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Yan YY, Wang YM, Shen JH, Jian YJ, Lei CC, Wang Q, Liu C, Zhang XX, Liu XH. The discovery of a novel pyrrolo[2,3-b]pyridine as a selective CDK8 inhibitor offers a new approach against psoriasis. Biomed Pharmacother 2024; 175:116705. [PMID: 38713949 DOI: 10.1016/j.biopha.2024.116705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024] Open
Abstract
Currently, the drugs used in clinical to treat psoriasis mainly broadly suppress cellular immunity. However, these drugs can only provide temporary and partial symptom relief, they do not cure the condition and may lead to recurrence or even serious toxic side effects. In this study, we describe the discovery of a novel potent CDK8 inhibitor as a treatment for psoriasis. Through structure-based design, compound 46 was identified as the most promising candidate, exhibiting a strong inhibitory effect on CDK8 (IC50 value of 57 nM) along with favourable inhibition against NF-κB. Additionally, it demonstrated a positive effect in an in vitro psoriasis model induced by TNF-α. Furthermore, this compound enhanced the thermal stability of CDK8 and exerted evident effects on the biological function of CDK8, and it had favourable selectivity across the CDK family and tyrosine kinase. This compound showed no obvious inhibitory effect on CYP450 enzyme. Further studies confirmed that compound 46 exhibited therapeutic effect on IMQ-induced psoriasis, alleviated the inflammatory response in mice, and enhanced the expression of Foxp3 and IL-10 in the dorsal skin in vivo. This discovery provides a new strategy for developing selective CDK8 inhibitors with anti-inflammatory activity for the treatment of psoriasis.
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Affiliation(s)
- Yao Yao Yan
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China
| | - Yu Meng Wang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China
| | - Jun Hao Shen
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China
| | - Yu Jie Jian
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China
| | - Cen Cen Lei
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China
| | - Quan Wang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China
| | - Chao Liu
- School of Biological and Food Engineering, Suzhou University, Suzhou 234000, PR China; Anhui Key Laboratory of Spin Electron and Nanomaterials, Suzhou 234000, PR China; School of Chemistry and Chemical Engineering, Suzhou University, Suzhou 234000, PR China.
| | - Xing Xing Zhang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China.
| | - Xin Hua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, PR China; School of Biological and Food Engineering, Suzhou University, Suzhou 234000, PR China.
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2
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Tai Y, Shang J. Wnt/β-catenin signaling pathway in the tumor progression of adrenocortical carcinoma. Front Endocrinol (Lausanne) 2024; 14:1260701. [PMID: 38269250 PMCID: PMC10806569 DOI: 10.3389/fendo.2023.1260701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
Adrenocortical carcinoma (ACC) is an uncommon, aggressive endocrine malignancy with a high rate of recurrence, a poor prognosis, and a propensity for metastasis. Currently, only mitotane has received certification from both the US Food and Drug Administration (FDA) and the European Medicines Agency for the therapy of advanced ACC. However, treatment in the advanced periods of the disorders is ineffective and has serious adverse consequences. Completely surgical excision is the only cure but has failed to effectively improve the survival of advanced patients. The aberrantly activated Wnt/β-catenin pathway is one of the catalysts for adrenocortical carcinogenesis. Research has concentrated on identifying methods that can prevent the stimulation of the Wnt/β-catenin pathway and are safe and advantageous for patients in view of the absence of effective treatments and the frequent alteration of the Wnt/β-catenin pathway in ACC. Comprehending the complex connection between the development of ACC and Wnt/β-catenin signaling is essential for accurate pharmacological targets. In this review, we summarize the potential targets between adrenocortical carcinoma and the Wnt/β-catenin signaling pathway. We analyze the relevant targets of drugs or inhibitors that act on the Wnt pathway. Finally, we provide new insights into how drugs or inhibitors may improve the treatment of ACC.
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Affiliation(s)
- Yanghao Tai
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences Tongji Shanxi Hospital, Taiyuan, China
| | - Jiwen Shang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences Tongji Shanxi Hospital, Taiyuan, China
- Department of Ambulatory Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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3
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Ghasemi S, Mahdavi M, Maleki M, Salahshourifar I, Kalayinia S. Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy. BMC Med Genomics 2023; 16:334. [PMID: 38129817 PMCID: PMC10734089 DOI: 10.1186/s12920-023-01780-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a major cause of sudden cardiac death and heart failure. Up to 50% of all DCM cases have a genetic background, with variants in over 250 genes reported in association with DCM. Whole-exome sequencing (WES) is a powerful tool to identify variants underlying genetic cardiomyopathies. Via WES, we sought to identify DCM causes in a family with 2 affected patients. METHODS WES was performed on the affected members of an Iranian family to identify the genetic etiology of DCM. The candidate variant was segregated via polymerase chain reaction and Sanger sequencing. Computational modeling and protein-protein docking were performed to survey the impact of the variant on the structure and function of the protein. RESULTS A novel single-nucleotide substitution (G > A) in exon 9 of MED12, c.1249G > A: p.Val417Ile, NM_005120.3, was identified. The c.1249G > A variant was validated in the family. Bioinformatic analysis and computational modeling confirmed that c.1249G > A was the pathogenic variant responsible for the DCM phenotype. CONCLUSION We detected a novel DCM-causing variant in MED12 using WES. The variant in MED12 may decrease binding to cyclin-dependent kinase 8 (CDK8), affect its activation, and cause alterations in calcium-handling gene expression in the heart, leading to DCM.
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Affiliation(s)
- Serwa Ghasemi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Mahdavi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Iman Salahshourifar
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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4
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Marelli S, Micaglio E, Taurino J, Salvi P, Rurali E, Perrucci GL, Dolci C, Udugampolage NS, Caruso R, Gentilini D, Trifiro' G, Callus E, Frigiola A, De Vincentiis C, Pappone C, Parati G, Pini A. Marfan Syndrome: Enhanced Diagnostic Tools and Follow-up Management Strategies. Diagnostics (Basel) 2023; 13:2284. [PMID: 37443678 DOI: 10.3390/diagnostics13132284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Marfan syndrome (MFS) is a rare inherited autosomic disorder, which encompasses a variety of systemic manifestations caused by mutations in the Fibrillin-1 encoding gene (FBN1). Cardinal clinical phenotypes of MFS are highly variable in terms of severity, and commonly involve cardiovascular, ocular, and musculoskeletal systems with a wide range of manifestations, such as ascending aorta aneurysms and dissection, mitral valve prolapse, ectopia lentis and long bone overgrowth, respectively. Of note, an accurate and prompt diagnosis is pivotal in order to provide the best treatment to the patients as early as possible. To date, the diagnosis of the syndrome has relied upon a systemic score calculation as well as DNA mutation identification. The aim of this review is to summarize the latest MFS evidence regarding the definition, differences and similarities with other connective tissue pathologies with severe systemic phenotypes (e.g., Autosomal dominant Weill-Marchesani syndrome, Loeys-Dietz syndrome, Ehlers-Danlos syndrome) and clinical assessment. In this regard, the management of MFS requires a multidisciplinary team in order to accurately control the evolution of the most severe and potentially life-threatening complications. Based on recent findings in the literature and our clinical experience, we propose a multidisciplinary approach involving specialists in different clinical fields (i.e., cardiologists, surgeons, ophthalmologists, orthopedics, pneumologists, neurologists, endocrinologists, geneticists, and psychologists) to comprehensively characterize, treat, and manage MFS patients with a personalized medicine approach.
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Affiliation(s)
- Susan Marelli
- Cardiovascular-Genetic Center, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Emanuele Micaglio
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Jacopo Taurino
- Cardiovascular-Genetic Center, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Paolo Salvi
- Istituto Auxologico Italiano, Cardiology Unit, IRCCS, 20133 Milan, Italy
| | - Erica Rurali
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy
| | - Gianluca L Perrucci
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy
| | - Claudia Dolci
- Laboratory of Functional Anatomy of the Stomatognathic System (LAFAS), Department of Biomedical Sciences for Health, Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Rosario Caruso
- Clinical Research Service, IRCCS Policlinico San Donato, 20097 Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, University of Milano-Bicocca, 20095 Milan, Italy
| | - Giuliana Trifiro'
- Cardiovascular-Genetic Center, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Edward Callus
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
- Clinical Psychology Service, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Alessandro Frigiola
- Department of Congenital Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
- Association "Bambini Cardiopatici nel Mondo" Non-Governmental Organization (NGO), 20123 Milan, Italy
| | - Carlo De Vincentiis
- Department of Cardiothoracic, Vascular Anaesthesia and Intensive Care, IRCCS Policlinico San Donato, 20097 Milan, Italy
- Department of Cardiac Surgery, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Carlo Pappone
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, 20097 Milan, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Gianfranco Parati
- Istituto Auxologico Italiano, Cardiology Unit, IRCCS, 20133 Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, 20126 Milan, Italy
| | - Alessandro Pini
- Cardiovascular-Genetic Center, IRCCS Policlinico San Donato, 20097 Milan, Italy
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5
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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6
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Wang R, Yu W, Zhu T, Lin F, Hua C, Ru L, Guo P, Wan X, Xue G, Guo Z, Han S, Lv K, Zhang G, Ge H, Guo W, Xu L, Deng W. MED27 plays a tumor-promoting role in breast cancer progression by targeting KLF4. Cancer Sci 2023. [PMID: 36786527 DOI: 10.1111/cas.15757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The mediator complex usually cooperates with transcription factors to be involved in RNA polymerase II-mediated gene transcription. As one component of this complex, MED27 has been reported in our previous studies to promote thyroid cancer and melanoma progression. However, the precise function of MED27 in breast cancer development remains poorly understood. Here, we found that MED27 was more highly expressed in breast cancer samples than in normal tissues, especially in triple-negative breast cancer, and its expression level was elevated with the increase in pathological stage. MED27 knockdown in triple-negative breast cancer cells inhibited cancer cell metastasis and stemness maintenance, which was accompanied by downregulation of the expression of EMT- and stem traits-associated proteins, and vice versa in non-triple-negative breast cancer. Furthermore, MED27 knockdown sensitized breast cancer cells to epirubicin treatment by inducing cellular apoptosis and reducing tumorsphere-forming ability. Based on RNA-seq, we identified KLF4 as the possible downstream target of MED27. KLF4 overexpression reversed the MED27 silencing-mediated arrest of cellular metastasis and stemness maintenance capacity in breast cancer in vitro and in vivo. Mechanistically, MED27 transcriptionally regulated KLF4 by binding to its promoter region at positions -156 to +177. Collectively, our study not only demonstrated the tumor-promoting role of MED27 in breast cancer progression by transcriptionally targeting KLF4, but also suggested the possibility of developing the MED27/KLF4 signaling axis as a potential therapeutic target in breast cancer.
