151
|
Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory. Nature 2017; 546:381-386. [PMID: 28562591 PMCID: PMC5505514 DOI: 10.1038/nature22405] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/28/2017] [Indexed: 12/17/2022]
Abstract
Metabolic production of acetyl-CoA is linked to histone acetylation and gene regulation, yet the precise mechanisms are largely unknown. Here we show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) is a direct regulator of histone acetylation in neurons and of spatial memory in mammals. In a neuronal cell culture model, ACSS2 increases in nuclei of differentiating neurons and localizes to upregulated neuronal genes near elevated histone acetylation. Reduction of ACSS2 lowers nuclear acetyl-CoA levels, histone acetylation, and responsive expression of the cohort of neuronal genes. In adult mice, attenuation of hippocampal ACSS2 expression impairs long-term spatial memory, a cognitive process reliant on histone acetylation. ACSS2 reduction in hippocampus also leads to defective upregulation of memory-related neuronal genes that are pre-bound by ACSS2. These results reveal a unique connection between cellular metabolism, gene regulation, and neural plasticity, establishing a link between acetyl-CoA generation “on-site” at chromatin for histone acetylation and the transcription of critical neuronal genes.
Collapse
|
152
|
Abstract
High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which gave rise to the field of “integrative genetics”. Other omics technologies, such as proteomics and metabolomics, are now often incorporated into the everyday methodology of biological researchers. In this review, we provide an overview of such omics technologies and focus on methods for their integration across multiple omics layers. As compared to studies of a single omics type, multi-omics offers the opportunity to understand the flow of information that underlies disease.
Collapse
Affiliation(s)
- Yehudit Hasin
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA.,Department of Human Genetics, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA
| | - Marcus Seldin
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA
| | - Aldons Lusis
- Department of Medicine, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA. .,Department of Microbiology, Immunology and Molecular Genetics, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA. .,Department of Human Genetics, University of California, 10833 Le Conte Avenue, A2-237 CHS, Los Angeles, CA, 90095, USA.
| |
Collapse
|
153
|
O-GlcNAcylation and chromatin remodeling in mammals: an up-to-date overview. Biochem Soc Trans 2017; 45:323-338. [PMID: 28408473 DOI: 10.1042/bst20160388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
Abstract
Post-translational modifications of histones and the dynamic DNA methylation cycle are finely regulated by a myriad of chromatin-binding factors and chromatin-modifying enzymes. Epigenetic modifications ensure local changes in the architecture of chromatin, thus controlling in fine the accessibility of the machinery of transcription, replication or DNA repair to the chromatin. Over the past decade, the nutrient-sensor enzyme O-GlcNAc transferase (OGT) has emerged as a modulator of chromatin remodeling. In mammals, OGT acts either directly through dynamic and reversible O-GlcNAcylation of histones and chromatin effectors, or in an indirect manner through its recruitment into chromatin-bound multiprotein complexes. In particular, there is an increasing amount of evidence of a cross-talk between OGT and the DNA dioxygenase ten-eleven translocation proteins that catalyze active DNA demethylation. Conversely, the stability of OGT itself can be controlled by the histone lysine-specific demethylase 2 (LSD2). Finally, a few studies have explored the role of O-GlcNAcase (OGA) in chromatin remodeling. In this review, we summarize the recent findings on the link between OGT, OGA and chromatin regulators in mammalian cellular models, and discuss their relevance in physiological and pathological conditions.
Collapse
|
154
|
Nie L, Shuai L, Zhu M, Liu P, Xie ZF, Jiang S, Jiang HW, Li J, Zhao Y, Li JY, Tan M. The Landscape of Histone Modifications in a High-Fat Diet-Induced Obese (DIO) Mouse Model. Mol Cell Proteomics 2017; 16:1324-1334. [PMID: 28450421 DOI: 10.1074/mcp.m117.067553] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Indexed: 12/24/2022] Open
Abstract
Type 2 diabetes (T2D) is a major chronic healthcare concern worldwide. Emerging evidence suggests that a histone-modification-mediated epigenetic mechanism underlies T2D. Nevertheless, the dynamics of histone marks in T2D have not yet been carefully analyzed. Using a mass spectrometry-based label-free and chemical stable isotope labeling quantitative proteomic approach, we systematically profiled liver histone post-translational modifications (PTMs) in a prediabetic high-fat diet-induced obese (DIO) mouse model. We identified 170 histone marks, 30 of which were previously unknown. Interestingly, about 30% of the histone marks identified in DIO mouse liver belonged to a set of recently reported lysine acylation modifications, including propionylation, butyrylation, malonylation, and succinylation, suggesting possible roles of these newly identified histone acylations in diabetes and obesity. These histone marks were detected without prior affinity enrichment with an antibody, demonstrating that the histone acylation marks are present at reasonably high stoichiometry. Fifteen histone marks differed in abundance in DIO mouse liver compared with liver from chow-fed mice in label-free quantification, and six histone marks in stable isotope labeling quantification. Analysis of hepatic histone modifications from metformin-treated DIO mice revealed that metformin, a drug widely used for T2D, could reverse DIO-stimulated histone H3K36me2 in prediabetes, suggesting that this mark is likely associated with T2D development. Our study thus offers a comprehensive landscape of histone marks in a prediabetic mouse model, provides a resource for studying epigenetic functions of histone modifications in obesity and T2D, and suggest a new epigenetic mechanism for the physiological function of metformin.
Collapse
Affiliation(s)
- Litong Nie
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lin Shuai
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Mingrui Zhu
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ping Liu
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Zhi-Fu Xie
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shangwen Jiang
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Hao-Wen Jiang
- ‖College of Chemistry and Molecular Engineering, East China Normal University, China, 200062
| | - Jia Li
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Yingming Zhao
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,**Ben May Department for Cancer Research, University of Chicago, Chicago, IL
| | - Jing-Ya Li
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203;
| | - Minjia Tan
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203; .,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| |
Collapse
|
155
|
Terranova R, Vitobello A, Del Rio Espinola A, Wolf CR, Schwarz M, Thomson J, Meehan R, Moggs J. Progress in identifying epigenetic mechanisms of xenobiotic-induced non-genotoxic carcinogenesis. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
156
|
The H3K27 demethylase, Utx, regulates adipogenesis in a differentiation stage-dependent manner. PLoS One 2017; 12:e0173713. [PMID: 28319137 PMCID: PMC5358847 DOI: 10.1371/journal.pone.0173713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/24/2017] [Indexed: 12/24/2022] Open
Abstract
Understanding the molecular mechanisms that drive adipogenesis is important in developing new treatments for obesity and diabetes. Epigenetic regulations determine the capacity of adipogenesis. In this study, we examined the role of a histone H3 lysine 27 demethylase, the ubiquitously transcribed tetratricopeptide repeat protein on the X chromosome (Utx), in the differentiation of mouse embryonic stem cells (mESCs) to adipocytes. Using gene trapping, we examined Utx-deficient male mESCs to determine whether loss of Utx would enhance or inhibit the differentiation of mESCs to adipocytes. Utx-deficient mESCs showed diminished potential to differentiate to adipocytes compared to that of controls. In contrast, Utx-deficient preadipocytes showed enhanced differentiation to adipocytes. Microarray analyses indicated that the β-catenin/c-Myc signaling pathway was differentially regulated in Utx-deficient cells during adipocyte differentiation. Therefore, our data suggest that Utx governs adipogenesis by regulating c-Myc in a differentiation stage-specific manner and that targeting the Utx signaling pathway could be beneficial for the treatment of obesity, diabetes, and congenital utx-deficiency disorders.
Collapse
|
157
|
Zhang X, Li B, Rezaeian AH, Xu X, Chou PC, Jin G, Han F, Pan BS, Wang CY, Long J, Zhang A, Huang CY, Tsai FJ, Tsai CH, Logothetis C, Lin HK. H3 ubiquitination by NEDD4 regulates H3 acetylation and tumorigenesis. Nat Commun 2017; 8:14799. [PMID: 28300060 PMCID: PMC5357315 DOI: 10.1038/ncomms14799] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 01/27/2017] [Indexed: 12/14/2022] Open
Abstract
Dynamic changes in histone modifications under various physiological cues play important roles in gene transcription and cancer. Identification of new histone marks critical for cancer development is of particular importance. Here we show that, in a glucose-dependent manner, E3 ubiquitin ligase NEDD4 ubiquitinates histone H3 on lysine 23/36/37 residues, which specifically recruits histone acetyltransferase GCN5 for subsequent H3 acetylation. Genome-wide analysis of chromatin immunoprecipitation followed by sequencing reveals that NEDD4 regulates glucose-induced H3 K9 acetylation at transcription starting site and enhancer regions. Integrative analysis of ChIP-seq and microarray data sets also reveals a consistent role of NEDD4 in transcription activation and H3 K9 acetylation in response to glucose. Functionally, we show that NEDD4-mediated H3 ubiquitination, by transcriptionally activating IL1α, IL1β and GCLM, is important for tumour sphere formation. Together, our study reveals the mechanism for glucose-induced transcriptome reprograming and epigenetic regulation in cancer by inducing NEDD4-dependent H3 ubiquitination. Histone modifications play important roles in gene transcription and cancer. Here the authors establish a role for the E3 ubiquitin ligase NEDD4 in modifying in a glucose-dependent manner the histone H3, thus regulating the expression of genes involved in tumorigenesis.
