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Mao Z, Gao F, Sun T, Xiao Y, Wu J, Xiao Y, Chu H, Wu D, Du M, Zheng R, Zhang Z. RB1 Mutations Induce Smoking-Related Bladder Cancer by Modulating the Cytochrome P450 Pathway. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 39239764 DOI: 10.1002/tox.24409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/14/2024] [Accepted: 08/10/2024] [Indexed: 09/07/2024]
Abstract
Cigarette smoking causes multiple cancers by directly influencing mutation burden of driver mutations. However, the mechanism between somatic mutation caused by cigarette smoking and bladder tumorigenesis remains elusive. Smoking-related mutation profile of bladder cancer was characterized by The Cancer Genome Atlas cohort. Integraticve OncoGenomics database was utilized to detect the smoking-related driver genes, and its biological mechanism predictions were interpreted based on bulk transcriptome and single-cell transcriptome, as well as cell experiments. Cigarette smoking was associated with an increased tumor mutational burden under 65 years old (p = 0.031), and generated specific mutational signatures in smokers. RB1 was identified as a differentially mutated driver gene between smokers and nonsmokers, and the mutation rate of RB1 increased twofold after smoking (p = 0.008). RB1 mutations and the 4-aminobiphenyl interference could significantly decrease the RB1 expression level and thus promote the proliferation, invasion, and migration ability of bladder cancer cells. Enrichment analysis and real-time quantitative PCR (RT-qPCR) data showed that RB1 mutations inhibited cytochrome P450 pathway by reducing expression levels of UGT1A6 and AKR1C2. In addition, we also observed that the component of immunological cells was regulated by RB1 mutations through the stronger cell-to-cell interactions between epithelial scissor+ cells and immune cells in smokers. This study highlighted that RB1 mutations could drive smoking-related bladder tumorigenesis through inhibiting cytochrome P450 pathway and regulating tumor immune microenvironment.
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Affiliation(s)
- Zhenguang Mao
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute of Clinical Research, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Fang Gao
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, China
| | - Tuo Sun
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute of Clinical Research, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Yi Xiao
- Department of Urology, Sir Run Run Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Jiajin Wu
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, China
| | - Yanping Xiao
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute of Clinical Research, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Haiyan Chu
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dongmei Wu
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Rui Zheng
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics and Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute of Clinical Research, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
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2
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Sanidas I, Lawrence MS, Dyson NJ. Patterns in the tapestry of chromatin-bound RB. Trends Cell Biol 2024; 34:288-298. [PMID: 37648594 PMCID: PMC10899529 DOI: 10.1016/j.tcb.2023.07.012] [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: 05/01/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
The retinoblastoma protein (RB)-mediated regulation of E2F is a component of a highly conserved cell cycle machine. However, RB's tumor suppressor activity, like RB's requirement in animal development, is tissue-specific, context-specific, and sometimes appears uncoupled from cell proliferation. Detailed new information about RB's genomic distribution provides a new perspective on the complexity of RB function, suggesting that some of its functional specificity results from context-specific RB association with chromatin. Here we summarize recent evidence showing that RB targets different types of chromatin regulatory elements at different cell cycle stages. RB controls traditional RB/E2F targets prior to S-phase, but, when cells proliferate, RB redistributes to cell type-specific chromatin loci. We discuss the broad implications of the new data for RB research.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149, 13th Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149, 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149, 13th Street, Charlestown, MA 02129, USA.
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3
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Zamalloa LG, Pruitt MM, Hermance NM, Gali H, Flynn RL, Manning AL. RB loss sensitizes cells to replication-associated DNA damage after PARP inhibition by trapping. Life Sci Alliance 2023; 6:e202302067. [PMID: 37704395 PMCID: PMC10500056 DOI: 10.26508/lsa.202302067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
The retinoblastoma tumor suppressor protein (RB) interacts physically and functionally with a number of epigenetic modifying enzymes to control transcriptional regulation, respond to replication stress, promote DNA damage response and repair, and regulate genome stability. To better understand how disruption of RB function impacts epigenetic regulation of genome stability and determine whether such changes represent exploitable weaknesses of RB-deficient cancer cells, we performed an imaging-based screen to identify epigenetic inhibitors that promote DNA damage and compromise the viability of RB-deficient cells. We found that loss of RB alone leads to high levels of replication-dependent poly-ADP ribosylation (PARylation) and that preventing PARylation by trapping PARP enzymes on chromatin enables RB-deficient cells to progress to mitosis with unresolved replication stress. These defects contribute to high levels of DNA damage and compromised cell viability. We demonstrate this sensitivity is conserved across a panel of drugs that target both PARP1 and PARP2 and can be suppressed by reexpression of the RB protein. Together, these data indicate that drugs that target PARP1 and PARP2 may be clinically relevant for RB-deficient cancers.
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Affiliation(s)
- Luis Gregory Zamalloa
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
| | - Margaret M Pruitt
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
| | - Nicole M Hermance
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
| | - Himabindu Gali
- Boston University School of Medicine, Pharmacology, Boston, MA, USA
| | - Rachel L Flynn
- Boston University School of Medicine, Pharmacology, Boston, MA, USA
| | - Amity L Manning
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
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4
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Cheung AHK, Hui CHL, Wong KY, Liu X, Chen B, Kang W, To KF. Out of the cycle: Impact of cell cycle aberrations on cancer metabolism and metastasis. Int J Cancer 2023; 152:1510-1525. [PMID: 36093588 DOI: 10.1002/ijc.34288] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 09/02/2022] [Indexed: 11/11/2022]
Abstract
The use of cell cycle inhibitors has necessitated a better understanding of the cell cycle in tumor biology to optimize the therapeutic approach. Cell cycle aberrations are common in cancers, and it is increasingly acknowledged that these aberrations exert oncogenic effects beyond the cell cycle. Multiple facets such as cancer metabolism, immunity and metastasis are also affected, all of which are beyond the effect of cell proliferation alone. This review comprehensively summarized the important recent findings and advances in these interrelated processes. In cancer metabolism, cell cycle regulators can modulate various pathways in aerobic glycolysis, glucose uptake and gluconeogenesis, mainly through transcriptional regulation and kinase activities. Amino acid metabolism is also regulated through cell cycle progression. On cancer metastasis, metabolic plasticity, immune evasion, tumor microenvironment adaptation and metastatic site colonization are intricately related to the cell cycle, with distinct regulatory mechanisms at each step of invasion and dissemination. Throughout the synthesis of current understanding, knowledge gaps and limitations in the literature are also highlighted, as are new therapeutic approaches such as combinational therapy and challenges in tackling emerging targeted therapy resistance. A greater understanding of how the cell cycle modulates diverse aspects of cancer biology can hopefully shed light on identifying new molecular targets by harnessing the vast potential of the cell cycle.
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Affiliation(s)
- Alvin Ho-Kwan Cheung
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris Ho-Lam Hui
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Kit Yee Wong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoli Liu
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, China
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5
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Zamalloa LG, Pruitt MM, Hermance NM, Gali H, Flynn RL, Manning AL. RB loss sensitizes cells to replication-associated DNA damage by PARP inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.532215. [PMID: 36993348 PMCID: PMC10055402 DOI: 10.1101/2023.03.25.532215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The retinoblastoma tumor suppressor protein (RB) interacts physically and functionally with a number of epigenetic modifying enzymes to control transcriptional regulation, respond to replication stress, promote DNA damage response and repair pathways, and regulate genome stability. To better understand how disruption of RB function impacts epigenetic regulation of genome stability and determine whether such changes may represent exploitable weaknesses of RB-deficient cancer cells, we performed an imaging-based screen to identify epigenetic inhibitors that promote DNA damage and compromise viability of RB-deficient cells. We found that loss of RB alone leads to high levels of replication-dependent poly-ADP ribosylation (PARylation) and that preventing PARylation through inhibition of PARP enzymes enables RB-deficient cells to progress to mitosis with unresolved replication stress and under-replicated DNA. These defects contribute to high levels of DNA damage, decreased proliferation, and compromised cell viability. We demonstrate this sensitivity is conserved across a panel of inhibitors that target both PARP1 and PARP2 and can be suppressed by re-expression of the RB protein. Together, these data indicate that inhibitors of PARP1 and PARP2 may be clinically relevant for RB-deficient cancers.