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Affiliation(s)
- Ruozhu Wang
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wendan Yu
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Tianhua Zhu
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fei Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Chunyu Hua
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Liyuan Ru
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ping Guo
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xinyu Wan
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Guoqing Xue
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ziyue Guo
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shilong Han
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Kuan Lv
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Guohui Zhang
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hanxiao Ge
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wei Guo
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Institute of Cancer Stem Cell & The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
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7
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Guo YY, Li BY, Xiao G, Liu Y, Guo L, Tang QQ. Cdo1 promotes PPARγ-mediated adipose tissue lipolysis in male mice. Nat Metab 2022; 4:1352-1368. [PMID: 36253617 DOI: 10.1038/s42255-022-00644-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/22/2022] [Indexed: 01/20/2023]
Abstract
Cysteine dioxygenase 1 (Cdo1) is a key enzyme in taurine synthesis. Here we show that Cdo1 promotes lipolysis in adipose tissue. Adipose-specific knockout of Cdo1 in mice impairs energy expenditure, cold tolerance and lipolysis, exacerbates diet-induced obesity (DIO) and decreases adipose expression of the key lipolytic genes encoding ATGL and HSL, with little effect on adipose taurine levels. White-adipose-specific overexpression of ATGL and HSL blunts the role of adipose Cdo1 deficiency in promoting DIO. Mechanistically, Cdo1 interacts with PPARγ and facilitates the recruitment of Med24, the core subunit of mediator complex, to ATGL and HSL gene promoters, thereby transactivating their expression. Further, mice with transgenic overexpression of Cdo1 show better cold tolerance, ameliorated DIO and higher lipolysis capacity. Thus, we uncover an unexpected and important role of Cdo1 in regulating adipose lipolysis.
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Affiliation(s)
- Ying-Ying Guo
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bai-Yu Li
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Gang Xiao
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Liu
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liang Guo
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Kinesiology, Shanghai University of Sport, Shanghai, China.
| | - Qi-Qun Tang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, China.
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8
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Yan YY, Zhang XX, Xiao Y, Shen XB, Jian YJ, Wang YM, She ZH, Liu MM, Liu XH. Design and Synthesis of a 2-Amino-pyridine Derivative as a Potent CDK8 Inhibitor for Anti-colorectal Cancer Therapy. J Med Chem 2022; 65:13216-13239. [PMID: 36126227 DOI: 10.1021/acs.jmedchem.2c01042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CDK8 is a transcriptional cyclin-dependent kinase and considered as a potential target in colon cancer therapeutics. Here, a novel selective CDK8 inhibitor was identified against colon cancer in vivo. Specifically, based on the structural information of the sorafenib-bound CDK8 structure, a series of novel 2-amino-pyridine derivatives were designed, synthesized, and evaluated. Among them, compound 29 showed strong inhibitory activity against CDK8 with an IC50 value of 46 nM and favorable selectivity. And there is an apparent interaction between the endogenous or overexpressed CDK8 and biotinylated-29. This compound exhibited antiproliferation potency on colon cancer cell lines with a high CDK8 expression level, suppressed the activation of WNT/β-catenin and transcriptional activity of the TCF family, and induced G1 phase arrested in HCT-116 cells. In addition, this compound showed potent activity against sorafenib-resistant HCT-116 cells. What's more, it exhibited low toxicity and suitable pharmacokinetic (PK) profiles and showed preferable antitumor effects in vivo.
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Affiliation(s)
- Yao Yao Yan
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Xing Xing Zhang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Yun Xiao
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Xiao Bao Shen
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang 236037, P.R. China
| | - Yu Jie Jian
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Yu Meng Wang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Zi Hao She
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Ming Ming Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
| | - Xin Hua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, P.R. China
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9
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Galouzis CC, Furlong EEM. Regulating specificity in enhancer-promoter communication. Curr Opin Cell Biol 2022; 75:102065. [PMID: 35240372 DOI: 10.1016/j.ceb.2022.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
Enhancers are cis-regulatory elements that can activate transcription remotely to regulate a specific pattern of a gene's expression. Genes typically have many enhancers that are often intermingled in the loci of other genes. To regulate expression, enhancers must therefore activate their correct promoter while ignoring others that may be in closer linear proximity. In this review, we discuss mechanisms by which enhancers engage with promoters, including recent findings on the role of cohesin and the Mediator complex, and how this specificity in enhancer-promoter communication is encoded. Genetic dissection of model loci, in addition to more recent findings using genome-wide approaches, highlight the core promoter sequence, its accessibility, cofactor-promoter preference, in addition to the surrounding genomic context, as key components.
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Affiliation(s)
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117, Heidelberg, Germany.
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10
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Han Z, Li W. Enhancer RNA: What we know and what we can achieve. Cell Prolif 2022; 55:e13202. [PMID: 35170113 PMCID: PMC9055912 DOI: 10.1111/cpr.13202] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/22/2021] [Accepted: 01/21/2022] [Indexed: 12/28/2022] Open
Abstract
Enhancers are important cis-acting elements that can regulate gene transcription and cell fate alongside promoters. In fact, many human cancers and diseases are associated with the malfunction of enhancers. Recent studies have shown that enhancers can produce enhancer RNAs (eRNAs) by RNA polymerase II. In this review, we discuss eRNA production, characteristics, functions and mechanics. eRNAs can determine chromatin accessibility, histone modification and gene expression by constructing a 'chromatin loop', thereby bringing enhancers to their target gene. eRNA can also be involved in the phase separation with enhancers and other proteins. eRNAs are abundant, and importantly, tissue-specific in tumours, various diseases and stem cells; thus, eRNAs can be a potential target for disease diagnosis and treatment. As eRNA is produced from the active transcription of enhancers and is involved in the regulation of cell fate, its manipulation will influence cell function, and therefore, it can be a new target for biological therapy.
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Affiliation(s)
- Zhenzhen Han
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Wei Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, China
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11
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Sooraj D, Sun C, Doan A, Garama DJ, Dannappel MV, Zhu D, Chua HK, Mahara S, Wan Hassan WA, Tay YK, Guanizo A, Croagh D, Prodanovic Z, Gough DJ, Wan C, Firestein R. MED12 and BRD4 cooperate to sustain cancer growth upon loss of mediator kinase. Mol Cell 2022; 82:123-139.e7. [PMID: 34910943 DOI: 10.1016/j.molcel.2021.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/27/2021] [Accepted: 11/13/2021] [Indexed: 11/23/2022]
Abstract
Mediator kinases (CDK8/19) are transcriptional regulators broadly implicated in cancer. Despite their central role in fine-tuning gene-expression programs, we find complete loss of CDK8/19 is tolerated in colorectal cancer (CRC) cells. Using orthogonal functional genomic and pharmacological screens, we identify BET protein inhibition as a distinct vulnerability in CDK8/19-depleted cells. Combined CDK8/19 and BET inhibition led to synergistic growth retardation in human and mouse models of CRC. Strikingly, depletion of CDK8/19 in these cells led to global repression of RNA polymerase II (Pol II) promoter occupancy and transcription. Concurrently, loss of Mediator kinase led to a profound increase in MED12 and BRD4 co-occupancy at enhancer elements and increased dependence on BET proteins for the transcriptional output of cell-essential genes. In total, this work demonstrates a synthetic lethal interaction between Mediator kinase and BET proteins and exposes a therapeutic vulnerability that can be targeted using combination therapies.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Binding Sites
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Proliferation/drug effects
- Colorectal Neoplasms/drug therapy
- Colorectal Neoplasms/enzymology
- Colorectal Neoplasms/genetics
- Cyclin-Dependent Kinase 8/genetics
- Cyclin-Dependent Kinase 8/metabolism
- Cyclin-Dependent Kinases/genetics
- Cyclin-Dependent Kinases/metabolism
- Enhancer Elements, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- HCT116 Cells
- Humans
- Male
- Mediator Complex/antagonists & inhibitors
- Mediator Complex/genetics
- Mediator Complex/metabolism
- Mice, Inbred BALB C
- Mice, Knockout
- Mice, Nude
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Kinase Inhibitors/pharmacology
- Receptors, Cell Surface/antagonists & inhibitors
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Signal Transduction
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Tumor Burden
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Dhanya Sooraj
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Claire Sun
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Anh Doan
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Daniel J Garama
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Marius V Dannappel
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Danxi Zhu
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Hui K Chua
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Sylvia Mahara
- Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Wan Amir Wan Hassan
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Yeng Kwang Tay
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Aleks Guanizo
- Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Daniel Croagh
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Zdenka Prodanovic
- Department of Pathology, Monash Medical Centre, Clayton, VIC, Australia
| | - Daniel J Gough
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Chunhua Wan
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
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12
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Ko H, Jang H, An S, Park IG, Ahn S, Gong J, Hwang SY, Oh S, Kwak SY, Choi WJ, Kim H, Noh M. Galangin 3-benzyl-5-methylether derivatives function as an adiponectin synthesis-promoting peroxisome proliferator-activated receptor γ partial agonist. Bioorg Med Chem 2021; 54:116564. [PMID: 34922307 DOI: 10.1016/j.bmc.2021.116564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/28/2022]
Abstract
The upregulation of adiponectin production has been suggested as a novel strategy for the treatment of metabolic diseases. Galangin, a natural flavonoid, exhibited adiponectin synthesis-promoting activity during adipogenesis in human bone marrow mesenchymal stem cells. In target identification, galangin bound both peroxisome proliferator-activated receptor (PPAR) γ and estrogen receptor (ER) β. Novel galangin derivatives were synthesized to improve adiponectin synthesis-promoting compounds by increasing the PPARγ activity of galangin and reducing its ERβ activity, because PPARγ functions can be inhibited by ERβ. Three galangin 3-benzyl-5-methylether derivatives significantly promoted adiponectin production by 2.88-, 4.47-, and 2.76-fold, respectively, compared to the effect of galangin. The most potent compound, galangin 3-benzyl-5,7-dimethylether, selectively bound to PPARγ (Ki, 1.7 μM), whereas it did not bind to ERβ. Galangin 3-benzyl-5,7-dimethylether was identified as a PPARγ partial agonist in docking and pharmacological competition studies, suggesting that it may have diverse therapeutic potential in a variety of metabolic diseases.
