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Fu D, Weng X, Su Y, Hong B, Zhao A, Lin J. Establishing a model composed of immune-related gene-modules to predict tumor immunotherapy response. Sci Rep 2024; 14:16630. [PMID: 39025898 PMCID: PMC11258235 DOI: 10.1038/s41598-024-67742-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024] Open
Abstract
At present, tumor immunotherapy has been widely applied to treat various cancers. However, the accuracy of predicting treatment efficacy has not yet achieved a significant breakthrough. This study aimed to construct a prediction model based on the modified WGCNA algorithm to precisely judge the anti-tumor immune response. First, we used a murine colon cancer model to screen corresponding DEGs according to different groups. GSEA was used to analyze the potential mechanisms of the immune-related DEGs (irDEGs) in each group. Subsequently, the intersection of the irDEGs in every group was acquired, and 7 gene-modules were mapped. Finally, 4 gene-modules including cogenes, antiPD-1 immu-genes, chemo immu-genes and comb immu-genes, were selected for subsequent study. Furthermore, a clinical dataset of gastric cancer patients receiving immunotherapy was enrolled, and the irDEGs were identified. A total of 34 vital irDEGs were obtained from the intersections of the vital irDEGs and the four gene-modules. Next, the vital irDEGs were analyzed by the modified WGCNA algorithm, and the correlation coefficients between the 4 gene-modules and the response status to immunotherapy were calculated. Thus, a prediction model based on correlation coefficients was built, and the corresponding model scores were acquired. The AUC calculated according to the model score was 0.727, which was non-inferior to that of the ESTIMATE score and the TIDE score. Meanwhile, the AUC calculated according to the classification of the model scores was 0.705, which was non-inferior to that of the ESTIMATE classification and the TIDE classification. The prediction accuracy of the model was validated in clinical datasets of other cancers.
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Affiliation(s)
- Deqiang Fu
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xiaoyuan Weng
- Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Quanzhou Medical College, Quanzhou, China
| | - Yunxia Su
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Binhuang Hong
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Aiyue Zhao
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
| | - Jianqing Lin
- Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
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Chen SF, Chao TC, Kim HJ, Tang HC, Khadka S, Li T, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator complex modulated by its dissociable Kinase module. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601608. [PMID: 39005267 PMCID: PMC11244988 DOI: 10.1101/2024.07.01.601608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), regulates RNA Polymerase II (Pol II)-dependent transcription. cMED recruits Pol II and promotes pre-initiation complex (PIC) formation in a manner inhibited by the CKM, which is also implicated in post-initiation control of gene expression. Herein we report cryo-electron microscopy structures of the human complete Mediator and its CKM, which explains the basis for CKM inhibition of cMED-activated transcription. The CKM binds to cMED through an intrinsically disordered region (IDR) in MED13 and HEAT repeats in MED12. The CKM inhibits transcription by allocating its MED13 IDR to occlude binding of Pol II and MED26 to cMED and further obstructing cMED-PIC assembly through steric hindrance with TFIIH and the +1 nucleosome. Notably, MED12 binds to the cMED Hook, positioning CDK8 downstream of the transcription start site, which sheds new light on its stimulatory function in post-initiation events.
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Voutsadakis IA. Mediator kinase module proteins, genetic alterations and expression of super-enhancer regulated genes in colorectal cancer. Pharmacol Rep 2024; 76:535-556. [PMID: 38602606 DOI: 10.1007/s43440-024-00589-2] [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: 01/08/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Genetic alterations are well characterized as contributors to the pathogenesis of cancers. Epigenetic abnormalities can lead to perturbations of the expression of genes in cancer cells without structural defects. Deregulation of proteins of the transcription machinery may result in perturbations of target genes. Mediator, a multiprotein component of the transcription machinery facilitates the function of RNA polymerase II, which transcribes most human genes. A part of the mediator with kinase activity, called the Mediator kinase module shows genetic alterations in a sub-set of colorectal cancers. METHODS Data from publicly available genomic series of colorectal cancer patients were examined to determine alterations of Mediator kinase module component genes, including MED12, MED12L, MED13, MED13L, CDK8, CDK19, and CCNC. The prevalence of alterations in genomically defined colorectal cancer sub-sets was also interrogated. The effect of Mediator kinase module member gene expression on colorectal cancer relapse-free survival was investigated. RESULTS Mutations in genes of the Mediator kinase module were present in a small percentage of colorectal cancers, ranging between 2 to 10% for MED12 and MED13 and alternative units MED12L and MED13L and below 2% for kinases CDK8 and CDK19 and cyclin C. Amplifications of the CDK8 gene were observed in 3% to 5% of colorectal cancers. The highest prevalence of mutations was observed in MSI cancers and the equivalent CMS1 group, with other genomic groups showing much lower frequency. An association of higher expression of MED12 with inferior relapse-free survival was observed. In contrast, higher expression of cyclin C was associated with improved survival. Colorectal cancer cell lines with CDK8 amplifications displayed sensitivity to several small molecule inhibitors of the KRAS/PI3K pathway but not to BET inhibitors. CONCLUSION The Mediator kinase module is deregulated in a sub-set of colorectal cancers with differences observed in genomically defined groups. These variations may result in differences in sensitivity to targeted therapies and may have to be taken into consideration as such therapies are developed.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste Marie, ON, P6B 0A8, Canada.
- Division of Clinical Sciences, Section of Internal Medicine, Northern Ontario School of Medicine, 750 Great Northern Road, Sudbury, ON, Canada.
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Li X, Liu M, Xing Y, Niu Y, Liu TH, Sun JL, Liu Y, Hemba-Waduge RUS, Ji JY. Distinct effects of CDK8 module subunits on cellular growth and proliferation in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591924. [PMID: 38746212 PMCID: PMC11092604 DOI: 10.1101/2024.04.30.591924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The Mediator complex, composed of about 30 conserved subunits, plays a pivotal role in facilitating RNA polymerase II-dependent transcription in eukaryotes. Within this complex, the CDK8 kinase module (CKM), comprising Med12, Med13, CDK8, and CycC (Cyclin C), serves as a dissociable subcomplex that modulates the activity of the small Mediator complex. Genetic studies in Drosophila have revealed distinct phenotypes of CDK8-CycC and Med12-Med13 mutations, yet the underlying mechanism has remained unknown. Here, using Drosophila as a model organism, we show that depleting CDK8-CycC enhances E2F1 target gene expression and promotes cell-cycle progression. Conversely, depletion of Med12-Med13 affects the expression of ribosomal protein genes and fibrillarin, indicating a more severe reduction in ribosome biogenesis and cellular growth compared to the loss of CDK8-CycC. Moreover, we found that the stability of CDK8 and CycC relies on Med12 and Med13, with a mutually interdependent relationship between Med12 and Med13. Furthermore, CycC stability depends on the other three CKM subunits. These findings reveal distinct roles for CKM subunits in vivo , with Med12-Med13 disruption exerting a more pronounced impact on ribosome biogenesis and cellular growth compared to the loss of CDK8-CycC. Significance The CDK8 kinase module (CKM), comprising CDK8, CycC, Med12, and Med13, is essential in the Mediator complex for RNA polymerase II-dependent transcription in eukaryotes. While expected to function jointly, CKM subunit mutations result in distinct phenotypes in Drosophila . This study investigates the mechanisms driving these differing effects. Our analysis reveals the role of Med12-Med13 pair in regulating ribosomal biogenesis and cellular growth, contrasting with the involvement of CDK8-CycC in E2F1-dependent cell-cycle progression. Additionally, an asymmetric interdependence in the stability of CDK8-CycC and Med12-Med13 was observed. CKM mutations or overexpression are associated with cancers and cardiovascular diseases. Our findings underscore the distinct impacts of CKM mutations on cellular growth and proliferation, advancing our understanding of their diverse consequences in vivo .
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Liao M, Yao D, Wu L, Luo C, Wang Z, Zhang J, Liu B. Targeting the Warburg effect: A revisited perspective from molecular mechanisms to traditional and innovative therapeutic strategies in cancer. Acta Pharm Sin B 2024; 14:953-1008. [PMID: 38487001 PMCID: PMC10935242 DOI: 10.1016/j.apsb.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 03/17/2024] Open
Abstract
Cancer reprogramming is an important facilitator of cancer development and survival, with tumor cells exhibiting a preference for aerobic glycolysis beyond oxidative phosphorylation, even under sufficient oxygen supply condition. This metabolic alteration, known as the Warburg effect, serves as a significant indicator of malignant tumor transformation. The Warburg effect primarily impacts cancer occurrence by influencing the aerobic glycolysis pathway in cancer cells. Key enzymes involved in this process include glucose transporters (GLUTs), HKs, PFKs, LDHs, and PKM2. Moreover, the expression of transcriptional regulatory factors and proteins, such as FOXM1, p53, NF-κB, HIF1α, and c-Myc, can also influence cancer progression. Furthermore, lncRNAs, miRNAs, and circular RNAs play a vital role in directly regulating the Warburg effect. Additionally, gene mutations, tumor microenvironment remodeling, and immune system interactions are closely associated with the Warburg effect. Notably, the development of drugs targeting the Warburg effect has exhibited promising potential in tumor treatment. This comprehensive review presents novel directions and approaches for the early diagnosis and treatment of cancer patients by conducting in-depth research and summarizing the bright prospects of targeting the Warburg effect in cancer.
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Affiliation(s)
- Minru Liao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen 518118, China
| | - Lifeng Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chaodan Luo
- Department of Psychology, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhiwen Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen 518118, China
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Jin Zhang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
| | - Bo Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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Fu X, Liu S, Cao D, Li C, Ji H, Wang G. Med23 deficiency reprograms the tumor microenvironment to promote lung tumorigenesis. Br J Cancer 2024; 130:716-727. [PMID: 38195889 PMCID: PMC10912217 DOI: 10.1038/s41416-023-02556-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death worldwide. We previously found that Mediator complex subunit 23 (MED23) is important for the tumourigenicity of lung cancer cells with hyperactive Ras activity in vitro, although the in vivo function of MED23 in lung tumourigenesis remains to be explored. METHODS In this study, we utilized well-characterized KrasG12D-driven non-small cell lung cancer mouse model to investigate the role of MED23 in lung cancer. The lung tumour progression was evaluated by H&E and IHC analysis. Western blotting and qRT-PCR assays were performed to detect changes in gene expression. Immune cells were analyzed by FACS technology. RNA-seq and reporter assays were conducted to explore the mechanism. RESULTS We observed that lung epithelial Med23 deletion by adeno-Cre resulted in a significant increase in KrasG12D tumour number and size, which was further verified with another mouse model with Med23 specifically deleted in alveolar type II cells. Mice with lung-specific Med23 deficiency also exhibited accelerated tumourigenesis, and a higher proliferation rate for tumour cells, along with increased ERK phosphorylation. Notably, the numbers of infiltrating CD4+ T cells and CD8+ T cells were significantly reduced in the lungs of Med23-deficient mice, while the numbers of myeloid-derived suppressor cells (MDSCs) and Treg cells were significantly increased, suggesting the enhanced immune escape capability of the Med23-deficient lung tumours. Transcriptomic analysis revealed that the downregulated genes in Med23-deficient lung tumour tissues were associated with the immune response. Specifically, Med23 deficiency may compromise the MHC-I complex formation, partially through down-regulating B2m expression. CONCLUSIONS Collectively, these findings revealed that MED23 may negatively regulate Kras-induced lung tumourigenesis in vivo, which would improve the precise classification of KRAS-mutant lung cancer patients and provide new insights for clinical interventions.
