1
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Huang PJ, Lin YL, Chen CH, Lin HY, Fang SC. A chloroplast sulphate transporter modulates glutathione-mediated redox cycling to regulate cell division. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39189939 DOI: 10.1111/pce.15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024]
Abstract
Glutathione redox cycling is important for cell cycle regulation, but its mechanisms are not well understood. We previously identified a small-sized mutant, suppressor of mat3 15-1 (smt15-1) that has elevated cellular glutathione. Here, we demonstrated that SMT15 is a chloroplast sulphate transporter. Reducing expression of γ-GLUTAMYLCYSTEINE SYNTHETASE, encoding the rate-limiting enzyme required for glutathione biosynthesis, corrected the size defect of smt15-1 cells. Overexpressing GLUTATHIONE SYNTHETASE (GSH2) recapitulated the small-size phenotype of smt15-1 mutant, confirming the role of glutathione in cell division. Hence, SMT15 may regulate chloroplast sulphate concentration to modulate cellular glutathione levels. In wild-type cells, glutathione and/or thiol-containing molecules (GSH/thiol) accumulated in the cytosol at the G1 phase and decreased as cells entered the S/M phase. While the cytosolic GSH/thiol levels in the small-sized mutants, smt15-1 and GSH2 overexpressors, mirrored those of wild-type cells (accumulating during G1 and declining at early S/M phase), GSH/thiol was specifically accumulated in the basal bodies at early S/M phase in the small-sized mutants. Therefore, we propose that GSH/thiol-mediated redox signalling in the basal bodies may regulate mitotic division number in Chlamydomonas reinhardtii. Our findings suggest a new mechanism by which glutathione regulates the multiple fission cell cycle in C. reinhardtii.
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Affiliation(s)
- Pin-Jui Huang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Ling Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
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2
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Huber K, Giralt A, Dreos R, Michenthaler H, Geller S, Barquissau V, Ziegler DV, Tavernari D, Gallart-Ayala H, Krajina K, Jonas K, Ciriello G, Ivanisevic J, Prokesch A, Pichler M, Fajas L. E2F transcription factor-1 modulates expression of glutamine metabolic genes in mouse embryonic fibroblasts and uterine sarcoma cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119721. [PMID: 38580088 DOI: 10.1016/j.bbamcr.2024.119721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Metabolic reprogramming is considered as a hallmark of cancer and is clinically exploited as a novel target for therapy. The E2F transcription factor-1 (E2F1) regulates various cellular processes, including proliferative and metabolic pathways, and acts, depending on the cellular and molecular context, as an oncogene or tumor suppressor. The latter is evident by the observation that E2f1-knockout mice develop spontaneous tumors, including uterine sarcomas. This dual role warrants a detailed investigation of how E2F1 loss impacts metabolic pathways related to cancer progression. Our data indicate that E2F1 binds to the promoter of several glutamine metabolism-related genes. Interestingly, the expression of genes in the glutamine metabolic pathway were increased in mouse embryonic fibroblasts (MEFs) lacking E2F1. In addition, we confirm that E2f1-/- MEFs are more efficient in metabolizing glutamine and producing glutamine-derived precursors for proliferation. Mechanistically, we observe a co-occupancy of E2F1 and MYC on glutamine metabolic promoters, increased MYC binding after E2F1 depletion and that silencing of MYC decreased the expression of glutamine-related genes in E2f1-/- MEFs. Analyses of transcriptomic profiles in 29 different human cancers identified uterine sarcoma that showed a negative correlation between E2F1 and glutamine metabolic genes. CRISPR/Cas9 knockout of E2F1 in the uterine sarcoma cell line SK-UT-1 confirmed elevated glutamine metabolic gene expression, increased proliferation and increased MYC binding to glutamine-related promoters upon E2F1 loss. Together, our data suggest a crucial role of E2F1 in energy metabolism and metabolic adaptation in uterine sarcoma cells.
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Affiliation(s)
- Katharina Huber
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Albert Giralt
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Helene Michenthaler
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Sarah Geller
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Valentin Barquissau
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Dorian V Ziegler
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Katarina Krajina
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Jonas
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria; Translational Oncology, II. Med. Clinics, University Hospital of Augsburg, Augsburg, Germany
| | - Lluis Fajas
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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3
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Zappia M, Kwon YJ, Westacott A, Liseth I, Lee H, Islam ABMMK, Kim J, Frolov M. E2F regulation of the Phosphoglycerate kinase gene is functionally important in Drosophila development. Proc Natl Acad Sci U S A 2023; 120:e2220770120. [PMID: 37011211 PMCID: PMC10104548 DOI: 10.1073/pnas.2220770120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/03/2023] [Indexed: 04/05/2023] Open
Abstract
The canonical role of the transcription factor E2F is to control the expression of cell cycle genes by binding to the E2F sites in their promoters. However, the list of putative E2F target genes is extensive and includes many metabolic genes, yet the significance of E2F in controlling the expression of these genes remains largely unknown. Here, we used the CRISPR/Cas9 technology to introduce point mutations in the E2F sites upstream of five endogenous metabolic genes in Drosophila melanogaster. We found that the impact of these mutations on both the recruitment of E2F and the expression of the target genes varied, with the glycolytic gene, Phosphoglycerate kinase (Pgk), being mostly affected. The loss of E2F regulation on the Pgk gene led to a decrease in glycolytic flux, tricarboxylic acid cycle intermediates levels, adenosine triphosphate (ATP) content, and an abnormal mitochondrial morphology. Remarkably, chromatin accessibility was significantly reduced at multiple genomic regions in PgkΔE2F mutants. These regions contained hundreds of genes, including metabolic genes that were downregulated in PgkΔE2F mutants. Moreover, PgkΔE2F animals had shortened life span and exhibited defects in high-energy consuming organs, such as ovaries and muscles. Collectively, our results illustrate how the pleiotropic effects on metabolism, gene expression, and development in the PgkΔE2F animals underscore the importance of E2F regulation on a single E2F target, Pgk.
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Affiliation(s)
- Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Yong-Jae Kwon
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Anton Westacott
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Isabel Liseth
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Hyun Min Lee
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Abul B. M. M. K. Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka1000, Bangladesh
| | - Jiyeon Kim
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Maxim V. Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
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4
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Yao Y, Gu X, Xu X, Ge S, Jia R. Novel insights into RB1 mutation. Cancer Lett 2022; 547:215870. [PMID: 35964818 DOI: 10.1016/j.canlet.2022.215870] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of the retinoblastoma susceptibility gene (RB1) decades ago, RB1 has been regarded as a prototype tumor suppressor gene providing a paradigm for tumor genetic research. Constant research has updated the understanding of RB1-related pathways and their impact on tumor and nontumor diseases. Mutation of RB1 gene has been observed in multiple types of malignant tumors including prostate cancer, lung cancer, breast cancer, and almost every familial and sporadic case of retinoblastoma. Even if well-known and long-investigated, the application potential of RB1 mutation has not been fully tapped. In this review, we focus on the mechanism underlying RB1 mutation during oncogenesis. Therapeutically, we have further discussed potential clinical strategies by targeting RB1-mutated cancers. The unsolved problems and prospects of RB1 mutation are also discussed.
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Affiliation(s)
- Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiaofang Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
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5
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Mandigo AC, Tomlins SA, Kelly WK, Knudsen KE. Relevance of pRB Loss in Human Malignancies. Clin Cancer Res 2022; 28:255-264. [PMID: 34407969 PMCID: PMC9306333 DOI: 10.1158/1078-0432.ccr-21-1565] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 01/07/2023]
Abstract
The retinoblastoma tumor suppressor protein (pRB) is a known regulator of cell-cycle control; however, recent studies identified critical functions for pRB in regulating cancer-associated gene networks that influence the DNA damage response, apoptosis, and cell metabolism. Understanding the impact of these pRB functions on cancer development and progression in the clinical setting will be essential, given the prevalence of pRB loss of function across disease types. Moreover, the current state of evidence supports the concept that pRB loss results in pleiotropic effects distinct from tumor proliferation. Here, the implications of pRB loss (and resultant pathway deregulation) on disease progression and therapeutic response will be reviewed, based on clinical observation. Developing a better understanding of the pRB-regulated pathways that underpin the aggressive features of pRB-deficient tumors will be essential for further developing pRB as a biomarker of disease progression and for stratifying pRB-deficient tumors into more effective treatment regimens.
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Affiliation(s)
- Amy C. Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Scott A. Tomlins
- Departments of Pathology and Urology, Michigan Center for Translational Pathology, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - William K. Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E. Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Corresponding Author: Karen E. Knudsen, Thomas Jefferson University, 233 South 10th Street, BLSB 1050, Philadelphia, PA 19107. Phone: 215-503-5692; E-mail:
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6
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Polat IH, Tarrado-Castellarnau M, Benito A, Hernandez-Carro C, Centelles J, Marin S, Cascante M. Glutamine Modulates Expression and Function of Glucose 6-Phosphate Dehydrogenase via NRF2 in Colon Cancer Cells. Antioxidants (Basel) 2021; 10:antiox10091349. [PMID: 34572981 PMCID: PMC8472416 DOI: 10.3390/antiox10091349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Nucleotide pools need to be constantly replenished in cancer cells to support cell proliferation. The synthesis of nucleotides requires glutamine and 5-phosphoribosyl-1-pyrophosphate produced from ribose-5-phosphate via the oxidative branch of the pentose phosphate pathway (ox-PPP). Both PPP and glutamine also play a key role in maintaining the redox status of cancer cells. Enhanced glutamine metabolism and increased glucose 6-phosphate dehydrogenase (G6PD) expression have been related to a malignant phenotype in tumors. However, the association between G6PD overexpression and glutamine consumption in cancer cell proliferation is still incompletely understood. In this study, we demonstrated that both inhibition of G6PD and glutamine deprivation decrease the proliferation of colon cancer cells and induce cell cycle arrest and apoptosis. Moreover, we unveiled that glutamine deprivation induce an increase of G6PD expression that is mediated through the activation of the nuclear factor (erythroid-derived 2)-like 2 (NRF2). This crosstalk between G6PD and glutamine points out the potential of combined therapies targeting oxidative PPP enzymes and glutamine catabolism to combat colon cancer.
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Affiliation(s)
- Ibrahim H. Polat
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- Equipe Environnement et Prédiction de la Santé des Populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, CEDEX, 38700 La Tronche, France
| | - Míriam Tarrado-Castellarnau
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Adrian Benito
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
| | - Claudia Hernandez-Carro
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
| | - Josep Centelles
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Correspondence: (S.M.); (M.C.)
