue
3
Publish Date
2016
Start Page
540
End Page
554
DOI
10.1016/j.immuni.2016.08.017

A Flux Balance of Glucose Metabolism Clarifies the Requirements of the Warburg Effect.

The Warburg effect, or aerobic glycolysis, is marked by the increased metabolism of glucose to lactate in the presence of oxygen. Despite its widespread prevalence in physiology and cancer biology, the causes and consequences remain incompletely understood. Here, we show that a simple balance of interacting fluxes in glycolysis creates constraints that impose the necessary conditions for glycolytic flux to generate lactate as opposed to entering into the mitochondria. These conditions are determined by cellular redox and energy demands. By analyzing the constraints and sampling the feasible region of the model, we further study how cell proliferation rate and mitochondria-associated NADH oxidizing and ATP producing fluxes are interlinked. Together this analysis illustrates the simplicity of the origins of the Warburg effect by identifying the flux distributions that are necessary for its instantiation.

Authors
Dai, Z; Shestov, AA; Lai, L; Locasale, JW
MLA Citation
Dai, Z, Shestov, AA, Lai, L, and Locasale, JW. "A Flux Balance of Glucose Metabolism Clarifies the Requirements of the Warburg Effect." Biophysical journal 111.5 (September 2016): 1088-1100.
PMID
27602736
Source
epmc
Published In
Biophysical Journal
Volume
111
Issue
5
Publish Date
2016
Start Page
1088
End Page
1100
DOI
10.1016/j.bpj.2016.07.028

IKKβ promotes metabolic adaptation to glutamine deprivation via phosphorylation and inhibition of PFKFB3.

Glutamine is an essential nutrient for cancer cell survival and proliferation. Enhanced utilization of glutamine often depletes its local supply, yet how cancer cells adapt to low glutamine conditions is largely unknown. Here, we report that IκB kinase β (IKKβ) is activated upon glutamine deprivation and is required for cell survival independently of NF-κB transcription. We demonstrate that IKKβ directly interacts with and phosphorylates 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase isoform 3 (PFKFB3), a major driver of aerobic glycolysis, at Ser269 upon glutamine deprivation to inhibit its activity, thereby down-regulating aerobic glycolysis when glutamine levels are low. Thus, due to lack of inhibition of PFKFB3, IKKβ-deficient cells exhibit elevated aerobic glycolysis and lactate production, leading to less glucose carbons contributing to tricarboxylic acid (TCA) cycle intermediates and the pentose phosphate pathway, which results in increased glutamine dependence for both TCA cycle intermediates and reactive oxygen species suppression. Therefore, coinhibition of IKKβ and glutamine metabolism results in dramatic synergistic killing of cancer cells both in vitro and in vivo. In all, our results uncover a previously unidentified role of IKKβ in regulating glycolysis, sensing low-glutamine-induced metabolic stress, and promoting cellular adaptation to nutrient availability.

Authors
Reid, MA; Lowman, XH; Pan, M; Tran, TQ; Warmoes, MO; Ishak Gabra, MB; Yang, Y; Locasale, JW; Kong, M
MLA Citation
Reid, MA, Lowman, XH, Pan, M, Tran, TQ, Warmoes, MO, Ishak Gabra, MB, Yang, Y, Locasale, JW, and Kong, M. "IKKβ promotes metabolic adaptation to glutamine deprivation via phosphorylation and inhibition of PFKFB3." Genes & development 30.16 (August 2016): 1837-1851.
PMID
27585591
Source
epmc
Published In
Genes & development
Volume
30
Issue
16
Publish Date
2016
Start Page
1837
End Page
1851
DOI
10.1101/gad.287235.116

Metabolism: A new layer of glycolysis.

Authors
Liberti, MV; Locasale, JW
MLA Citation
Liberti, MV, and Locasale, JW. "Metabolism: A new layer of glycolysis." Nature chemical biology 12.8 (July 2016): 577-578.
PMID
27434766
Source
epmc
Published In
Nature Chemical Biology
Volume
12
Issue
8
Publish Date
2016
Start Page
577
End Page
578
DOI
10.1038/nchembio.2133

The metabolic co-regulator PGC1α suppresses prostate cancer metastasis.

Cellular transformation and cancer progression is accompanied by changes in the metabolic landscape. Master co-regulators of metabolism orchestrate the modulation of multiple metabolic pathways through transcriptional programs, and hence constitute a probabilistically parsimonious mechanism for general metabolic rewiring. Here we show that the transcriptional co-activator peroxisome proliferator-activated receptor gamma co-activator 1α (PGC1α) suppresses prostate cancer progression and metastasis. A metabolic co-regulator data mining analysis unveiled that PGC1α is downregulated in prostate cancer and associated with disease progression. Using genetically engineered mouse models and xenografts, we demonstrated that PGC1α opposes prostate cancer progression and metastasis. Mechanistically, the use of integrative metabolomics and transcriptomics revealed that PGC1α activates an oestrogen-related receptor alpha (ERRα)-dependent transcriptional program to elicit a catabolic state and metastasis suppression. Importantly, a signature based on the PGC1α-ERRα pathway exhibited prognostic potential in prostate cancer, thus uncovering the relevance of monitoring and manipulating this pathway for prostate cancer stratification and treatment.

Authors
Torrano, V; Valcarcel-Jimenez, L; Cortazar, AR; Liu, X; Urosevic, J; Castillo-Martin, M; Fernández-Ruiz, S; Morciano, G; Caro-Maldonado, A; Guiu, M; Zúñiga-García, P; Graupera, M; Bellmunt, A; Pandya, P; Lorente, M; Martín-Martín, N; David Sutherland, J; Sanchez-Mosquera, P; Bozal-Basterra, L; Zabala-Letona, A; Arruabarrena-Aristorena, A; Berenguer, A; Embade, N; Ugalde-Olano, A; Lacasa-Viscasillas, I; Loizaga-Iriarte, A; Unda-Urzaiz, M; Schultz, N; Aransay, AM; Sanz-Moreno, V; Barrio, R et al.
MLA Citation
Torrano, V, Valcarcel-Jimenez, L, Cortazar, AR, Liu, X, Urosevic, J, Castillo-Martin, M, Fernández-Ruiz, S, Morciano, G, Caro-Maldonado, A, Guiu, M, Zúñiga-García, P, Graupera, M, Bellmunt, A, Pandya, P, Lorente, M, Martín-Martín, N, David Sutherland, J, Sanchez-Mosquera, P, Bozal-Basterra, L, Zabala-Letona, A, Arruabarrena-Aristorena, A, Berenguer, A, Embade, N, Ugalde-Olano, A, Lacasa-Viscasillas, I, Loizaga-Iriarte, A, Unda-Urzaiz, M, Schultz, N, Aransay, AM, Sanz-Moreno, V, and Barrio, R et al. "The metabolic co-regulator PGC1α suppresses prostate cancer metastasis." Nature cell biology 18.6 (June 2016): 645-656.
PMID
27214280
Source
epmc
Published In
Nature Cell Biology
Volume
18
Issue
6
Publish Date
2016
Start Page
645
End Page
656
DOI
10.1038/ncb3357

Targeting One Carbon Metabolism with an Antimetabolite Disrupts Pyrimidine Homeostasis and Induces Nucleotide Overflow.

Antimetabolites that affect nucleotide metabolism are frontline chemotherapy agents in several cancers and often successfully target one carbon metabolism. However, the precise mechanisms and resulting determinants of their therapeutic value are unknown. We show that 5-fluorouracil (5-FU), a commonly used antimetabolite therapeutic with varying efficacy, induces specific alterations to nucleotide metabolism by disrupting pyrimidine homeostasis. An integrative metabolomics analysis of the cellular response to 5-FU reveals intracellular uracil accumulation, whereas deoxyuridine levels exhibited increased flux into the extracellular space, resulting in an induction of overflow metabolism. Subsequent analysis from mice bearing colorectal tumors treated with 5-FU show specific secretion of metabolites in tumor-bearing mice into serum that results from alterations in nucleotide flux and reduction in overflow metabolism. Together, these findings identify a determinant of an antimetabolite response that may be exploited to more precisely define the tumors that could respond to targeting cancer metabolism.

Authors
Ser, Z; Gao, X; Johnson, C; Mehrmohamadi, M; Liu, X; Li, S; Locasale, JW
MLA Citation
Ser, Z, Gao, X, Johnson, C, Mehrmohamadi, M, Liu, X, Li, S, and Locasale, JW. "Targeting One Carbon Metabolism with an Antimetabolite Disrupts Pyrimidine Homeostasis and Induces Nucleotide Overflow." Cell reports 15.11 (June 2016): 2367-2376.
PMID
27264180
Source
epmc
Published In
Cell Reports
Volume
15
Issue
11
Publish Date
2016
Start Page
2367
End Page
2376
DOI
10.1016/j.celrep.2016.05.035

Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function.

Cellular metabolites, such as acyl-CoA, can modify proteins, leading to protein posttranslational modifications (PTMs). One such PTM is lysine succinylation, which is regulated by sirtuin 5 (SIRT5). Although numerous proteins are modified by lysine succinylation, the physiological significance of lysine succinylation and SIRT5 remains elusive. Here, by profiling acyl-CoA molecules in various mouse tissues, we have discovered that different tissues have different acyl-CoA profiles and that succinyl-CoA is the most abundant acyl-CoA molecule in the heart. This interesting observation has prompted us to examine protein lysine succinylation in different mouse tissues in the presence and absence of SIRT5. Protein lysine succinylation predominantly accumulates in the heart whenSirt5is deleted. Using proteomic studies, we have identified many cardiac proteins regulated by SIRT5. Our data suggest that ECHA, a protein involved in fatty acid oxidation, is a major enzyme that is regulated by SIRT5 and affects heart function.Sirt5knockout (KO) mice have lower ECHA activity, increased long-chain acyl-CoAs, and decreased ATP in the heart under fasting conditions.Sirt5KO mice develop hypertrophic cardiomyopathy, as evident from the increased heart weight relative to body weight, as well as reduced shortening and ejection fractions. These findings establish that regulating heart metabolism and function is a major physiological function of lysine succinylation and SIRT5.

Authors
Sadhukhan, S; Liu, X; Ryu, D; Nelson, OD; Stupinski, JA; Li, Z; Chen, W; Zhang, S; Weiss, RS; Locasale, JW; Auwerx, J; Lin, H
MLA Citation
Sadhukhan, S, Liu, X, Ryu, D, Nelson, OD, Stupinski, JA, Li, Z, Chen, W, Zhang, S, Weiss, RS, Locasale, JW, Auwerx, J, and Lin, H. "Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function." Proceedings of the National Academy of Sciences of the United States of America 113.16 (April 5, 2016): 4320-4325.
PMID
27051063
Source
epmc
Published In
Proceedings of the National Academy of Sciences of USA
Volume
113
Issue
16
Publish Date
2016
Start Page
4320
End Page
4325
DOI
10.1073/pnas.1519858113

ERRα-Regulated Lactate Metabolism Contributes to Resistance to Targeted Therapies in Breast Cancer.

Imaging studies in animals and in humans have indicated that the oxygenation and nutritional status of solid tumors is dynamic. Furthermore, the extremely low level of glucose within tumors, while reflecting its rapid uptake and metabolism, also suggests that cancer cells must rely on other energy sources in some circumstances. Here, we find that some breast cancer cells can switch to utilizing lactate as a primary source of energy, allowing them to survive glucose deprivation for extended periods, and that this activity confers resistance to PI3K/mTOR inhibitors. The nuclear receptor, estrogen-related receptor alpha (ERRα), was shown to regulate the expression of genes required for lactate utilization, and isotopomer analysis revealed that genetic or pharmacological inhibition of ERRα activity compromised lactate oxidation. Importantly, ERRα antagonists increased the in vitro and in vivo efficacy of PI3K/mTOR inhibitors, highlighting the potential clinical utility of this drug combination.

Authors
Park, S; Chang, C-Y; Safi, R; Liu, X; Baldi, R; Jasper, JS; Anderson, GR; Liu, T; Rathmell, JC; Dewhirst, MW; Wood, KC; Locasale, JW; McDonnell, DP
MLA Citation
Park, S, Chang, C-Y, Safi, R, Liu, X, Baldi, R, Jasper, JS, Anderson, GR, Liu, T, Rathmell, JC, Dewhirst, MW, Wood, KC, Locasale, JW, and McDonnell, DP. "ERRα-Regulated Lactate Metabolism Contributes to Resistance to Targeted Therapies in Breast Cancer." Cell reports 15.2 (April 2016): 323-335.
PMID
27050525
Source
epmc
Published In
Cell Reports
Volume
15
Issue
2
Publish Date
2016
Start Page
323
End Page
335
DOI
10.1016/j.celrep.2016.03.026

AMPK Is Essential to Balance Glycolysis and Mitochondrial Metabolism to Control T-ALL Cell Stress and Survival.

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy associated with Notch pathway mutations. While both normal activated and leukemic T cells can utilize aerobic glycolysis to support proliferation, it is unclear to what extent these cell populations are metabolically similar and if differences reveal T-ALL vulnerabilities. Here we show that aerobic glycolysis is surprisingly less active in T-ALL cells than proliferating normal T cells and that T-ALL cells are metabolically distinct. Oncogenic Notch promoted glycolysis but also induced metabolic stress that activated 5' AMP-activated kinase (AMPK). Unlike stimulated T cells, AMPK actively restrained aerobic glycolysis in T-ALL cells through inhibition of mTORC1 while promoting oxidative metabolism and mitochondrial Complex I activity. Importantly, AMPK deficiency or inhibition of Complex I led to T-ALL cell death and reduced disease burden. Thus, AMPK simultaneously inhibits anabolic growth signaling and is essential to promote mitochondrial pathways that mitigate metabolic stress and apoptosis in T-ALL.

Authors
Kishton, RJ; Barnes, CE; Nichols, AG; Cohen, S; Gerriets, VA; Siska, PJ; Macintyre, AN; Goraksha-Hicks, P; de Cubas, AA; Liu, T; Warmoes, MO; Abel, ED; Yeoh, AEJ; Gershon, TR; Rathmell, WK; Richards, KL; Locasale, JW; Rathmell, JC
MLA Citation
Kishton, RJ, Barnes, CE, Nichols, AG, Cohen, S, Gerriets, VA, Siska, PJ, Macintyre, AN, Goraksha-Hicks, P, de Cubas, AA, Liu, T, Warmoes, MO, Abel, ED, Yeoh, AEJ, Gershon, TR, Rathmell, WK, Richards, KL, Locasale, JW, and Rathmell, JC. "AMPK Is Essential to Balance Glycolysis and Mitochondrial Metabolism to Control T-ALL Cell Stress and Survival." Cell metabolism 23.4 (April 2016): 649-662.
PMID
27076078
Source
epmc
Published In
Cell Metabolism
Volume
23
Issue
4
Publish Date
2016
Start Page
649
End Page
662
DOI
10.1016/j.cmet.2016.03.008

Downregulation of hepatic betaine:homocysteine methyltransferase (BHMT) expression in taurine-deficient mice is reversed by taurine supplementation in vivo.

The cysteine dioxygenase (Cdo1)-null and the cysteine sulfinic acid decarboxylase (Csad)-null mouse are not able to synthesize hypotaurine/taurine by the cysteine/cysteine sulfinate pathway and have very low tissue taurine levels. These mice provide excellent models for studying the effects of taurine on biological processes. Using these mouse models, we identified betaine:homocysteine methyltransferase (BHMT) as a protein whose in vivo expression is robustly regulated by taurine. BHMT levels are low in liver of both Cdo1-null and Csad-null mice, but are restored to wild-type levels by dietary taurine supplementation. A lack of BHMT activity was indicated by an increase in the hepatic betaine level. In contrast to observations in liver of Cdo1-null and Csad-null mice, BHMT was not affected by taurine supplementation of primary hepatocytes from these mice. Likewise, CSAD abundance was not affected by taurine supplementation of primary hepatocytes, although it was robustly upregulated in liver of Cdo1-null and Csad-null mice and lowered to wild-type levels by dietary taurine supplementation. The mechanism by which taurine status affects hepatic CSAD and BHMT expression appears to be complex and to require factors outside of hepatocytes. Within the liver, mRNA abundance for both CSAD and BHMT was upregulated in parallel with protein levels, indicating regulation of BHMT and CSAD mRNA synthesis or degradation.

Authors
Jurkowska, H; Niewiadomski, J; Hirschberger, LL; Roman, HB; Mazor, KM; Liu, X; Locasale, JW; Park, E; Stipanuk, MH
MLA Citation
Jurkowska, H, Niewiadomski, J, Hirschberger, LL, Roman, HB, Mazor, KM, Liu, X, Locasale, JW, Park, E, and Stipanuk, MH. "Downregulation of hepatic betaine:homocysteine methyltransferase (BHMT) expression in taurine-deficient mice is reversed by taurine supplementation in vivo." Amino acids 48.3 (March 2016): 665-676.
PMID
26481005
Source
epmc
Published In
Amino Acids
Volume
48
Issue
3
Publish Date
2016
Start Page
665
End Page
676
DOI
10.1007/s00726-015-2108-9

The Warburg Effect: How Does it Benefit Cancer Cells?

