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Wang Y, Hou Q, Wu Y, Xu Y, Liu Y, Chen J, Xu L, Guo Y, Gao S, Yuan J. Methionine deficiency and its hydroxy analogue influence chicken intestinal 3-dimensional organoid development. ANIMAL NUTRITION 2022; 8:38-51. [PMID: 34977374 PMCID: PMC8669257 DOI: 10.1016/j.aninu.2021.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022]
Abstract
Methionine and its hydroxy analogue (MHA) have been shown to benefit mouse intestinal regeneration. The intestinal organoid is a good model that directly reflects the impact of certain nutrients or chemicals on intestinal development. Here, we aimed to establish a chicken intestinal organoid culture method first and then use the model to explore the influence of methionine deficiency and MHA on intestinal organoid development. The results showed that 125-μm cell strainer exhibited the highest efficiency for chicken embryo crypt harvesting. We found that transforming growth factor-β inhibitor (A8301) supplementation promoted enterocyte differentiation at the expense of the proliferation of intestinal stem cells (ISC). The mitogen-activated protein kinase p38 inhibitor (SB202190) promoted intestinal organoid formation and enterocyte differentiation but suppressed the differentiation of enteroendocrine cells, goblet cells and Paneth cells. However, the suppression of enteroendocrine cell and Paneth cell differentiation by SB202190 was alleviated at the presence of A8301. The glycogen synthase kinase 3 inhibitor (CHIR99021), valproic acid (VPA) alone and their combination promoted chicken intestinal organoid formation and enterocyte differentiation at the expense of the expression of Paneth cells and goblet cells. Chicken serum significantly improved organoid formation, especially in the presence of A8301, SB202190, CHIR99021, and VPA, but inhibited the differentiation of Paneth cells and enteroendocrine cells. Chicken serum at a concentration of 0.25% meets the requirement of chicken intestinal organoid development, and the beneficial effect of chicken serum on chicken intestinal organoid culture could not be replaced by fetal bovine serum and insulin-like growth factor-1. Moreover, commercial mouse organoid culture medium supplemented with A8301, SB202190, CHIR99021, VPA, and chicken serum promotes chicken organoid budding. Based on the chicken intestinal organoid model, we found that methionine deficiency mimicked by cycloleucine suppressed organoid formation and organoid size, and this effect was reinforced with increased cycloleucine concentrations. Methionine hydroxy analogue promoted regeneration of ISC but decreased cell differentiation compared with the results obtained with L-methionine. In conclusion, our results provide a potentially excellent guideline for chicken intestinal organoid culture and insights into methionine function in crypt development.
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Affiliation(s)
- Youli Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qihang Hou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuqin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanwei Xu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jing Chen
- Sichuan New Hope Liuhe Co. Ltd, Chengdu, 610100, China
| | - Lingling Xu
- Beijing Dafa Chia Tai Co. Ltd., Beijing, 101206, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shuai Gao
- Key Laboratory of Animal Gene Breeding and Reproductivity, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Corresponding authors.
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Corresponding authors.