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Affiliation(s)
- Xiaobo Fu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Siming Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Cao
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chonghui Li
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Gang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
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Huang W, Zhang T, Wang H, Liu Z, Zhai P, Wang X, Wang S. Intravenous metastasis of unexpected uterine sarcoma in the context of uterine fibroids: case report and literature review. Front Oncol 2024; 14:1354032. [PMID: 38425345 PMCID: PMC10902127 DOI: 10.3389/fonc.2024.1354032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Objective Endometrial stromal tumors are rare and complex mesenchymal tumors that often present with clinical symptoms similar to uterine leiomyomas. Due to their atypical nature, they are prone to be misdiagnosed or overlooked by healthcare professionals. This study presents a case report of an incidentally discovered endometrial stromal sarcoma with venous metastasis, which was initially misdiagnosed as a uterine leiomyoma. In addition, this study reviews previously documented cases of similar tumors. Case report During a routine medical examination in 2016, a 50-year-old woman was diagnosed with uterine fibroids. In June 2020, she began experiencing moderate, irregular vaginal bleeding. Nevertheless, a histopathological examination indicated an endometrial stromal sarcoma with a striking amalgamation of both low-grade and high-grade features. Molecular analysis identified a rare MED12 gene mutation. The patient underwent total hysterectomy, bilateral salpingectomy, and resection of the metastatic lesions. Postoperative management included radiotherapy, chemotherapy, and hormone therapy. After completion of chemotherapy, the patient was followed up for 27 months with no evidence of tumor recurrence. Conclusion This case report highlights the importance of pathological, immunohistochemical, and molecular aspects of this rare tumor involving the inferior vena cava and showing the presence of atypical gene mutations. The successful treatment outcome further emphasizes the importance of advances in diagnostic modalities for managing rare tumors like this.
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Affiliation(s)
- Wenying Huang
- School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Tianwei Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
- Department of Hematology and Radiotherapy, Zibo 148 Hospital, Zibo, Shandong, China
| | - Hui Wang
- Department of Gynecology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhengchun Liu
- School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Peiling Zhai
- Department of Gynecology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Xinbo Wang
- Department of Gynecology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Shuai Wang
- Department of Radiotherapy, School of Medical Imaging, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
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Li T, Tang HC, Tsai KL. Unveiling the noncanonical activation mechanism of CDKs: insights from recent structural studies. Front Mol Biosci 2023; 10:1290631. [PMID: 38028546 PMCID: PMC10666765 DOI: 10.3389/fmolb.2023.1290631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The Cyclin-dependent kinases (CDKs) play crucial roles in a range of essential cellular processes. While the classical two-step activation mechanism is generally applicable to cell cycle-related CDKs, both CDK7 and CDK8, involved in transcriptional regulation, adopt distinct mechanisms for kinase activation. In both cases, binding to their respective cyclin partners results in only partial activity, while their full activation requires the presence of an additional subunit. Recent structural studies of these two noncanonical kinases have provided unprecedented insights into their activation mechanisms, enabling us to understand how the third subunit coordinates the T-loop stabilization and enhances kinase activity. In this review, we summarize the structure and function of CDK7 and CDK8 within their respective functional complexes, while also describing their noncanonical activation mechanisms. These insights open new avenues for targeted drug discovery and potential therapeutic interventions in various diseases related to CDK7 and CDK8.
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Affiliation(s)
- Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hui-Chi Tang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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Buyukcelebi K, Chen X, Abdula F, Elkafas H, Duval AJ, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Bulun SE, Wei JJ, Yue F, Adli M. Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. Nat Commun 2023; 14:4057. [PMID: 37429859 DOI: 10.1038/s41467-023-39684-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Nearly 70% of Uterine fibroid (UF) tumors are driven by recurrent MED12 hotspot mutations. Unfortunately, no cellular models could be generated because the mutant cells have lower fitness in 2D culture conditions. To address this, we employ CRISPR to precisely engineer MED12 Gly44 mutations in UF-relevant myometrial smooth muscle cells. The engineered mutant cells recapitulate several UF-like cellular, transcriptional, and metabolic alterations, including altered Tryptophan/kynurenine metabolism. The aberrant gene expression program in the mutant cells is, in part, driven by a substantial 3D genome compartmentalization switch. At the cellular level, the mutant cells gain enhanced proliferation rates in 3D spheres and form larger lesions in vivo with elevated production of collagen and extracellular matrix deposition. These findings indicate that the engineered cellular model faithfully models key features of UF tumors and provides a platform for the broader scientific community to characterize genomics of recurrent MED12 mutations.
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Affiliation(s)
- Kadir Buyukcelebi
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Xintong Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Fatih Abdula
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Hoda Elkafas
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Alexander James Duval
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Harun Ozturk
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Fidan Seker-Polat
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Ping Yin
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Yue Feng
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Serdar E Bulun
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Jian Jun Wei
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Mazhar Adli
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA.
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Buyukcelebi K, Chen X, Abdula F, Duval A, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Wei JJ, Bulun S, Yue F, Adli M. Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. RESEARCH SQUARE 2023:rs.3.rs-2537075. [PMID: 36798375 PMCID: PMC9934745 DOI: 10.21203/rs.3.rs-2537075/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Uterine fibroid (UF) tumors originate from a mutated smooth muscle cell (SMC). Nearly 70% of these tumors are driven by hotspot recurrent somatic mutations in the MED12 gene; however, there are no tractable genetic models to study the biology of UF tumors because, under culture conditions, the non-mutant fibroblasts outgrow the mutant SMC cells, resulting in the conversion of the population to WT phenotype. The lack of faithful cellular models hampered our ability to delineate the molecular pathways downstream of MED12 mutations and identify therapeutics that may selectively target the mutant cells. To overcome this challenge, we employed CRISPR knock-in with a sensitive PCR-based screening strategy to precisely engineer cells with mutant MED12 Gly44, which constitutes 50% of MED12 exon two mutations. Critically, the engineered myometrial SMC cells recapitulate several UF-like cellular, transcriptional and metabolic alterations, including enhanced proliferation rates in 3D spheres and altered Tryptophan/kynurenine metabolism. Our transcriptomic analysis supported by DNA synthesis tracking reveals that MED12 mutant cells, like UF tumors, have heightened expression of DNA repair genes but reduced DNA synthesis rates. Consequently, these cells accumulate significantly higher rates of DNA damage and are selectively more sensitive to common DNA-damaging chemotherapy, indicating mutation-specific and therapeutically relevant vulnerabilities. Our high-resolution 3D chromatin interaction analysis demonstrates that the engineered MED12 mutations drive aberrant genomic activity due to a genome-wide chromatin compartmentalization switch. These findings indicate that the engineered cellular model faithfully models key features of UF tumors and provides a novel platform for the broader scientific community to characterize genomics of recurrent MED12 mutations and discover potential therapeutic targets.
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Maia N, Ibarluzea N, Misra-Isrie M, Koboldt DC, Marques I, Soares G, Santos R, Marcelis CLM, Keski-Filppula R, Guitart M, Gabau Vila E, Lehman A, Hickey S, Mori M, Terhal P, Valenzuela I, Lasa-Aranzasti A, Cueto-González AM, Chhouk BH, Yeh RC, Neil JE, Abu-Libde B, Kleefstra T, Elting MW, Császár A, Kárteszi J, Bessenyei B, van Bokhoven H, Jorge P, van Hagen JM, de Brouwer APM. Missense MED12 variants in 22 males with intellectual disability: From nonspecific symptoms to complete syndromes. Am J Med Genet A 2023; 191:135-143. [PMID: 36271811 PMCID: PMC10092556 DOI: 10.1002/ajmg.a.63004] [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: 05/05/2022] [Revised: 07/26/2022] [Accepted: 08/13/2022] [Indexed: 12/14/2022]
Abstract
We describe the phenotype of 22 male patients (20 probands) carrying a hemizygous missense variant in MED12. The phenotypic spectrum is very broad ranging from nonspecific intellectual disability (ID) to the three well-known syndromes: Opitz-Kaveggia syndrome, Lujan-Fryns syndrome, or Ohdo syndrome. The identified variants were randomly distributed throughout the gene (p = 0.993, χ2 test), but mostly outside the functional domains (p = 0.004; χ2 test). Statistical analyses did not show a correlation between the MED12-related phenotypes and the locations of the variants (p = 0.295; Pearson correlation), nor the protein domain involved (p = 0.422; Pearson correlation). In conclusion, establishing a genotype-phenotype correlation in MED12-related diseases remains challenging. Therefore, we think that patients with a causative MED12 variant are currently underdiagnosed due to the broad patients' clinical presentations.
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Affiliation(s)
- Nuno Maia
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Daniel C Koboldt
- Steve and Cindy Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Isabel Marques
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Gabriela Soares
- Unidade de Genética Médica, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal
| | - Rosário Santos
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Carlo L M Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riikka Keski-Filppula
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Miriam Guitart
- Paediatric Unit, ParcTaulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí, I3PTUniversitat Autònoma de Barcelona, Sabadell, Spain
| | - Elisabeth Gabau Vila
- Paediatric Unit, ParcTaulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí, I3PTUniversitat Autònoma de Barcelona, Sabadell, Spain
| | - April Lehman
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Scott Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mari Mori
- Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Paulien Terhal
- Division Laboratories, Pharmacy and Biomedical Genetics, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Anna Maria Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Brian H Chhouk
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Rebecca C Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mariet W Elting
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrea Császár
- Paediatric Ward, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Judit Kárteszi
- Genetic Counselling, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Beáta Bessenyei
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paula Jorge
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Johanna M van Hagen
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
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12
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Jamaluddin MFB, Nagendra PB, Ko YA, Bajwa P, Scott RJ, Nahar P, Tanwar PS. Prevalence and clinical significance of co-existing mutations in MED12 and FH in uterine fibroids of Australian women. FRONTIERS IN REPRODUCTIVE HEALTH 2023; 5:1081092. [PMID: 37113812 PMCID: PMC10126294 DOI: 10.3389/frph.2023.1081092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
Uterine fibroids are exceedingly common benign tumours of the female reproductive system and cause severe symptoms, including acute pain, bleeding, and infertility. Fibroids are frequently associated with genetic alterations affecting mediator complex subunit 12 (MED12), fumarate hydratase (FH), high mobility group AT-hook 2 (HMGA2) and collagen, type IV alpha 5 and alpha 6 (COL4A5-COL4A6). Recently, we reported MED12 exon 2 mutations in 39 out of 65 uterine fibroids (60%) from 14 Australian patients. The aim of this study was to evaluate the status of FH mutations in MED12 mutation-positive and mutation-negative uterine fibroids. FH mutation screening of altogether 65 uterine fibroids and corresponding adjacent normal myometrium (n = 14) was carried out by Sanger sequencing. Three out of 14 patients displayed somatic mutations in FH exon 1 in addition to harbouring MED12 mutation in uterine fibroids. This study is the first to report that the mutations in MED12 and FH co-exist in uterine fibroids of Australian women.