Collapse
Affiliation(s)
- Xian Zhang
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030, USA
| | - Binkui Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Abdol Hossein Rezaeian
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiaohong Xu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ping-Chieh Chou
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Guoxiang Jin
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Fei Han
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030, USA
| | - Bo-Syong Pan
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chi-Yun Wang
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jie Long
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Anmei Zhang
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chih-Yang Huang
- Graduate Institute of Basic Medical Science, China Medical University, Taichung 404, Taiwan.,Department of Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Fuu-Jen Tsai
- College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan.,Department of Medical Genetics, Pediatrics and Medical Research, China Medical University Hospital, Taichung 40402, Taiwan
| | - Chang-Hai Tsai
- Department of Biotechnology, Asia University, Taichung 41354, Taiwan.,Center of Molecular Medicine, China Medical University Hospital, Taichung 40402, Taiwan
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030, USA.,Graduate Institute of Basic Medical Science, China Medical University, Taichung 404, Taiwan.,Department of Biotechnology, Asia University, Taichung 41354, Taiwan
| |
Collapse
|
158
|
Yang SJ, Park YS, Cho JH, Moon B, An HJ, Lee JY, Xie Z, Wang Y, Pocalyko D, Lee DC, Sohn HA, Kang M, Kim JY, Kim E, Park KC, Kim JA, Yeom YI. Regulation of hypoxia responses by flavin adenine dinucleotide-dependent modulation of HIF-1α protein stability. EMBO J 2017; 36:1011-1028. [PMID: 28279976 DOI: 10.15252/embj.201694408] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 01/04/2023] Open
Abstract
Oxygen deprivation induces a range of cellular adaptive responses that enable to drive cancer progression. Here, we report that lysine-specific demethylase 1 (LSD1) upregulates hypoxia responses by demethylating RACK1 protein, a component of hypoxia-inducible factor (HIF) ubiquitination machinery, and consequently suppressing the oxygen-independent degradation of HIF-1α. This ability of LSD1 is attenuated during prolonged hypoxia, with a decrease in the cellular level of flavin adenine dinucleotide (FAD), a metabolic cofactor of LSD1, causing HIF-1α downregulation in later stages of hypoxia. Exogenously provided FAD restores HIF-1α stability, indicating a rate-limiting role for FAD in LSD1-mediated HIF-1α regulation. Transcriptomic analyses of patient tissues show that the HIF-1 signature is highly correlated with the expression of LSD1 target genes as well as the enzymes of FAD biosynthetic pathway in triple-negative breast cancers, reflecting the significance of FAD-dependent LSD1 activity in cancer progression. Together, our findings provide a new insight into HIF-mediated hypoxia response regulation by coupling the FAD dependence of LSD1 activity to the regulation of HIF-1α stability.
Collapse
Affiliation(s)
- Suk-Jin Yang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Young Soo Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea
| | - Jung Hee Cho
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Byul Moon
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea
| | - Hyun-Jung An
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, South Korea
| | - Zhi Xie
- Pfizer Global Research and Development, San Diego, CA, USA
| | - Yuli Wang
- Pfizer Global Research and Development, San Diego, CA, USA
| | - David Pocalyko
- Pfizer Global Research and Development, San Diego, CA, USA
| | - Dong Chul Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Hyun Ahm Sohn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minho Kang
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, South Korea
| | - Eunhee Kim
- Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Kyung Chan Park
- Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea .,Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Ae Kim
- Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea .,Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Young Il Yeom
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea .,Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
159
|
Carrer A, Parris JLD, Trefely S, Henry RA, Montgomery DC, Torres A, Viola JM, Kuo YM, Blair IA, Meier JL, Andrews AJ, Snyder NW, Wellen KE. Impact of a High-fat Diet on Tissue Acyl-CoA and Histone Acetylation Levels. J Biol Chem 2017; 292:3312-3322. [PMID: 28077572 PMCID: PMC5336165 DOI: 10.1074/jbc.m116.750620] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
Cellular metabolism dynamically regulates the epigenome via availability of the metabolite substrates of chromatin-modifying enzymes. The impact of diet on the metabolism-epigenome axis is poorly understood but could alter gene expression and influence metabolic health. ATP citrate-lyase produces acetyl-CoA in the nucleus and cytosol and regulates histone acetylation levels in many cell types. Consumption of a high-fat diet (HFD) results in suppression of ATP citrate-lyase levels in tissues such as adipose and liver, but the impact of diet on acetyl-CoA and histone acetylation in these tissues remains unknown. Here we examined the effects of HFD on levels of acyl-CoAs and histone acetylation in mouse white adipose tissue (WAT), liver, and pancreas. We report that mice consuming a HFD have reduced levels of acetyl-CoA and/or acetyl-CoA:CoA ratio in these tissues. In WAT and the pancreas, HFD also impacted the levels of histone acetylation; in particular, histone H3 lysine 23 acetylation was lower in HFD-fed mice. Genetic deletion of Acly in cultured adipocytes also suppressed acetyl-CoA and histone acetylation levels. In the liver, no significant effects on histone acetylation were observed with a HFD despite lower acetyl-CoA levels. Intriguingly, acetylation of several histone lysines correlated with the acetyl-CoA: (iso)butyryl-CoA ratio in liver. Butyryl-CoA and isobutyryl-CoA interacted with the acetyltransferase P300/CBP-associated factor (PCAF) in liver lysates and inhibited its activity in vitro This study thus provides evidence that diet can impact tissue acyl-CoA and histone acetylation levels and that acetyl-CoA abundance correlates with acetylation of specific histone lysines in WAT but not in the liver.
Collapse
Affiliation(s)
- Alessandro Carrer
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - Joshua L D Parris
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - Sophie Trefely
- Department of Cancer Biology, Abramson Family Cancer Research Institute; A. J. Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania 19104
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702
| | - AnnMarie Torres
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - John M Viola
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Nathaniel W Snyder
- A. J. Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania 19104
| | - Kathryn E Wellen
- Department of Cancer Biology, Abramson Family Cancer Research Institute.
| |
Collapse
|
160
|
Castex J, Willmann D, Kanouni T, Arrigoni L, Li Y, Friedrich M, Schleicher M, Wöhrle S, Pearson M, Kraut N, Méret M, Manke T, Metzger E, Schüle R, Günther T. Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4. Cell Death Dis 2017; 8:e2631. [PMID: 28230862 PMCID: PMC5386490 DOI: 10.1038/cddis.2017.48] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/22/2016] [Accepted: 01/23/2017] [Indexed: 11/24/2022]
Abstract
Coordination of energy metabolism is essential for homeostasis of stem cells, whereas an imbalance in energy homeostasis causes disease and accelerated aging. Here we show that deletion or enzymatic inactivation of lysine-specific demethylase 1 (Lsd1) triggers senescence in trophoblast stem cells (TSCs). Genome-wide transcriptional profiling of TSCs following Lsd1 inhibition shows gene set enrichment of aging and metabolic pathways. Consistently, global metabolomic and phenotypic analyses disclose an unbalanced redox status, decreased glutamine anaplerosis and mitochondrial function. Loss of homeostasis is caused by increased expression of sirtuin 4 (Sirt4), a Lsd1-repressed direct target gene. Accordingly, Sirt4 overexpression in wild-type TSCs recapitulates the senescence phenotype initiated by Lsd1 deletion or inhibition. Inversely, absence of Lsd1 enzymatic activity concomitant with knockdown of Sirt4 reestablishes normal glutamine anaplerosis, redox balance and mitochondrial function. In conclusion, by repression of Sirt4, Lsd1 directs the epigenetic control of TSC immortality via maintenance of metabolic flexibility.
Collapse
Affiliation(s)
- Josefina Castex
- Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dominica Willmann
- Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Yan Li
- metaSysX GmbH, Potsdam-Golm, Germany
| | - Marcel Friedrich
- Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | | | | | | | | | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Eric Metzger
- Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
| | - Roland Schüle
- Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany.,BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Thomas Günther
- Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| |
Collapse
|
161
|
Kaput J, Perozzi G, Radonjic M, Virgili F. Propelling the paradigm shift from reductionism to systems nutrition. GENES & NUTRITION 2017; 12:3. [PMID: 28138347 PMCID: PMC5264346 DOI: 10.1186/s12263-016-0549-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease. Animal, cell, and microbial models have been extensively used to address questions that could not be pursued experimentally in humans, posing an additional level of complexity in translation of the results to healthy and diseased metabolism. The past few decades have witnessed a surge in development of increasingly sensitive molecular techniques and bioinformatic tools for storing, managing, and analyzing increasingly large datasets. Application of such powerful means to molecular nutrition research led to a major leap in study designs and experimental approaches yielding experimental data connecting dietary components to human health. Scientific journals bear major responsibilities in the advancement of science. As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. Such policies evolve in parallel with the evolution of novel approaches and emerging challenges and therefore require constant updating. We highlight in this manuscript the major scientific issues that led to formulating new, updated journal policies for Genes & Nutrition, a journal which targets the growing field of nutritional systems biology interfacing personalized nutrition and preventive medicine, with the ultimate goal of promoting health and preventing or treating disease. We focus here on relevant issues requiring standardization in nutrition research. We also introduce new sections on human genetic variation and nutritional bioinformatics which follow the evolution of nutritional science into the twenty-first century.