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Affiliation(s)
- Hyejin Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hongjun Jang
- Research Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Seungchan An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - In Guk Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sungjin Ahn
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Junpyo Gong
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seok Young Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Soyeon Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Soo Yeon Kwak
- Research Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Won Jun Choi
- College of Pharmacy, Dongguk University-Seoul, 32 Dongguk-ro, Goyang, Gyeonggi-do 10326, Republic of Korea
| | - Hyoungsu Kim
- Research Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi-do 16499, Republic of Korea.
| | - Minsoo Noh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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13
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Jain M, Garg R. Enhancers as potential targets for engineering salinity stress tolerance in crop plants. PHYSIOLOGIA PLANTARUM 2021; 173:1382-1391. [PMID: 33837536 DOI: 10.1111/ppl.13421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/19/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Enhancers represent noncoding regulatory regions of the genome located distantly from their target genes. They regulate gene expression programs in a context-specific manner via interacting with promoters of one or more target genes and are generally associated with transcription factor binding sites and epi(genomic)/chromatin features, such as regions of chromatin accessibility and histone modifications. The enhancers are difficult to identify due to the modularity of their associated features. Although enhancers have been studied extensively in human and animals, only a handful of them has been identified in few plant species till date due to nonavailability of plant-specific experimental and computational approaches for their discovery. Being an important regulatory component of the genome, enhancers represent potential targets for engineering agronomic traits, including salinity stress tolerance in plants. Here, we provide a review of the available experimental and computational approaches along with the associated sequence and chromatin/epigenetic features for the discovery of enhancers in plants. In addition, we provide insights into the challenges and future prospects of enhancer research in plant biology with emphasis on potential applications in engineering salinity stress tolerance in crop plants.
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Affiliation(s)
- Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
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14
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Chen H, Li M, Qi G, Zhao M, Liu L, Zhang J, Chen G, Wang D, Liu F, Fu ZQ. Two interacting transcriptional coactivators cooperatively control plant immune responses. SCIENCE ADVANCES 2021; 7:eabl7173. [PMID: 34739308 PMCID: PMC8570602 DOI: 10.1126/sciadv.abl7173] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The phytohormone salicylic acid (SA) plays a pivotal role in plant defense against biotrophic and hemibiotrophic pathogens. NPR1 and EDS1 function as two central hubs in plant local and systemic immunity. However, it is unclear how NPR1 orchestrates gene regulation and whether EDS1 directly participates in transcriptional reprogramming. Here, we show that NPR1 and EDS1 synergistically activate pathogenesis-related (PR) genes and plant defenses by forming a protein complex and recruiting Mediator. We discover that EDS1 functions as an autonomous transcriptional coactivator with intrinsic transactivation domains and physically interacts with the CDK8 subunit of Mediator. Upon SA induction, EDS1 is directly recruited by NPR1 onto the PR1 promoter via physical NPR1-EDS1 interactions, thereby potentiating PR1 activation. We further demonstrate that EDS1 stabilizes NPR1 protein and NPR1 transcriptionally up-regulates EDS1. Our results reveal an elegant interplay of key coactivators with Mediator and elucidate important molecular mechanisms for activating transcription during immune responses.
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Affiliation(s)
- Huan Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety–State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Min Li
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Guang Qi
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
- State Key Laboratory of Wheat and Maize Crop Science and College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Ming Zhao
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Longyu Liu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingyi Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety–State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science and College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety–State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Corresponding author. (F.L.); (Z.Q.F.)
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
- Corresponding author. (F.L.); (Z.Q.F.)
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15
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Discovery of a potent, highly selective, and orally bioavailable inhibitor of CDK8 through a structure-based optimisation. Eur J Med Chem 2021; 218:113391. [PMID: 33823391 DOI: 10.1016/j.ejmech.2021.113391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022]
Abstract
CDK8 is deregulated in multiple types of human cancer and is viewed as a therapeutic target for the treatment of the disease. Accordingly, the search for small-molecule inhibitors of CDK8 is being intensified. Capitalising on our initial discovery of AU1-100, a potent CDK8 inhibitor yet with a limited degree of kinase selectivity, a structure-based optimisation was carried out, with a series of new multi-substituted pyridines rationally designed, chemically prepared and biologically evaluated. Such endeavour has culminated in the identification of 42, a more potent CDK8 inhibitor with superior kinomic selectivity and oral bioavailability. The mechanism underlying the anti-proliferative effect of 42 on MV4-11 cells was studied, revealing that the compound arrested the G1 cell cycle and triggered apoptosis. The low risk of hepato- and cardio-toxicity of 42 was estimated. These findings merit further investigation of 42 as a targeted cancer therapeutic.
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16
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Sorokin V, Vickneson K, Kofidis T, Woo CC, Lin XY, Foo R, Shanahan CM. Role of Vascular Smooth Muscle Cell Plasticity and Interactions in Vessel Wall Inflammation. Front Immunol 2020; 11:599415. [PMID: 33324416 PMCID: PMC7726011 DOI: 10.3389/fimmu.2020.599415] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
The pathobiology of atherosclerotic disease requires further elucidation to discover new approaches to address its high morbidity and mortality. To date, over 17 million cardiovascular-related deaths have been reported annually, despite a multitude of surgical and nonsurgical interventions and advances in medical therapy. Existing strategies to prevent disease progression mainly focus on management of risk factors, such as hypercholesterolemia. Even with optimum current medical therapy, recurrent cardiovascular events are not uncommon in patients with atherosclerosis, and their incidence can reach 10–15% per year. Although treatments targeting inflammation are under investigation and continue to evolve, clinical breakthroughs are possible only if we deepen our understanding of vessel wall pathobiology. Vascular smooth muscle cells (VSMCs) are one of the most abundant cells in vessel walls and have emerged as key players in disease progression. New technologies, including in situ hybridization proximity ligation assays, in vivo cell fate tracing with the CreERT2-loxP system and single-cell sequencing technology with spatial resolution, broaden our understanding of the complex biology of these intriguing cells. Our knowledge of contractile and synthetic VSMC phenotype switching has expanded to include macrophage-like and even osteoblast-like VSMC phenotypes. An increasing body of data suggests that VSMCs have remarkable plasticity and play a key role in cell-to-cell crosstalk with endothelial cells and immune cells during the complex process of inflammation. These are cells that sense, interact with and influence the behavior of other cellular components of the vessel wall. It is now more obvious that VSMC plasticity and the ability to perform nonprofessional phagocytic functions are key phenomena maintaining the inflammatory state and senescent condition and actively interacting with different immune competent cells.
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Affiliation(s)
- Vitaly Sorokin
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Cardiac, Thoracic and Vascular Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Keeran Vickneson
- School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Theo Kofidis
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Cardiac, Thoracic and Vascular Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Chin Cheng Woo
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiao Yun Lin
- Department of Cardiac, Thoracic and Vascular Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Roger Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, ASTAR, Singapore, Singapore
| | - Catherine M Shanahan
- School of Cardiovascular Medicine and Sciences, James Black Centre, King's College London, London, United Kingdom
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17
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Dash S, Bhatt S, Sandell LL, Seidel CW, Ahn Y, Krumlauf RE, Trainor PA. The Mediator Subunit, Med23 Is Required for Embryonic Survival and Regulation of Canonical WNT Signaling During Cranial Ganglia Development. Front Physiol 2020; 11:531933. [PMID: 33192541 PMCID: PMC7642510 DOI: 10.3389/fphys.2020.531933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
Development of the vertebrate head is a complex and dynamic process, which requires integration of all three germ layers and their derivatives. Of special importance are ectoderm-derived cells that form the cranial placodes, which then differentiate into the cranial ganglia and sensory organs. Critical to a fully functioning head, defects in cranial placode and sensory organ development can result in congenital craniofacial anomalies. In a forward genetic screen aimed at identifying novel regulators of craniofacial development, we discovered an embryonically lethal mouse mutant, snouty, which exhibits malformation of the facial prominences, cranial nerves and vasculature. The snouty mutation was mapped to a single nucleotide change in a ubiquitously expressed gene, Med23, which encodes a subunit of the global transcription co-factor complex, Mediator. Phenotypic analyses revealed that the craniofacial anomalies, particularly of the cranial ganglia, were caused by a failure in the proper specification of cranial placode neuronal precursors. Molecular analyses determined that defects in cranial placode neuronal differentiation in Med23 sn/sn mutants were associated with elevated WNT/β-catenin signaling, which can be partially rescued through combined Lrp6 and Wise loss-of-function. Our work therefore reveals a surprisingly tissue specific role for the ubiquitously expressed mediator complex protein Med23 in placode differentiation during cranial ganglia development. This highlights the importance of coupling general transcription to the regulation of WNT signaling during embryogenesis.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Shachi Bhatt
- Stowers Institute for Medical Research, Kansas City, MO, United States.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Lisa L Sandell
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, United States
| | | | - Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Robb E Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, United States.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, United States
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18
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Uehara T, Abe K, Oginuma M, Ishitani S, Yoshihashi H, Okamoto N, Takenouchi T, Kosaki K, Ishitani T. Pathogenesis of CDK8-associated disorder: two patients with novel CDK8 variants and in vitro and in vivo functional analyses of the variants. Sci Rep 2020; 10:17575. [PMID: 33067521 PMCID: PMC7567849 DOI: 10.1038/s41598-020-74642-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 09/03/2020] [Indexed: 11/09/2022] Open
Abstract
Cyclin-dependent kinase 8 (CDK8) is a member of the CDK/Cyclin module of the mediator complex. A recent study reported that heterozygous missense CDK8 mutations cause a neurodevelopmental disorder in humans. The mechanistic basis of CDK8-related disorder has yet to be delineated. Here, we report 2 patients with de novo missense mutations within the kinase domain of CDK8 along with the results of in vitro and in vivo functional analyses using a zebrafish model. Patient 1 and Patient 2 had intellectual disabilities and congenital anomalies. Exome analyses showed that patient 1 had a heterozygous de novo missense p.G28A variant in the CDK8 (NM_001260.3) gene and patient 2 had a heterozygous de novo missense p.N156S variant in the CDK8 gene. We assessed the pathogenicity of these two variants using cultured-cells and zebrafish model. An in vitro kinase assay of human CDK8 showed that enzymes with a p.G28A or p.N156S substitution showed decreased kinase activity. An in vivo assays of zebrafish overexpression analyses also showed that the p.G28A and p.N156S alleles were hypomorphic alleles. Importantly, the inhibition of CDK8 kinase activity in zebrafish embryos using a specific chemical inhibitor induced craniofacial and heart defects similar to the patients' phenotype. Taken together, zebrafish studies showed that non-synonymous variants in the kinase domain of CDK8 act as hypomorphic alleles causing human congenital disorder.