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Affiliation(s)
- M. Fairuz B. Jamaluddin
- Global Centre for Gynecological Diseases, University of Newcastle, Callaghan, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Prathima B. Nagendra
- Global Centre for Gynecological Diseases, University of Newcastle, Callaghan, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Yi-An Ko
- Global Centre for Gynecological Diseases, University of Newcastle, Callaghan, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Preety Bajwa
- Global Centre for Gynecological Diseases, University of Newcastle, Callaghan, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Rodney J. Scott
- Global Centre for Gynecological Diseases, University of Newcastle, Callaghan, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Division of Molecular Medicine, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Pravin Nahar
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, New Lambton Heights, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Pradeep S. Tanwar
- Global Centre for Gynecological Diseases, University of Newcastle, Callaghan, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Correspondence: Pradeep S. Tanwar
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13
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Duong TM, Araujo Rincon M, Myneni N, Burleson M. Genetic alterations in MED12 promote castration-resistant prostate cancer through modulation of GLI3 signaling. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2023; 12:63-70. [PMID: 37520466 PMCID: PMC10382901 DOI: 10.22099/mbrc.2023.47346.1828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Prostate cancer is a disease that depends on androgenic stimulation and is thus commonly treated with androgen deprivation therapy (ADT). ADT is highly successful initially; however, patients inevitably relapse at which point the cancer grows independently of androgens and is termed castration-resistant prostate cancer (CRPC). CRPC develops through various mechanisms, one of these being crosstalk of the androgen receptor (AR) signaling pathway with other signaling pathways. Congruently, prior work has shown that androgen deprivation induces SHH signaling, which subsequently promotes activation of AR-dependent gene expression to promote cell growth. Mechanistically, this crosstalk involves a physical interaction between AR and components of SHH signaling, specifically proteins of the GLI transcription factor family. These findings thus suggest that activation of SHH signaling could promote the recurrence of cell growth in the absence of androgens to ultimately lead to progression towards CRPC. In this study, we have investigated this mechanism in a subset of prostate cancer that harbors genetic alterations within the Mediator subunit 12 (MED12). We found that loss of MED12 promotes the expression of GLI3 target genes which subsequently drives excessive cell growth in the absence of androgens. Thus, we conclude that genetic alterations within MED12 promote CRPC through hyperactivated GLI3 dependent sonic hedgehog signaling.
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Affiliation(s)
- Thu Minh Duong
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX, USA
| | | | - Nishanth Myneni
- Department of Biology, University of the Incarnate Word, San Antonio, TX, USA
| | - Marieke Burleson
- Department of Biology, University of the Incarnate Word, San Antonio, TX, USA
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14
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Dannappel MV, Zhu D, Sun X, Chua HK, Poppelaars M, Suehiro M, Khadka S, Lim Kam Sian TC, Sooraj D, Loi M, Gao H, Croagh D, Daly RJ, Faridi P, Boyer TG, Firestein R. CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF. J Clin Invest 2022; 132:158593. [PMID: 36006697 PMCID: PMC9566890 DOI: 10.1172/jci158593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Initiation and maintenance of transcriptional states are critical for controlling normal tissue homeostasis and differentiation. The cyclin dependent kinases CDK8 and CDK19 (Mediator kinases) are regulatory components of Mediator, a highly conserved complex that orchestrates enhancer-mediated transcriptional output. While Mediator kinases have been implicated in the transcription of genes necessary for development and growth, its function in mammals has not been well defined. Using genetically defined models and pharmacological inhibitors, we showed that CDK8 and CDK19 function in a redundant manner to regulate intestinal lineage specification in humans and mice. The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF) in intestinal epithelial cells. Concomitantly, SWI/SNF and MED12-Mediator colocalized at distinct lineage-specifying enhancers in a CDK8/19-dependent manner. Thus, these studies reveal a transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase.
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Affiliation(s)
- Marius V Dannappel
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Danxi Zhu
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Hui Kheng Chua
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Marle Poppelaars
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Monica Suehiro
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Subash Khadka
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Terry Cc Lim Kam Sian
- Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology
| | - Dhanya Sooraj
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Melissa Loi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Hugh Gao
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | | | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology
| | - Pouya Faridi
- Department of Medicine, School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Thomas G Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
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15
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Multiple Mechanisms of NOTCH1 Activation in Chronic Lymphocytic Leukemia: NOTCH1 Mutations and Beyond. Cancers (Basel) 2022; 14:cancers14122997. [PMID: 35740661 PMCID: PMC9221163 DOI: 10.3390/cancers14122997] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Mutations of the NOTCH1 gene are a validated prognostic marker in chronic lymphocytic leukemia and a potential predictive marker for anti-CD20-based therapies. At present, the most frequent pathological alteration of the NOTCH1 gene is due to somatic genetic mutations, which have a multifaceted functional impact. However, beside NOTCH1 mutations, other factors may lead to activation of the NOTCH1 pathway, and these include mutations of FBXW7, MED12, SPEN, SF3B1 as well as other B-cell pathways. Understanding the preferential strategies though which CLL cells hijack NOTCH1 signaling may present important clues for designing targeted treatment strategies for the management of CLL. Abstract The Notch signaling pathway plays a fundamental role for the terminal differentiation of multiple cell types, including B and T lymphocytes. The Notch receptors are transmembrane proteins that, upon ligand engagement, undergo multiple processing steps that ultimately release their intracytoplasmic portion. The activated protein ultimately operates as a nuclear transcriptional co-factor, whose stability is finely regulated. The Notch pathway has gained growing attention in chronic lymphocytic leukemia (CLL) because of the high rate of somatic mutations of the NOTCH1 gene. In CLL, NOTCH1 mutations represent a validated prognostic marker and a potential predictive marker for anti-CD20-based therapies, as pathological alterations of the Notch pathway can provide significant growth and survival advantage to neoplastic clone. However, beside NOTCH1 mutation, other events have been demonstrated to perturb the Notch pathway, namely somatic mutations of upstream, or even apparently unrelated, proteins such as FBXW7, MED12, SPEN, SF3B1, as well as physiological signals from other pathways such as the B-cell receptor. Here we review these mechanisms of activation of the NOTCH1 pathway in the context of CLL; the resulting picture highlights how multiple different mechanisms, that might occur under specific genomic, phenotypic and microenvironmental contexts, ultimately result in the same search for proliferative and survival advantages (through activation of MYC), as well as immune escape and therapy evasion (from anti-CD20 biological therapies). Understanding the preferential strategies through which CLL cells hijack NOTCH1 signaling may present important clues for designing targeted treatment strategies for the management of CLL.
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16
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Muralimanoharan S, Shamby R, Stansbury N, Schenken R, de la Pena Avalos B, Javanmardi S, Dray E, Sung P, Boyer TG. Aberrant R-loop-induced replication stress in MED12-mutant uterine fibroids. Sci Rep 2022; 12:6169. [PMID: 35418189 PMCID: PMC9008039 DOI: 10.1038/s41598-022-10188-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
Uterine fibroid (UF) driver mutations in Mediator complex subunit 12 (MED12) trigger genomic instability and tumor development through unknown mechanisms. Herein, we show that MED12 mutations trigger aberrant R-loop-induced replication stress, suggesting a possible route to genomic instability and a novel therapeutic vulnerability in this dominant UF subclass. Immunohistochemical analyses of patient-matched tissue samples revealed that MED12 mutation-positive UFs, compared to MED12 mutation-negative UFs and myometrium, exhibited significantly higher levels of R-loops and activated markers of Ataxia Telangiectasia and Rad3-related (ATR) kinase-dependent replication stress signaling in situ. Single molecule DNA fiber analysis revealed that primary cells from MED12 mutation-positive UFs, compared to those from patient-matched MED12 mutation-negative UFs and myometrium, exhibited defects in replication fork dynamics, including reduced fork speeds, increased and decreased numbers of stalled and restarted forks, respectively, and increased asymmetrical bidirectional forks. Notably, these phenotypes were recapitulated and functionally linked in cultured uterine smooth muscle cells following chemical inhibition of Mediator-associated CDK8/19 kinase activity that is known to be disrupted by UF driver mutations in MED12. Thus, Mediator kinase inhibition triggered enhanced R-loop formation and replication stress leading to an S-phase cell cycle delay, phenotypes that were rescued by overexpression of the R-loop resolving enzyme RNaseH. Altogether, these findings reveal MED12-mutant UFs to be uniquely characterized by aberrant R-loop induced replication stress, suggesting a possible basis for genomic instability and new avenues for therapeutic intervention that involve the replication stress phenotype in this dominant UF subtype.
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Affiliation(s)
- Sribalasubashini Muralimanoharan
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA
| | - Ross Shamby
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA
| | - Nicholas Stansbury
- Department of Obstetrics and Gynecology, UT Health San Antonio, San Antonio, TX, USA
| | - Robert Schenken
- Department of Obstetrics and Gynecology, UT Health San Antonio, San Antonio, TX, USA
| | | | - Samin Javanmardi
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Thomas G Boyer
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA.
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17
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Srivastava S, Makala H, Sharma V, Suri V, Sarkar C, Kulshreshtha R. MED12 is overexpressed in glioblastoma patients and serves as an oncogene by targeting the VDR/BCL6/p53 axis. Cell Mol Life Sci 2022; 79:104. [PMID: 35091793 PMCID: PMC11071957 DOI: 10.1007/s00018-021-04056-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/08/2021] [Accepted: 11/21/2021] [Indexed: 11/03/2022]
Abstract
Glioblastoma is the most life-threatening tumor of the central nervous system. Despite recent therapeutic advancements, maximum survival of glioblastoma patients remains dismal. The mediator complex is a set of proteins, essential for eukaryotic gene expression. Abnormal expression/mutations of specific mediator genes have been associated with progression of various cancers, however, its role and status in glioblastoma remains largely unknown. Our work shows overexpression of a subunit of kinase assembly of mediator complex, MED12, in various glioblastoma patient cohorts including Indian glioblastoma patients and cell lines. Functional characterization of MED12 using both overexpression and knockdown approach revealed that it promotes glioblastoma cell proliferation, migration and inhibits apoptosis. Transcriptome analysis post MED12 knockdown revealed Vitamin D receptor (VDR) pathway to be one of the key pathways affected by MED12 in glioblastoma. We studied direct interaction of MED12 with VDR protein using docking studies and co-immunoprecipitation assay. We identify BCL6, a secondary regulator of VDR signaling, to be directly regulated by MED12 through a combination of chromatin immunoprecipitation, qRT-PCR and western analyses. We further show that MED12 brings about the inhibition of p53 levels and apoptosis partly through induction of BCL6 in glioblastoma. Overall, this stands as the first report of MED12 over-expression and involvement in glioblastoma pathogenesis and identifies MED12 as an important mediator of VDR signaling and an attractive molecule for development of new therapeutic interventions.
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Affiliation(s)
- Srishti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Hima Makala
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vikas Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vaishali Suri
- Neuropathology Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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18
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Zhang Y, Qin P, Xu X, Li M, Huang H, Yan J, Zhou Y. Mediator Complex Subunit 19 Promotes the Development of Hepatocellular Carcinoma by Regulating the AKT/mTOR Signaling Pathway. Front Oncol 2022; 11:792285. [PMID: 35047403 PMCID: PMC8761619 DOI: 10.3389/fonc.2021.792285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/10/2021] [Indexed: 01/13/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, the pathogenesis of which remains unclear. Mediator complex subunit 19 (MED19), a subunit of the Mediator complex, is a multi-protein co-activator necessary for DNA transcription factors to induce RNA polymerase II transcription. In the current study, we aimed to study the role of MED19 in HCC and elucidate its mechanism. Methods MED19 expression in HCC tissues was determined. The relationship between MED19 and the clinical prognosis was explored. The influence of MED19 on HCC cell viability, migration, invasion, and apoptosis was studied. The expression of AKT/mTOR pathway genes and proteins was detected by qRT-PCR and western blot. The correlation between MED19 and immune infiltration was investigated. Results MED19 was upregulated in HCC tissues compared with tumor-adjacent tissues, and was associated with a poor prognosis. Furthermore, high MED19 expression was correlated with race, gender, etc. Knockdown of MED19 inhibited cell proliferation, migration, invasion, and promoted apoptosis. Knockdown of MED19 decreased p-AKT and p-mTOR protein expression. Additionally, the downstream effectors of the AKT/mTOR pathway, p70S6K1 and 4EBP1, were affected by MED19. Notably, MED19 expression was positively correlated with the infiltration levels of B cells, CD4+ T cells, CD8+ T cells, macrophages, etc. Conclusion MED19 is significantly upregulated in HCC tissues and cells. MED19 may promote the progression of HCC in vitro and may be related to immune infiltration. Together, our data show that MED19 could be considered as a new possible biomarker as well as a novel therapeutic target for HCC.