Collapse
Affiliation(s)
- Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - Fabio Virgili
- CREA-NUT, Food & Nutrition Research Centre, Rome, Italy
| |
Collapse
|
162
|
Qu J, Sun W, Zhong J, Lv H, Zhu M, Xu J, Jin N, Xie Z, Tan M, Lin SH, Geng M, Ding J, Huang M. Phosphoglycerate mutase 1 regulates dNTP pool and promotes homologous recombination repair in cancer cells. J Cell Biol 2017; 216:409-424. [PMID: 28122957 PMCID: PMC5294784 DOI: 10.1083/jcb.201607008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 11/02/2016] [Accepted: 01/17/2017] [Indexed: 02/04/2023] Open
Abstract
Phosphoglycerate mutase 1 (PGAM1) regulates metabolism in cancer cells. Qu et al. show that PGAM1 maintains the intracellular dNTP pool, promotes the stability of CTBP-interacting protein, and is required for homologous recombination repair. PGAM1 inhibition sensitizes BRCA1/2-proficient breast cancer to PARP inhibitors. Glycolytic enzymes are known to play pivotal roles in cancer cell survival, yet their molecular mechanisms remain poorly understood. Phosphoglycerate mutase 1 (PGAM1) is an important glycolytic enzyme that coordinates glycolysis, pentose phosphate pathway, and serine biosynthesis in cancer cells. Herein, we report that PGAM1 is required for homologous recombination (HR) repair of DNA double-strand breaks (DSBs) caused by DNA-damaging agents. Mechanistically, PGAM1 facilitates DSB end resection by regulating the stability of CTBP-interacting protein (CtIP). Knockdown of PGAM1 in cancer cells accelerates CtIP degradation through deprivation of the intracellular deoxyribonucleotide triphosphate pool and associated activation of the p53/p73 pathway. Enzymatic inhibition of PGAM1 decreases CtIP protein levels, impairs HR repair, and hence sensitizes BRCA1/2-proficient breast cancer to poly(ADP-ribose) polymerase (PARP) inhibitors. Together, this study identifies a metabolically dependent function of PGAM1 in promoting HR repair and reveals a potential therapeutic opportunity for PGAM1 inhibitors in combination with PARP inhibitors.
Collapse
Affiliation(s)
- Jia Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenyi Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Zhong
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hao Lv
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingrui Zhu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Nan Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zuoquan Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shu-Hai Lin
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Meiyu Geng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China .,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Min Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
163
|
Tabe Y, Yamamoto S, Saitoh K, Sekihara K, Monma N, Ikeo K, Mogushi K, Shikami M, Ruvolo V, Ishizawa J, Hail N, Kazuno S, Igarashi M, Matsushita H, Yamanaka Y, Arai H, Nagaoka I, Miida T, Hayashizaki Y, Konopleva M, Andreeff M. Bone Marrow Adipocytes Facilitate Fatty Acid Oxidation Activating AMPK and a Transcriptional Network Supporting Survival of Acute Monocytic Leukemia Cells. Cancer Res 2017; 77:1453-1464. [PMID: 28108519 DOI: 10.1158/0008-5472.can-16-1645] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 01/05/2023]
Abstract
Leukemia cells in the bone marrow must meet the biochemical demands of increased cell proliferation and also survive by continually adapting to fluctuations in nutrient and oxygen availability. Thus, targeting metabolic abnormalities in leukemia cells located in the bone marrow is a novel therapeutic approach. In this study, we investigated the metabolic role of bone marrow adipocytes in supporting the growth of leukemic blasts. Prevention of nutrient starvation-induced apoptosis of leukemic cells by bone marrow adipocytes, as well as the metabolic and molecular mechanisms involved in this process, was investigated using various analytic techniques. In acute monocytic leukemia (AMoL) cells, the prevention of spontaneous apoptosis by bone marrow adipocytes was associated with an increase in fatty acid β-oxidation (FAO) along with the upregulation of PPARγ, FABP4, CD36, and BCL2 genes. In AMoL cells, bone marrow adipocyte coculture increased adiponectin receptor gene expression and its downstream target stress response kinase AMPK, p38 MAPK with autophagy activation, and upregulated antiapoptotic chaperone HSPs. Inhibition of FAO disrupted metabolic homeostasis, increased reactive oxygen species production, and induced the integrated stress response mediator ATF4 and apoptosis in AMoL cells cocultured with bone marrow adipocytes. Our results suggest that bone marrow adipocytes support AMoL cell survival by regulating their metabolic energy balance and that the disruption of FAO in bone marrow adipocytes may be an alternative, novel therapeutic strategy for AMoL therapy. Cancer Res; 77(6); 1453-64. ©2017 AACR.
Collapse
Affiliation(s)
- Yoko Tabe
- Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan.,Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Next Generation Hematology Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Shinichi Yamamoto
- Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan.,Leading Center for the Development and Research of Cancer Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Kaori Saitoh
- Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Kazumasa Sekihara
- Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Norikazu Monma
- Center for Information Biology, National Institute of Genetics, Sizuoka, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Sizuoka, Japan
| | - Kaoru Mogushi
- Center for Genomic and Regenerative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Masato Shikami
- Department of Hematology, Aichi Medical University, Aichi, Japan
| | - Vivian Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Numsen Hail
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Saiko Kazuno
- Division of Proteomics and BioMolecular Science, Juntendo University School of Medicine, Tokyo, Japan
| | - Mamoru Igarashi
- Department of Host Defense and Biochemical Research, Juntendo University School of Medicine, Tokyo, Japan
| | - Hiromichi Matsushita
- Department of Laboratory Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Yasunari Yamanaka
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Kanagawa, Japan
| | - Hajime Arai
- Division of Proteomics and BioMolecular Science, Juntendo University School of Medicine, Tokyo, Japan
| | - Isao Nagaoka
- Department of Host Defense and Biochemical Research, Juntendo University School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | | | - Marina Konopleva
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
164
|
Maury E, Hashizume R. Epigenetic modification in chromatin machinery and its deregulation in pediatric brain tumors: Insight into epigenetic therapies. Epigenetics 2017; 12:353-369. [PMID: 28059591 DOI: 10.1080/15592294.2016.1278095] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Malignancies are characterized by the reprogramming of epigenetic patterns. This reprogramming includes gains or losses in DNA methylation and disruption of normal patterns of covalent histone modifications, which are associated with changes in chromatin remodeling processes. This review will focus on the mechanisms underlying this reprogramming and, specifically, on the role of histone modification in chromatin machinery and the modifications in epigenetic processes occurring in brain cancer, with a specific focus on epigenetic therapies for pediatric brain tumors.
Collapse
Affiliation(s)
- Eleonore Maury
- a Department of Neurological Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA.,b Science in Society , Northwestern University , Evanston , IL , USA
| | - Rintaro Hashizume
- a Department of Neurological Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA.,c Department of Biochemistry and Molecular Genetics , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| |
Collapse
|
165
|
Histone Post-Translational Modifications and Nucleosome Organisation in Transcriptional Regulation: Some Open Questions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 28639249 DOI: 10.1007/5584_2017_58] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The organisation of chromatin is first discussed to conclude that nucleosomes play both structural and transcription-regulatory roles. The presence of nucleosomes makes difficult the access of transcriptional factors to their target sequences and the action of RNA polymerases. The histone post-translational modifications and nucleosome remodelling are first discussed, from a historical point of view, as mechanisms to remove the obstacles imposed by chromatin structure to transcription. Instead of reviewing the state of the art of the whole field, this review is centred on some open questions. First, some "non-classical" histone modifications, such as short-chain acylations other than acetylation, are considered to conclude that their relationship with the concentration of metabolic intermediaries might make of them a sensor of the physiological state of the cells. Then attention is paid to the interest of studying chromatin organisation and epigenetic marks at a single nucleosome level as a complement to genome-wide approaches. Finally, as a consequence of the above questions, the review focuses on the presence of multiple histone post-translational modifications on a single nucleosome. The methods to detect them and their meaning, with special emphasis on bivalent marks, are discussed.
Collapse
|
166
|
Navarro E, Funtikova AN, Fíto M, Schröder H. Prenatal nutrition and the risk of adult obesity: Long-term effects of nutrition on epigenetic mechanisms regulating gene expression. J Nutr Biochem 2017; 39:1-14. [DOI: 10.1016/j.jnutbio.2016.03.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/19/2022]
|
167
|
Woods JK, Rogina B. The effects of Rpd3 on fly metabolism, health, and longevity. Exp Gerontol 2016; 86:124-128. [PMID: 26927903 PMCID: PMC5002259 DOI: 10.1016/j.exger.2016.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/29/2022]
Abstract
The epigenetic regulation of DNA structure and function is essential for changes in gene expression involved in development, growth, and maintenance of cellular function. Epigenetic changes include histone modifications such as methylation, acetylation, ubiquitination, and phosphorylation. Histone deacetylase (HDAC) proteins have a major role in epigenetic regulation of chromatin structure. HDACs are enzymes that catalyze the removal of acetyl groups from lysine residues within histones, as well as a range of other proteins including transcriptional factors. HDACs are highly conserved proteins divided into two families and based on sequence similarity in four classes. Here we will discuss the roles of Rpd3 in physiology and longevity with emphasis on its role in flies. Rpd3, the Drosophila HDAC1 homolog, is a class I lysine deacetylase and a member of a large family of HDAC proteins. Rpd3 has multiple functions including control of proliferation, development, metabolism, and aging. Pharmacological and dietary HDAC inhibitors have been used as therapeutics in psychiatry, cancer, and neurology.
Collapse
Affiliation(s)
- Jared K Woods
- Department of Genetics & Genome Sciences, School of Medicine, University of Connecticut Health, Farmington, CT, USA
| | - Blanka Rogina
- Department of Genetics & Genome Sciences, School of Medicine, University of Connecticut Health, Farmington, CT, USA; Institute for Systems Genomics, School of Medicine, University of Connecticut Health, Farmington, CT, USA.
| |
Collapse
|
168
|
Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism. Nat Commun 2016; 7:13666. [PMID: 27966532 PMCID: PMC5171841 DOI: 10.1038/ncomms13666] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022] Open
Abstract
Altered DNA methylation is common in cancer and often considered an early event in tumorigenesis. However, the sources of heterogeneity of DNA methylation among tumours remain poorly defined. Here we capitalize on the availability of multi-platform data on thousands of human tumours to build integrative models of DNA methylation. We quantify the contribution of clinical and molecular factors in explaining intertumoral variability in DNA methylation. We show that the levels of a set of metabolic genes involved in the methionine cycle is predictive of several features of DNA methylation in tumours, including the methylation of cancer genes. Finally, we demonstrate that patients whose DNA methylation can be predicted from the methionine cycle exhibited improved survival over cases where this regulation is disrupted. This study represents a comprehensive analysis of the determinants of methylation and demonstrates the surprisingly large interaction between metabolism and DNA methylation variation. Together, our results quantify links between tumour metabolism and epigenetics and outline clinical implications.