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (A.B.); (C.H.-C.); (J.C.)
- Institute of Biomedicine, Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Correspondence: (S.M.); (M.C.)
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7
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Rajasekaran S, Siddiqui J, Rakijas J, Nicolay B, Lin C, Khan E, Patel R, Morris R, Wyler E, Boukhali M, Balasubramanyam J, Ranjith Kumar R, Van Rechem C, Vogel C, Elchuri SV, Landthaler M, Obermayer B, Haas W, Dyson N, Miles W. Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses. Commun Biol 2021; 4:977. [PMID: 34404904 PMCID: PMC8371045 DOI: 10.1038/s42003-021-02495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/26/2021] [Indexed: 11/09/2022] Open
Abstract
Inactivation of RB is one of the hallmarks of cancer, however gaps remain in our understanding of how RB-loss changes human cells. Here we show that pRB-depletion results in cellular reprogramming, we quantitatively measured how RB-depletion altered the transcriptional, proteomic and metabolic output of non-tumorigenic RPE1 human cells. These profiles identified widespread changes in metabolic and cell stress response factors previously linked to E2F function. In addition, we find a number of additional pathways that are sensitive to RB-depletion that are not E2F-regulated that may represent compensatory mechanisms to support the growth of RB-depleted cells. To determine whether these molecular changes are also present in RB1-/- tumors, we compared these results to Retinoblastoma and Small Cell Lung Cancer data, and identified widespread conservation of alterations found in RPE1 cells. To define which of these changes contribute to the growth of cells with de-regulated E2F activity, we assayed how inhibiting or depleting these proteins affected the growth of RB1-/- cells and of Drosophila E2f1-RNAi models in vivo. From this analysis, we identify key metabolic pathways that are essential for the growth of pRB-deleted human cells.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jalal Siddiqui
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jessica Rakijas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Brandon Nicolay
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.,Harvard Medical School, Boston, MA, USA.,Agios Pharmaceutical, Cambridge, MA, USA
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rahi Patel
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jayashree Balasubramanyam
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - R Ranjith Kumar
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | | | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Sailaja V Elchuri
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Benedikt Obermayer
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Nicholas Dyson
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA. .,The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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8
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Shen Y, Zhang Y, Li W, Chen K, Xiang M, Ma H. Glutamine metabolism: from proliferating cells to cardiomyocytes. Metabolism 2021; 121:154778. [PMID: 33901502 DOI: 10.1016/j.metabol.2021.154778] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Glutamine is a major energy source for rapidly dividing cells, such as hematopoietic stem cells and cancer cells. Reliance on glutamine is therefore regarded as a metabolic hallmark of proliferating cells. Moreover, reprogramming glutamine metabolism by various factors, including tissue type, microenvironment, pro-oncogenes, and tumor suppressor genes, can facilitate stem cell fate decisions, tumor recurrence, and drug resistance. However, the significance of glutamine metabolism in cardiomyocytes, an end-differentiated cell type, is not fully understood. Existing evidence suggests important roles of glutamine metabolism in the development of cardiovascular diseases. In this review, we have focused on glutaminolysis and its regulatory network in proliferating cells. We have summarized current findings about the role of glutamine utilization in cardiomyocytes and have discussed possibilities of targeting glutamine metabolism for the treatment of cardiovascular diseases.
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Affiliation(s)
- Yimin Shen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yuhao Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Wudi Li
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Kaijie Chen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Meixiang Xiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
| | - Hong Ma
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
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9
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Zappia MP, Guarner A, Kellie-Smith N, Rogers A, Morris R, Nicolay B, Boukhali M, Haas W, Dyson NJ, Frolov MV. E2F/Dp inactivation in fat body cells triggers systemic metabolic changes. eLife 2021; 10:67753. [PMID: 34251339 PMCID: PMC8298092 DOI: 10.7554/elife.67753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/11/2021] [Indexed: 11/25/2022] Open
Abstract
The E2F transcription factors play a critical role in controlling cell fate. In Drosophila, the inactivation of E2F in either muscle or fat body results in lethality, suggesting an essential function for E2F in these tissues. However, the cellular and organismal consequences of inactivating E2F in these tissues are not fully understood. Here, we show that the E2F loss exerts both tissue-intrinsic and systemic effects. The proteomic profiling of E2F-deficient muscle and fat body revealed that E2F regulates carbohydrate metabolism, a conclusion further supported by metabolomic profiling. Intriguingly, animals with E2F-deficient fat body had a lower level of circulating trehalose and reduced storage of fat. Strikingly, a sugar supplement was sufficient to restore both trehalose and fat levels, and subsequently rescued animal lethality. Collectively, our data highlight the unexpected complexity of E2F mutant phenotype, which is a result of combining both tissue-specific and systemic changes that contribute to animal development.
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Affiliation(s)
| | - Ana Guarner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, United States
| | | | - Alice Rogers
- University of Illinois at Chicago, Chicago, United States
| | - Robert Morris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, United States
| | - Brandon Nicolay
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, United States
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, United States
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, United States
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, United States
| | - Maxim V Frolov
- University of Illinois at Chicago, Chicago, United States
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10
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Abooshahab R, Hooshmand K, Razavi F, Dass CR, Hedayati M. A glance at the actual role of glutamine metabolism in thyroid tumorigenesis. EXCLI JOURNAL 2021; 20:1170-1183. [PMID: 34345235 PMCID: PMC8326501 DOI: 10.17179/excli2021-3826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022]
Abstract
Thyroid cancers (TCs) are the most prevalent malignancy of the endocrine system and the seventh most common cancer in women. According to estimates from the Global Cancer Observatory (GCO) in 2020, the incidence of thyroid cancer globally was 586,000 cases. As thyroid cancer incidences have dramatically increased, identifying the most important metabolic pathways and biochemical markers involved in thyroid tumorigenesis can be critical strategies for controlling the prevalence and ultimately treatment of this disease. Cancer cells undergo cellular metabolism and energy alteration in order to promote cell proliferation and invasion. Glutamine is one of the most abundant free amino acids in the human body that contributes to cancer metabolic remodeling as a carbon and nitrogen source to sustain cell growth and proliferation. In the present review, glutamine metabolism and its regulation in cancer cells are highlighted. Thereafter, emphasis is given to the perturbation of glutamine metabolism in thyroid cancer, focusing on metabolomics studies.
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Affiliation(s)
- Raziyeh Abooshahab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Curtin Medical School, Curtin University, Bentley 6102, Australia
| | | | - Fatemeh Razavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Crispin R Dass
- Curtin Medical School, Curtin University, Bentley 6102, Australia.,Curtin Health Innovation Research Institute, Bentley, 6102, Australia
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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11
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Prusinkiewicz MA, Mymryk JS. Metabolic Control by DNA Tumor Virus-Encoded Proteins. Pathogens 2021; 10:560. [PMID: 34066504 PMCID: PMC8148605 DOI: 10.3390/pathogens10050560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Viruses co-opt a multitude of host cell metabolic processes in order to meet the energy and substrate requirements for successful viral replication. However, due to their limited coding capacity, viruses must enact most, if not all, of these metabolic changes by influencing the function of available host cell regulatory proteins. Typically, certain viral proteins, some of which can function as viral oncoproteins, interact with these cellular regulatory proteins directly in order to effect changes in downstream metabolic pathways. This review highlights recent research into how four different DNA tumor viruses, namely human adenovirus, human papillomavirus, Epstein-Barr virus and Kaposi's associated-sarcoma herpesvirus, can influence host cell metabolism through their interactions with either MYC, p53 or the pRb/E2F complex. Interestingly, some of these host cell regulators can be activated or inhibited by the same virus, depending on which viral oncoprotein is interacting with the regulatory protein. This review highlights how MYC, p53 and pRb/E2F regulate host cell metabolism, followed by an outline of how each of these DNA tumor viruses control their activities. Understanding how DNA tumor viruses regulate metabolism through viral oncoproteins could assist in the discovery or repurposing of metabolic inhibitors for antiviral therapy or treatment of virus-dependent cancers.
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Affiliation(s)
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada;
- Department of Otolaryngology, Head & Neck Surgery, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
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12
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Mandigo AC, Yuan W, Xu K, Gallagher P, Pang A, Guan YF, Shafi AA, Thangavel C, Sheehan B, Bogdan D, Paschalis A, McCann JJ, Laufer TS, Gordon N, Vasilevskaya IA, Dylgjeri E, Chand SN, Schiewer MJ, Domingo-Domenech J, Den RB, Holst J, McCue PA, de Bono JS, McNair C, Knudsen KE. RB/E2F1 as a Master Regulator of Cancer Cell Metabolism in Advanced Disease. Cancer Discov 2021; 11:2334-2353. [PMID: 33879449 DOI: 10.1158/2159-8290.cd-20-1114] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/20/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
Loss of the retinoblastoma (RB) tumor suppressor protein is a critical step in reprogramming biological networks that drive cancer progression, although mechanistic insight has been largely limited to the impact of RB loss on cell-cycle regulation. Here, isogenic modeling of RB loss identified disease stage-specific rewiring of E2F1 function, providing the first-in-field mapping of the E2F1 cistrome and transcriptome after RB loss across disease progression. Biochemical and functional assessment using both in vitro and in vivo models identified an unexpected, prominent role for E2F1 in regulation of redox metabolism after RB loss, driving an increase in the synthesis of the antioxidant glutathione, specific to advanced disease. These E2F1-dependent events resulted in protection from reactive oxygen species in response to therapeutic intervention. On balance, these findings reveal novel pathways through which RB loss promotes cancer progression and highlight potentially new nodes of intervention for treating RB-deficient cancers. SIGNIFICANCE: This study identifies stage-specific consequences of RB loss across cancer progression that have a direct impact on tumor response to clinically utilized therapeutics. The study herein is the first to investigate the effect of RB loss on global metabolic regulation and link RB/E2F1 to redox control in multiple advanced diseases.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Amy C Mandigo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Kexin Xu
- The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Peter Gallagher
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Angel Pang
- School of Medical Sciences and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Yi Fang Guan
- School of Medical Sciences and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ayesha A Shafi
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chellappagounder Thangavel
- Departments of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Dermatology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Beshara Sheehan
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Denisa Bogdan
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alec Paschalis
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jennifer J McCann
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Talya S Laufer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Nicolas Gordon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Irina A Vasilevskaya
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Saswati N Chand
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Matthew J Schiewer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Robert B Den
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Departments of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jeff Holst
- Department of Dermatology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Peter A McCue
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher McNair
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. .,Departments of Urology, Medical Oncology and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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13
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Parkhitko AA, Singh A, Hsieh S, Hu Y, Binari R, Lord CJ, Hannenhalli S, Ryan CJ, Perrimon N. Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells. PLoS Genet 2021; 17:e1009354. [PMID: 33591981 PMCID: PMC7909629 DOI: 10.1371/journal.pgen.1009354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/26/2021] [Accepted: 01/11/2021] [Indexed: 01/02/2023] Open
Abstract
The RB1 tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, triple-negative breast cancers, prostate cancers, and osteosarcomas. Finding new synthetic lethal (SL) interactions with RB1 could lead to new approaches to treating cancers with inactivated RB1. We identified 95 SL partners of RB1 based on a Drosophila screen for genetic modifiers of the eye phenotype caused by defects in the RB1 ortholog, Rbf1. We validated 38 mammalian orthologs of Rbf1 modifiers as RB1 SL partners in human cancer cell lines with defective RB1 alleles. We further show that for many of the RB1 SL genes validated in human cancer cell lines, low activity of the SL gene in human tumors, when concurrent with low levels of RB1 was associated with improved patient survival. We investigated higher order combinatorial gene interactions by creating a novel Drosophila cancer model with co-occurring Rbf1, Pten and Ras mutations, and found that targeting RB1 SL genes in this background suppressed the dramatic tumor growth and rescued fly survival whilst having minimal effects on wild-type cells. Finally, we found that drugs targeting the identified RB1 interacting genes/pathways, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol also elicit SL in human cancer cell lines. In summary, we identified several high confidence, evolutionarily conserved, novel targets for RB1-deficient cells that may be further adapted for the treatment of human cancer.