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Li B, He Y, Li P, Chen X. Leptin Receptor Overlapping Transcript (LEPROT) Is Associated with the Tumor Microenvironment and a Prognostic Predictor in Pan-Cancer. Front Genet 2021; 12:749435. [PMID: 34804118 PMCID: PMC8596502 DOI: 10.3389/fgene.2021.749435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background Leptin receptor overlapping transcript (LEPROT) is reported to be involved in metabolism regulation and energy balance as well as molecular signaling of breast cancer and osteosarcoma. LEPROT is expressed in various tissue and is suggested to be involved in cancer developments but with contradictory roles. The comprehensive knowledge of the effects of LEPROT on cancer development and progression across pan-cancer is still missing. Methods The expressions of LEPROT in cancers were compared with corresponding normal tissues across pan-cancer types. The relationships between expression and methylation of LEPROT were then demonstrated. The correlations of LEPROT with the tumor microenvironment (TME), including immune checkpoints, tumor immune cells infiltration (TII), and cancer-associated fibroblasts (CAFs), were also investigated. Co-expression analyses and functional enrichments were conducted to suggest the most relevant genes and the mechanisms of the effects in cancers for LEPROT. Finally, the correlations of LEPROT with patient survival and immunotherapy response were explored. Results LEPROT expression was found to be significantly aberrant in 15/19 (78.9%) cancers compared with corresponding normal tissues; LEPROT was downregulated in 12 cancers and upregulated in three cancers. LEPROT expressions were overall negatively correlated with its methylation alterations. Moreover, LEPROT was profoundly correlated with the TME, including immune checkpoints, TIIs, and CAFs. According to co-expression analyses and functional enrichments, the interactions of LEPROT with the TME may be mediated by the interleukin six signal transducer/the Janus kinase/signal transducers and activators of the transcription signaling pathway. Prognostic values may exist for LEPROT to predict patient survival and immunotherapy response in a context-dependent way. Conclusions LEPROT affects cancer development by interfering with the TME and regulating inflammatory or immune signals. LEPROT may also serve as a potential prognostic marker or a target in cancer therapy. This is the first study to investigate the roles of LEPROT across pan-cancer.
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Affiliation(s)
- Bingsheng Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.,Department of Urology, University Hospital Munich, LMU Munich, Munich, Germany
| | - Yao He
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Pan Li
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Xiang Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
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Sumei S, Xiangyun K, Fenrong C, Xueguang S, Sijun H, Bin B, Xiaolei S, Yongjiu T, Kaichun W, Qingchuan Z, Yongzhan N, Bin X. Hypermethylation of DHRS3 as a Novel Tumor Suppressor Involved in Tumor Growth and Prognosis in Gastric Cancer. Front Cell Dev Biol 2021; 9:624871. [PMID: 33553182 PMCID: PMC7859350 DOI: 10.3389/fcell.2021.624871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background/Aims The role of DHRS3 in human cancer remains unclear. Our study explored the role of DHRS3 in gastric cancer (GC) and its clinicopathological significance and associated mechanisms. Materials Bisulfite-assisted genomic sequencing PCR and a Mass-Array system were used to evaluate and quantify the methylation levels of the promoter. The expression levels and biological function of DHRS3 was examined by both in vitro and in vivo assays. A two-way hierarchical cluster analysis was used to classify the methylation profiles, and the correlation between the methylation status of the DHRS3 promoter and the clinicopathological characteristics of GC were then assessed. Results The DHRS3 promoter was hypermethylated in GC samples, while the mRNA and protein levels of DHRS3 were significantly downregulated. Ectopic expression of DHRS3 in GC cells inhibited cell proliferation and migration in vitro, decreased tumor growth in vivo. DHRS3 methylation was correlated with histological type and poor differentiation of tumors. GC patients with high degrees of CpG 9.10 methylation had shorter survival times than those with lower methylation. Conclusion DHRS3 was hypermethylated and downregulated in GC patients. Reduced expression of DHRS3 is implicated in gastric carcinogenesis, which suggests DHRS3 is a tumor suppressor.
