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Enhancer RNA: biogenesis, function, and regulation. Essays Biochem 2021; 64:883-894. [PMID: 33034351 DOI: 10.1042/ebc20200014] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
Enhancers are noncoding DNA elements that are present upstream or downstream of a gene to control its spatial and temporal expression. Specific histone modifications, such as monomethylation on histone H3 lysine 4 (H3K4me1) and H3K27ac, have been widely used to assign enhancer regions in mammalian genomes. In recent years, emerging evidence suggests that active enhancers are bidirectionally transcribed to produce enhancer RNAs (eRNAs). This finding not only adds a new reliable feature to define enhancers but also raises a fundamental question of how eRNAs function to activate transcription. Although some believe that eRNAs are merely transcriptional byproducts, many studies have demonstrated that eRNAs execute crucial tasks in regulating chromatin conformation and transcription activation. In this review, we summarize the current understanding of eRNAs from their biogenesis, functions, and regulation to their pathological significance. Additionally, we discuss the challenges and possible mechanisms of eRNAs in regulated transcription.
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Mushimiyimana I, Tomas Bosch V, Niskanen H, Downes NL, Moreau PR, Hartigan K, Ylä-Herttuala S, Laham-Karam N, Kaikkonen MU. Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells. Mol Cell Biol 2021; 41:e0059420. [PMID: 33875575 PMCID: PMC8224232 DOI: 10.1128/mcb.00594-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/29/2020] [Accepted: 04/03/2021] [Indexed: 12/26/2022] Open
Abstract
Vascular endothelial growth factors (VEGFs) are best known as key regulators of angiogenesis and lymphangiogenesis. Although VEGFs have been promising therapeutic targets for various cardiovascular diseases, their regulatory landscape in endothelial cells remains elusive. Several studies have highlighted the involvement of noncoding RNAs (ncRNAs) in the modulation of VEGF expression. In this study, we investigated the role of two classes of ncRNAs, long ncRNAs (lncRNAs) and enhancer RNAs (eRNAs), in the transcriptional regulation of VEGFA and VEGFC. By integrating genome-wide global run-on sequencing (GRO-Seq) and chromosome conformation capture (Hi-C) data, we identified putative lncRNAs and eRNAs associated with VEGFA and VEGFC genes in endothelial cells. A subset of the identified putative enhancers demonstrated regulatory activity in a reporter assay. Importantly, we demonstrate that deletion of enhancers and lncRNAs by CRISPR/Cas9 promoted significant changes in VEGFA and VEGFC expression. Transcriptome sequencing (RNA-Seq) data from lncRNA deletions showed downstream factors implicated in VEGFA- and VEGFC-linked pathways, such as angiogenesis and lymphangiogenesis, suggesting functional roles for these lncRNAs. Our study uncovers novel lncRNAs and eRNAs regulating VEGFA and VEGFC that can be targeted to modulate the expression of these important molecules in endothelial cells.
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Affiliation(s)
- Isidore Mushimiyimana
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vanesa Tomas Bosch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nicholas L. Downes
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pierre R. Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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Wang Y, Cen A, Yang Y, Ye H, Li J, Liu S, Zhao L. miR-181a, delivered by hypoxic PTC-secreted exosomes, inhibits DACT2 by downregulating MLL3, leading to YAP-VEGF-mediated angiogenesis. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:610-621. [PMID: 33898109 PMCID: PMC8054101 DOI: 10.1016/j.omtn.2021.02.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Papillary thyroid cancer (PTC) is the most common type of thyroid cancer, and angiogenesis plays critical roles in its recurrence and metastasis. In this study, we investigated the effects of hypoxia-induced exosomal microRNA-181 (miR-181a) from PTC on tumor growth and angiogenesis. Thyroid-cancer-related differentially expressed miR-181a was identified by microarray-based analysis in the Gene Expression Omnibus (GEO) database. We validated that miR-181a was highly expressed in PTC cells and even more so in cells cultured under hypoxic conditions, which also augmented exosome secretion from PTC cells. Exosomes extracted from PTC cells with manipulated miR-181a and mixed-lineage leukemia 3 (MLL3) were subjected to normoxic or hypoxic conditions. Human umbilical vein endothelial cells (HUVECs) were transfected with miR-181a inhibitor/mimic or small interfering RNA (siRNA)-MLL3 or treated with exosomes from hypoxic PTC cells. Hypoxic exosomal miR-181a delivery promoted proliferation and capillary-like network formation in HUVECs. Mechanistically, miR-181a targeted and inhibited MLL3. Furthermore, miR-181a downregulated DACT2 and upregulated YAP and vascular endothelial growth factor (VEGF). Further, hypoxic exosomal miR-181a induced angiogenesis and tumor growth in vivo, which was reversed by hypoxic exosomal miR-181a inhibitor. In conclusion, exosomal miR-181a from hypoxic PTC cells promotes tumor angiogenesis and growth through MLL3 and DACT2 downregulation, as well as VEGF upregulation.