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Affiliation(s)
- Andrey A. Parkhitko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Aging Institute of UPMC and the University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Arashdeep Singh
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sharon Hsieh
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Christopher J. Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Colm J. Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
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14
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RB Regulates DNA Double Strand Break Repair Pathway Choice by Mediating CtIP Dependent End Resection. Int J Mol Sci 2020; 21:ijms21239176. [PMID: 33271982 PMCID: PMC7730402 DOI: 10.3390/ijms21239176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 01/15/2023] Open
Abstract
Inactivation of the retinoblastoma tumor suppressor gene (RB1) leads to genome instability, and can be detected in retinoblastoma and other cancers. One damaging effect is causing DNA double strand breaks (DSB), which, however, can be repaired by homologous recombination (HR), classical non-homologous end joining (C-NHEJ), and micro-homology mediated end joining (MMEJ). We aimed to study the mechanistic roles of RB in regulating multiple DSB repair pathways. Here we show that HR and C-NHEJ are decreased, but MMEJ is elevated in RB-depleted cells. After inducing DSB by camptothecin, RB co-localizes with CtIP, which regulates DSB end resection. RB depletion leads to less RPA and native BrdU foci, which implies less end resection. In RB-depleted cells, less CtIP foci, and a lack of phosphorylation on CtIP Thr847, are observed. According to the synthetic lethality principle, based on the altered DSB repair pathway choice, after inducing DSBs by camptothecin, RB depleted cells are more sensitive to co-treatment with camptothecin and MMEJ blocker poly-ADP ribose polymerase 1 (PARP1) inhibitor. We propose a model whereby RB can regulate DSB repair pathway choice by mediating the CtIP dependent DNA end resection. The use of PARP1 inhibitor could potentially improve treatment outcomes for RB-deficient cancers.
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15
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Huber K, Mestres-Arenas A, Fajas L, Leal-Esteban LC. The multifaceted role of cell cycle regulators in the coordination of growth and metabolism. FEBS J 2020; 288:3813-3833. [PMID: 33030287 PMCID: PMC8359344 DOI: 10.1111/febs.15586] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/08/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022]
Abstract
Adapting to changes in nutrient availability and environmental conditions is a fundamental property of cells. This adaptation requires a multi‐directional coordination between metabolism, growth, and the cell cycle regulators (consisting of the family of cyclin‐dependent kinases (CDKs), their regulatory subunits known as cyclins, CDK inhibitors, the retinoblastoma family members, and the E2F transcription factors). Deciphering the mechanisms accountable for this coordination is crucial for understanding various patho‐physiological processes. While it is well established that metabolism and growth affect cell division, this review will focus on recent observations that demonstrate how cell cycle regulators coordinate metabolism, cell cycle progression, and growth. We will discuss how the cell cycle regulators directly regulate metabolic enzymes and pathways and summarize their involvement in the endolysosomal pathway and in the functions and dynamics of mitochondria.
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Affiliation(s)
- Katharina Huber
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Lluis Fajas
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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16
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Yan L, Zhao Z, Wang X, Lyu T, Li J, Qi Y, Wang X, Guo X. Short-term in vitro glutamine restriction differentially impacts the chromosomal stability of transformed and non-transformed cells. Mutagenesis 2020; 35:geaa026. [PMID: 33043986 DOI: 10.1093/mutage/geaa026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/10/2020] [Indexed: 11/13/2022] Open
Abstract
Glutamine (Gln) is a non-essential amino acid central for generating building blocks and cellular energy in tumours and rapidly proliferating non-transformed cells. However, the influence of Gln on regulating chromosomal stability of transformed and non-transformed cells remain poorly understand. We hypothesised that Gln is required for maintaining a homeostatic level of chromosomal stability. To this end, transformed cells HeLa and A375 and non-transformed cells NCM460 and HUVEC cells were intervened with varying concentrations of Gln (10, 1, 0.1 and 0.01 mM), with or without cisplatin (0.1 µg/ml), for 24 h. The cytokinesis-block micronucleus (MN) assay was used to determine chromosomal instability (CIN), the extent of which is reflected by the frequency of MN, nucleoplasmic bridge (NPB) and nuclear bud (NB). We demonstrated an unexpected decrease in the spontaneous rate of MN, but not NPB and NB, after Gln restriction in HeLa and A375 cells. Gln restriction reduced cisplatin-induced MN, but not NPB and NB, in HeLa and A375 cells. We further revealed that Gln restriction suppressed the proliferation of HeLa cells with high CIN induced by nocodazole, partially explaining why Gln restriction decreased the frequency of spontaneous and cisplatin-induced MN in transformed cells. In contrast, Gln restriction increased MN and NB, but not NPB, in NCM460 cells. In HUVEC cells, Gln restriction increased MN, NPB and NB. Meanwhile, Gln restriction sensitised NCM460 cells to cisplatin-induced genotoxicity. A similar but more pronounced pattern was observed in HUVEC cells. Collectively, these results suggest that the in vitro influences of Gln metabolism on CIN depend on cellular contexts: Transformed cells require high Gln to fine tune their CIN in an optimal rate to maximise genomic heterogeneity and fitness, whereas non-transformed cells need high Gln to prevent CIN.
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Affiliation(s)
- Ling Yan
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
| | - Ziru Zhao
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
| | - Xiaoran Wang
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
| | - Ting Lyu
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
| | - Jianfei Li
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
| | - Yanmei Qi
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
| | - Xu Wang
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Chenggong District, Kunming, Yunnan, China
- Yunnan Environmental Society, Chenggong District, Kunming, Yunnan, China
| | - Xihan Guo
- School of Life Sciences, Yunnan Normal University, Chenggong District, Kunming, Yunnan, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Chenggong District, Kunming, Yunnan, China
- Yunnan Environmental Society, Chenggong District, Kunming, Yunnan, China
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17
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IsoSearch: An Untargeted and Unbiased Metabolite and Lipid Isotopomer Tracing Strategy from HR-LC-MS/MS Datasets. Methods Protoc 2020; 3:mps3030054. [PMID: 32751454 PMCID: PMC7563207 DOI: 10.3390/mps3030054] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
Stable isotopic tracer analysis is a technique used to determine carbon or nitrogen atom incorporation into biological systems. A number of mass spectrometry based approaches have been developed for this purpose, including high-resolution tandem mass spectrometry (HR-LC-MS/MS), selected reaction monitoring (SRM) and parallel reaction monitoring (PRM). We have developed an approach for analyzing untargeted metabolomic and lipidomic datasets using high-resolution mass spectrometry with polarity switching and implemented our approach in the open-source R script IsoSearch and in Scaffold Elements software. Using our strategy, which requires an unlabeled reference dataset and isotope labeled datasets across various biological conditions, we traced metabolic isotopomer alterations in breast cancer cells (MCF-7) treated with the metabolic drugs 2-deoxy-glucose, 6-aminonicotinamide, compound 968, and rapamycin. Metabolites and lipids were first identified by the commercial software Scaffold Elements and LipidSearch, then IsoSearch successfully profiled the 13C-isotopomers extracted metabolites and lipids from 13C-glucose labeled MCF-7 cells. The results interpreted known models, such as glycolysis and pentose phosphate pathway inhibition, but also helped to discover new metabolic/lipid flux patterns, including a reactive oxygen species (ROS) defense mechanism induced by 6AN and triglyceride accumulation in rapamycin treated cells. The results suggest the IsoSearch/Scaffold Elements platform is effective for studying metabolic tracer analysis in diseases, drug metabolism, and metabolic engineering for both polar metabolites and non-polar lipids.
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18
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Zappia MP, Rogers A, Islam ABMMK, Frolov MV. Rbf Activates the Myogenic Transcriptional Program to Promote Skeletal Muscle Differentiation. Cell Rep 2020; 26:702-719.e6. [PMID: 30650361 PMCID: PMC6344057 DOI: 10.1016/j.celrep.2018.12.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 11/18/2018] [Accepted: 12/18/2018] [Indexed: 11/25/2022] Open
Abstract
The importance of the retinoblastoma tumor suppressor protein pRB in cell cycle control is well established. However, less is known about its role in differentiation during animal development. Here, we investigated the role of Rbf, the Drosophila pRB homolog, in adult skeletal muscles. We found that the depletion of Rbf severely reduced muscle growth and altered myofibrillogenesis but only minimally affected myoblast proliferation. We identified an Rbf-dependent transcriptional program in late muscle development that is distinct from the canonical role of Rbf in cell cycle control. Unexpectedly, Rbf acts as a transcriptional activator of the myogenic and metabolic genes in the growing muscles. The genomic regions bound by Rbf contained the binding sites of several factors that genetically interacted with Rbf by modulating Rbf-dependent phenotype. Thus, our results reveal a distinctive role for Rbf as a direct activator of the myogenic transcriptional program that drives late muscle differentiation. Inactivation of the tumor suppressor RB, an obligatory step in most cancers, results in unrestrained cell cycle progression. Zappia et al. show that Rbf, the RB Drosophila ortholog, directly activates the metabolic program that accompanies muscle development. This work expands the understanding of the plethora of Rbf functions.