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Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics, Keio University Hospital, Tokyo, Japan
| | - Kota Abe
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayuki Oginuma
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shizuka Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Yoshihashi
- Department of Genetics, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University Hospital, Tokyo, Japan
| | - Tohru Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan. .,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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19
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Pyrido[2,3-b][1,5]benzoxazepin-5(6H)-one derivatives as CDK8 inhibitors. Eur J Med Chem 2020; 201:112443. [DOI: 10.1016/j.ejmech.2020.112443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 01/07/2023]
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20
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Selective Mediator dependence of cell-type-specifying transcription. Nat Genet 2020; 52:719-727. [PMID: 32483291 PMCID: PMC7610447 DOI: 10.1038/s41588-020-0635-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.
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21
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Rubinato E, Rondeau S, Giuliano F, Kossorotoff M, Parodi M, Gherbi S, Steffan J, Jonard L, Marlin S. MED12 missense mutation in a three-generation family. Clinical characterization of MED12-related disorders and literature review. Eur J Med Genet 2020; 63:103768. [DOI: 10.1016/j.ejmg.2019.103768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/23/2019] [Accepted: 09/15/2019] [Indexed: 10/26/2022]
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22
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Hiebert CW, Moscou MJ, Hewitt T, Steuernagel B, Hernández-Pinzón I, Green P, Pujol V, Zhang P, Rouse MN, Jin Y, McIntosh RA, Upadhyaya N, Zhang J, Bhavani S, Vrána J, Karafiátová M, Huang L, Fetch T, Doležel J, Wulff BBH, Lagudah E, Spielmeyer W. Stem rust resistance in wheat is suppressed by a subunit of the mediator complex. Nat Commun 2020; 11:1123. [PMID: 32111840 PMCID: PMC7048732 DOI: 10.1038/s41467-020-14937-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar ‘Canthatch’ suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat. Stem rust is an important disease of wheat and resistance present in some cultivars can be suppressed by the SuSr-D1 locus. Here the authors show that SuSr-D1 encodes a subunit of the Mediator Complex and that nonsense mutations are sufficient to abolish suppression and confer stem rust resistance.
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Affiliation(s)
- Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK.
| | - Tim Hewitt
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia.,CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Inma Hernández-Pinzón
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Vincent Pujol
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Yue Jin
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Robert A McIntosh
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | | | - Jianping Zhang
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sridhar Bhavani
- CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market, Nairobi, 00621, Kenya
| | - Jan Vrána
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Li Huang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Tom Fetch
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | | | - Evans Lagudah
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia.
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Wang C, Lin L, Xue Y, Wang Y, Liu Z, Ou Z, Wu S, Lan X, Zhang Y, Yuan F, Luo X, Wang C, Xi J, Sun X, Chen Y. MED12-Related Disease in a Chinese Girl: Clinical Characteristics and Underlying Mechanism. Front Genet 2020; 11:129. [PMID: 32174975 PMCID: PMC7056888 DOI: 10.3389/fgene.2020.00129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
The RNA polymerase II transcription subunit 12 homolog (MED12) is a member of the mediator complex, which plays a critical role in RNA transcription. Mutations in MED12 cause X-linked intellectual disability and other anomalies collectively grouped as MED12-related disorders. While MED12 mutations have been most commonly reported in male patients, we present the case of a 1-year-old girl with clinical characteristics similar to MED12-related disorders. To explore the clinical characteristics of the condition and its possible pathogenesis, we analyzed the patient's clinical data; genetic testing by whole-exome sequencing revealed a de novo heterozygous mutation (c.1249-1G > C) in MED12. Further cDNA experiments revealed that the patient had an abnormal splicing at the skipping of exon9, which may have produced a truncated protein. qPCR showed decreased MED12 gene expression level in the patient, and an X-chromosome inactivation test confirmed a skewed inactivation of the X-chromosome. The lymphoblast transcription levels of the genes involved in the Gli3-dependent sonic hedgehog (SHH) signaling pathway, namely, CREB5, BMP4, and NEUROG2, were found to be significantly elevated compared with those of her parents and sex- and age-matched controls. Our results support the view that MED12 mutations may dysregulate the SHH signaling pathway, which may have accounted for the aberrant craniofacial morphology of our patient.
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Affiliation(s)
- Chao Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Longlong Lin
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Xue
- Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yilin Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhao Liu
- Division of Pediatric Neurology, Department of Pediatrics, University of Illinois and Children's Hospital of Illinois, Peoria, IL, United States
| | - Zicheng Ou
- Department of Pediatrics, JianNing General Hospital, Fujian, China
| | - Shengnan Wu
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoping Lan
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanfeng Zhang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Yuan
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaona Luo
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chunmei Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaming Xi
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaomin Sun
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yucai Chen
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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24
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A precisely positioned MED12 activation helix stimulates CDK8 kinase activity. Proc Natl Acad Sci U S A 2020; 117:2894-2905. [PMID: 31988137 DOI: 10.1073/pnas.1917635117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mediator kinase module regulates eukaryotic transcription by phosphorylating transcription-related targets and by modulating the association of Mediator and RNA polymerase II. The activity of its catalytic core, cyclin-dependent kinase 8 (CDK8), is controlled by Cyclin C and regulatory subunit MED12, with its deregulation contributing to numerous malignancies. Here, we combine in vitro biochemistry, cross-linking coupled to mass spectrometry, and in vivo studies to describe the binding location of the N-terminal segment of MED12 on the CDK8/Cyclin C complex and to gain mechanistic insights into the activation of CDK8 by MED12. Our data demonstrate that the N-terminal portion of MED12 wraps around CDK8, whereby it positions an "activation helix" close to the T-loop of CDK8 for its activation. Intriguingly, mutations in the activation helix that are frequently found in cancers do not diminish the affinity of MED12 for CDK8, yet likely alter the exact positioning of the activation helix. Furthermore, we find the transcriptome-wide gene-expression changes in human cells that result from a mutation in the MED12 activation helix to correlate with deregulated genes in breast and colon cancer. Finally, functional assays in the presence of kinase inhibitors reveal that binding of MED12 remodels the active site of CDK8 and thereby precludes the inhibition of ternary CDK8 complexes by type II kinase inhibitors. Taken together, our results not only allow us to propose a revised model of how CDK8 activity is regulated by MED12, but also offer a path forward in developing small molecules that target CDK8 in its MED12-bound form.
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25
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van der Vorst EPC, Weber C. Novel Features of Monocytes and Macrophages in Cardiovascular Biology and Disease. Arterioscler Thromb Vasc Biol 2019; 39:e30-e37. [PMID: 30673349 DOI: 10.1161/atvbaha.118.312002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Emiel P C van der Vorst
- From the Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany (E.P.C.v.d.V., C.W.)
| | - Christian Weber
- From the Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany (E.P.C.v.d.V., C.W.).,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Germany (C.W.).,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, the Netherlands (C.W.)
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26
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Legrand N, Bretscher CL, Zielke S, Wilke B, Daude M, Fritz B, Diederich WE, Adhikary T. PPARβ/δ recruits NCOR and regulates transcription reinitiation of ANGPTL4. Nucleic Acids Res 2019; 47:9573-9591. [PMID: 31428774 PMCID: PMC6765110 DOI: 10.1093/nar/gkz685] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/20/2019] [Accepted: 07/28/2019] [Indexed: 12/24/2022] Open
Abstract
In the absence of ligands, the nuclear receptor PPARβ/δ recruits the NCOR and SMRT corepressors, which form complexes with HDAC3, to canonical target genes. Agonistic ligands cause dissociation of corepressors and enable enhanced transcription. Vice versa, synthetic inverse agonists augment corepressor recruitment and repression. Both basal repression of the target gene ANGPTL4 and reinforced repression elicited by inverse agonists are partially insensitive to HDAC inhibition. This raises the question how PPARβ/δ represses transcription mechanistically. We show that the PPARβ/δ inverse agonist PT-S264 impairs transcription initiation by decreasing recruitment of activating Mediator subunits, RNA polymerase II, and TFIIB, but not of TFIIA, to the ANGPTL4 promoter. Mass spectrometry identifies NCOR as the main PT-S264-dependent interactor of PPARβ/δ. Reconstitution of knockout cells with PPARβ/δ mutants deficient in basal repression results in diminished recruitment of NCOR, SMRT, and HDAC3 to PPAR target genes, while occupancy by RNA polymerase II is increased. PT-S264 restores binding of NCOR, SMRT, and HDAC3 to the mutants, resulting in reduced polymerase II occupancy. Our findings corroborate deacetylase-dependent and -independent repressive functions of HDAC3-containing complexes, which act in parallel to downregulate transcription.