Cancer cells rewire their metabolism to promote growth, survival, proliferation, and long-term maintenance. The common feature of this altered metabolism is the increased glucose uptake and fermentation of glucose to lactate. This phenomenon is observed even in the presence of completely functioning mitochondria and, together, is known as the 'Warburg Effect'. The Warburg Effect has been documented for over 90 years and extensively studied over the past 10 years, with thousands of papers reporting to have established either its causes or its functions. Despite this intense interest, the function of the Warburg Effect remains unclear. Here, we analyze several proposed explanations for the function of Warburg Effect, emphasize their rationale, and discuss their controversies.

Authors
Liberti, MV; Locasale, JW
MLA Citation
Liberti, MV, and Locasale, JW. "The Warburg Effect: How Does it Benefit Cancer Cells?." Trends in biochemical sciences 41.3 (March 2016): 211-218. (Review)
PMID
26778478
Source
epmc
Published In
Trends in Biochemical Sciences
Volume
41
Issue
3
Publish Date
2016
Start Page
211
End Page
218
DOI
10.1016/j.tibs.2015.12.001

Correction to: ‘The Warburg Effect: How Does it Benefit Cancer Cells?’

Authors
Liberti, MV; Locasale, JW
MLA Citation
Liberti, MV, and Locasale, JW. "Correction to: ‘The Warburg Effect: How Does it Benefit Cancer Cells?’." Trends in Biochemical Sciences 41.3 (March 2016): 287-287.
Source
crossref
Published In
Trends in Biochemical Sciences
Volume
41
Issue
3
Publish Date
2016
Start Page
287
End Page
287
DOI
10.1016/j.tibs.2016.01.004

Sphingosine kinase 1 as a mediator and predictor of metformin's protective effect in ovarian cancer.

Authors
Chiyoda, T; Liu, X; Lengyel, E; Locasale, J; Romero, I
MLA Citation
Chiyoda, T, Liu, X, Lengyel, E, Locasale, J, and Romero, I. "Sphingosine kinase 1 as a mediator and predictor of metformin's protective effect in ovarian cancer." CLINICAL CANCER RESEARCH 22 (January 15, 2016).
Source
wos-lite
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
22
Publish Date
2016

The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis.

While cellular GTP concentration dramatically changes in response to an organism's cellular status, whether it serves as a metabolic cue for biological signaling remains elusive due to the lack of molecular identification of GTP sensors. Here we report that PI5P4Kβ, a phosphoinositide kinase that regulates PI(5)P levels, detects GTP concentration and converts them into lipid second messenger signaling. Biochemical analyses show that PI5P4Kβ preferentially utilizes GTP, rather than ATP, for PI(5)P phosphorylation, and its activity reflects changes in direct proportion to the physiological GTP concentration. Structural and biological analyses reveal that the GTP-sensing activity of PI5P4Kβ is critical for metabolic adaptation and tumorigenesis. These results demonstrate that PI5P4Kβ is the missing GTP sensor and that GTP concentration functions as a metabolic cue via PI5P4Kβ. The critical role of the GTP-sensing activity of PI5P4Kβ in cancer signifies this lipid kinase as a cancer therapeutic target.

Authors
Sumita, K; Lo, Y-H; Takeuchi, K; Senda, M; Kofuji, S; Ikeda, Y; Terakawa, J; Sasaki, M; Yoshino, H; Majd, N; Zheng, Y; Kahoud, ER; Yokota, T; Emerling, BM; Asara, JM; Ishida, T; Locasale, JW; Daikoku, T; Anastasiou, D; Senda, T; Sasaki, AT
MLA Citation
Sumita, K, Lo, Y-H, Takeuchi, K, Senda, M, Kofuji, S, Ikeda, Y, Terakawa, J, Sasaki, M, Yoshino, H, Majd, N, Zheng, Y, Kahoud, ER, Yokota, T, Emerling, BM, Asara, JM, Ishida, T, Locasale, JW, Daikoku, T, Anastasiou, D, Senda, T, and Sasaki, AT. "The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis." Molecular cell 61.2 (January 5, 2016): 187-198.
PMID
26774281
Source
epmc
Published In
Molecular Cell
Volume
61
Issue
2
Publish Date
2016
Start Page
187
End Page
198
DOI
10.1016/j.molcel.2015.12.011

One-carbon metabolism and epigenetics: understanding the specificity.

One-carbon metabolism is a metabolic network that integrates nutrient status from the environment to yield multiple biological functions. The folate and methionine cycles generate S-adenosylmethionine (SAM), which is the universal methyl donor for methylation reactions, including histone and DNA methylation. Histone methylation is a crucial part of the epigenetic code and plays diverse roles in the establishment of chromatin states that mediate the regulation of gene expression. The activities of histone methyltransferases (HMTs) are dependent on intracellular levels of SAM, which fluctuate based on cellular nutrient availability, providing a link between cell metabolism and histone methylation. Here we discuss the biochemical properties of HMTs, their role in gene regulation, and the connection to cellular metabolism. Our emphasis is on understanding the specificity of this intriguing link.

Authors
Mentch, SJ; Locasale, JW
MLA Citation
Mentch, SJ, and Locasale, JW. "One-carbon metabolism and epigenetics: understanding the specificity." Annals of the New York Academy of Sciences 1363 (January 2016): 91-98. (Review)
PMID
26647078
Source
epmc
Published In
Annals of the New York Academy of Sciences
Volume
1363
Publish Date
2016
Start Page
91
End Page
98
DOI
10.1111/nyas.12956

Effects of a block in cysteine catabolism on energy balance and fat metabolism in mice.

To gain further insights into the effects of elevated cysteine levels on energy metabolism and the possible mechanisms underlying these effects, we conducted studies in cysteine dioxygenase (Cdo1)-null mice. Cysteine dioxygenase (CDO) catalyzes the first step of the major pathway for cysteine catabolism. When CDO is absent, tissue and plasma cysteine levels are elevated, resulting in enhanced flux of cysteine through desulfhydration reactions. When Cdo1-null mice were fed a high-fat diet, they gained more weight than their wild-type controls, regardless of whether the diet was supplemented with taurine. Cdo1-null mice had markedly lower leptin levels, higher feed intakes, and markedly higher abundance of hepatic stearoyl-CoA desaturase 1 (SCD1) compared to wild-type control mice, and these differences were not affected by the fat or taurine content of the diet. Thus, reported associations of elevated cysteine levels with greater weight gain and with elevated hepatic Scd1 expression are also seen in the Cdo1-null mouse model. Hepatic accumulation of acylcarnitines suggests impaired mitochondrial β-oxidation of fatty acids in Cdo1-null mice. The strong associations of elevated cysteine levels with excess H2 S production and impairments in energy metabolism suggest that H2 S signaling could be involved.

Authors
Niewiadomski, J; Zhou, JQ; Roman, HB; Liu, X; Hirschberger, LL; Locasale, JW; Stipanuk, MH
MLA Citation
Niewiadomski, J, Zhou, JQ, Roman, HB, Liu, X, Hirschberger, LL, Locasale, JW, and Stipanuk, MH. "Effects of a block in cysteine catabolism on energy balance and fat metabolism in mice." Annals of the New York Academy of Sciences 1363 (January 2016): 99-115.
PMID
26995761
Source
epmc
Published In
Annals of the New York Academy of Sciences
Volume
1363
Publish Date
2016
Start Page
99
End Page
115
DOI
10.1111/nyas.13021

A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data.

A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with high-throughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability and improve our understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present an algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation, the ability to handle large enzyme complex rules that may incorporate multiple isoforms, and either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB.

Authors
Barker, BE; Sadagopan, N; Wang, Y; Smallbone, K; Myers, CR; Xi, H; Locasale, JW; Gu, Z
MLA Citation
Barker, BE, Sadagopan, N, Wang, Y, Smallbone, K, Myers, CR, Xi, H, Locasale, JW, and Gu, Z. "A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data." Computational biology and chemistry 59 Pt B (December 2015): 98-112.
PMID
26381164
Source
epmc
Published In
Computational Biology and Chemistry
Volume
59 Pt B
Publish Date
2015
Start Page
98
End Page
112
DOI
10.1016/j.compbiolchem.2015.08.002

Dysregulated metabolism contributes to oncogenesis.

Cancer is a disease characterized by unrestrained cellular proliferation. In order to sustain growth, cancer cells undergo a complex metabolic rearrangement characterized by changes in metabolic pathways involved in energy production and biosynthetic processes. The relevance of the metabolic transformation of cancer cells has been recently included in the updated version of the review "Hallmarks of Cancer", where dysregulation of cellular metabolism was included as an emerging hallmark. While several lines of evidence suggest that metabolic rewiring is orchestrated by the concerted action of oncogenes and tumor suppressor genes, in some circumstances altered metabolism can play a primary role in oncogenesis. Recently, mutations of cytosolic and mitochondrial enzymes involved in key metabolic pathways have been associated with hereditary and sporadic forms of cancer. Together, these results demonstrate that aberrant metabolism, once seen just as an epiphenomenon of oncogenic reprogramming, plays a key role in oncogenesis with the power to control both genetic and epigenetic events in cells. In this review, we discuss the relationship between metabolism and cancer, as part of a larger effort to identify a broad-spectrum of therapeutic approaches. We focus on major alterations in nutrient metabolism and the emerging link between metabolism and epigenetics. Finally, we discuss potential strategies to manipulate metabolism in cancer and tradeoffs that should be considered. More research on the suite of metabolic alterations in cancer holds the potential to discover novel approaches to treat it.

Authors
Hirschey, MD; DeBerardinis, RJ; Diehl, AME; Drew, JE; Frezza, C; Green, MF; Jones, LW; Ko, YH; Le, A; Lea, MA; Locasale, JW; Longo, VD; Lyssiotis, CA; McDonnell, E; Mehrmohamadi, M; Michelotti, G; Muralidhar, V; Murphy, MP; Pedersen, PL; Poore, B; Raffaghello, L; Rathmell, JC; Sivanand, S; Vander Heiden, MG; Wellen, KE
MLA Citation
Hirschey, MD, DeBerardinis, RJ, Diehl, AME, Drew, JE, Frezza, C, Green, MF, Jones, LW, Ko, YH, Le, A, Lea, MA, Locasale, JW, Longo, VD, Lyssiotis, CA, McDonnell, E, Mehrmohamadi, M, Michelotti, G, Muralidhar, V, Murphy, MP, Pedersen, PL, Poore, B, Raffaghello, L, Rathmell, JC, Sivanand, S, Vander Heiden, MG, and Wellen, KE. "Dysregulated metabolism contributes to oncogenesis." Seminars in cancer biology 35 Suppl (December 2015): S129-S150. (Review)
PMID
26454069
Source
epmc
Published In
Seminars in Cancer Biology
Volume
35 Suppl
Publish Date
2015
Start Page
S129
End Page
S150
DOI
10.1016/j.semcancer.2015.10.002

Designing a broad-spectrum integrative approach for cancer prevention and treatment.

Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment. Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered.

Authors
Block, KI; Gyllenhaal, C; Lowe, L; Amedei, A; Amin, ARMR; Amin, A; Aquilano, K; Arbiser, J; Arreola, A; Arzumanyan, A; Ashraf, SS; Azmi, AS; Benencia, F; Bhakta, D; Bilsland, A; Bishayee, A; Blain, SW; Block, PB; Boosani, CS; Carey, TE; Carnero, A; Carotenuto, M; Casey, SC; Chakrabarti, M; Chaturvedi, R; Chen, GZ; Chen, H; Chen, S; Chen, YC; Choi, BK; Ciriolo, MR; Coley, HM; Collins, AR; Connell, M; Crawford, S; Curran, CS; Dabrosin, C; Damia, G; Dasgupta, S; DeBerardinis, RJ; Decker, WK et al.
MLA Citation
Block, KI, Gyllenhaal, C, Lowe, L, Amedei, A, Amin, ARMR, Amin, A, Aquilano, K, Arbiser, J, Arreola, A, Arzumanyan, A, Ashraf, SS, Azmi, AS, Benencia, F, Bhakta, D, Bilsland, A, Bishayee, A, Blain, SW, Block, PB, Boosani, CS, Carey, TE, Carnero, A, Carotenuto, M, Casey, SC, Chakrabarti, M, Chaturvedi, R, Chen, GZ, Chen, H, Chen, S, Chen, YC, Choi, BK, Ciriolo, MR, Coley, HM, Collins, AR, Connell, M, Crawford, S, Curran, CS, Dabrosin, C, Damia, G, Dasgupta, S, DeBerardinis, RJ, and Decker, WK et al. "Designing a broad-spectrum integrative approach for cancer prevention and treatment." Seminars in cancer biology 35 Suppl (December 2015): S276-S304. (Review)
PMID
26590477
Source
epmc
Published In
Seminars in Cancer Biology
Volume
35 Suppl
Publish Date
2015
Start Page
S276
End Page
S304
DOI
10.1016/j.semcancer.2015.09.007

Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation.

The protein substrates of sirtuin 5-regulated lysine malonylation (Kmal) remain unknown, hindering its functional analysis. In this study, we carried out proteomic screening, which identified 4042 Kmal sites on 1426 proteins in mouse liver and 4943 Kmal sites on 1822 proteins in human fibroblasts. Increased malonyl-CoA levels in malonyl-CoA decarboxylase (MCD)-deficient cells induces Kmal levels in substrate proteins. We identified 461 Kmal sites showing more than a 2-fold increase in response to MCD deficiency as well as 1452 Kmal sites detected only in MCD-/- fibroblast but not MCD+/+ cells, suggesting a pathogenic role of Kmal in MCD deficiency. Cells with increased lysine malonylation displayed impaired mitochondrial function and fatty acid oxidation, suggesting that lysine malonylation plays a role in pathophysiology of malonic aciduria. Our study establishes an association between Kmal and a genetic disease and offers a rich resource for elucidating the contribution of the Kmal pathway and malonyl-CoA to cellular physiology and human diseases.

Authors
Colak, G; Pougovkina, O; Dai, L; Tan, M; Te Brinke, H; Huang, H; Cheng, Z; Park, J; Wan, X; Liu, X; Yue, WW; Wanders, RJA; Locasale, JW; Lombard, DB; de Boer, VCJ; Zhao, Y
MLA Citation
Colak, G, Pougovkina, O, Dai, L, Tan, M, Te Brinke, H, Huang, H, Cheng, Z, Park, J, Wan, X, Liu, X, Yue, WW, Wanders, RJA, Locasale, JW, Lombard, DB, de Boer, VCJ, and Zhao, Y. "Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation." Molecular & cellular proteomics : MCP 14.11 (November 2015): 3056-3071.
PMID
26320211
Source
epmc
Published In
Molecular & cellular proteomics : MCP
Volume
14
Issue
11
Publish Date
2015
Start Page
3056
End Page
3071
DOI
10.1074/mcp.m115.048850

Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism.

S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) link one-carbon metabolism to methylation status. However, it is unknown whether regulation of SAM and SAH by nutrient availability can be directly sensed to alter the kinetics of key histone methylation marks. We provide evidence that the status of methionine metabolism is sufficient to determine levels of histone methylation by modulating SAM and SAH. This dynamic interaction led to rapid changes in H3K4me3, altered gene transcription, provided feedback regulation to one-carbon metabolism, and could be fully recovered upon restoration of methionine. Modulation of methionine in diet led to changes in metabolism and histone methylation in the liver. In humans, methionine variability in fasting serum was commensurate with concentrations needed for these dynamics and could be partly explained by diet. Together these findings demonstrate that flux through methionine metabolism and the sensing of methionine availability may allow direct communication to the chromatin state in cells.

Authors
Mentch, SJ; Mehrmohamadi, M; Huang, L; Liu, X; Gupta, D; Mattocks, D; Gómez Padilla, P; Ables, G; Bamman, MM; Thalacker-Mercer, AE; Nichenametla, SN; Locasale, JW
MLA Citation
Mentch, SJ, Mehrmohamadi, M, Huang, L, Liu, X, Gupta, D, Mattocks, D, Gómez Padilla, P, Ables, G, Bamman, MM, Thalacker-Mercer, AE, Nichenametla, SN, and Locasale, JW. "Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism." Cell metabolism 22.5 (November 2015): 861-873.
PMID
26411344
Source
epmc
Published In
Cell Metabolism
Volume
22
Issue
5
Publish Date
2015
Start Page
861
End Page
873
DOI
10.1016/j.cmet.2015.08.024

Adaptive changes in amino acid metabolism permit normal longevity in mice consuming a low-carbohydrate ketogenic diet.