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Affiliation(s)
- Sha Sumei
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Kong Xiangyun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,Xi'an No.1 Hospital, Xi'an, China
| | - Chen Fenrong
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Sun Xueguang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Hu Sijun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Bai Bin
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Shi Xiaolei
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,Dongfang Hospital of Xiamen University, Fuzhou, China
| | - Tu Yongjiu
- The General Surgery Department of Chenggong Hospital of Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen, China
| | - Wu Kaichun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Zhao Qingchuan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Nie Yongzhan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Xu Bin
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,The General Surgery Department of Chenggong Hospital of Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen, China
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4
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Wu J, Zhao Y, Wang X, Kong L, Johnston LJ, Lu L, Ma X. Dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications. Crit Rev Food Sci Nutr 2020; 62:783-797. [PMID: 33043708 DOI: 10.1080/10408398.2020.1828813] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jianmin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xian Wang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Lingchang Kong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lee J. Johnston
- West Central Research & Outreach Centre, University of Minnesota, Morris, Minnesota, USA
| | - Lin Lu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Bifidobacteria and Mucosal-Associated Invariant T (MAIT) Cells: A New Approach to Colorectal Cancer Prevention? GASTROINTESTINAL DISORDERS 2019. [DOI: 10.3390/gidisord1020022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer is the most preventable form of cancer worldwide. The pathogenesis of colorectal cancer includes gut inflammation, genetic and microbial composition factors. İmpairment of the gut microbiota has been associated with development of colorectal cancer. The genus Bifidobacterium is an important component of the commensal gut microbiota. Bifidobacteria are considered to have important roles in multiple homeostatic functions: immunologic, hormonal and metabolic. Mucosal-associated invariant T cells (MAIT) are components of the immune system involved in protection against infectious pathogens and regulate the pathogenesis of various inflammatory diseases and, potentially, colorectal cancer. Engagement between Bifidobacterium and MAIT cells could exert a beneficial effect on colorectal cancer prevention and treatment.
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Aberrant methylation status of SPG20 promoter in hepatocellular carcinoma: A potential tumor metastasis biomarker. Cancer Genet 2019; 233-234:48-55. [PMID: 31109594 DOI: 10.1016/j.cancergen.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/01/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE The aim of this study is to analyze the methylation levels of SPG20 promotor region and explore the association between the methylation levels and clinical features in hepatocellular carcinoma (HCC). MATERIALS AND METHODS We collected paired of HCC and adjacent non-cancerous tissues (ANT) from 160 HCC patients and analyze the methylation levels through MassARRAY Analyzer 4. The statistical calculations were performed using SPSS version 22.0. Real-time-quantification PCR was performed to assess expression levels of SPG20 in HCC cell lines. Wound healing assay and transwell assay was used to measure cell migration capacity. RESULT We found that mean methylation level of SPG20 in tumor tissues was significantly higher than that in ANT (7.3% vs. 16.2%, P<0.0013). There was a significantly negative correlation between expression level and methylation level of SPG20 (P<0.01). In addition, the methylation levels in HCC were correlated with age and HBV infection. Meanwhile, micro-satellite tumors (P = 0.016) and tumor number (P = 0.018) was found significantly associated with increased methylation levels of several CpG sites and the mean levels of SPG20 promotor in ANT. In addtion, the capacity of cell migration was significantly enhanced in SPG20 knock-down HCC cells. CONCLUSION The hypermethylation status of SPG20 gene promoter is significantly associated with intra-hepatic metastasis and contribute to HCC metastasis.
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Liu Y, Xing J, Li Y, Luo Q, Su Z, Zhang X, Zhang H. Chronic hypoxia–induced Cirbp hypermethylation attenuates hypothermic cardioprotection via down-regulation of ubiquinone biosynthesis. Sci Transl Med 2019; 11:11/489/eaat8406. [PMID: 31019028 DOI: 10.1126/scitranslmed.aat8406] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 10/25/2018] [Accepted: 03/25/2019] [Indexed: 12/24/2022]
Abstract
Therapeutic hypothermia is commonly used during cardiopulmonary bypass (CPB) to protect the heart against myocardial injury in cardiac surgery. Patients who suffer from chronic hypoxia (CH), such as those with certain heart or lung conditions, are at high risk of severe myocardial injury after cardiac surgery, but the underlying mechanisms are unknown. This study tested whether CH attenuates hypothermic cardioprotection during CPB. Using a rat model of CPB, we found that hypothermic cardioprotection was impaired in CH rats but was preserved in normoxic rats. Cardiac proteomes showed that cold-inducible RNA binding protein (CIRBP) was significantly (P = 0.03) decreased in CH rats during CPB. Methylation analysis of neonatal rat cardiomyocytes under CH and myocardium specimens from patients with CH showed that CH induced hypermethylation of the Cirbp promoter region, resulting in its depression and failure to respond to cold stress. Cirbp-knockout rats showed attenuated hypothermic cardioprotection, whereas Cirbp-transgenic rats showed an enhanced response. Proteomics analysis revealed that the cardiac ubiquinone biosynthesis pathway was down-regulated during CPB in Cirbp-knockout rats, resulting in a significantly (P = 0.01) decreased concentration of ubiquinone (CoQ10). Consequently, cardiac oxidative stress was aggravated and adenosine 5′-triphosphate production was impaired, leading to increased myocardial injury during CPB. CoQ10-supplemented cardioplegic solution improved cardioprotection in rats exposed to CH, but its effect was limited in normoxic rats. Our study suggests that an individualized cardioprotection strategy should be used to fully compensate for the consequences of epigenetic modification of Cirbp in patients with CH who require therapeutic hypothermia.