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6
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A novel defined risk signature of endoplasmic reticulum stress-related genes for predicting the prognosis and immune infiltration status of ovarian cancer. J Zhejiang Univ Sci B 2023; 24:64-77. [PMID: 36632751 PMCID: PMC9837372 DOI: 10.1631/jzus.b2200272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Endoplasmic reticulum (ER) stress, as an emerging hallmark feature of cancer, has a considerable impact on cell proliferation, metastasis, invasion, and chemotherapy resistance. Ovarian cancer (OvCa) is one of the leading causes of cancer-related mortality across the world due to the late stage of disease at diagnosis. Studies have explored the influence of ER stress on OvCa in recent years, while the predictive role of ER stress-related genes in OvCa prognosis remains unexplored. Here, we enrolled 552 cases of ER stress-related genes involved in OvCa from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts for the screening of prognosis-related genes. The least absolute shrinkage and selection operator (LASSO) regression was applied to establish an ER stress-related risk signature based on the TCGA cohort. A seven-gene signature revealed a favorable predictive efficacy for the TCGA, International Cancer Genome Consortium (ICGC), and another GEO cohort (P<0.001, P<0.001, and P=0.04, respectively). Moreover, functional annotation indicated that this signature was enriched in cellular response and senescence, cytokines interaction, as well as multiple immune-associated terms. The immune infiltration profiles further delineated an immunologic unresponsive status in the high-risk group. In conclusion, ER stress-related genes are vital factors predicting the prognosis of OvCa, and possess great application potential in the clinic.
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7
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Romani A, Zauli E, Zauli G, AlMesfer S, Al-Swailem S, Voltan R. MDM2 inhibitors-mediated disruption of mitochondrial metabolism: A novel therapeutic strategy for retinoblastoma. Front Oncol 2022; 12:1000677. [PMID: 36338723 PMCID: PMC9632280 DOI: 10.3389/fonc.2022.1000677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/07/2022] [Indexed: 12/04/2022] Open
Abstract
MDM2 is the principal inhibitor of p53, and MDM2 inhibitors can disrupt the physical interaction between MDM2 and p53. The half-life of p53 is very short in normal cells and tissues, and an uncontrolled increase in p53 levels has potential harmful effects. It has been shown that p53 is frequently mutated in most cancers; however, p53 mutations are rare in retinoblastoma. Therefore, therapeutic strategies aimed at increasing the expression levels of wild-type p53 are attractive. In this minireview, we discuss the potential use of nutlin-3, the prototype small molecule inhibitor that disrupts the MDM2-p53 interaction, for the treatment of retinoblastoma. Although p53 has pleiotropic biological effects, the functions of p53 depend on its sub-cellular localization. In the nucleus, p53 induces the transcription of a vast array of genes, while in mitochondria, p53 regulates mitochondrial metabolism. This review also discusses the relative contribution of p53-mediated gene transcription and mitochondrial perturbation for retinoblastoma treatment.
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Affiliation(s)
- Arianna Romani
- Department of Environmental and Prevention Sciences and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA) Centre, University of Ferrara, Ferrara, Italy
| | - Enrico Zauli
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Research Department, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Saleh AlMesfer
- Research Department, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Samar Al-Swailem
- Research Department, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Rebecca Voltan
- Department of Environmental and Prevention Sciences and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA) Centre, University of Ferrara, Ferrara, Italy
- *Correspondence: Rebecca Voltan,
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8
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Dual roles of β-arrestin 1 in mediating cell metabolism and proliferation in gastric cancer. Proc Natl Acad Sci U S A 2022; 119:e2123231119. [PMID: 36161910 DOI: 10.1073/pnas.2123231119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
β-Arrestin 1 (ARRB1) has been recognized as a multifunctional adaptor protein in the last decade, beyond its original role in desensitizing G protein-coupled receptor signaling. Here, we identify that ARRB1 plays essential roles in mediating gastric cancer (GC) cell metabolism and proliferation, by combining cohort analysis and functional investigation using patient-derived preclinical models. Overexpression of ARRB1 was associated with poor outcome of GC patients and knockdown of ARRB1 impaired cell proliferation both ex vivo and in vivo. Intriguingly, ARRB1 depicted diverse subcellular localizations during a passage of organoid cultures (7 d) to exert dual functions. Further analysis revealed that nuclear ARRB1 binds with transcription factor E2F1 triggering up-regulation of proliferative genes, while cytoplasmic ARRB1 modulates metabolic flux by binding with the pyruvate kinase M2 isoform (PKM2) and hindering PKM2 tetramerization, which reduces pyruvate kinase activity and leads to cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis. As ARRB1 localization was shown mostly in the cytoplasm in human GC samples, therapeutic potential of the ARRB1-PKM2 axis was tested, and we found tumor proliferation could be attenuated by the PKM2 activator DASA-58, especially in ARRB1high organoids. Together, the data in our study highlight a spatiotemporally dependent role of ARRB1 in mediating GC cell metabolism and proliferation and implies reactivating PKM2 may be a promising therapeutic strategy in a subset of GC patients.
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9
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Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression. Mol Cell 2022; 82:3333-3349.e9. [PMID: 35981542 PMCID: PMC9481721 DOI: 10.1016/j.molcel.2022.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/19/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023]
Abstract
The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Hanjun Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Purva H Rumde
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gaylor Boulay
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gabriel Golczer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Marcelo Stanzione
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Soroush Hajizadeh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Meagan B Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Benjamin J Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA.
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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10
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Tian Q, Wang G, Ma X, Shen Q, Ding M, Yang X, Luo X, Li R, Wang Z, Wang X, Fu Z, Yang Q, Tang J, Wang G. Riboflavin integrates cellular energetics and cell cycle to regulate maize seed development. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1487-1501. [PMID: 35426230 PMCID: PMC9342611 DOI: 10.1111/pbi.13826] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/10/2022] [Indexed: 05/23/2023]
Abstract
Riboflavin is the precursor of essential cofactors for diverse metabolic processes. Unlike animals, plants can de novo produce riboflavin through an ancestrally conserved pathway, like bacteria and fungi. However, the mechanism by which riboflavin regulates seed development is poorly understood. Here, we report a novel maize (Zea mays L.) opaque mutant o18, which displays an increase in lysine accumulation, but impaired endosperm filling and embryo development. O18 encodes a rate-limiting bifunctional enzyme ZmRIBA1, targeted to plastid where to initiate riboflavin biosynthesis. Loss of function of O18 specifically disrupts respiratory complexes I and II, but also decreases SDH1 flavinylation, and in turn shifts the mitochondrial tricarboxylic acid (TCA) cycle to glycolysis. The deprivation of cellular energy leads to cell-cycle arrest at G1 and S phases in both mitosis and endoreduplication during endosperm development. The unexpected up-regulation of cell-cycle genes in o18 correlates with the increase of H3K4me3 levels, revealing a possible H3K4me-mediated epigenetic back-up mechanism for cell-cycle progression under unfavourable circumstances. Overexpression of O18 increases riboflavin production and confers osmotic tolerance. Altogether, our results substantiate a key role of riboflavin in coordinating cellular energy and cell cycle to modulate maize endosperm development.
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Affiliation(s)
- Qiuzhen Tian
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Gang Wang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xuexia Ma
- Shanghai Key Laboratory of Bio‐Energy CropsSchool of Life SciencesShanghai UniversityShanghaiChina
| | - Qingwen Shen
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Mengli Ding
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xueyi Yang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiaoli Luo
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Rongrong Li
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhenghui Wang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiangyang Wang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Qinghua Yang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guifeng Wang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
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11
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Sainz de la Maza D, Hof-Michel S, Phillimore L, Bökel C, Amoyel M. Cell-cycle exit and stem cell differentiation are coupled through regulation of mitochondrial activity in the Drosophila testis. Cell Rep 2022; 39:110774. [PMID: 35545055 PMCID: PMC9350557 DOI: 10.1016/j.celrep.2022.110774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 02/21/2022] [Accepted: 04/12/2022] [Indexed: 11/27/2022] Open
Abstract
Whereas stem and progenitor cells proliferate to maintain tissue homeostasis, fully differentiated cells exit the cell cycle. How cell identity and cell-cycle state are coordinated during differentiation is still poorly understood. The Drosophila testis niche supports germline stem cells and somatic cyst stem cells (CySCs). CySCs give rise to post-mitotic cyst cells, providing a tractable model to study the links between stem cell identity and proliferation. We show that, while cell-cycle progression is required for CySC self-renewal, the E2f1/Dp transcription factor is dispensable for self-renewal but instead must be silenced by the Drosophila retinoblastoma homolog, Rbf, to permit differentiation. Continued E2f1/Dp activity inhibits the expression of genes important for mitochondrial activity. Furthermore, promoting mitochondrial biogenesis rescues the differentiation of CySCs with ectopic E2f1/Dp activity but not their cell-cycle exit. In sum, E2f1/Dp coordinates cell-cycle progression with stem cell identity by regulating the metabolic state of CySCs. CycE is critical for CySC self-renewal E2f/Dp does not act in self-renewal but must be silenced for differentiation E2f/Dp inhibits increases in oxidative metabolism involved in normal differentiation Increased mitochondrial biogenesis rescues differentiation of E2f/Dp-active cells
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Affiliation(s)
- Diego Sainz de la Maza
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Silvana Hof-Michel
- Department of Developmental Genetics, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Lee Phillimore
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Christian Bökel
- Department of Developmental Genetics, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany.