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Affiliation(s)
- Yingxue Wang
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, Guangzhou 510630, P.R. China
| | - Aiying Cen
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, Guangzhou 510630, P.R. China
| | - Yuxian Yang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Huilin Ye
- Department of Hepatopancreatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou 510120, P.R. China
| | - Jiaying Li
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, Guangzhou 510630, P.R. China
| | - Shiliang Liu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Lei Zhao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
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Wang R, Tang Q. Current Advances on the Important Roles of Enhancer RNAs in Molecular Pathways of Cancer. Int J Mol Sci 2021; 22:5640. [PMID: 34073237 PMCID: PMC8198447 DOI: 10.3390/ijms22115640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 01/08/2023] Open
Abstract
Enhancers are critical genomic elements that can cooperate with promoters to regulate gene transcription in both normal and cancer cells. Recent studies reveal that enhancer regions are transcribed to produce a class of noncoding RNAs referred to as enhancer RNAs (eRNAs). Emerging evidence shows that eRNAs play important roles in enhancer activation and enhancer-driven gene regulation, and the expression of eRNAs may be a critical factor in tumorigenesis. The important roles of eRNAs in cancer signaling pathways are also gradually unveiled, providing a new insight into cancer therapy. Here, we review the roles of eRNAs in regulating cancer signaling pathways and discuss the potential of eRNA-targeted therapy for human cancers.
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Affiliation(s)
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
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Adhikary S, Roy S, Chacon J, Gadad SS, Das C. Implications of Enhancer Transcription and eRNAs in Cancer. Cancer Res 2021; 81:4174-4182. [PMID: 34016622 DOI: 10.1158/0008-5472.can-20-4010] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Despite extensive progress in developing anticancer therapies, therapy resistance remains a major challenge that promotes disease relapse. The changes that lead to therapy resistance can be intrinsically present or may be initiated during treatment. Genetic and epigenetic heterogeneity in tumors make it more challenging to deal with therapy resistance. Recent advances in genome-wide analyses have revealed that the deregulation of distal gene regulatory elements, such as enhancers, appears in several pathophysiological conditions, including cancer. Beyond the conventional function of enhancers in recruiting transcription factors to gene promoters, enhancer elements are also transcribed into noncoding RNAs known as enhancer RNAs (eRNA). Accumulating evidence suggests that uncontrolled enhancer activity with aberrant eRNA expression promotes oncogenesis. Interestingly, tissue-specific, transcribed eRNAs from active enhancers can serve as potential therapeutic targets or biomarkers in several cancer types. This review provides a comprehensive overview of the mechanisms of enhancer transcription and eRNAs as well as their potential roles in cancer and drug resistance.
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Affiliation(s)
- Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jessica Chacon
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas
| | - Shrikanth S Gadad
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas. .,Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India. .,Homi Bhaba National Institute, Mumbai, Maharashtra, India
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Anshabo AT, Milne R, Wang S, Albrecht H. CDK9: A Comprehensive Review of Its Biology, and Its Role as a Potential Target for Anti-Cancer Agents. Front Oncol 2021; 11:678559. [PMID: 34041038 PMCID: PMC8143439 DOI: 10.3389/fonc.2021.678559] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are proteins pivotal to a wide range of cellular functions, most importantly cell division and transcription, and their dysregulations have been implicated as prominent drivers of tumorigenesis. Besides the well-established role of cell cycle CDKs in cancer, the involvement of transcriptional CDKs has been confirmed more recently. Most cancers overtly employ CDKs that serve as key regulators of transcription (e.g., CDK9) for a continuous production of short-lived gene products that maintain their survival. As such, dysregulation of the CDK9 pathway has been observed in various hematological and solid malignancies, making it a valuable anticancer target. This therapeutic potential has been utilized for the discovery of CDK9 inhibitors, some of which have entered human clinical trials. This review provides a comprehensive discussion on the structure and biology of CDK9, its role in solid and hematological cancers, and an updated review of the available inhibitors currently being investigated in preclinical and clinical settings.
