51
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CD98hc (SLC3A2) sustains amino acid and nucleotide availability for cell cycle progression. Sci Rep 2019; 9:14065. [PMID: 31575908 PMCID: PMC6773781 DOI: 10.1038/s41598-019-50547-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
CD98 heavy chain (CD98hc) forms heteromeric amino acid (AA) transporters by interacting with different light chains. Cancer cells overexpress CD98hc-transporters in order to meet their increased nutritional and antioxidant demands, since they provide branched-chain AA (BCAA) and aromatic AA (AAA) availability while protecting cells from oxidative stress. Here we show that BCAA and AAA shortage phenocopies the inhibition of mTORC1 signalling, protein synthesis and cell proliferation caused by CD98hc ablation. Furthermore, our data indicate that CD98hc sustains glucose uptake and glycolysis, and, as a consequence, the pentose phosphate pathway (PPP). Thus, loss of CD98hc triggers a dramatic reduction in the nucleotide pool, which leads to replicative stress in these cells, as evidenced by the enhanced DNA Damage Response (DDR), S-phase delay and diminished rate of mitosis, all recovered by nucleoside supplementation. In addition, proper BCAA and AAA availability sustains the expression of the enzyme ribonucleotide reductase. In this regard, BCAA and AAA shortage results in decreased content of deoxynucleotides that triggers replicative stress, also recovered by nucleoside supplementation. On the basis of our findings, we conclude that CD98hc plays a central role in AA and glucose cellular nutrition, redox homeostasis and nucleotide availability, all key for cell proliferation.
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Dai S, Funk LM, von Pappenheim FR, Sautner V, Paulikat M, Schröder B, Uranga J, Mata RA, Tittmann K. Low-barrier hydrogen bonds in enzyme cooperativity. Nature 2019; 573:609-613. [PMID: 31534226 DOI: 10.1038/s41586-019-1581-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/12/2019] [Indexed: 11/09/2022]
Abstract
The underlying molecular mechanisms of cooperativity and allosteric regulation are well understood for many proteins, with haemoglobin and aspartate transcarbamoylase serving as prototypical examples1,2. The binding of effectors typically causes a structural transition of the protein that is propagated through signalling pathways to remote sites and involves marked changes on the tertiary and sometimes even the quaternary level1-5. However, the origin of these signals and the molecular mechanism of long-range signalling at an atomic level remain unclear5-8. The different spatial scales and timescales in signalling pathways render experimental observation challenging; in particular, the positions and movement of mobile protons cannot be visualized by current methods of structural analysis. Here we report the experimental observation of fluctuating low-barrier hydrogen bonds as switching elements in cooperativity pathways of multimeric enzymes. We have observed these low-barrier hydrogen bonds in ultra-high-resolution X-ray crystallographic structures of two multimeric enzymes, and have validated their assignment using computational calculations. Catalytic events at the active sites switch between low-barrier hydrogen bonds and ordinary hydrogen bonds in a circuit that consists of acidic side chains and water molecules, transmitting a signal through the collective repositioning of protons by behaving as an atomistic Newton's cradle. The resulting communication synchronizes catalysis in the oligomer. Our studies provide several lines of evidence and a working model for not only the existence of low-barrier hydrogen bonds in proteins, but also a connection to enzyme cooperativity. This finding suggests new principles of drug and enzyme design, in which sequences of residues can be purposefully included to enable long-range communication and thus the regulation of engineered biomolecules.
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Affiliation(s)
- Shaobo Dai
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Lisa-Marie Funk
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Viktor Sautner
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Mirko Paulikat
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany
| | - Benjamin Schröder
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany
| | - Jon Uranga
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany. .,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany.