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Affiliation(s)
- Yuting Zhang
- Department of Microbiology, Guilin Medical University, Guilin, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Peifang Qin
- Department of Microbiology, Guilin Medical University, Guilin, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Xingfeng Xu
- Department of Physiology, Guilin Medical University, Guilin, China
| | - Mao Li
- Department of Physiology, Guilin Medical University, Guilin, China
| | - Haitao Huang
- Department of Microbiology, Guilin Medical University, Guilin, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Jianguo Yan
- Department of Physiology, Guilin Medical University, Guilin, China
| | - Yali Zhou
- Department of Microbiology, Guilin Medical University, Guilin, China.,Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
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19
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Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress. Microorganisms 2021; 9:microorganisms9102152. [PMID: 34683473 PMCID: PMC8540245 DOI: 10.3390/microorganisms9102152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways.
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20
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Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, Chen Z, Zhao Z, Chen J. Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. Nucleic Acids Res 2021; 49:7476-7491. [PMID: 34197614 PMCID: PMC8287926 DOI: 10.1093/nar/gkab540] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/04/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitor (PARPi)-based therapies initially reduce tumor burden but eventually lead to acquired resistance in cancer patients with BRCA1 or BRCA2 mutation. To understand the potential PARPi resistance mechanisms, we performed whole-genome CRISPR screens to discover genetic alterations that change the gene essentiality in cells with inducible depletion of BRCA2. We identified that several RNA Polymerase II transcription Mediator complex components, especially Cyclin C (CCNC) as synthetic survival targets upon BRCA2 loss. Total mRNA sequencing demonstrated that loss of CCNC could activate the transforming growth factor (TGF)-beta signaling pathway and extracellular matrix (ECM)-receptor interaction pathway, however the inhibition of these pathways could not reverse cell survival in BRCA2 depleted CCNC-knockout cells, indicating that the activation of these pathways is not required for the resistance. Moreover, we showed that the improved survival is not due to restoration of homologous recombination repair although decreased DNA damage signaling was observed. Interestingly, loss of CCNC could restore replication fork stability in BRCA2 deficient cells, which may contribute to PARPi resistance. Taken together, our data reveal CCNC as a critical genetic determinant upon BRCA2 loss of function, which may help the development of novel therapeutic strategies that overcome PARPi resistance.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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21
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Jiang J, Yang G, Xin Y, Wang Z, Yan W, Chen Z, Tang X, Xia J. Overexpression of OsMed16 Inhibits the Growth of Rice and Causes Spontaneous Cell Death. Genes (Basel) 2021; 12:genes12050656. [PMID: 33925652 PMCID: PMC8145620 DOI: 10.3390/genes12050656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022] Open
Abstract
The Mediator complex transduces information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. Research on plant Mediator subunits has primarily been performed in Arabidopsis, while very few of them have been functionally characterized in rice. In this study, the rice Mediator subunit 16, OsMed16, was examined. OsMed16 encodes a putative protein of 1301 amino acids, which is longer than the version previously reported. It was expressed in various rice organs and localized to the nucleus. The knockout of OsMed16 resulted in rice seedling lethality. Its overexpression led to the retardation of rice growth, low yield, and spontaneous cell death in the leaf blade and sheath. RNA sequencing suggested that the overexpression of OsMed16 altered the expression of a large number of genes. Among them, the upregulation of some defense-related genes was verified. OsMed16 can regulate the expression of a wealth of genes, and alterations in its expression have a profound impact on plant growth, development, and defense responses in rice.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Guangzhe Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Yafeng Xin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Zhigang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China;
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China;
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China;
- Shenzhen Agricultural Technology Promotion Center, Shenzhen 518055, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China;
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China;
- Correspondence: (X.T.); (J.X.)
| | - Jixing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
- Correspondence: (X.T.); (J.X.)
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22
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Osman S, Mohammad E, Lidschreiber M, Stuetzer A, Bazsó FL, Maier KC, Urlaub H, Cramer P. The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II. J Biol Chem 2021; 296:100734. [PMID: 33933450 PMCID: PMC8191332 DOI: 10.1016/j.jbc.2021.100734] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a dissociable part of the coactivator complex mediator, which regulates gene transcription by RNA polymerase II. The CKM has both negative and positive functions in gene transcription that remain poorly understood at the mechanistic level. In order to reconstitute the role of the CKM in transcription initiation, we prepared recombinant CKM from the yeast Saccharomyces cerevisiae. We showed that CKM bound to the core mediator (cMed) complex, sterically inhibiting cMed from binding to the polymerase II preinitiation complex (PIC) in vitro. We further showed that the Cdk8 kinase activity of the CKM weakened CKM-cMed interaction, thereby facilitating dissociation of the CKM and enabling mediator to bind the PIC in order to stimulate transcription initiation. Finally, we report that the kinase activity of Cdk8 is required for gene activation during the stressful condition of heat shock in vivo but not under steady-state growth conditions. Based on these results, we propose a model in which the CKM negatively regulates mediator function at upstream-activating sequences by preventing mediator binding to the PIC at the gene promoter. However, during gene activation in response to stress, the Cdk8 kinase activity of the CKM may release mediator and allow its binding to the PIC, thereby accounting for the positive function of CKM. This may impart improved adaptability to stress by allowing a rapid transcriptional response to environmental changes, and we speculate that a similar mechanism in metazoans may allow the precise timing of developmental transcription programs.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Eusra Mohammad
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexandra Stuetzer
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Fanni Laura Bazsó
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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23
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Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang CE, Murakami K, Garcia BA, Boyer TG, Tsai KL. Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module. SCIENCE ADVANCES 2021; 7:7/3/eabd4484. [PMID: 33523904 PMCID: PMC7810384 DOI: 10.1126/sciadv.abd4484] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/25/2020] [Indexed: 05/02/2023]
Abstract
The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.
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Affiliation(s)
- Yi-Chuan Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chia-En Chang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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24
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Scholl SM, Beal J, de Koning L, Girard E, Popovic M, de la Rochefordière A, Lecuru F, Fourchotte V, Ngo C, Floquet A, Berns EM, Kenter G, Gestraud P, von der Leyen H, Lecerf C, Puard V, Roman SR, Latouche A, Kereszt A, Balint B, Rouzier R, Kamal M. Genetic markers and phosphoprotein forms of beta-catenin pβ-Cat552 and pβ-Cat675 are prognostic biomarkers of cervical cancer. EBioMedicine 2020; 61:103049. [PMID: 33096476 PMCID: PMC7581879 DOI: 10.1016/j.ebiom.2020.103049] [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: 05/12/2020] [Revised: 07/10/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality world wide and constitutes the third most common malignancy in women. The RAIDs consortium (http://www.raids-fp7.eu/) conducted a prospective European study [BioRAIDs (NCT02428842)] with the objective to stratify CC patients for innovative treatments. A "metagene" of genomic markers in the PI3K pathway and epigenetic regulators had been previously associated with poor outcome [2]. METHODS To detect new, more specific, targets for treatment of patients who resist standard chemo-radiation, a high-dimensional Cox model was applied to define dominant molecular variants, copy number variations, and reverse phase protein arrays (RPPA). FINDINGS Survival analysis on 89 patients with all omics data available, suggested loss-of-function (LOF) or activating molecular alterations in nine genes to be candidate biomarkers for worse prognosis in patients treated by chemo-radiation while LOF of ATRX, MED13 as well as CASP8 were associated with better prognosis. When protein expression data by RPPA were factored in, the supposedly low molecular weight and nuclear form, of beta-catenin, phosphorylated in Ser552 (pβ-Cat552), ranked highest for good prognosis, while pβ-Cat675 was associated with worse prognosis. INTERPRETATION These findings call for molecularly targeted treatments involving p53, Wnt pathway, PI3K pathway, and epigenetic regulator genes. Pβ-Cat552 and pβ-Cat675 may be useful biomarkers to predict outcome to chemo-radiation, which targets the DNA repair axis. FUNDING European Union's Seventh Program for research, technological development and demonstration (agreement N°304,810), the Fondation ARC pour la recherche contre le cancer.
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Affiliation(s)
- Suzy M Scholl
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France.
| | - Jonas Beal
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Leanne de Koning
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Elodie Girard
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Marina Popovic
- Oncology Institute of Vojvodina, Put doktora Goldmana, 421204 Sremska Kamenica, Serbia
| | | | - Fabrice Lecuru
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Virginie Fourchotte
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Charlotte Ngo
- Service de chirurgie cancérologique gynécologique et du sein, Hôpital Européen Georges Pompidou, APHP et faculté de médecine, Université Paris Descartes, France
| | - Anne Floquet
- Chirurgie onco-gynécologique and Oncology, Institut Bergonié, Centre Régional de Lutte contre le Cancer Bordeaux-Aquitaine, France
| | - Els Mjj Berns
- Dept Medical Oncology, Erasmus MC, 3000 CA Rotterdam, Netherlands
| | - Gemma Kenter
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Department of Gynaecologic Oncology Amsterdam, Amsterdam UMC and The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Pierre Gestraud
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Heiko von der Leyen
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Hannover Clinical Trial Center, Hannover Medical School Germany
| | - Charlotte Lecerf
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Vincent Puard
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Sergio Roman Roman
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Aurelien Latouche
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France; Conservatoire national des arts et métiers, Paris, France
| | - Attila Kereszt
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; SeqOmics Biotechnology Ltd, Vallalkozok utja 7, Morahalom, Hungary
| | - Balazs Balint
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Roman Rouzier
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
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25
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Otsuji K, Sasaki T, Tanabe M, Seto Y. Droplet-digital PCR reveals frequent mutations in TERT promoter region in breast fibroadenomas and phyllodes tumours, irrespective of the presence of MED12 mutations. Br J Cancer 2020; 124:466-473. [PMID: 33046803 PMCID: PMC7852881 DOI: 10.1038/s41416-020-01109-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Breast fibroadenoma (FA) and phyllodes tumour (PT) often have variations of gene mediator complex subunit 12 (MED12) and mutations in the telomerase reverse transcriptase promoter region (TERTp). TERTp mutation is usually tested by Sanger sequencing. In this study, we compared Sanger sequencing and droplet-digital PCR (ddPCR) to measure TERTp mutations in FA and PT samples. METHODS FA and PT samples were collected from 82 patients who underwent surgery at our institution from 2005 to 2016. MED12 mutations for all cases and TERTp mutations for 17 tumours were detected by Sanger sequencing. ddPCR was performed to analyse TERTp mutation in all cases. RESULTS A total of 75 samples were eligible for analysis. Sanger sequencing detected MED12 mutations in 19/44 FA (42%) and 21/31 PT (68%). Among 17 Sanger sequencing-tested samples, 2/17 (12%) were TERTp mutation-positive. In ddPCR analyses, a significantly greater percentage of PT (19/31, 61%) was TERTp mutation-positive than was FA (13/44, 30%; P = 0.0046). The mutation positivity of TERTp and MED12 did not correlate, in either FA or PT. CONCLUSIONS ddPCR was more sensitive for detecting TERTp mutation than Sanger sequencing, being able to elucidate tumorigenesis in FA and PT.