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Affiliation(s)
- Abel Tesfaye Anshabo
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Robert Milne
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Shudong Wang
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Hugo Albrecht
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
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FOXP4-AS1 is a favorable prognostic-related enhancer RNA in ovarian cancer. Biosci Rep 2021; 41:228414. [PMID: 33870423 PMCID: PMC8150160 DOI: 10.1042/bsr20204008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/22/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Ovarian cancer (OV) is the main cause of deaths worldwide in female reproductive system malignancies. Enhancer RNAs (eRNAs) are derived from the transcription of enhancers and has attracted increasing attention in cancers recently. However, the biological functions and clinical significance of eRNAs in OV have not been well described presently. We used an integrated data analysis to identify prognostic-related eRNAs in OV. Tissue-specific enhancer-derived RNAs and their regulating genes were considered as putative eRNA–target pairs using the computational pipeline PreSTIGE. Gene expression profiles and clinical data of OV and 32 other cancer types were obtained from the UCSC Xena platform. Altogether, 71 eRNAs candidates showed significant correlation with overall survival (OS) of OV samples (Kaplan–Meier log-rank test, P<0.05). Among which, 23 were determined to be correlated with their potential target genes (Spearman’s r > 0.3, P<0.001). It was found that among the 23 prognostic-related eRNAs, the expression of forkhead box P4 antisense RNA 1 (FOXP4-AS1) had the highest positive correlation with its predicted target gene FOXP4 (Spearman’s r = 0.61). Moreover, the results were further validated by RT-qPCR analysis in an independent OV cohort. Our results suggested the eRNA FOXP4-AS1 expression index may be a favorable independent prognostic biomarker candidate in OV.
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Yang M, Lee JH, Zhang Z, De La Rosa R, Bi M, Tan Y, Liao Y, Hong J, Du B, Wu Y, Scheirer J, Hong T, Li W, Fei T, Hsieh CL, Liu Z, Li W, Rosenfeld MG, Xu K. Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor. Cell Rep 2021; 31:107803. [PMID: 32579929 PMCID: PMC8564762 DOI: 10.1016/j.celrep.2020.107803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/26/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
The function of enhancer RNAs (eRNAs) in transcriptional regulation remains obscure. By analyzing the genome-wide nascent transcript profiles in breast cancer cells, we identify a special group of eRNAs that are essential for estrogen-induced transcriptional repression. Using eRNAs of TM4SF1 and EFEMP1 as the paradigms, we find that these RNA molecules not only stabilize promoter-enhancer interactions but also recruit liganded estrogen receptor α (ERα) to particular enhancer regions, facilitate the formation of a functional transcriptional complex, and cause gene silencing. Interestingly, ERα is shown to directly bind with eRNAs by its DNA-binding domain. These eRNAs help with the formation of a specific ERα-centered transcriptional complex and promote the association of the histone demethylase KDM2A, which dismisses RNA polymerase II from designated enhancers and suppresses the transcription of target genes. Our work demonstrates a complete mechanism underlying the action of eRNAs in modulating and refining the locus-specific transcriptional program. Yang et al. identified a group of eRNAs that are essential for estrogen-induced transcriptional repression by assisting with the chromatin recruitment of ERα through binding to its DNA-binding domain and facilitating the interaction of ERα with its cofactors, which leads to the dismissal of RNA polymerase II.