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53
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Baloni P, Sangar V, Yurkovich JT, Robinson M, Taylor S, Karbowski CM, Hamadeh HK, He YD, Price ND. Genome-scale metabolic model of the rat liver predicts effects of diet restriction. Sci Rep 2019; 9:9807. [PMID: 31285465 PMCID: PMC6614411 DOI: 10.1038/s41598-019-46245-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/25/2019] [Indexed: 12/19/2022] Open
Abstract
Mapping network analysis in cells and tissues can provide insights into metabolic adaptations to changes in external environment, pathological conditions, and nutrient deprivation. Here, we reconstructed a genome-scale metabolic network of the rat liver that will allow for exploration of systems-level physiology. The resulting in silico model (iRatLiver) contains 1,882 reactions, 1,448 metabolites, and 994 metabolic genes. We then used this model to characterize the response of the liver’s energy metabolism to a controlled perturbation in diet. Transcriptomics data were collected from the livers of Sprague Dawley rats at 4 or 14 days of being subjected to 15%, 30%, or 60% diet restriction. These data were integrated with the iRatLiver model to generate condition-specific metabolic models, allowing us to explore network differences under each condition. We observed different pathway usage between early and late time points. Network analysis identified several highly connected “hub” genes (Pklr, Hadha, Tkt, Pgm1, Tpi1, and Eno3) that showed differing trends between early and late time points. Taken together, our results suggest that the liver’s response varied with short- and long-term diet restriction. More broadly, we anticipate that the iRatLiver model can be exploited further to study metabolic changes in the liver under other conditions such as drug treatment, infection, and disease.
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Affiliation(s)
- Priyanka Baloni
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Vineet Sangar
- Institute for Systems Biology, Seattle, WA, United States of America
| | - James T Yurkovich
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Max Robinson
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Scott Taylor
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Christine M Karbowski
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Hisham K Hamadeh
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America.,Genmab, Princeton, NJ, United States of America
| | - Yudong D He
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, United States of America.
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54
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Villa E, Ali ES, Sahu U, Ben-Sahra I. Cancer Cells Tune the Signaling Pathways to Empower de Novo Synthesis of Nucleotides. Cancers (Basel) 2019; 11:E688. [PMID: 31108873 PMCID: PMC6562601 DOI: 10.3390/cancers11050688] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022] Open
Abstract
Cancer cells exhibit a dynamic metabolic landscape and require a sufficient supply of nucleotides and other macromolecules to grow and proliferate. To meet the metabolic requirements for cell growth, cancer cells must stimulate de novo nucleotide synthesis to obtain adequate nucleotide pools to support nucleic acid and protein synthesis along with energy preservation, signaling activity, glycosylation mechanisms, and cytoskeletal function. Both oncogenes and tumor suppressors have recently been identified as key molecular determinants for de novo nucleotide synthesis that contribute to the maintenance of homeostasis and the proliferation of cancer cells. Inactivation of tumor suppressors such as TP53 and LKB1 and hyperactivation of the mTOR pathway and of oncogenes such as MYC, RAS, and AKT have been shown to fuel nucleotide synthesis in tumor cells. The molecular mechanisms by which these signaling hubs influence metabolism, especially the metabolic pathways for nucleotide synthesis, continue to emerge. Here, we focus on the current understanding of the molecular mechanisms by which oncogenes and tumor suppressors modulate nucleotide synthesis in cancer cells and, based on these insights, discuss potential strategies to target cancer cell proliferation.
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Affiliation(s)
- Elodie Villa
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA; (E.V.); (E.S.A.); (U.S.)
| | - Eunus S. Ali
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA; (E.V.); (E.S.A.); (U.S.)
| | - Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA; (E.V.); (E.S.A.); (U.S.)
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA; (E.V.); (E.S.A.); (U.S.)
- Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL 60611, USA
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55
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Guo J, Cui L, Lu Q, Zhang Y, Liu Q, Wang X, Wang Y, Liu Z, Yuan Z, Dai M. Cyadox regulates the transcription of different genes by activation of the PI3K signaling pathway in porcine primary hepatocytes. J Cell Biochem 2019; 120:7623-7634. [PMID: 30417433 DOI: 10.1002/jcb.28037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 10/15/2018] [Indexed: 01/24/2023]
Abstract
Cyadox, a new derivative of quinoxalines, has been ascertained as an antibiotic with significant growth promoting, low poison, quick absorption, swift elimination, brief residual period, and noncumulative effect. Seven differential expressed genes, including Insulin-like Growth Factor-1 ( IGF-1), Epidermal Growth Factor ( EGF), Poly ADP-ribose polymerase ( PARP), the Defender Against Apoptotic Death 1 ( DAD1), Complement Component 3 ( C3), Transketolase ( TK) and a New gene, were induced by cyadox in swine liver tissues by messenger RNA differential display reverse transcription polymerase chain reaction (DDRT-PCR) in our laboratory. However, the signal mechanism that cyadox altered these genes expression is not completely elucidated. The signaling pathways involved in the expressions of seven genes induced by cyadox were determined in porcine primary hepatocytes by RT-qPCR and the application of various signal pathway inhibitors. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed that cyadox could stimulate proliferation of porcine primary hepatocytes in a time-dependent manner. In porcine primary cultured hepatocytes, phosphoinositide 3-kinase (PI3K) and transforming growth factor-β (TGF-β) signal pathways were the main signal pathways involved in the expressions of seven genes induced by cyadox. Taken together, these results demonstrate for the first time that seven cyadox-related genes expressions in porcine primary hepatocytes treated with cyadox are mediated mainly through the PI3K signaling pathway, potentially leading to enhanced cell growth and cell immunity. EGF might be the early response gene of cyadox, and a primary regulator of the other gene expressions such as IGF-1 and DAD1, playing an important role in cell proliferation promoted by cyadox.
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Affiliation(s)
- Ju Guo
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Luqing Cui
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Qirong Lu
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Yinfeng Zhang
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Qianying Liu
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Xu Wang
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Yulian Wang
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Zhenli Liu
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Zonghui Yuan
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Menghong Dai
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
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56
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Liu C, Knudsen GM, Pedley AM, He J, Johnson JL, Yaron TM, Cantley LC, Benkovic SJ. Mapping Post-Translational Modifications of de Novo Purine Biosynthetic Enzymes: Implications for Pathway Regulation. J Proteome Res 2019; 18:2078-2087. [PMID: 30964683 DOI: 10.1021/acs.jproteome.8b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Purines represent a class of essential metabolites produced by the cell to maintain cellular homeostasis and facilitate cell proliferation. In times of high purine demand, the de novo purine biosynthetic pathway is activated; however, the mechanisms that facilitate this process are largely unknown. One plausible mechanism is through intracellular signaling, which results in enzymes within the pathway becoming post-translationally modified to enhance their individual enzyme activities and the overall pathway metabolic flux. Here, we employ a proteomic strategy to investigate the extent to which de novo purine biosynthetic pathway enzymes are post-translationally modified in 293T cells. We identified 7 post-translational modifications on 135 residues across the 6 human pathway enzymes. We further asked whether there were differences in the post-translational modification state of each pathway enzyme isolated from cells cultured in the presence or absence of purines. Of the 174 assigned modifications, 67% of them were only detected in one experimental growth condition in which a significant number of serine and threonine phosphorylations were noted. A survey of the most-probable kinases responsible for these phosphorylation events uncovered a likely AKT phosphorylation site at residue Thr397 of PPAT, which was only detected in cells under purine-supplemented growth conditions. These data suggest that this modification might alter enzyme activity or modulate its interaction(s) with downstream pathway enzymes. Together, these findings propose a role for post-translational modifications in pathway regulation and activation to meet intracellular purine demand.