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Affiliation(s)
- Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Alice Rogers
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Abul B M M K Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA.
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19
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Tumor Milieu Controlled by RB Tumor Suppressor. Int J Mol Sci 2020; 21:ijms21072450. [PMID: 32244804 PMCID: PMC7177274 DOI: 10.3390/ijms21072450] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/31/2020] [Indexed: 02/08/2023] Open
Abstract
The RB gene is one of the most frequently mutated genes in human cancers. Canonically, RB exerts its tumor suppressive activity through the regulation of the G1/S transition during cell cycle progression by modulating the activity of E2F transcription factors. However, aberration of the RB gene is most commonly detected in tumors when they gain more aggressive phenotypes, including metastatic activity or drug resistance, rather than accelerated proliferation. This implicates RB controls' malignant progression to a considerable extent in a cell cycle-independent manner. In this review, we highlight the multifaceted functions of the RB protein in controlling tumor lineage plasticity, metabolism, and the tumor microenvironment (TME), with a focus on the mechanism whereby RB controls the TME. In brief, RB inactivation in several types of cancer cells enhances production of pro-inflammatory cytokines, including CCL2, through upregulation of mitochondrial reactive oxygen species (ROS) production. These factors not only accelerate the growth of cancer cells in a cell-autonomous manner, but also stimulate non-malignant cells in the TME to generate a pro-tumorigenic niche in a non-cell-autonomous manner. Here, we discuss the biological and pathological significance of the non-cell-autonomous functions of RB and attempt to predict their potential clinical relevance to cancer immunotherapy.
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20
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Nelson BS, Lin L, Kremer DM, Sousa CM, Cotta-Ramusino C, Myers A, Ramos J, Gao T, Kovalenko I, Wilder-Romans K, Dresser J, Davis M, Lee HJ, Nwosu ZC, Campit S, Mashadova O, Nicolay BN, Tolstyka ZP, Halbrook CJ, Chandrasekaran S, Asara JM, Crawford HC, Cantley LC, Kimmelman AC, Wahl DR, Lyssiotis CA. Tissue of origin dictates GOT1 dependence and confers synthetic lethality to radiotherapy. Cancer Metab 2020; 8:1. [PMID: 31908776 PMCID: PMC6941320 DOI: 10.1186/s40170-019-0202-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Metabolic programs in cancer cells are influenced by genotype and the tissue of origin. We have previously shown that central carbon metabolism is rewired in pancreatic ductal adenocarcinoma (PDA) to support proliferation through a glutamate oxaloacetate transaminase 1 (GOT1)-dependent pathway. METHODS We utilized a doxycycline-inducible shRNA-mediated strategy to knockdown GOT1 in PDA and colorectal cancer (CRC) cell lines and tumor models of similar genotype. These cells were analyzed for the ability to form colonies and tumors to test if tissue type impacted GOT1 dependence. Additionally, the ability of GOT1 to impact the response to chemo- and radiotherapy was assessed. Mechanistically, the associated specimens were examined using a combination of steady-state and stable isotope tracing metabolomics strategies and computational modeling. Statistics were calculated using GraphPad Prism 7. One-way ANOVA was performed for experiments comparing multiple groups with one changing variable. Student's t test (unpaired, two-tailed) was performed when comparing two groups to each other. Metabolomics data comparing three PDA and three CRC cell lines were analyzed by performing Student's t test (unpaired, two-tailed) between all PDA metabolites and CRC metabolites. RESULTS While PDA exhibits profound growth inhibition upon GOT1 knockdown, we found CRC to be insensitive. In PDA, but not CRC, GOT1 inhibition disrupted glycolysis, nucleotide metabolism, and redox homeostasis. These insights were leveraged in PDA, where we demonstrate that radiotherapy potently enhanced the effect of GOT1 inhibition on tumor growth. CONCLUSIONS Taken together, these results illustrate the role of tissue type in dictating metabolic dependencies and provide new insights for targeting metabolism to treat PDA.
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Affiliation(s)
- Barbara S. Nelson
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139 USA
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016 USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139 USA
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016 USA
| | - Daniel M. Kremer
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Cristovão M. Sousa
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139 USA
| | - Cecilia Cotta-Ramusino
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Amy Myers
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Johanna Ramos
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Tina Gao
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Ilya Kovalenko
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Joseph Dresser
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Mary Davis
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Zeribe C. Nwosu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Scott Campit
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Oksana Mashadova
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
| | | | - Zachary P. Tolstyka
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Christopher J. Halbrook
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - John M. Asara
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115 USA
| | - Howard C. Crawford
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
| | - Alec C. Kimmelman
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016 USA
| | - Daniel R. Wahl
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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Dolfini D, Minuzzo M, Sertic S, Mantovani R. NF-YA overexpression protects from glutamine deprivation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118571. [PMID: 31706909 DOI: 10.1016/j.bbamcr.2019.118571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/20/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022]
Abstract
The heterotrimeric transcription factor NF-Y binds to CCAAT boxes of genes of glutamine metabolism. We set out to study the role of the regulatory NF-YA subunit in this pathway. We produced U2OS and A549 clones stably overexpressing -OE- the two splicing isoforms of NF-YA. NF-YA OE cells show normal growth and colony formation rates, but they become resistant to cell death upon glutamine deprivation. Increased mRNA and protein expression of the key biosynthetic enzyme GLUL in U2OS entails increased production of endogenous glutamine upon deprivation. The use of GLUL inhibitors dampens the NF-YA-mediated effect. NF-YA OE prevents activation of the pro-apoptotic transcription factor CHOP/DDIT3. Elevated basal levels of SERCA1/2, coding for the molecular target of Thapsigargin, correlate with resistance of NF-YA OE cells to the drug. The work represents a proof-of-principle that elevated levels of NF-YA, as found in some tumor types, helps altering cancer metabolic pathways.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Mario Minuzzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sarah Sertic
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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22
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Lupberger J, Croonenborghs T, Roca Suarez AA, Van Renne N, Jühling F, Oudot MA, Virzì A, Bandiera S, Jamey C, Meszaros G, Brumaru D, Mukherji A, Durand SC, Heydmann L, Verrier ER, El Saghire H, Hamdane N, Bartenschlager R, Fereshetian S, Ramberger E, Sinha R, Nabian M, Everaert C, Jovanovic M, Mertins P, Carr SA, Chayama K, Dali-Youcef N, Ricci R, Bardeesy NM, Fujiwara N, Gevaert O, Zeisel MB, Hoshida Y, Pochet N, Baumert TF. Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development. Gastroenterology 2019; 157:537-551.e9. [PMID: 30978357 PMCID: PMC8318381 DOI: 10.1053/j.gastro.2019.04.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The mechanisms of hepatitis C virus (HCV) infection, liver disease progression, and hepatocarcinogenesis are only partially understood. We performed genomic, proteomic, and metabolomic analyses of HCV-infected cells and chimeric mice to learn more about these processes. METHODS Huh7.5.1dif (hepatocyte-like cells) were infected with culture-derived HCV and used in RNA sequencing, proteomic, metabolomic, and integrative genomic analyses. uPA/SCID (urokinase-type plasminogen activator/severe combined immunodeficiency) mice were injected with serum from HCV-infected patients; 8 weeks later, liver tissues were collected and analyzed by RNA sequencing and proteomics. Using differential expression, gene set enrichment analyses, and protein interaction mapping, we identified pathways that changed in response to HCV infection. We validated our findings in studies of liver tissues from 216 patients with HCV infection and early-stage cirrhosis and paired biopsy specimens from 99 patients with hepatocellular carcinoma, including 17 patients with histologic features of steatohepatitis. Cirrhotic liver tissues from patients with HCV infection were classified into 2 groups based on relative peroxisome function; outcomes assessed included Child-Pugh class, development of hepatocellular carcinoma, survival, and steatohepatitis. Hepatocellular carcinomas were classified according to steatohepatitis; the outcome was relative peroxisomal function. RESULTS We quantified 21,950 messenger RNAs (mRNAs) and 8297 proteins in HCV-infected cells. Upon HCV infection of hepatocyte-like cells and chimeric mice, we observed significant changes in levels of mRNAs and proteins involved in metabolism and hepatocarcinogenesis. HCV infection of hepatocyte-like cells significantly increased levels of the mRNAs, but not proteins, that regulate the innate immune response; we believe this was due to the inhibition of translation in these cells. HCV infection of hepatocyte-like cells increased glucose consumption and metabolism and the STAT3 signaling pathway and reduced peroxisome function. Peroxisomes mediate β-oxidation of very long-chain fatty acids; we found intracellular accumulation of very long-chain fatty acids in HCV-infected cells, which is also observed in patients with fatty liver disease. Cells in livers from HCV-infected mice had significant reductions in levels of the mRNAs and proteins associated with peroxisome function, indicating perturbation of peroxisomes. We found that defects in peroxisome function were associated with outcomes and features of HCV-associated cirrhosis, fatty liver disease, and hepatocellular carcinoma in patients. CONCLUSIONS We performed combined transcriptome, proteome, and metabolome analyses of liver tissues from HCV-infected hepatocyte-like cells and HCV-infected mice. We found that HCV infection increases glucose metabolism and the STAT3 signaling pathway and thereby reduces peroxisome function; alterations in the expression levels of peroxisome genes were associated with outcomes of patients with liver diseases. These findings provide insights into liver disease pathogenesis and might be used to identify new therapeutic targets.