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Affiliation(s)
- Mei Yang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ji Hoon Lee
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Richard De La Rosa
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Mingjun Bi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yuliang Tan
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, CA 92093, USA
| | - Yiji Liao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Juyeong Hong
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Baowen Du
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yanming Wu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jessica Scheirer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tao Hong
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Division of Biostatistics, Dan L. Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Chen-Lin Hsieh
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Zhijie Liu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX 77030, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, CA 92093, USA
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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Uddin F, Srivastava M. Characterization of transcripts emanating from enhancer Eβ of the murine TCRβ locus. FEBS Open Bio 2021; 11:1014-1028. [PMID: 33426767 PMCID: PMC8016127 DOI: 10.1002/2211-5463.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 11/08/2022] Open
Abstract
Enhancers are well established as critical regulators of gene expression, but the mechanisms underlying the molecular basis of their specificity and activity are only partly understood. One of the most exciting recent observations is the discovery of enhancer RNA (eRNA), a class of noncoding RNAs derived from enhancer regions. Transcription of developmentally regulated enhancers has been observed to be associated with their active state. The nature of transcripts (eRNA) and their functional attributes are diverse and context dependent. The majority of eRNA are nonpolyadenylated and present in low abundance owing to their low stability, and may represent transcriptional noise. However, some eRNAs have been reported to be reasonably long and stable, are enriched in nuclei, exhibit tissue-specific expression and may contribute to enhancer function. Transcription of enhancers has been postulated to mediate enhancer function through either the act of transcription or via the transcribed RNA per se and is a useful feature to be analysed to understand mechanisms underlying enhancer activity. Enhancer Eβ at the murine TCRβ locus has been reported to exhibit enhanced occupancy of RNA polymerase II in developing thymocytes. Here, we investigated the transcriptional potential of Eβ in developing thymocytes and detected overlapping bidirectional transcripts at Eβ ranging between 0.7 and 1.7 kb. These noncoding transcripts are capped, polyadenylated, nuclear and expressed specifically in thymocytes. Delineation of these characteristics is important to further investigate their functional roles in mediating enhancer activity.
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Affiliation(s)
- Faizan Uddin
- Epigenetics Research Laboratory, National Institute of Immunology, New Delhi, India
| | - Madhulika Srivastava
- Epigenetics Research Laboratory, National Institute of Immunology, New Delhi, India
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Pan CW, Wen S, Chen L, Wei Y, Niu Y, Zhao Y. Functional roles of antisense enhancer RNA for promoting prostate cancer progression. Am J Cancer Res 2021; 11:1780-1794. [PMID: 33408781 PMCID: PMC7778597 DOI: 10.7150/thno.51931] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Rationale: Enhancer RNA (eRNA) bi-directionally expresses from enhancer region and sense eRNA regulates adjacent mRNA in cis and in trans. However, it has remained unclear whether antisense eRNAs in different direction are functional or merely a reflection of enhancer activation. Methods: Strand-specific, ribosome-minus RNA sequencing (RNA-seq) were performed in AR positive prostate cancer cells. RNA-seq, GRO-seq, ChIP-seq, 4C-seq and DNA-methylation-seq that published in our and other labs were re-analyzed to define bi-directional enhancer RNA and DNA methylation regions. Molecular mechanisms were demonstrated by 3C, ChIP, ChIRP, CLIP, RT-PCR and western blot assays. The biological functions of antisense-eRNA were assessed using mice xenograft model and RT-PCR analysis in human tissues. Results: In this study, we identified that antisense eRNA was regulated by androgen receptor (AR) activity in prostate cancer cells. Antisense eRNA negatively regulated antisense ncRNA in AR-related target genes' loci, through recruiting DNMT1 on the antisense enhancer in the gene-ending regions and elevating DNA methylation. Importantly, the chromatin exhibited a double looping manner that facilitated sense-eRNA to promoter and antisense-eRNA to gene-ending region in cis. Depletion of antisense eRNA impaired its neighbor mRNA expression, cancer growth and invasion. The expressions of antisense eRNA were correlated with biochemical recurrence and clinical marker PSA's levels in patients' tissues. Conclusions: The findings indicated that antisense eRNA was a functional RNA and may be a novel target that when suppressed improved prostate cancer therapy and diagnosis. New chromatin interaction among enhancer, promoter and gene-ending region might provide new insight into the spatiotemporal mechanism of the gene transcription and acting of bi-directional eRNAs.