Altered DNA methylation is a feature of cancer and between-patient variability is prevalent. Here, the authors integrate data on thousands of human tumours, and find that expression levels of methionine metabolism genes are predictive of methylation features, and that the breakdown of this relationship is a negative prognostic marker.
Collapse
|
169
|
Field AE, Adams PD. Targeting chromatin aging - The epigenetic impact of longevity-associated interventions. Exp Gerontol 2016; 94:29-33. [PMID: 27986499 DOI: 10.1016/j.exger.2016.12.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 12/27/2022]
Abstract
A rapidly growing body of evidence has shown that chromatin undergoes radical alterations as an organism ages, but how these changes relate to aging itself is an open question. It is likely that these processes contribute to genomic instability and loss of transcriptional fidelity, which in turn drives deleterious age-related phenotypes. Interventions associated with increased healthspan and longevity such as reduced insulin/IGF signalling (IIS), inhibition of mTOR and energy depletion resulting in SIRT1/AMPK activation, all have beneficial effects which ameliorate multiple facets of age-associated decline. The impact of these interventions on the epigenome is less certain. In this review we highlight the potential of these interventions to act directly upon the epigenome and promote a youthful chromatin landscape, maintaining genetic and transcriptional memory throughout the lifecourse. We propose that this is a fundamental mechanism through which these interventions are able to curtail the incidence of age-related disease. By revisiting these well characterised interventions, we may be able to identify targetable effectors of chromatin function and use this knowledge to enhance healthspan and longevity in human populations through the measured application of dietary and small molecule interventions.
Collapse
Affiliation(s)
- Adam E Field
- University of Glasgow, CRUK Beatson Institute, United Kingdom.
| | - Peter D Adams
- University of Glasgow, CRUK Beatson Institute, United Kingdom
| |
Collapse
|
170
|
Mitochondrial control through nutritionally regulated global histone H3 lysine-4 demethylation. Sci Rep 2016; 6:37942. [PMID: 27897198 PMCID: PMC5126570 DOI: 10.1038/srep37942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/02/2016] [Indexed: 12/13/2022] Open
Abstract
Histone demethylation by Jumonji-family proteins is coupled with the decarboxylation of α-ketoglutarate (αKG) to yield succinate, prompting hypotheses that their activities are responsive to levels of these metabolites in the cell. Consistent with this paradigm we show here that the Saccharomyces cerevisiae Jumonji demethylase Jhd2 opposes the accumulation of H3K4me3 in fermenting cells only when they are nutritionally manipulated to contain an elevated αKG/succinate ratio. We also find that Jhd2 opposes H3K4me3 in respiratory cells that do not exhibit such an elevated αKG/succinate ratio. While jhd2∆ caused only limited gene expression defects in fermenting cells, transcript profiling and physiological measurements show that JHD2 restricts mitochondrial respiratory capacity in cells grown in non-fermentable carbon in an H3K4me-dependent manner. In association with these phenotypes, we find that JHD2 limits yeast proliferative capacity under physiologically challenging conditions as measured by both replicative lifespan and colony growth on non-fermentable carbon. JHD2’s impact on nutrient response may reflect an ancestral role of its gene family in mediating mitochondrial regulation.
Collapse
|
171
|
Kottakis F, Nicolay BN, Roumane A, Karnik R, Gu H, Nagle JM, Boukhali M, Hayward MC, Li YY, Chen T, Liesa M, Hammerman PS, Wong KK, Hayes DN, Shirihai OS, Dyson NJ, Haas W, Meissner A, Bardeesy N. LKB1 loss links serine metabolism to DNA methylation and tumorigenesis. Nature 2016; 539:390-395. [PMID: 27799657 PMCID: PMC5988435 DOI: 10.1038/nature20132] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
Intermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that is central to oncogenic transformation downstream of the liver kinase B1 (LKB1, also known as STK11) tumour suppressor, an integrator of nutrient availability, metabolism and growth. By developing genetically engineered mouse models and primary pancreatic epithelial cells, and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation is fuelled by pronounced mTOR-dependent induction of the serine-glycine-one-carbon pathway coupled to S-adenosylmethionine generation. At the same time, DNA methyltransferases are upregulated, leading to elevation in DNA methylation with particular enrichment at retrotransposon elements associated with their transcriptional silencing. Correspondingly, LKB1 deficiency sensitizes cells and tumours to inhibition of serine biosynthesis and DNA methylation. Thus, we define a hypermetabolic state that incites changes in the epigenetic landscape to support tumorigenic growth of LKB1-mutant cells, while resulting in potential therapeutic vulnerabilities.
Collapse
Affiliation(s)
- Filippos Kottakis
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Brandon N. Nicolay
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Ahlima Roumane
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Rahul Karnik
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Julia M. Nagle
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Myriam Boukhali
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | | | - Yvonne Y. Li
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ting Chen
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Marc Liesa
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Peter S. Hammerman
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kwok Kin Wong
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - D. Neil Hayes
- UNC, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Orian S. Shirihai
- Evans Center for Interdisciplinary Research, Department of Medicine, Mitochondria ARC, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, UCLA David Geffen School of Medicine, Los Angeles, CA 90095
| | - Nicholas J. Dyson
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Wilhelm Haas
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nabeel Bardeesy
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114
| |
Collapse
|
172
|
Capitanio D, Vasso M, De Palma S, Fania C, Torretta E, Cammarata FP, Magnaghi V, Procacci P, Gelfi C. Specific protein changes contribute to the differential muscle mass loss during ageing. Proteomics 2016; 16:645-56. [PMID: 26698593 DOI: 10.1002/pmic.201500395] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/12/2015] [Accepted: 12/16/2015] [Indexed: 11/11/2022]
Abstract
In the skeletal muscle, the ageing process is characterized by a loss of muscle mass and strength, coupled with a decline of mitochondrial function and a decrease of satellite cells. This profile is more pronounced in hindlimb than in forelimb muscles, both in humans and in rodents. Utilizing light and electron microscopy, myosin heavy chain isoform distribution, proteomic analysis by 2D-DIGE, MALDI-TOF MS and quantitative immunoblotting, this study analyzes the protein levels and the nuclear localization of specific molecules, which can contribute to a preferential muscle loss. Our results identify the molecular changes in the hindlimb (gastrocnemius) and forelimb (triceps) muscles during ageing in rats (3- and 22-month-old). Specifically, the oxidative metabolism contributes to tissue homeostasis in triceps, whereas respiratory chain disruption and oxidative-stress-induced damage imbalance the homeostasis in gastrocnemius muscle. High levels of dihydrolipoyllysine-residue acetyltransferase (Dlat) and ATP synthase subunit alpha (Atp5a1) are detected in triceps and gastrocnemius, respectively. Interestingly, in triceps, both molecules are increased in the nucleus in aged rats and are associated to an increased protein acetylation and myoglobin availability. Furthermore, autophagy is retained in triceps whereas an enhanced fusion, decrement of mitophagy and of regenerative potential is observed in aged gastrocnemius muscle.
Collapse
Affiliation(s)
- Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Policlinico San Donato, San Donato Milanese (MI), Italy
| | - Michele Vasso
- Institute of Bioimaging and Molecular Physiology, National Research Council, Segrate (MI) - Cefalù (PA), Italy
| | - Sara De Palma
- Institute of Bioimaging and Molecular Physiology, National Research Council, Segrate (MI) - Cefalù (PA), Italy
| | - Chiara Fania
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Policlinico San Donato, San Donato Milanese (MI), Italy
| | - Enrica Torretta
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Policlinico San Donato, San Donato Milanese (MI), Italy
| | - Francesco P Cammarata
- Institute of Bioimaging and Molecular Physiology, National Research Council, Segrate (MI) - Cefalù (PA), Italy
| | - Valerio Magnaghi
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Patrizia Procacci
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Policlinico San Donato, San Donato Milanese (MI), Italy.,Institute of Bioimaging and Molecular Physiology, National Research Council, Segrate (MI) - Cefalù (PA), Italy
| |
Collapse
|
173
|
Wende AR, Young ME, Chatham J, Zhang J, Rajasekaran NS, Darley-Usmar VM. Redox biology and the interface between bioenergetics, autophagy and circadian control of metabolism. Free Radic Biol Med 2016; 100:94-107. [PMID: 27242268 PMCID: PMC5124549 DOI: 10.1016/j.freeradbiomed.2016.05.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 12/01/2022]
Abstract
Understanding molecular mechanisms that underlie the recent emergence of metabolic diseases such as diabetes and heart failure has revealed the need for a multi-disciplinary research integrating the key metabolic pathways which change the susceptibility to environmental or pathologic stress. At the physiological level these include the circadian control of metabolism which aligns metabolism with temporal demand. The mitochondria play an important role in integrating the redox signals and metabolic flux in response to the changing activities associated with chronobiology, exercise and diet. At the molecular level this involves dynamic post-translational modifications regulating transcription, metabolism and autophagy. In this review we will discuss different examples of mechanisms which link these processes together. An important pathway capable of linking signaling to metabolism is the post-translational modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc). This is a nutrient regulated protein modification that plays an important role in impaired cellular stress responses. Circadian clocks have also emerged as critical regulators of numerous cardiometabolic processes, including glucose/lipid homeostasis, hormone secretion, redox status and cardiovascular function. Central to these pathways are the response of autophagy, bioenergetics to oxidative stress, regulated by Keap1/Nrf2 and mechanisms of metabolic control. The extension of these ideas to the emerging concept of bioenergetic health will be discussed.