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Affiliation(s)
- Chunliang Liu
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry , University of California San Francisco Mass Spectrometry Facility , San Francisco , California 94158 , United States
| | - Anthony M Pedley
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Jingxuan He
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | | | | | - Lewis C Cantley
- Department of Medicine , Beth Israel Deaconess Medical Center , Boston , Massachusetts 02115 , United States.,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Stephen J Benkovic
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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57
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Qin Z, Xiang C, Zhong F, Liu Y, Dong Q, Li K, Shi W, Ding C, Qin L, He F. Transketolase (TKT) activity and nuclear localization promote hepatocellular carcinoma in a metabolic and a non-metabolic manner. J Exp Clin Cancer Res 2019; 38:154. [PMID: 30971297 PMCID: PMC6458711 DOI: 10.1186/s13046-019-1131-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/08/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Metabolic reprogramming is one of the hallmarks of cancer cells. The pentose phosphate pathway (PPP), a branch of glycolysis, is an important metabolic pathway for the survival and biosynthesis of cancer cells. Transketolase (TKT) is a key enzyme in the non-oxidative phase of PPP. The mechanistic details of TKT in hepatocellular carcinoma (HCC) development remain unclear. METHODS TKT level and subcellular location were examined in HCC cell lines and tissue samples. We established the TKT overexpression and knocking-down stable cells in HCC cell lines. Proliferation, migration, viability and enzyme activity assays in vitro, tumor growth and metastasis assays in vivo were employed to test the effects of TKT on HCC development. GFP-tagged TKT truncations and mutants were used to locate the nuclear localization sequence (NLSs) of TKT. Cross-linking co-IP/MS was applied to identify the interaction proteins of nuclear TKT. RESULTS We showed that TKT increased the proliferation and migration of HCC cells, as well as the viability under oxidative stress in vitro and accelerated the growth and metastasis of HCC cells in vivo. We found as a key enzyme of PPP, TKT could promote the proliferation, cell cycle, migration and viability by regulating the metabolic flux. Moreover, it was firstly reported that unlike other key enzymes in PPP, TKT showed a strong nuclear localization in HCC cells. We found not only high TKT expression, but also its nuclear localization was a prediction for poor prognosis of HCC patients. We further identified the nuclear localization sequences (NLS) for TKT and demonstrated the NLS mutations decreased the pro-tumor function of TKT independent of the enzyme activity. Cross-linking Co-IP/MS showed that nuclear TKT interacted with kinases and transcriptional coregulators such as EGFR and MAPK3, which are associated with cell activation or stress response processes. EGF treatment significantly increased the viability and proliferation of HCC cells in the enzyme-inactivating mutation TKT-D155A overexpression cells but not in the NLS-D155A double mutant group, which could be blocked by EGFR inhibitor erlotinib treatment. CONCLUSIONS Our research suggests that in addition to the metabolic manner, TKT can promote the development of HCC in a non-metabolic manner via its nuclear localization and EGFR pathway.
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Affiliation(s)
- Zhaoyu Qin
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Fan Zhong
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Yang Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Qiongzhu Dong
- Department of Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai, 200040 China
| | - Kai Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China
| | - Wenhao Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China
| | - Chen Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Lunxiu Qin
- Department of Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai, 200040 China
| | - Fuchu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China
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58
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Weighing In on mTOR Complex 2 Signaling: The Expanding Role in Cell Metabolism. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:7838647. [PMID: 30510625 PMCID: PMC6232796 DOI: 10.1155/2018/7838647] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 12/21/2022]
Abstract
In all eukaryotes, the mechanistic target of rapamycin (mTOR) signaling emerges as a master regulator of homeostasis, which integrates environmental inputs, including nutrients, energy, and growth factors, to regulate many fundamental cellular processes such as cell growth and metabolism. mTOR signaling functions through two structurally and functionally distinct complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), which correspond to two major branches of signal output. While mTORC1 is well characterized for its structure, regulation, and function in the last decade, information of mTORC2 signaling is only rapidly expanding in recent years, from structural biology, signaling network, to functional impact. Here we review the recent advances in many aspects of the mTORC2 signaling, with particular focus on its involvement in the control of cell metabolism and its physiological implications in metabolic diseases and aging.