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Wen S, Wei Y, Zen C, Xiong W, Niu Y, Zhao Y. Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine. Mol Cancer 2020; 19:171. [PMID: 33308223 PMCID: PMC7733260 DOI: 10.1186/s12943-020-01293-4] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) is the most prevalent messenger RNA modification in mammalian cells. However, the disease relevant function of m6A on specific oncogenic long non-coding RNAs (ncRNAs) is not well understood. Methods We analyzed the m6A status using patients samples and bone metastatic PDXs. Through m6A high-throughput sequencing, we identified the m6A sites on NEAT1–1 in prostate bone metastatic PDXs. Mass spec assay showed interaction among NEAT1–1, CYCLINL1 and CDK19. RNA EMSA, RNA pull-down, mutagenesis, CLIP, western blot, ChIP and ChIRP assays were used to investigate the molecular mechanisms underlying the functions of m6A on NEAT1–1. Loss-of function and rescued experiments were executed to detect the biological roles of m6A on NEAT1–1 in the PDX cell phenotypes in vivo. Results In this study, we identified 4 credible m6A sites on long ncRNA NEAT1–1. High m6A level of NEAT1–1 was related to bone metastasis of prostate cancer and m6A level of NEAT1–1 was a powerful predictor of eventual death. Transcribed NEAT1–1 served as a bridge to facility the binding between CYCLINL1 and CDK19 and promoted the Pol II ser2 phosphorylation. Importantly, depletion of NEAT1–1or decreased m6A of NEAT1–1 impaired Pol II Ser-2p level in the promoter of RUNX2. Overexpression of NEAT1–1 induced cancer cell metastasis to lung and bone; xenograft growth and shortened the survival of mice, but NEAT1–1 with m6A site mutation failed to do these. Conclusion Collectively, the findings indicate that m6A on ncRNA NEAT1–1 takes critical role in regulating Pol II ser2 phosphorylation and may be novel specific target for bone metastasis cancer therapy and diagnosis. New complex CYCLINL1/CDK19/NEAT1–1 might provide new insight into the potential mechanism of the pathogenesis and development of bone metastatic prostate cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-020-01293-4.
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Affiliation(s)
- Simeng Wen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China
| | - Yulei Wei
- Department of Gynecology and Obstetrics, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Chong Zen
- Department of Urology, Central South University, Changsha, 410011, China
| | - Wei Xiong
- Department of Urology, Central South University, Changsha, 410011, China
| | - Yuanjie Niu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China.
| | - Yu Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
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Aprile M, Katopodi V, Leucci E, Costa V. LncRNAs in Cancer: From garbage to Junk. Cancers (Basel) 2020; 12:E3220. [PMID: 33142861 PMCID: PMC7692075 DOI: 10.3390/cancers12113220] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing-based transcriptomics has significantly redefined the concept of genome complexity, leading to the identification of thousands of lncRNA genes identification of thousands of lncRNA genes whose products possess transcriptional and/or post-transcriptional regulatory functions that help to shape cell functionality and fate. Indeed, it is well-established now that lncRNAs play a key role in the regulation of gene expression through epigenetic and posttranscriptional mechanims. The rapid increase of studies reporting lncRNAs alteration in cancers has also highlighted their relevance for tumorigenesis. Herein we describe the most prominent examples of well-established lncRNAs having oncogenic and/or tumor suppressive activity. We also discuss how technical advances have provided new therapeutic strategies based on their targeting, and also report the challenges towards their use in the clinical settings.
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Affiliation(s)
- Marianna Aprile
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Valerio Costa
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
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Noncoding RNAs Set the Stage for RNA Polymerase II Transcription. Trends Genet 2020; 37:279-291. [PMID: 33046273 DOI: 10.1016/j.tig.2020.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022]
Abstract
Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional regulators. Understanding the mode of action of these non-protein regulators has been an intense area of research in recent years. Here, we describe how these ncRNAs influence key regulatory steps of the transcription process, to affect large numbers of genes. Through direct association with pol II or by modulating the activity of transcription or RNA processing factors, these regulatory RNAs perform critical roles in gene expression.