Collapse
Affiliation(s)
- Adam R Wende
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Martin E Young
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Chatham
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Namakkal S Rajasekaran
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Victor M Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; UAB Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
174
|
Molina-Serrano D, Schiza V, Demosthenous C, Stavrou E, Oppelt J, Kyriakou D, Liu W, Zisser G, Bergler H, Dang W, Kirmizis A. Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity. EMBO Rep 2016; 17:1829-1843. [PMID: 27799288 PMCID: PMC5167350 DOI: 10.15252/embr.201642540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/07/2023] Open
Abstract
Changes in histone modifications are an attractive model through which environmental signals, such as diet, could be integrated in the cell for regulating its lifespan. However, evidence linking dietary interventions with specific alterations in histone modifications that subsequently affect lifespan remains elusive. We show here that deletion of histone N‐alpha‐terminal acetyltransferase Nat4 and loss of its associated H4 N‐terminal acetylation (N‐acH4) extend yeast replicative lifespan. Notably, nat4Δ‐induced longevity is epistatic to the effects of calorie restriction (CR). Consistent with this, (i) Nat4 expression is downregulated and the levels of N‐acH4 within chromatin are reduced upon CR, (ii) constitutive expression of Nat4 and maintenance of N‐acH4 levels reduces the extension of lifespan mediated by CR, and (iii) transcriptome analysis indicates that nat4Δ largely mimics the effects of CR, especially in the induction of stress‐response genes. We further show that nicotinamidase Pnc1, which is typically upregulated under CR, is required for nat4Δ‐mediated longevity. Collectively, these findings establish histone N‐acH4 as a regulator of cellular lifespan that links CR to increased stress resistance and longevity.
Collapse
Affiliation(s)
| | - Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Wei Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Gertrude Zisser
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Helmut Bergler
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| |
Collapse
|
175
|
Singhal NK, Huang H, Li S, Clements R, Gadd J, Daniels A, Kooijman EE, Bannerman P, Burns T, Guo F, Pleasure D, Freeman E, Shriver L, McDonough J. The neuronal metabolite NAA regulates histone H3 methylation in oligodendrocytes and myelin lipid composition. Exp Brain Res 2016; 235:279-292. [PMID: 27709268 DOI: 10.1007/s00221-016-4789-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 09/27/2016] [Indexed: 01/01/2023]
Abstract
The neuronal mitochondrial metabolite N-acetylaspartate (NAA) is decreased in the multiple sclerosis (MS) brain. NAA is synthesized in neurons by the enzyme N-acetyltransferase-8-like (NAT8L) and broken down in oligodendrocytes by aspartoacylase (ASPA) into acetate and aspartate. We have hypothesized that NAA links the metabolism of axons with oligodendrocytes to support myelination. To test this hypothesis, we performed lipidomic analyses using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and high-performance thin-layer chromatography (HPTLC) to identify changes in myelin lipid composition in postmortem MS brains and in NAT8L knockout (NAT8L-/-) mice which do not synthesize NAA. We found reduced levels of sphingomyelin in MS normal appearing white matter that mirrored decreased levels of NAA. We also discovered decreases in the amounts of sphingomyelin and sulfatide lipids in the brains of NAT8L-/- mice compared to controls. Metabolomic analysis of primary cultures of oligodendrocytes treated with NAA revealed increased levels of α-ketoglutarate, which has been reported to regulate histone demethylase activity. Consistent with this, NAA treatment resulted in alterations in the levels of histone H3 methylation, including H3K4me3, H3K9me2, and H3K9me3. The H3K4me3 histone mark regulates cellular energetics, metabolism, and growth, while H3K9me3 has been linked to alterations in transcriptional repression in developing oligodendrocytes. We also noted the NAA treatment was associated with increases in the expression of genes involved in sulfatide and sphingomyelin synthesis in cultured oligodendrocytes. This is the first report demonstrating that neuronal-derived NAA can signal to the oligodendrocyte nucleus. These data suggest that neuronal-derived NAA signals through epigenetic mechanisms in oligodendrocytes to support or maintain myelination.
Collapse
Affiliation(s)
- N K Singhal
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - H Huang
- Department of Chemistry and Biology, University of Akron, Akron, OH, 44325, USA
| | - S Li
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - R Clements
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - J Gadd
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - A Daniels
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - E E Kooijman
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - P Bannerman
- Department of Cell Biology and Human Anatomy, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - T Burns
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - F Guo
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - D Pleasure
- Department of Neurology, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - E Freeman
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA
| | - L Shriver
- Department of Chemistry and Biology, University of Akron, Akron, OH, 44325, USA
| | - J McDonough
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, OH, 44242, USA.
| |
Collapse
|
176
|
Cameron AM, Lawless SJ, Pearce EJ. Metabolism and acetylation in innate immune cell function and fate. Semin Immunol 2016; 28:408-416. [PMID: 28340958 PMCID: PMC10911065 DOI: 10.1016/j.smim.2016.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
Innate immunity is the first line of defense against invading pathogens. Changes in both metabolism and chromatin accessibility contribute to the shaping of these innate immune responses, and we are beginning to appreciate that cross-talk between these two systems plays an important role in determining innate immune cell differentiation and function. In this review we focus on acetylation, a post-translational modification important for both regulating chromatin accessibility by modulating histone function, and for functional regulation of non-histone proteins, which has many links to both immune signaling and metabolism. We discuss the interactions between metabolism and acetylation, including the requirement for metabolic intermediates as substrates and co-factors for acetylation, and the regulation of metabolic proteins and enzymes by acetylation. Here we highlight recent findings, which demonstrate the role that the metabolism-acetylation axis has in coordinating the responses of innate immune cells to the availability of nutrients and the microenvironment.
Collapse
Affiliation(s)
- Alanna M Cameron
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Simon J Lawless
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Edward J Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
177
|
He X, Yan B, Liu S, Jia J, Lai W, Xin X, Tang CE, Luo D, Tan T, Jiang Y, Shi Y, Liu Y, Xiao D, Chen L, Liu S, Mao C, Yin G, Cheng Y, Fan J, Cao Y, Muegge K, Tao Y. Chromatin Remodeling Factor LSH Drives Cancer Progression by Suppressing the Activity of Fumarate Hydratase. Cancer Res 2016; 76:5743-5755. [PMID: 27302170 PMCID: PMC7821962 DOI: 10.1158/0008-5472.can-16-0268] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/26/2016] [Indexed: 12/26/2022]
Abstract
Chromatin modification is pivotal to the epithelial-mesenchymal transition (EMT), which confers potent metastatic potential to cancer cells. Here, we report a role for the chromatin remodeling factor lymphoid-specific helicase (LSH) in nasopharyngeal carcinoma (NPC), a prevalent cancer in China. LSH expression was increased in NPC, where it was controlled by the Epstein-Barr virus-encoded protein LMP1. In NPC cells in vitro and in vivo, LSH promoted cancer progression in part by regulating expression of fumarate hydratase (FH), a core component of the tricarboxylic acid cycle. LSH bound to the FH promoter, recruiting the epigenetic silencer factor G9a to repress FH transcription. Clinically, we found that the concentration of TCA intermediates in NPC patient sera was deregulated in the presence of LSH. RNAi-mediated silencing of FH mimicked LSH overexpression, establishing FH as downstream mediator of LSH effects. The TCA intermediates α-KG and citrate potentiated the malignant character of NPC cells, in part by altering IKKα-dependent EMT gene expression. In this manner, LSH furthered malignant progression of NPC by modifying cancer cell metabolism to support EMT. Cancer Res; 76(19); 5743-55. ©2016 AACR.
Collapse
Affiliation(s)
- Xiaozhen He
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Bin Yan
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Shuang Liu
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiantao Jia
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China
| | - Weiwei Lai
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China
| | - Xing Xin
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Can-E Tang
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dixian Luo
- National and Local Joint Engineering Laboratory of High-throughput Molecular Diagnosis Technology, Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Chenzhou, Hunan, China
| | - Tan Tan
- National and Local Joint Engineering Laboratory of High-throughput Molecular Diagnosis Technology, Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Chenzhou, Hunan, China
| | - Yiqun Jiang
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China
| | - Ying Shi
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Yating Liu
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ling Chen
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chao Mao
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China
| | - Gang Yin
- Department of Pathology, School of Basic Medicine, Central South University, Hunan, China
| | - Yan Cheng
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Jia Fan
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Fudan University, Shanghai, China. Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ya Cao
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, National Cancer Institute, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Yongguang Tao
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, China. Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China. Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, China. Key Laboratory of Carcinogenesis (Central South University), Ministry of Health, Hunan, China.
| |
Collapse
|
178
|
Arts RJ, Joosten LA, Netea MG. Immunometabolic circuits in trained immunity. Semin Immunol 2016; 28:425-430. [DOI: 10.1016/j.smim.2016.09.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
|
179
|
Bromodomain Inhibitors Correct Bioenergetic Deficiency Caused by Mitochondrial Disease Complex I Mutations. Mol Cell 2016; 64:163-175. [PMID: 27666594 DOI: 10.1016/j.molcel.2016.08.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/01/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]
Abstract
Mitochondrial diseases comprise a heterogeneous group of genetically inherited disorders that cause failures in energetic and metabolic function. Boosting residual oxidative phosphorylation (OXPHOS) activity can partially correct these failures. Herein, using a high-throughput chemical screen, we identified the bromodomain inhibitor I-BET 525762A as one of the top hits that increases COX5a protein levels in complex I (CI) mutant cybrid cells. In parallel, bromodomain-containing protein 4 (BRD4), a target of I-BET 525762A, was identified using a genome-wide CRISPR screen to search for genes whose loss of function rescues death of CI-impaired cybrids grown under conditions requiring OXPHOS activity for survival. We show that I-BET525762A or loss of BRD4 remodeled the mitochondrial proteome to increase the levels and activity of OXPHOS protein complexes, leading to rescue of the bioenergetic defects and cell death caused by mutations or chemical inhibition of CI. These studies show that BRD4 inhibition may have therapeutic implications for the treatment of mitochondrial diseases.