Ingestion of very low-carbohydrate ketogenic diets (KD) is associated with weight loss, lowering of glucose and insulin levels and improved systemic insulin sensitivity. However, the beneficial effects of long-term feeding have been the subject of debate. We therefore studied the effects of lifelong consumption of this diet in mice. Complete metabolic analyses were performed after 8 and 80weeks on the diet. In addition we performed a serum metabolomic analysis and examined hepatic gene expression. Lifelong consumption of KD had no effect on morbidity or mortality (KD vs. Chow, 676 vs. 630days) despite hepatic steatosis and inflammation in KD mice. The KD fed mice lost weight initially as previously reported (Kennnedy et al., 2007) and remained lighter and had less fat mass; KD consuming mice had higher levels of energy expenditure, improved glucose homeostasis and higher circulating levels of β-hydroxybutyrate and triglycerides than chow-fed controls. Hepatic expression of the critical metabolic regulators including fibroblast growth factor 21 were also higher in KD-fed mice while expression levels of lipogenic enzymes such as stearoyl-CoA desaturase-1 was reduced. Metabolomic analysis revealed compensatory changes in amino acid metabolism, primarily involving down-regulation of catabolic processes, demonstrating that mice eating KD can shift amino acid metabolism to conserve amino acid levels. Long-term KD feeding caused profound and persistent metabolic changes, the majority of which are seen as health promoting, and had no adverse effects on survival in mice.

Authors
Douris, N; Melman, T; Pecherer, JM; Pissios, P; Flier, JS; Cantley, LC; Locasale, JW; Maratos-Flier, E
MLA Citation
Douris, N, Melman, T, Pecherer, JM, Pissios, P, Flier, JS, Cantley, LC, Locasale, JW, and Maratos-Flier, E. "Adaptive changes in amino acid metabolism permit normal longevity in mice consuming a low-carbohydrate ketogenic diet." Biochimica et biophysica acta 1852.10 Pt A (October 2015): 2056-2065.
PMID
26170063
Source
epmc
Published In
Biochimica et Biophysica Acta: international journal of biochemistry and biophysics
Volume
1852
Issue
10 Pt A
Publish Date
2015
Start Page
2056
End Page
2065
DOI
10.1016/j.bbadis.2015.07.009

Context dependent utilization of serine in cancer.

Serine and glycine have diverse biological functions but the general and context dependent utilizations of these nutrients in cancer are unknown. Our recent work integrates genomics data and isotope tracing using computational tools to study serine utilization across multiple cancer and normal human samples.

Authors
Mehrmohamadi, M; Locasale, JW
MLA Citation
Mehrmohamadi, M, and Locasale, JW. "Context dependent utilization of serine in cancer." Molecular & cellular oncology 2.4 (October 2015): e996418-.
PMID
26550606
Source
epmc
Published In
Molecular & cellular oncology
Volume
2
Issue
4
Publish Date
2015
Start Page
e996418
DOI
10.1080/23723556.2014.996418

Mitophagy defects arising from BNip3 loss promote mammary tumor progression to metastasis.

BNip3 is a hypoxia-inducible protein that targets mitochondria for autophagosomal degradation. We report a novel tumor suppressor role for BNip3 in a clinically relevant mouse model of mammary tumorigenesis. BNip3 delays primary mammary tumor growth and progression by preventing the accumulation of dysfunctional mitochondria and resultant excess ROS production. In the absence of BNip3, mammary tumor cells are unable to reduce mitochondrial mass effectively and elevated mitochondrial ROS increases the expression of Hif-1α and Hif target genes, including those involved in glycolysis and angiogenesis—two processes that are also markedly increased in BNip3-null tumors. Glycolysis inhibition attenuates the growth of BNip3-null tumor cells, revealing an increased dependence on autophagy for survival. We also demonstrate that BNIP3 deletion can be used as a prognostic marker of tumor progression to metastasis in human triple-negative breast cancer (TNBC). These studies show that mitochondrial dysfunction—caused by defects in mitophagy—can promote the Warburg effect and tumor progression, and suggest better approaches to stratifying TNBC for treatment.

Authors
Chourasia, AH; Tracy, K; Frankenberger, C; Boland, ML; Sharifi, MN; Drake, LE; Sachleben, JR; Asara, JM; Locasale, JW; Karczmar, GS; Macleod, KF
MLA Citation
Chourasia, AH, Tracy, K, Frankenberger, C, Boland, ML, Sharifi, MN, Drake, LE, Sachleben, JR, Asara, JM, Locasale, JW, Karczmar, GS, and Macleod, KF. "Mitophagy defects arising from BNip3 loss promote mammary tumor progression to metastasis." EMBO reports 16.9 (September 2015): 1145-1163.
PMID
26232272
Source
epmc
Published In
EMBO Reports
Volume
16
Issue
9
Publish Date
2015
Start Page
1145
End Page
1163
DOI
10.15252/embr.201540759

Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses.

Activated T cells engage aerobic glycolysis and anabolic metabolism for growth, proliferation, and effector functions. We propose that a glucose-poor tumor microenvironment limits aerobic glycolysis in tumor-infiltrating T cells, which suppresses tumoricidal effector functions. We discovered a new role for the glycolytic metabolite phosphoenolpyruvate (PEP) in sustaining T cell receptor-mediated Ca(2+)-NFAT signaling and effector functions by repressing sarco/ER Ca(2+)-ATPase (SERCA) activity. Tumor-specific CD4 and CD8 T cells could be metabolically reprogrammed by increasing PEP production through overexpression of phosphoenolpyruvate carboxykinase 1 (PCK1), which bolstered effector functions. Moreover, PCK1-overexpressing T cells restricted tumor growth and prolonged the survival of melanoma-bearing mice. This study uncovers new metabolic checkpoints for T cell activity and demonstrates that metabolic reprogramming of tumor-reactive T cells can enhance anti-tumor T cell responses, illuminating new forms of immunotherapy.

Authors
Ho, P-C; Bihuniak, JD; Macintyre, AN; Staron, M; Liu, X; Amezquita, R; Tsui, Y-C; Cui, G; Micevic, G; Perales, JC; Kleinstein, SH; Abel, ED; Insogna, KL; Feske, S; Locasale, JW; Bosenberg, MW; Rathmell, JC; Kaech, SM
MLA Citation
Ho, P-C, Bihuniak, JD, Macintyre, AN, Staron, M, Liu, X, Amezquita, R, Tsui, Y-C, Cui, G, Micevic, G, Perales, JC, Kleinstein, SH, Abel, ED, Insogna, KL, Feske, S, Locasale, JW, Bosenberg, MW, Rathmell, JC, and Kaech, SM. "Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses." Cell 162.6 (September 2015): 1217-1228.
PMID
26321681
Source
epmc
Published In
Cell
Volume
162
Issue
6
Publish Date
2015
Start Page
1217
End Page
1228
DOI
10.1016/j.cell.2015.08.012

Abstract POSTER-TECH-1123: Advancing metformin as therapeutic for ovarian cancer: metabolomic profiling of mouse ovarian tumors identifies metformin-induced global metabolic changes

Authors
Romero, IL; Liu, X; Mitra, AK; Lengyel, E; Locasale, JW
MLA Citation
Romero, IL, Liu, X, Mitra, AK, Lengyel, E, and Locasale, JW. "Abstract POSTER-TECH-1123: Advancing metformin as therapeutic for ovarian cancer: metabolomic profiling of mouse ovarian tumors identifies metformin-induced global metabolic changes." August 15, 2015.
Source
crossref
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
21
Issue
16 Supplement
Publish Date
2015
Start Page
POSTER-TECH-1123
End Page
POSTER-TECH-1123
DOI
10.1158/1557-3265.OVCASYMP14-POSTER-TECH-1123

A roadmap for interpreting (13)C metabolite labeling patterns from cells.

Measuring intracellular metabolism has increasingly led to important insights in biomedical research. (13)C tracer analysis, although less information-rich than quantitative (13)C flux analysis that requires computational data integration, has been established as a time-efficient method to unravel relative pathway activities, qualitative changes in pathway contributions, and nutrient contributions. Here, we review selected key issues in interpreting (13)C metabolite labeling patterns, with the goal of drawing accurate conclusions from steady state and dynamic stable isotopic tracer experiments.

Authors
Buescher, JM; Antoniewicz, MR; Boros, LG; Burgess, SC; Brunengraber, H; Clish, CB; DeBerardinis, RJ; Feron, O; Frezza, C; Ghesquiere, B; Gottlieb, E; Hiller, K; Jones, RG; Kamphorst, JJ; Kibbey, RG; Kimmelman, AC; Locasale, JW; Lunt, SY; Maddocks, ODK; Malloy, C; Metallo, CM; Meuillet, EJ; Munger, J; Nöh, K; Rabinowitz, JD; Ralser, M; Sauer, U; Stephanopoulos, G; St-Pierre, J; Tennant, DA; Wittmann, C; Vander Heiden, MG; Vazquez, A; Vousden, K; Young, JD; Zamboni, N; Fendt, S-M
MLA Citation
Buescher, JM, Antoniewicz, MR, Boros, LG, Burgess, SC, Brunengraber, H, Clish, CB, DeBerardinis, RJ, Feron, O, Frezza, C, Ghesquiere, B, Gottlieb, E, Hiller, K, Jones, RG, Kamphorst, JJ, Kibbey, RG, Kimmelman, AC, Locasale, JW, Lunt, SY, Maddocks, ODK, Malloy, C, Metallo, CM, Meuillet, EJ, Munger, J, Nöh, K, Rabinowitz, JD, Ralser, M, Sauer, U, Stephanopoulos, G, St-Pierre, J, Tennant, DA, Wittmann, C, Vander Heiden, MG, Vazquez, A, Vousden, K, Young, JD, Zamboni, N, and Fendt, S-M. "A roadmap for interpreting (13)C metabolite labeling patterns from cells." Current opinion in biotechnology 34 (August 2015): 189-201. (Review)
PMID
25731751
Source
epmc
Published In
Current Opinion in Biotechnology
Volume
34
Publish Date
2015
Start Page
189
End Page
201
DOI
10.1016/j.copbio.2015.02.003

Metabolic plasticity of metastatic breast cancer cells: adaptation to changes in the microenvironment.

Cancer cells adapt their metabolism during tumorigenesis. We studied two isogenic breast cancer cells lines (highly metastatic 4T1; nonmetastatic 67NR) to identify differences in their glucose and glutamine metabolism in response to metabolic and environmental stress. Dynamic magnetic resonance spectroscopy of (13)C-isotopomers showed that 4T1 cells have higher glycolytic and tricarboxylic acid (TCA) cycle flux than 67NR cells and readily switch between glycolysis and oxidative phosphorylation (OXPHOS) in response to different extracellular environments. OXPHOS activity increased with metastatic potential in isogenic cell lines derived from the same primary breast cancer: 4T1 > 4T07 and 168FARN (local micrometastasis only) > 67NR. We observed a restricted TCA cycle flux at the succinate dehydrogenase step in 67NR cells (but not in 4T1 cells), leading to succinate accumulation and hindering OXPHOS. In the four isogenic cell lines, environmental stresses modulated succinate dehydrogenase subunit A expression according to metastatic potential. Moreover, glucose-derived lactate production was more glutamine dependent in cell lines with higher metastatic potential. These studies show clear differences in TCA cycle metabolism between 4T1 and 67NR breast cancer cells. They indicate that metastases-forming 4T1 cells are more adept at adjusting their metabolism in response to environmental stress than isogenic, nonmetastatic 67NR cells. We suggest that the metabolic plasticity and adaptability are more important to the metastatic breast cancer phenotype than rapid cell proliferation alone, which could 1) provide a new biomarker for early detection of this phenotype, possibly at the time of diagnosis, and 2) lead to new treatment strategies of metastatic breast cancer by targeting mitochondrial metabolism.

Authors
Simões, RV; Serganova, IS; Kruchevsky, N; Leftin, A; Shestov, AA; Thaler, HT; Sukenick, G; Locasale, JW; Blasberg, RG; Koutcher, JA; Ackerstaff, E
MLA Citation
Simões, RV, Serganova, IS, Kruchevsky, N, Leftin, A, Shestov, AA, Thaler, HT, Sukenick, G, Locasale, JW, Blasberg, RG, Koutcher, JA, and Ackerstaff, E. "Metabolic plasticity of metastatic breast cancer cells: adaptation to changes in the microenvironment." Neoplasia (New York, N.Y.) 17.8 (August 2015): 671-684.
PMID
26408259
Source
epmc
Published In
Neoplasia (New York, N.Y.)
Volume
17
Issue
8
Publish Date
2015
Start Page
671
End Page
684
DOI
10.1016/j.neo.2015.08.005

High-Resolution Metabolomics with Acyl-CoA Profiling Reveals Widespread Remodeling in Response to Diet.

The availability of acyl-Coenzyme A (acyl-CoA) thioester compounds affects numerous cellular functions including autophagy, lipid oxidation and synthesis, and post-translational modifications. Consequently, the acyl-CoA level changes tend to be associated with other metabolic alterations that regulate these critical cellular functions. Despite their biological importance, this class of metabolites remains difficult to detect and quantify using current analytical methods. Here we show a universal method for metabolomics that allows for the detection of an expansive set of acyl-CoA compounds and hundreds of other cellular metabolites. We apply this method to profile the dynamics of acyl-CoA compounds and corresponding alterations in metabolism across the metabolic network in response to high fat feeding in mice. We identified targeted metabolites (>50) and untargeted features (>1000) with significant changes (FDR < 0.05) in response to diet. A substantial extent of this metabolic remodeling exhibited correlated changes in acyl-CoA metabolism with acyl-carnitine metabolism and other features of the metabolic network that together can lead to the discovery of biomarkers of acyl-CoA metabolism. These findings show a robust acyl-CoA profiling method and identify coordinated changes of acyl-CoA metabolism in response to nutritional stress.

Authors
Liu, X; Sadhukhan, S; Sun, S; Wagner, GR; Hirschey, MD; Qi, L; Lin, H; Locasale, JW
MLA Citation
Liu, X, Sadhukhan, S, Sun, S, Wagner, GR, Hirschey, MD, Qi, L, Lin, H, and Locasale, JW. "High-Resolution Metabolomics with Acyl-CoA Profiling Reveals Widespread Remodeling in Response to Diet." Molecular & cellular proteomics : MCP 14.6 (June 2015): 1489-1500.
PMID
25795660
Source
epmc
Published In
Molecular & cellular proteomics : MCP
Volume
14
Issue
6
Publish Date
2015
Start Page
1489
End Page
1500
DOI
10.1074/mcp.m114.044859

Extraction parameters for metabolomics from cultured cells.

The successful extraction of metabolites is a critical step in metabolite profiling. By optimizing metabolite extraction, the range and quantitative capacity of metabolomics studies can be improved. We considered eight separate extraction protocols for the preparation of a metabolite extract from cultured mammalian cells. Parameters considered included temperature, pH, and cell washing before extraction. The effects on metabolite recovery were studied using a liquid chromatography high-resolution mass spectrometry (LC-HRMS) platform that measures metabolites of diverse chemical classes, including amino acids, lipids, and sugar derivatives. The temperature considered during the extraction or the presence of formic acid, a commonly used additive, was shown to have minimal effects on the measured ion intensities of metabolites. However, washing of samples before metabolite extraction, whether with water or phosphate-buffered saline, exhibited dramatic effects on measured intensities of both intracellular and extracellular metabolites. Together, these findings present a systematic assessment of extraction conditions for metabolite profiling.

Authors
Ser, Z; Liu, X; Tang, NN; Locasale, JW
MLA Citation
Ser, Z, Liu, X, Tang, NN, and Locasale, JW. "Extraction parameters for metabolomics from cultured cells." Analytical biochemistry 475 (April 2015): 22-28.
PMID
25613493
Source
epmc
Published In
Analytical Biochemistry
Volume
475
Publish Date
2015
Start Page
22
End Page
28
DOI
10.1016/j.ab.2015.01.003

Gain of glucose-independent growth upon metastasis of breast cancer cells to the brain.

Breast cancer brain metastasis is resistant to therapy and a particularly poor prognostic feature in patient survival. Altered metabolism is a common feature of cancer cells, but little is known as to what metabolic changes benefit breast cancer brain metastases. We found that brain metastatic breast cancer cells evolved the ability to survive and proliferate independent of glucose due to enhanced gluconeogenesis and oxidations of glutamine and branched chain amino acids, which together sustain the nonoxidative pentose pathway for purine synthesis. Silencing expression of fructose-1,6-bisphosphatases (FBP) in brain metastatic cells reduced their viability and improved the survival of metastasis-bearing immunocompetent hosts. Clinically, we showed that brain metastases from human breast cancer patients expressed higher levels of FBP and glycogen than the corresponding primary tumors. Together, our findings identify a critical metabolic condition required to sustain brain metastasis and suggest that targeting gluconeogenesis may help eradicate this deadly feature in advanced breast cancer patients.