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59
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Ahn WS, Dong W, Zhang Z, Cantor JR, Sabatini DM, Iliopoulos O, Stephanopoulos G. Glyceraldehyde 3-phosphate dehydrogenase modulates nonoxidative pentose phosphate pathway to provide anabolic precursors in hypoxic tumor cells. AIChE J 2018. [DOI: 10.1002/aic.16423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Woo S. Ahn
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - Wentao Dong
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - Zhe Zhang
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - Jason R. Cantor
- Dept. of Biology; Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology; Cambridge MA 02142
- Dept. of Biology; Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge MA 02139
- Koch Institute for Integrative Cancer Research; Cambridge MA 02139
- Broad Institute of Harvard and Massachusetts Institute of Technology; Cambridge MA 02142
| | - David M. Sabatini
- Dept. of Biology; Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology; Cambridge MA 02142
- Dept. of Biology; Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge MA 02139
- Koch Institute for Integrative Cancer Research; Cambridge MA 02139
- Broad Institute of Harvard and Massachusetts Institute of Technology; Cambridge MA 02142
| | - Othon Iliopoulos
- Center for Cancer Research; Massachusetts General Hospital Cancer Center; Boston MA 02114
- Dept. of Medicine; Harvard Medical School; Boston MA 02115
- Division of Hematology-Oncology, Dept. of Medicine; Massachusetts General Hospital; Boston MA 02114
| | - Gregory Stephanopoulos
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
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60
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Makinoshima H, Umemura S, Suzuki A, Nakanishi H, Maruyama A, Udagawa H, Mimaki S, Matsumoto S, Niho S, Ishii G, Tsuboi M, Ochiai A, Esumi H, Sasaki T, Goto K, Tsuchihara K. Metabolic Determinants of Sensitivity to Phosphatidylinositol 3-Kinase Pathway Inhibitor in Small-Cell Lung Carcinoma. Cancer Res 2018; 78:2179-2190. [PMID: 29490947 DOI: 10.1158/0008-5472.can-17-2109] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/15/2017] [Accepted: 02/22/2018] [Indexed: 11/16/2022]
Abstract
Comprehensive genomic analysis has revealed that the PI3K/AKT/mTOR pathway is a feasible therapeutic target in small-cell lung carcinoma (SCLC). However, biomarkers to identify patients likely to benefit from inhibitors of this pathway have not been identified. Here, we show that metabolic features determine sensitivity to the PI3K/mTOR dual inhibitor gedatolisib in SCLC cells. Substantial phosphatidyl lipid analysis revealed that a specific phosphatidylinositol (3,4,5)-trisphosphate (PIP3) subspecies lipid product PIP3 (38:4) is predictive in assessing sensitivity to PI3K/mTOR dual inhibitor. Notably, we found that higher amounts of purine-related aqueous metabolites such as hypoxanthine, which are characteristic of SCLC biology, lead to resistance to PI3K pathway inhibition. In addition, the levels of the mRNA encoding hypoxanthine phosphoribosyl transferase 1, a key component of the purine salvage pathway, differed significantly between SCLC cells sensitive or resistant to gedatolisib. Moreover, complementation with purine metabolites could reverse the vulnerability to targeting of the PI3K pathway in SCLC cells normally sensitive to gedatolisib. These results indicate that the resistance mechanism of PI3K pathway inhibitors is mediated by the activation of the purine salvage pathway, supplying purine resource to nucleotide biosynthesis. Metabolomics is a powerful approach for finding novel therapeutic biomarkers in SCLC treatment.Significance: These findings identify features that determine sensitivity of SCLC to PI3K pathway inhibition and support metabolomics as a tool for finding novel therapeutic biomarkers. Cancer Res; 78(9); 2179-90. ©2018 AACR.