Collapse
|
180
|
Metabolic interactions with cancer epigenetics. Mol Aspects Med 2016; 54:50-57. [PMID: 27620316 DOI: 10.1016/j.mam.2016.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/30/2016] [Accepted: 09/03/2016] [Indexed: 01/31/2023]
Abstract
Cancer cells have epigenetic alterations that are known to drive cancer progression. The reversibility of the epigenetic posttranslational modifications on chromatin and DNA renders targeting these modifications an attractive means for cancer therapy. Cellular epigenetic status interacts with cell metabolism, and we are now beginning to understand the nature of how this interaction occurs and the biological contexts that mediate its function. Given the tremendous interest in understanding and targeting metabolic reprogramming in cancer, this nexus also provides opportunities for exploring the liabilities of cancers. This review summarizes recent developments in our understanding of the interaction of cancer metabolism and epigenetics.
Collapse
|
181
|
Ligand-Bound GeneSwitch Causes Developmental Aberrations in Drosophila that Are Alleviated by the Alternative Oxidase. G3-GENES GENOMES GENETICS 2016; 6:2839-46. [PMID: 27412986 PMCID: PMC5015941 DOI: 10.1534/g3.116.030882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Culture of Drosophila expressing the steroid-dependent GeneSwitch transcriptional activator under the control of the ubiquitous α-tubulin promoter was found to produce extensive pupal lethality, as well as a range of dysmorphic adult phenotypes, in the presence of high concentrations of the inducing drug RU486. Prominent among these was cleft thorax, seen previously in flies bearing mutant alleles of the nuclear receptor Ultraspiracle and many other mutants, as well as notched wings, leg malformations, and bristle abnormalities. Neither the α-tubulin-GeneSwitch driver nor the inducing drug on their own produced any of these effects. A second GeneSwitch driver, under the control of the daughterless promoter, which gave much lower and more tissue-restricted transgene expression, exhibited only mild bristle abnormalities in the presence of high levels of RU486. Coexpression of the alternative oxidase (AOX) from Ciona intestinalis produced a substantial shift in the developmental outcome toward a wild-type phenotype, which was dependent on the AOX expression level. Neither an enzymatically inactivated variant of AOX, nor GFP, or the alternative NADH dehydrogenase Ndi1 from yeast gave any such rescue. Users of the GeneSwitch system should be aware of the potential confounding effects of its application in developmental studies.
Collapse
|
182
|
Picard M, Wallace DC, Burelle Y. The rise of mitochondria in medicine. Mitochondrion 2016; 30:105-16. [PMID: 27423788 PMCID: PMC5023480 DOI: 10.1016/j.mito.2016.07.003] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/04/2016] [Accepted: 07/12/2016] [Indexed: 12/11/2022]
Abstract
Once considered exclusively the cell's powerhouse, mitochondria are now recognized to perform multiple essential functions beyond energy production, impacting most areas of cell biology and medicine. Since the emergence of molecular biology and the discovery of pathogenic mitochondrial DNA defects in the 1980's, research advances have revealed a number of common human diseases which share an underlying pathogenesis involving mitochondrial dysfunction. Mitochondria undergo function-defining dynamic shape changes, communicate with each other, regulate gene expression within the nucleus, modulate synaptic transmission within the brain, release molecules that contribute to oncogenic transformation and trigger inflammatory responses systemically, and influence the regulation of complex physiological systems. Novel mitopathogenic mechanisms are thus being uncovered across a number of medical disciplines including genetics, oncology, neurology, immunology, and critical care medicine. Increasing knowledge of the bioenergetic aspects of human disease has provided new opportunities for diagnosis, therapy, prevention, and in connecting various domains of medicine. In this article, we overview specific aspects of mitochondrial biology that have contributed to - and likely will continue to enhance the progress of modern medicine.
Collapse
Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA; Department of Neurology and CTNI, H Houston Merritt Center, Columbia University Medical Center, New York, NY, USA.
| | - Douglas C Wallace
- The Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yan Burelle
- Faculty of Pharmacy, Université de Montreal, Montreal, QC, Canada
| |
Collapse
|
183
|
Rensvold JW, Krautkramer KA, Dowell JA, Denu JM, Pagliarini DJ. Iron Deprivation Induces Transcriptional Regulation of Mitochondrial Biogenesis. J Biol Chem 2016; 291:20827-20837. [PMID: 27497435 DOI: 10.1074/jbc.m116.727701] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/31/2023] Open
Abstract
Mitochondria are essential organelles that adapt to stress and environmental changes. Among the nutrient signals that affect mitochondrial form and function is iron, whose depletion initiates a rapid and reversible decrease in mitochondrial biogenesis through unclear means. Here we demonstrate that, unlike the canonical iron-induced alterations to transcript stability, loss of iron dampens the transcription of genes encoding mitochondrial proteins with no change to transcript half-life. Using mass spectrometry, we demonstrate that these transcriptional changes are accompanied by dynamic alterations to histone acetylation and methylation levels that are largely reversible upon readministration of iron. Moreover, histone deacetylase inhibition abrogates the decreased histone acetylation observed upon iron deprivation and restores normal transcript levels at genes encoding mitochondrial proteins. Collectively, we demonstrate that deprivation of an essential nutrient induces transcriptional repression of organellar biogenesis involving epigenetic alterations.
Collapse
Affiliation(s)
| | - Kimberly A Krautkramer
- the Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, and
| | - James A Dowell
- the Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, and
| | - John M Denu
- From the Morgridge Institute for Research, Madison, Wisconsin 53715, the Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, and
| | - David J Pagliarini
- From the Morgridge Institute for Research, Madison, Wisconsin 53715, the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
184
|
Hernández-Aguilera A, Fernández-Arroyo S, Cuyàs E, Luciano-Mateo F, Cabre N, Camps J, Lopez-Miranda J, Menendez JA, Joven J. Epigenetics and nutrition-related epidemics of metabolic diseases: Current perspectives and challenges. Food Chem Toxicol 2016; 96:191-204. [PMID: 27503834 DOI: 10.1016/j.fct.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 02/07/2023]
Abstract
We live in a world fascinated by the relationship between disease and nutritional disequilibrium. The subtle and slow effects of chronic nutrient toxicity are a major public health concern. Since food is potentially important for the development of "metabolic memory", there is a need for more information on the type of nutrients causing adverse or toxic effects. We now know that metabolic alterations produced by excessive intake of some nutrients, drugs and chemicals directly impact epigenetic regulation. We envision that understanding how metabolic pathways are coordinated by environmental and genetic factors will provide novel insights for the treatment of metabolic diseases. New methods will enable the assembly and analysis of large sets of complex molecular and clinical data for understanding how inflammation and mitochondria affect bioenergetics, epigenetics and health. Collectively, the observations we highlight indicate that energy utilization and disease are intimately connected by epigenetics. The challenge is to incorporate metabolo-epigenetic data in better interpretations of disease, to expedite therapeutic targeting of key pathways linking nutritional toxicity and metabolism. An additional concern is that changes in the parental phenotype are detectable in the methylome of subsequent offspring. The effect might create a menace to future generations and preconceptional considerations.
Collapse
Affiliation(s)
- Anna Hernández-Aguilera
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Elisabet Cuyàs
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain
| | - Fedra Luciano-Mateo
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Noemi Cabre
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Jose Lopez-Miranda
- Lipid and Atherosclerosis Unit, IMIBIC, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier A Menendez
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain; The Campus of International Excellence Southern Catalonia, Tarragona, Spain.
| |
Collapse
|
185
|
Liu S, Tao YG. Chromatin remodeling factor LSH affects fumarate hydratase as a cancer driver. CHINESE JOURNAL OF CANCER 2016; 35:72. [PMID: 27473869 PMCID: PMC4967323 DOI: 10.1186/s40880-016-0138-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 07/21/2016] [Indexed: 12/23/2022]
Abstract
Cancer metabolism and epigenetic alteration are two critical mechanisms for tumorigenesis and cancer progression; however, the dynamic interplay between them remains poorly understood. As reported in the article entitled "Chromatin remodeling factor LSH drives cancer progression by suppressing the activity of fumarate hydratase," which was recently published in Cancer Research, our group examined the physiological role of lymphocyte-specific helicase (LSH) in nasopharyngeal carcinoma (NPC) by focusing on cancer progression and the tricarboxylic acid cycle. We found that LSH was overexpressed in NPC, and its expression associated with Epstein-Barr virus infection. We also found that LSH directly suppressed fumarate hydratase (FH), a key component of the tricarboxylic acid cycle, in combination with euchromatic histone-lysine N-methyltransferase 2 (EHMT2), also known as G9a. Depletion of FH promoted epithelial-mesenchymal transition (EMT). Moreover, LSH controlled expression of tricarboxylic acid cycle intermediates that promote cancer progression, including EMT, through activation by inhibitor of nuclear factor kappa-B kinase alpha (IKKα), a chromatin modifier and transcriptional activator. Our study showed that LSH plays a critical role in cancer progression, which has important implications for the development of novel strategies to treat NPC.
Collapse
Affiliation(s)
- Shuang Liu
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P. R. China
| | - Yong-Guang Tao
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P. R. China. .,Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, 410078, Hunan, P. R. China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Changsha, 410078, Hunan, P. R. China.
| |
Collapse
|
186
|
Lemaire K, Thorrez L, Schuit F. Disallowed and Allowed Gene Expression: Two Faces of Mature Islet Beta Cells. Annu Rev Nutr 2016; 36:45-71. [DOI: 10.1146/annurev-nutr-071715-050808] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Lieven Thorrez
- Gene Expression Unit, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven B3000, Belgium; , ,
| | - Frans Schuit
- Gene Expression Unit, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven B3000, Belgium; , ,
| |
Collapse
|
187
|
Abstract
Over the past 20 years, breakthrough discoveries of chromatin-modifying enzymes and associated mechanisms that alter chromatin in response to physiological or pathological signals have transformed our knowledge of epigenetics from a collection of curious biological phenomena to a functionally dissected research field. Here, we provide a personal perspective on the development of epigenetics, from its historical origins to what we define as 'the modern era of epigenetic research'. We primarily highlight key molecular mechanisms of and conceptual advances in epigenetic control that have changed our understanding of normal and perturbed development.