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Affiliation(s)
- Nathalie Legrand
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Clemens L Bretscher
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Svenja Zielke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Bernhard Wilke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Michael Daude
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Barbara Fritz
- Centre for Human Genetics, Universitätsklinikum Giessen und Marburg GmbH, Baldingerstrasse, 35043 Marburg, Germany
| | - Wibke E Diederich
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Pharmacy, Institute for Pharmaceutical Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Till Adhikary
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
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27
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Zhai Q, Li C. The plant Mediator complex and its role in jasmonate signaling. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3415-3424. [PMID: 31089685 PMCID: PMC6609880 DOI: 10.1093/jxb/erz233] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/07/2019] [Indexed: 05/20/2023]
Abstract
The Mediator complex is an essential, multisubunit transcriptional coactivator that is highly conserved in eukaryotes. Mediator interacts with gene-specific transcription factors, the RNA polymerase II transcriptional machinery, as well as several other factors involved in transcription, and acts as an integral hub to regulate various aspects of transcription. Recent studies of the plant Mediator complex have established that it functions in diverse aspects of plant development and fitness. Jasmonate (JA) is an oxylipin-derived plant hormone that regulates plant immunity and development. The basic helix-loop-helix transcription factor MYC2, which is a master regulator of JA signaling, orchestrates genome-wide transcriptional reprogramming of plant cells to coordinate defense- and growth-related processes. Here, we review the function of the plant Mediator complex in regulating JA signaling. We focus on the multifunctional Mediator subunit MED25, which emerges as an integrative hub for the transcriptional regulation of jasmonate signaling.
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Affiliation(s)
- Qingzhe Zhai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Correspondence:
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28
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Xu M, Wang F, Li G, Wang X, Fang X, Jin H, Chen Z, Zhang J, Fu L. MED12 exerts an emerging role in actin-mediated cytokinesis via LIMK2/cofilin pathway in NSCLC. Mol Cancer 2019; 18:93. [PMID: 31072327 PMCID: PMC6509838 DOI: 10.1186/s12943-019-1020-4] [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: 01/30/2019] [Accepted: 04/22/2019] [Indexed: 12/31/2022] Open
Abstract
Background Mediator complex subunit 12 (MED12) is an essential hub for transcriptional regulation, in which mutations and overexpression were reported to be associated with several kinds of malignancies. Nevertheless, the role of MED12 in non-small cell lung cancer (NSCLC) remains to be elucidated. Methods MED12 mutation was detected by Next-generation sequencing. The expression of MED12 in 179 human NSCLC tissue samples and 73 corresponding adjacent normal lung tissue samples was measured by immunohistochemistry (IHC). CRISPR-Cas9 was used to knock out MED12 in PC9 and SPC-A1 cells. MED12 rescued stable cell lines were generated by lentivirus infection. We traced cell division process by live cell imaging. The molecular mechanism of aborted cytokinesis resulted by MED12 knockout was investigated by RNA-seq. Effects of MED12 deletion on the proliferation of NSCLC cells were determined by MTT assay and Colony-formation assay in vitro and xenograft tumor model in nude mouse. Cell senescence was measured by SA-β-gal staining. Results In our study, no MED12 exon mutation was detected in NSCLC samples, whereas we found that MED12 was overexpressed in human NSCLC tissues, which positively correlated with the tumor volume and adversely affected patient survival. Furthermore, knockout MED12 in NSCLC cell lines resulted in cytokinesis failure, displayed a multinuclear phenotype, and disposed to senescence, and become non-viable. Lack of MED12 decreased the proliferative potential of NSCLC cells and limited the tumor growth in vivo. Mechanism investigations revealed that MED12 knockout activated LIMK2, caused aberrant actin cytoskeleton remodeling, and disrupted the abscission of intercellular bridge, which led to the cytokinesis failure. Reconstitution of exogenous MED12 restored actin dynamics, normal cytokinesis and cell proliferation capacity in MED12 knockout cells. Conclusions These results revealed a novel role of MED12 as an important regulator for maintaining accurate cytokinesis and survival in NSCLC cells, which may offer a therapeutic strategy to control tumor growth for NSCLC patients especially those highly expressed MED12. Electronic supplementary material The online version of this article (10.1186/s12943-019-1020-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng East Road, Guangzhou, 510060, Guangdong, China.,Radiotherapy Department of Thorax & Abdomen Tumor, Cancer Center, The First People's Hospital of Foshan Affiliated to Sun Yat-sen University, Foshan, 528000, China
| | - Fang Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng East Road, Guangzhou, 510060, Guangdong, China
| | - Guibo Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Xiaokun Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng East Road, Guangzhou, 510060, Guangdong, China
| | - Xiaona Fang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng East Road, Guangzhou, 510060, Guangdong, China
| | - Haoxuan Jin
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zhen Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng East Road, Guangzhou, 510060, Guangdong, China
| | - Jianye Zhang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Liwu Fu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng East Road, Guangzhou, 510060, Guangdong, China.
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29
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Twenty years of Mediator complex structural studies. Biochem Soc Trans 2019; 47:399-410. [PMID: 30733343 PMCID: PMC6393861 DOI: 10.1042/bst20180608] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/18/2022]
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit kinase module. For nearly 20 years, because of its size and complexity, Mediator has posed a formidable challenge to structural biologists. The first two-dimensional electron microscopy (EM) projection map of Mediator leading to the canonical view of its division in three topological modules named Head, Middle and Tail, was published in 1999. Within the last few years, optimization of Mediator purification combined with technical and methodological advances in cryo-electron microscopy (cryo-EM) have revealed unprecedented details of Mediator subunit organization, interactions with RNA polymerase II and parts of its core structure at high resolution. To celebrate the twentieth anniversary of the first Mediator EM reconstruction, we look back on the structural studies of Mediator complex from a historical perspective and discuss them in the light of our current understanding of its role in transcriptional regulation.
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30
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Chen W, Ren X, Chang CEA. Discovery of CDK8/CycC Ligands with a New Virtual Screening Tool. ChemMedChem 2018; 14:107-118. [PMID: 30403831 DOI: 10.1002/cmdc.201800559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/02/2018] [Indexed: 12/15/2022]
Abstract
Selective inhibition of cyclin-dependent kinase 8 and cyclin C (CDK8/CycC) has been suggested as a promising strategy for decreasing mitogenic signals in cancer cells with reduced toxicity toward normal cells. We developed a novel virtual screening protocol for drug development and applied it to the discovery of new CDK8/CycC type II ligands, which is likely to achieve long residence time and specificity. We first analyzed the binding thermodynamics of 11 published pyrazolourea ligands using molecular dynamics simulations and a free-energy calculation method, VM2, and extracted the key binding information to assist virtual screening. The urea moiety was found to be the critical structural contributor of the reference ligands. Starting with the urea moiety, we conducted substructure-based searches with our newly developed superposition and single-point energy evaluation method, followed by free-energy calculations, and singled out three purchasable compounds for bioassay testing. The ranking from the experimental results is completely consistent with the predicted rankings. A potent drug-like compound was found to have a Kd value of 42.5 nm, which is similar to those of the most potent reference ligands; this provided a good starting point for further improvement. This study shows that our novel virtual screening protocol is an accurate and efficient tool for drug development.
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Affiliation(s)
- Wei Chen
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.,ChemConsulting LLC, Frederick, MD, 21704, USA.,NanChang Lead Biotech LLC, NanChang, JiangXi, 330096, China
| | - Xiaodong Ren
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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31
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Pérez-Martín F, Yuste-Lisbona FJ, Pineda B, García-Sogo B, Olmo ID, de Dios Alché J, Egea I, Flores FB, Piñeiro M, Jarillo JA, Angosto T, Capel J, Moreno V, Lozano R. Developmental role of the tomato Mediator complex subunit MED18 in pollen ontogeny. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:300-315. [PMID: 30003619 DOI: 10.1111/tpj.14031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/17/2018] [Accepted: 06/26/2018] [Indexed: 05/06/2023]
Abstract
Pollen development is a crucial step in higher plants, which not only makes possible plant fertilization and seed formation, but also determines fruit quality and yield in crop species. Here, we reported a tomato T-DNA mutant, pollen deficient1 (pod1), characterized by an abnormal anther development and the lack of viable pollen formation, which led to the production of parthenocarpic fruits. Genomic analyses and the characterization of silencing lines proved that pod1 mutant phenotype relies on the tomato SlMED18 gene encoding the subunit 18 of Mediator multi-protein complex involved in RNA polymerase II transcription machinery. The loss of SlMED18 function delayed tapetum degeneration, which resulted in deficient microspore development and scarce production of viable pollen. A detailed histological characterization of anther development proved that changes during microgametogenesis and a significant delay in tapetum degeneration are associated with a high proportion of degenerated cells and, hence, should be responsible for the low production of functional pollen grains. Expression of pollen marker genes indicated that SlMED18 is essential for the proper transcription of a subset of genes specifically required to pollen formation and fruit development, revealing a key role of SlMED18 in male gametogenesis of tomato. Additionally, SlMED18 is able to rescue developmental abnormalities of the Arabidopsis med18 mutant, indicating that most biological functions have been conserved in both species.