Authors
Chen, J; Lee, H-J; Wu, X; Huo, L; Kim, S-J; Xu, L; Wang, Y; He, J; Bollu, LR; Gao, G; Su, F; Briggs, J; Liu, X; Melman, T; Asara, JM; Fidler, IJ; Cantley, LC; Locasale, JW; Weihua, Z
MLA Citation
Chen, J, Lee, H-J, Wu, X, Huo, L, Kim, S-J, Xu, L, Wang, Y, He, J, Bollu, LR, Gao, G, Su, F, Briggs, J, Liu, X, Melman, T, Asara, JM, Fidler, IJ, Cantley, LC, Locasale, JW, and Weihua, Z. "Gain of glucose-independent growth upon metastasis of breast cancer cells to the brain." Cancer research 75.3 (February 2015): 554-565.
PMID
25511375
Source
epmc
Published In
Cancer Research
Volume
75
Issue
3
Publish Date
2015
Start Page
554
End Page
565
DOI
10.1158/0008-5472.can-14-2268

Organization of enzyme concentration across the metabolic network in cancer cells.

Rapid advances in mass spectrometry have allowed for estimates of absolute concentrations across entire proteomes, permitting the interrogation of many important biological questions. Here, we focus on a quantitative aspect of human cancer cell metabolism that has been limited by a paucity of available data on the abundance of metabolic enzymes. We integrate data from recent measurements of absolute protein concentration to analyze the statistics of protein abundance across the human metabolic network. At a global level, we find that the enzymes in glycolysis comprise approximately half of the total amount of metabolic proteins and can constitute up to 10% of the entire proteome. We then use this analysis to investigate several outstanding problems in cancer metabolism, including the diversion of glycolytic flux for biosynthesis, the relative contribution of nitrogen assimilating pathways, and the origin of cellular redox potential. We find many consistencies with current models, identify several inconsistencies, and find generalities that extend beyond current understanding. Together our results demonstrate that a relatively simple analysis of the abundance of metabolic enzymes was able to reveal many insights into the organization of the human cancer cell metabolic network.

Authors
Madhukar, NS; Warmoes, MO; Locasale, JW
MLA Citation
Madhukar, NS, Warmoes, MO, and Locasale, JW. "Organization of enzyme concentration across the metabolic network in cancer cells." PloS one 10.1 (January 26, 2015): e0117131-.
PMID
25621879
Source
epmc
Published In
PloS one
Volume
10
Issue
1
Publish Date
2015
Start Page
e0117131
DOI
10.1371/journal.pone.0117131

Cancer metabolism

© Cambridge University Press 2015.Recent technological developments in combination with novel computational approaches for analysis of large-scale datasets have provided novel insights into genetic changes that are associated with tumorigenesis. Better genetic understanding of this process forms the basis for personalized approaches to pharmacologic intervention that promises more successful therapeutics. Yet the vast diversity of cancer-promoting genetic changes along with the economic burden associated with the development of individualized therapies and corresponding diagnostic tools constitute a great challenge: to devise drugs that target a broad spectrum of cancers while minimizing unwanted effects. Thus better understanding the common characteristics that distinguish cancer cells from normal tissues is imperative for devising novel therapeutic strategies to complement “targeted” treatments that focus on specific genetic events. Aberrations in cell cycle regulatory circuits underlie one such common feature of cancer cells, which is uncontrolled proliferation. During proliferation, accumulation of biomass for cell growth is the first discernable process preceding cell division. This occurs primarily during the G1 phase of the eukaryotic cell cycle before committing to a new round of DNA replication and ensures that sufficient nucleotides, lipids, and amino acids are available to build a functioning daughter cell. Thus highly proliferative cancer cells have an increased demand for biosynthetic processes to provide these building blocks.

Authors
Anastasiou, D; Locasale, JW; Vander Heiden, MG
MLA Citation
Anastasiou, D, Locasale, JW, and Vander Heiden, MG. "Cancer metabolism." Systems Biology of Cancer. January 1, 2015. 295-308.
Source
scopus
Publish Date
2015
Start Page
295
End Page
308
DOI
10.1017/9780511979811.020

Metabolic programming and PDHK1 control CD4+ T cell subsets and inflammation.

Activation of CD4+ T cells results in rapid proliferation and differentiation into effector and regulatory subsets. CD4+ effector T cell (Teff) (Th1 and Th17) and Treg subsets are metabolically distinct, yet the specific metabolic differences that modify T cell populations are uncertain. Here, we evaluated CD4+ T cell populations in murine models and determined that inflammatory Teffs maintain high expression of glycolytic genes and rely on high glycolytic rates, while Tregs are oxidative and require mitochondrial electron transport to proliferate, differentiate, and survive. Metabolic profiling revealed that pyruvate dehydrogenase (PDH) is a key bifurcation point between T cell glycolytic and oxidative metabolism. PDH function is inhibited by PDH kinases (PDHKs). PDHK1 was expressed in Th17 cells, but not Th1 cells, and at low levels in Tregs, and inhibition or knockdown of PDHK1 selectively suppressed Th17 cells and increased Tregs. This alteration in the CD4+ T cell populations was mediated in part through ROS, as N-acetyl cysteine (NAC) treatment restored Th17 cell generation. Moreover, inhibition of PDHK1 modulated immunity and protected animals against experimental autoimmune encephalomyelitis, decreasing Th17 cells and increasing Tregs. Together, these data show that CD4+ subsets utilize and require distinct metabolic programs that can be targeted to control specific T cell populations in autoimmune and inflammatory diseases.

Authors
Gerriets, VA; Kishton, RJ; Nichols, AG; Macintyre, AN; Inoue, M; Ilkayeva, O; Winter, PS; Liu, X; Priyadharshini, B; Slawinska, ME; Haeberli, L; Huck, C; Turka, LA; Wood, KC; Hale, LP; Smith, PA; Schneider, MA; MacIver, NJ; Locasale, JW; Newgard, CB; Shinohara, ML; Rathmell, JC
MLA Citation
Gerriets, VA, Kishton, RJ, Nichols, AG, Macintyre, AN, Inoue, M, Ilkayeva, O, Winter, PS, Liu, X, Priyadharshini, B, Slawinska, ME, Haeberli, L, Huck, C, Turka, LA, Wood, KC, Hale, LP, Smith, PA, Schneider, MA, MacIver, NJ, Locasale, JW, Newgard, CB, Shinohara, ML, and Rathmell, JC. "Metabolic programming and PDHK1 control CD4+ T cell subsets and inflammation." The Journal of clinical investigation 125.1 (January 2015): 194-207.
Website
http://hdl.handle.net/10161/10313
PMID
25437876
Source
epmc
Published In
Journal of Clinical Investigation
Volume
125
Issue
1
Publish Date
2015
Start Page
194
End Page
207
DOI
10.1172/jci76012

Epigenetics and cancer metabolism.

Cancer cells adapt their metabolism to support proliferation and survival. A hallmark of cancer, this alteration is characterized by dysfunctional metabolic enzymes, changes in nutrient availability, tumor microenvironment and oncogenic mutations. Metabolic rewiring in cancer is tightly connected to changes at the epigenetic level. Enzymes that mediate epigenetic status of cells catalyze posttranslational modifications of DNA and histones and influence metabolic gene expression. These enzymes require metabolites that are used as cofactors and substrates to carry out reactions. This interaction of epigenetics and metabolism constitutes a new avenue of cancer biology and could lead to new insights for the development of anti-cancer therapeutics.

Authors
Johnson, C; Warmoes, MO; Shen, X; Locasale, JW
MLA Citation
Johnson, C, Warmoes, MO, Shen, X, and Locasale, JW. "Epigenetics and cancer metabolism." Cancer letters 356.2 Pt A (January 2015): 309-314. (Review)
PMID
24125862
Source
epmc
Published In
Cancer Letters
Volume
356
Issue
2 Pt A
Publish Date
2015
Start Page
309
End Page
314
DOI
10.1016/j.canlet.2013.09.043

The rate of glycolysis quantitatively mediates specific histone acetylation sites.

Glucose metabolism links metabolic status to protein acetylation. However, it remains poorly understood to what extent do features of glucose metabolism contribute to protein acetylation and whether the process can be dynamically and quantitatively regulated by differing rates of glycolysis.Here, we show that titratable rates of glycolysis with corresponding changes in the levels of glycolytic intermediates result in a graded remodeling of a bulk of the metabolome and resulted in gradual changes in total histone acetylation levels. Dynamic histone acetylation levels were found and most strongly correlated with acetyl coenzyme A (ac-CoA) levels and inversely associated with the ratio of ac-CoA to free CoA. A multiplexed stable isotopic labeling by amino acids in cell culture (SILAC)-based proteomics approach revealed that the levels of half of identified histone acetylation sites as well as other lysine acylation modifications are tuned by the rate of glycolysis demonstrating that glycolytic rate affects specific acylation sites.We demonstrate that histone acylation is directly sensed by glucose flux in a titratable, dose-dependent manner that is modulated by glycolytic flux and that a possible function of the Warburg Effect, a metabolic state observed in cancers with enhanced glucose metabolism, is to confer specific signaling effects on cells.

Authors
Cluntun, AA; Huang, H; Dai, L; Liu, X; Zhao, Y; Locasale, JW
MLA Citation
Cluntun, AA, Huang, H, Dai, L, Liu, X, Zhao, Y, and Locasale, JW. "The rate of glycolysis quantitatively mediates specific histone acetylation sites." Cancer & metabolism 3 (January 2015): 10-.
PMID
26401273
Source
epmc
Published In
Cancer and Metabolism
Volume
3
Publish Date
2015
Start Page
10
DOI
10.1186/s40170-015-0135-3

Estimating relative changes of metabolic fluxes.

Fluxes are the central trait of metabolism and Kinetic Flux Profiling (KFP) is an effective method of measuring them. To generalize its applicability, we present an extension of the method that estimates the relative changes of fluxes using only relative quantitation of 13C-labeled metabolites. Such features are directly tailored to the more common experiment that performs only relative quantitation and compares fluxes between two conditions. We call our extension rKFP. Moreover, we examine the effects of common missing data and common modeling assumptions on (r)KFP, and provide practical suggestions. We also investigate the selection of measuring times for (r)KFP and provide a simple recipe. We then apply rKFP to 13C-labeled glucose time series data collected from cells under normal and glucose-deprived conditions, estimating the relative flux changes of glycolysis and its branching pathways. We identify an adaptive response in which de novo serine biosynthesis is compromised to maintain the glycolytic flux backbone. Together, these results greatly expand the capabilities of KFP and are suitable for broad biological applications.

Authors
Huang, L; Kim, D; Liu, X; Myers, CR; Locasale, JW
MLA Citation
Huang, L, Kim, D, Liu, X, Myers, CR, and Locasale, JW. "Estimating relative changes of metabolic fluxes." PLoS computational biology 10.11 (November 20, 2014): e1003958-.
PMID
25412287
Source
epmc
Published In
PLoS computational biology
Volume
10
Issue
11
Publish Date
2014
Start Page
e1003958
DOI
10.1371/journal.pcbi.1003958

Characterization of the usage of the serine metabolic network in human cancer.

The serine, glycine, one-carbon (SGOC) metabolic network is implicated in cancer pathogenesis, but its general functions are unknown. We carried out a computational reconstruction of the SGOC network and then characterized its expression across thousands of cancer tissues. Pathways including methylation and redox metabolism exhibited heterogeneous expression indicating a strong context dependency of their usage in tumors. From an analysis of coexpression, simultaneous up- or downregulation of nucleotide synthesis, NADPH, and glutathione synthesis was found to be a common occurrence in all cancers. Finally, we developed a method to trace the metabolic fate of serine using stable isotopes, high-resolution mass spectrometry, and a mathematical model. Although the expression of single genes didn't appear indicative of flux, the collective expression of several genes in a given pathway allowed for successful flux prediction. Altogether, these findings identify expansive and heterogeneous functions for the SGOC metabolic network in human cancer.

Authors
Mehrmohamadi, M; Liu, X; Shestov, AA; Locasale, JW
MLA Citation
Mehrmohamadi, M, Liu, X, Shestov, AA, and Locasale, JW. "Characterization of the usage of the serine metabolic network in human cancer." Cell reports 9.4 (November 6, 2014): 1507-1519.
PMID
25456139
Source
epmc
Published In
Cell Reports
Volume
9
Issue
4
Publish Date
2014
Start Page
1507
End Page
1519
DOI
10.1016/j.celrep.2014.10.026

Heterogeneity of glycolysis in cancers and therapeutic opportunities.

Upregulated glycolysis, both in normoxic and hypoxic environments, is a nearly universal trait of cancer cells. The enormous difference in glucose metabolism offers a target for therapeutic intervention with a potentially low toxicity profile. The past decade has seen a steep rise in the development and clinical assessment of small molecules that target glycolysis. The enzymes in glycolysis have a highly heterogeneous nature that allows for the different bioenergetic, biosynthetic, and signaling demands needed for various tissue functions. In cancers, these properties enable them to respond to the variable requirements of cell survival, proliferation and adaptation to nutrient availability. Heterogeneity in glycolysis occurs through the expression of different isoforms, posttranslational modifications that affect the kinetic and regulatory properties of the enzyme. In this review, we will explore this vast heterogeneity of glycolysis and discuss how this information might be exploited to better target glucose metabolism and offer possibilities for biomarker development.

Authors
Warmoes, MO; Locasale, JW
MLA Citation
Warmoes, MO, and Locasale, JW. "Heterogeneity of glycolysis in cancers and therapeutic opportunities." Biochemical pharmacology 92.1 (November 2014): 12-21. (Review)
PMID
25093285
Source
epmc
Published In
Biochemical Pharmacology
Volume
92
Issue
1
Publish Date
2014
Start Page
12
End Page
21
DOI
10.1016/j.bcp.2014.07.019

Glucose transporter 1-mediated glucose uptake is limiting for B-cell acute lymphoblastic leukemia anabolic metabolism and resistance to apoptosis.

The metabolic profiles of cancer cells have long been acknowledged to be altered and to provide new therapeutic opportunities. In particular, a wide range of both solid and liquid tumors use aerobic glycolysis to supply energy and support cell growth. This metabolic program leads to high rates of glucose consumption through glycolysis with secretion of lactate even in the presence of oxygen. Identifying the limiting events in aerobic glycolysis and the response of cancer cells to metabolic inhibition is now essential to exploit this potential metabolic dependency. Here, we examine the role of glucose uptake and the glucose transporter Glut1 in the metabolism and metabolic stress response of BCR-Abl+ B-cell acute lymphoblastic leukemia cells (B-ALL). B-ALL cells were highly glycolytic and primary human B-ALL samples were dependent on glycolysis. We show B-ALL cells express multiple glucose transporters and conditional genetic deletion of Glut1 led to a partial loss of glucose uptake. This reduced glucose transport capacity, however, was sufficient to metabolically reprogram B-ALL cells to decrease anabolic and increase catabolic flux. Cell proliferation decreased and a limited degree of apoptosis was also observed. Importantly, Glut1-deficient B-ALL cells failed to accumulate in vivo and leukemic progression was suppressed by Glut1 deletion. Similarly, pharmacologic inhibition of aerobic glycolysis with moderate doses of 2-deoxyglucose (2-DG) slowed B-ALL cell proliferation, but extensive apoptosis only occurred at high doses. Nevertheless, 2-DG induced the pro-apoptotic protein Bim and sensitized B-ALL cells to the tyrosine kinase inhibitor Dasatinib in vivo. Together, these data show that despite expression of multiple glucose transporters, B-ALL cells are reliant on Glut1 to maintain aerobic glycolysis and anabolic metabolism. Further, partial inhibition of glucose metabolism is sufficient to sensitize cancer cells to specifically targeted therapies, suggesting inhibition of aerobic glycolysis as a plausible adjuvant approach for B-ALL therapies.

Authors
Liu, T; Kishton, RJ; Macintyre, AN; Gerriets, VA; Xiang, H; Liu, X; Abel, ED; Rizzieri, D; Locasale, JW; Rathmell, JC
MLA Citation
Liu, T, Kishton, RJ, Macintyre, AN, Gerriets, VA, Xiang, H, Liu, X, Abel, ED, Rizzieri, D, Locasale, JW, and Rathmell, JC. "Glucose transporter 1-mediated glucose uptake is limiting for B-cell acute lymphoblastic leukemia anabolic metabolism and resistance to apoptosis." Cell death & disease 5 (October 16, 2014): e1470-.
PMID
25321477
Source
epmc
Published In
Cell Death and Disease
Volume
5
Publish Date
2014
Start Page
e1470
DOI
10.1038/cddis.2014.431

Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step.

Aerobic glycolysis or the Warburg Effect (WE) is characterized by the increased metabolism of glucose to lactate. It remains unknown what quantitative changes to the activity of metabolism are necessary and sufficient for this phenotype. We developed a computational model of glycolysis and an integrated analysis using metabolic control analysis (MCA), metabolomics data, and statistical simulations. We identified and confirmed a novel mode of regulation specific to aerobic glycolysis where flux through GAPDH, the enzyme separating lower and upper glycolysis, is the rate-limiting step in the pathway and the levels of fructose (1,6) bisphosphate (FBP), are predictive of the rate and control points in glycolysis. Strikingly, negative flux control was found and confirmed for several steps thought to be rate-limiting in glycolysis. Together, these findings enumerate the biochemical determinants of the WE and suggest strategies for identifying the contexts in which agents that target glycolysis might be most effective.

