1
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Watanabe T, Hayashi S, Zhaoyu Y, Inada H, Nagaoka K, Tateyama M, Tanaka Y. A novel, small anti-HBV compound reduces HBsAg and HBV-DNA by destabilizing HBV-RNA. J Gastroenterol 2024; 59:315-328. [PMID: 38315437 DOI: 10.1007/s00535-023-02070-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/17/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Currently, standard treatments for chronic hepatitis B such as nucleos(t)ide analogs (NAs), effectively reduce hepatitis B virus (HBV) loads but rarely result in a functional cure (defined as sustained HBsAg loss). We report the discovery of a novel, 4-pyridone compound, SAG-524, a potent and orally bioavailable small molecule inhibitor of HBV replication. METHODS The antiviral characteristics and selectivity of SAG-524 and its derivative compound against HBV were evaluated in HBV-infection assays and HBV-infected chimeric urokinase-type plasminogen activator/severe combined immunodeficiency mice with humanized livers (PXB mice), alone or in combination with entecavir. Toxicity studies were conducted in mice and monkeys. RESULTS SAG-524 reduced HBV-DNA (IC50 = 0.92 nM) and HBsAg (IC50 = 1.4 nM) in the supernatant of the HepG2.2.15 cells. SAG-524 selectively destabilized HBV-RNA via PAPD5, but not GAPDH or albumin mRNA, by shortening the poly(A) tail. PAPD5 may also be involved in HBV regulation via ELAVL1. In a study of HBV-infected PXB mice, SAG-524 produced potent reductions of serum HBsAg and HBcrAg, and the minimum effective dose was estimated to be 6 mg/kg/day. The combination therapy with entecavir greatly reduced HBsAg and cccDNA in the liver due to reduction of human hepatocytes with good tolerability. Administration of SAG-524 to monkeys, up to 1000 mg/kg/day for two weeks, led to no significant toxicity, as determined by blood tests and pathological images. CONCLUSIONS We have identified SAG-524 as novel and orally bioavailable HBV-RNA destabilizers which can reduce HBsAg and HBV-DNA levels, and possibly contribute a functional cure.
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Affiliation(s)
- Takehisa Watanabe
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan
| | - Sanae Hayashi
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan
| | - Yan Zhaoyu
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan
| | - Hiroki Inada
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan
| | - Katsuya Nagaoka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan
| | - Masakuni Tateyama
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo, Kumamoto, 860-8556, Japan.
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Science, Nagoya, Japan.
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2
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Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
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Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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3
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Narahara S, Watanabe T, Nagaoka K, Fujimoto N, Furuta Y, Tanaka K, Tokunaga T, Kawasaki T, Yoshimaru Y, Setoyama H, Oniki K, Saruwatari J, Tateyama M, Naoe H, Tanaka M, Tanaka Y, Sasaki Y. Clusterin and Related Scoring Index as Potential Early Predictors of Response to Sorafenib in Hepatocellular Carcinoma. Hepatol Commun 2022; 6:1198-1212. [PMID: 34837478 PMCID: PMC9035573 DOI: 10.1002/hep4.1872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022] Open
Abstract
Advanced hepatocellular carcinoma (HCC) remains a highly lethal malignancy, although several systemic therapeutic options are available, including sorafenib (SFN), which has been one of the standard treatment agents for almost a decade. As early prediction of response to SFN remains challenging, biomarkers that enable early prediction using a clinically feasible method are needed. Here, we report that the serum secretory form of clusterin (sCLU) protein and its related predictive index are potential beneficial biomarkers for early prediction of SFN response. Using high-throughput screening and subsequent multivariate analysis in the derivation cohort, we found that changes in the concentrations of CLU, vascular cell adhesion molecule-1 (VCAM1), and α-fetoprotein were significantly associated with response to SFN. Furthermore, we confirmed that an increase in CLU serum level 1 month after treatment initiation was significantly associated with shorter progression-free survival. In addition, "NR-index," which comprises these proteins, was evaluated as a tool for accurately predicting the efficacy of SFN and confirmed in the validation cohort. We also established SFN-resistant HepG2 cells (HepG2-SR) and found that sCLU significantly increased in HepG2-SR cells compared with normal HepG2 cells, and confirmed that HepG2-SR cells treated with SFN were resistant to apoptosis. The mechanism underlying activation of sCLU expression in acquired SFN resistance involves aberrant signaling and expression of Akt, mammalian target of rapamycin (mTOR), and a nutrient-related transcription factor, sterol regulatory element binding protein 1c (SREBP-1c). Furthermore, the PI3K and mTOR inhibitor BEZ235 markedly decreased sCLU expression in HepG2-SR cells. Conclusion: These results suggest that measurement of sCLU serum levels and the sCLU-related NR-index are promising clinical tools for the early prediction of SFN response in HCC. Additionally, sCLU-overexpressing HCC might be susceptible to mTOR inhibition.