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Affiliation(s)
- Yiwei Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Junyue Xing
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Heart Center of Henan Provincial People Hospital and Key Laboratory of Cardiac Regenerative Medicine, National Health Commission, Zhengzhou 451464, China
| | - Yongnan Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou 730030, China
| | - Qipeng Luo
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Zhanhao Su
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Xiaoling Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Heart Center of Henan Provincial People Hospital and Key Laboratory of Cardiac Regenerative Medicine, National Health Commission, Zhengzhou 451464, China
| | - Hao Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China.
- Heart Center of Henan Provincial People Hospital and Key Laboratory of Cardiac Regenerative Medicine, National Health Commission, Zhengzhou 451464, China
- Center for Pediatric Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Heart Center and Shanghai Institute of Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China
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Bozkurt HS, Quigley EM, Kara B. Bifidobacterium animalis subspecies lactis engineered to produce mycosporin-like amino acids in colorectal cancer prevention. SAGE Open Med 2019; 7:2050312119825784. [PMID: 30719295 PMCID: PMC6348500 DOI: 10.1177/2050312119825784] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is the third most common cancer and the third leading cause of cancer-related death. The pathogensesis of colorectal cancer involves a multi-step and multi-factorial process. Disruption of the gut microbiota has been associated with gastrointestinal diseases such as colorectal cancer. The genus Bifidobacterium is considered an important component of the commensal microbiota and plays important roles in several homeostatic functions: immune, neurohormonal, and metabolic. Bifidobacterium animalis subsp. lactis is a well-documented probiotic within the species Bifidobacterium. Mycosporin-like amino acids are low molecular weight amino acids demonstrated to exert prebiotic effects and to modulate host immunity by regulating the proliferation and differentiation of intestinal epithelial cells, macrophages and lymphocytes, as well as cytokine production.Their modulation of the metabolism of the immune system and transcription factors could exert a beneficial effect on colorectal cancer. B. animalis does not produce mycosporin-like amino acids. If one could create a B. animalis–producing mycosporin-like amino acids via genetic open reading frame engineering it should exert more potent immuno-stimulatory properties and, thereby, become a potent strain-specific microbial based therapy in colorectal cancer prevention.