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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12
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Xie B, Tan G, Ren J, Lu W, Pervaz S, Ren X, Otoo AA, Tang J, Li F, Wang Y, Wang M. RB1 Is an Immune-Related Prognostic Biomarker for Ovarian Cancer. Front Oncol 2022; 12:830908. [PMID: 35299734 PMCID: PMC8920998 DOI: 10.3389/fonc.2022.830908] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/03/2022] [Indexed: 01/06/2023] Open
Abstract
Background Ovarian cancer (OC) is one of the most lethal gynecologic malignancies and a leading cause of death in the world. Thus, this necessitates identification of prognostic biomarkers which will be helpful in its treatment. Methods The gene expression profiles from The Cancer Genome Atlas (TCGA) and GSE31245 were selected as the training cohort and validation cohort, respectively. The Kaplan–Meier (KM) survival analysis was used to analyze the difference in overall survival (OS) between high and low RB transcriptional corepressor 1 (RB1) expression groups. To confirm whether RB1 was an independent risk factor for OC, we constructed a multivariate Cox regression model. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were conducted to identify the functions of differentially expressed genes (DEGs). The associations of RB1 with immune infiltration and immune checkpoints were studied by the Tumor Immune Estimation Resource (TIMER 2.0) and the Gene Expression Profiling Interactive Analysis (GEPIA). The immunohistochemistry (IHC) was performed to compare the expression level of RB1 in normal tissues and tumor samples, and to predict the prognosis of OC. Results The KM survival curve of the TCGA indicated that the OS in the high-risk group was lower than that in the low-risk group (HR = 1.61, 95% CI: 1.28-2.02, P = 3×10-5), which was validated in GSE31245 (HR = 4.08, 95% CI: 1.21–13.74, P = 0.01) and IHC. Multivariate Cox regression analysis revealed that RB1 was an independent prognostic biomarker (HR = 1.66, 95% CI: 1.31-2.10, P = 2.02×10-5). Enrichment analysis suggested that the DEGs were mainly involved in cell cycle, DNA replication, and mitochondrial transition. The infiltration levels of fibroblast, neutrophil, monocyte and macrophage were positively correlated with RB1. Furthermore, RB1 was associated with immune checkpoint molecules (CTLA4, LAG3, and CD274). The IHC staining revealed higher expression of RB1 in tumor tissues as compared to that in normal tissues (P = 0.019). Overexpression of RB1 was associated with poor prognosis of OC (P = 0.01). Conclusion These findings suggest that RB1 was a novel and immune-related prognostic biomarker for OC, which may be a promising target for OC treatment.
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Affiliation(s)
- Biao Xie
- Department of Biostatistics, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Guangqing Tan
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Jingyi Ren
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Weiyu Lu
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Sadaf Pervaz
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Xinyi Ren
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Antonia Adwoa Otoo
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Jing Tang
- Department of Bioinformatics, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Fangfang Li
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Meijiao Wang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China.,Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
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13
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Krishnan B, Yasuhara T, Rumde P, Stanzione M, Lu C, Lee H, Lawrence MS, Zou L, Nieman LT, Sanidas I, Dyson NJ. Active RB causes visible changes in nuclear organization. J Cell Biol 2022; 221:212957. [PMID: 35019938 PMCID: PMC8759594 DOI: 10.1083/jcb.202102144] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 10/21/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
RB restricts G1/S progression by inhibiting E2F. Here, we show that sustained expression of active RB, and prolonged G1 arrest, causes visible changes in chromosome architecture that are not directly associated with E2F inhibition. Using FISH probes against two euchromatin RB-associated regions, two heterochromatin domains that lack RB-bound loci, and two whole-chromosome probes, we found that constitutively active RB (ΔCDK-RB) promoted a more diffuse, dispersed, and scattered chromatin organization. These changes were RB dependent, were driven by specific isoforms of monophosphorylated RB, and required known RB-associated activities. ΔCDK-RB altered physical interactions between RB-bound genomic loci, but the RB-induced changes in chromosome architecture were unaffected by dominant-negative DP1. The RB-induced changes appeared to be widespread and influenced chromosome localization within nuclei. Gene expression profiles revealed that the dispersion phenotype was associated with an increased autophagy response. We infer that, after cell cycle arrest, RB acts through noncanonical mechanisms to significantly change nuclear organization, and this reorganization correlates with transitions in cellular state.
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Affiliation(s)
- Badri Krishnan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Takaaki Yasuhara
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Purva Rumde
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Hanjun Lee
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Linda T Nieman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Ioannis Sanidas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
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14
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Coronel L, Häckes D, Schwab K, Riege K, Hoffmann S, Fischer M. p53-mediated AKT and mTOR inhibition requires RFX7 and DDIT4 and depends on nutrient abundance. Oncogene 2022; 41:1063-1069. [PMID: 34907345 PMCID: PMC8837532 DOI: 10.1038/s41388-021-02147-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/08/2022]
Abstract
In recent years the tumor suppressor p53 has been increasingly recognized as a potent regulator of the cell metabolism and for its ability to inhibit the critical pro-survival kinases AKT and mTOR. The mechanisms through which p53 controls AKT and mTOR, however, are largely unclear. Here, we demonstrate that p53 activates the metabolic regulator DDIT4 indirectly through the regulatory factor X 7 (RFX7). We provide evidence that DDIT4 is required for p53 to inhibit mTOR complex 2 (mTORC2)-dependent AKT activation. Most strikingly, we also find that the DDIT4 regulator RFX7 is required for p53-mediated inhibition of mTORC1 and AKT. Our results suggest that AMPK activation plays no role and p53-mediated AKT inhibition is not critical for p53-mediated mTORC1 inhibition. Moreover, using recently developed physiological cell culture media we uncover that basal p53 and RFX7 activity can play a critical role in restricting mTORC1 activity under physiological nutrient conditions, and we propose a nutrient-dependent model for p53-RFX7-mediated mTORC1 inhibition. These results establish RFX7 and its downstream target DDIT4 as essential effectors in metabolic control elicited by p53.
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Affiliation(s)
- Luis Coronel
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - David Häckes
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Katjana Schwab
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
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15
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Merle DA, Provenzano F, Jarboui MA, Kilger E, Clark SJ, Deleidi M, Armento A, Ueffing M. mTOR Inhibition via Rapamycin Treatment Partially Reverts the Deficit in Energy Metabolism Caused by FH Loss in RPE Cells. Antioxidants (Basel) 2021; 10:1944. [PMID: 34943047 PMCID: PMC8750186 DOI: 10.3390/antiox10121944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex degenerative disease of the retina with multiple risk-modifying factors, including aging, genetics, and lifestyle choices. The combination of these factors leads to oxidative stress, inflammation, and metabolic failure in the retinal pigment epithelium (RPE) with subsequent degeneration of photoreceptors in the retina. The alternative complement pathway is tightly linked to AMD. In particular, the genetic variant in the complement factor H gene (CFH), which leads to the Y402H polymorphism in the factor H protein (FH), confers the second highest risk for the development and progression of AMD. Although the association between the FH Y402H variant and increased complement system activation is known, recent studies have uncovered novel FH functions not tied to this activity and highlighted functional relevance for intracellular FH. In our previous studies, we show that loss of CFH expression in RPE cells causes profound disturbances in cellular metabolism, increases the vulnerability towards oxidative stress, and modulates the activation of pro-inflammatory signaling pathways, most importantly the NF-kB pathway. Here, we silenced CFH in hTERT-RPE1 cells to investigate the mechanism by which intracellular FH regulates RPE cell homeostasis. We found that silencing of CFH results in hyperactivation of mTOR signaling along with decreased mitochondrial respiration and that mTOR inhibition via rapamycin can partially rescue these metabolic defects. To obtain mechanistic insight into the function of intracellular FH in hTERT-RPE1 cells, we analyzed the interactome of FH via immunoprecipitation followed by mass spectrometry-based analysis. We found that FH interacts with essential components of the ubiquitin-proteasomal pathway (UPS) as well as with factors associated with RB1/E2F signalling in a complement-pathway independent manner. Moreover, we found that FH silencing affects mRNA levels of the E3 Ubiquitin-Protein Ligase Parkin and PTEN induced putative kinase (Pink1), both of which are associated with UPS. As inhibition of mTORC1 was previously shown to result in increased overall protein degradation via UPS and as FH mRNA and protein levels were shown to be affected by inhibition of UPS, our data stress a potential regulatory link between endogenous FH activity and the UPS.
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Affiliation(s)
- David A. Merle
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; (D.A.M.); (M.A.J.); (E.K.); (S.J.C.)
- Department of Ophthalmology, Medical University of Graz, 8036 Graz, Austria
| | - Francesca Provenzano
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany; (F.P.); (M.D.)
| | - Mohamed Ali Jarboui
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; (D.A.M.); (M.A.J.); (E.K.); (S.J.C.)
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Eberhard-Karls University of Tuebingen, 72076 Tübingen, Germany
| | - Ellen Kilger
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; (D.A.M.); (M.A.J.); (E.K.); (S.J.C.)
| | - Simon J. Clark
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; (D.A.M.); (M.A.J.); (E.K.); (S.J.C.)
- Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Michela Deleidi
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany; (F.P.); (M.D.)
| | - Angela Armento
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; (D.A.M.); (M.A.J.); (E.K.); (S.J.C.)
| | - Marius Ueffing
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; (D.A.M.); (M.A.J.); (E.K.); (S.J.C.)
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany; (F.P.); (M.D.)
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16
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p107 mediated mitochondrial function controls muscle stem cell proliferative fates. Nat Commun 2021; 12:5977. [PMID: 34645816 PMCID: PMC8514468 DOI: 10.1038/s41467-021-26176-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
Muscle diseases and aging are associated with impaired myogenic stem cell self-renewal and fewer proliferating progenitors (MPs). Importantly, distinct metabolic states induced by glycolysis or oxidative phosphorylation have been connected to MP proliferation and differentiation. However, how these energy-provisioning mechanisms cooperate remain obscure. Herein, we describe a mechanism by which mitochondrial-localized transcriptional co-repressor p107 regulates MP proliferation. We show p107 directly interacts with the mitochondrial DNA, repressing mitochondrial-encoded gene transcription. This reduces ATP production by limiting electron transport chain complex formation. ATP output, controlled by the mitochondrial function of p107, is directly associated with the cell cycle rate. Sirt1 activity, dependent on the cytoplasmic glycolysis product NAD+, directly interacts with p107, impeding its mitochondrial localization. The metabolic control of MP proliferation, driven by p107 mitochondrial function, establishes a cell cycle paradigm that might extend to other dividing cell types. The connection between cell cycle, metabolic state and mitochondrial activity is unclear. Here, the authors show that p107 represses mitochondrial transcription and ATP output in response to glycolytic byproducts, causing metabolic control of the cell cycle rate in myogenic progenitors.
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17
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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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18
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Kaulich M, Link VM, Lapek JD, Lee YJ, Glass CK, Gonzalez DJ, Dowdy SF. A Cdk4/6-dependent phosphorylation gradient regulates the early to late G1 phase transition. Sci Rep 2021; 11:14736. [PMID: 34282211 PMCID: PMC8290049 DOI: 10.1038/s41598-021-94200-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/30/2021] [Indexed: 11/29/2022] Open
Abstract
During early G1 phase, Rb is exclusively mono-phosphorylated by cyclin D:Cdk4/6, generating 14 different isoforms with specific binding patterns to E2Fs and other cellular protein targets. While mono-phosphorylated Rb is dispensable for early G1 phase progression, interfering with cyclin D:Cdk4/6 kinase activity prevents G1 phase progression, questioning the role of cyclin D:Cdk4/6 in Rb inactivation. To dissect the molecular functions of cyclin D:Cdk4/6 during cell cycle entry, we generated a single cell reporter for Cdk2 activation, RB inactivation and cell cycle entry by CRISPR/Cas9 tagging endogenous p27 with mCherry. Through single cell tracing of Cdk4i cells, we identified a time-sensitive early G1 phase specific Cdk4/6-dependent phosphorylation gradient that regulates cell cycle entry timing and resides between serum-sensing and cyclin E:Cdk2 activation. To reveal the substrate identity of the Cdk4/6 phosphorylation gradient, we performed whole proteomic and phospho-proteomic mass spectrometry, and identified 147 proteins and 82 phospho-peptides that significantly changed due to Cdk4 inhibition in early G1 phase. In summary, we identified novel (non-Rb) cyclin D:Cdk4/6 substrates that connects early G1 phase functions with cyclin E:Cdk2 activation and Rb inactivation by hyper-phosphorylation.
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Affiliation(s)
- Manuel Kaulich
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. .,Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany.
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John D Lapek
- Department of Pharmacology, University of California San Diego, La Jolla, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yeon J Lee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California San Diego, La Jolla, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Steven F Dowdy
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
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19
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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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20
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O'Connor MJ, Thakar T, Nicolae CM, Moldovan GL. PARP14 regulates cyclin D1 expression to promote cell-cycle progression. Oncogene 2021; 40:4872-4883. [PMID: 34158578 PMCID: PMC8384455 DOI: 10.1038/s41388-021-01881-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022]
Abstract
Cyclin D1 is an essential regulator of the G1-S cell-cycle transition and is overexpressed in many cancers. Expression of cyclin D1 is under tight cellular regulation that is controlled by many signaling pathways. Here we report that PARP14, a member of the poly(ADP-ribose) polymerase (PARP) family, is a regulator of cyclin D1 expression. Depletion of PARP14 leads to decreased cyclin D1 protein levels. In cells with a functional retinoblastoma (RB) protein pathway, this results in G1 cell-cycle arrest and reduced proliferation. Mechanistically, we found that PARP14 controls cyclin D1 mRNA levels. Using luciferase assays, we show that PARP14 specifically regulates cyclin D1 3'UTR mRNA stability. Finally, we also provide evidence that G1 arrest in PARP14-depleted cells is dependent on an intact p53-p21 pathway. Our work uncovers a new role for PARP14 in promoting cell-cycle progression through both cyclin D1 and the p53 pathway.
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Affiliation(s)
- Michael J O'Connor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
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21
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Inoue Y, Nikolic A, Farnsworth D, Shi R, Johnson FD, Liu A, Ladanyi M, Somwar R, Gallo M, Lockwood WW. Extracellular signal-regulated kinase mediates chromatin rewiring and lineage transformation in lung cancer. eLife 2021; 10:66524. [PMID: 34121659 PMCID: PMC8337080 DOI: 10.7554/elife.66524] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022] Open
Abstract
Lineage transformation between lung cancer subtypes is a poorly understood phenomenon associated with resistance to treatment and poor patient outcomes. Here, we aimed to model this transition to define underlying biological mechanisms and identify potential avenues for therapeutic intervention. Small cell lung cancer (SCLC) is neuroendocrine in identity and, in contrast to non-SCLC (NSCLC), rarely contains mutations that drive the MAPK pathway. Likewise, NSCLCs that transform to SCLC concomitantly with development of therapy resistance downregulate MAPK signaling, suggesting an inverse relationship between pathway activation and lineage state. To test this, we activated MAPK in SCLC through conditional expression of mutant KRAS or EGFR, which revealed suppression of the neuroendocrine differentiation program via ERK. We found that ERK induces the expression of ETS factors that mediate transformation into a NSCLC-like state. ATAC-seq demonstrated ERK-driven changes in chromatin accessibility at putative regulatory regions and global chromatin rewiring at neuroendocrine and ETS transcriptional targets. Further, ERK-mediated induction of ETS factors as well as suppression of neuroendocrine differentiation were dependent on histone acetyltransferase activities of CBP/p300. Overall, we describe how the ERK-CBP/p300-ETS axis promotes a lineage shift between neuroendocrine and non-neuroendocrine lung cancer phenotypes and provide rationale for the disruption of this program during transformation-driven resistance to targeted therapy.
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Affiliation(s)
- Yusuke Inoue
- Department of Integrative Oncology, BC Cancer Agency, Columbia, Canada
| | - Ana Nikolic
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Dylan Farnsworth
- Department of Integrative Oncology, BC Cancer Agency, Columbia, Canada
| | - Rocky Shi
- Department of Integrative Oncology, BC Cancer Agency, Columbia, Canada
| | - Fraser D Johnson
- Department of Integrative Oncology, BC Cancer Agency, Columbia, Canada
| | - Alvin Liu
- Department of Integrative Oncology, BC Cancer Agency, Columbia, Canada
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Romel Somwar
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Marco Gallo
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Agency, Columbia, Canada.,Department of Pathology & Laboratory Medicine, University of British Columbia, Columbia, Canada
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22
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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: 36] [Impact Index Per Article: 12.0] [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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23
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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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24
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Chinopoulos C. From Glucose to Lactate and Transiting Intermediates Through Mitochondria, Bypassing Pyruvate Kinase: Considerations for Cells Exhibiting Dimeric PKM2 or Otherwise Inhibited Kinase Activity. Front Physiol 2020; 11:543564. [PMID: 33335484 PMCID: PMC7736077 DOI: 10.3389/fphys.2020.543564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
A metabolic hallmark of many cancers is the increase in glucose consumption coupled to excessive lactate production. Mindful that L-lactate originates only from pyruvate, the question arises as to how can this be sustained in those tissues where pyruvate kinase activity is reduced due to dimerization of PKM2 isoform or inhibited by oxidative/nitrosative stress, posttranslational modifications or mutations, all widely reported findings in the very same cells. Hereby 17 pathways connecting glucose to lactate bypassing pyruvate kinase are reviewed, some of which transit through the mitochondrial matrix. An additional 69 converging pathways leading to pyruvate and lactate, but not commencing from glucose, are also examined. The minor production of pyruvate and lactate by glutaminolysis is scrutinized separately. The present review aims to highlight the ways through which L-lactate can still be produced from pyruvate using carbon atoms originating from glucose or other substrates in cells with kinetically impaired pyruvate kinase and underscore the importance of mitochondria in cancer metabolism irrespective of oxidative phosphorylation.