Collapse
Affiliation(s)
- C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York 10065, New York, USA
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg D-79108, Germany
| |
Collapse
|
188
|
Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 518] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
Collapse
Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
| |
Collapse
|
189
|
Mews P, Berger SL. Exploring the Dynamic Relationship Between Cellular Metabolism and Chromatin Structure Using SILAC-Mass Spec and ChIP-Sequencing. Methods Enzymol 2016; 574:311-329. [PMID: 27423866 DOI: 10.1016/bs.mie.2016.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Metabolic state and chromatin structure are tightly linked, enabling adaptation of gene expression to changing environment and metabolism. The bioenergetic pathways and enzymes that provide metabolic cofactors for histone modification have recently emerged as central regulators of chromatin. Current research therefore focuses on the dynamic interface of cellular metabolism and chromatin structure. Here, we provide an adaptable approach to examine broadly in changing physiological states, how chromatin structure is dynamically modulated by metabolic activity. We employ two complementary methods: high-throughput sequencing to establish the location of epigenetic changes, and stable isotope tracing using mass spectrometry to evaluate chromatin modification dynamics. Our two-pronged approach is of particular advantage when interrogating how metabolic and oncogenic mutations influence the dynamic relationship between metabolism, nutritional environment, and chromatin regulation.
Collapse
Affiliation(s)
- P Mews
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - S L Berger
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
190
|
Scovell WM. High mobility group protein 1: A collaborator in nucleosome dynamics and estrogen-responsive gene expression. World J Biol Chem 2016; 7:206-222. [PMID: 27247709 PMCID: PMC4877529 DOI: 10.4331/wjbc.v7.i2.206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 02/19/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023] Open
Abstract
High mobility group protein 1 (HMGB1) is a multifunctional protein that interacts with DNA and chromatin to influence the regulation of transcription, DNA replication and repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, adenosine triphosphate-independent manner. As a result, the canonical nucleosome is converted to two stable, physically distinct nucleosome conformers. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes (N’ and N’’) remain stable and exhibit a number of characteristics that are distinctly different from the canonical nucleosome. These findings complement previous studies that showed (1) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and (2) knock down of HMGB1 expression by siRNA precipitously reduced transcriptional activation. The findings indicate that a major facet of the mechanism of HMGB1 action involves a restructuring of aspects of the nucleosome that appear to relax structural constraints within the nucleosome. The findings are extended to reveal the differences between ER and the other steroid hormone receptors. A working proposal outlines mechanisms that highlight the multiple facets that HMGB1 may utilize in restructuring the nucleosome.
Collapse
|
191
|
Abstract
O-GlcNAc-ylation is the post-translational addition of an O-linked β-N-acetylglucosamine to the serine and threonine residues of thousands of proteins in eukaryotic cells. Specifically, half of the thirty different types of protein components in the nuclear pore complex (NPC) are modified by O-GlcNAc, of which the majority are intrinsically disordered nucleoporins (Nups) containing multiple phenylalanine-glycine (FG) repeats. Moreover, these FG-Nups form a strict selectivity barrier with a high density of O-GlcNAc in the NPC to mediate bidirectional trafficking between the cytoplasm and nucleus. However, the roles that O-GlcNAc plays in the structure and function of the NPC remain obscure. In this review paper, we will discuss the current knowledge of O-GlcNAc-ylated Nups, highlight some new techniques used to probe O-GlcNAc's roles in the nuclear pore, and finally propose a new model for the effect of O-GlcNAc on the NPC's permeability.
Collapse
Affiliation(s)
- Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA
| |
Collapse
|
192
|
Christ A, Bekkering S, Latz E, Riksen NP. Long-term activation of the innate immune system in atherosclerosis. Semin Immunol 2016; 28:384-93. [PMID: 27113267 DOI: 10.1016/j.smim.2016.04.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/12/2016] [Indexed: 01/05/2023]
Abstract
Efforts to reverse the pathologic consequences of vulnerable plaques are often stymied by the complex treatment resistant pro-inflammatory environment within the plaque. This suggests that pro-atherogenic stimuli, such as LDL cholesterol and high fat diets may impart longer lived signals on (innate) immune cells that persist even after reversing the pro-atherogenic stimuli. Recently, a series of studies challenged the traditional immunological paradigm that innate immune cells cannot display memory characteristics. Epigenetic reprogramming in these myeloid cell subsets, after exposure to certain stimuli, has been shown to alter the expression of genes upon re-exposure. This phenomenon has been termed trained innate immunity or innate immune memory. The changed responses of 'trained' innate immune cells can confer nonspecific protection against secondary infections, suggesting that innate immune memory has likely evolved as an ancient mechanism to protect against pathogens. However, dysregulated processes of immunological imprinting mediated by trained innate immunity may also be detrimental under certain conditions as the resulting exaggerated immune responses could contribute to autoimmune and inflammatory diseases, such as atherosclerosis. Pro-atherogenic stimuli most likely cause epigenetic modifications that persist for prolonged time periods even after the initial stimulus has been removed. In this review we discuss the concept of trained innate immunity in the context of a hyperlipidemic environment and atherosclerosis. According to this idea the epigenome of myeloid (progenitor) cells is presumably modified for prolonged periods of time, which, in turn, could evoke a condition of continuous immune cell over-activation.
Collapse
Affiliation(s)
- Anette Christ
- Institute of Innate Immunity, University Hospitals Bonn, University of Bonn, Bonn, Germany; Department of Infectious Diseases and Immunology, UMass Medical School, Worcester, MA, USA
| | - Siroon Bekkering
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eicke Latz
- Institute of Innate Immunity, University Hospitals Bonn, University of Bonn, Bonn, Germany; Department of Infectious Diseases and Immunology, UMass Medical School, Worcester, MA, USA; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.
| |
Collapse
|
193
|
Netea MG, Joosten LAB, Latz E, Mills KHG, Natoli G, Stunnenberg HG, O'Neill LAJ, Xavier RJ. Trained immunity: A program of innate immune memory in health and disease. Science 2016; 352:aaf1098. [PMID: 27102489 DOI: 10.1126/science.aaf1098] [Citation(s) in RCA: 1598] [Impact Index Per Article: 199.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The general view that only adaptive immunity can build immunological memory has recently been challenged. In organisms lacking adaptive immunity, as well as in mammals, the innate immune system can mount resistance to reinfection, a phenomenon termed "trained immunity" or "innate immune memory." Trained immunity is orchestrated by epigenetic reprogramming, broadly defined as sustained changes in gene expression and cell physiology that do not involve permanent genetic changes such as mutations and recombination, which are essential for adaptive immunity. The discovery of trained immunity may open the door for novel vaccine approaches, new therapeutic strategies for the treatment of immune deficiency states, and modulation of exaggerated inflammation in autoinflammatory diseases.
Collapse
Affiliation(s)
- Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Eicke Latz
- Institute of Innate Immunity, Bonn University, Bonn, Germany. Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA. German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute of Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| |
Collapse
|
194
|
Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Duale genetische Kodierung von Acetyllysin und nicht-hydrolysierbarem Thioacetyllysin mittels Flexizym. Angew Chem Int Ed Engl 2016; 128:4151-4154. [DOI: 10.1002/ange.201511750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hai Xiong
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Noah M. Reynolds
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Chenguang Fan
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery; Yale University; West Haven CT 06516 USA
| | - Scott J. Miller
- Department of Chemistry; Yale University; 225 Prospect Street New Haven CT 06511 USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
- Department of Chemistry; Yale University; 225 Prospect Street New Haven CT 06511 USA
| |
Collapse
|
195
|
Abstract
Growing evidence demonstrates that metabolism and chromatin dynamics are not separate processes but that they functionally intersect in many ways. For example, the lysine biosynthetic enzyme homocitrate synthase was recently shown to have unexpected functions in DNA damage repair, raising the question of whether other amino acid metabolic enzymes participate in chromatin regulation. Using an in silico screen combined with reporter assays, we discovered that a diverse range of metabolic enzymes function in heterochromatin regulation. Extended analysis of the glutamate dehydrogenase 1 (Gdh1) revealed that it regulates silent information regulator complex recruitment to telomeres and ribosomal DNA. Enhanced N-terminal histone H3 proteolysis is observed in GDH1 mutants, consistent with telomeric silencing defects. A conserved catalytic Asp residue is required for Gdh1's functions in telomeric silencing and H3 clipping. Genetic modulation of α-ketoglutarate levels demonstrates a key regulatory role for this metabolite in telomeric silencing. The metabolic activity of glutamate dehydrogenase thus has important and previously unsuspected roles in regulating chromatin-related processes.
Collapse
|
196
|
Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Dual Genetic Encoding of Acetyl-lysine and Non-deacetylatable Thioacetyl-lysine Mediated by Flexizyme. Angew Chem Int Ed Engl 2016; 55:4083-6. [PMID: 26914285 DOI: 10.1002/anie.201511750] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 11/10/2022]
Abstract
Acetylation of lysine residues is an important post-translational protein modification. Lysine acetylation in histones and its crosstalk with other post-translational modifications in histone and non-histone proteins are crucial to DNA replication, DNA repair, and transcriptional regulation. We incorporated acetyl-lysine (AcK) and the non-hydrolyzable thioacetyl-lysine (ThioAcK) into full-length proteins in vitro, mediated by flexizyme. ThioAcK and AcK were site-specifically incorporated at different lysine positions into human histone H3, either individually or in pairs. We demonstrate that the thioacetyl group in histone H3 could not be removed by the histone deacetylase sirtuin type 1. This method provides a powerful tool to study protein acetylation and its role in crosstalk between post-translational modifications.