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Affiliation(s)
- Joachim Lupberger
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France.
| | - Tom Croonenborghs
- Department of Neurology, Harvard Medical School, Boston, Massachusetts; Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Armando Andres Roca Suarez
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Nicolaas Van Renne
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Frank Jühling
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Marine A Oudot
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Alessia Virzì
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Simonetta Bandiera
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Carole Jamey
- Université de Strasbourg, Strasbourg, France; Laboratoire de Biochimie et de Biologie Moléculaire, Pôle de biologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Gergö Meszaros
- Université de Strasbourg, Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France
| | - Daniel Brumaru
- Université de Strasbourg, Strasbourg, France; Laboratoire de Biochimie et de Biologie Moléculaire, Pôle de biologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Atish Mukherji
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Sarah C Durand
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Laura Heydmann
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Eloi R Verrier
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Hussein El Saghire
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Nourdine Hamdane
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shaunt Fereshetian
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Evelyn Ramberger
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany; Berlin Institute of Health, Berlin, Germany
| | - Rileen Sinha
- Department of Neurology, Harvard Medical School, Boston, Massachusetts; Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Mohsen Nabian
- Department of Neurology, Harvard Medical School, Boston, Massachusetts; Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Celine Everaert
- Department of Neurology, Harvard Medical School, Boston, Massachusetts; Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Marko Jovanovic
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Department of Biological Sciences, Columbia University, New York, New York
| | - Philipp Mertins
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany; Berlin Institute of Health, Berlin, Germany
| | - Steven A Carr
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Nassim Dali-Youcef
- Université de Strasbourg, Strasbourg, France; Laboratoire de Biochimie et de Biologie Moléculaire, Pôle de biologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France
| | - Romeo Ricci
- Université de Strasbourg, Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France
| | | | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Olivier Gevaert
- Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, California
| | - Mirjam B Zeisel
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Nathalie Pochet
- Department of Neurology, Harvard Medical School, Boston, Massachusetts; Cell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Thomas F Baumert
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), Strasbourg, France; Université de Strasbourg, Strasbourg, France; Pôle Hépato-digestif, Institut Hopitalo-Universitaire, Strasbourg, France.
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23
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Mitochondria as playmakers of apoptosis, autophagy and senescence. Semin Cell Dev Biol 2019; 98:139-153. [PMID: 31154010 DOI: 10.1016/j.semcdb.2019.05.022] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022]
Abstract
Mitochondria are the key energy-producing organelles and cellular source of reactive species. They are responsible for managing cell life and death by a balanced homeostasis passing through a network of structures, regulated principally via fission and fusion. Herein we discuss about the most advanced findings considering mitochondria as dynamic biophysical systems playing compelling roles in the regulation of energy metabolism in both physiologic and pathologic processes controlling cell death and survival. Precisely, we focus on the mitochondrial commitment to the onset, maintenance and counteraction of apoptosis, autophagy and senescence in the bioenergetic reprogramming of cancer cells. In this context, looking for a pharmacological manipulation of cell death processes as a successful route for future targeted therapies, there is major biotechnological challenge in underlining the location, function and molecular mechanism of mitochondrial proteins. Based on the critical role of mitochondrial functions for cellular health, a better knowledge of the main molecular players in mitochondria disfunction could be decisive for the therapeutical control of degenerative diseases, including cancer.
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24
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de Jong Y, Ingola M, Briaire-de Bruijn IH, Kruisselbrink AB, Venneker S, Palubeckaite I, Heijs BPAM, Cleton-Jansen AM, Haas RLM, Bovée JVMG. Radiotherapy resistance in chondrosarcoma cells; a possible correlation with alterations in cell cycle related genes. Clin Sarcoma Res 2019; 9:9. [PMID: 31160965 PMCID: PMC6540537 DOI: 10.1186/s13569-019-0119-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
Background Conventional chondrosarcomas are malignant cartilage tumors considered radioresistant. Nevertheless, retrospective series show a small but significant survival benefit for patients with locally advanced disease treated with radiotherapy. And, in daily practice when considered inoperable their irradiation is an accepted indication for proton beam radiotherapy. Therefore, we investigated the sensitivity of chondrosarcoma cell lines and -tissue samples towards radiotherapy and screened for biomarkers to identify predictors of radiosensitivity. Methods Proliferation and clonogenic assays were performed in chondrosarcoma cell lines after γ-radiation in combination with mutant IDH1 inhibitor AGI-5198. In addition, glutathione levels were measured using mass spectrometry. Chondrosarcoma tumor explants were irradiated after which γ-H2AX foci were counted. Mutation analysis was performed using the Ion AmpliSeq™ Cancer Hotspot Panel and immunohistochemical staining’s were performed for P-S6, LC-3B, P53, Bcl-2, Bcl-xl and Survivin. Results were correlated with the number of γ-H2AX foci. Results Chondrosarcoma cell lines were variably γ-radiation resistant. No difference in radiosensitivity, nor glutathione levels was observed after treatment with AGI-5198. Irradiated chondrosarcoma patient tissue presented a variable increase in γ-H2AX foci compared to non-radiated tissue. Samples were divided into two groups, high and low radioresistant, based on the amount of γ-H2AX foci. All four highly resistant tumors exhibited mutations in the pRb pathway, while none of the less radioresistant tumors showed mutations in these genes. Conclusions Chondrosarcoma cell lines as well as primary tumors are variably radioresistant, particularly in case of a defective Rb pathway. Whether selection for radiotherapy can be based upon an intact Rb pathway should be further investigated. Electronic supplementary material The online version of this article (10.1186/s13569-019-0119-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yvonne de Jong
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Martha Ingola
- 2Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Inge H Briaire-de Bruijn
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Alwine B Kruisselbrink
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Sanne Venneker
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Ieva Palubeckaite
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Bram P A M Heijs
- 2Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anne-Marie Cleton-Jansen
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Rick L M Haas
- 3Department of Radiation Oncology, Leiden University Medical Center, Leiden, The Netherlands.,4Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Judith V M G Bovée
- 1Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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25
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Qie S, Diehl JA. Glutamine addiction: an Achilles heel in esophageal cancers with dysregulation of CDK4/6. Mol Cell Oncol 2019; 6:1610257. [PMID: 31211239 DOI: 10.1080/23723556.2019.1610257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 10/26/2022]
Abstract
Understanding and overcoming resistance to cyclin-dependent kinase 4/6 (CDK4/6) inhibitors will be challenging. Recent work reveals that dysregulation of F-Box Protein 4 (FBXO4)-Cyclin D1 axis leads to mitochondrial dysfunction and drives glutamine-addiction in esophageal squamous cell carcinoma. This metabolism feature makes these tumors susceptible to combined treatment with glutaminase (GLS) inhibitor and metformin even when resisting to CDK4/6 inhibitors.
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Affiliation(s)
- Shuo Qie
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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26
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Ex vivo and in vivo stable isotope labelling of central carbon metabolism and related pathways with analysis by LC-MS/MS. Nat Protoc 2019; 14:313-330. [PMID: 30683937 DOI: 10.1038/s41596-018-0102-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Targeted tandem mass spectrometry (LC-MS/MS) has been extremely useful for profiling small molecules extracted from biological sources, such as cells, bodily fluids and tissues. Here, we present a protocol for analysing incorporation of the non-radioactive stable isotopes carbon-13 (13C) and nitrogen-15 (15N) into polar metabolites in central carbon metabolism and related pathways. Our platform utilizes selected reaction monitoring (SRM) with polarity switching and amide hydrophilic interaction liquid chromatography (HILIC) to capture transitions for carbon and nitrogen incorporation into selected metabolites using a hybrid triple quadrupole (QQQ) mass spectrometer. This protocol represents an extension of a previously published protocol for targeted metabolomics of unlabeled species and has been used extensively in tracing the metabolism of nutrients such as 13C-labeled glucose, 13C-glutamine and 15N-glutamine in a variety of biological settings (e.g., cell culture experiments and in vivo mouse labelling via i.p. injection). SRM signals are integrated to produce an array of peak areas for each labelling form that serve as the output for further analysis. The processed data are then used to obtain the degree and distribution of labelling of the targeted molecules (termed fluxomics). Each method can be customized on the basis of known unlabeled Q1/Q3 SRM transitions and adjusted to account for the corresponding 13C or 15N incorporation. The entire procedure takes ~6-7 h for a single sample from experimental labelling and metabolite extraction to peak integration.
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27
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Qie S, Yoshida A, Parnham S, Oleinik N, Beeson GC, Beeson CC, Ogretmen B, Bass AJ, Wong KK, Rustgi AK, Diehl JA. Targeting glutamine-addiction and overcoming CDK4/6 inhibitor resistance in human esophageal squamous cell carcinoma. Nat Commun 2019; 10:1296. [PMID: 30899002 PMCID: PMC6428878 DOI: 10.1038/s41467-019-09179-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/20/2019] [Indexed: 02/08/2023] Open
Abstract
The dysregulation of Fbxo4-cyclin D1 axis occurs at high frequency in esophageal squamous cell carcinoma (ESCC), where it promotes ESCC development and progression. However, defining a therapeutic vulnerability that results from this dysregulation has remained elusive. Here we demonstrate that Rb and mTORC1 contribute to Gln-addiction upon the dysregulation of the Fbxo4-cyclin D1 axis, which leads to the reprogramming of cellular metabolism. This reprogramming is characterized by reduced energy production and increased sensitivity of ESCC cells to combined treatment with CB-839 (glutaminase 1 inhibitor) plus metformin/phenformin. Of additional importance, this combined treatment has potent efficacy in ESCC cells with acquired resistance to CDK4/6 inhibitors in vitro and in xenograft tumors. Our findings reveal a molecular basis for cancer therapy through targeting glutaminolysis and mitochondrial respiration in ESCC with dysregulated Fbxo4-cyclin D1 axis as well as cancers resistant to CDK4/6 inhibitors.
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Affiliation(s)
- Shuo Qie
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Akihiro Yoshida
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Stuart Parnham
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Natalia Oleinik
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Gyda C Beeson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Craig C Beeson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anil K Rustgi
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.,Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
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28
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Sahoo S, Ravi Kumar RK, Nicolay B, Mohite O, Sivaraman K, Khetan V, Rishi P, Ganesan S, Subramanyan K, Raman K, Miles W, Elchuri SV. Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma. FEBS Lett 2018; 593:23-41. [PMID: 30417337 DOI: 10.1002/1873-3468.13294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/25/2018] [Accepted: 11/06/2018] [Indexed: 11/06/2022]
Abstract
Retinoblastoma (RB) is a childhood eye cancer. Currently, chemotherapy, local therapy, and enucleation are the main ways in which these tumors are managed. The present work is the first study that uses constraint-based reconstruction and analysis approaches to identify and explain RB-specific survival strategies, which are RB tumor specific. Importantly, our model-specific secretion profile is also found in RB1-depleted human retinal cells in vitro and suggests that novel biomarkers involved in lipid metabolism may be important. Finally, RB-specific synthetic lethals have been predicted as lipid and nucleoside transport proteins that can aid in novel drug target development.