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Affiliation(s)
- Fernando Pérez-Martín
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120, Almería, Spain
| | - Fernando J Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120, Almería, Spain
| | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, 46022, Valencia, Spain
| | - Begoña García-Sogo
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, 46022, Valencia, Spain
| | - Iván Del Olmo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Juan de Dios Alché
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, EEZ-CSIC, 18008, Granada, Spain
| | - Isabel Egea
- Departamento de Biología del Estrés y Patología Vegetal, CEBAS-CSIC, 30100, Espinardo-Murcia, Spain
| | - Francisco B Flores
- Departamento de Biología del Estrés y Patología Vegetal, CEBAS-CSIC, 30100, Espinardo-Murcia, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120, Almería, Spain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120, Almería, Spain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, 46022, Valencia, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120, Almería, Spain
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32
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Światowy W, Jagodzińśki PP. Molecules derived from tRNA and snoRNA: Entering the degradome pool. Biomed Pharmacother 2018; 108:36-42. [PMID: 30216797 DOI: 10.1016/j.biopha.2018.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/03/2018] [Accepted: 09/04/2018] [Indexed: 02/02/2023] Open
Abstract
Molecules built of RNA have been the subjects of numerous studies, which have made known new functions and structures that these molecules can create. In recent years, thanks to next-generation sequencing, it is possible to observe very small RNAs and the number of newly discovered RNA molecules is rapidly increasing. Among other small oligonucleotides, structures derived from tRNA and snoRNA molecules have been observed, and these molecules were determined to not be precursors of known RNA molecules. These structures have attracted the attention of researchers because the level of accumulation of tRNA or snoRNA fragments was relatively high. Additionally, other parts of the parent molecules were absent. Derivatives of well-known RNA molecules also have functions that are different from their parent molecules. They are mainly involved in regulating the expression of genetic information in a similar way to miRNA. In addition, some of the miRNAs that have been described are derivatives of tRNA or snoRNA. Most of the research on these newly discovered molecules is based on their detection and on the study of the macro effects that they exert, in the absence of a description of the molecular mechanism by which they arise and work.
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Affiliation(s)
- Witold Światowy
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poland.
| | - Paweł P Jagodzińśki
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poland
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33
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Cholko T, Chen W, Tang Z, Chang CEA. A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery. J Comput Aided Mol Des 2018; 32:671-685. [PMID: 29737445 DOI: 10.1007/s10822-018-0120-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 05/02/2018] [Indexed: 12/13/2022]
Abstract
Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein-ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein-ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.
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Affiliation(s)
- Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Wei Chen
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Zhiye Tang
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA.
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Luo XL, Deng CC, Su XD, Wang F, Chen Z, Wu XP, Liang SB, Liu JH, Fu LW. Loss of MED12 Induces Tumor Dormancy in Human Epithelial Ovarian Cancer via Downregulation of EGFR. Cancer Res 2018; 78:3532-3543. [PMID: 29735544 DOI: 10.1158/0008-5472.can-18-0134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/24/2018] [Accepted: 04/26/2018] [Indexed: 11/16/2022]
Abstract
A high rate of disease relapse makes epithelial ovarian cancer (EOC) the leading cause of death among all gynecologic malignancies. These relapses are often due to tumor dormancy. Here we identify the RNA polymerase II transcriptional mediator subunit 12 (MED12) as an important molecular regulator of tumor dormancy. MED12 knockout (KO) induced dormancy of EOC cells in vitro and in vivo, and microarray analysis showed that MED12 KO decreased expression of EGFR. Restoration of EGFR expression in MED12 KO cells restored proliferation. Additionally, MED12 bound to the promoter of EGFR, and correlation studies showed that MED12 expression positively correlated with EGFR expression in EOC patient samples. Clinical data demonstrated that chemotherapy-resistant patients expressed lower levels of MED12 compared with responsive patients. Overall, our data show that MED12 plays an important role in regulating dormancy of EOC through regulation of EGFR.Significance: MED12 is identified as a novel, important regulator of tumor dormancy in human ovarian cancer. Cancer Res; 78(13); 3532-43. ©2018 AACR.
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Affiliation(s)
- Xiao-Lin Luo
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Gynecologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cheng-Cheng Deng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiao-Dong Su
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Fang Wang
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhen Chen
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xing-Ping Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shao-Bo Liang
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ji-Hong Liu
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Li-Wu Fu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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Snijders Blok L, Hiatt SM, Bowling KM, Prokop JW, Engel KL, Cochran JN, Bebin EM, Bijlsma EK, Ruivenkamp CAL, Terhal P, Simon MEH, Smith R, Hurst JA, McLaughlin H, Person R, Crunk A, Wangler MF, Streff H, Symonds JD, Zuberi SM, Elliott KS, Sanders VR, Masunga A, Hopkin RJ, Dubbs HA, Ortiz-Gonzalez XR, Pfundt R, Brunner HG, Fisher SE, Kleefstra T, Cooper GM. De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder. Hum Genet 2018; 137:375-388. [PMID: 29740699 PMCID: PMC5973976 DOI: 10.1007/s00439-018-1887-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/21/2018] [Indexed: 01/15/2023]
Abstract
Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders. Other features that were reported in two or more patients include autism spectrum disorder, attention deficit hyperactivity disorder, optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphisms. Six affected individuals had mutations that are predicted to truncate the MED13 protein, six had missense mutations, and one had an in-frame-deletion of one amino acid. Out of the seven non-truncating mutations, six clustered in two specific locations of the MED13 protein: an N-terminal and C-terminal region. The four N-terminal clustering mutations affect two adjacent amino acids that are known to be involved in MED13 ubiquitination and degradation, p.Thr326 and p.Pro327. MED13 is a component of the CDK8-kinase module that can reversibly bind Mediator, a multi-protein complex that is required for Polymerase II transcription initiation. Mutations in several other genes encoding subunits of Mediator have been previously shown to associate with DD/ID, including MED13L, a paralog of MED13. Thus, our findings add MED13 to the group of CDK8-kinase module-associated disease genes.
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Affiliation(s)
- Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Krysta L Engel
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paulien Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Jane A Hurst
- Great Ormond Street Hospital for Children, London, UK
| | | | | | - Amy Crunk
- GeneDx, 207 Perry Parkway, Gaithersburg, MD, 20877, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | | | - Victoria R Sanders
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Abigail Masunga
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Rolph Pfundt
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Han G Brunner
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
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Abstract
Background Monosomy of the X chromosome is the most frequent genetic abnormality in human as it is present in approximately 2% of all conceptions, although 99% of these embryos are spontaneously miscarried. In postnatal life, clinical features of Turner syndrome may include typical dysmorphic stigmata, short stature, sexual infantilism, and renal, cardiac, skeletal, endocrine and metabolic abnormalities. Main text Turner syndrome is due to a partial or total loss of the second sexual chromosome, resulting in the development of highly variable clinical features. This phenotype may not merely be due to genomic imbalance from deleted genes but may also result from additive influences on associated genes within a given gene network, with an altered regulation of gene expression triggered by the absence of the second sex chromosome. Current studies in human and mouse models have demonstrated that this chromosomal abnormality leads to epigenetic changes, including differential DNA methylation in specific groups of downstream target genes in pathways associated with several clinical and metabolic features, mostly on autosomal chromosomes. In this article, we begin exploring the potential involvement of both genetic and epigenetic factors in the origin of X chromosome monosomy. We review the dispute between the meiotic and post-zygotic origins of 45,X monosomy, by mainly analyzing the findings from several studies that compare gene expression of the 45,X monosomy to their euploid and/or 47,XXX trisomic cell counterparts on peripheral blood mononuclear cells, amniotic fluid, human fibroblast cells, and induced pluripotent human cell lines. From these studies, a profile of epigenetic changes seems to emerge in response to chromosomal imbalance. An interesting finding of all these studies is that methylation-based and expression-based pathway analyses are complementary, rather than overlapping, and are correlated with the clinical picture displayed by TS subjects. Conclusions The clarification of these possible causal pathways may have future implications in increasing the life expectancy of these patients and may provide informative targets for early pharmaceutical intervention.
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Affiliation(s)
- Francisco Álvarez-Nava
- Biological Sciences School, Faculty of Biological Sciences, Central University of Ecuador, Quito, Ecuador
| | - Roberto Lanes
- Pediatric Endocrine Unit, Hospital de Clínicas Caracas, Caracas, Venezuela
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Shrimp JH, Grose C, Widmeyer SRT, Thorpe AL, Jadhav A, Meier JL. Chemical Control of a CRISPR-Cas9 Acetyltransferase. ACS Chem Biol 2018; 13:455-460. [PMID: 29309117 PMCID: PMC6320253 DOI: 10.1021/acschembio.7b00883] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lysine acetyltransferases (KATs) play a critical role in the regulation of transcription and other genomic functions. However, a persistent challenge is the development of assays capable of defining KAT activity directly in living cells. Toward this goal, here we report the application of a previously reported dCas9-p300 fusion as a transcriptional reporter of KAT activity. First, we benchmark the activity of dCas9-p300 relative to other dCas9-based transcriptional activators and demonstrate its compatibility with second generation short guide RNA architectures. Next, we repurpose this technology to rapidly identify small molecule inhibitors of acetylation-dependent gene expression. These studies validate a recently reported p300 inhibitor chemotype and reveal a role for p300s bromodomain in dCas9-p300-mediated transcriptional activation. Comparison with other CRISPR-Cas9 transcriptional activators highlights the inherent ligand tunable nature of dCas9-p300 fusions, suggesting new opportunities for orthogonal gene expression control. Overall, our studies highlight dCas9-p300 as a powerful tool for studying gene expression mechanisms in which acetylation plays a causal role and provide a foundation for future applications requiring spatiotemporal control over acetylation at specific genomic loci.