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Affiliation(s)
- Kazutaka Otsuji
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Sasaki
- Department of Next-Generation Pathology Information and Networking, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Masahiko Tanabe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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26
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Xu W, Xie XJ, Faust AK, Liu M, Li X, Chen F, Naquin AA, Walton AC, Kishbaugh PW, Ji JY. All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site. Int J Mol Sci 2020; 21:E7511. [PMID: 33053834 PMCID: PMC7590003 DOI: 10.3390/ijms21207511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 are required for the normal larval-to-pupal transition in Drosophila. Second, our molecular dynamic analyses have revealed that hCDK8 has higher hydrogen bond occupation of His149-Asp151 and Asp151-Asn156 than dCDK8. Third, the substructure of Asp282, Phe283, Arg285, Thr287 and Cys291 can distinguish human and Drosophila CDK8 structures. In addition, there are two hydrogen bonds in the LXXLL motif: a lower occupation between L312 and L315, and a relatively higher occupation between L312 and L316. Human CDK8 has higher hydrogen bond occupation between L312 and L316 than dCDK8. Moreover, L312, L315 and L316 in the LXXLL motif of CDK8 have the specific pattern of hydrogen bonds and geometries, which could be crucial for the binding to nuclear receptors. Furthermore, the P154L mutation dramatically decreases the hydrogen bond between L312 and L315 in hCDK8, but not in dCDK8. The mutations of P154L and AQKAA modestly alter the local structures around residues 154. Finally, we identified the inhibitor-induced conformational changes of hCDK8, and our results suggest a structural difference in the drug-binding site between hCDK8 and dCDK8. Taken together, these results provide the structural insights into the roles of the LXXLL motif and the kinase activity of CDK8 in vivo.
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Affiliation(s)
- Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; (A.K.F.); (A.A.N.); (A.C.W.); (P.W.K.)
| | - Xiao-Jun Xie
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX 77807, USA; (X.-J.X.); (M.L.); (X.L.)
| | - Ali K. Faust
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; (A.K.F.); (A.A.N.); (A.C.W.); (P.W.K.)
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX 77807, USA; (X.-J.X.); (M.L.); (X.L.)
| | - Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX 77807, USA; (X.-J.X.); (M.L.); (X.L.)
| | - Feng Chen
- High Performance Computing, 329 Frey Computing Services Center, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Ashlin A. Naquin
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; (A.K.F.); (A.A.N.); (A.C.W.); (P.W.K.)
| | - Avery C. Walton
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; (A.K.F.); (A.A.N.); (A.C.W.); (P.W.K.)
| | - Peter W. Kishbaugh
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; (A.K.F.); (A.A.N.); (A.C.W.); (P.W.K.)
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX 77807, USA; (X.-J.X.); (M.L.); (X.L.)
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27
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Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases. Nat Cell Biol 2020; 22:1223-1238. [PMID: 32989249 DOI: 10.1038/s41556-020-0573-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/07/2020] [Indexed: 12/11/2022]
Abstract
Pluripotent stem cells (PSCs) transition between cell states in vitro, reflecting developmental changes in the early embryo. PSCs can be stabilized in the naive state by blocking extracellular differentiation stimuli, particularly FGF-MEK signalling. Here, we report that multiple features of the naive state in human and mouse PSCs can be recapitulated without affecting FGF-MEK signalling or global DNA methylation. Mechanistically, chemical inhibition of CDK8 and CDK19 (hereafter CDK8/19) kinases removes their ability to repress the Mediator complex at enhancers. CDK8/19 inhibition therefore increases Mediator-driven recruitment of RNA polymerase II (RNA Pol II) to promoters and enhancers. This efficiently stabilizes the naive transcriptional program and confers resistance to enhancer perturbation by BRD4 inhibition. Moreover, naive pluripotency during embryonic development coincides with a reduction in CDK8/19. We conclude that global hyperactivation of enhancers drives naive pluripotency, and this can be achieved in vitro by inhibiting CDK8/19 kinase activity. These principles may apply to other contexts of cellular plasticity.
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28
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Stieg DC, Cooper KF, Strich R. The extent of cyclin C promoter occupancy directs changes in stress-dependent transcription. J Biol Chem 2020; 295:16280-16291. [PMID: 32934007 DOI: 10.1074/jbc.ra120.015215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/09/2020] [Indexed: 12/20/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a detachable Mediator subunit composed of cyclin C and one each of paralogs Cdk8/Cdk19, Med12/Med12L, and Med13/Med13L. Our previous RNA-Seq studies demonstrated that cyclin C represses a subset of hydrogen peroxide-induced genes under normal conditions but is involved in activating other loci following stress. Here, we show that cyclin C directs this transcriptional reprograming through changes in its promoter occupancy. Following peroxide stress, cyclin C promoter occupancy increased for genes it activates while decreasing at loci it represses under normal conditions. Promoter occupancy of other CKM components generally mirrored cyclin C, indicating that the CKM moves as a single unit. It has previously been shown that some cyclin C leaves the nucleus following cytotoxic stress to induce mitochondrial fragmentation and apoptosis. We observed that CKM integrity appeared compromised at a subset of repressed promoters, suggesting a source of cyclin C that is targeted for nuclear release. Interestingly, mTOR inhibition induced a new pattern of cyclin C promoter occupancy indicating that this control is fine-tuned to the individual stress. Using inhibitors, we found that Cdk8 kinase activity is not required for CKM movement or repression but was necessary for full gene activation. In conclusion, this study revealed that different stress stimuli elicit specific changes in CKM promoter occupancy correlating to altered transcriptional outputs. Finally, although CKM components were recruited or expelled from promoters as a unit, heterogeneity was observed at individual promoters, suggesting a mechanism to generate gene- and stress-specific responses.
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Affiliation(s)
- David C Stieg
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Randy Strich
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA.
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29
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Gene Transcription as a Limiting Factor in Protein Production and Cell Growth. G3-GENES GENOMES GENETICS 2020; 10:3229-3242. [PMID: 32694199 PMCID: PMC7466996 DOI: 10.1534/g3.120.401303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell growth is driven by the synthesis of proteins, genes, and other cellular components. Defining processes that limit biosynthesis rates is fundamental for understanding the determinants of cell physiology. Here, we analyze the consequences of engineering cells to express extremely high levels of mCherry proteins, as a tool to define limiting processes that fail to adapt upon increasing biosynthetic demands. Protein-burdened cells were transcriptionally and phenotypically similar to mutants of the Mediator, a transcription coactivator complex. However, our binding data suggest that the Mediator was not depleted from endogenous promoters. Burdened cells showed an overall increase in the abundance of the majority of endogenous transcripts, except for highly expressed genes. Our results, supported by mathematical modeling, suggest that wild-type cells transcribe highly expressed genes at the maximal possible rate, as defined by the transcription machinery’s physical properties. We discuss the possible cellular benefit of maximal transcription rates to allow a coordinated optimization of cell size and cell growth.
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30
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Postlmayr A, Dumeau CE, Wutz A. Cdk8 is required for establishment of H3K27me3 and gene repression by Xist and mouse development. Development 2020; 147:dev175141. [PMID: 32439758 PMCID: PMC7295591 DOI: 10.1242/dev.175141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/14/2020] [Indexed: 10/30/2022]
Abstract
We previously identified the cyclin dependent kinase Cdk8 as a putative silencing factor for Xist To investigate its role in X inactivation, we engineered a Cdk8 mutation in mouse embryonic stem cells (ESCs) carrying an inducible system for studying Xist function. We found that Xist repressed X-linked genes at half of the expression level in Cdk8 mutant cells, whereas they were almost completely silenced in the controls. Lack of Cdk8 impaired Ezh2 recruitment and the establishment of histone H3 lysine 27 tri-methylation but not PRC1 recruitment by Xist Transgenic expression of wild-type but not catalytically inactive Cdk8 restored efficient gene repression and PRC2 recruitment. Mutation of the paralogous kinase Cdk19 did not affect Xist function, and combined mutations of Cdk8 and Cdk19 resembled the Cdk8 mutation. In mice, a Cdk8 mutation caused post-implantation lethality. We observed that homozygous Cdk8 mutant female embryos showed a greater developmental delay than males on day 10.5. Together with the inefficient repression of X-linked genes in differentiating Cdk8 mutant female ESCs, these data show a requirement for Cdk8 in the initiation of X inactivation.
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Affiliation(s)
- Andreas Postlmayr
- D-BIOL, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, HPL E12, Otto-Stern-Weg 7, 8049 Zurich, Switzerland
| | - Charles Etienne Dumeau
- D-BIOL, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, HPL E12, Otto-Stern-Weg 7, 8049 Zurich, Switzerland
| | - Anton Wutz
- D-BIOL, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, HPL E12, Otto-Stern-Weg 7, 8049 Zurich, Switzerland
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Feldmann A, Dimitrova E, Kenney A, Lastuvkova A, Klose RJ. CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions. Nucleic Acids Res 2020; 48:2942-2955. [PMID: 31996894 PMCID: PMC7102981 DOI: 10.1093/nar/gkaa064] [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: 10/03/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 02/05/2023] Open
Abstract
Appropriate developmental gene regulation relies on the capacity of gene promoters to integrate inputs from distal regulatory elements, yet how this is achieved remains poorly understood. In embryonic stem cells (ESCs), a subset of silent developmental gene promoters are primed for activation by FBXL19, a CpG island binding protein, through its capacity to recruit CDK-Mediator. How mechanistically these proteins function together to prime genes for activation during differentiation is unknown. Here we discover that in mouse ESCs FBXL19 and CDK-Mediator support long-range interactions between silent gene promoters that rely on FBXL19 for their induction during differentiation and gene regulatory elements. During gene induction, these distal regulatory elements behave in an atypical manner, in that the majority do not acquire histone H3 lysine 27 acetylation and no longer interact with their target gene promoter following gene activation. Despite these atypical features, we demonstrate by targeted deletions that these distal elements are required for appropriate gene induction during differentiation. Together these discoveries demonstrate that CpG-island associated gene promoters can prime genes for activation by communicating with atypical distal gene regulatory elements to achieve appropriate gene expression.
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Affiliation(s)
- Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Emilia Dimitrova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Kenney
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Li X, Liu M, Ren X, Loncle N, Wang Q, Hemba-Waduge RUS, Yu SH, Boube M, Bourbon HMG, Ni JQ, Ji JY. The Mediator CDK8-Cyclin C complex modulates Dpp signaling in Drosophila by stimulating Mad-dependent transcription. PLoS Genet 2020; 16:e1008832. [PMID: 32463833 PMCID: PMC7282676 DOI: 10.1371/journal.pgen.1008832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/09/2020] [Accepted: 05/05/2020] [Indexed: 11/19/2022] Open
Abstract
Dysregulation of CDK8 (Cyclin-Dependent Kinase 8) and its regulatory partner CycC (Cyclin C), two subunits of the conserved Mediator (MED) complex, have been linked to diverse human diseases such as cancer. Thus, it is essential to understand the regulatory network modulating the CDK8-CycC complex in both normal development and tumorigenesis. To identify upstream regulators or downstream effectors of CDK8, we performed a dominant modifier genetic screen in Drosophila based on the defects in vein patterning caused by specific depletion or overexpression of CDK8 or CycC in developing wing imaginal discs. We identified 26 genomic loci whose haploinsufficiency can modify these CDK8- or CycC-specific phenotypes. Further analysis of two overlapping deficiency lines and mutant alleles led us to identify genetic interactions between the CDK8-CycC pair and the components of the Decapentaplegic (Dpp, the Drosophila homolog of TGFβ, or Transforming Growth Factor-β) signaling pathway. We observed that CDK8-CycC positively regulates transcription activated by Mad (Mothers against dpp), the primary transcription factor downstream of the Dpp/TGFβ signaling pathway. CDK8 can directly interact with Mad in vitro through the linker region between the DNA-binding MH1 (Mad homology 1) domain and the carboxy terminal MH2 (Mad homology 2) transactivation domain. Besides CDK8 and CycC, further analyses of other subunits of the MED complex have revealed six additional subunits that are required for Mad-dependent transcription in the wing discs: Med12, Med13, Med15, Med23, Med24, and Med31. Furthermore, our analyses confirmed the positive roles of CDK9 and Yorkie in regulating Mad-dependent gene expression in vivo. These results suggest that CDK8 and CycC, together with a few other subunits of the MED complex, may coordinate with other transcription cofactors in regulating Mad-dependent transcription during wing development in Drosophila.