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Affiliation(s)
- Satoshi Narahara
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Takehisa Watanabe
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Katsuya Nagaoka
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Nahoko Fujimoto
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Yoki Furuta
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Kentaro Tanaka
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Takayuki Tokunaga
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Takeshi Kawasaki
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Yoko Yoshimaru
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Hiroko Setoyama
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Kentaro Oniki
- Department of Pharmacology and Therapeutics Graduate School of Pharmaceutical SciencesKumamoto UniversityKumamotoJapan
| | - Junji Saruwatari
- Department of Pharmacology and Therapeutics Graduate School of Pharmaceutical SciencesKumamoto UniversityKumamotoJapan
| | - Masakuni Tateyama
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Hideaki Naoe
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Motohiko Tanaka
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan.,Public Health and Welfare BureauCity of KumamotoKumamotoJapan
| | - Yasuhito Tanaka
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Yutaka Sasaki
- Department of Gastroenterology and HepatologyFaculty of Life SciencesKumamoto UniversityKumamotoJapan.,Department of Health and NutritionFaculty of Health ManagementNagasaki International UniversityNagasakiJapan
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4
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Regulation of Transcription Factor NF-κB in Its Natural Habitat: The Nucleus. Cells 2021; 10:cells10040753. [PMID: 33805563 PMCID: PMC8066257 DOI: 10.3390/cells10040753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 01/11/2023] Open
Abstract
Activation of the transcription factor NF-κB elicits an individually tailored transcriptional response in order to meet the particular requirements of specific cell types, tissues, or organs. Control of the induction kinetics, amplitude, and termination of gene expression involves multiple layers of NF-κB regulation in the nucleus. Here we discuss some recent advances in our understanding of the mutual relations between NF-κB and chromatin regulators also in the context of different levels of genome organization. Changes in the 3D folding of the genome, as they occur during senescence or in cancer cells, can causally contribute to sustained increases in NF-κB activity. We also highlight the participation of NF-κB in the formation of hierarchically organized super enhancers, which enable the coordinated expression of co-regulated sets of NF-κB target genes. The identification of mechanisms allowing the specific regulation of NF-κB target gene clusters could potentially enable targeted therapeutic interventions, allowing selective interference with subsets of the NF-κB response without a complete inactivation of this key signaling system.
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5
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Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders affecting the gastrointestinal tract. The incidence of IBD is increasing, with more cases occurring in developed countries. Multiple factors such as genetics, environmental changes, gut microbiota, and immune abnormalities have been associated with development of IBD. In recent years, it has become increasingly apparent that epigenetic modifications of chromatin and the manner in which chromatin is organized in the nucleus are additionally important elements that can influence responses induced by the factors described above, and may therefore contribute to the onset and pathogenesis of IBD. Epigenetics and chromatin organization regulate diverse functions that include maintenance of homeostasis in the intestinal epithelium, the development and differentiation of immune cells, and modulation of responses generated by the immune system to defend against potential pathogens. Furthermore, changes in epigenetic chromatin marks and in chromatin organization have now been linked to differential gene expression in IBD patient cells. Although direct evidence for a role of histone modifications in IBD is currently very limited, in this review, we summarize the links between various epigenetic modifications, the proteins that catalyze or recognize these modifications, and the development or progression of IBD in human and experimental IBD. We also discuss how epigenetics influence the organization of DNA contacts to regulate gene expression and the implications this may have for diagnosing and treating IBD.
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Affiliation(s)
- Greeshma Ray
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michelle S Longworth
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA,Address correspondence to: Michelle S. Longworth, 9500 Euclid Ave NC22, Cleveland, OH 44195 ()
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6
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Peterson JM, Wang DJ, Shettigar V, Roof SR, Canan BD, Bakkar N, Shintaku J, Gu JM, Little SC, Ratnam NM, Londhe P, Lu L, Gaw CE, Petrosino JM, Liyanarachchi S, Wang H, Janssen PML, Davis JP, Ziolo MT, Sharma SM, Guttridge DC. NF-κB inhibition rescues cardiac function by remodeling calcium genes in a Duchenne muscular dystrophy model. Nat Commun 2018; 9:3431. [PMID: 30143619 PMCID: PMC6109146 DOI: 10.1038/s41467-018-05910-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 07/25/2018] [Indexed: 12/20/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a neuromuscular disorder causing progressive muscle degeneration. Although cardiomyopathy is a leading mortality cause in DMD patients, the mechanisms underlying heart failure are not well understood. Previously, we showed that NF-κB exacerbates DMD skeletal muscle pathology by promoting inflammation and impairing new muscle growth. Here, we show that NF-κB is activated in murine dystrophic (mdx) hearts, and that cardiomyocyte ablation of NF-κB rescues cardiac function. This physiological improvement is associated with a signature of upregulated calcium genes, coinciding with global enrichment of permissive H3K27 acetylation chromatin marks and depletion of the transcriptional repressors CCCTC-binding factor, SIN3 transcription regulator family member A, and histone deacetylase 1. In this respect, in DMD hearts, NF-κB acts differently from its established role as a transcriptional activator, instead promoting global changes in the chromatin landscape to regulate calcium genes and cardiac function.
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Affiliation(s)
- Jennifer M Peterson
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Binghamton, NY, 13902, USA
| | - David J Wang
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, 29425, USA
| | - Vikram Shettigar
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA
| | - Steve R Roof
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA.,Q Test Labs, Columbus, OH, 43235, USA
| | - Benjamin D Canan
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA
| | - Nadine Bakkar
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Neurobiology, St Joseph's Hospital and Medical Center-Barrow Neurological Institute, Phoenix, AZ, 85013, USA
| | - Jonathan Shintaku
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Jin-Mo Gu
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Biomedical Engineering and Pediatrics, Emory University, Decatur, GA, 30322, USA
| | - Sean C Little
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA.,Bristol-Myers Squibb, Wallingford, CT, 06492, USA
| | - Nivedita M Ratnam
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA
| | - Priya Londhe
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, 02111, USA
| | - Leina Lu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Christopher E Gaw
- The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jennifer M Petrosino
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA
| | - Sandya Liyanarachchi
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul M L Janssen
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA
| | - Jonathan P Davis
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA
| | - Mark T Ziolo
- Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA.,The Ohio State University Medical Center, Columbus, OH, 43210, USA.,Department of Physiology and Cell Biology, The Ohio State University Medical Center, Columbus, 43210, Ohio, USA
| | - Sudarshana M Sharma
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Denis C Guttridge
- Department of Cancer Biology and Genetics, Columbus, OH, 43210, USA. .,Center for Muscle Health and Neuromuscular Disorders, Columbus, OH, 43210, USA. .,The Ohio State University Medical Center, Columbus, OH, 43210, USA. .,Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, 29425, USA.