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Affiliation(s)
- Hideki Makinoshima
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan.,Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan
| | - Shigeki Umemura
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan.
| | - Ayako Suzuki
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | | | - Ami Maruyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan
| | - Hibiki Udagawa
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Sachiyo Mimaki
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Shingo Matsumoto
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan.,Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Seiji Niho
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Genichiro Ishii
- Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Atsushi Ochiai
- Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Hiroyasu Esumi
- Division of Clinical Research, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Takehiko Sasaki
- Research Center for Biosignal, Akita University, Akita, Japan.,Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
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61
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ATR inhibition facilitates targeting of leukemia dependence on convergent nucleotide biosynthetic pathways. Nat Commun 2017; 8:241. [PMID: 28808226 PMCID: PMC5556071 DOI: 10.1038/s41467-017-00221-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 06/13/2017] [Indexed: 01/08/2023] Open
Abstract
Leukemia cells rely on two nucleotide biosynthetic pathways, de novo and salvage, to produce dNTPs for DNA replication. Here, using metabolomic, proteomic, and phosphoproteomic approaches, we show that inhibition of the replication stress sensing kinase ataxia telangiectasia and Rad3-related protein (ATR) reduces the output of both de novo and salvage pathways by regulating the activity of their respective rate-limiting enzymes, ribonucleotide reductase (RNR) and deoxycytidine kinase (dCK), via distinct molecular mechanisms. Quantification of nucleotide biosynthesis in ATR-inhibited acute lymphoblastic leukemia (ALL) cells reveals substantial remaining de novo and salvage activities, and could not eliminate the disease in vivo. However, targeting these remaining activities with RNR and dCK inhibitors triggers lethal replication stress in vitro and long-term disease-free survival in mice with B-ALL, without detectable toxicity. Thus the functional interplay between alternative nucleotide biosynthetic routes and ATR provides therapeutic opportunities in leukemia and potentially other cancers. Leukemic cells depend on the nucleotide synthesis pathway to proliferate. Here the authors use metabolomics and proteomics to show that inhibition of ATR reduced the activity of these pathways thus providing a valuable therapeutic target in leukemia.
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Garcia-Carbonell R, Divakaruni AS, Lodi A, Vicente-Suarez I, Saha A, Cheroutre H, Boss GR, Tiziani S, Murphy AN, Guma M. Critical Role of Glucose Metabolism in Rheumatoid Arthritis Fibroblast-like Synoviocytes. Arthritis Rheumatol 2017; 68:1614-26. [PMID: 26815411 DOI: 10.1002/art.39608] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/19/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Up-regulation of glucose metabolism has been implicated not only in tumor cell growth but also in immune cells upon activation. However, little is known about the metabolite profile in rheumatoid arthritis (RA), particularly in fibroblast-like synoviocytes (FLS). This study was undertaken to evaluate whether changes in glucose metabolism in RA FLS could play a role in inflammation and joint damage. METHODS Synovium and FLS were obtained from patients with RA and patients with osteoarthritis (OA). The rate of glycolysis after stimulation of FLS with lipopolysaccharide and platelet-derived growth factor BB was measured using glycolysis stress test technology. FLS function was evaluated using a glycolysis inhibitor, 2-deoxy-d-glucose (2-DG). After stimulation of the FLS, a migration scratch assay, MTT assay, and enzyme-linked immunosorbent assay were performed to measure the effect of 2-DG on FLS migration, viability of the FLS, and cytokine secretion, respectively. IRDye 800CW 2-DG was used to assess glucose uptake in the arthritic joints and stromal cells of mice after K/BxN mouse serum transfer. The mice were injected daily, intraperitoneally, with 3-bromopyruvate (BrPa; 5 mg/kg) to assess the effect of inhibition of glycolysis in vivo. RESULTS Compared to human OA FLS, the balance between glycolysis and oxidative phosphorylation was shifted toward glycolysis in RA FLS. Glucose transporter 1 (GLUT1) messenger RNA (mRNA) expression correlated with baseline functions of the RA FLS. Glucose deprivation or incubation of the FLS with glycolytic inhibitors impaired cytokine secretion and decreased the rate of proliferation and migration of the cells. In a mouse model of inflammatory arthritis, GLUT1 mRNA expression in the synovial lining cells was observed, and increased levels of glucose uptake and glycolytic gene expression were detected in the stromal compartment of the arthritic mouse joints. Inhibition of glycolysis by BrPa, administered in vivo, significantly decreased the severity of arthritis in this mouse model. CONCLUSION Targeting metabolic pathways is a novel approach to understanding the mechanisms of disease. Inhibition of glycolysis may directly modulate synoviocyte-mediated inflammatory functions and could be an effective treatment strategy for arthritis.