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Affiliation(s)
| | - Eamonn Mm Quigley
- Division of Gastroenterology and Hepatology, Lynda K and David M Underwood Center for Digestive Disorders, Houston Methodist Hospital and Weill Cornell Medical College, Houston, TX, USA
| | - Banu Kara
- Clinic of Gastroenterology, Adana Numune Research and Education Hospital, University of Health Sciences, Adana, Turkey
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Poupeau A, Garde C, Sulek K, Citirikkaya K, Treebak JT, Arumugam M, Simar D, Olofsson LE, Bäckhed F, Barrès R. Genes controlling the activation of natural killer lymphocytes are epigenetically remodeled in intestinal cells from germ-free mice. FASEB J 2018; 33:2719-2731. [PMID: 30303739 PMCID: PMC6338647 DOI: 10.1096/fj.201800787r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Remodeling of the gut microbiota is implicated in various metabolic and inflammatory diseases of the gastrointestinal tract. We hypothesized that the gut microbiota affects the DNA methylation profile of intestinal epithelial cells (IECs) which could, in turn, alter intestinal function. In this study, we used mass spectrometry and methylated DNA capture to respectively investigate global and genome-wide DNA methylation of intestinal epithelial cells from germ-free (GF) and conventionally raised mice. In colonic IECs from GF mice, DNA was markedly hypermethylated. This was associated with a dramatic loss of ten-eleven-translocation activity, a lower DNA methyltransferase activity and lower circulating levels of the 1-carbon metabolite, folate. At the gene level, we found an enrichment for differentially methylated regions proximal to genes regulating the cytotoxicity of NK cells (false-discovery rate < 8.9E−6), notably genes regulating the cross-talk between NK cells and target cells, such as members of the NK group 2 member D ligand superfamily Raet. This distinct epigenetic signature was associated with a marked decrease in Raet1 expression and a loss of CD56+/CD45+ cells in the intestine of GF mice. Thus, our results indicate that altered activity of methylation-modifying enzymes in GF mice influences the IEC epigenome and modulates the crosstalk between IECs and NK cells. Epigenetic reprogramming of IECs may modulate intestinal function in diseases associated with altered gut microbiota.—Poupeau, A., Garde, C., Sulek, K., Citirikkaya, K., Treebak, J. T., Arumugam, M., Simar, D., Olofsson, L. E., Bäckhed, F., Barrès, R. Genes controlling the activation of natural killer lymphocytes are epigenetically remodeled in intestinal cells from germ-free mice.
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Affiliation(s)
- Audrey Poupeau
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Garde
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kiymet Citirikkaya
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Simar
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Mechanisms of Disease and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia; and
| | - Louise E Olofsson
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Molecular and Clinical Medicine, Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Basson MD, Wang Q, Chaturvedi LS, More S, Vomhof-DeKrey EE, Al-Marsoummi S, Sun K, Kuhn LA, Kovalenko P, Kiupel M. Schlafen 12 Interaction with SerpinB12 and Deubiquitylases Drives Human Enterocyte Differentiation. Cell Physiol Biochem 2018; 48:1274-1290. [PMID: 30045019 PMCID: PMC6123821 DOI: 10.1159/000492019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/25/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND/AIMS Human enterocytic differentiation is altered during development, fasting, adaptation, and bariatric surgery, but its intracellular control remains unclear. We hypothesized that Schlafen 12 (SLFN12) regulates enterocyte differentiation. METHODS We used laser capture dissection of epithelium, qRT-PCR, and immunohistochemistry to evaluate SLFN12 expression in biopsies of control and fasting human duodenal mucosa, and viral overexpression and siRNA to trace the SLFN12 pathway in human Caco-2 and HIEC6 intestinal epithelial cells. RESULTS Fasting human duodenal mucosa expressed less SLFN12 mRNA and protein, accompanied by decreases in enterocytic markers like sucrase-isomaltase. SLFN12 overexpression increased Caco-2 sucrase-isomaltase promoter activity, mRNA, and protein independently of proliferation, and activated the SLFN12 putative promoter. SLFN12 coprecipitated Serpin B12 (SERPB12). An inactivating SLFN12 point mutation prevented both SERPB12 binding and sucrase-isomaltase induction. SERPB12 overexpression also induced sucrase-isomaltase, while reducing SERPB12 prevented the SLFN12 effect on sucrase-isomaltase. Sucrase-isomaltase induction by both SLFN12 and SERPB12 was attenuated by reducing UCHL5 or USP14, and blocked by reducing both. SERPB12 stimulated USP14 but not UCHL5 activity. SERPB12 coprecipitated USP14 but not UCHL5. Moreover, SLFN12 increased protein levels of the sucrase-isomaltase-promoter-binding transcription factor cdx2 without altering Cdx2 mRNA. This was prevented by reducing UCHL5 and USP14. We further validated this pathway in vitro and in vivo. SLFN12 or SERPB12 overexpression induced sucrase-isomaltase in human non-malignant HIEC-6 enterocytes. CONCLUSIONS SLFN12 regulates human enterocytic differentiation by a pathway involving SERPB12, the deubiquitylases, and Cdx2. This pathway may be targeted to manipulate human enterocytic differentiation in mucosal atrophy, short gut or obesity.