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25
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Abstract
ATP is required for mammalian cells to remain viable and to perform genetically programmed functions. Maintenance of the ΔG′ATP hydrolysis of −56 kJ/mole is the endpoint of both genetic and metabolic processes required for life. Various anomalies in mitochondrial structure and function prevent maximal ATP synthesis through OxPhos in cancer cells. Little ATP synthesis would occur through glycolysis in cancer cells that express the dimeric form of pyruvate kinase M2. Mitochondrial substrate level phosphorylation (mSLP) in the glutamine-driven glutaminolysis pathway, substantiated by the succinate-CoA ligase reaction in the TCA cycle, can partially compensate for reduced ATP synthesis through both OxPhos and glycolysis. A protracted insufficiency of OxPhos coupled with elevated glycolysis and an auxiliary, fully operational mSLP, would cause a cell to enter its default state of unbridled proliferation with consequent dedifferentiation and apoptotic resistance, i.e., cancer. The simultaneous restriction of glucose and glutamine offers a therapeutic strategy for managing cancer.
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Affiliation(s)
- Thomas N Seyfried
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | - Gabriel Arismendi-Morillo
- Electron Microscopy Laboratory, Biological Researches Institute, Faculty of Medicine, University of Zulia, Maracaibo, Venezuela
| | - Purna Mukherjee
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | - Christos Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary
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26
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Venkatesh S, Baljinnyam E, Tong M, Kashihara T, Yan L, Liu T, Li H, Xie LH, Nakamura M, Oka SI, Suzuki CK, Fraidenraich D, Sadoshima J. Proteomic analysis of mitochondrial biogenesis in cardiomyocytes differentiated from human induced pluripotent stem cells. Am J Physiol Regul Integr Comp Physiol 2020; 320:R547-R562. [PMID: 33112656 DOI: 10.1152/ajpregu.00207.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondria play key roles in the differentiation and maturation of human cardiomyocytes (CMs). As human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) hold potential in the treatment of heart diseases, we sought to identify key mitochondrial pathways and regulators, which may provide targets for improving cardiac differentiation and maturation. Proteomic analysis was performed on enriched mitochondrial protein extracts isolated from hiPSC-CMs differentiated from dermal fibroblasts (dFCM) and cardiac fibroblasts (cFCM) at time points between 12 and 115 days of differentiation, and from adult and neonatal mouse hearts. Mitochondrial proteins with a twofold change at time points up to 120 days relative to 12 days were subjected to ingenuity pathway analysis (IPA). The highest upregulation was in metabolic pathways for fatty acid oxidation (FAO), the tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and branched chain amino acid (BCAA) degradation. The top upstream regulators predicted to be activated were peroxisome proliferator-activated receptor γ coactivator 1 α (PGC1-α), the insulin receptor (IR), and the retinoblastoma protein (Rb1) transcriptional repressor. IPA and immunoblotting showed upregulation of the mitochondrial LonP1 protease-a regulator of mitochondrial proteostasis, energetics, and metabolism. LonP1 knockdown increased FAO in neonatal rat ventricular cardiomyocytes (nRVMs). Our results support the notion that LonP1 upregulation negatively regulates FAO in cardiomyocytes to calibrate the flux between glucose and fatty acid oxidation. We discuss potential mechanisms by which IR, Rb1, and LonP1 regulate the metabolic shift from glycolysis to OXPHOS and FAO. These newly identified factors and pathways may help in optimizing the maturation of iPSC-CMs.
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Affiliation(s)
- Sundararajan Venkatesh
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Erdene Baljinnyam
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Mingming Tong
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Toshihide Kashihara
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Lin Yan
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Tong Liu
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Hong Li
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Lai-Hua Xie
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Michinari Nakamura
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Shin-Ichi Oka
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Carolyn K Suzuki
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Diego Fraidenraich
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
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27
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Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion. Oncogene 2020; 39:5690-5707. [PMID: 32694611 DOI: 10.1038/s41388-020-1381-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
RB1 gene is often homozygously deleted or mutated in prostate adenocarcinomas following acquirement of castration resistance and/or metastatic ability. We found that SUCLA2 gene is frequently involved in the deletion of the RB1 gene region in advanced prostate cancer. SUCLA2 constitutes the β-subunit of succinate CoA ligase heterodimer that reversibly converts succinyl CoA into succinate. We sought the possibility that deletion of SUCLA2 gives rise to a metabolic vulnerability that could be targeted therapeutically. We found a significant metabolic shift in SUCLA2-deleted prostate cancer cells, including lower mitochondrial respiratory activity. By screening a number of libraries for compounds that induce cell death selectively in SUCLA2-deficient prostate cancer cells, we identified thymoquinone (2-isopropyl-5-methylbenzo-1,4-quinone) and PMA (phorbol-12-myristate-13-acetate) from a natural compound library. These findings indicate that the metabolic vulnerability in SUCLA2-deficient prostate cancer cells is pharmacologically targetable.
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28
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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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29
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Seyfried TN, Mukherjee P, Iyikesici MS, Slocum A, Kalamian M, Spinosa JP, Chinopoulos C. Consideration of Ketogenic Metabolic Therapy as a Complementary or Alternative Approach for Managing Breast Cancer. Front Nutr 2020; 7:21. [PMID: 32219096 PMCID: PMC7078107 DOI: 10.3389/fnut.2020.00021] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer remains as a significant cause of morbidity and mortality in women. Ultrastructural and biochemical evidence from breast biopsy tissue and cancer cells shows mitochondrial abnormalities that are incompatible with energy production through oxidative phosphorylation (OxPhos). Consequently, breast cancer, like most cancers, will become more reliant on substrate level phosphorylation (fermentation) than on oxidative phosphorylation (OxPhos) for growth consistent with the mitochondrial metabolic theory of cancer. Glucose and glutamine are the prime fermentable fuels that underlie therapy resistance and drive breast cancer growth through substrate level phosphorylation (SLP) in both the cytoplasm (Warburg effect) and the mitochondria (Q-effect), respectively. Emerging evidence indicates that ketogenic metabolic therapy (KMT) can reduce glucose availability to tumor cells while simultaneously elevating ketone bodies, a non-fermentable metabolic fuel. It is suggested that KMT would be most effective when used together with glutamine targeting. Information is reviewed for suggesting how KMT could reduce systemic inflammation and target tumor cells without causing damage to normal cells. Implementation of KMT in the clinic could improve progression free and overall survival for patients with breast cancer.
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Affiliation(s)
| | - Purna Mukherjee
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Mehmet S. Iyikesici
- Medical Oncology, Kemerburgaz University Bahcelievler Medical Park Hospital, Istanbul, Turkey
| | - Abdul Slocum
- Medical Oncology, Chemo Thermia Oncology Center, Istanbul, Turkey
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30
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Maugein A, Diedisheim M, Bailly K, Scharfmann R, Albagli O. The RB gene family controls the maturation state of the EndoC-βH2 human pancreatic β-cells. Differentiation 2020; 113:1-9. [PMID: 32120156 DOI: 10.1016/j.diff.2020.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 01/18/2023]
Abstract
The functional maturation of human pancreatic β-cells remains poorly understood. EndoC-βH2 is a human β-cell line with a reversible immortalized phenotype. Removal of the two oncogenes, SV40LT and hTERT introduced for its propagation, stops proliferation, triggers cell size increase and senescence, promotes mitochondrial activity and amplifies several β-cell traits and functions. Overall, these events recapitulate several aspects of functional β-cell maturation. We report here that selective depletion of SV40LT, but not of hTERT, is sufficient to revert EndoC-βH2 immortalization. SV40LT inhibits the activity of the RB family members and of P53. In EndoC-βH2 cells, the knock-down of RB itself, and, to a lesser extent, of its relative P130, precludes most events triggered by SV40LT depletion. In contrast, the knock-down of P53 does not prevent reversion of immortalization. Thus, an increase in RB and P130 activity, but not in P53 activity, is required for functional maturation of EndoC-βH2 cells upon SV40LT-depletion. In addition, RB and/or P130 depletion in SV40LT-expressing EndoC-βH2 cells decreases cell size, stimulates proliferation, and decreases the expression of key β-cell genes. Thus, despite SV40LT expression, EndoC-βH2 cells have a residual RB activity, which when suppressed reverts them to a more immature phenotype. These results show that the expression and activity levels of RB family members, especially RB itself, regulate the maturation state of EndoC-βH2 cells.
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Affiliation(s)
- Alicia Maugein
- Paris University, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 75014, Paris, France
| | - Marc Diedisheim
- Assistance Publique - Hôpitaux de Paris, Diabetology Department, Paris University, Cochin Hospital, and INSERM, UMRS 1138, Centre de Recherche des Cordeliers, Paris University, 75006, Paris, France
| | - Karine Bailly
- Paris University, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 75014, Paris, France
| | - Raphaël Scharfmann
- Paris University, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 75014, Paris, France
| | - Olivier Albagli
- Paris University, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 75014, Paris, France.