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Affiliation(s)
- Swagatika Sahoo
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
| | | | - Brandon Nicolay
- Department of Molecular Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA, USA.,Agios Pharmaceutical, 88 Sidney Street, Cambridge, MA, USA
| | - Omkar Mohite
- Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Sankara Nethralaya, Chennai, India
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Sankara Nethralaya, Chennai, India
| | - Suganeswari Ganesan
- Department of Histopathology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | | | - Karthik Raman
- Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), Indian Institute of Technology Madras, Chennai, India
| | - Wayne Miles
- Department of Molecular Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA, USA.,Department of Molecular Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Sailaja V Elchuri
- Department of Nanotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
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29
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Elchuri SV, Rajasekaran S, Miles WO. RNA-Sequencing of Primary Retinoblastoma Tumors Provides New Insights and Challenges Into Tumor Development. Front Genet 2018; 9:170. [PMID: 29868118 PMCID: PMC5966869 DOI: 10.3389/fgene.2018.00170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
Retinoblastoma is rare tumor of the retina caused by the homozygous loss of the Retinoblastoma 1 tumor suppressor gene (RB1). Loss of the RB1 protein, pRB, results in de-regulated activity of the E2F transcription factors, chromatin changes and developmental defects leading to tumor development. Extensive microarray profiles of these tumors have enabled the identification of genes sensitive to pRB disruption, however, this technology has a number of limitations in the RNA profiles that they generate. The advent of RNA-sequencing has enabled the global profiling of all of the RNA within the cell including both coding and non-coding features and the detection of aberrant RNA processing events. In this perspective, we focus on discussing how RNA-sequencing of rare Retinoblastoma tumors will build on existing data and open up new area's to improve our understanding of the biology of these tumors. In particular, we discuss how the RB-research field may be to use this data to determine how RB1 loss results in the expression of; non-coding RNAs, causes aberrant RNA processing events and how a deeper analysis of metabolic RNA changes can be utilized to model tumor specific shifts in metabolism. Each section discusses new opportunities and challenges associated with these types of analyses and aims to provide an honest assessment of how understanding these different processes may contribute to the treatment of Retinoblastoma.
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Affiliation(s)
- Sailaja V. Elchuri
- Department of Nanotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Swetha Rajasekaran
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Wayne O. Miles
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
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30
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Glutamine Synthetase: Localization Dictates Outcome. Genes (Basel) 2018; 9:genes9020108. [PMID: 29463059 PMCID: PMC5852604 DOI: 10.3390/genes9020108] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 01/03/2023] Open
Abstract
Glutamine synthetase (GS) is the adenosine triphosphate (ATP)-dependent enzyme that catalyses the synthesis of glutamine by condensing ammonium to glutamate. In the circulatory system, glutamine carries ammonia from muscle and brain to the kidney and liver. In brain reduction of GS activity has been suggested as a mechanism mediating neurotoxicity in neurodegenerative disorders. In cancer, the delicate balance between glutamine synthesis and catabolism is a critical event. In vitro evidence, confirmed in vivo in some cases, suggests that reduced GS activity in cancer cells associates with a more invasive and aggressive phenotype. However, GS is known to be highly expressed in cells of the tumor microenvironment, such as fibroblasts, adipocytes and immune cells, and their ability to synthesize glutamine is responsible for the acquisition of protumoral phenotypes. This has opened a new window into the complex scenario of the tumor microenvironment, in which the balance of glutamine consumption versus glutamine synthesis influences cellular function. Since GS expression responds to glutamine starvation, a lower glutamine synthesizing power due to the absence of GS in cancer cells might apply a metabolic pressure on stromal cells. This event might push stroma towards a GS-high/protumoral phenotype. When referred to stromal cells, GS expression might acquire a ‘bad’ significance to the point that GS inhibition might be considered a conceivable strategy against cancer metastasis.
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31
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Metabolomics: State-of-the-Art Technologies and Applications on Drosophila melanogaster. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:257-276. [PMID: 29951824 DOI: 10.1007/978-981-13-0529-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Metabolomics is one of the latest "omics" technology concerned with the high-throughput identification and quantification of metabolites, the final products of cellular processes. The revealed data provide an instantaneous snapshot of an organism's metabolic pathways, which can be used to explain its phenotype or physiology. On the other hand, Drosophila has shown its power in studying metabolism and related diseases. At this stage, we have the state-of-the-art knowledge in place: a potential candidate to study cellular metabolism (Drosophila melanogaster) and a powerful methodology for metabolic network decipherer (metabolomics). Yet missing is advanced metabolomics technologies like isotope-assisted metabolomics optimized for Drosophila. In this chapter, we will discuss on the current status and future perspectives in technologies and applications of Drosophila metabolomics.
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32
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Zacksenhaus E, Shrestha M, Liu JC, Vorobieva I, Chung PE, Ju Y, Nir U, Jiang Z. Mitochondrial OXPHOS Induced by RB1 Deficiency in Breast Cancer: Implications for Anabolic Metabolism, Stemness, and Metastasis. Trends Cancer 2017; 3:768-779. [DOI: 10.1016/j.trecan.2017.09.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/26/2022]
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33
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Kitajima S, Takahashi C. Intersection of retinoblastoma tumor suppressor function, stem cells, metabolism, and inflammation. Cancer Sci 2017; 108:1726-1731. [PMID: 28865172 PMCID: PMC5581511 DOI: 10.1111/cas.13312] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/27/2022] Open
Abstract
The Retinoblastoma (RB) tumor suppressor regulates G1/S transition during cell cycle progression by modulating the activity of E2F transcription factors. The RB pathway plays a central role in the suppression of most cancers, and RB mutation was initially discovered by virtue of its role in tumor initiation. However, as cancer genome sequencing has evolved to profile more advanced and treatment‐resistant cancers, it has become increasingly clear that, in the majority of cancers, somatic RB inactivation occurs during tumor progression. Furthermore, despite the presence of deregulation of cell cycle control due to an INK4A deletion, additional CCND amplification and/or other mutations in the RB pathway, mutation or deletion of the RB gene is often observed during cancer progression. Of note, RB inactivation during cancer progression not only facilitates G1/S transition but also enhances some characteristics of malignancy, including altered drug sensitivity and a return to the undifferentiated state. Recently, we reported that RB inactivation enhances pro‐inflammatory signaling through stimulation of the interleukin‐6/STAT3 pathway, which directly promotes various malignant features of cancer cells. In this review, we highlight the consequences of RB inactivation during cancer progression, and discuss the biological and pathological significance of the interaction between RB and pro‐inflammatory signaling.
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Affiliation(s)
- Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
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34
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Bruntz RC, Lane AN, Higashi RM, Fan TWM. Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM). J Biol Chem 2017; 292:11601-11609. [PMID: 28592486 PMCID: PMC5512057 DOI: 10.1074/jbc.r117.776054] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metabolic reprogramming is a hallmark of cancer. The changes in metabolism are adaptive to permit proliferation, survival, and eventually metastasis in a harsh environment. Stable isotope-resolved metabolomics (SIRM) is an approach that uses advanced approaches of NMR and mass spectrometry to analyze the fate of individual atoms from stable isotope-enriched precursors to products to deduce metabolic pathways and networks. The approach can be applied to a wide range of biological systems, including human subjects. This review focuses on the applications of SIRM to cancer metabolism and its use in understanding drug actions.
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Affiliation(s)
- Ronald C Bruntz
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506.
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506.
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35
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Wang H, Nicolay BN, Chick JM, Gao X, Geng Y, Ren H, Gao H, Yang G, Williams JA, Suski JM, Keibler MA, Sicinska E, Gerdemann U, Haining WN, Roberts TM, Polyak K, Gygi SP, Dyson NJ, Sicinski P. The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival. Nature 2017; 546:426-430. [PMID: 28607489 DOI: 10.1038/nature22797] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/28/2017] [Indexed: 01/08/2023]
Abstract
D-type cyclins (D1, D2 and D3) and their associated cyclin-dependent kinases (CDK4 and CDK6) are components of the core cell cycle machinery that drives cell proliferation. Inhibitors of CDK4 and CDK6 are currently being tested in clinical trials for patients with several cancer types, with promising results. Here, using human cancer cells and patient-derived xenografts in mice, we show that the cyclin D3-CDK6 kinase phosphorylates and inhibits the catalytic activity of two key enzymes in the glycolytic pathway, 6-phosphofructokinase and pyruvate kinase M2. This re-directs the glycolytic intermediates into the pentose phosphate (PPP) and serine pathways. Inhibition of cyclin D3-CDK6 in tumour cells reduces flow through the PPP and serine pathways, thereby depleting the antioxidants NADPH and glutathione. This, in turn, increases the levels of reactive oxygen species and causes apoptosis of tumour cells. The pro-survival function of cyclin D-associated kinase operates in tumours expressing high levels of cyclin D3-CDK6 complexes. We propose that measuring the levels of cyclin D3-CDK6 in human cancers might help to identify tumour subsets that undergo cell death and tumour regression upon inhibition of CDK4 and CDK6. Cyclin D3-CDK6, through its ability to link cell cycle and cell metabolism, represents a particularly powerful oncoprotein that affects cancer cells at several levels, and this property can be exploited for anti-cancer therapy.
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Affiliation(s)
- Haizhen Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Brandon N Nicolay
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts 02129, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xueliang Gao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hong Ren
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hui Gao
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Guizhi Yang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Juliet A Williams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jan M Suski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mark A Keibler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ulrike Gerdemann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Thomas M Roberts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts 02129, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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36
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Activated E2F activity induces cell death in papillary thyroid carcinoma K1 cells with enhanced Wnt signaling. PLoS One 2017; 12:e0178908. [PMID: 28570681 PMCID: PMC5453581 DOI: 10.1371/journal.pone.0178908] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/19/2017] [Indexed: 11/19/2022] Open
Abstract
Disruption of Wnt signaling often happens in tumorigenesis, but whether Wnt signaling affects the early stages of thyroid tumor, such as papillary thyroid carcinoma, is still a question, especially in the papillary thyroid carcinoma without genomic RET/PTC mutation. In this study, we demonstrated the important function of Wnt signaling in papillary thyroid carcinoma K1 cells, which have no RET/PTC mutation. We found that K1 cells have enhanced Wnt signaling in comparison to normal thyroid cells. We further demonstrated that K1 cells require the enhanced Wnt signaling for growth and survival. Interestingly, we identified that enhancing E2F activity by either knockdown of Rb or overexpression of Cyclin D1 induces cell death in K1 cells. And we further revealed that the cell death is caused by enhanced oxidative stress. Our studies present a novel cell model to support the key roles of Wnt signaling in early stage of thyroid tumor, and also provide an alternative way to limit thyroid cancer.