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Affiliation(s)
- Marc D Basson
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
| | - Qinggang Wang
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
| | - Lakshmi S Chaturvedi
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
- Currently at Departments of Pharmaceutical Sciences and Biomedical Sciences-College of Pharmacy, Departments of Basic Sciences and Surgery-College of Medicine, California Northstate University, Cambridge, Massachusetts, USA
| | - Shyam More
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
| | - Emilie E Vomhof-DeKrey
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
| | - Sarmad Al-Marsoummi
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
| | - Kelian Sun
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
| | - Leslie A Kuhn
- Department of Biochemistry and Molecular Biology, Colleges of National Science, Human Medicine, Osteopathic Medicine and Engineering, Michigan State University, Cambridge, Massachusetts, USA
| | - Pavlo Kovalenko
- Departments of Surgery, Pathology, and Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, Cambridge, Massachusetts, USA
- Currently at Sarepta Therapeutics, Cambridge, Massachusetts, USA
| | - Matti Kiupel
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, Lansing, Michigan, USA
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11
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Urinary 1-hydroxypyrene and smoking are determinants of LINE-1 and AhRR promoter methylation in coke oven workers. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 826:33-40. [PMID: 29412867 DOI: 10.1016/j.mrgentox.2018.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 12/28/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
Abstract
Coke oven emissions (COE) containing polycyclic aromatic hydrocarbons (PAHs) are predominant toxic constituents of particulate air pollution that have been linked to increased risk of lung cancer. Aberrant DNA methylation is one of the best known epigenetic changes in human cancers and healthy subjects exposed to carcinogens. The purpose of this study is to explore the factors influencing the methylation of long interspersed nuclear element-1 (LINE-1) and aryl-hydrocarbon receptor repressor (AhRR) in coke oven workers. The study population is composed by coke oven workers (348) and water treatment workers (131). And their urinary PAH metabolites were analyzed by high performance liquid chromatography; DNA methylation were measured by pyrosequencing. The urinary PAHs metabolites were significantly elevated in coke oven workers (P < 0.01). The results from multivariate logistic regression analysis showed that a high level of urinary 1-hydroxypyrene was associated with a significantly increased risk of hypomethylation of LINE-1 (OR: 1.80; 95% CI: 1.25, 2.60), and heavy smoking was associated with a significantly increased risk of hypomethylation of AhRR (OR: 1.44; 95% CI: 1.04, 2.00). Our findings demonstrate that urinary 1-hydroxypyrene may be a useful biomarker for evaluating the role of PAHs exposure on hypomethylation of LINE-1 among coke oven workers and that smoking may be an important factor affecting hypomethylation of AhRR.
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Baek SJ, Kim M, Bae DH, Kim JH, Kim HJ, Han ME, Oh SO, Kim YS, Kim SY. Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer. Oncotarget 2018; 7:25620-31. [PMID: 27016420 PMCID: PMC5041931 DOI: 10.18632/oncotarget.8239] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/10/2016] [Indexed: 12/13/2022] Open
Abstract
Abnormal DNA methylation is an epigenetic mechanism that promotes gastric carcinogenesis. While the abnormal methylation at promoter regions has been characterized for many genes, the function of DNA methylation marks at distal regulatory regions in gastric cancer remains poorly described. Here, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines to understand the epigenetic changes in the distal as well as the proximal regulatory regions. In total, 257,651 significant DMRs (Differentially methylated regions) were identified in gastric cancer, and the majority of these DMRs were located in the intergenic, intronic, and non-coding RNA regions. We identified the aberrant expression of many genes and lncRNAs due to changes in DNA methylation. Furthermore, we profiled the molecular subtype-specific methylation patterns in gastric cancer to characterize subtype-specific regulators that undergo DNA methylation changes. Our findings provide insights for understanding methylation changes at distal regulatory regions and reveal novel epigenetic targets in gastric cancer.