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Affiliation(s)
- Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Xingjie Ren
- School of Medicine, Tsinghua University, Beijing, China
| | - Nicolas Loncle
- Centre de Biologie Intégrative, Centre de Biologie du Développement, UMR5544 du CNRS, Université de Toulouse, Toulouse, France
| | - Qun Wang
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Rajitha-Udakara-Sampath Hemba-Waduge
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Stephen H. Yu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Muriel Boube
- Centre de Biologie Intégrative, Centre de Biologie du Développement, UMR5544 du CNRS, Université de Toulouse, Toulouse, France
| | - Henri-Marc G. Bourbon
- Centre de Biologie Intégrative, Centre de Biologie du Développement, UMR5544 du CNRS, Université de Toulouse, Toulouse, France
| | - Jian-Quan Ni
- School of Medicine, Tsinghua University, Beijing, China
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
- Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
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Network Structure Analysis Identifying Key Genes of Autism and Its Mechanism. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:3753080. [PMID: 32273901 PMCID: PMC7125446 DOI: 10.1155/2020/3753080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/04/2019] [Accepted: 02/22/2020] [Indexed: 01/16/2023]
Abstract
Identifying the key genes of autism is of great significance for understanding its pathogenesis and improving the clinical level of medicine. In this paper, we use the structural parameters (average degree) of gene correlation networks to identify genes related to autism and study its pathogenesis. Based on the gene expression profiles of 82 autistic patients (the experimental group, E) and 64 healthy persons (the control group, C) in NCBI database, spearman correlation networks are established, and their average degrees under different thresholds are analyzed. It is found that average degrees of C and E are basically separable at the full thresholds. This indicates that there is a clear difference between the network structures of C and E, and it also suggests that this difference is related to the mechanism of disease. By annotating and enrichment analysis of the first 20 genes (MD-Gs) with significant difference in the average degree, we find that they are significantly related to gland development, cardiovascular development, and embryogenesis of nervous system, which support the results in Alter et al.'s original research. In addition, FIGF and CSF3 may play an important role in the mechanism of autism.
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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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Introduction of Somatic Mutation in MED12 Induces Wnt4/β-Catenin and Disrupts Autophagy in Human Uterine Myometrial Cell. Reprod Sci 2020; 27:823-832. [PMID: 32046450 DOI: 10.1007/s43032-019-00084-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022]
Abstract
Uterine fibroids (UFs) or leiomyoma are frequently associated with somatic mutations in the mediator complex subunit 12 (MED12) gene; however, the function of these mutations in human UF biology is yet to be determined. Herein, we determined the functional role of the most common MED12 somatic mutation in the modulation of oncogenic Wnt4/β-catenin and mammalian target of rapamycin (mTOR) signaling pathways. Using an immortalized human uterine myometrial smooth muscle cell line (UtSM), we constitutively overexpressed either MED12-Wild Type or the most common MED12 somatic mutation (c.131G>A), and the effects of this MED12 mutation were compared between these cell lines. This immortalized cell line was used as a model because it expresses wild type MED12 protein and do not possess MED12 somatic mutations. By comparing the effect between MED12-WT and MED12-mutant (mut) stable cell populations, we observed increased levels of protein expression of Wnt4 and β-catenin in MED12-mut cells as compared with MED12-WT cells. MED12-mut cells also expressed increased levels of mTOR protein and oncogenic cyclin D1 which are hallmarks of cell growth and tumorigenicity. This somatic mutation in MED12 showed an effect on cell-cycle progression by induction of S-phase cells. MED12-mut cells also showed inhibition of autophagy as compared with MED12-WT cells. Together, these findings indicate that the MED12 somatic mutation has the potentials for myometrial cell transformation by dysregulating oncogenic Wnt4/β-catenin and its downstream mTOR signaling which might be associated with autophagy abrogation, cell proliferation, and tumorigenicity.
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Zhang S, O'Regan R, Xu W. The emerging role of mediator complex subunit 12 in tumorigenesis and response to chemotherapeutics. Cancer 2019; 126:939-948. [PMID: 31869450 DOI: 10.1002/cncr.32672] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022]
Abstract
Transcriptional dysregulation induced by disease-defining genetic alterations of proteins in transcriptional machinery is a key feature of cancers. Mediator complex subunit 12 (MED12) is the central architectural subunit in the kinase module of Mediator, a large transcriptional regulatory complex that controls essential steps of transcription. Emerging evidence links deregulated MED12 to human cancers. MED12 is frequently mutated in benign tumors and cancers. Although the missense mutations of MED12 in benign tumors disrupt the kinase activity of Mediator, MED12 mutations in cancers could eliminate the interaction between Mediator complex and RNA polymerase II, leading to severe transcriptional misregulation. Aberrant expression of MED12 is associated with the prognosis of various types of human cancers. Loss of MED12 function has been associated with the development of resistance to chemotherapeutics. Moreover, MED12 is modified by posttranscriptional regulations. Arginine methylation of MED12 has been shown to regulate MED12-mediated transcriptional regulation and response to chemotherapeutics in human cancer cell lines. In this mini-review, the authors provide an overview of the roles of MED12 in the development of benign and malignant tumors as well as its roles in chemoresistance. The studies of MED12 exemplify that aberrant transcriptional programming is a therapeutic vulnerability for certain types of cancer.
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Affiliation(s)
- Shengjie Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin.,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Ruth O'Regan
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
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37
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Dufour C, Perbet R, Leblond P, Vasseur R, Stechly L, Pierache A, Reyns N, Touzet G, Le Rhun E, Vinchon M, Maurage CA, Escande F, Renaud F. Identification of prognostic markers in diffuse midline gliomas H3K27M-mutant. Brain Pathol 2019; 30:179-190. [PMID: 31348837 DOI: 10.1111/bpa.12768] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022] Open
Abstract
Pediatric diffuse midline gliomas are devastating diseases. Among them, diffuse midline gliomas H3K27M-mutant are associated with worse prognosis. However, recent studies have highlighted significant differences in clinical behavior and biological alterations within this specific subgroup. In this context, simple markers are needed to refine the prognosis of diffuse midline gliomas H3K27M-mutant and guide the clinical management of patients. The aims of this study were (i) to describe the molecular, immunohistochemical and, especially, chromosomal features of a cohort of diffuse midline gliomas and (ii) to focus on H3K27M-mutant tumors to identify new prognostic markers. Patients were retrospectively selected from 2001 to 2017. Tumor samples were analyzed by immunohistochemistry (including H3K27me3, EGFR, c-MET and p53), next-generation sequencing and comparative genomic hybridization array. Forty-nine patients were included in the study. The median age at diagnosis was 9 years, and the median overall survival (OS) was 9.4 months. H3F3A or HIST1H3B mutations were identified in 80% of the samples. Within the H3K27M-mutant tumors, PDGFRA amplification, loss of 17p and a complex chromosomal profile were significantly associated with worse survival. Three prognostic markers were identified in diffuse midline gliomas H3K27M-mutant: PDGFRA amplification, loss of 17p and a complex chromosomal profile. These markers are easy to detect in daily practice and should be considered to refine the prognosis of this entity.
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Affiliation(s)
- Charlotte Dufour
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France
| | - Romain Perbet
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France.,Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
| | - Pierre Leblond
- Department of Paediatric Oncology, Centre Oscar Lambret, Lille, F-59000, France
| | - Romain Vasseur
- Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
| | - Laurence Stechly
- Department of Biochemistry and Molecular Biology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France
| | - Adeline Pierache
- Department of Biostatistics and Data Management, Lille University Hospital, Lille, F-59000, France
| | - Nicolas Reyns
- Department of Stereotactic Neurosurgery, Lille University Hospital, Lille, F-59000, France
| | - Gustavo Touzet
- Department of Stereotactic Neurosurgery, Lille University Hospital, Lille, F-59000, France
| | - Emilie Le Rhun
- Univ Lille, Inserm, U-1192, Lille, F-59000, France.,Department of Neuro-Oncology and Neurosurgery, Lille University Hospital, Lille, F-59000, France.,Department of Neurology, Breast Cancer, Centre Oscar Lambret, Lille, F-59000, France
| | - Matthieu Vinchon
- Department of Paediatric Neurosurgery, Lille University Hospital, Lille, F-59000, France
| | - Claude-Alain Maurage
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France.,Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
| | - Fabienne Escande
- Department of Biochemistry and Molecular Biology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France
| | - Florence Renaud
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France.,Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
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Miao YL, Gambini A, Zhang Y, Padilla-Banks E, Jefferson WN, Bernhardt ML, Huang W, Li L, Williams CJ. Mediator complex component MED13 regulates zygotic genome activation and is required for postimplantation development in the mouse. Biol Reprod 2019; 98:449-464. [PMID: 29325037 DOI: 10.1093/biolre/ioy004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Understanding factors that regulate zygotic genome activation (ZGA) is critical for determining how cells are reprogrammed to become totipotent or pluripotent. There is limited information regarding how this process occurs physiologically in early mammalian embryos. Here, we identify a mediator complex subunit, MED13, as translated during mouse oocyte maturation and transcribed early from the zygotic genome. Knockdown and conditional knockout approaches demonstrate that MED13 is essential for ZGA in the mouse, in part by regulating expression of the embryo-specific chromatin remodeling complex, esBAF. The role of MED13 in ZGA is mediated in part by interactions with E2F transcription factors. In addition to MED13, its paralog, MED13L, is required for successful preimplantation embryo development. MED13L partially compensates for loss of MED13 function in preimplantation knockout embryos, but postimplantation development is not rescued by MED13L. Our data demonstrate an essential role for MED13 in supporting chromatin reprogramming and directed transcription of essential genes during ZGA.
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Affiliation(s)
- Yi-Liang Miao
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.,Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education College of Animal Science and Technology, Huazhong Agricultural University, China
| | - Andrés Gambini
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Yingpei Zhang
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Elizabeth Padilla-Banks
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Wendy N Jefferson
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Miranda L Bernhardt
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Weichun Huang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Leping Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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Variants in MED12L, encoding a subunit of the mediator kinase module, are responsible for intellectual disability associated with transcriptional defect. Genet Med 2019; 21:2713-2722. [PMID: 31155615 PMCID: PMC7243155 DOI: 10.1038/s41436-019-0557-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose Mediator is a multiprotein complex that allows the transfer of
genetic information from DNA binding proteins to the RNA polymerase II
during transcription initiation. MED12L is a subunit of the kinase module,
which is one of the four sub-complexes of the mediator complex. Other
subunits of the kinase module have been already implicated in intellectual
disability, namely MED12, MED13L, MED13 and CDK19. Methods We describe an international cohort of seven affected individuals
harboring variants involving MED12L identified by array
CGH, exome or genome sequencing. Results All affected individuals presented with intellectual disability
and/or developmental delay, including speech impairment. Other features
included autism spectrum disorder, aggressive behavior, corpus callosum
abnormality and mild facial morphological features. Three individuals had a
MED12L deletion or duplication. The other four
individuals harbored single nucleotide variants (one nonsense, one
frameshift and two splicing variants). Functional analysis confirmed a
moderate and significant alteration of RNA synthesis in two individuals. Conclusion Overall data suggest that MED12L haploinsufficiency is responsible
for intellectual disability and transcriptional defect. Our findings confirm
that the integrity of this kinase module is a critical factor for
neurological development.