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37
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Abstract
In this review, Dyson summarizes some recent developments in pRB research and focuses on progress toward answers for the three fundamental questions that sit at the heart of the pRB literature: What does pRB do? How does the inactivation of RB change the cell? How can our knowledge of RB function be exploited to provide better treatment for cancer patients? The retinoblastoma susceptibility gene (RB1) was the first tumor suppressor gene to be molecularly defined. RB1 mutations occur in almost all familial and sporadic forms of retinoblastoma, and this gene is mutated at variable frequencies in a variety of other human cancers. Because of its early discovery, the recessive nature of RB1 mutations, and its frequency of inactivation, RB1 is often described as a prototype for the class of tumor suppressor genes. Its gene product (pRB) regulates transcription and is a negative regulator of cell proliferation. Although these general features are well established, a precise description of pRB's mechanism of action has remained elusive. Indeed, in many regards, pRB remains an enigma. This review summarizes some recent developments in pRB research and focuses on progress toward answers for the three fundamental questions that sit at the heart of the pRB literature: What does pRB do? How does the inactivation of RB change the cell? How can our knowledge of RB function be exploited to provide better treatment for cancer patients?
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38
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The RB–IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity. Oncogene 2017; 36:5145-5157. [DOI: 10.1038/onc.2017.124] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022]
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39
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Abstract
Reliance on glutamine has long been considered a hallmark of cancer cell metabolism. However, some recent studies have challenged this notion in vivo, prompting a need for further clarifications on 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.
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Affiliation(s)
- Ahmad A Cluntun
- Graduate Field of Biochemistry, Molecular & Cell Biology, Cornell University, Ithaca, NY, USA; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Michael J Lukey
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Richard A Cerione
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA; Department of Chemistry and Chemical Biology, Cornell University, Ithaca NY 14853, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
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40
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Breitkopf SB, Ricoult SJH, Yuan M, Xu Y, Peake DA, Manning BD, Asara JM. A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source. Metabolomics 2017; 13:30. [PMID: 28496395 PMCID: PMC5421409 DOI: 10.1007/s11306-016-1157-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/21/2016] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Advances in high-resolution mass spectrometry have created renewed interest for studying global lipid biochemistry in disease and biological systems. OBJECTIVES Here, we present an untargeted 30 min. LC-MS/MS platform that utilizes positive/negative polarity switching to perform unbiased data dependent acquisitions (DDA) via higher energy collisional dissociation (HCD) fragmentation to profile more than 1000-1500 lipid ions mainly from methyl-tert-butyl ether (MTBE) or chloroform:methanol extractions. METHODS The platform uses C18 reversed-phase chromatography coupled to a hybrid QExactive Plus/HF Orbitrap mass spectrometer and the entire procedure takes ~10 h from lipid extraction to identification/quantification for a data set containing 12 samples (~4 h for a single sample). Lipids are identified by both accurate precursor ion mass and fragmentation features and quantified using Lipid-Search and Elements software. RESULTS Using this approach, we are able to profile intact lipid ions from up to 18 different main lipid classes and 66 subclasses. We show several studies from different biological sources, including cultured cancer cells, resected tissues from mice such as lung and breast tumors and biological fluids such as plasma and urine. CONCLUSIONS Using mouse embryonic fibroblasts, we showed that TSC2-/- KD significantly abrogates lipid biosynthesis and that rapamycin can rescue triglyceride (TG) lipids and we show that SREBP-/- shuts down lipid biosynthesis significantly via mTORC1 signaling pathways. We show that in mouse EGFR driven lung tumors, a large number of TGs and phosphatidylmethanol (PMe) lipids are elevated while some phospholipids (PLs) show some of the largest decrease in lipid levels from ~ 2000 identified lipid ions. In addition, we identified more than 1500 unique lipid species from human blood plasma.
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Affiliation(s)
- Susanne B Breitkopf
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Stéphane J H Ricoult
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Min Yuan
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ying Xu
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - David A Peake
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA 95134, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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41
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Kottakis F, Nicolay BN, Roumane A, Karnik R, Gu H, Nagle JM, Boukhali M, Hayward MC, Li YY, Chen T, Liesa M, Hammerman PS, Wong KK, Hayes DN, Shirihai OS, Dyson NJ, Haas W, Meissner A, Bardeesy N. LKB1 loss links serine metabolism to DNA methylation and tumorigenesis. Nature 2016; 539:390-395. [PMID: 27799657 PMCID: PMC5988435 DOI: 10.1038/nature20132] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
Intermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that is central to oncogenic transformation downstream of the liver kinase B1 (LKB1, also known as STK11) tumour suppressor, an integrator of nutrient availability, metabolism and growth. By developing genetically engineered mouse models and primary pancreatic epithelial cells, and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation is fuelled by pronounced mTOR-dependent induction of the serine-glycine-one-carbon pathway coupled to S-adenosylmethionine generation. At the same time, DNA methyltransferases are upregulated, leading to elevation in DNA methylation with particular enrichment at retrotransposon elements associated with their transcriptional silencing. Correspondingly, LKB1 deficiency sensitizes cells and tumours to inhibition of serine biosynthesis and DNA methylation. Thus, we define a hypermetabolic state that incites changes in the epigenetic landscape to support tumorigenic growth of LKB1-mutant cells, while resulting in potential therapeutic vulnerabilities.
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Affiliation(s)
- Filippos Kottakis
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Brandon N. Nicolay
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Ahlima Roumane
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Rahul Karnik
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Julia M. Nagle
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Myriam Boukhali
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | | | - Yvonne Y. Li
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ting Chen
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Marc Liesa
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Peter S. Hammerman
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kwok Kin Wong
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - D. Neil Hayes
- UNC, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Orian S. Shirihai
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Nicholas J. Dyson
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Wilhelm Haas
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nabeel Bardeesy
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
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42
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Nagel R, Semenova EA, Berns A. Drugging the addict: non-oncogene addiction as a target for cancer therapy. EMBO Rep 2016; 17:1516-1531. [PMID: 27702988 PMCID: PMC5090709 DOI: 10.15252/embr.201643030] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
Historically, cancers have been treated with chemotherapeutics aimed to have profound effects on tumor cells with only limited effects on normal tissue. This approach was followed by the development of small‐molecule inhibitors that can target oncogenic pathways critical for the survival of tumor cells. The clinical targeting of these so‐called oncogene addictions, however, is in many instances hampered by the outgrowth of resistant clones. More recently, the proper functioning of non‐mutated genes has been shown to enhance the survival of many cancers, a phenomenon called non‐oncogene addiction. In the current review, we will focus on the distinct non‐oncogenic addictions found in cancer cells, including synthetic lethal interactions, the underlying stress phenotypes, and arising therapeutic opportunities.
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Affiliation(s)
- Remco Nagel
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ekaterina A Semenova
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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43
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Glucose-dependent anaplerosis in cancer cells is required for cellular redox balance in the absence of glutamine. Sci Rep 2016; 6:32606. [PMID: 27605385 PMCID: PMC5015067 DOI: 10.1038/srep32606] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/09/2016] [Indexed: 12/11/2022] Open
Abstract
Cancer cells have altered metabolism compared to normal cells, including dependence on glutamine (GLN) for survival, known as GLN addiction. However, some cancer cell lines do not require GLN for survival and the basis for this discrepancy is not well understood. GLN is a precursor for antioxidants such as glutathione (GSH) and NADPH, and GLN deprivation is therefore predicted to deplete antioxidants and increase reactive oxygen species (ROS). Using diverse human cancer cell lines we show that this occurs only in cells that rely on GLN for survival. Thus, the preference for GLN as a dominant antioxidant source defines GLN addiction. We show that despite increased glucose uptake, GLN addicted cells do not metabolize glucose via the TCA cycle when GLN is depleted, as revealed by 13C-glucose labeling. In contrast, GLN independent cells can compensate by diverting glucose-derived pyruvate into the TCA cycle. GLN addicted cells exhibit reduced PDH activity, increased PDK1 expression, and PDK inhibition partially rescues GLN starvation-induced ROS and cell death. Finally, we show that combining GLN starvation with pro-oxidants selectively kills GLN addicted cells. These data highlight a major role for GLN in maintaining redox balance in cancer cells that lack glucose-dependent anaplerosis.
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44
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Jones RA, Robinson TJ, Liu JC, Shrestha M, Voisin V, Ju Y, Chung PED, Pellecchia G, Fell VL, Bae S, Muthuswamy L, Datti A, Egan SE, Jiang Z, Leone G, Bader GD, Schimmer A, Zacksenhaus E. RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation. J Clin Invest 2016; 126:3739-3757. [PMID: 27571409 DOI: 10.1172/jci81568] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/12/2016] [Indexed: 01/03/2023] Open
Abstract
Triple-negative breast cancer (TNBC) includes basal-like and claudin-low subtypes for which no specific treatment is currently available. Although the retinoblastoma tumor-suppressor gene (RB1) is frequently lost together with TP53 in TNBC, it is not directly targetable. There is thus great interest in identifying vulnerabilities downstream of RB1 that can be therapeutically exploited. Here, we determined that combined inactivation of murine Rb and p53 in diverse mammary epithelial cells induced claudin-low-like TNBC with Met, Birc2/3-Mmp13-Yap1, and Pvt1-Myc amplifications. Gene set enrichment analysis revealed that Rb/p53-deficient tumors showed elevated expression of the mitochondrial protein translation (MPT) gene pathway relative to tumors harboring p53 deletion alone. Accordingly, bioinformatic, functional, and biochemical analyses showed that RB1-E2F complexes bind to MPT gene promoters to regulate transcription and control MPT. Additionally, a screen of US Food and Drug Administration-approved (FDA-approved) drugs identified the MPT antagonist tigecycline (TIG) as a potent inhibitor of Rb/p53-deficient tumor cell proliferation. TIG preferentially suppressed RB1-deficient TNBC cell proliferation, targeted both the bulk and cancer stem cell fraction, and strongly attenuated xenograft growth. It also cooperated with sulfasalazine, an FDA-approved inhibitor of cystine xCT antiporter, in culture and xenograft assays. Our results suggest that RB1 deficiency promotes cancer cell proliferation in part by enhancing mitochondrial function and identify TIG as a clinically approved drug for RB1-deficient TNBC.