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7
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DDX39 promotes hepatocellular carcinoma growth and metastasis through activating Wnt/β-catenin pathway. Cell Death Dis 2018; 9:675. [PMID: 29867138 PMCID: PMC5986742 DOI: 10.1038/s41419-018-0591-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/20/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer related death worldwide; however, the molecular mechanisms regulating HCC progression remain largely unknown. In this study, we determined the role of DDX39 which a DEAD-box RNA helicase in HCC progression, and found DDX39 was upregulated in HCC tissues and cells, DDX39 expression was positive correlated with advanced clinical stage, survival analysis showed patients with high-DDX39 levels had poor outcome, it was an independent prognostic factor. Functional analysis revealed that DDX39 overexpression promoted HCC cell migration, invasion, growth, and metastasis, DDX39 knockdown inhibited HCC cell migration, invasion, growth, and metastasis. Mechanism analysis suggested DDX39 overexpression increased β-catenin expression in nucleus and increased Wnt/β-catenin pathway target genes levels, while DDX39 knockdown reduced this effect. Knockdown of Wnt/β-catenin pathway co-activators TCF4 and LEF1 in DDX39 overexpressing HCC cells inhibited Wnt/β-catenin pathway target genes. The invasion ability was also reduced, confirming DDX39 regulates HCC progression by activating Wnt/β-catenin pathway. In conclusion, we found DDX39 is a target and prognostic factor for HCC, and promotes HCC migration, invasion, growth, and metastasis by activating Wnt/β-catenin pathway.
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8
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Carini C, Hunter E, Ramadass AS, Green J, Akoulitchev A, McInnes IB, Goodyear CS. Chromosome conformation signatures define predictive markers of inadequate response to methotrexate in early rheumatoid arthritis. J Transl Med 2018; 16:18. [PMID: 29378619 PMCID: PMC5789697 DOI: 10.1186/s12967-018-1387-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/13/2018] [Indexed: 12/15/2022] Open
Abstract
Background There is a pressing need in rheumatoid arthritis (RA) to identify patients who will not respond to first-line disease-modifying anti-rheumatic drugs (DMARD). We explored whether differences in genomic architecture represented by a chromosome conformation signature (CCS) in blood taken from early RA patients before methotrexate (MTX) treatment could assist in identifying non-response to DMARD and, whether there is an association between such a signature and RA specific expression quantitative trait loci (eQTL). Methods We looked for the presence of a CCS in blood from early RA patients commencing MTX using chromosome conformation capture by EpiSwitch™. Using blood samples from MTX responders, non-responders and healthy controls, a custom designed biomarker discovery array was refined to a 5-marker CCS that could discriminate between responders and non-responders to MTX. We cross-validated the predictive power of the CCS by generating 150 randomized groups of 59 early RA patients (30 responders and 29 non-responders) before MTX treatment. The CCS was validated using a blinded, independent cohort of 19 early RA patients (9 responders and 10 non-responders). Last, the loci of the CCS markers were mapped to RA-specific eQTL. Results We identified a 5-marker CCS that could identify, at baseline, responders and non-responders to MTX. The CCS consisted of binary chromosome conformations in the genomic regions of IFNAR1, IL-21R, IL-23, CXCL13 and IL-17A. When tested on a cohort of 59 RA patients, the CCS provided a negative predictive value of 90.0% for MTX response. When tested on a blinded independent validation cohort of 19 early RA patients, the signature demonstrated a true negative response rate of 86 and a 90% sensitivity for detection of non-responders to MTX. Only conformations in responders mapped to RA-specific eQTL. Conclusions Here we demonstrate that detection of a CCS in blood in early RA is able to predict inadequate response to MTX with a high degree of accuracy. Our results provide a proof of principle that a priori stratification of response to MTX is possible, offering a mechanism to provide alternative treatments for non-responders to MTX earlier in the course of the disease. Electronic supplementary material The online version of this article (10.1186/s12967-018-1387-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudio Carini
- Pfizer Inc., Cambridge, USA. .,Department of Asthma, Allergy & Lung Biology, GSTT Campus, King's College School of Medicine, London, UK.
| | | | | | | | | | | | - Iain B McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Carl S Goodyear
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
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9
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Wang X, Ma C, Zong Z, Xiao Y, Li N, Guo C, Zhang L, Shi Y. A20 inhibits the motility of HCC cells induced by TNF-α. Oncotarget 2018; 7:14742-54. [PMID: 26909601 PMCID: PMC4924748 DOI: 10.18632/oncotarget.7521] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 01/26/2016] [Indexed: 02/06/2023] Open
Abstract
Metastasis of hepatocellular carcinoma (HCC) can be facilitated by TNF-α, a prototypical inflammatory cytokine in the HCC microenvironment. A20 is a negative regulator of NF-κB signaling pathway. In the present study we ask whether A20 plays a role in HCC metastasis. We found that A20 expression was downregulated in the invasive cells of microvascular invasions (MVI) compared with the noninvasive cells in 89 tissue samples from patients with HCC by immunochemistry methods. Overexpression of A20 in HCC cell lines inhibited their motility induced by TNF-α. Furthermore, the overexpression of A20 inhibited epithelial-mesenchymal transition (EMT), FAK activation and RAC1 activity. By contrast, knockdown of A20 in one HCC cell line results in the converse. In addition, the overexpression of A20 restrained the formation of MVI in HCC xenograft in nude mice treated with TNF-α. All the results suggested that A20 functioned as a negative regulator in motility of HCC cells induced by TNF-α.