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Affiliation(s)
| | | | | | | | - Arindam Saha
- University of California, San Diego School of Medicine, La Jolla
| | - Hilde Cheroutre
- La Jolla Institute for Allergy & Immunology, La Jolla, California
| | - Gerry R Boss
- University of California, San Diego School of Medicine, La Jolla
| | | | - Anne N Murphy
- University of California, San Diego School of Medicine, La Jolla
| | - Monica Guma
- University of California, San Diego School of Medicine, La Jolla
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Bughani U, Saha A, Kuriakose A, Nair R, Sadashivarao RB, Venkataraman R, Patel S, Deshchougule AT, S. SK, Montero E, Pai HV, Palanivelu DV, Melarkode R, Nair P. T cell activation and differentiation is modulated by a CD6 domain 1 antibody Itolizumab. PLoS One 2017; 12:e0180088. [PMID: 28672038 PMCID: PMC5495335 DOI: 10.1371/journal.pone.0180088] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 06/09/2017] [Indexed: 12/24/2022] Open
Abstract
CD6 is associated with T-cell modulation and is implicated in several autoimmune diseases. We previously demonstrated that Itolizumab, a CD6 domain 1 (CD6D1) specific humanized monoclonal antibody, inhibited the proliferation and cytokine production by T lymphocytes stimulated with anti-CD3 antibody or when co-stimulated with ALCAM. Aberrant IL-17 producing CD4+ helper T-cells (Th17) have been identified as pivotal for the pathogenesis of certain inflammatory autoimmune disorders, including psoriasis. Itolizumab has demonstrated efficacy in human diseases known to have an IL-17 driven pathogenesis. Here, in in vitro experiments we show that by day 3 of human PBMC activation using anti-CD3 and anti-CD28 co-stimulation in a Th17 polarizing milieu, 15-35% of CD4+ T-cells overexpress CD6 and there is an establishment of differentiated Th17 cells. Addition of Itolizumab reduces the activation and differentiation of T cells to Th17 cells and decreases production of IL-17. These effects are associated with the reduction of key transcription factors pSTAT3 and RORγT. Further, transcription analysis studies in these conditions indicate that Itolizumab suppressed T cell activation by primarily reducing cell cycle, DNA transcription and translation associated genes. To understand the mechanism of this inhibition, we evaluated the effect of this anti-human CD6D1 mAb on ALCAM-CD6 as well as TCR-mediated T cell activation. We show that Itolizumab but not its F(ab')2 fragment directly inhibits CD6 receptor hyper-phosphorylation and leads to subsequent decrease in associated ZAP70 kinase and docking protein SLP76. Since Itolizumab binds to CD6 expressed only on human and chimpanzee, we developed an antibody binding specifically to mouse CD6D1. This antibody successfully ameliorated the incidence of experimental autoimmune encephalitis in the mice model. These results position CD6 as a key molecule in sustaining the activation and differentiation of T cells and an important target for modulating autoimmune diseases.