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Affiliation(s)
- Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Carissa Grose
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. , Frederick, Maryland 21702, United States
| | - Stephanie R T Widmeyer
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. , Frederick, Maryland 21702, United States
| | - Abigail L Thorpe
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville, Maryland 20850, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
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Banerji R, Skibbens RV, Iovine MK. How many roads lead to cohesinopathies? Dev Dyn 2017; 246:881-888. [PMID: 28422453 DOI: 10.1002/dvdy.24510] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/10/2017] [Accepted: 04/11/2017] [Indexed: 12/16/2023] Open
Abstract
Genetic mapping studies reveal that mutations in cohesion pathways are responsible for multispectrum developmental abnormalities termed cohesinopathies. These include Roberts syndrome (RBS), Cornelia de Lange Syndrome (CdLS), and Warsaw Breakage Syndrome (WABS). The cohesinopathies are characterized by overlapping phenotypes ranging from craniofacial deformities, limb defects, and mental retardation. Though these syndromes share a similar suite of phenotypes and arise due to mutations in a common cohesion pathway, the underlying mechanisms are currently believed to be distinct. Defects in mitotic failure and apoptosis i.e. trans DNA tethering events are believed to be the underlying cause of RBS, whereas the underlying cause of CdLS is largely modeled as occurring through defects in transcriptional processes i.e. cis DNA tethering events. Here, we review recent findings described primarily in zebrafish, paired with additional studies in other model systems, including human patient cells, which challenge the notion that cohesinopathies represent separate syndromes. We highlight numerous studies that illustrate the utility of zebrafish to provide novel insights into the phenotypes, genes affected and the possible mechanisms underlying cohesinopathies. We propose that transcriptional deregulation is the predominant mechanism through which cohesinopathies arise. Developmental Dynamics 246:881-888, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rajeswari Banerji
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
| | - Robert V Skibbens
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
| | - M Kathryn Iovine
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
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Ko YA, Jamaluddin MFB, Adebayo M, Bajwa P, Scott RJ, Dharmarajan AM, Nahar P, Tanwar PS. Extracellular matrix (ECM) activates β-catenin signaling in uterine fibroids. Reproduction 2017; 155:61-71. [PMID: 29066531 DOI: 10.1530/rep-17-0339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/16/2017] [Accepted: 10/23/2017] [Indexed: 12/26/2022]
Abstract
Recent studies showed that genetic aberrations in the MED12 gene, probably through the canonical WNT/β-catenin pathway, lead to the pathogenesis of uterine fibroids. However, a comprehensive analysis of the WNT pathway in MED12-mutated and MED12-wild-type fibroids has not been performed. The objective of this study was to determine the status of the WNT pathway in human fibroids. We performed Sanger sequencing to define the MED12 mutational status of fibroids and normal myometrium samples. qPCR arrays were carried out to determine the status of the WNT signaling pathway in MED12-mutated and MED12-wild-type fibroids. Liquid chromatography-mass spectrometry (LC-MS), Western blotting and immunohistochemistry were used to monitor the expression of β-catenin. We showed that β-catenin expression was increased in fibroids compared to the adjacent myometrium samples. However, β-catenin expression showed no correlation with MED12 mutation status. Of all the WNT signaling components, WNT inhibitors showed the greatest differences in expression between fibroids and controls. WIF1, a WNT inhibitor, was identified as the most significantly upregulated gene in fibroids. We cultured primary fibroid cells on hydrogels of known stiffness to decipher the influence of biomechanical cues on β-catenin expression and revealed increased levels of β-catenin when cells were cultured on a stiffer surface. In conclusion, our data showed that β-catenin expression in fibroids occurs independently of MED12 mutations. Biomechanical changes upregulate β-catenin expression in fibroids, providing an attractive avenue for developing new treatments for this disease.
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Affiliation(s)
- Yi-An Ko
- School of Biomedical Sciences and PharmacyUniversity of Newcastle, Callaghan, New South Wales, Australia
| | - M Fairuz B Jamaluddin
- School of Biomedical Sciences and PharmacyUniversity of Newcastle, Callaghan, New South Wales, Australia
| | - Mariam Adebayo
- School of Biomedical Sciences and PharmacyUniversity of Newcastle, Callaghan, New South Wales, Australia
| | - Preety Bajwa
- School of Biomedical Sciences and PharmacyUniversity of Newcastle, Callaghan, New South Wales, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and PharmacyUniversity of Newcastle, Callaghan, New South Wales, Australia.,Division of Molecular MedicineNSW Health Pathology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Arunasalam M Dharmarajan
- Stem Cell and Cancer Biology LaboratorySchool of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Pravin Nahar
- School of Medicine and Public HealthUniversity of Newcastle, Callaghan, New South Wales, Australia.,Department of Maternity and GynecologyJohn Hunter Hospital, New Lambton, New South Wales, Australia
| | - Pradeep S Tanwar
- School of Biomedical Sciences and PharmacyUniversity of Newcastle, Callaghan, New South Wales, Australia
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GH/IGF-1 Signaling and Current Knowledge of Epigenetics; a Review and Considerations on Possible Therapeutic Options. Int J Mol Sci 2017; 18:ijms18101624. [PMID: 28981462 PMCID: PMC5666699 DOI: 10.3390/ijms18101624] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 01/01/2023] Open
Abstract
Epigenetic mechanisms play an important role in the regulation of the Growth Hormone- Insulin-like Growth Factor 1 (GH-IGF1) axis and in processes for controlling long bone growth, and carbohydrate and lipid metabolism. Improvement of methodologies that allow for the assessment of epigenetic regulation have contributed enormously to the understanding of GH action, but many questions still remain to be clarified. The reversible nature of epigenetic factors and, particularly, their role as mediators between the genome and the environment, make them viable therapeutic target candidates. Rather than reviewing the molecular and epigenetic pathways regulated by GH action, in this review we have focused on the use of epigenetic modulators as potential drugs to improve the GH response. We first discuss recent progress in the understanding of intracellular molecular mechanisms controlling GH and IGF-I action. We then emphasize current advances in genetic and epigenetic mechanisms that control gene expression, and which support a key role for epigenetic regulation in the cascade of intracellular events that trigger GH action when coupled to its receptor. Thirdly, we focus on fetal programming and epigenetic regulation at the IGF1 locus. We then discuss epigenetic alterations in intrauterine growth retardation, and the possibility for a potential epigenetic pharmaceutical approach in short stature associated with this fetal condition. Lastly, we review an example of epigenetic therapeutics in the context of growth-related epigenetic deregulation disorders. The advance of our understanding of epigenetic changes and the impact they are having on new forms of therapy creates exciting prospects for the future.
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ScMED7, a sugarcane mediator subunit gene, acts as a regulator of plant immunity and is responsive to diverse stress and hormone treatments. Mol Genet Genomics 2017; 292:1363-1375. [DOI: 10.1007/s00438-017-1352-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
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Bai L, Li Z, Li Q, Guan H, Zhao S, Liu R, Wang R, Zhang J, Jia Y, Fan J, Wang N, Reddy JK, Shyy JYJ, Liu E. Mediator 1 Is Atherosclerosis Protective by Regulating Macrophage Polarization. Arterioscler Thromb Vasc Biol 2017. [PMID: 28642237 DOI: 10.1161/atvbaha.117.309672] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE MED1 (mediator 1) interacts with transcription factors to regulate transcriptional machinery. The role of MED1 in macrophage biology and the relevant disease state remains to be investigated. APPROACH AND RESULTS To study the molecular mechanism by which MED1 regulates the M1/M2 phenotype switch of macrophage and the effect on atherosclerosis, we generated MED1/apolipoprotein E (ApoE) double-deficient (MED1ΔMac/ApoE-/-) mice and found that atherosclerosis was greater in MED1ΔMac/ApoE-/- mice than in MED1fl/fl/ApoE-/- littermates. The gene expression of M1 markers was increased and that of M2 markers decreased in both aortic wall and peritoneal macrophages from MED1ΔMac/ApoE-/- mice, whereas MED1 overexpression rectified the changes in M1/M2 expression. Moreover, LDLR (low-density lipoprotein receptor)-deficient mice received bone marrow from MED1ΔMac mice showed greater atherosclerosis. Mechanistically, MED1 ablation decreased the binding of PPARγ (peroxisome proliferator-activated receptor γ) and enrichment of H3K4me1 and H3K27ac to upstream region of M2 marker genes. Furthermore, interleukin 4 induction of PPARγ and MED1 increased the binding of PPARγ or MED1 to the PPAR response elements of M2 marker genes. CONCLUSIONS Our data suggest that MED1 is required for the PPARγ-mediated M2 phenotype switch, with M2 marker genes induced but M1 marker genes suppressed. MED1 in macrophages has an antiatherosclerotic role via PPARγ-regulated transactivation.
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Affiliation(s)
- Liang Bai
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Zhao Li
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Qianwei Li
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Hua Guan
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Sihai Zhao
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Ruihan Liu
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Rong Wang
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Jin Zhang
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Yuzhi Jia
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Jianglin Fan
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Nanping Wang
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - Janardan K Reddy
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.)
| | - John Y-J Shyy
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.).
| | - Enqi Liu
- From the Research Institute of Atherosclerotic Disease, Health Science Center and Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Laboratory Animal Center, Health Science Center (L.B., Q.L., H.G., S.Z., R.L., R.W., E.L.), Cardiovascular Research Center, School of Basic Medical Sciences, Health Science Center (L.B., Z.L., J.Z., N.W., J.Y.-J.S.), Xi'an Jiaotong University, Shaanxi, China; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (Y.J., J.K.R.); Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Japan (J.F.); and Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (J.Y.-J.S.).
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Malik N, Agarwal P, Tyagi A. Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 2017; 52:475-502. [DOI: 10.1080/10409238.2017.1325830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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44
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Wang T, Yang Z, Zhang Y, Yan W, Wang F, He L, Zhou Y, Chen L. Discovery of novel CDK8 inhibitors using multiple crystal structures in docking-based virtual screening. Eur J Med Chem 2017; 129:275-286. [DOI: 10.1016/j.ejmech.2017.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/13/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
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Yamamoto S, Hagihara T, Horiuchi Y, Okui A, Wani S, Yoshida T, Inoue T, Tanaka A, Ito T, Hirose Y, Ohkuma Y. Mediator cyclin-dependent kinases upregulate transcription of inflammatory genes in cooperation with NF-κB and C/EBPβ on stimulation of Toll-like receptor 9. Genes Cells 2017; 22:265-276. [PMID: 28151579 DOI: 10.1111/gtc.12475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/27/2016] [Indexed: 12/17/2022]
Abstract
In eukaryotes, the Mediator complex has important roles in regulation of transcription by RNA polymerase II. Mediator is a large complex with more than 20 subunits that form head, middle, tail and CDK/cyclin modules. Among them, CDK8 and/or CDK19 (CDK8/19), and their counterpart cyclin C, form the CDK/cyclin module together with Mediator subunits MED12 and MED13. Despite evidences of both activation and repression, the precise functional roles of CDK8/19 in transcription are still elusive. Our previous results indicate that CDK8/19 recruits epigenetic regulators to repress immunoresponse genes. Here, this study focused on Toll-like receptors (TLRs), which exert innate immune responses through recognition of pathogen-associated molecular patterns and examined the functional roles of CDK8/19. As a result, CDK8/19 regulated transcription of inflammatory genes on stimulation of TLR9 in myeloma-derived RPMI8226 cells, which led to expression of inflammation-associated genes such as IL8, IL10, PTX3 and CCL2. Mediator subunits CDK8/19 and MED1, inflammation-related transcriptional activator NF-κB and C/EBPβ, and general transcription factors TFIIE and TFIIB colocalized at the promoter regions of these genes under this condition. Our results show that CDK8/19 positively regulates inflammatory gene transcription in cooperation with NF-κB and C/EBPβ on stimulation of TLR9.