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40
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MED28 Over-Expression Shortens the Cell Cycle and Induces Genomic Instability. Int J Mol Sci 2019; 20:ijms20071746. [PMID: 30970566 PMCID: PMC6479353 DOI: 10.3390/ijms20071746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 01/01/2023] Open
Abstract
The mammalian mediator complex subunit 28 (MED28) is overexpressed in a variety of cancers and it regulates cell migration/invasion and epithelial-mesenchymal transition. However, transcription factors that increase MED28 expression have not yet been identified. In this study, we performed a luciferase reporter assay to identify and characterize the prospective transcription factors, namely E2F transcription factor 1, nuclear respiratory factor 1, E-26 transforming sequence 1, and CCAAT/enhancer-binding protein β, which increased MED28 expression. In addition, the release from the arrest at the G1−S or G2−M phase transition after cell cycle synchronization using thymidine or nocodazole, respectively, showed enhanced MED28 expression at the G1−S transition and mitosis. Furthermore, the overexpression of MED28 significantly decreased the duration of interphase and mitosis. Conversely, a knockdown of MED28 using si-RNA increased the duration of interphase and mitosis. Of note, the overexpression of MED28 significantly increased micronucleus and nuclear budding in HeLa cells. In addition, flow cytometry and fluorescence microscopy analyses showed that the overexpression of MED28 significantly increased aneuploid cells. Taken together, these results suggest that MED28 expression is increased by oncogenic transcription factors and its overexpression disturbs the cell cycle, which results in genomic instability and aneuploidy.
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Calpena E, Hervieu A, Kaserer T, Swagemakers SM, Goos JA, Popoola O, Ortiz-Ruiz MJ, Barbaro-Dieber T, Bownass L, Brilstra EH, Brimble E, Foulds N, Grebe TA, Harder AV, Lees MM, Monaghan KG, Newbury-Ecob RA, Ong KR, Osio D, Reynoso Santos FJ, Ruzhnikov MR, Telegrafi A, van Binsbergen E, van Dooren MF, van der Spek PJ, Blagg J, Twigg SR, Mathijssen IM, Clarke PA, Wilkie AO, Wilkie AOM. De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder. Am J Hum Genet 2019; 104:709-720. [PMID: 30905399 PMCID: PMC6451695 DOI: 10.1016/j.ajhg.2019.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022] Open
Abstract
The Mediator is an evolutionarily conserved, multi-subunit complex that regulates multiple steps of transcription. Mediator activity is regulated by the reversible association of a four-subunit module comprising CDK8 or CDK19 kinases, together with cyclin C, MED12 or MED12L, and MED13 or MED13L. Mutations in MED12, MED13, and MED13L were previously identified in syndromic developmental disorders with overlapping phenotypes. Here, we report CDK8 mutations (located at 13q12.13) that cause a phenotypically related disorder. Using whole-exome or whole-genome sequencing, and by international collaboration, we identified eight different heterozygous missense CDK8 substitutions, including 10 shown to have arisen de novo, in 12 unrelated subjects; a recurrent mutation, c.185C>T (p.Ser62Leu), was present in five individuals. All predicted substitutions localize to the ATP-binding pocket of the kinase domain. Affected individuals have overlapping phenotypes characterized by hypotonia, mild to moderate intellectual disability, behavioral disorders, and variable facial dysmorphism. Congenital heart disease occurred in six subjects; additional features present in multiple individuals included agenesis of the corpus callosum, ano-rectal malformations, seizures, and hearing or visual impairments. To evaluate the functional impact of the mutations, we measured phosphorylation at STAT1-Ser727, a known CDK8 substrate, in a CDK8 and CDK19 CRISPR double-knockout cell line transfected with wild-type (WT) or mutant CDK8 constructs. These experiments demonstrated a reduction in STAT1 phosphorylation by all mutants, in most cases to a similar extent as in a kinase-dead control. We conclude that missense mutations in CDK8 cause a developmental disorder that has phenotypic similarity to syndromes associated with mutations in other subunits of the Mediator kinase module, indicating probable overlap in pathogenic mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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Lerario AM, Nanba K, Blinder AR, Suematsu S, Omura M, Nishikawa T, Giordano TJ, Rainey WE, Else T. Genetics of aldosterone-producing adenomas with pathogenic KCNJ5 variants. Endocr Relat Cancer 2019; 26:463-470. [PMID: 30753137 PMCID: PMC7869655 DOI: 10.1530/erc-18-0364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/11/2019] [Indexed: 12/27/2022]
Abstract
Somatic variants in genes that regulate intracellular ion homeostasis have been identified in aldosterone-producing adenomas (APA). Although the mechanisms leading to an increased aldosterone production in APA cells has been well studied, the molecular events that cause cell proliferation and tumor formation are poorly understood. In the present study, we have performed whole exome sequencing (WES) to characterize the landscape of somatic alterations in a homogeneous series of APA with pathogenic KCNJ5 variants. In the WES analysis on eleven APA, 84 exonic somatic events were called by 3 different somatic callers. Besides the KCNJ5 gene, only two genes (MED13 and ZNF669) harbored somatic variants in more than one APA. Unlike adrenocortical carcinomas, no chromosomal instability was observed by the somatic copy-number alteration and loss of heterozygosity analyses. The estimated tumor purity ranged from 0.35 to 0.67, suggesting a significant proportion of normal cell infiltration. Based on the results of PureCN analysis, the KCNJ5 variants appear to be clonal. In conclusion, in addition to KCNJ5 somatic pathogenic variant, no significant somatic event that would obviously explain proliferation or tumor growth was observed in our homogeneous cohort of KCNJ5-mutated APA. The molecular mechanisms causing APA growth and tumorigenesis remain to be elucidated.
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Affiliation(s)
- Antonio M. Lerario
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Kazutaka Nanba
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Amy R. Blinder
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Sachiko Suematsu
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, Japan
| | - Masao Omura
- Medical Checkup Clinic, Minatomirai Medical Square, Sowa-Group, Yokohama, Japan
| | - Tetsuo Nishikawa
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, Japan
| | - Thomas J. Giordano
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - William E. Rainey
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Tobias Else
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Corresponding author: Tobias Else, MD, 1150 West Medical Center Dr. Ann Arbor, MI, 48109, USA,
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Ibrahimpasic T, Ghossein R, Shah JP, Ganly I. Poorly Differentiated Carcinoma of the Thyroid Gland: Current Status and Future Prospects. Thyroid 2019; 29:311-321. [PMID: 30747050 PMCID: PMC6437626 DOI: 10.1089/thy.2018.0509] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Poorly differentiated thyroid cancer (PDTC) is a rare but clinically highly significant entity because it accounts for most fatalities from non-anaplastic follicular cell-derived thyroid cancer. Due to the relative rarity of the disease and heterogeneous diagnostic criteria, studies on PDTC have been limited. In light of the evolution of ultra-deep next-generation sequencing technologies and through correlation of clinicopathologic and genomic characteristics of PDTC, an improved understanding of the biology of PDTC has been facilitated. Here, the diagnostic criteria, clinicopathologic characteristics, management, and outcomes in PDTC, as well as genomic drivers in PDTC reported in recent next-generation sequencing studies, are reviewed. In addition, future prospects in improving the outcomes in PDTC patients are reviewed. SUMMARY PDTC patients tend to present with adverse clinicopathologic characteristics: older age, male predominance, advanced locoregional disease, and distant metastases. Surgery with clearance of all gross disease can achieve satisfactory locoregional control. However, the majority of PDTC patients die of distant disease. Five-year disease-specific survival for PDTC patients has been reported at 66%. On multivariate analysis, reported predictors of poor survival in PDTC patients have been older age (>45 years), T4a pathological stage, extrathyroidal extension, high mitotic rate, tumor necrosis, and distant metastasis at presentation. BRAFV600E or RAS mutations (27% and 24% of cases, respectively) remain mutually exclusive main drivers in PDTC. TERT promoter mutations represent the most common alteration in PDTC (40%). Mutation in translation initiation factor EIF1AX (11%) and tumor suppressor TP53 (16%) have also been reported in PDTC. High rates of novel mutations (MED12 and RBM10) have been reported in fatal PDTC (15% and 12%, respectively). Chromosome 1q gains represent the most common arm-level alterations in PDTC, and those patients show worse survival rates. Chromosome 22q losses are also found in PDTC and show strong association with RAS mutation. CONCLUSIONS These new insights into the clinicopathologic and molecular characteristics of PDTC, together with further advancement in ultra-deep sequencing technologies, will be conducive in narrowing the focus in order to develop novel targeted therapies and improve the outcomes in PDTC patients.
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Affiliation(s)
- Tihana Ibrahimpasic
- Department of Surgery, Head and Neck Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jatin P. Shah
- Department of Surgery, Head and Neck Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ian Ganly
- Department of Surgery, Head and Neck Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Address correspondence to: Ian Ganly, MD, PhD, Department of Surgery, Head and Neck Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
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Ježek J, Smethurst DGJ, Stieg DC, Kiss ZAC, Hanley SE, Ganesan V, Chang KT, Cooper KF, Strich R. Cyclin C: The Story of a Non-Cycling Cyclin. BIOLOGY 2019; 8:biology8010003. [PMID: 30621145 PMCID: PMC6466611 DOI: 10.3390/biology8010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
The class I cyclin family is a well-studied group of structurally conserved proteins that interact with their associated cyclin-dependent kinases (Cdks) to regulate different stages of cell cycle progression depending on their oscillating expression levels. However, the role of class II cyclins, which primarily act as transcription factors and whose expression remains constant throughout the cell cycle, is less well understood. As a classic example of a transcriptional cyclin, cyclin C forms a regulatory sub-complex with its partner kinase Cdk8 and two accessory subunits Med12 and Med13 called the Cdk8-dependent kinase module (CKM). The CKM reversibly associates with the multi-subunit transcriptional coactivator complex, the Mediator, to modulate RNA polymerase II-dependent transcription. Apart from its transcriptional regulatory function, recent research has revealed a novel signaling role for cyclin C at the mitochondria. Upon oxidative stress, cyclin C leaves the nucleus and directly activates the guanosine 5’-triphosphatase (GTPase) Drp1, or Dnm1 in yeast, to induce mitochondrial fragmentation. Importantly, cyclin C-induced mitochondrial fission was found to increase sensitivity of both mammalian and yeast cells to apoptosis. Here, we review and discuss the biology of cyclin C, focusing mainly on its transcriptional and non-transcriptional roles in tumor promotion or suppression.
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Affiliation(s)
- Jan Ježek
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Daniel G J Smethurst
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - David C Stieg
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Z A C Kiss
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Sara E Hanley
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Vidyaramanan Ganesan
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Kai-Ti Chang
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Katrina F Cooper
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Randy Strich
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
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Li X, Liu M, Ji JY. Understanding Obesity as a Risk Factor for Uterine Tumors Using Drosophila. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1167:129-155. [PMID: 31520353 DOI: 10.1007/978-3-030-23629-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple large-scale epidemiological studies have identified obesity as an important risk factor for a variety of human cancers, particularly cancers of the uterus, gallbladder, kidney, liver, colon, and ovary, but there is much uncertainty regarding how obesity increases the cancer risks. Given that obesity has been consistently identified as a major risk factor for uterine tumors, the most common malignancies of the female reproductive system, we use uterine tumors as a pathological context to survey the relevant literature and propose a novel hypothesis: chronic downregulation of the cyclin-dependent kinase 8 (CDK8) module, composed of CDK8 (or its paralog CDK19), Cyclin C, MED12 (or MED12L), and MED13 (or MED13L), by elevated insulin or insulin-like growth factor signaling in obese women may increase the chances to dysregulate the activities of transcription factors regulated by the CDK8 module, thereby increasing the risk of uterine tumors. Although we focus on endometrial cancer and uterine leiomyomas (or fibroids), two major forms of uterine tumors, our model may offer additional insights into how obesity increases the risk of other types of cancers and diseases. To illustrate the power of model organisms for studying human diseases, here we place more emphasis on the findings obtained from Drosophila melanogaster.