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31
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Organ-level protein networks as a reference for the host effects of the microbiome. Genome Res 2020; 30:276-286. [PMID: 31992612 PMCID: PMC7050531 DOI: 10.1101/gr.256875.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 02/07/2023]
Abstract
Connections between the microbiome and health are rapidly emerging in a wide range of diseases. However, a detailed mechanistic understanding of how different microbial communities are influencing their hosts is often lacking. One method researchers have used to understand these effects are germ-free (GF) mouse models. Differences found within the organ systems of these model organisms may highlight generalizable mechanisms that microbiome dysbioses have throughout the host. Here, we applied multiplexed, quantitative proteomics on the brains, spleens, hearts, small intestines, and colons of conventionally raised and GF mice, identifying associations to colonization state in over 7000 proteins. Highly ranked associations were constructed into protein–protein interaction networks and visualized onto an interactive 3D mouse model for user-guided exploration. These results act as a resource for microbiome researchers hoping to identify host effects of microbiome colonization on a given organ of interest. Our results include validation of previously reported effects in xenobiotic metabolism, the innate immune system, and glutamate-associated proteins while simultaneously providing organism-wide context. We highlight organism-wide differences in mitochondrial proteins including consistent increases in NNT, a mitochondrial protein with essential roles in influencing levels of NADH and NADPH, in all analyzed organs of conventional mice. Our networks also reveal new associations for further exploration, including protease responses in the spleen, high-density lipoproteins in the heart, and glutamatergic signaling in the brain. In total, our study provides a resource for microbiome researchers through detailed tables and visualization of the protein-level effects of microbial colonization on several organ systems.
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Loss of Rb1 Enhances Glycolytic Metabolism in Kras-Driven Lung Tumors In Vivo. Cancers (Basel) 2020; 12:cancers12010237. [PMID: 31963621 PMCID: PMC7016860 DOI: 10.3390/cancers12010237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/30/2019] [Accepted: 01/14/2020] [Indexed: 01/31/2023] Open
Abstract
Dysregulated metabolism is a hallmark of cancer cells and is driven in part by specific genetic alterations in various oncogenes or tumor suppressors. The retinoblastoma protein (pRb) is a tumor suppressor that canonically regulates cell cycle progression; however, recent studies have highlighted a functional role for pRb in controlling cellular metabolism. Here, we report that loss of the gene encoding pRb (Rb1) in a transgenic mutant Kras-driven model of lung cancer results in metabolic reprogramming. Our tracer studies using bolus dosing of [U-13C]-glucose revealed an increase in glucose carbon incorporation into select glycolytic intermediates. Consistent with this result, Rb1-depleted tumors exhibited increased expression of key glycolytic enzymes. Interestingly, loss of Rb1 did not alter mitochondrial pyruvate oxidation compared to lung tumors with intact Rb1. Additional tracer studies using [U-13C,15N]-glutamine and [U-13C]-lactate demonstrated that loss of Rb1 did not alter glutaminolysis or utilization of circulating lactate within the tricarboxylic acid cycle (TCA) in vivo. Taken together, these data suggest that the loss of Rb1 promotes a glycolytic phenotype, while not altering pyruvate oxidative metabolism or glutamine anaplerosis in Kras-driven lung tumors.
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Delos Santos K, Kim M, Yergeau C, Jean S, Moon NS. Pleiotropic role of Drosophila phosphoribosyl pyrophosphate synthetase in autophagy and lysosome homeostasis. PLoS Genet 2019; 15:e1008376. [PMID: 31487280 PMCID: PMC6748441 DOI: 10.1371/journal.pgen.1008376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/17/2019] [Accepted: 08/17/2019] [Indexed: 01/07/2023] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRPS) is a rate-limiting enzyme whose function is important for the biosynthesis of purines, pyrimidines, and pyridines. Importantly, while missense mutations of PRPS1 have been identified in neurological disorders such as Arts syndrome, how they contribute to neuropathogenesis is still unclear. We identified the Drosophila ortholog of PRPS (dPRPS) as a direct target of RB/E2F in Drosophila, a vital cell cycle regulator, and engineered dPRPS alleles carrying patient-derived mutations. Interestingly, while they are able to develop normally, dPRPS mutant flies have a shortened lifespan and locomotive defects, common phenotypes associated with neurodegeneration. Careful analysis of the fat body revealed that patient-derived PRPS mutations result in profound defects in lipolysis, macroautophagy, and lysosome function. Significantly, we show evidence that the nervous system of dPRPS mutant flies is affected by these defects. Overall, we uncovered an unexpected link between nucleotide metabolism and autophagy/lysosome function, providing a possible mechanism by which PRPS-dysfunction contributes to neurological disorders.
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Affiliation(s)
- Keemo Delos Santos
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Minhee Kim
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Christine Yergeau
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Département d’Anatomie et de Biologie Cellulaire, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nam-Sung Moon
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
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RB1 Deletion in Retinoblastoma Protein Pathway-Disrupted Cells Results in DNA Damage and Cancer Progression. Mol Cell Biol 2019; 39:MCB.00105-19. [PMID: 31138663 DOI: 10.1128/mcb.00105-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
Proliferative control in cancer cells is frequently disrupted by mutations in the retinoblastoma protein (RB) pathway. Intriguingly, RB1 mutations can arise late in tumorigenesis in cancer cells whose RB pathway is already compromised by another mutation. In this study, we present evidence for increased DNA damage and instability in cancer cells with RB pathway defects when RB1 mutations are induced. We generated isogenic RB1 mutant genotypes with CRISPR/Cas9 in a number of cell lines. Cells with even one mutant copy of RB1 have increased basal levels of DNA damage and increased mitotic errors. Elevated levels of reactive oxygen species as well as impaired homologous recombination repair underlie this DNA damage. When xenografted into immunocompromised mice, RB1 mutant cells exhibit an elevated propensity to seed new tumors in recipient lungs. This study offers evidence that late-arising RB1 mutations can facilitate genome instability and cancer progression that are beyond the preexisting proliferative control deficit.
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Drp1 and RB interaction to mediate mitochondria-dependent necroptosis induced by cadmium in hepatocytes. Cell Death Dis 2019; 10:523. [PMID: 31285421 PMCID: PMC6614419 DOI: 10.1038/s41419-019-1730-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial quality control (MQC) is implicated in cell death induced by heavy metal pollutants. Dynamin-related protein 1 (Drp1) regulates mitochondrial fission, which is an important part of MQC. Retinoblastoma (RB) protein can regulate MQC in a transcription-independent manner. Necroptosis plays a critical role in hepatic pathologies such as inflammatory, infectious, and xenobiotics-induced injury and diseases. We aimed to explore the role and mechanism of Drp1 interaction with RB in hepatocyte's necroptosis caused by cadmium (Cd). CdCl2 was employed to expose to Institute of Cancer Research (ICR) mice and human hepatic L02 cells. CdCl2 exposure induced necroptosis and hepatic injury both in vivo and in vitro. Moreover, Drp1 and RB protein were up-regulated and translocated to mitochondria in CdCl2-exposed hepatocytes. Inhibition of Drp1 with siRNA (siDNM1L) or inhibitors not only suppressed the RB expression and its mitochondrial translocation, but also alleviated MQC disorder, necroptosis, and hepatotoxicity caused by CdCl2. Moreover, blocking Drp1 with metformin rescued necroptosis and hepatic injury triggered by CdCl2. RB was proved to directly interact with Drp1 at mitochondria to form a complex which then bound to receptor interaction protein kinase (RIPK3) and enhanced the formation of necrosome after CdCl2 exposure. In summary, we found a new molecular mechanism of regulated cell death that Drp1 interacted with RB and promoted them mitochondrial translocation to mediate necroptosis and hepatic injury in hepatocytes induced by Cd-exposure. The mitochondrial Drp1-RB axis would be a novel target for the protection cells from xenobiotics triggering hepatic injury and diseases involved in necroptosis.
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What if? Mouse proteomics after gene inactivation. J Proteomics 2019; 199:102-122. [DOI: 10.1016/j.jprot.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022]
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Seyfried TN, Shelton L, Arismendi-Morillo G, Kalamian M, Elsakka A, Maroon J, Mukherjee P. Provocative Question: Should Ketogenic Metabolic Therapy Become the Standard of Care for Glioblastoma? Neurochem Res 2019; 44:2392-2404. [PMID: 31025151 DOI: 10.1007/s11064-019-02795-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022]
Abstract
No major advances have been made in improving overall survival for glioblastoma (GBM) in almost 100 years. The current standard of care (SOC) for GBM involves immediate surgical resection followed by radiotherapy with concomitant temozolomide chemotherapy. Corticosteroid (dexamethasone) is often prescribed to GBM patients to reduce tumor edema and inflammation. The SOC disrupts the glutamate-glutamine cycle thus increasing availability of glucose and glutamine in the tumor microenvironment. Glucose and glutamine are the prime fermentable fuels that underlie therapy resistance and drive GBM growth through substrate level phosphorylation in the cytoplasm and the mitochondria, respectively. Emerging evidence indicates that ketogenic metabolic therapy (KMT) can reduce glucose availability while elevating ketone bodies that are neuroprotective and non-fermentable. Information is presented from preclinical and case report studies showing how KMT could target tumor cells without causing neurochemical damage thus improving progression free and overall survival for patients with GBM.