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Affiliation(s)
- Seiji Yamamoto
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.,Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Tomoko Hagihara
- Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Yoshiyuki Horiuchi
- Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Akira Okui
- Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Shotaro Wani
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 153-8501, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 153-8501, Japan
| | - Aki Tanaka
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.,Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
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46
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Yu S, Wang Y, Yuan H, Zhao H, Lv W, Chen J, Wan F, Liu D, Gao Z, Wu J. Knockdown of Mediator Complex Subunit 19 Suppresses the Growth and Invasion of Prostate Cancer Cells. PLoS One 2017; 12:e0171134. [PMID: 28125713 PMCID: PMC5270333 DOI: 10.1371/journal.pone.0171134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 01/16/2017] [Indexed: 12/29/2022] Open
Abstract
Prostate cancer (PCa) is one of the most common cancers in elderly men. Mediator Complex Subunit 19 (Med19) is overexpressed and plays promotional roles in many cancers. However, the roles of Med19 in PCa are still obscure. In this study, by using immunohistochemical staining, we found higher expression level of Med19 in PCa tissues than in adjacent benign prostate tissues. We then knocked down the Med19 expression in PCa cell lines LNCaP and PC3 by using lentivirus siRNA. Cell proliferation, anchor-independent growth, migration, and invasion were suppressed in Med19 knockdown PCa cells. In nude mice xenograft model, we found that Med19 knockdown PCa cells formed smaller tumors with lower proliferation index than did control cells. In the mechanism study, we found that Med19 could regulate genes involved in cell proliferation, cell cycle, and epithelial-mesenchymal transition, including P27, pAKT, pPI3K, IGF1R, E-Cadherin, N-Cadherin, Vimentin, ZEB2, Snail-1 and Snail-2. Targeting Med19 in PCa cells could inhibit the PCa growth and metastasis, and might be a therapeutic option for PCa in the future.
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Affiliation(s)
- Shengqiang Yu
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
- * E-mail: (SY); (JW)
| | - Yanwei Wang
- Central Laboratory, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Hejia Yuan
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Hongwei Zhao
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Wei Lv
- Department of Nephrology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Jian Chen
- Central Laboratory, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Fengchun Wan
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Dongfu Liu
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Zhenli Gao
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Jitao Wu
- Department of Urology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
- * E-mail: (SY); (JW)
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47
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Kylie K, Romero J, Lindamulage IK, Knockleby J, Lee H. Dynamic regulation of histone H3K9 is linked to the switch between replication and transcription at the Dbf4 origin-promoter locus. Cell Cycle 2016; 15:2321-35. [PMID: 27341472 PMCID: PMC5004705 DOI: 10.1080/15384101.2016.1201254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/20/2016] [Accepted: 06/08/2016] [Indexed: 02/07/2023] Open
Abstract
The co-regulation of DNA replication and gene transcription is still poorly understood. To gain a better understanding of this important control mechanism, we examined the DNA replication and transcription using the Dbf4 origin-promoter and Dbf4 pseudogene models. We found that origin firing and Dbf4 transcription activity were inversely regulated in a cell cycle-dependent manner. We also found that proteins critical for the regulation of replication (ORC, MCM), transcription (SP1, TFIIB), and cohesin (Smc1, Smc3) and Mediator functions (Med1, Med12) interact with specific sites within and the surrounding regions of the Dbf4 locus in a cell cycle-dependent manner. As expected, replication initiation occurred within a nucleosome-depleted region, and nucleosomes flanked the 2 replication initiation zones. Further, the histone H3 in this region was distinctly acetylated or trimethylated on lysine 9 in a cell cycle-dependent fluctuation pattern: H3K9ac was most prevalent when the Dbf4 transcription level was highest whereas the H3K9me3 level was greatest during and just after replication. The KDM4A histone demethylase, which is responsible for the H3K9me3 modification, was enriched at the Dbf4 origin in a manner coinciding with H3K9me3. Finally, HP1γ, a protein known to interact with H3K9me3 in the heterochromatin was also found enriched at the origin during DNA replication, indicating that H3K9me3 may be required for the regulation of replication at both heterochromatin and euchromatin regions. Taken together, our data show that mammalian cells employ an extremely sophisticated and multilayered co-regulation mechanism for replication and transcription in a highly coordinated manner.
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Affiliation(s)
- Kathleen Kylie
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | - Julia Romero
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | | | - James Knockleby
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
| | - Hoyun Lee
- Tumour Biology Group, Health Sciences North Research Institute, Sudbury, Ontario, Canada
- Department of Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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48
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Chhun T, Chong SY, Park BS, Wong ECC, Yin JL, Kim M, Chua NH. HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth. PLANT & CELL PHYSIOLOGY 2016; 57:1689-706. [PMID: 27335347 DOI: 10.1093/pcp/pcw095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/01/2016] [Indexed: 05/25/2023]
Abstract
Arabidopsis HSI2 (HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE 2) which carries a EAR (ERF-associated amphiphilic repression) motif acts as a repressor of seed maturation genes and lipid biosynthesis, whereas MEDIATOR (MED) is a conserved multiprotein complex linking DNA-bound transcription factors to RNA polymerase II transcription machinery. How HSI2 executes its repressive function through MED is hitherto unknown. Here, we show that HSI2 and its homolog, HSI2-lik (HSL1), are able to form homo- and heterocomplexes. Both factors bind to the TRAP240 domain of MED13, a subunit of the MED CDK8 module. Mutant alleles of the med13 mutant show elevated seed maturation gene expression and increased lipid accumulation in cotyledons; in contrast, HSI2- or MED13-overexpressing plants display the opposite phenotypes. The overexpression phenotypes of HSI2 and MED13 are abolished in med13 and hsi2 hsl1, respectively, indicating that HSI2 and MED13 together are required for these functions. The HSI2 C-terminal region interacts with HDA6, whose overexpression also reduces seed maturation gene expression and lipid accumulation. Moreover, HSI2, MED13 and HDA6 bind to the proximal promoter and 5'-coding regions of seed maturation genes. Taken together, our results suggest that HSI2 recruits MED13 and HDA6 to suppress directly a subset of seed maturation genes post-germination.
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Affiliation(s)
- Tory Chhun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Suet Yen Chong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Eriko Chi Cheng Wong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Jun-Lin Yin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Mijung Kim
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
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49
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Prontera P, Ottaviani V, Rogaia D, Isidori I, Mencarelli A, Malerba N, Cocciadiferro D, Rolph P, Stangoni G, Vulto-van Silfhout A, Merla G. A novel MED12 mutation: Evidence for a fourth phenotype. Am J Med Genet A 2016; 170:2377-82. [PMID: 27312080 DOI: 10.1002/ajmg.a.37805] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/30/2016] [Indexed: 11/11/2022]
Abstract
Mutations of the MED12 gene have been reported mainly in males with FG (Opitz-Kaveggia), Lujan-Fryns, or X-linked Ohdo syndromes. Recently, a different phenotype characterized by minor anomalies, severe intellectual disability (ID), and absent language was reported in female and male patients belonging to the same family and carrying a frameshift MED12 mutation (c.5898dupC). Here, we report on two brothers and their niece affected by severe and mild ID, respectively, where whole exome sequencing combined with variant analysis within a panel of ID-related genes, disclosed a novel c.2312T>C (p.Ile771Thr) MED12 mutation. This variant, which has not been reported as a polymorphism, was not present in a third unaffected brother, and was predicted to be deleterious by five bioinformatic databases. This finding together with the phenotypic analogies shared with the carriers of c.5898dupC mutation suggests the existence of a fourth MED12-related disorder, characterized by severe ID, absent or deficient language and, milder, clinical manifestation in heterozygotes. We have reviewed the literature on MED12 heterozygotes, their clinical manifestations, and discuss the possible biological causes of this condition. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Paolo Prontera
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Valentina Ottaviani
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniela Rogaia
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Ilenia Isidori
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Amedea Mencarelli
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Natascia Malerba
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Dario Cocciadiferro
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy.,Ph.D. Program in Experimental and Regenerative Medicine, University of Foggia, Foggia, Italy
| | - Pfundt Rolph
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Gabriela Stangoni
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Anneke Vulto-van Silfhout
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Giuseppe Merla
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
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50
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Marand AP, Zhang T, Zhu B, Jiang J. Towards genome-wide prediction and characterization of enhancers in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:131-139. [PMID: 27321818 DOI: 10.1016/j.bbagrm.2016.06.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 11/19/2022]
Abstract
Enhancers are important cis-regulatory DNA elements that regulate transcription programs by recruiting transcription factors and directing them to the promoters of target genes in a cell-type/tissue-specific manner. The expression of a gene can be regulated by one or multiple enhancers at different developmental stages and/or in different tissues. Enhancers are difficult to identify because of their unpredictable positions relative to their cognate promoters. Remarkably, only a handful of enhancers have been identified in plant species largely due to the lack of general approaches for enhancer identification. Extensive genomic and epigenomic research in mammalian species has revealed that the genomic locations of enhancers can be predicted based on the binding sites of transcriptional co-factors and several distinct features associated with open chromatin. Here we review the methodologies used in enhancer prediction in mammalian species. We also review the recent applications of these methodologies in Arabidopsis thaliana and discuss the future directions of enhancer identification in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
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