Authors
Shestov, AA; Liu, X; Ser, Z; Cluntun, AA; Hung, YP; Huang, L; Kim, D; Le, A; Yellen, G; Albeck, JG; Locasale, JW
MLA Citation
Shestov, AA, Liu, X, Ser, Z, Cluntun, AA, Hung, YP, Huang, L, Kim, D, Le, A, Yellen, G, Albeck, JG, and Locasale, JW. "Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step." eLife 3 (July 9, 2014).
PMID
25009227
Source
epmc
Published In
eLife
Volume
3
Publish Date
2014
DOI
10.7554/elife.03342

Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step

Authors
Shestov, AA; Liu, X; Ser, Z; Cluntun, AA; Hung, YP; Huang, L; Kim, D; Le, A; Yellen, G; Albeck, JG; Locasale, JW
MLA Citation
Shestov, AA, Liu, X, Ser, Z, Cluntun, AA, Hung, YP, Huang, L, Kim, D, Le, A, Yellen, G, Albeck, JG, and Locasale, JW. "Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step." ELIFE 3 (July 9, 2014).
Source
wos-lite
Published In
eLife
Volume
3
Publish Date
2014
DOI
10.7554/eLife.03342

A strategy for sensitive, large scale quantitative metabolomics.

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.  Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases.

Authors
Liu, X; Ser, Z; Cluntun, AA; Mentch, SJ; Locasale, JW
MLA Citation
Liu, X, Ser, Z, Cluntun, AA, Mentch, SJ, and Locasale, JW. "A strategy for sensitive, large scale quantitative metabolomics." Journal of visualized experiments : JoVE 87 (May 27, 2014).
PMID
24894601
Source
epmc
Published In
Journal of Visualized Experiments
Issue
87
Publish Date
2014
DOI
10.3791/51358

A fundamental trade-off in covalent switching and its circumvention by enzyme bifunctionality in glucose homeostasis.

Covalent modification provides a mechanism for modulating molecular state and regulating physiology. A cycle of competing enzymes that add and remove a single modification can act as a molecular switch between "on" and "off" and has been widely studied as a core motif in systems biology. Here, we exploit the recently developed "linear framework" for time scale separation to determine the general principles of such switches. These methods are not limited to Michaelis-Menten assumptions, and our conclusions hold for enzymes whose mechanisms may be arbitrarily complicated. We show that switching efficiency improves with increasing irreversibility of the enzymes and that the on/off transition occurs when the ratio of enzyme levels reaches a value that depends only on the rate constants. Fluctuations in enzyme levels, which habitually occur due to cellular heterogeneity, can cause flipping back and forth between on and off, leading to incoherent mosaic behavior in tissues, that worsens as switching becomes sharper. This trade-off can be circumvented if enzyme levels are correlated. In particular, if the competing catalytic domains are on the same protein but do not influence each other, the resulting bifunctional enzyme can switch sharply while remaining coherent. In the mammalian liver, the switch between glycolysis and gluconeogenesis is regulated by the bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2/FBPase-2). We suggest that bifunctionality of PFK-2/FBPase-2 complements the metabolic zonation of the liver by ensuring coherent switching in response to insulin and glucagon.

Authors
Dasgupta, T; Croll, DH; Owen, JA; Vander Heiden, MG; Locasale, JW; Alon, U; Cantley, LC; Gunawardena, J
MLA Citation
Dasgupta, T, Croll, DH, Owen, JA, Vander Heiden, MG, Locasale, JW, Alon, U, Cantley, LC, and Gunawardena, J. "A fundamental trade-off in covalent switching and its circumvention by enzyme bifunctionality in glucose homeostasis." The Journal of biological chemistry 289.19 (May 2014): 13010-13025.
PMID
24634222
Source
epmc
Published In
The Journal of biological chemistry
Volume
289
Issue
19
Publish Date
2014
Start Page
13010
End Page
13025
DOI
10.1074/jbc.m113.546515

Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 5, (E582-E591) doi:10.1073/pnas.1318114111)

Authors
Sun, S; Shi, G; Han, X; Francisco, AB; Ji, Y; Mendonça, N; Liu, X; Locasale, JW; Simpson, KW; Duhamel, GE; Kersten, S; Yates, JR; Long, Q; Qi, L
MLA Citation
Sun, S, Shi, G, Han, X, Francisco, AB, Ji, Y, Mendonça, N, Liu, X, Locasale, JW, Simpson, KW, Duhamel, GE, Kersten, S, Yates, JR, Long, Q, and Qi, L. "Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 5, (E582-E591) doi:10.1073/pnas.1318114111)." Proceedings of the National Academy of Sciences of the United States of America 111.16 (April 22, 2014): 6115-.
Source
scopus
Published In
Proceedings of the National Academy of Sciences of USA
Volume
111
Issue
16
Publish Date
2014
Start Page
6115
DOI
10.1073/pnas.1405563111

Development and quantitative evaluation of a high-resolution metabolomics technology.

Recent advances in mass spectrometry have allowed for unprecedented characterization of human metabolism and its contribution to disease. Despite these advances, limitations in metabolomics technology remain. Here, we describe a metabolomics strategy that consolidates several recent improvements in mass spectrometry technology. The platform involves a high-resolution Orbitrap mass spectrometer coupled to faster scanning speeds, allowing for polarity switching and improved ion optics resulting in enhanced sensitivity. When coupled to HILIC chromatography, we are able to quantify over 339 metabolites from an extract of HCT8 cells with a linear range of over 4 orders of magnitude in a single chromatographic run. These metabolites include diverse chemical classes ranging from amino acids to polar lipids. In addition, we also detect over 3000 additional potential metabolites present in mammalian cells. We applied this platform to characterize the metabolome of eight colorectal cancer cell lines and observed both commonalities and heterogeneities across their metabolic profiles when cells are grown in identical conditions. Together these results demonstrate that simultaneous profiling and quantitation of the human metabolome is feasible.

Authors
Liu, X; Ser, Z; Locasale, JW
MLA Citation
Liu, X, Ser, Z, and Locasale, JW. "Development and quantitative evaluation of a high-resolution metabolomics technology." Analytical chemistry 86.4 (February 2014): 2175-2184.
PMID
24410464
Source
epmc
Published In
Analytical Chemistry
Volume
86
Issue
4
Publish Date
2014
Start Page
2175
End Page
2184
DOI
10.1021/ac403845u

Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival.

Suppressor/Enhancer of Lin-12-like (Sel1L) is an adaptor protein for the E3 ligase hydroxymethylglutaryl reductase degradation protein 1 (Hrd1) involved in endoplasmic reticulum-associated degradation (ERAD). Sel1L's physiological importance in mammalian ERAD, however, remains to be established. Here, using the inducible Sel1L knockout mouse and cell models, we show that Sel1L is indispensable for Hrd1 stability, ER homeostasis, and survival. Acute loss of Sel1L leads to premature death in adult mice within 3 wk with profound pancreatic atrophy. Contrary to current belief, our data show that mammalian Sel1L is required for Hrd1 stability and ERAD function both in vitro and in vivo. Sel1L deficiency disturbs ER homeostasis, activates ER stress, attenuates translation, and promotes cell death. Serendipitously, using a biochemical approach coupled with mass spectrometry, we found that Sel1L deficiency causes the aggregation of both small and large ribosomal subunits. Thus, Sel1L is an indispensable component of the mammalian Hrd1 ERAD complex and ER homeostasis, which is essential for protein translation, pancreatic function, and cellular and organismal survival.

Authors
Sun, S; Shi, G; Han, X; Francisco, AB; Ji, Y; Mendonça, N; Liu, X; Locasale, JW; Simpson, KW; Duhamel, GE; Kersten, S; Yates, JR; Long, Q; Qi, L
MLA Citation
Sun, S, Shi, G, Han, X, Francisco, AB, Ji, Y, Mendonça, N, Liu, X, Locasale, JW, Simpson, KW, Duhamel, GE, Kersten, S, Yates, JR, Long, Q, and Qi, L. "Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival." Proceedings of the National Academy of Sciences of the United States of America 111.5 (February 2014): E582-E591.
PMID
24453213
Source
epmc
Published In
Proceedings of the National Academy of Sciences of USA
Volume
111
Issue
5
Publish Date
2014
Start Page
E582
End Page
E591
DOI
10.1073/pnas.1318114111

A metabolic signature of colon cancer initiating cells.

Colon cancer initiating cells (CCICs) are more tumorigenic and metastatic than the majority of colorectal cancer (CRC) cells. CCICs have also been associated with stem cell-like properties. However, there is a lack of system-level understanding of what mechanisms distinguish CCICs from common CRC cells. We compared the transcriptomes of CD133+ CCICs and CD133- CRC cells from multiple sources, which identified a distinct metabolic signature for CD133(high) CCICs. High-resolution unbiased metabolomics was then performed to validate this CCIC metabolic signature. Specifically, levels of enzymes and metabolites involved in glycolysis, the citric acid (TCA) cycle, and cysteine and methionine metabolism are altered in CCICs. Analyses of the alterations further suggest an epigenetic link. This metabolic signature provides mechanistic insights into CCIC phenotypes and may serve as potential biomarkers and therapeutic targets for future CRC treatment.

Authors
Chen, K-Y; Liu, X; Bu, P; Lin, C-S; Rakhilin, N; Locasale, JW; Shen, X
MLA Citation
Chen, K-Y, Liu, X, Bu, P, Lin, C-S, Rakhilin, N, Locasale, JW, and Shen, X. "A metabolic signature of colon cancer initiating cells." Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 2014 (January 2014): 4759-4762.
PMID
25571056
Source
epmc
Published In
Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
Volume
2014
Publish Date
2014
Start Page
4759
End Page
4762
DOI
10.1109/embc.2014.6944688

Autophagy-dependent metabolic reprogramming sensitizes TSC2-deficient cells to the antimetabolite 6-aminonicotinamide.

The mammalian target of rapamycin complex 1 (mTORC1) is hyperactive in many human cancers and in tuberous sclerosis complex (TSC). Autophagy, a key mTORC1-targeted process, is a critical determinant of metabolic homeostasis. Metabolomic profiling was performed to elucidate the cellular consequences of autophagy dysregulation under conditions of hyperactive mTORC1. It was discovered that TSC2-null cells have distinctive autophagy-dependent pentose phosphate pathway (PPP) alterations. This was accompanied by enhanced glucose uptake and utilization, decreased mitochondrial oxygen consumption, and increased mitochondrial reactive oxygen species (ROS) production. Importantly, these findings revealed that the PPP is a key autophagy-dependent compensatory metabolic mechanism. Furthermore, PPP inhibition with 6-aminonicotinamide (6-AN) in combination with autophagy inhibition suppressed proliferation and prompted the activation of NF-κB and CASP1 in TSC2-deficient, but not TSC2-proficient cells. These data demonstrate that TSC2-deficient cells can be therapeutically targeted, without mTORC1 inhibitors, by focusing on their metabolic vulnerabilities.This study provides proof-of-concept that therapeutic targeting of diseases with hyperactive mTORC1 can be achieved without the application of mTORC1 inhibitors.

Authors
Parkhitko, AA; Priolo, C; Coloff, JL; Yun, J; Wu, JJ; Mizumura, K; Xu, W; Malinowska, IA; Yu, J; Kwiatkowski, DJ; Locasale, JW; Asara, JM; Choi, AMK; Finkel, T; Henske, EP
MLA Citation
Parkhitko, AA, Priolo, C, Coloff, JL, Yun, J, Wu, JJ, Mizumura, K, Xu, W, Malinowska, IA, Yu, J, Kwiatkowski, DJ, Locasale, JW, Asara, JM, Choi, AMK, Finkel, T, and Henske, EP. "Autophagy-dependent metabolic reprogramming sensitizes TSC2-deficient cells to the antimetabolite 6-aminonicotinamide." Molecular cancer research : MCR 12.1 (January 2014): 48-57.
PMID
24296756
Source
epmc
Published In
Molecular cancer research : MCR
Volume
12
Issue
1
Publish Date
2014
Start Page
48
End Page
57
DOI
10.1158/1541-7786.mcr-13-0258-t

Glucose transporter 1-mediated glucose uptake is limiting for B-cell acute lymphoblastic leukemia anabolic metabolism and resistance to apoptosis.

Authors
Liu, T; Kishton, RJ; Macintyre, AN; Gerriets, VA; Xiang, H; Liu, X; Abel, ED; Rizzieri, D; Locasale, JW; Rathmell, JC
MLA Citation
Liu, T, Kishton, RJ, Macintyre, AN, Gerriets, VA, Xiang, H, Liu, X, Abel, ED, Rizzieri, D, Locasale, JW, and Rathmell, JC. "Glucose transporter 1-mediated glucose uptake is limiting for B-cell acute lymphoblastic leukemia anabolic metabolism and resistance to apoptosis." Cell death & disease 5 (2014): e1516-.
PMID
25375381
Source
epmc
Published In
Cell Death and Disease
Volume
5
Publish Date
2014
Start Page
e1516
DOI
10.1038/cddis.2014.493

Computational approaches for understanding energy metabolism.

There has been a surge of interest in understanding the regulation of metabolic networks involved in disease in recent years. Quantitative models are increasingly being used to interrogate the metabolic pathways that are contained within this complex disease biology. At the core of this effort is the mathematical modeling of central carbon metabolism involving glycolysis and the citric acid cycle (referred to as energy metabolism). Here, we discuss several approaches used to quantitatively model metabolic pathways relating to energy metabolism and discuss their formalisms, successes, and limitations.

Authors
Shestov, AA; Barker, B; Gu, Z; Locasale, JW
MLA Citation
Shestov, AA, Barker, B, Gu, Z, and Locasale, JW. "Computational approaches for understanding energy metabolism." Wiley interdisciplinary reviews. Systems biology and medicine 5.6 (November 2013): 733-750. (Review)
PMID
23897661
Source
epmc
Published In
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
Volume
5
Issue
6
Publish Date
2013
Start Page
733
End Page
750
DOI
10.1002/wsbm.1238

Serine, glycine and one-carbon units: cancer metabolism in full circle.

One-carbon metabolism involving the folate and methionine cycles integrates nutritional status from amino acids, glucose and vitamins, and generates diverse outputs, such as the biosynthesis of lipids, nucleotides and proteins, the maintenance of redox status and the substrates for methylation reactions. Long considered a 'housekeeping' process, this pathway has recently been shown to have additional complexity. Genetic and functional evidence suggests that hyperactivation of this pathway is a driver of oncogenesis and establishes a link to cellular epigenetic status. Given the wealth of clinically available agents that target one-carbon metabolism, these new findings could present opportunities for translation into precision cancer medicine.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Serine, glycine and one-carbon units: cancer metabolism in full circle." Nature reviews. Cancer 13.8 (August 2013): 572-583. (Review)
PMID
23822983
Source
epmc
Published In
Nature Reviews Cancer
Volume
13
Issue
8
Publish Date
2013
Start Page
572
End Page
583
DOI
10.1038/nrc3557

Heterogeneity of tumor-induced gene expression changes in the human metabolic network.

Reprogramming of cellular metabolism is an emerging hallmark of neoplastic transformation. However, it is not known how the expression of metabolic genes in tumors differs from that in normal tissues, or whether different tumor types exhibit similar metabolic changes. Here we compare expression patterns of metabolic genes across 22 diverse types of human tumors. Overall, the metabolic gene expression program in tumors is similar to that in the corresponding normal tissues. Although expression changes of some metabolic pathways (e.g., upregulation of nucleotide biosynthesis and glycolysis) are frequently observed across tumors, expression changes of other pathways (e.g., oxidative phosphorylation) are very heterogeneous. Our analysis also suggests that the expression changes of some metabolic genes (e.g., isocitrate dehydrogenase and fumarate hydratase) may enhance or mimic the effects of recurrent mutations in tumors. On the level of individual biochemical reactions, many hundreds of metabolic isoenzymes show significant and tumor-specific expression changes. These isoenzymes are potential targets for anticancer therapy.

Authors
Hu, J; Locasale, JW; Bielas, JH; O'Sullivan, J; Sheahan, K; Cantley, LC; Vander Heiden, MG; Vitkup, D
MLA Citation
Hu, J, Locasale, JW, Bielas, JH, O'Sullivan, J, Sheahan, K, Cantley, LC, Vander Heiden, MG, and Vitkup, D. "Heterogeneity of tumor-induced gene expression changes in the human metabolic network." Nature biotechnology 31.6 (June 2013): 522-529.
PMID
23604282
Source
epmc
Published In
Nature Biotechnology
Volume
31
Issue
6
Publish Date
2013
Start Page
522
End Page
529
DOI
10.1038/nbt.2530

Human melanoma metabolic network analysis with combined 13C NMR/bioreactor technique: testing the Warburg effect

Authors
Shestov, A; Mancuso, A; Locasale, JW; Glickson, JD
MLA Citation
Shestov, A, Mancuso, A, Locasale, JW, and Glickson, JD. "Human melanoma metabolic network analysis with combined 13C NMR/bioreactor technique: testing the Warburg effect." April 2013.
Source
wos-lite
Published In
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Volume
27
Publish Date
2013

Ras Activity Regulation by Monoubiquitination

Authors
Campbell, SL; Baker, R; Lewis, S; Sasaki, A; Wilkerson, EM; Locasale, J; Cantley, LC; Kuhlman, B; Dohlman, H
MLA Citation
Campbell, SL, Baker, R, Lewis, S, Sasaki, A, Wilkerson, EM, Locasale, J, Cantley, LC, Kuhlman, B, and Dohlman, H. "Ras Activity Regulation by Monoubiquitination." April 2013.
Source
wos-lite
Published In
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Volume
27
Publish Date
2013

Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function.