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Affiliation(s)
- Su-Jin Baek
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Genomic Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Mirang Kim
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Dong-Hyuck Bae
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hee-Jin Kim
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Myoung-Eun Han
- Departments of Anatomy and Surgery, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Sae-Ock Oh
- Departments of Anatomy and Surgery, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Yong Sung Kim
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seon-Young Kim
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.,Genomic Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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Huang CZ, Xu JH, Zhong W, Xia ZS, Wang SY, Cheng D, Li JY, Wu TF, Chen QK, Yu T. Sox9 transcriptionally regulates Wnt signaling in intestinal epithelial stem cells in hypomethylated crypts in the diabetic state. Stem Cell Res Ther 2017; 8:60. [PMID: 28279198 PMCID: PMC5345140 DOI: 10.1186/s13287-017-0507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/19/2017] [Accepted: 02/11/2017] [Indexed: 12/16/2022] Open
Abstract
Background Distinctive structures called crypts harbor intestinal epithelial stem cells (IESCs) which generate progenitor and terminally differentiated cells in the intestinal epithelium. Mammalian IESCs and their daughter cells require the participation of DNA methylation and the transcription factor Sox9 for proliferation and differentiation. However, the association between Sox9 and DNA methylation in this process remains elusive. Methods The DNA methylation of small intestinal epithelial crypts in db/db mice was detected via combining methylated DNA immunoprecipitation with microarray hybridization. DNA methylation of Sox9 promoter in crypts and IESCs was validated using bisulfite sequence analysis. The target sequence of the transcription factor Sox9 in IESCs was investigated via chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq). Results Increased Sox9 expression is accompanied by the loss of methylation in its promoter in IESCs. Sox9 targets the enhancers of the Wnt signaling pathway-related genes. Sox9 predominantly acts as a transcriptional activator at proximal enhancers of Wnt4, Tab2, Sox4, and Fzd8, but also functions as a potential transcriptional inhibitor at a distant enhancer of Cdk1. Lack of Sox9 transcriptional activation in specific repressors of the Wnt signaling pathway leads to the loss of intrinsic inhibitory action and ultimately produces overactivation of this pathway in db/db mice. Conclusions Our study sheds light on the connections among DNA methylation, transcription factor modulation, and Wnt signaling in IESCs in the diabetic state. Hypomethylation in the Sox9 promoter is correlated to increased Sox9 expression in db/db IESCs. Although there is increased expression of Sox9 in db/db IESCs, the loss of Sox9 transcriptional activation in specific repressors of the Wnt signaling pathway might result in abnormalities in this pathway. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0507-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Can-Ze Huang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Ji-Hao Xu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Wa Zhong
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Zhong-Sheng Xia
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Si-Yi Wang
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Di Cheng
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Jie-Yao Li
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Ting-Feng Wu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China
| | - Qi-Kui Chen
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China.
| | - Tao Yu
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China. .,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang Xi Road, Guangzhou, Guangdong, 510120, China.