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Affiliation(s)
- Xianteng Wang
- Department of Immunology, Shandong University School of Medicine, Jinan, China
| | - Chao Ma
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Zhaoyun Zong
- Department of Immunology, Shandong University School of Medicine, Jinan, China
| | - Ying Xiao
- Laboratory of Cellular and Molecular Medicine, Shandong University School of Medicine, Jinan, China
| | - Na Li
- Department of Immunology, Shandong University School of Medicine, Jinan, China
| | - Chun Guo
- Department of Immunology, Shandong University School of Medicine, Jinan, China
| | - Lining Zhang
- Department of Immunology, Shandong University School of Medicine, Jinan, China
| | - Yongyu Shi
- Department of Immunology, Shandong University School of Medicine, Jinan, China
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10
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Ishihara K, Nakamoto M, Nakao M. DNA methylation-independent removable insulator controls chromatin remodeling at the HOXA locus via retinoic acid signaling. Hum Mol Genet 2017; 25:5383-5394. [PMID: 27798106 DOI: 10.1093/hmg/ddw354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/12/2016] [Indexed: 11/14/2022] Open
Abstract
Chromatin insulators partition the genome into functional units to control gene expression, particularly in complex chromosomal regions. The CCCTC-binding factor (CTCF) is an insulator-binding protein that functions in transcriptional regulation and higher-order chromatin formation. Variable CTCF-binding sites have been identified to be cell type-specific partly due to differential DNA methylation. Here, we show that DNA methylation-independent removable CTCF insulator is responsible for retinoic acid (RA)-mediated higher-order chromatin remodeling in the human HOXA gene locus. Detailed chromatin analysis characterized multiple CTCF-enriched sites and RA-responsive enhancers at this locus. These regulatory elements and transcriptionally silent HOXA genes are closely positioned under basal conditions. Notably, upon RA signaling, the RAR/RXR transcription factor induced loss of adjacent CTCF binding and changed the higher-order chromatin conformation of the overall locus. Targeted disruption of a CTCF site by genome editing with zinc finger nucleases and CRISPR/Cas9 system showed that the site is required for chromatin conformations that maintain the initial associations among insulators, enhancers and promoters. The results indicate that the initial chromatin conformation affects subsequent RA-induced HOXA gene activation. Our study uncovers that a removable insulator spatiotemporally switches higher-order chromatin and multiple gene activities via cooperation of CTCF and key transcription factors.
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Affiliation(s)
- Ko Ishihara
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan.,Core Research for Evolutionary Science and Technology (CREST), Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Masafumi Nakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.,Core Research for Evolutionary Science and Technology (CREST), Japan Agency for Medical Research and Development, Tokyo, Japan
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11
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Higher-Order Chromatin Regulation of Inflammatory Gene Expression. Mediators Inflamm 2017; 2017:7848591. [PMID: 28490839 PMCID: PMC5401750 DOI: 10.1155/2017/7848591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Whether it is caused by viruses and bacteria infection, or low-grade chronic inflammation of atherosclerosis and cellular senescence, the transcription factor (TF) NF-κB plays a central role in the inducible expression of inflammatory genes. Accumulated evidence has indicated that the chromatin environment is the main determinant of TF binding in gene expression regulation, including the stimulus-responsive NF-κB. Dynamic changes in intra- and interchromosomes are the key regulatory mechanisms promoting the binding of TFs. When an inflammatory process is triggered, NF-κB binds to enhancers or superenhancers, triggering the transcription of enhancer RNA (eRNA), driving the chromatin of the NF-κB-binding gene locus to construct transcriptional factories, and forming intra- or interchromosomal contacts. These processes reveal a mechanism in which intrachromosomal contacts appear to be cis-control enhancer-promoter communications, whereas interchromosomal regulatory elements construct trans-form relationships with genes on other chromosomes. This article will review emerging evidence on the genome organization hierarchy underlying the inflammatory response.
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12
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Nakamoto M, Ishihara K, Watanabe T, Hirosue A, Hino S, Shinohara M, Nakayama H, Nakao M. The Glucocorticoid Receptor Regulates the ANGPTL4 Gene in a CTCF-Mediated Chromatin Context in Human Hepatic Cells. PLoS One 2017; 12:e0169225. [PMID: 28056052 PMCID: PMC5215901 DOI: 10.1371/journal.pone.0169225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
Glucocorticoid signaling through the glucocorticoid receptor (GR) plays essential roles in the response to stress and in energy metabolism. This hormonal action is integrated to the transcriptional control of GR-target genes in a cell type-specific and condition-dependent manner. In the present study, we found that the GR regulates the angiopoietin-like 4 gene (ANGPTL4) in a CCCTC-binding factor (CTCF)-mediated chromatin context in the human hepatic HepG2 cells. There are at least four CTCF-enriched sites and two GR-binding sites within the ANGPTL4 locus. Among them, the major CTCF-enriched site is positioned near the ANGPTL4 enhancer that binds GR. We showed that CTCF is required for induction and subsequent silencing of ANGPTL4 expression in response to dexamethasone (Dex) and that transcription is diminished after long-term treatment with Dex. Although the ANGPTL4 locus maintains a stable higher-order chromatin conformation in the presence and absence of Dex, the Dex-bound GR activated transcription of ANGPTL4 but not that of the neighboring three genes through interactions among the ANGPTL4 enhancer, promoter, and CTCF sites. These results reveal that liganded GR spatiotemporally controls ANGPTL4 transcription in a chromosomal context.