Cell growth and differentiation are controlled by growth factor receptors coupled to the GTPase Ras. Oncogenic mutations disrupt GTPase activity, leading to persistent Ras signaling and cancer progression. Recent evidence indicates that monoubiquitination of Ras leads to Ras activation. Mutation of the primary site of monoubiquitination impairs the ability of activated K-Ras (one of the three mammalian isoforms of Ras) to promote tumor growth. To determine the mechanism of human Ras activation, we chemically ubiquitinated the protein and analyzed its function by NMR, computational modeling and biochemical activity measurements. We established that monoubiquitination has little effect on the binding of Ras to guanine nucleotide, GTP hydrolysis or exchange-factor activation but severely abrogates the response to GTPase-activating proteins in a site-specific manner. These findings reveal a new mechanism by which Ras can trigger persistent signaling in the absence of receptor activation or an oncogenic mutation.

Authors
Baker, R; Lewis, SM; Sasaki, AT; Wilkerson, EM; Locasale, JW; Cantley, LC; Kuhlman, B; Dohlman, HG; Campbell, SL
MLA Citation
Baker, R, Lewis, SM, Sasaki, AT, Wilkerson, EM, Locasale, JW, Cantley, LC, Kuhlman, B, Dohlman, HG, and Campbell, SL. "Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function." Nature structural & molecular biology 20.1 (January 2013): 46-52.
PMID
23178454
Source
epmc
Published In
Nature Structural & Molecular Biology
Volume
20
Issue
1
Publish Date
2013
Start Page
46
End Page
52
DOI
10.1038/nsmb.2430

Influence of threonine metabolism on S-adenosylmethionine and histone methylation.

Threonine is the only amino acid critically required for the pluripotency of mouse embryonic stem cells (mESCs), but the detailed mechanism remains unclear. We found that threonine and S-adenosylmethionine (SAM) metabolism are coupled in pluripotent stem cells, resulting in regulation of histone methylation. Isotope labeling of mESCs revealed that threonine provides a substantial fraction of both the cellular glycine and the acetyl-coenzyme A (CoA) needed for SAM synthesis. Depletion of threonine from the culture medium or threonine dehydrogenase (Tdh) from mESCs decreased accumulation of SAM and decreased trimethylation of histone H3 lysine 4 (H3K4me3), leading to slowed growth and increased differentiation. Thus, abundance of SAM appears to influence H3K4me3, providing a possible mechanism by which modulation of a metabolic pathway might influence stem cell fate.

Authors
Shyh-Chang, N; Locasale, JW; Lyssiotis, CA; Zheng, Y; Teo, RY; Ratanasirintrawoot, S; Zhang, J; Onder, T; Unternaehrer, JJ; Zhu, H; Asara, JM; Daley, GQ; Cantley, LC
MLA Citation
Shyh-Chang, N, Locasale, JW, Lyssiotis, CA, Zheng, Y, Teo, RY, Ratanasirintrawoot, S, Zhang, J, Onder, T, Unternaehrer, JJ, Zhu, H, Asara, JM, Daley, GQ, and Cantley, LC. "Influence of threonine metabolism on S-adenosylmethionine and histone methylation." Science (New York, N.Y.) 339.6116 (January 2013): 222-226.
PMID
23118012
Source
epmc
Published In
Science
Volume
339
Issue
6116
Publish Date
2013
Start Page
222
End Page
226
DOI
10.1126/science.1226603

The consequences of enhanced cell-autonomous glucose metabolism.

The intake and metabolism of carbohydrates for the generation of energy and biomass is evolutionarily conserved, down to the most primitive of cells. Although a basal rate of glucose metabolism occurs in all cells, the processing rates of glucose can become dramatically enhanced when cells acquire malignant properties, or remain undifferentiated. This article investigates the consequences of how increased glucose metabolism affects cellular physiology by altering the physicochemical properties of the whole metabolic network. As a result, enhanced lactate production in the presence of oxygen (the Warburg effect) is required, and metabolism is consequently reconfigured, through multiple mechanisms, to confer numerous physiological and possibly regulatory properties to cells.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "The consequences of enhanced cell-autonomous glucose metabolism." Trends in endocrinology and metabolism: TEM 23.11 (November 2012): 545-551.
PMID
22920571
Source
epmc
Published In
Trends in Endocrinology and Metabolism
Volume
23
Issue
11
Publish Date
2012
Start Page
545
End Page
551
DOI
10.1016/j.tem.2012.07.005

Metabolomics of human cerebrospinal fluid identifies signatures of malignant glioma.

Cerebrospinal fluid is routinely collected for the diagnosis and monitoring of patients with neurological malignancies. However, little is known as to how its constituents may change in a patient when presented with a malignant glioma. Here, we used a targeted mass-spectrometry based metabolomics platform using selected reaction monitoring with positive/negative switching and profiled the relative levels of over 124 polar metabolites present in patient cerebrospinal fluid. We analyzed the metabolic profiles from 10 patients presenting malignant gliomas and seven control patients that did not present malignancy to test whether a small sample size could provide statistically significant signatures. We carried out multiple unbiased forms of classification using a series of unsupervised techniques and identified metabolic signatures that distinguish malignant glioma patients from the control patients. One subtype identified contained metabolites enriched in citric acid cycle components. Newly diagnosed patients segregated into a different subtype and exhibited low levels of metabolites involved in tryptophan metabolism, which may indicate the absence of an inflammatory signature. Together our results provide the first global assessment of the polar metabolic composition in cerebrospinal fluid that accompanies malignancy, and demonstrate that data obtained from high throughput mass spectrometry technology may have suitable predictive capabilities for the identification of biomarkers and classification of neurological diseases.

Authors
Locasale, JW; Melman, T; Song, S; Yang, X; Swanson, KD; Cantley, LC; Wong, ET; Asara, JM
MLA Citation
Locasale, JW, Melman, T, Song, S, Yang, X, Swanson, KD, Cantley, LC, Wong, ET, and Asara, JM. "Metabolomics of human cerebrospinal fluid identifies signatures of malignant glioma." Molecular & cellular proteomics : MCP 11.6 (June 2012): M111.014688-.
PMID
22240505
Source
epmc
Published In
Molecular & cellular proteomics : MCP
Volume
11
Issue
6
Publish Date
2012
Start Page
M111.014688
DOI
10.1074/mcp.m111.014688

Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism.

Tumor maintenance relies on continued activity of driver oncogenes, although their rate-limiting role is highly context dependent. Oncogenic Kras mutation is the signature event in pancreatic ductal adenocarcinoma (PDAC), serving a critical role in tumor initiation. Here, an inducible Kras(G12D)-driven PDAC mouse model establishes that advanced PDAC remains strictly dependent on Kras(G12D) expression. Transcriptome and metabolomic analyses indicate that Kras(G12D) serves a vital role in controlling tumor metabolism through stimulation of glucose uptake and channeling of glucose intermediates into the hexosamine biosynthesis and pentose phosphate pathways (PPP). These studies also reveal that oncogenic Kras promotes ribose biogenesis. Unlike canonical models, we demonstrate that Kras(G12D) drives glycolysis intermediates into the nonoxidative PPP, thereby decoupling ribose biogenesis from NADP/NADPH-mediated redox control. Together, this work provides in vivo mechanistic insights into how oncogenic Kras promotes metabolic reprogramming in native tumors and illuminates potential metabolic targets that can be exploited for therapeutic benefit in PDAC.

Authors
Ying, H; Kimmelman, AC; Lyssiotis, CA; Hua, S; Chu, GC; Fletcher-Sananikone, E; Locasale, JW; Son, J; Zhang, H; Coloff, JL; Yan, H; Wang, W; Chen, S; Viale, A; Zheng, H; Paik, J-H; Lim, C; Guimaraes, AR; Martin, ES; Chang, J; Hezel, AF; Perry, SR; Hu, J; Gan, B; Xiao, Y; Asara, JM; Weissleder, R; Wang, YA; Chin, L; Cantley, LC; DePinho, RA
MLA Citation
Ying, H, Kimmelman, AC, Lyssiotis, CA, Hua, S, Chu, GC, Fletcher-Sananikone, E, Locasale, JW, Son, J, Zhang, H, Coloff, JL, Yan, H, Wang, W, Chen, S, Viale, A, Zheng, H, Paik, J-H, Lim, C, Guimaraes, AR, Martin, ES, Chang, J, Hezel, AF, Perry, SR, Hu, J, Gan, B, Xiao, Y, Asara, JM, Weissleder, R, Wang, YA, Chin, L, Cantley, LC, and DePinho, RA. "Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism." Cell 149.3 (April 2012): 656-670.
PMID
22541435
Source
epmc
Published In
Cell
Volume
149
Issue
3
Publish Date
2012
Start Page
656
End Page
670
DOI
10.1016/j.cell.2012.01.058

Cellular control mechanisms that regulate pyruvate kinase M2 activity and promote cancer growth

Authors
Lyssiotis, CA; Anastasiou, D; Locasale, JW; Vander Heiden, MG; Christofk, HR; Cantley, LC
MLA Citation
Lyssiotis, CA, Anastasiou, D, Locasale, JW, Vander Heiden, MG, Christofk, HR, and Cantley, LC. "Cellular control mechanisms that regulate pyruvate kinase M2 activity and promote cancer growth." Biomedical Research 23.SPEC. ISSUE (February 23, 2012): 213-217.
Source
scopus
Published In
Biomedical Research
Volume
23
Issue
SPEC. ISSUE
Publish Date
2012
Start Page
213
End Page
217

Interactions between epigenetics and metabolism in cancers.

Cancer progression is accompanied by widespread transcriptional changes and metabolic alterations. While it is widely accepted that the origin of cancer can be traced to the mutations that accumulate over time, relatively recent evidence favors a similarly fundamental role for alterations in the epigenome during tumorigenesis. Changes in epigenetics that arise from post-translational modifications of histones and DNA are exploited by cancer cells to upregulate and/or downregulate the expression levels of oncogenes and tumor suppressors, respectively. Although the mechanisms behind these modifications, in particular how they lead to gene silencing and activation, are still being understood, most of the enzymatic machinery of epigenetics require metabolites as substrates or cofactors. As a result, their activities can be influenced by the metabolic state of the cell. The purpose of this review is to give an overview of cancer epigenetics and metabolism and provide examples of where they converge.

Authors
Yun, J; Johnson, JL; Hanigan, CL; Locasale, JW
MLA Citation
Yun, J, Johnson, JL, Hanigan, CL, and Locasale, JW. "Interactions between epigenetics and metabolism in cancers." Frontiers in oncology 2 (January 2012): 163-.
PMID
23162793
Source
epmc
Published In
Frontiers in Oncology
Volume
2
Publish Date
2012
Start Page
163
DOI
10.3389/fonc.2012.00163

Metabolic rewiring drives resistance to targeted cancer therapy.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Metabolic rewiring drives resistance to targeted cancer therapy." Molecular systems biology 8 (January 2012): 597-.
PMID
22806144
Source
epmc
Published In
Molecular systems biology
Volume
8
Publish Date
2012
Start Page
597
DOI
10.1038/msb.2012.30

Maximizing the efficacy of angiogenesis inhibitors.

Authors
Locasale, JW; Zeskind, BJ
MLA Citation
Locasale, JW, and Zeskind, BJ. "Maximizing the efficacy of angiogenesis inhibitors." Journal of clinical oncology : official journal of the American Society of Clinical Oncology 30.3 (January 2012): 337-338.
PMID
22147743
Source
epmc
Published In
Journal of Clinical Oncology
Volume
30
Issue
3
Publish Date
2012
Start Page
337
End Page
338
DOI
10.1200/jco.2011.38.5435

Metabolomics of human cerebrospinal fluid identifies signatures of malignant glioma.

Cerebrospinal fluid is routinely collected for the diagnosis and monitoring of patients with neurological malignancies. However, little is known as to how its constituents may change in a patient when presented with a malignant glioma. Here, we used a targeted mass-spectrometry based metabolomics platform using selected reaction monitoring with positive/negative switching and profiled the relative levels of over 124 polar metabolites present in patient cerebrospinal fluid. We analyzed the metabolic profiles from 10 patients presenting malignant gliomas and seven control patients that did not present malignancy to test whether a small sample size could provide statistically significant signatures. We carried out multiple unbiased forms of classification using a series of unsupervised techniques and identified metabolic signatures that distinguish malignant glioma patients from the control patients. One subtype identified contained metabolites enriched in citric acid cycle components. Newly diagnosed patients segregated into a different subtype and exhibited low levels of metabolites involved in tryptophan metabolism, which may indicate the absence of an inflammatory signature. Together our results provide the first global assessment of the polar metabolic composition in cerebrospinal fluid that accompanies malignancy, and demonstrate that data obtained from high throughput mass spectrometry technology may have suitable predictive capabilities for the identification of biomarkers and classification of neurological diseases.

Authors
Locasale, JW; Melman, T; Song, S; Yang, X; Swanson, KD; Cantley, LC; Wong, ET; Asara, JM
MLA Citation
Locasale, JW, Melman, T, Song, S, Yang, X, Swanson, KD, Cantley, LC, Wong, ET, and Asara, JM. "Metabolomics of human cerebrospinal fluid identifies signatures of malignant glioma." Molecular & cellular proteomics : MCP 11.6 (2012): M111.014688-.
Source
scival
Published In
Molecular & cellular proteomics : MCP
Volume
11
Issue
6
Publish Date
2012
Start Page
M111.014688
DOI
10.1074/mcp.M111.014688

Human pluripotent stem cells decouple respiration from energy production.

Authors
Shyh-Chang, N; Zheng, Y; Locasale, JW; Cantley, LC
MLA Citation
Shyh-Chang, N, Zheng, Y, Locasale, JW, and Cantley, LC. "Human pluripotent stem cells decouple respiration from energy production." The EMBO journal 30.24 (December 14, 2011): 4851-4852.
PMID
22166995
Source
epmc
Published In
EMBO Journal
Volume
30
Issue
24
Publish Date
2011
Start Page
4851
End Page
4852
DOI
10.1038/emboj.2011.436

IL-6 and ovarian cancer--letter.

Authors
Locasale, JW; Zeskind, B
MLA Citation
Locasale, JW, and Zeskind, B. "IL-6 and ovarian cancer--letter." Clinical cancer research : an official journal of the American Association for Cancer Research 17.24 (December 6, 2011): 7837-.
PMID
22147939
Source
epmc
Published In
Clinical cancer research : an official journal of the American Association for Cancer Research
Volume
17
Issue
24
Publish Date
2011
Start Page
7837
DOI
10.1158/1078-0432.ccr-11-2170

Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses.

Control of intracellular reactive oxygen species (ROS) concentrations is critical for cancer cell survival. We show that, in human lung cancer cells, acute increases in intracellular concentrations of ROS caused inhibition of the glycolytic enzyme pyruvate kinase M2 (PKM2) through oxidation of Cys(358). This inhibition of PKM2 is required to divert glucose flux into the pentose phosphate pathway and thereby generate sufficient reducing potential for detoxification of ROS. Lung cancer cells in which endogenous PKM2 was replaced with the Cys(358) to Ser(358) oxidation-resistant mutant exhibited increased sensitivity to oxidative stress and impaired tumor formation in a xenograft model. Besides promoting metabolic changes required for proliferation, the regulatory properties of PKM2 may confer an additional advantage to cancer cells by allowing them to withstand oxidative stress.

Authors
Anastasiou, D; Poulogiannis, G; Asara, JM; Boxer, MB; Jiang, J-K; Shen, M; Bellinger, G; Sasaki, AT; Locasale, JW; Auld, DS; Thomas, CJ; Vander Heiden, MG; Cantley, LC
MLA Citation
Anastasiou, D, Poulogiannis, G, Asara, JM, Boxer, MB, Jiang, J-K, Shen, M, Bellinger, G, Sasaki, AT, Locasale, JW, Auld, DS, Thomas, CJ, Vander Heiden, MG, and Cantley, LC. "Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses." Science (New York, N.Y.) 334.6060 (December 2011): 1278-1283.
PMID
22052977
Source
epmc
Published In
Science
Volume
334
Issue
6060
Publish Date
2011
Start Page
1278
End Page
1283
DOI
10.1126/science.1211485

PHGDH amplification and altered glucose metabolism in human melanoma.