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45
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Duminuco R, Noble JW, Goody J, Sharma M, Ksander BR, Roskelley CD, Cox ME, Mills J. Integrin-linked kinase regulates senescence in an Rb-dependent manner in cancer cell lines. Cell Cycle 2016; 14:2924-37. [PMID: 26176204 DOI: 10.1080/15384101.2015.1064205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Anti-integrin-linked kinase (ILK) therapies result in aberrant mitosis including altered mitotic spindle organization, centrosome declustering and mitotic arrest. In contrast to cells that expressed the retinoblastoma tumor suppressor protein Rb, we have shown that in retinoblastoma cell lines that do not express Rb, anti-ILK therapies induced aberrant mitosis that led to the accumulation of temporarily viable multinucleated cells. The present work was undertaken to: 1) determine the ultimate fate of cells that had survived anti-ILK therapies and 2) determine whether or not Rb expression altered the outcome of these cells. Our data indicate that ILK, a chemotherapy drug target is expressed in both well-differentiated, Rb-negative and relatively undifferentiated, Rb-positive retinoblastoma tissue. We show that small molecule targeting of ILK in Rb-positive and Rb-deficient cancer cells results in increased centrosomal declustering, aberrant mitotic spindle formation and multinucleation. However, anti-ILK therapies in vitro have different outcomes in retinoblastoma and glioblastoma cell lines that depend on Rb expression. TUNEL labeling and propidium iodide FACS analysis indicate that Rb-positive cells exposed to anti-ILK therapies are more susceptible to apoptosis and senescence than their Rb-deficient counterparts wherein aberrant mitosis induced by anti-ILK therapies exhibit mitotic arrest instead. These studies are the first to show a role for ILK in chemotherapy-induced senescence in Rb-positive cancer lines. Taken together these results indicate that the oncosuppressive outcomes for anti-ILK therapies in vitro, depend on the expression of the tumor suppressor Rb, a known G1 checkpoint and senescence regulator.
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Affiliation(s)
- Rose Duminuco
- a Department of Biology ; Trinity Western University ; Langley , British Columbia , Canada
| | - Jake W Noble
- a Department of Biology ; Trinity Western University ; Langley , British Columbia , Canada
| | - Joseph Goody
- a Department of Biology ; Trinity Western University ; Langley , British Columbia , Canada
| | - Manju Sharma
- b Vancouver Prostate Center; Vancouver Coastal Health Research Institute ; Vancouver , British Columbia
| | - Bruce R Ksander
- d Department of Ophthalmology ; Schepens Eye Research Institute; Harvard Medical School ; Boston , Massachusetts , United States of America
| | - Calvin D Roskelley
- c Department of Cellular and Physiological Sciences ; University of British Columbia ; Canada
| | - Michael E Cox
- b Vancouver Prostate Center; Vancouver Coastal Health Research Institute ; Vancouver , British Columbia
| | - Julia Mills
- a Department of Biology ; Trinity Western University ; Langley , British Columbia , Canada.,e Adjunct in the Department of Molecular Biology and Biochemistry ; Simon Fraser University ; Burnaby , British Columbia , Canada
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46
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Coloff JL, Murphy JP, Braun CR, Harris IS, Shelton LM, Kami K, Gygi SP, Selfors LM, Brugge JS. Differential Glutamate Metabolism in Proliferating and Quiescent Mammary Epithelial Cells. Cell Metab 2016; 23:867-80. [PMID: 27133130 DOI: 10.1016/j.cmet.2016.03.016] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 02/14/2016] [Accepted: 03/29/2016] [Indexed: 12/29/2022]
Abstract
Mammary epithelial cells transition between periods of proliferation and quiescence during development, menstrual cycles, and pregnancy, and as a result of oncogenic transformation. Utilizing an organotypic 3D tissue culture model coupled with quantitative metabolomics and proteomics, we identified significant differences in glutamate utilization between proliferating and quiescent cells. Relative to quiescent cells, proliferating cells catabolized more glutamate via transaminases to couple non-essential amino acid (NEAA) synthesis to α-ketoglutarate generation and tricarboxylic acid (TCA) cycle anaplerosis. As cells transitioned to quiescence, glutamine consumption and transaminase expression were reduced, while glutamate dehydrogenase (GLUD) was induced, leading to decreased NEAA synthesis. Highly proliferative human tumors display high transaminase and low GLUD expression, suggesting that proliferating cancer cells couple glutamine consumption to NEAA synthesis to promote biosynthesis. These findings describe a competitive and partially redundant relationship between transaminases and GLUD, and they reveal how coupling of glutamate-derived carbon and nitrogen metabolism can be regulated to support cell proliferation.
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Affiliation(s)
- Jonathan L Coloff
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Patrick Murphy
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Craig R Braun
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Shelton
- Human Metabolome Technologies America, Boston, MA 02134, USA
| | - Kenjiro Kami
- Human Metabolome Technologies, Tsuruoka, 997-0052 Japan
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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47
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Kohno S, Kitajima S, Sasaki N, Takahashi C. Retinoblastoma tumor suppressor functions shared by stem cell and cancer cell strategies. World J Stem Cells 2016; 8:170-84. [PMID: 27114748 PMCID: PMC4835675 DOI: 10.4252/wjsc.v8.i4.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/30/2015] [Accepted: 02/14/2016] [Indexed: 02/06/2023] Open
Abstract
Carcinogenic transformation of somatic cells resembles nuclear reprogramming toward the generation of pluripotent stem cells. These events share eternal escape from cellular senescence, continuous self-renewal in limited but certain population of cells, and refractoriness to terminal differentiation while maintaining the potential to differentiate into cells of one or multiple lineages. As represented by several oncogenes those appeared to be first keys to pluripotency, carcinogenesis and nuclear reprogramming seem to share a number of core mechanisms. The retinoblastoma tumor suppressor product retinoblastoma (RB) seems to be critically involved in both events in highly complicated manners. However, disentangling such complicated interactions has enabled us to better understand how stem cell strategies are shared by cancer cells. This review covers recent findings on RB functions related to stem cells and stem cell-like behaviors of cancer cells.
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Affiliation(s)
- Susumu Kohno
- Susumu Kohno, Chiaki Takahashi, Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Shunsuke Kitajima
- Susumu Kohno, Chiaki Takahashi, Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Nobunari Sasaki
- Susumu Kohno, Chiaki Takahashi, Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Chiaki Takahashi
- Susumu Kohno, Chiaki Takahashi, Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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48
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Franco J, Balaji U, Freinkman E, Witkiewicz AK, Knudsen ES. Metabolic Reprogramming of Pancreatic Cancer Mediated by CDK4/6 Inhibition Elicits Unique Vulnerabilities. Cell Rep 2016; 14:979-990. [PMID: 26804906 PMCID: PMC4757440 DOI: 10.1016/j.celrep.2015.12.094] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/23/2015] [Accepted: 12/19/2015] [Indexed: 12/22/2022] Open
Abstract
Due to loss of p16ink4a in pancreatic ductal adenocarcinoma (PDA), pharmacological suppression of CDK4/6 could represent a potent target for treatment. In PDA models, CDK4/6 inhibition had a variable effect on cell cycle but yielded accumulation of ATP and mitochondria. Pharmacological CDK4/6 inhibitors induce cyclin D1 protein levels; however, RB activation was required and sufficient for mitochondrial accumulation. CDK4/6 inhibition stimulated glycolytic and oxidative metabolism and was associated with an increase in mTORC1 activity. MTOR and MEK inhibitors potently cooperate with CDK4/6 inhibition in eliciting cell-cycle exit. However, MTOR inhibition fully suppressed metabolism and yielded apoptosis and suppression of tumor growth in xenograft models. The metabolic state mediated by CDK4/6 inhibition increases mitochondrial number and reactive oxygen species (ROS). Concordantly, the suppression of ROS scavenging or BCL2 antagonists cooperated with CDK4/6 inhibition. Together, these data define the impact of therapeutics on PDA metabolism and provide strategies for converting cytostatic response to tumor cell killing.
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Affiliation(s)
- Jorge Franco
- McDermott Center University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Uthra Balaji
- McDermott Center University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Elizaveta Freinkman
- Whitehead Institute, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Agnieszka K Witkiewicz
- McDermott Center University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Erik S Knudsen
- McDermott Center University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.
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49
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Identification of a small molecule inhibitor of 3-phosphoglycerate dehydrogenase to target serine biosynthesis in cancers. Proc Natl Acad Sci U S A 2016; 113:1778-83. [PMID: 26831078 DOI: 10.1073/pnas.1521548113] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cancer cells reprogram their metabolism to promote growth and proliferation. The genetic evidence pointing to the importance of the amino acid serine in tumorigenesis is striking. The gene encoding the enzyme 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the first committed step of serine biosynthesis, is overexpressed in tumors and cancer cell lines via focal amplification and nuclear factor erythroid-2-related factor 2 (NRF2)-mediated up-regulation. PHGDH-overexpressing cells are exquisitely sensitive to genetic ablation of the pathway. Here, we report the discovery of a selective small molecule inhibitor of PHGDH, CBR-5884, identified by screening a library of 800,000 drug-like compounds. CBR-5884 inhibited de novo serine synthesis in cancer cells and was selectively toxic to cancer cell lines with high serine biosynthetic activity. Biochemical characterization of the inhibitor revealed that it was a noncompetitive inhibitor that showed a time-dependent onset of inhibition and disrupted the oligomerization state of PHGDH. The identification of a small molecule inhibitor of PHGDH not only enables thorough preclinical evaluation of PHGDH as a target in cancers, but also provides a tool with which to study serine metabolism.
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50
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Recruitment of Pontin/Reptin by E2f1 amplifies E2f transcriptional response during cancer progression. Nat Commun 2015; 6:10028. [PMID: 26639898 PMCID: PMC4686657 DOI: 10.1038/ncomms10028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022] Open
Abstract
Changes in gene expression during tumorigenesis are often considered the consequence of de novo mutations occurring in the tumour. An alternative possibility is that the transcriptional response of oncogenic transcription factors evolves during tumorigenesis. Here we show that aberrant E2f activity, following inactivation of the Rb gene family in a mouse model of liver cancer, initially activates a robust gene expression programme associated with the cell cycle. Slowly accumulating E2f1 progressively recruits a Pontin/Reptin complex to open the chromatin conformation at E2f target genes and amplifies the E2f transcriptional response. This mechanism enhances the E2f-mediated transactivation of cell cycle genes and initiates the activation of low binding affinity E2f target genes that regulate non-cell-cycle functions, such as the Warburg effect. These data indicate that both the physiological and the oncogenic activities of E2f result in distinct transcriptional responses, which could be exploited to target E2f oncogenic activity for therapy. E2F transcription factors are primarily known for the regulation of the cell cycle and are often dysregulated in cancer. Here, the authors show that during cancer progression E2F1 recruits a Pontin/Reptin complex to E2F target genes to open chromatin and increase E2F transcriptional response.
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