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Affiliation(s)
- Masafumi Nakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ko Ishihara
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
- * E-mail: (MiN); (KI)
| | - Takehisa Watanabe
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Akiyuki Hirosue
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideki Nakayama
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Agency for Medical Research and Development, Tokyo, Japan
- * E-mail: (MiN); (KI)
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13
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Ito K, Sanosaka T, Igarashi K, Ideta-Otsuka M, Aizawa A, Uosaki Y, Noguchi A, Arakawa H, Nakashima K, Takizawa T. Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation. Sci Rep 2016; 6:23903. [PMID: 27041678 PMCID: PMC4819225 DOI: 10.1038/srep23903] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2016] [Indexed: 01/15/2023] Open
Abstract
Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus, and gene clustering is of great significance in transcriptional regulation. However, the relevance of gene clustering and their expression during the differentiation of neural precursor cells (NPCs) into astrocytes remains unclear. We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen for genes associated with the astrocyte-specific gene glial fibrillary acidic protein (Gfap) during astrocyte differentiation. We identified 18 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes. Our results provide additional evidence for the functional significance of gene clustering in transcriptional regulation during NPC differentiation.
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Affiliation(s)
- Kenji Ito
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Tsukasa Sanosaka
- Stem Cell Biology and Medicine, Department of Stem cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Katsuhide Igarashi
- Life Science Tokyo Advanced Research Center (L-StaR), Pharmacy and Pharmaceutical Science, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Maky Ideta-Otsuka
- Life Science Tokyo Advanced Research Center (L-StaR), Pharmacy and Pharmaceutical Science, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Akira Aizawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Yuichi Uosaki
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Azumi Noguchi
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Hirokazu Arakawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Kinichi Nakashima
- Stem Cell Biology and Medicine, Department of Stem cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takumi Takizawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
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14
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The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome. Proc Natl Acad Sci U S A 2016; 113:3054-9. [PMID: 26929370 DOI: 10.1073/pnas.1423199113] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human T-lymphotropic virus type 1 (HTLV-1) is a retrovirus that causes malignant and inflammatory diseases in ∼10% of infected people. A typical host has between 10(4) and 10(5) clones of HTLV-1-infected T lymphocytes, each clone distinguished by the genomic integration site of the single-copy HTLV-1 provirus. The HTLV-1 bZIP (HBZ) factor gene is constitutively expressed from the minus strand of the provirus, whereas plus-strand expression, required for viral propagation to uninfected cells, is suppressed or intermittent in vivo, allowing escape from host immune surveillance. It remains unknown what regulates this pattern of proviral transcription and latency. Here, we show that CTCF, a key regulator of chromatin structure and function, binds to the provirus at a sharp border in epigenetic modifications in the pX region of the HTLV-1 provirus in T cells naturally infected with HTLV-1. CTCF is a zinc-finger protein that binds to an insulator region in genomic DNA and plays a fundamental role in controlling higher order chromatin structure and gene expression in vertebrate cells. We show that CTCF bound to HTLV-1 acts as an enhancer blocker, regulates HTLV-1 mRNA splicing, and forms long-distance interactions with flanking host chromatin. CTCF-binding sites (CTCF-BSs) have been propagated throughout the genome by transposons in certain primate lineages, but CTCF binding has not previously been described in present-day exogenous retroviruses. The presence of an ectopic CTCF-BS introduced by the retrovirus in tens of thousands of genomic locations has the potential to cause widespread abnormalities in host cell chromatin structure and gene expression.
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15
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Abe Y, Rozqie R, Matsumura Y, Kawamura T, Nakaki R, Tsurutani Y, Tanimura-Inagaki K, Shiono A, Magoori K, Nakamura K, Ogi S, Kajimura S, Kimura H, Tanaka T, Fukami K, Osborne TF, Kodama T, Aburatani H, Inagaki T, Sakai J. JMJD1A is a signal-sensing scaffold that regulates acute chromatin dynamics via SWI/SNF association for thermogenesis. Nat Commun 2015; 6:7052. [PMID: 25948511 PMCID: PMC4432656 DOI: 10.1038/ncomms8052] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/27/2015] [Indexed: 12/11/2022] Open
Abstract
Histone 3 lysine 9 (H3K9) demethylase JMJD1A regulates β-adrenergic-induced systemic metabolism and body weight control. Here we show that JMJD1A is phosphorylated at S265 by protein kinase A (PKA), and this is pivotal to activate the β1-adrenergic receptor gene (Adrb1) and downstream targets including Ucp1 in brown adipocytes (BATs). Phosphorylation of JMJD1A by PKA increases its interaction with the SWI/SNF nucleosome remodelling complex and DNA-bound PPARγ. This complex confers β-adrenergic-induced rapid JMJD1A recruitment to target sites and facilitates long-range chromatin interactions and target gene activation. This rapid gene induction is dependent on S265 phosphorylation but not on demethylation activity. Our results show that JMJD1A has two important roles in regulating hormone-stimulated chromatin dynamics that modulate thermogenesis in BATs. In one role, JMJD1A is recruited to target sites and functions as a cAMP-responsive scaffold that facilitates long-range chromatin interactions, and in the second role, JMJD1A demethylates H3K9 di-methylation. Demethylase JMJD1A activates thermogenesis-related target genes in response to β-adrenergic hormones. Here, the authors show that phosphorylation of JMJD1A at S265 increases its interaction with the SWI/SNF chromatin remodeler, leading to long-range chromatin interactions and target gene activation.