The metabolic requirements of cancer cells differ from that of their normal counterparts. To support their proliferation, cancer cells switch to a fermentative metabolism that is thought to support biomass production. Instances where metabolic enzymes promote tumorigenesis remain rare. However, an enzyme involved in the de novo synthesis of serine, 3-phosphoglycerate dehydrogenase (PHGDH), was recently identified as a putative oncogene. The potential mechanisms by which PHGDH promotes cancer are discussed.

Authors
Mullarky, E; Mattaini, KR; Vander Heiden, MG; Cantley, LC; Locasale, JW
MLA Citation
Mullarky, E, Mattaini, KR, Vander Heiden, MG, Cantley, LC, and Locasale, JW. "PHGDH amplification and altered glucose metabolism in human melanoma." Pigment cell & melanoma research 24.6 (December 2011): 1112-1115.
PMID
21981974
Source
epmc
Published In
Pigment Cell and Melanoma Research
Volume
24
Issue
6
Publish Date
2011
Start Page
1112
End Page
1115
DOI
10.1111/j.1755-148x.2011.00919.x

Genetic selection for enhanced serine metabolism in cancer development.

Authors
Locasale, JW; Cantley, LC
MLA Citation
Locasale, JW, and Cantley, LC. "Genetic selection for enhanced serine metabolism in cancer development." Cell cycle (Georgetown, Tex.) 10.22 (November 15, 2011): 3812-3813.
PMID
22064516
Source
epmc
Published In
Cell Cycle
Volume
10
Issue
22
Publish Date
2011
Start Page
3812
End Page
3813
DOI
10.4161/cc.10.22.18224

METABOLOMICS PROFILING OF PATIENT CEREBROSPINAL FLUID IDENTIFIES SIGNATURES OF MALIGNANT GLIOMA

Authors
Locasale, JW; Melman, T; Song, SS; Yang, X; Swanson, KD; Cantley, LC; Asara, JM; Wong, ET
MLA Citation
Locasale, JW, Melman, T, Song, SS, Yang, X, Swanson, KD, Cantley, LC, Asara, JM, and Wong, ET. "METABOLOMICS PROFILING OF PATIENT CEREBROSPINAL FLUID IDENTIFIES SIGNATURES OF MALIGNANT GLIOMA." NEURO-ONCOLOGY 13 (November 2011): 69-69.
Source
wos-lite
Published In
Neuro-Oncology
Volume
13
Publish Date
2011
Start Page
69
End Page
69

mTOR drives its own activation via SCF(βTrCP)-dependent degradation of the mTOR inhibitor DEPTOR.

The activities of both mTORC1 and mTORC2 are negatively regulated by their endogenous inhibitor, DEPTOR. As such, the abundance of DEPTOR is a critical determinant in the activity status of the mTOR network. DEPTOR stability is governed by the 26S-proteasome through a largely unknown mechanism. Here we describe an mTOR-dependent phosphorylation-driven pathway for DEPTOR destruction via SCF(βTrCP). DEPTOR phosphorylation by mTOR in response to growth signals, and in collaboration with casein kinase I (CKI), generates a phosphodegron that binds βTrCP. Failure to degrade DEPTOR through either degron mutation or βTrCP depletion leads to reduced mTOR activity, reduced S6 kinase activity, and activation of autophagy to reduce cell growth. This work expands the current understanding of mTOR regulation by revealing a positive feedback loop involving mTOR and CKI-dependent turnover of its inhibitor, DEPTOR, suggesting that misregulation of the DEPTOR destruction pathway might contribute to aberrant activation of mTOR in disease.

Authors
Gao, D; Inuzuka, H; Tan, M-KM; Fukushima, H; Locasale, JW; Liu, P; Wan, L; Zhai, B; Chin, YR; Shaik, S; Lyssiotis, CA; Gygi, SP; Toker, A; Cantley, LC; Asara, JM; Harper, JW; Wei, W
MLA Citation
Gao, D, Inuzuka, H, Tan, M-KM, Fukushima, H, Locasale, JW, Liu, P, Wan, L, Zhai, B, Chin, YR, Shaik, S, Lyssiotis, CA, Gygi, SP, Toker, A, Cantley, LC, Asara, JM, Harper, JW, and Wei, W. "mTOR drives its own activation via SCF(βTrCP)-dependent degradation of the mTOR inhibitor DEPTOR." Molecular cell 44.2 (October 2011): 290-303.
PMID
22017875
Source
epmc
Published In
Molecular Cell
Volume
44
Issue
2
Publish Date
2011
Start Page
290
End Page
303
DOI
10.1016/j.molcel.2011.08.030

Metabolic flux and the regulation of mammalian cell growth.

The study of normal mammalian cell growth and the defects that contribute to disease pathogenesis links metabolism to cell growth. Here, we visit several aspects of growth-promoting metabolism, emphasizing recent advances in our understanding of how alterations in glucose metabolism affect cytosolic and mitochondrial redox potential and ATP generation. These alterations drive cell proliferation not only through supporting biosynthesis, energy metabolism, and maintaining redox potential but also through initiating signaling mechanisms that are still poorly characterized. The evolutionary basis of these additional layers of growth control is also discussed.

Authors
Locasale, JW; Cantley, LC
MLA Citation
Locasale, JW, and Cantley, LC. "Metabolic flux and the regulation of mammalian cell growth." Cell metabolism 14.4 (October 2011): 443-451. (Review)
PMID
21982705
Source
epmc
Published In
Cell Metabolism
Volume
14
Issue
4
Publish Date
2011
Start Page
443
End Page
451
DOI
10.1016/j.cmet.2011.07.014

Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival.

Previous experiments suggest a connection between the N-alpha-acetylation of proteins and sensitivity of cells to apoptotic signals. Here, we describe a biochemical assay to detect the acetylation status of proteins and demonstrate that protein N-alpha-acetylation is regulated by the availability of acetyl-CoA. Because the antiapoptotic protein Bcl-xL is known to influence mitochondrial metabolism, we reasoned that Bcl-xL may provide a link between protein N-alpha-acetylation and apoptosis. Indeed, Bcl-xL overexpression leads to a reduction in levels of acetyl-CoA and N-alpha-acetylated proteins in the cell. This effect is independent of Bax and Bak, the known binding partners of Bcl-xL. Increasing cellular levels of acetyl-CoA by addition of acetate or citrate restores protein N-alpha-acetylation in Bcl-xL-expressing cells and confers sensitivity to apoptotic stimuli. We propose that acetyl-CoA serves as a signaling molecule that couples apoptotic sensitivity to metabolism by regulating protein N-alpha-acetylation.

Authors
Yi, CH; Pan, H; Seebacher, J; Jang, I-H; Hyberts, SG; Heffron, GJ; Vander Heiden, MG; Yang, R; Li, F; Locasale, JW; Sharfi, H; Zhai, B; Rodriguez-Mias, R; Luithardt, H; Cantley, LC; Daley, GQ; Asara, JM; Gygi, SP; Wagner, G; Liu, C-F; Yuan, J
MLA Citation
Yi, CH, Pan, H, Seebacher, J, Jang, I-H, Hyberts, SG, Heffron, GJ, Vander Heiden, MG, Yang, R, Li, F, Locasale, JW, Sharfi, H, Zhai, B, Rodriguez-Mias, R, Luithardt, H, Cantley, LC, Daley, GQ, Asara, JM, Gygi, SP, Wagner, G, Liu, C-F, and Yuan, J. "Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival." Cell 146.4 (August 2011): 607-620.
PMID
21854985
Source
epmc
Published In
Cell
Volume
146
Issue
4
Publish Date
2011
Start Page
607
End Page
620
DOI
10.1016/j.cell.2011.06.050

Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis.

Most tumors exhibit increased glucose metabolism to lactate, however, the extent to which glucose-derived metabolic fluxes are used for alternative processes is poorly understood. Using a metabolomics approach with isotope labeling, we found that in some cancer cells a relatively large amount of glycolytic carbon is diverted into serine and glycine metabolism through phosphoglycerate dehydrogenase (PHGDH). An analysis of human cancers showed that PHGDH is recurrently amplified in a genomic region of focal copy number gain most commonly found in melanoma. Decreasing PHGDH expression impaired proliferation in amplified cell lines. Increased expression was also associated with breast cancer subtypes, and ectopic expression of PHGDH in mammary epithelial cells disrupted acinar morphogenesis and induced other phenotypic alterations that may predispose cells to transformation. Our findings show that the diversion of glycolytic flux into a specific alternate pathway can be selected during tumor development and may contribute to the pathogenesis of human cancer.

Authors
Locasale, JW; Grassian, AR; Melman, T; Lyssiotis, CA; Mattaini, KR; Bass, AJ; Heffron, G; Metallo, CM; Muranen, T; Sharfi, H; Sasaki, AT; Anastasiou, D; Mullarky, E; Vokes, NI; Sasaki, M; Beroukhim, R; Stephanopoulos, G; Ligon, AH; Meyerson, M; Richardson, AL; Chin, L; Wagner, G; Asara, JM; Brugge, JS; Cantley, LC; Vander Heiden, MG
MLA Citation
Locasale, JW, Grassian, AR, Melman, T, Lyssiotis, CA, Mattaini, KR, Bass, AJ, Heffron, G, Metallo, CM, Muranen, T, Sharfi, H, Sasaki, AT, Anastasiou, D, Mullarky, E, Vokes, NI, Sasaki, M, Beroukhim, R, Stephanopoulos, G, Ligon, AH, Meyerson, M, Richardson, AL, Chin, L, Wagner, G, Asara, JM, Brugge, JS, Cantley, LC, and Vander Heiden, MG. "Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis." Nature genetics 43.9 (July 31, 2011): 869-874.
PMID
21804546
Source
epmc
Published In
Nature Genetics
Volume
43
Issue
9
Publish Date
2011
Start Page
869
End Page
874
DOI
10.1038/ng.890

Abstract LB-255: A mass spectrometry platform to quantitatively profile cancer cell metabolism from cells, tumors, and fixed tissue

Authors
Yang, X; Locasale, J; Rahal, R; Breitkopf, S; VanderHeiden, M; Spentzos, D; Wu, C-L; Perrimon, N; Cantley, L; Wong, E; Asara, J
MLA Citation
Yang, X, Locasale, J, Rahal, R, Breitkopf, S, VanderHeiden, M, Spentzos, D, Wu, C-L, Perrimon, N, Cantley, L, Wong, E, and Asara, J. "Abstract LB-255: A mass spectrometry platform to quantitatively profile cancer cell metabolism from cells, tumors, and fixed tissue." Cancer Research 71.8 Supplement (April 15, 2011): LB-255-LB-255.
Source
crossref
Published In
Cancer Research
Volume
71
Issue
8 Supplement
Publish Date
2011
Start Page
LB-255
End Page
LB-255
DOI
10.1158/1538-7445.AM2011-LB-255

Ubiquitination of K-Ras enhances activation and facilitates binding to select downstream effectors.

The guanosine triphosphate (GTP)--loaded form of the guanosine triphosphatase (GTPase) Ras initiates multiple signaling pathways by binding to various effectors, such as the kinase Raf and phosphatidylinositol 3-kinase (PI3K). Ras activity is increased by guanine nucleotide exchange factors that stimulate guanosine diphosphate release and GTP loading and is inhibited by GTPase-activating proteins that stimulate GTP hydrolysis. KRAS is the most frequently mutated RAS gene in cancer. Here, we report that monoubiquitination of lysine-147 in the guanine nucleotide-binding motif of wild-type K-Ras could lead to enhanced GTP loading. Furthermore, ubiquitination increased the binding of the oncogenic Gly12Val mutant of K-Ras to the downstream effectors PI3K and Raf. Thus, monoubiquitination could enhance GTP loading on K-Ras and increase its affinity for specific downstream effectors, providing a previously unidentified mechanism for Ras activation.

Authors
Sasaki, AT; Carracedo, A; Locasale, JW; Anastasiou, D; Takeuchi, K; Kahoud, ER; Haviv, S; Asara, JM; Pandolfi, PP; Cantley, LC
MLA Citation
Sasaki, AT, Carracedo, A, Locasale, JW, Anastasiou, D, Takeuchi, K, Kahoud, ER, Haviv, S, Asara, JM, Pandolfi, PP, and Cantley, LC. "Ubiquitination of K-Ras enhances activation and facilitates binding to select downstream effectors." Science signaling 4.163 (March 8, 2011): ra13-.
PMID
21386094
Source
epmc
Published In
Science Signaling
Volume
4
Issue
163
Publish Date
2011
Start Page
ra13
DOI
10.1126/scisignal.2001518

Metabolic pathway alterations that support cell proliferation.

Proliferating cells adapt metabolism to support the conversion of available nutrients into biomass. How cell metabolism is regulated to balance the production of ATP, metabolite building blocks, and reducing equivalents remains uncertain. Proliferative metabolism often involves an increased rate of glycolysis. A key regulated step in glycolysis is catalyzed by pyruvate kinase to convert phosphoenolpyruvate (PEP) to pyruvate. Surprisingly, there is strong selection for expression of the less active M2 isoform of pyruvate kinase (PKM2) in tumors and other proliferative tissues. Cell growth signals further decrease PKM2 activity, and cells with less active PKM2 use another pathway with separate regulatory properties to convert PEP to pyruvate. One consequence of using this alternative pathway is an accumulation of 3-phosphoglycerate (3PG) that leads to the diversion of 3PG into the serine biosynthesis pathway. In fact, in some cancers a substantial portion of the total glucose flux is directed toward serine synthesis, and genetic evidence suggests that glucose flux into this pathway can promote cell transformation. Environmental conditions can also influence the pathways that cells use to generate biomass with the source of carbon for lipid synthesis changing based on oxygen availability. Together, these findings argue that distinct metabolic phenotypes exist among proliferating cells, and both genetic and environmental factors influence how metabolism is regulated to support cell growth.

Authors
Vander Heiden, MG; Lunt, SY; Dayton, TL; Fiske, BP; Israelsen, WJ; Mattaini, KR; Vokes, NI; Stephanopoulos, G; Cantley, LC; Metallo, CM; Locasale, JW
MLA Citation
Vander Heiden, MG, Lunt, SY, Dayton, TL, Fiske, BP, Israelsen, WJ, Mattaini, KR, Vokes, NI, Stephanopoulos, G, Cantley, LC, Metallo, CM, and Locasale, JW. "Metabolic pathway alterations that support cell proliferation." Cold Spring Harbor symposia on quantitative biology 76 (January 2011): 325-334.
PMID
22262476
Source
epmc
Published In
Cold Spring Harbor Laboratory: Symposia on Quantitative Biology
Volume
76
Publish Date
2011
Start Page
325
End Page
334
DOI
10.1101/sqb.2012.76.010900

Rewiring of glycolysis in cancer cell metabolism.

Authors
Locasale, JW; Vander Heiden, MG; Cantley, LC
MLA Citation
Locasale, JW, Vander Heiden, MG, and Cantley, LC. "Rewiring of glycolysis in cancer cell metabolism." Cell cycle (Georgetown, Tex.) 9.21 (November 7, 2010): 4253-.
PMID
21045562
Source
epmc
Published In
Cell Cycle
Volume
9
Issue
21
Publish Date
2010
Start Page
4253
DOI
10.4161/cc.9.21.13925

Evidence for an alternative glycolytic pathway in rapidly proliferating cells.

Proliferating cells, including cancer cells, require altered metabolism to efficiently incorporate nutrients such as glucose into biomass. The M2 isoform of pyruvate kinase (PKM2) promotes the metabolism of glucose by aerobic glycolysis and contributes to anabolic metabolism. Paradoxically, decreased pyruvate kinase enzyme activity accompanies the expression of PKM2 in rapidly dividing cancer cells and tissues. We demonstrate that phosphoenolpyruvate (PEP), the substrate for pyruvate kinase in cells, can act as a phosphate donor in mammalian cells because PEP participates in the phosphorylation of the glycolytic enzyme phosphoglycerate mutase (PGAM1) in PKM2-expressing cells. We used mass spectrometry to show that the phosphate from PEP is transferred to the catalytic histidine (His11) on human PGAM1. This reaction occurred at physiological concentrations of PEP and produced pyruvate in the absence of PKM2 activity. The presence of histidine-phosphorylated PGAM1 correlated with the expression of PKM2 in cancer cell lines and tumor tissues. Thus, decreased pyruvate kinase activity in PKM2-expressing cells allows PEP-dependent histidine phosphorylation of PGAM1 and may provide an alternate glycolytic pathway that decouples adenosine triphosphate production from PEP-mediated phosphotransfer, allowing for the high rate of glycolysis to support the anabolic metabolism observed in many proliferating cells.