Collapse
Affiliation(s)
- Hai Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Chenguang Fan
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Scott J Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.
| |
Collapse
|
197
|
Role of Natural Radiosensitizers and Cancer Cell Radioresistance: An Update. Anal Cell Pathol (Amst) 2016; 2016:6146595. [PMID: 26998418 PMCID: PMC4779816 DOI: 10.1155/2016/6146595] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/01/2016] [Indexed: 11/17/2022] Open
Abstract
Cancer originates from genetic mutations accumulation. Cancer stem cells have been depicted as tumorigenic cells that can differentiate and self-renew. Cancer stem cells are thought to be resistant to conventional therapy like chemotherapy and radiation therapy. Radiation therapy and chemotherapy damage carcinomic DNA cells. Because of the ability of cancer stem cells to self-renew and reproduce malignant tumors, they are the subject of intensive research. In this review, CSCs radioresistant mechanisms which include DNA damage response and natural radiosensitizers have been summed up. Reactive oxygen species play an important role in different physiological processes. ROS scavenging is responsible for regulation of reactive oxygen species generation. A researcher has proved that microRNAs regulate tumor radiation resistance. Ionizing radiation does not kill the cancer cells; rather, IR just slows down the signs and symptoms. Ionizing radiation damages DNA directly/indirectly. IR is given mostly in combination with other chemo/radiotherapies. We briefly described here the behavior of cancer stem cells and radioresistance therapies in cancer treatment. To overcome radioresistance in treatment of cancer, strategies like fractionation modification, treatment in combination, inflammation modification, and overcoming hypoxic tumor have been practiced. Natural radiosensitizers, for example, curcumin, genistein, and quercetin, are more beneficial than synthetic compounds.
Collapse
|
198
|
Covarrubias AJ, Aksoylar HI, Yu J, Snyder NW, Worth AJ, Iyer SS, Wang J, Ben-Sahra I, Byles V, Polynne-Stapornkul T, Espinosa EC, Lamming D, Manning BD, Zhang Y, Blair IA, Horng T. Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation. eLife 2016; 5. [PMID: 26894960 PMCID: PMC4769166 DOI: 10.7554/elife.11612] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022] Open
Abstract
Macrophage activation/polarization to distinct functional states is critically supported by metabolic shifts. How polarizing signals coordinate metabolic and functional reprogramming, and the potential implications for control of macrophage activation, remains poorly understood. Here we show that IL-4 signaling co-opts the Akt-mTORC1 pathway to regulate Acly, a key enzyme in Ac-CoA synthesis, leading to increased histone acetylation and M2 gene induction. Only a subset of M2 genes is controlled in this way, including those regulating cellular proliferation and chemokine production. Moreover, metabolic signals impinge on the Akt-mTORC1 axis for such control of M2 activation. We propose that Akt-mTORC1 signaling calibrates metabolic state to energetically demanding aspects of M2 activation, which may define a new role for metabolism in supporting macrophage activation.
Collapse
Affiliation(s)
- Anthony J Covarrubias
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Halil Ibrahim Aksoylar
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Jiujiu Yu
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Nathaniel W Snyder
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, United States.,A.J. Drexel Autism Institute, Drexel University, Philadelphia, United States
| | - Andrew J Worth
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, United States
| | - Shankar S Iyer
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
| | - Jiawei Wang
- Institute for Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Issam Ben-Sahra
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Vanessa Byles
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Tiffany Polynne-Stapornkul
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Erika C Espinosa
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Dudley Lamming
- Department of Medicine, University of Wisconsin-Madison, Madison, United States
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Yijing Zhang
- Institute for Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ian A Blair
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, United States
| | - Tiffany Horng
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| |
Collapse
|
199
|
Menendez JA, Corominas-Faja B, Cuyàs E, García MG, Fernández-Arroyo S, Fernández AF, Joven J, Fraga MF, Alarcón T. Oncometabolic Nuclear Reprogramming of Cancer Stemness. Stem Cell Reports 2016; 6:273-83. [PMID: 26876667 PMCID: PMC4788754 DOI: 10.1016/j.stemcr.2015.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 12/18/2022] Open
Abstract
By impairing histone demethylation and locking cells into a reprogramming-prone state, oncometabolites can partially mimic the process of induced pluripotent stem cell generation. Using a systems biology approach, combining mathematical modeling, computation, and proof-of-concept studies with live cells, we found that an oncometabolite-driven pathological version of nuclear reprogramming increases the speed and efficiency of dedifferentiating committed epithelial cells into stem-like states with only a minimal core of stemness transcription factors. Our biomathematical model, which introduces nucleosome modification and epigenetic regulation of cell differentiation genes to account for the direct effects of oncometabolites on nuclear reprogramming, demonstrates that oncometabolites markedly lower the “energy barriers” separating non-stem and stem cell attractors, diminishes the average time of nuclear reprogramming, and increases the size of the basin of attraction of the macrostate occupied by stem cells. These findings establish the concept of oncometabolic nuclear reprogramming of stemness as a bona fide metabolo-epigenetic mechanism for generation of cancer stem-like cells. Oncometabolites facilitate the reprogramming process evoked by stemness factors Oncometabolites lower the epigenetic barriers to nuclear reprogramming Cancer stem-like states arise through oncometabolic nuclear reprogramming phenomena Oncometabolic regulation of epigenetics can drive stemness in cancer tissues
Collapse
Affiliation(s)
- Javier A Menendez
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism and Cancer Group, Catalan Institute of Oncology, 17007 Girona, Catalonia, Spain; Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), 17190 Salt, Catalonia, Spain; Girona Biomedical Research Institute (IDIBGI), Parc Hospitalari Martí i Julià, Edifici M2, E-17190 Salt, Girona, Spain.
| | - Bruna Corominas-Faja
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), 17190 Salt, Catalonia, Spain
| | - Elisabet Cuyàs
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), 17190 Salt, Catalonia, Spain
| | - María G García
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Campus of International Excellence Southern Catalonia, 43201 Reus, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Campus of International Excellence Southern Catalonia, 43201 Reus, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain; Nanomaterials and Nanotechnology Research Center (CINN-CSIC), 33940 San Martín del Rey Aurelio, Spain
| | - Tomás Alarcón
- Institució Catalana d'Estudis i Recerca Avançats (ICREA), 08010 Barcelona, Spain; Computational & Mathematical Biology Research Group, Centre de Recerca Matemàtica (CRM), 08193 Barcelona, Spain; Departament de Matemàtiques, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; Barcelona Graduate School of Mathematics (BGSMath), 08193 Barcelona, Spain; Centre de Recerca Matemàtica (CRM), Office 29 (C3b/140), Edifici C, Campus de Bellaterra, E-08193 Bellaterra, Barcelona, Spain.
| |
Collapse
|
200
|
Efimova EV, Takahashi S, Shamsi NA, Wu D, Labay E, Ulanovskaya OA, Weichselbaum RR, Kozmin SA, Kron SJ. Linking Cancer Metabolism to DNA Repair and Accelerated Senescence. Mol Cancer Res 2016; 14:173-84. [PMID: 26538285 PMCID: PMC4755886 DOI: 10.1158/1541-7786.mcr-15-0263] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/22/2015] [Indexed: 01/14/2023]
Abstract
UNLABELLED Conventional wisdom ascribes metabolic reprogramming in cancer to meeting increased demands for intermediates to support rapid proliferation. Prior models have proposed benefits toward cell survival, immortality, and stress resistance, although the recent discovery of oncometabolites has shifted attention to chromatin targets affecting gene expression. To explore further effects of cancer metabolism and epigenetic deregulation, DNA repair kinetics were examined in cells treated with metabolic intermediates, oncometabolites, and/or metabolic inhibitors by tracking resolution of double-strand breaks (DSB) in irradiated MCF7 breast cancer cells. Disrupting cancer metabolism revealed roles for both glycolysis and glutaminolysis in promoting DSB repair and preventing accelerated senescence after irradiation. Targeting pathways common to glycolysis and glutaminolysis uncovered opposing effects of the hexosamine biosynthetic pathway (HBP) and tricarboxylic acid (TCA) cycle. Treating cells with the HBP metabolite N-acetylglucosamine (GlcNAc) or augmenting protein O-GlcNAcylation with small molecules or RNAi targeting O-GlcNAcase each enhanced DSB repair, while targeting O-GlcNAc transferase reversed GlcNAc's effects. Opposing the HBP, TCA metabolites including α-ketoglutarate blocked DSB resolution. Strikingly, DNA repair could be restored by the oncometabolite 2-hydroxyglutarate (2-HG). Targeting downstream effectors of histone methylation and demethylation implicated the PRC1/2 polycomb complexes as the ultimate targets for metabolic regulation, reflecting known roles for Polycomb group proteins in nonhomologous end-joining DSB repair. Our findings that epigenetic effects of cancer metabolic reprogramming may promote DNA repair provide a molecular mechanism by which deregulation of metabolism may not only support cell growth but also maintain cell immortality, drive therapeutic resistance, and promote genomic instability. IMPLICATIONS By defining a pathway from deregulated metabolism to enhanced DNA damage response in cancer, these data provide a rationale for targeting downstream epigenetic effects of metabolic reprogramming to block cancer cell immortality and overcome resistance to genotoxic stress.
Collapse
Affiliation(s)
- Elena V Efimova
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois. Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois
| | - Satoe Takahashi
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois. Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois
| | - Noumaan A Shamsi
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Ding Wu
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois. Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois
| | - Edwardine Labay
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois. Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois
| | | | - Ralph R Weichselbaum
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois. Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois
| | - Sergey A Kozmin
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois. Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois.
| |
Collapse
|