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Affiliation(s)
- Yohei Abe
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Royhan Rozqie
- 1] Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [2] Department of Cardiology and Vascular Medicine, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Yoshihiro Matsumura
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Takeshi Kawamura
- 1] Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [2] The Translational Systems Biology and Medicine Initiative, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Ryo Nakaki
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Yuya Tsurutani
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Kyoko Tanimura-Inagaki
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Akira Shiono
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Kenta Magoori
- 1] Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [2] The Translational Systems Biology and Medicine Initiative, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Kanako Nakamura
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Shotaro Ogi
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Shingo Kajimura
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143-0669, USA
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Toshiya Tanaka
- 1] Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [2] Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [3] The Translational Systems Biology and Medicine Initiative, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Kiyoko Fukami
- Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Timothy F Osborne
- Metabolic Disease Program, Sanford-Burnham Medical Research Institute, Orlando, Florida 32827, USA
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Hiroyuki Aburatani
- 1] The Translational Systems Biology and Medicine Initiative, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8655, Japan [2] Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Takeshi Inagaki
- 1] Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [2] The Translational Systems Biology and Medicine Initiative, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Juro Sakai
- 1] Division of Metabolic Medicine, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan [2] The Translational Systems Biology and Medicine Initiative, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-8655, Japan
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16
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Sakamoto A, Hino S, Nagaoka K, Anan K, Takase R, Matsumori H, Ojima H, Kanai Y, Arita K, Nakao M. Lysine Demethylase LSD1 Coordinates Glycolytic and Mitochondrial Metabolism in Hepatocellular Carcinoma Cells. Cancer Res 2015; 75:1445-56. [PMID: 25649769 DOI: 10.1158/0008-5472.can-14-1560] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/22/2014] [Indexed: 11/16/2022]
Abstract
The hallmark of most cancer cells is the metabolic shift from mitochondrial to glycolytic metabolism for adapting to the surrounding environment. Although epigenetic modification is intimately linked to cancer, the molecular mechanism, by which epigenetic factors regulate cancer metabolism, is poorly understood. Here, we show that lysine-specific demethylase-1 (LSD1, KDM1A) has an essential role in maintaining the metabolic shift in human hepatocellular carcinoma cells. Inhibition of LSD1 reduced glucose uptake and glycolytic activity, with a concurrent activation of mitochondrial respiration. These metabolic changes coexisted with the inactivation of the hypoxia-inducible factor HIF1α, resulting in a decreased expression of GLUT1 and glycolytic enzymes. In contrast, during LSD1 inhibition, a set of mitochondrial metabolism genes was activated with the concomitant increase of methylated histone H3 at lysine 4 in the promoter regions. Consistently, both LSD1 and GLUT1 were significantly overexpressed in carcinoma tissues. These findings demonstrate the epigenetic plasticity of cancer cell metabolism, which involves an LSD1-mediated mechanism.
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Affiliation(s)
- Akihisa Sakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan Department of Neurosurgery, Faculty of Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Katsuya Nagaoka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Kotaro Anan
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Ryuta Takase
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Haruka Matsumori
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Hidenori Ojima
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazunori Arita
- Department of Neurosurgery, Faculty of Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan.
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17
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Lu TT, Browning JL. Role of the Lymphotoxin/LIGHT System in the Development and Maintenance of Reticular Networks and Vasculature in Lymphoid Tissues. Front Immunol 2014; 5:47. [PMID: 24575096 PMCID: PMC3920476 DOI: 10.3389/fimmu.2014.00047] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/27/2014] [Indexed: 01/08/2023] Open
Abstract
Lymphoid organs are meeting zones where lymphocytes come together and encounter antigens present in the blood and lymph or as delivered by cells migrating from the draining tissue bed. The exquisite efficiency of this process relies heavily on highly specialized anatomy to direct and position the various players. Gated entry and exit control access to these theaters and reticular networks and associated chemokines guide cells into the proper sections. Lymphoid tissues are remarkably plastic, being able to expand dramatically and then involute upon resolution of the danger. All of the reticular scaffolds and vascular and lymphatic components adapt accordingly. As such, the lymph node (LN) is a wonderful example of a physiologic remodeling process and is potentially a guide to study such elements in pathological settings such as fibrosis, chronic infection, and tumor metastasis. The lymphotoxin/LIGHT axis delivers critical differentiation signals that direct and hone differentiation of both reticular networks and the vasculature. Considerable progress has been made recently in understanding the mesenchymal differentiation pathways leading to these specialized networks and in the remodeling that occurs in reactive LNs. In this article, we will review some new advances in the area in terms of developmental, differentiation, and maintenance events mediated by this axis.