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Bomer N, den Hollander W, Suchiman H, Houtman E, Slieker RC, Heijmans BT, Slagboom PE, Nelissen RGHH, Ramos YFM, Meulenbelt I. Neo-cartilage engineered from primary chondrocytes is epigenetically similar to autologous cartilage, in contrast to using mesenchymal stem cells. Osteoarthritis Cartilage 2016; 24:1423-30. [PMID: 26995110 DOI: 10.1016/j.joca.2016.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/16/2016] [Accepted: 03/10/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVES To compare the epigenetic landscape of 3D cell models of human primary articular chondrocytes (hPACs) and human bone-marrow derived mesenchymal stem cells (hBMSCs) and their respective autologous articular cartilage. DESIGN Using Illumina Infinium HumanMethylation450 BeadChip arrays, the DNA methylation landscape of the different cell sources and autologous cartilage was determined. Pathway enrichment was analyzed using DAVID. RESULTS Principal Component Analysis (PCA) of methylation data revealed separate clustering of hBMSC samples. Between hBMSCs and autologous cartilage 86,881 cytosine-phosphate-guanine dinucleotides (CpGs) (20.2%), comprising 3,034 differentially methylated regions (DMRs; Δβ > 0.1; with the same direction of effect), were significantly differentially methylated. In contrast, between hPACs and autologous cartilage only 5,706 CpGs (1.33%) were differentially methylated. Of interest was the finding of the transcriptionally active, hyper-methylation of a Cartilage Intermediate Layer Protein (CILP) annotated DMR (Δβ = 0.16) in PAC-cartilage, corresponding to a profound decrease in CILP expression after in vitro culturing of hPACs as compared to autologous cartilage. CONCLUSIONS In vitro engineered neo-cartilage tissue from primary chondrocytes, hPACs, exhibits a DNA methylation landscape that is almost identical (99% similarity) to autologous cartilage, in contrast to neo-cartilage engineered from bone marrow-derived mesenchymal stem cells (MSCs). Although hBMSCs are widely used for cartilage engineering purposes the effects of these vast differences on cartilage regeneration and long term consequences of implantation, are not known. The use of hBMSCs or hPACs for future cartilage tissue regeneration purposes should therefore be investigated in more depth in future endeavors to better understand the consequences of the differential methylome on neo-cartilage.
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Affiliation(s)
- N Bomer
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands; IDEAL, LUMC, Leiden, The Netherlands
| | - W den Hollander
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - H Suchiman
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - E Houtman
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - R C Slieker
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands; IDEAL, LUMC, Leiden, The Netherlands
| | - B T Heijmans
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands; IDEAL, LUMC, Leiden, The Netherlands
| | - P E Slagboom
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands; IDEAL, LUMC, Leiden, The Netherlands
| | | | - Y F M Ramos
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - I Meulenbelt
- Dept. of Molecular Epidemiology, LUMC, Leiden, The Netherlands.
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NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds. Acta Pharmacol Sin 2016; 37:984-93. [PMID: 27238211 DOI: 10.1038/aps.2016.19] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/04/2016] [Indexed: 12/13/2022] Open
Abstract
AIM Fragment-based lead discovery (FBLD) is a complementary approach in drug research and development. In this study, we established an NMR-based FBLD platform that was used to screen novel scaffolds targeting human bromodomain of BRD4, and investigated the binding interactions between hit compounds and the target protein. METHODS 1D NMR techniques were primarily used to generate the fragment library and to screen compounds. The inhibitory activity of hits on the first bromodomain of BRD4 [BRD4(I)] was examined using fluorescence anisotropy binding assay. 2D NMR and X-ray crystallography were applied to characterize the binding interactions between hit compounds and the target protein. RESULTS An NMR-based fragment library containing 539 compounds was established, which were clustered into 56 groups (8-10 compounds in each group). Eight hits with new scaffolds were found to inhibit BRD4(I). Four out of the 8 hits (compounds 1, 2, 8 and 9) had IC50 values of 100-260 μmol/L, demonstrating their potential for further BRD4-targeted hit-to-lead optimization. Analysis of the binding interactions revealed that compounds 1 and 2 shared a common quinazolin core structure and bound to BRD4(I) in a non-acetylated lysine mimetic mode. CONCLUSION An NMR-based platform for FBLD was established and used in discovery of BRD4-targeted compounds. Four potential hit-to-lead optimization candidates have been found, two of them bound to BRD4(I) in a non-acetylated lysine mimetic mode, being selective BRD4(I) inhibitors.
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