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64
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Aberrant activation of super enhancer and choline metabolism drive antiandrogen therapy resistance in prostate cancer. Oncogene 2020; 39:6556-6571. [PMID: 32917955 DOI: 10.1038/s41388-020-01456-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/20/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022]
Abstract
Next generation antiandrogens such as enzalutamide (Enz) are effective initially for the treatment of castration-resistant prostate cancer (CRPC). However, the disease often relapses and the underlying mechanisms remain elusive. By performing H3-lysine-27 acetylation (H3K27ac) ChIP-seq in Enz-resistant CRPC cells, we identified a group of super enhancers (SEs) that are abnormally activated in Enz-resistant CRPC cells and associated with enhanced transcription of a subset of tumor promoting genes such as CHPT1, which catalyzes phosphatidylcholine (PtdCho) synthesis and regulates choline metabolism. Increased CHPT1 conferred CRPC resistance to Enz in vitro and in mice. While androgen receptor (AR) primarily binds to a putative CHPT1 enhancer and mediates androgen-dependent expression of CHPT1 gene in Enz-sensitive prostate cancer cells, AR binds to a different enhancer within the CHPT1 SE locus and facilities androgen-independent expression of CHPT1 in Enz-resistant cells. We further identified a long-non coding RNA transcribed at CHPT1 enhancer (also known as enhancer RNA) that binds to the H3K27ac reader BRD4 and participates in regulating CHPT1 SE activity and CHPT1 gene expression. Our findings demonstrate that aberrantly activated SE upregulates CHPT1 expression and confers Enz resistance in CRPC, suggesting that SE-mediated expression of downstream effectors such as CHPT1 can be viable targets to overcome Enz resistance in PCa.
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65
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Hou TY, Kraus WL. Spirits in the Material World: Enhancer RNAs in Transcriptional Regulation. Trends Biochem Sci 2020; 46:138-153. [PMID: 32888773 DOI: 10.1016/j.tibs.2020.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
Responses to developmental and environmental cues depend on precise spatiotemporal control of gene transcription. Enhancers, which comprise DNA elements bound by regulatory proteins, can activate target genes in response to these external signals. Recent studies have shown that enhancers are transcribed to produce enhancer RNAs (eRNAs). Do eRNAs play a functional role in activating gene expression or are they non-functional byproducts of nearby transcription machinery? The unstable nature of eRNAs and over-reliance on knockdown approaches have made elucidating the possible functions of eRNAs challenging. We focus here on studies using cloned eRNAs to study their function as transcripts, revealing roles for eRNAs in enhancer-promoter looping, recruiting transcriptional machinery, and facilitating RNA polymerase pause-release to regulate gene expression.
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Affiliation(s)
- Tim Y Hou
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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66
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Erb HHH, Bodenbender J, Handle F, Diehl T, Donix L, Tsaur I, Gleave M, Haferkamp A, Huber J, Fuessel S, Juengel E, Culig Z, Thomas C. Assessment of STAT5 as a potential therapy target in enzalutamide-resistant prostate cancer. PLoS One 2020; 15:e0237248. [PMID: 32790723 PMCID: PMC7425943 DOI: 10.1371/journal.pone.0237248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/22/2020] [Indexed: 12/18/2022] Open
Abstract
Despite enzalutamide's efficacy in delaying the progression of metastatic castration-resistant prostate cancer (CRPC), resistance to this anti-androgen inevitably occurs. Several studies have revealed that the signal transducer and activator of transcription (STAT) 5 plays a role in tumour progression and development of drug resistance such as enzalutamide. Data mining revealed heterogeneous expression of STAT5 in enzalutamide-treated mCRPC patients and enzalutamide-resistant prostate cancer (PCa). Isobologram analysis revealed that the STAT5 inhibitor pimozide combined with enzalutamide has? additive and synergistic inhibitory effects on cell viability in the used models. Functional analysis with siRNA-mediated STAT5 knockdown yielded divergent results. The LNCaP-derived cell line MR49F could be resensitised to enzalutamide by siRNA-mediated STAT5b-knock-down. In contrast, neither STAT5a nor STAT5b knockdown resensitised enzalutamide-resistant LAPC4-EnzaR cells to enzalutamide. In conclusion, our results indicate that STAT5 may be a possible target in a subgroup of enzalutamide-resistant PCa. However, based on the data presented here, a general role of STAT5 in enzalutamide-resistance and its potential as a therapeutic target could not be shown.