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Affiliation(s)
- Theresa T Lu
- Autoimmunity and Inflammation Program and Pediatric Rheumatology, Hospital for Special Surgery , New York, NY , USA ; Department of Microbiology and Immunology, Weill Cornell Medical College , New York, NY , USA
| | - Jeffrey L Browning
- Department of Microbiology and Section of Rheumatology, Boston University School of Medicine , Boston, MA , USA
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18
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Saito Y, Hibino S, Saito H. Alterations of epigenetics and microRNA in hepatocellular carcinoma. Hepatol Res 2014; 44:31-42. [PMID: 23617364 DOI: 10.1111/hepr.12147] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/12/2013] [Accepted: 04/21/2013] [Indexed: 01/05/2023]
Abstract
Studies have shown that alterations of epigenetics and microRNA (miRNA) play critical roles in the initiation and progression of hepatocellular carcinoma (HCC). Epigenetic silencing of tumor suppressor genes in HCC is generally mediated by DNA hypermethylation of CpG island promoters and histone modifications such as histone deacetylation, methylation of histone H3 lysine 9 (H3K9) and tri-methylation of H3K27. Chromatin-modifying drugs such as DNA methylation inhibitors and histone deacetylase inhibitors have shown clinical promise for cancer therapy. miRNA are small non-coding RNA that regulate expression of various target genes. Specific miRNA are aberrantly expressed and play roles as tumor suppressors or oncogenes during hepatocarcinogenesis. We and other groups have demonstrated that important tumor suppressor miRNA are silenced by epigenetic alterations, resulting in activation of target oncogenes in human malignancies including HCC. Restoring the expression of tumor suppressor miRNA by inhibitors of DNA methylation and histone deacetylase may be a promising therapeutic strategy for HCC.
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Affiliation(s)
- Yoshimasa Saito
- Division of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Tokyo, Japan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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19
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Marshall AD, Bailey CG, Rasko JEJ. CTCF and BORIS in genome regulation and cancer. Curr Opin Genet Dev 2013; 24:8-15. [PMID: 24657531 DOI: 10.1016/j.gde.2013.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 10/25/2022]
Abstract
CTCF plays a vital role in chromatin structure and function. CTCF is ubiquitously expressed and plays diverse roles in gene regulation, imprinting, insulation, intra/interchromosomal interactions, nuclear compartmentalisation, and alternative splicing. CTCF has a single paralogue, the testes-specific CTCF-like gene (CTCFL)/BORIS. CTCF and BORIS can be deregulated in cancer. The tumour suppressor gene CTCF can be mutated or deleted in cancer, or CTCF DNA binding can be altered by epigenetic changes. BORIS is aberrantly expressed frequently in cancer, leading some to propose a pro-tumourigenic role for BORIS. However, BORIS can inhibit cell proliferation, and is mutated in cancer similarly to CTCF suggesting BORIS activation in cancer may be due to global genetic or epigenetic changes typical of malignant transformation.
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Affiliation(s)
- Amy D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, NSW, Australia.
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20
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Song K, Han C, Zhang J, Lu D, Dash S, Feitelson M, Lim K, Wu T. Epigenetic regulation of MicroRNA-122 by peroxisome proliferator activated receptor-gamma and hepatitis b virus X protein in hepatocellular carcinoma cells. Hepatology 2013; 58:1681-92. [PMID: 23703729 PMCID: PMC3773012 DOI: 10.1002/hep.26514] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 03/12/2013] [Accepted: 05/02/2013] [Indexed: 12/14/2022]
Abstract
UNLABELLED MicroRNA-122 (miR-122), a pivotal liver-specific miRNA, has been implicated in several liver diseases including hepatocellular carcinoma (HCC) and hepatitis C and B viral infection. This study aimed to explore epigenetic regulation of miR-122 in human HCC cells and to examine the effect of hepatitis C virus (HCV) and hepatitis B virus (HBV). We performed microRNA microarray analysis and identified miR-122 as the most up-regulated miRNA (6-fold) in human HCC cells treated with 5'aza-2'deoxycytidine (5-Aza-CdR, DNA methylation inhibitor) and 4-phenylbutyric acid (PBA, histone deacetylation inhibitor). Real-time polymerase chain reaction (PCR) analysis verified significant up-regulation of miR-122 by 5'aza and PBA in HCC cells, and to a lesser extent in primary hepatocytes. Peroxisome proliferator activated receptor-gamma (PPARγ) and retinoid X receptor alpha (RXRα) complex was found to be associated with the DR1 and DR2 consensus site in the miR-122 gene promoter which enhanced miR-122 gene transcription. 5-Aza-CdR and PBA treatment increased the association of PPARγ/RXRα, but decreased the association of its corepressors (N-CoR and SMRT), with the miR-122 DR1 and DR2 motifs. The aforementioned DNA-protein complex also contains SUV39H1, an H3K9 histone methyl transferase, which down-regulates miR-122 expression. CONCLUSIONS These findings establish a novel role of the PPARγ binding complex for epigenetic regulation of miR-122 in human HCC cells. Moreover, we show that hepatitis B virus X protein binds PPARγ and inhibits the transcription of miR-122, whereas hepatitis C viral particles exhibited no significant effect; these findings provide mechanistic insight into reduction of miR-122 in patients with HBV but not with HCV infection.