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Affiliation(s)
- Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA.
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Abstract
The Mediator-associated kinases CDK8 and CDK19 function in the context of three additional proteins: CCNC and MED12, which activate CDK8/CDK19 kinase function, and MED13, which enables their association with the Mediator complex. The Mediator kinases affect RNA polymerase II (pol II) transcription indirectly, through phosphorylation of transcription factors and by controlling Mediator structure and function. In this review, we discuss cellular roles of the Mediator kinases and mechanisms that enable their biological functions. We focus on sequence-specific, DNA-binding transcription factors and other Mediator kinase substrates, and how CDK8 or CDK19 may enable metabolic and transcriptional reprogramming through enhancers and chromatin looping. We also summarize Mediator kinase inhibitors and their therapeutic potential. Throughout, we note conserved and divergent functions between yeast and mammalian CDK8, and highlight many aspects of kinase module function that remain enigmatic, ranging from potential roles in pol II promoter-proximal pausing to liquid-liquid phase separation.
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Affiliation(s)
- Charli B Fant
- a Department of Biochemistry , University of Colorado , Boulder , CO , USA
| | - Dylan J Taatjes
- a Department of Biochemistry , University of Colorado , Boulder , CO , USA
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47
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Gao X, Xie XJ, Hsu FN, Li X, Liu M, Hemba-Waduge RUS, Xu W, Ji JY. CDK8 mediates the dietary effects on developmental transition in Drosophila. Dev Biol 2018; 444:62-70. [PMID: 30352217 PMCID: PMC6263851 DOI: 10.1016/j.ydbio.2018.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/08/2018] [Accepted: 10/07/2018] [Indexed: 01/29/2023]
Abstract
The complex interplay between genetic and environmental factors, such as diet and lifestyle, defines the initiation and progression of multifactorial diseases, including cancer, cardiovascular and metabolic diseases, and neurological disorders. Given that most of the studies have been performed in controlled experimental settings to ensure the consistency and reproducibility, the impacts of environmental factors, such as dietary perturbation, on the development of animals with different genotypes and the pathogenesis of these diseases remain poorly understood. By analyzing the cdk8 and cyclin C (cycC) mutant larvae in Drosophila, we have previously reported that the CDK8-CycC complex coordinately regulates lipogenesis by repressing dSREBP (sterol regulatory element-binding protein)-activated transcription and developmental timing by activating EcR (ecdysone receptor)-dependent gene expression. Here we report that dietary nutrients, particularly proteins and carbohydrates, modulate the developmental timing through the CDK8/CycC/EcR pathway. We observed that cdk8 and cycC mutants are sensitive to the levels of dietary proteins and seven amino acids (arginine, glutamine, isoleucine, leucine, methionine, threonine, and valine). Those mutants are also sensitive to dietary carbohydrates, and they are more sensitive to monosaccharides than disaccharides. These results suggest that CDK8-CycC mediates the dietary effects on lipid metabolism and developmental timing in Drosophila larvae.
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Affiliation(s)
- Xinsheng Gao
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Xiao-Jun Xie
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Fu-Ning Hsu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | | | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA.
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Heikkinen T, Äyräväinen A, Hänninen J, Ahvenainen T, Bützow R, Pasanen A, Vahteristo P. MED12 mutations and fumarate hydratase inactivation in uterine adenomyomas. Hum Reprod Open 2018; 2018:hoy020. [PMID: 30895261 PMCID: PMC6276694 DOI: 10.1093/hropen/hoy020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/09/2018] [Accepted: 10/26/2018] [Indexed: 01/16/2023] Open
Abstract
STUDY QUESTION Do the uterine leiomyoma driver events – mediator complex subunit 12 (MED12) mutations, high mobility group AT-hook (HMGA2) overexpression, and fumarate hydratase (FH) inactivation – also contribute to the development of uterine adenomyomas? SUMMARY ANSWER MED12 mutations and FH deficiency occur in a subset of uterine adenomyomas, but at lower frequencies than in leiomyomas. WHAT IS KNOWN ALREADY Uterine adenomyomas are benign tumours with clinical features very similar to uterine leiomyomas. Mutations affecting MED12, HMGA2 and FH account for up to 80–90% of leiomyomas, but their contribution to adenomyomas is not known. STUDY DESIGN, SIZE, DURATION Formalin-fixed paraffin-embedded adenomyoma samples from 21 patients operated on during 2012–2014 were collected at the pathology department’s archives and analysed for uterine leiomyoma driver events. PARTICIPANTS/MATERIALS, SETTING, METHODS Adenomyoma diagnoses were verified by a specialized pathologist and representative areas were marked on haematoxylin-eosin slides. DNA was extracted from the tissue samples and sequenced to detect mutations in MED12. Expression levels of HMGA2 and 2SC, a robust indirect method to detect FH inactivation, were analysed by immunohistochemistry (IHC). The coding region of FH was sequenced in one adenomyoma sample showing strong 2SC staining as well as in the same patient’s normal tissue sample. All patients’ medical histories were collected and reviewed. MAIN RESULTS AND THE ROLE OF CHANCE MED12 mutation c.131G > A, p.G44D, the most common mutation in uterine leiomyomas, was identified in two samples (2/21; 9.5%). One adenomyoma displayed strong 2SC positivity and subsequent sequencing revealed a frameshift FH mutation c.911delC, p.P304fs in the tumour. The mutation was also present in the patient’s normal tissue sample, indicating that she has a hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome. HMGA2 protein expression was normal in all adenomyomas. LIMITATIONS, REASONS FOR CAUTION Restricted sample size limits the determination of exact mutation frequencies of the studied aberrations in adenomyomas. WIDER IMPLICATIONS OF THE FINDINGS Uterine leiomyoma driver mutations do contribute to the development of some adenomyomas. We also report an adenomyoma in the context of hereditary HLRCC syndrome. Despite clinical similarities, the pathogenic mechanisms of adenomyomas and leiomyomas are likely different. Large-scale genomic analyses are warranted to elucidate the complete molecular background of adenomyomas. STUDY FUNDING/COMPETING INTERESTS This study was supported by The Academy of Finland, the Sigrid Jusélius Foundation, and the Cancer Society of Finland. The authors declare no conflict of interest.
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Affiliation(s)
- Tuomas Heikkinen
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics., FIN-00014 University of Helsinki, Helsinki, Finland
| | - Anna Äyräväinen
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics., FIN-00014 University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Janne Hänninen
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics., FIN-00014 University of Helsinki, Helsinki, Finland
| | - Terhi Ahvenainen
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics., FIN-00014 University of Helsinki, Helsinki, Finland
| | - Ralf Bützow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Annukka Pasanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pia Vahteristo
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics., FIN-00014 University of Helsinki, Helsinki, Finland
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Abstract
The fact that many cancer types display transcriptional addiction driven by dysregulation of oncogenic enhancers and transcription factors has led to increased interest in a group of protein kinases, known as transcriptional cyclin dependent kinases (tCDKs), as potential therapeutic targets. Despite early reservations about targeting a process that is essential to healthy cell types, there is now evidence that targeting tCDKs could provide enough therapeutic window to be effective in the clinic. Here, we discuss recent developments in this field, with an emphasis on highly-selective inhibitors and the challenges to be addressed before these inhibitors could be used for therapeutic purposes. Abbreviations: CAK: CDK-activating kinase;CDK: cyclin-dependent kinase;CMGC group: CDK-, MAPK-, GSK3-, and CLK-like;CTD: C-terminal repeat domain of the RPB1 subunit of RNA polymerase II;DRB: 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole;mCRPC: metastatic castration-resistant prostate cancer;NSCLC: non-small cell lung cancer;P-TEFb: positive elongation factor b;RNAPII: RNA polymerase II;S2: serine-2 of CTD repeats;S5: serine-5 of CTD repeats;S7: serine-7 of CTD repeats;SEC: super elongation complex;tCDK: transcriptional cyclin-dependent kinase;TNBC: triple-negative breast cancer
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Affiliation(s)
- Matthew D Galbraith
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA
| | - Heather Bender
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA
| | - Joaquín M Espinosa
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,c Department of Molecular, Cellular and Developmental Biology , University of Colorado Boulder , Boulder , CO , USA
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50
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Park MJ, Shen H, Kim NH, Gao F, Failor C, Knudtson JF, McLaughlin J, Halder SK, Heikkinen TA, Vahteristo P, Al-Hendy A, Schenken RS, Boyer TG. Mediator Kinase Disruption in MED12-Mutant Uterine Fibroids From Hispanic Women of South Texas. J Clin Endocrinol Metab 2018; 103:4283-4292. [PMID: 30099503 PMCID: PMC6194812 DOI: 10.1210/jc.2018-00863] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/01/2018] [Indexed: 01/09/2023]
Abstract
CONTEXT Mutations in the gene encoding Mediator complex subunit MED12 are dominant drivers of uterine fibroids (UFs) in women of diverse racial and ethnic origins. Previously, we showed that UF-linked mutations in MED12 disrupt its ability to activate cyclin C-CDK8/19 in Mediator. However, validation of Mediator kinase disruption in the clinically relevant setting of MED12-mutant UFs is currently lacking. OBJECTIVE The objective of this study was twofold. First, to extend the ethnic distribution profile of MED12 mutations by establishing their frequency in UFs from Hispanic women of South Texas. Second, to examine the impact of MED12 mutations on Mediator kinase activity in patient-derived UFs. METHODS We screened 219 UFs from 76 women, including 170 tumors from 57 Hispanic patients, for MED12 exon 2 mutations, and further examined CDK8/19 activity in Mediator complexes immunoprecipitated from MED12 mutation-negative and MED12 mutation-positive UFs. RESULTS MED12 exon 2 mutations in UFs from Hispanic women are somatic in nature, predominantly monoallelic, and occur at high frequency (54.1%). We identified a minimal cyclin C-CDK8 activation domain on MED12 spanning amino acids 15 through 80 that includes all recorded UF-linked mutations in MED12, suggesting that disruption of Mediator kinase activity is a principal biochemical defect arising from these pathogenic alterations. Analysis of Mediator complexes recovered from patient UFs confirmed this, revealing that Mediator kinase activity is selectively impaired in MED12-mutant UFs. CONCLUSIONS MED12 mutations are important drivers of UF formation in Hispanic women of South Texas. MED12 mutations disrupt Mediator kinase activity, implicating altered CDK8/19 function in UF pathogenesis.
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Affiliation(s)
- Min Ju Park
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Hailian Shen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Nam Hee Kim
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Fangjian Gao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Courtney Failor
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Jennifer F Knudtson
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Jessica McLaughlin
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sunil K Halder
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Tuomas A Heikkinen
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Pia Vahteristo
- Research Programs Unit, Genome-Scale Biology Research Program and Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Robert S Schenken
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
- Correspondence and Reprint Requests: Thomas G. Boyer, PhD, Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, Mail Code 8257, San Antonio, Texas 78229. E-mail:
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