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Affiliation(s)
- Thomas N Seyfried
- Biology Department, Boston College, 140 Commonwealth Ave, Chestnut Hill, MA, 02467, USA.
| | - Laura Shelton
- Human Metabolome Technologies America, 24 Denby Rd., Boston, MA, 02134, USA
| | - Gabriel Arismendi-Morillo
- Instituto de Investigaciones Biológicas, Facultad de Medicina, Universidad del Zulia, Maracaibo, 526, Venezuela
| | | | - Ahmed Elsakka
- Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Joseph Maroon
- Department of Neurosurgery, University of Pittsburgh Medical Center, Suite 5C, 200 Lothrop St., Pittsburgh, PA, USA
| | - Purna Mukherjee
- Biology Department, Boston College, 140 Commonwealth Ave, Chestnut Hill, MA, 02467, USA
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Rajasekaran S, Nagarajha Selvan LD, Dotts K, Kumar R, Rishi P, Khetan V, Bisht M, Sivaraman K, Krishnakumar S, Sahoo D, Campbell MJ, Elchuri SV, Miles WO. Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors. Front Oncol 2019; 9:221. [PMID: 31058073 PMCID: PMC6477087 DOI: 10.3389/fonc.2019.00221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
Retinoblastoma is a rare pediatric tumor of the retina, caused by the homozygous loss of the Retinoblastoma 1 (RB1) tumor suppressor gene. Previous microarray studies have identified changes in the expression profiles of coding genes; however, our understanding of how non-coding genes change in this tumor is absent. This is an important area of research, as in many adult malignancies, non-coding genes including LNC-RNAs are used as biomarkers to predict outcome and/or relapse. To establish a complete and in-depth RNA profile, of both coding and non-coding genes, in Retinoblastoma tumors, we conducted RNA-seq from a cohort of tumors and normal retina controls. This analysis identified widespread transcriptional changes in the levels of both coding and non-coding genes. Unexpectedly, we also found rare RNA fusion products resulting from genomic alterations, specific to Retinoblastoma tumor samples. We then determined whether these gene expression changes, of both coding and non-coding genes, were also found in a completely independent Retinoblastoma cohort. Using our dataset, we then profiled the potential effects of deregulated LNC-RNAs on the expression of neighboring genes, the entire genome, and on mRNAs that contain a putative area of homology. This analysis showed that most deregulated LNC-RNAs do not act locally to change the transcriptional environment, but potentially function to modulate genes at distant sites. From this analysis, we selected a strongly down-regulated LNC-RNA in Retinoblastoma, DRAIC, and found that restoring DRAIC RNA levels significantly slowed the growth of the Y79 Retinoblastoma cell line. Collectively, our work has generated the first non-coding RNA profile of Retinoblastoma tumors and has found that these tumors show widespread transcriptional deregulation.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | | | - Kathleen Dotts
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Ranjith Kumar
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Madhoolika Bisht
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | | | | | - Debashis Sahoo
- Department of Pediatrics and Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Sailaja V Elchuri
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Wayne O Miles
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.,The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.,Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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Barger CJ, Branick C, Chee L, Karpf AR. Pan-Cancer Analyses Reveal Genomic Features of FOXM1 Overexpression in Cancer. Cancers (Basel) 2019; 11:cancers11020251. [PMID: 30795624 PMCID: PMC6406812 DOI: 10.3390/cancers11020251] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 01/22/2023] Open
Abstract
FOXM1 is frequently overexpressed in cancer, but this has not been studied in a comprehensive manner. We utilized genotype-tissue expression (GTEx) normal and The Cancer Genome Atlas (TCGA) tumor data to define FOXM1 expression, including its isoforms, and to determine the genetic alterations that promote FOXM1 expression in cancer. Additionally, we used human fallopian tube epithelial (FTE) cells to dissect the role of Retinoblastoma (Rb)-E2F and Cyclin E1 in FOXM1 regulation, and a novel human embryonic kidney cell (HEK293T) CRISPR FOXM1 knockout model to define isoform-specific transcriptional programs. FOXM1 expression, at the mRNA and protein level, was significantly elevated in tumors with FOXM1 amplification, p53 inactivation, and Rb-E2F deregulation. FOXM1 expression was remarkably high in testicular germ cell tumors (TGCT), high-grade serous ovarian cancer (HGSC), and basal breast cancer (BBC). FOXM1 expression in cancer was associated with genomic instability, as measured using aneuploidy signatures. FTE models confirmed a role for Rb-E2F signaling in FOXM1 regulation and in particular identified Cyclin E1 as a novel inducer of FOXM1 expression. Among the three FOXM1 isoforms, FOXM1c showed the highest expression in normal and tumor tissues and cancer cell lines. The CRISPR knockout model demonstrated that FOXM1b and FOXM1c are transcriptionally active, while FOXM1a is not. Finally, we were unable to confirm the existence of a FOXM1 auto-regulatory loop. This study provides significant and novel information regarding the frequency, causes, and consequences of elevated FOXM1 expression in human cancer.
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Affiliation(s)
- Carter J Barger
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Connor Branick
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Linda Chee
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Adam R Karpf
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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Knudsen ES, Witkiewicz AK. The transcriptome of CDK4/6 inhibition. Aging (Albany NY) 2019; 9:1859-1860. [PMID: 28860413 PMCID: PMC5611978 DOI: 10.18632/aging.101285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/28/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Erik S Knudsen
- Department of Medicine, ,, University of Arizona, Tucson, AZ 85721, USA
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Sanidas I, Morris R, Fella KA, Rumde PH, Boukhali M, Tai EC, Ting DT, Lawrence MS, Haas W, Dyson NJ. A Code of Mono-phosphorylation Modulates the Function of RB. Mol Cell 2019; 73:985-1000.e6. [PMID: 30711375 DOI: 10.1016/j.molcel.2019.01.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/26/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022]
Abstract
Hyper-phosphorylation of RB controls its interaction with E2F and inhibits its tumor suppressor properties. However, during G1 active RB can be mono-phosphorylated on any one of 14 CDK phosphorylation sites. Here, we used quantitative proteomics to profile protein complexes formed by each mono-phosphorylated RB isoform (mP-RB) and identified the associated transcriptional outputs. The results show that the 14 sites of mono-phosphorylation co-ordinate RB's interactions and confer functional specificity. All 14 mP-RBs interact with E2F/DP proteins, but they provide different shades of E2F regulation. RB mono-phosphorylation at S811, for example, alters RB transcriptional activity by promoting its association with NuRD complexes. The greatest functional differences between mP-RBs are evident beyond the cell cycle machinery. RB mono-phosphorylation at S811 or T826 stimulates the expression of oxidative phosphorylation genes, increasing cellular oxygen consumption. These results indicate that RB activation signals are integrated in a phosphorylation code that determines the diversity of RB activity.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Katerina A Fella
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Purva H Rumde
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Eric C Tai
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA.
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Pseudopodium-enriched atypical kinase 1 mediates angiogenesis by modulating GATA2-dependent VEGFR2 transcription. Cell Discov 2018; 4:26. [PMID: 29872538 PMCID: PMC5972149 DOI: 10.1038/s41421-018-0024-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
PEAK1 is a newly described tyrosine kinase and scaffold protein that transmits integrin-mediated extracellular matrix (ECM) signals to facilitate cell movement and growth. While aberrant expression of PEAK1 has been linked to cancer progression, its normal physiological role in vertebrate biology is not known. Here we provide evidence that PEAK1 plays a central role in orchestrating new vessel formation in vertebrates. Deletion of the PEAK1 gene in zebrafish, mice, and human endothelial cells (ECs) induced severe defects in new blood vessel formation due to deficiencies in EC proliferation, survival, and migration. Gene transcriptional and proteomic analyses of PEAK1-deficient ECs revealed a significant loss of vascular endothelial growth factor receptor 2 (VEGFR2) mRNA and protein expression, as well as downstream signaling to its effectors, ERK, Akt, and Src kinase. PEAK1 regulates VEGFR2 expression by binding to and increasing the protein stability of the transcription factor GATA-binding protein 2 (GATA2), which controls VEGFR2 transcription. Importantly, PEAK1-GATA2-dependent VEGFR2 expression is mediated by EC adhesion to the ECM and is required for breast cancer-induced new vessel formation in mice. Also, elevated expression of PEAK1 and VEGFR2 mRNA are highly correlated in many human cancers including breast cancer. Together, our findings reveal a novel PEAK1-GATA2-VEGFR2 signaling axis that integrates cell adhesion and growth factor cues from the extracellular environment necessary for new vessel formation during vertebrate development and cancer.