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Affiliation(s)
- Kyoungsub Song
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Chang Han
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Jinqiang Zhang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Dongdong Lu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Srikanta Dash
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Mark Feitelson
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122
| | - Kyu Lim
- Department of Biochemistry, College of Medicine, Cancer Research Institute and Infection Signaling Network Research Center, Chungnam National University, Daejeon, Korea
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
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21
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Yu X, Huang Y, Li C, Yang H, Lu C, Duan S. Positive association between lymphotoxin-alpha variation rs909253 and cancer risk: a meta-analysis based on 36 case-control studies. Tumour Biol 2013; 35:1973-83. [PMID: 24136744 DOI: 10.1007/s13277-013-1263-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/25/2013] [Indexed: 01/14/2023] Open
Abstract
Lymphotoxin-alpha (LTA) polymorphism rs909253 has been reported to be a risk factor for cancers, but some results are inconsistent. To establish a more conclusive association, we performed a meta-analysis of this variant with cancers. A systematic search was performed for informative case-control studies of rs909253 with cancers among literature databases, including PubMed, Web of Science, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang Chinese Periodical Database. After a comprehensive filtration procedure, 36 publications involved with 35,677 participants were selected for the current meta-analysis. Stratified factors, such as cancer type, populations, and source of control, were used for a better interpretation of this variant. Minimal heterogeneity was shown in the current meta-analysis (I (2) = 0.0%, P = 0.48). Our results show a significant association of rs909253 and cancer risk (odds ratio (OR) = 1.12, P (z) < 0.001). In the subgroup analysis, significant association of rs909253 was found in adenocarcinoma (OR = 1.16, P (z) < 0.001) and hematological malignancy (OR = 1.10, P (z) < 0.001). Our meta-analyses established a significant association of rs909253 with cancer risk among multiple populations including North Americans, Asians, and Europeans.
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Affiliation(s)
- Xi Yu
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, 315041, China
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22
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Shebzukhov YV, Horn K, Brazhnik KI, Drutskaya MS, Kuchmiy AA, Kuprash DV, Nedospasov SA. Dynamic changes in chromatin conformation at the TNF transcription start site in T helper lymphocyte subsets. Eur J Immunol 2013; 44:251-64. [PMID: 24009130 DOI: 10.1002/eji.201243297] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 07/23/2013] [Accepted: 09/02/2013] [Indexed: 12/21/2022]
Abstract
Tumor necrosis factor (TNF) is one of the key primary response genes in the immune system that can be activated by a variety of stimuli. Previous analysis of chromatin accessibility to DNaseI demonstrated open chromatin conformation of the TNF proximal promoter in T cells. Here, using chromatin probing with restriction enzyme EcoNI and micrococcal nuclease we show that in contrast to the proximal promoter, the TNF transcription start site remains in a closed chromatin configuration in primary T helper (Th) cells, but acquires an open state after activation or polarization under Th1 and Th17 conditions. We further demonstrate that transcription factor c-Jun plays a pivotal role in the maintenance of open chromatin conformation at the transcription start site of the TNF gene.
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Affiliation(s)
- Yury V Shebzukhov
- German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany
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23
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The DNA-binding factor Ctcf critically controls gene expression in macrophages. Cell Mol Immunol 2013; 11:58-70. [PMID: 24013844 DOI: 10.1038/cmi.2013.41] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 07/11/2013] [Accepted: 07/21/2013] [Indexed: 12/18/2022] Open
Abstract
Macrophages play an important role in immunity and homeostasis. Upon pathogen recognition via specific receptors, they rapidly induce inflammatory responses. This process is tightly controlled at the transcriptional level. The DNA binding zinc-finger protein CCCTC-binding factor (Ctcf) is a crucial regulator of long-range chromatin interactions and coordinates specific communication between transcription factors and gene expression processes. In this study, the Ctcf gene was specifically deleted in myeloid cells by making use of the transgenic Cre-LoxP system. Conditional deletion of the Ctcf gene in myeloid cells induced a mild phenotype in vivo. Ctcf-deficient mice exhibited significantly reduced expression of major histocompatibility complex (MHC) class II in the liver. Ctcf-deficient macrophages demonstrated a normal surface phenotype and phagocytosis capacity. Upon Toll-like receptor (TLR) stimulation, they produced normal levels of the pro-inflammatory cytokines IL-12 and IL-6, but manifested a strongly impaired capacity to produce tumor-necrosis factor (TNF) and IL-10, as well as to express the IL-10 family members IL-19, IL-20 and IL-24. Taken together, our data demonstrate a role of Ctcf that involves fine-tuning of macrophage function.
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24
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Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation. Adv Immunol 2013; 118:37-128. [PMID: 23683942 DOI: 10.1016/b978-0-12-407708-9.00002-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Epigenetics encompasses transient and heritable modifications to DNA and nucleosomes in the native chromatin context. For example, enzymatic addition of chemical moieties to the N-terminal "tails" of histones, particularly acetylation and methylation of lysine residues in the histone tails of H3 and H4, plays a key role in regulation of gene transcription. The modified histones, which are physically associated with gene regulatory regions that typically occur within conserved noncoding sequences, play a functional role in active, poised, or repressed gene transcription. The "histone code" defined by these modifications, along with the chromatin-binding acetylases, deacetylases, methylases, demethylases, and other enzymes that direct modifications resulting in specific patterns of histone modification, shows considerable evolutionary conservation from yeast to humans. Direct modifications at the DNA level, such as cytosine methylation at CpG motifs that represses promoter activity, are another highly conserved epigenetic mechanism of gene regulation. Furthermore, epigenetic modifications at the nucleosome or DNA level can also be coupled with higher-order intra- or interchromosomal interactions that influence the location of regulatory elements and that can place them in an environment of specific nucleoprotein complexes associated with transcription. In the mammalian immune system, epigenetic gene regulation is a crucial mechanism for a range of physiological processes, including the innate host immune response to pathogens and T cell differentiation driven by specific patterns of cytokine gene expression. Here, we will review current findings regarding epigenetic regulation of cytokine genes important in innate and/or adaptive immune responses, with a special focus upon the tumor necrosis factor/lymphotoxin locus and cytokine-driven CD4+ T cell differentiation into the Th1, Th2, and Th17 lineages.
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