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Affiliation(s)
- Usha Bughani
- Research and Development, Biocon Research Limited, Bangalore, India
| | - Arindam Saha
- Research and Development, Biocon Research Limited, Bangalore, India
| | - Anshu Kuriakose
- Research and Development, Biocon Research Limited, Bangalore, India
| | - Reshmi Nair
- Research and Development, Biocon Research Limited, Bangalore, India
| | | | | | - Swati Patel
- Research and Development, Biocon Research Limited, Bangalore, India
| | | | - Satish Kumar S.
- Research and Development, Biocon Research Limited, Bangalore, India
| | - Enrique Montero
- Research and Development, Biocon Research Limited, Bangalore, India
| | - Harish V. Pai
- Research and Development, Biocon Research Limited, Bangalore, India
| | | | | | - Pradip Nair
- Research and Development, Biocon Research Limited, Bangalore, India
- * E-mail:
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Choudhary KS, Rohatgi N, Halldorsson S, Briem E, Gudjonsson T, Gudmundsson S, Rolfsson O. EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT. PLoS Comput Biol 2016; 12:e1004924. [PMID: 27253373 PMCID: PMC4890760 DOI: 10.1371/journal.pcbi.1004924] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/17/2016] [Indexed: 01/05/2023] Open
Abstract
Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E) and mesenchymal (EGFR_M) networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend.
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Affiliation(s)
- Kumari Sonal Choudhary
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Neha Rohatgi
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Skarphedinn Halldorsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| | - Eirikur Briem
- Biomedical Center, University of Iceland, Reykjavik, Iceland
- Stem Cell Research Unit, Department of Anatomy, School of Health Sciences, University of Iceland, Reykjavík, Iceland
- Department of Laboratory Hematology, Landspitali-University Hospital, Reykjavik, Iceland
| | - Thorarinn Gudjonsson
- Biomedical Center, University of Iceland, Reykjavik, Iceland
- Stem Cell Research Unit, Department of Anatomy, School of Health Sciences, University of Iceland, Reykjavík, Iceland
- Department of Laboratory Hematology, Landspitali-University Hospital, Reykjavik, Iceland
| | | | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
- * E-mail:
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Mesquita A, Tábara LC, Martinez-Costa O, Santos-Rodrigo N, Vincent O, Escalante R. Dissecting the function of Atg1 complex in Dictyostelium autophagy reveals a connection with the pentose phosphate pathway enzyme transketolase. Open Biol 2016; 5:rsob.150088. [PMID: 26246495 PMCID: PMC4554924 DOI: 10.1098/rsob.150088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The network of protein–protein interactions of the Dictyostelium discoideum autophagy pathway was investigated by yeast two-hybrid screening of the conserved autophagic proteins Atg1 and Atg8. These analyses confirmed expected interactions described in other organisms and also identified novel interactors that highlight the complexity of autophagy regulation. The Atg1 kinase complex, an essential regulator of autophagy, was investigated in detail here. The composition of the Atg1 complex in D. discoideum is more similar to mammalian cells than to Saccharomyces cerevisiae as, besides Atg13, it contains Atg101, a protein not conserved in this yeast. We found that Atg101 interacts with Atg13 and genetic disruption of these proteins in Dictyostelium leads to an early block in autophagy, although the severity of the developmental phenotype and the degree of autophagic block is higher in Atg13-deficient cells. We have also identified a protein containing zinc-finger B-box and FNIP motifs that interacts with Atg101. Disruption of this protein increases autophagic flux, suggesting that it functions as a negative regulator of Atg101. We also describe the interaction of Atg1 kinase with the pentose phosphate pathway enzyme transketolase (TKT). We found changes in the activity of endogenous TKT activity in strains lacking or overexpressing Atg1, suggesting the presence of an unsuspected regulatory pathway between autophagy and the pentose phosphate pathway in Dictyostelium that seems to be conserved in mammalian cells.
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Affiliation(s)
- Ana Mesquita
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
| | - Luis C Tábara
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
| | | | | | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
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