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Lapek JD, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ. Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Cell Syst 2018; 6:579-592.e4. [PMID: 29778837 PMCID: PMC7868092 DOI: 10.1016/j.cels.2018.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/30/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022]
Abstract
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues. From this analysis, an atlas of dynamically regulated proteins and pathways was constructed. Through statistical methods, we narrowed organ-specific markers of infection to 34 from the defined atlas. We show these markers are trackable in blood of infected mice, and a subset has been observed in plasma samples from GAS-infected clinical patients. This proteomics-based strategy provides insight into host defense responses, establishes potentially useful targets for therapeutic intervention, and presents biomarkers for determining affected organs during bacterial infection.
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Affiliation(s)
- John D Lapek
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ronnie H Fang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xiaoli Wei
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kirsten van de Groep
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands; Department of Intensive Care Medicine, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Araceli Perez-Lopez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Manuela Raffatellu
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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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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45
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Bhattacharya D, Ydfors M, Hughes MC, Norrbom J, Perry CGR, Scimè A. Decreased transcriptional corepressor p107 is associated with exercise-induced mitochondrial biogenesis in human skeletal muscle. Physiol Rep 2017; 5:5/5/e13155. [PMID: 28270591 PMCID: PMC5350169 DOI: 10.14814/phy2.13155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/24/2022] Open
Abstract
Increased mitochondrial content is a hallmark of exercise-induced skeletal muscle remodeling. For this process, considerable evidence underscores the involvement of transcriptional coactivators in mediating mitochondrial biogenesis. However, our knowledge regarding the role of transcriptional corepressors is lacking. In this study, we assessed the association of the transcriptional corepressor Rb family proteins, Rb and p107, with endurance exercise-induced mitochondrial adaptation in human skeletal muscle. We showed that p107, but not Rb, protein levels decrease by 3 weeks of high-intensity interval training. This is associated with significant inverse association between p107 and exercise-induced improved mitochondrial oxidative phosphorylation. Indeed, p107 showed significant reciprocal correlations with the protein contents of representative markers of mitochondrial electron transport chain complexes. These findings in human skeletal muscle suggest that attenuated transcriptional repression through p107 may be a novel mechanism by which exercise stimulates mitochondrial biogenesis following exercise.
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Affiliation(s)
- Debasmita Bhattacharya
- Stem Cell Research Group, Molecular, Cellular and Integrative Physiology, Faculty of Health York University, Toronto, Canada.,Molecular, Cellular and Integrative Physiology, Faculty of Health York University, Toronto, Canada
| | - Mia Ydfors
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Meghan C Hughes
- Molecular, Cellular and Integrative Physiology, Faculty of Health York University, Toronto, Canada
| | - Jessica Norrbom
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Christopher G R Perry
- Molecular, Cellular and Integrative Physiology, Faculty of Health York University, Toronto, Canada
| | - Anthony Scimè
- Stem Cell Research Group, Molecular, Cellular and Integrative Physiology, Faculty of Health York University, Toronto, Canada .,Molecular, Cellular and Integrative Physiology, Faculty of Health York University, Toronto, Canada
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46
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Zhao X, Bai X, Guan L, Li J, Song X, Ma X, Guo J, Zhang Z, Du Q, Huang Y, Tong D. microRNA-4331 Promotes Transmissible Gastroenteritis Virus (TGEV)-induced Mitochondrial Damage Via Targeting RB1, Upregulating Interleukin-1 Receptor Accessory Protein (IL1RAP), and Activating p38 MAPK Pathway In Vitro. Mol Cell Proteomics 2017; 17:190-204. [PMID: 29217619 PMCID: PMC5795386 DOI: 10.1074/mcp.ra117.000432] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Indexed: 11/06/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV), a member of the coronaviridae family, could cause fatal diarrhea of piglets and result in numerous economic losses. Previous studies demonstrated that TGEV infection could lead to mitochondrial damage and upregulate miR-4331 level. So miR-4331 may play an important regulatory role in the control of mitochondrial function. To explore the potential role of miR-4331 in mitochondrial damage, we adopted a strategy consisting of quantitative proteomic analysis of porcine kidney (PK-15) cells in response to miR-4331 and TGEV infection. Eventually, 69 differentially expressed proteins were gained. The target of miR-4331 was identified. The effects of miR-4331 and its target RB1 on mitochondrial Ca2+ level, mitochondrial membrane potential (MMP), interleukin-1 receptor accessory protein (IL1RAP), p38 MAPK signaling pathway were investigated. The results showed that miR-4331 elevated mitochondrial Ca2+ level, reduced MMP, targets Retinoblastoma 1 (RB1), upregulated IL1RAP, and induced activation of p38 MAPK pathway during TGEV infection. RB1 was identified as the direct targets of miR-4331 and downregulated IL1RAP, suppressed the activation of p38 MPAK, and attenuated TGEV-induced mitochondrial damage. In addition, IL1RAP played a positive role in activating p38 MAPK signaling and negative role in TGEV-induced mitochondrial damage. The data indicate that miR-4331 aggravates TGEV-induced mitochondrial damage by repressing expression of RB1, promoting IL1RAP, and activating p38 MAPK pathway.
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Affiliation(s)
- Xiaomin Zhao
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xiaoyuan Bai
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Lijuan Guan
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Juejun Li
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xiangjun Song
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xuelian Ma
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jianxiong Guo
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhichao Zhang
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Qian Du
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yong Huang
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Dewen Tong
- From the ‡College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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47
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Tanaka H, Takebayashi SI, Sakamoto A, Igata T, Nakatsu Y, Saitoh N, Hino S, Nakao M. The SETD8/PR-Set7 Methyltransferase Functions as a Barrier to Prevent Senescence-Associated Metabolic Remodeling. Cell Rep 2017; 18:2148-2161. [PMID: 28249161 DOI: 10.1016/j.celrep.2017.02.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/29/2016] [Accepted: 02/06/2017] [Indexed: 01/01/2023] Open
Abstract
Cellular senescence is an irreversible growth arrest that contributes to development, tumor suppression, and age-related conditions. Senescent cells show active metabolism compared with proliferating cells, but the underlying mechanisms remain unclear. Here we show that the SETD8/PR-Set7 methyltransferase, which catalyzes mono-methylation of histone H4 at lysine 20 (H4K20me1), suppresses nucleolar and mitochondrial activities to prevent cellular senescence. SETD8 protein was selectively downregulated in both oncogene-induced and replicative senescence. Inhibition of SETD8 alone was sufficient to trigger senescence. Under these states, the expression of genes encoding ribosomal proteins (RPs) and ribosomal RNAs as well as the cyclin-dependent kinase (CDK) inhibitor p16INK4A was increased, with a corresponding reduction of H4K20me1 at each locus. As a result, the loss of SETD8 concurrently stimulated nucleolar function and retinoblastoma protein-mediated mitochondrial metabolism. In conclusion, our data demonstrate that SETD8 acts as a barrier to prevent cellular senescence through chromatin-mediated regulation of senescence-associated metabolic remodeling.
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Affiliation(s)
- Hiroshi Tanaka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shin-Ichiro Takebayashi
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Akihisa Sakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Tomoka Igata
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yuko Nakatsu
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Noriko Saitoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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48
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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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49
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Tarrado-Castellarnau M, de Atauri P, Tarragó-Celada J, Perarnau J, Yuneva M, Thomson TM, Cascante M. De novo MYC addiction as an adaptive response of cancer cells to CDK4/6 inhibition. Mol Syst Biol 2017; 13:940. [PMID: 28978620 PMCID: PMC5658703 DOI: 10.15252/msb.20167321] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Cyclin‐dependent kinases (CDK) are rational cancer therapeutic targets fraught with the development of acquired resistance by tumor cells. Through metabolic and transcriptomic analyses, we show that the inhibition of CDK4/6 leads to a metabolic reprogramming associated with gene networks orchestrated by the MYC transcription factor. Upon inhibition of CDK4/6, an accumulation of MYC protein ensues which explains an increased glutamine metabolism, activation of the mTOR pathway and blunting of HIF‐1α‐mediated responses to hypoxia. These MYC‐driven adaptations to CDK4/6 inhibition render cancer cells highly sensitive to inhibitors of MYC, glutaminase or mTOR and to hypoxia, demonstrating that metabolic adaptations to antiproliferative drugs unveil new vulnerabilities that can be exploited to overcome acquired drug tolerance and resistance by cancer cells.
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Affiliation(s)
- Míriam Tarrado-Castellarnau
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
| | - Josep Tarragó-Celada
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
| | - Jordi Perarnau
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
| | | | - Timothy M Thomson
- Institute of Molecular Biology of Barcelona, National Research Council (IBMB-CSIC), Barcelona, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
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50
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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: 27] [Impact Index Per Article: 3.9] [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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