Authors
Vander Heiden, MG; Locasale, JW; Swanson, KD; Sharfi, H; Heffron, GJ; Amador-Noguez, D; Christofk, HR; Wagner, G; Rabinowitz, JD; Asara, JM; Cantley, LC
MLA Citation
Vander Heiden, MG, Locasale, JW, Swanson, KD, Sharfi, H, Heffron, GJ, Amador-Noguez, D, Christofk, HR, Wagner, G, Rabinowitz, JD, Asara, JM, and Cantley, LC. "Evidence for an alternative glycolytic pathway in rapidly proliferating cells." Science (New York, N.Y.) 329.5998 (September 2010): 1492-1499.
PMID
20847263
Source
epmc
Published In
Science
Volume
329
Issue
5998
Publish Date
2010
Start Page
1492
End Page
1499
DOI
10.1126/science.1188015

Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases.

The Mycobacterium tuberculosis genome encodes 11 serine/threonine protein kinases (STPKs) that are structurally related to eukaryotic kinases. To gain insight into the role of Ser/Thr phosphorylation in this major global pathogen, we used a phosphoproteomic approach to carry out an extensive analysis of protein phosphorylation in M. tuberculosis. We identified more than 500 phosphorylation events in 301 proteins that are involved in a broad range of functions. Bioinformatic analysis of quantitative in vitro kinase assays on peptides containing a subset of these phosphorylation sites revealed a dominant motif shared by six of the M. tuberculosis STPKs. Kinase assays on a second set of peptides incorporating targeted substitutions surrounding the phosphoacceptor validated this motif and identified additional residues preferred by individual kinases. Our data provide insight into processes regulated by STPKs in M. tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins.

Authors
Prisic, S; Dankwa, S; Schwartz, D; Chou, MF; Locasale, JW; Kang, C-M; Bemis, G; Church, GM; Steen, H; Husson, RN
MLA Citation
Prisic, S, Dankwa, S, Schwartz, D, Chou, MF, Locasale, JW, Kang, C-M, Bemis, G, Church, GM, Steen, H, and Husson, RN. "Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases." Proceedings of the National Academy of Sciences of the United States of America 107.16 (April 5, 2010): 7521-7526.
PMID
20368441
Source
epmc
Published In
Proceedings of the National Academy of Sciences of USA
Volume
107
Issue
16
Publish Date
2010
Start Page
7521
End Page
7526
DOI
10.1073/pnas.0913482107

Altered metabolism in cancer.

Cancer cells have different metabolic requirements from their normal counterparts. Understanding the consequences of this differential metabolism requires a detailed understanding of glucose metabolism and its relation to energy production in cancer cells. A recent study in BMC Systems Biology by Vasquez et al. developed a mathematical model to assess some features of this altered metabolism. Here, we take a broader look at the regulation of energy metabolism in cancer cells, considering their anabolic as well as catabolic needs. See research article: http://www.biomedcentral.com/1752-0509/4/58/

Authors
Locasale, JW; Cantley, LC
MLA Citation
Locasale, JW, and Cantley, LC. "Altered metabolism in cancer." BMC biology 8 (January 2010): 88-.
PMID
20598111
Source
epmc
Published In
BMC Biology
Volume
8
Publish Date
2010
Start Page
88
DOI
10.1186/1741-7007-8-88

Cancer's insatiable appetite.

Authors
Locasale, JW; Cantley, LC; Vander Heiden, MG
MLA Citation
Locasale, JW, Cantley, LC, and Vander Heiden, MG. "Cancer's insatiable appetite." Nature biotechnology 27.10 (October 2009): 916-917.
PMID
19816448
Source
epmc
Published In
Nature Biotechnology
Volume
27
Issue
10
Publish Date
2009
Start Page
916
End Page
917
DOI
10.1038/nbt1009-916

Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data.

Advances in mass spectrometry among other technologies have allowed for quantitative, reproducible, proteome-wide measurements of levels of phosphorylation as signals propagate through complex networks in response to external stimuli under different conditions. However, computational approaches to infer elements of the signaling network strictly from the quantitative aspects of proteomics data are not well established. We considered a method using the principle of maximum entropy to infer a network of interacting phosphotyrosine sites from pairwise correlations in a mass spectrometry data set and derive a phosphorylation-dependent interaction network solely from quantitative proteomics data. We first investigated the applicability of this approach by using a simulation of a model biochemical signaling network whose dynamics are governed by a large set of coupled differential equations. We found that in a simulated signaling system, the method detects interactions with significant accuracy. We then analyzed a growth factor mediated signaling network in a human mammary epithelial cell line that we inferred from mass spectrometry data and observe a biologically interpretable, small-world structure of signaling nodes, as well as a catalog of predictions regarding the interactions among previously uncharacterized phosphotyrosine sites. For example, the calculation places a recently identified tumor suppressor pathway through ARHGEF7 and Scribble, in the context of growth factor signaling. Our findings suggest that maximum entropy derived network models are an important tool for interpreting quantitative proteomics data.

Authors
Locasale, JW; Wolf-Yadlin, A
MLA Citation
Locasale, JW, and Wolf-Yadlin, A. "Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data." PloS one 4.8 (August 26, 2009): e6522-.
PMID
19707567
Source
epmc
Published In
PloS one
Volume
4
Issue
8
Publish Date
2009
Start Page
e6522
DOI
10.1371/journal.pone.0006522

Signatures of protein-DNA recognition in free DNA binding sites.

One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel beta strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition.

Authors
Locasale, JW; Napoli, AA; Chen, S; Berman, HM; Lawson, CL
MLA Citation
Locasale, JW, Napoli, AA, Chen, S, Berman, HM, and Lawson, CL. "Signatures of protein-DNA recognition in free DNA binding sites." Journal of molecular biology 386.4 (March 2009): 1054-1065.
PMID
19244617
Source
epmc
Published In
Journal of Molecular Biology
Volume
386
Issue
4
Publish Date
2009
Start Page
1054
End Page
1065
DOI
10.1016/j.jmb.2009.01.007

Signal duration and the time scale dependence of signal integration in biochemical pathways.

Signal duration (e.g. the time over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments. Accompanying differences in signal duration are numerous downstream biological processes that require multiple steps of biochemical regulation.Here we present an analysis that investigates how simple biochemical motifs that involve multiple stages of regulation can be constructed to differentially process signals that persist at different time scales. We compute the dynamic, frequency dependent gain within these networks and resulting power spectra to better understand how biochemical networks can integrate signals at different time scales. We identify topological features of these networks that allow for different frequency dependent signal processing properties.We show that multi-staged cascades are effective in integrating signals of long duration whereas multi-staged cascades that operate in the presence of negative feedback are effective in integrating signals of short duration. Our studies suggest principles for why signal duration in connection with multiple steps of downstream regulation is a ubiquitous motif in biochemical systems.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Signal duration and the time scale dependence of signal integration in biochemical pathways." BMC systems biology 2 (December 17, 2008): 108-.
PMID
19091071
Source
epmc
Published In
BMC Systems Biology
Volume
2
Publish Date
2008
Start Page
108
DOI
10.1186/1752-0509-2-108

Three-state kinetic mechanism for scaffold-mediated signal transduction.

Signaling events in eukaryotic cells are often guided by a scaffolding protein. Scaffold proteins assemble multiple proteins into a spatially localized signaling complex and exert numerous physical effects on signaling pathways. To study these effects, we consider a minimal, three-state kinetic model of scaffold-mediated kinase activation. We first introduce and apply a path summation technique to obtain approximate solutions to a single molecule master equation that governs protein kinase activation. We then consider exact numerical solutions. We comment on when this approximation is appropriate and then use this analysis to illustrate the competition of processes occurring at many time scales that are involved in signal transduction in the presence of a scaffold protein. We find that our minimal model captures how scaffold concentration can influence the times over which signaling is distributed in kinase cascades. For a range of scaffold concentrations, scaffolds allow for signaling to be distributed over multiple decades. The findings are consistent with recent experiments and simulation data. These results provide a framework and offer a mechanism for understanding how scaffold proteins can influence the shape of the waiting time distribution of kinase activation and effectively broaden the times over which protein kinases are activated in the course of cell signaling.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Three-state kinetic mechanism for scaffold-mediated signal transduction." Physical review. E, Statistical, nonlinear, and soft matter physics 78.5 Pt 1 (November 21, 2008): 051921-.
PMID
19113169
Source
epmc
Published In
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume
78
Issue
5 Pt 1
Publish Date
2008
Start Page
051921
DOI
10.1103/physreve.78.051921

Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins.

Scaffolding proteins that direct the assembly of multiple kinases into a spatially localized signaling complex are often essential for the maintenance of an appropriate biological response. Although scaffolds are widely believed to have dramatic effects on the dynamics of signal propagation, the mechanisms that underlie these consequences are not well understood. Here, Monte Carlo simulations of a model kinase cascade are used to investigate how the temporal characteristics of signaling cascades can be influenced by the presence of scaffold proteins. Specifically, we examine the effects of spatially localizing kinase components on a scaffold on signaling dynamics. The simulations indicate that a major effect that scaffolds exert on the dynamics of cell signaling is to control how the activation of protein kinases is distributed over time. Scaffolds can influence the timing of kinase activation by allowing for kinases to become activated over a broad range of times, thus allowing for signaling at both early and late times. Scaffold concentrations that result in optimal signal amplitude also result in the broadest distributions of times over which kinases are activated. These calculations provide insights into one mechanism that describes how the duration of a signal can potentially be regulated in a scaffold mediated protein kinase cascade. Our results illustrate another complexity in the broad array of control properties that emerge from the physical effects of spatially localizing components of kinase cascades on scaffold proteins.

Authors
Locasale, JW; Chakraborty, AK
MLA Citation
Locasale, JW, and Chakraborty, AK. "Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins." PLoS computational biology 4.6 (June 27, 2008): e1000099-.
PMID
18584022
Source
epmc
Published In
PLoS computational biology
Volume
4
Issue
6
Publish Date
2008
Start Page
e1000099
DOI
10.1371/journal.pcbi.1000099

Importance of signal duration and the time scale dependence of signal integration in biochemical networks

Authors
Locasale, JW; Chakraborty, AK
MLA Citation
Locasale, JW, and Chakraborty, AK. "Importance of signal duration and the time scale dependence of signal integration in biochemical networks." FASEB JOURNAL 22 (April 2008).
Source
wos-lite
Published In
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Volume
22
Publish Date
2008

Allovalency revisited: an analysis of multisite phosphorylation and substrate rebinding.

The utilization of multiple phosphorylation sites in regulating a biological response is ubiquitous in cell signaling. If each site contributes an additional, equivalent binding site, then one consequence of an increase in the number of phosphorylations may be to increase the probability that, upon dissociation, a ligand immediately rebinds to its receptor. How such effects may influence cell signaling systems is not well understood. Here, a self-consistent integral equation formalism for ligand rebinding, in conjunction with Monte Carlo simulations, is employed to further investigate the effects of multiple, equivalent binding sites on shaping biological responses. Multiple regimes that characterize qualitatively different physics due to the differential prevalence of rebinding effects are predicted. Calculations suggest that when ligand rebinding contributes significantly to the dose response, a purely allovalent model can influence the binding curves nonlinearly. The model also predicts that ligand rebinding in itself appears insufficient to generate a highly cooperative biological response.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Allovalency revisited: an analysis of multisite phosphorylation and substrate rebinding." The Journal of chemical physics 128.11 (March 2008): 115106-.
PMID
18361621
Source
epmc
Published In
Journal of Chemical Physics
Volume
128
Issue
11
Publish Date
2008
Start Page
115106
DOI
10.1063/1.2841124

Scaffold proteins tune the regulatory properties of protein kinase cascades

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Scaffold proteins tune the regulatory properties of protein kinase cascades." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 (August 19, 2007).
Source
wos-lite
Published In
ACS National Meeting Book of Abstracts
Volume
234
Publish Date
2007

Scaffold proteins confer diverse regulatory properties to protein kinase cascades.

The assembly of multiple signaling proteins into a complex by a scaffold protein guides many cellular decisions. Despite recent advances, the overarching principles that govern scaffold function are not well understood. We carried out a computational study using kinetic Monte Carlo simulations to understand how spatial localization of kinases on a scaffold may regulate signaling under different physiological conditions. Our studies identify regulatory properties of scaffold proteins that allow them to both amplify and attenuate incoming signals in different biological contexts. These properties are not caused by the well established prozone or combinatorial inhibition effect. These results bring coherence to seemingly paradoxical observations and suggest that cells have evolved design rules that enable scaffold proteins to regulate widely disparate cellular functions.

Authors
Locasale, JW; Shaw, AS; Chakraborty, AK
MLA Citation
Locasale, JW, Shaw, AS, and Chakraborty, AK. "Scaffold proteins confer diverse regulatory properties to protein kinase cascades." Proceedings of the National Academy of Sciences of the United States of America 104.33 (August 8, 2007): 13307-13312.
PMID
17686969
Source
epmc
Published In
Proceedings of the National Academy of Sciences of USA
Volume
104
Issue
33
Publish Date
2007
Start Page
13307
End Page
13312
DOI
10.1073/pnas.0706311104

Scaffold proteins confer diverse regulatory properties to protein kinase cascades

Authors
Locasale, JW; Chakraborty, AK; Shaw, A
MLA Citation
Locasale, JW, Chakraborty, AK, and Shaw, A. "Scaffold proteins confer diverse regulatory properties to protein kinase cascades." April 2007.
Source
wos-lite
Published In
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Volume
21
Issue
5
Publish Date
2007
Start Page
A264
End Page
A264

The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse.

T cell activation is predicated on the interaction between the T cell receptor and peptide-major histocompatibility (pMHC) ligands. The factors that determine the stimulatory potency of a pMHC molecule remain unclear. We describe results showing that a peptide exhibiting many hallmarks of a weak agonist stimulates T cells to proliferate more than the wild-type agonist ligand. An in silico approach suggested that the inability to form the central supramolecular activation cluster (cSMAC) could underlie the increased proliferation. This conclusion was supported by experiments that showed that enhancing cSMAC formation reduced stimulatory capacity of the weak peptide. Our studies highlight the fact that a complex interplay of factors determines the quality of a T cell antigen.

Authors
Cemerski, S; Das, J; Locasale, J; Arnold, P; Giurisato, E; Markiewicz, MA; Fremont, D; Allen, PM; Chakraborty, AK; Shaw, AS
MLA Citation
Cemerski, S, Das, J, Locasale, J, Arnold, P, Giurisato, E, Markiewicz, MA, Fremont, D, Allen, PM, Chakraborty, AK, and Shaw, AS. "The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse." Immunity 26.3 (March 8, 2007): 345-355.
PMID
17346997
Source
epmc
Published In
Immunity
Volume
26
Issue
3
Publish Date
2007
Start Page
345
End Page
355
DOI
10.1016/j.immuni.2007.01.013

The Stimulatory Potency of T Cell Antigens Is Influenced by the Formation of the Immunological Synapse

Authors
Čemerski, S; Das, J; Locasale, J; Arnold, P; Giurisato, E; Markiewicz, MA; Fremont, D; Allen, PM; Chakraborty, AK; Shaw, AS
MLA Citation
Čemerski, S, Das, J, Locasale, J, Arnold, P, Giurisato, E, Markiewicz, MA, Fremont, D, Allen, PM, Chakraborty, AK, and Shaw, AS. "The Stimulatory Potency of T Cell Antigens Is Influenced by the Formation of the Immunological Synapse." Immunity 26.3 (March 2007): 345-355.
Source
crossref
Published In
Immunity
Volume
26
Issue
3
Publish Date
2007
Start Page
345
End Page
355
DOI
10.1016/j.immuni.2007.01.013

Computational investigations into the origins of short-term biochemical memory in T cell activation.

Recent studies have reported that T cells can integrate signals between interrupted encounters with Antigen Presenting Cells (APCs) in such a way that the process of signal integration exhibits a form of memory. Here, we carry out a computational study using a simple mathematical model of T cell activation to investigate the ramifications of interrupted T cell-APC contacts on signal integration. We consider several mechanisms of how signal integration at these time scales may be achieved and conclude that feedback control of immediate early gene products (IEGs) appears to be a highly plausible mechanism that allows for effective signal integration and cytokine production from multiple exposures to APCs. Analysis of these computer simulations provides an experimental roadmap involving several testable predictions.

Authors
Locasale, JW
MLA Citation
Locasale, JW. "Computational investigations into the origins of short-term biochemical memory in T cell activation." PloS one 2.7 (January 2007): e627-.
PMID
17637843
Source
epmc
Published In
PloS one
Volume
2
Issue
7
Publish Date
2007
Start Page
e627
DOI
10.1371/journal.pone.0000627

Friction, dynamics, and length scales in hydrophilic polymers.

Authors
Castner, EW; Lee, BJ; Diken, EG; Shirota, H; DeRitter, M; Wiewior, PP; Locasale, JW
MLA Citation
Castner, EW, Lee, BJ, Diken, EG, Shirota, H, DeRitter, M, Wiewior, PP, and Locasale, JW. "Friction, dynamics, and length scales in hydrophilic polymers." March 2003.
Source
wos-lite
Published In
ACS National Meeting Book of Abstracts
Volume
225
Publish Date
2003
Start Page
U446
End Page
U446
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