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Affiliation(s)
- Holger H. H. Erb
- Department of Urology, Technische Universität Dresden, Dresden, Germany
| | - Julia Bodenbender
- Department of Urology and Pediatric Urology, University Medical Center Mainz, Mainz, Germany
| | - Florian Handle
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Tamara Diehl
- Department of Urology and Pediatric Urology, University Medical Center Mainz, Mainz, Germany
| | - Lukas Donix
- Department of Urology, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Igor Tsaur
- Department of Urology and Pediatric Urology, University Medical Center Mainz, Mainz, Germany
| | - Martin Gleave
- The Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Axel Haferkamp
- Department of Urology and Pediatric Urology, University Medical Center Mainz, Mainz, Germany
| | - Johannes Huber
- Department of Urology, Technische Universität Dresden, Dresden, Germany
| | - Susanne Fuessel
- Department of Urology, Technische Universität Dresden, Dresden, Germany
| | - Eva Juengel
- Department of Urology and Pediatric Urology, University Medical Center Mainz, Mainz, Germany
| | - Zoran Culig
- Experimental Urology, Department of Urology, University of Innsbruck, Innsbruck, Austria
| | - Christian Thomas
- Department of Urology, Technische Universität Dresden, Dresden, Germany
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67
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Patty BJ, Hainer SJ. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. BIOLOGY 2020; 9:E213. [PMID: 32784701 PMCID: PMC7465399 DOI: 10.3390/biology9080213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an important role in transcriptional regulation. Recent findings show that ncRNAs regulate nucleosome remodeler activities at many levels and that ncRNAs are regulatory targets of nucleosome remodelers. Further, a series of recent screens indicate this network of regulatory interactions is more expansive than previously appreciated. Here, we discuss currently described regulatory interactions between ncRNAs and nucleosome remodelers and contextualize their biological functions.
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Affiliation(s)
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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68
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Enhancer RNAs are an important regulatory layer of the epigenome. Nat Struct Mol Biol 2020; 27:521-528. [PMID: 32514177 DOI: 10.1038/s41594-020-0446-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 05/07/2020] [Indexed: 12/20/2022]
Abstract
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. Leading the charge in the RNA revolution is a class of ncRNAs that are synthesized at active enhancers, called enhancer RNAs (eRNAs). Here, we review recent insights into the biogenesis of eRNAs and the mechanisms underlying their multifaceted functions and consider how these findings could inform future investigations into enhancer transcription and eRNA function.
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69
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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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70
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Zhang M, Lai Y, Vasquez JL, James DI, Smith KM, Waddell ID, Ogilvie DJ, Liu Y, Agoulnik IU. Androgen Receptor and Poly(ADP-ribose) Glycohydrolase Inhibition Increases Efficiency of Androgen Ablation in Prostate Cancer Cells. Sci Rep 2020; 10:3836. [PMID: 32123273 PMCID: PMC7052214 DOI: 10.1038/s41598-020-60849-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
There is mounting evidence of androgen receptor signaling inducing genome instability and changing DNA repair capacity in prostate cancer cells. Expression of genes associated with base excision repair (BER) is increased with prostate cancer progression and correlates with poor prognosis. Poly(ADP-ribose) polymerase (PARP) and poly(ADP-ribose) glycohydrolase (PARG) are key enzymes in BER that elongate and degrade PAR polymers on target proteins. While PARP inhibitors have been tested in clinical trials and are a promising therapy for prostate cancer patients with TMPRSS2-ERG fusions and mutations in DNA repair genes, PARG inhibitors have not been evaluated. We show that PARG is a direct androgen receptor (AR) target gene. AR is recruited to the PARG locus and induces PARG expression. Androgen ablation combined with PARG inhibition synergistically reduces BER capacity in independently derived LNCaP and LAPC4 prostate cancer cell lines. A combination of PARG inhibition with androgen ablation or with the DNA damaging drug, temozolomide, significantly reduces cellular proliferation and increases DNA damage. PARG inhibition alters AR transcriptional output without changing AR protein levels. Thus, AR and PARG are engaged in reciprocal regulation suggesting that the success of androgen ablation therapy can be enhanced by PARG inhibition in prostate cancer patients.
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Affiliation(s)
- Manqi Zhang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, College of Arts, Sciences and Education, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Judy L Vasquez
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Dominic I James
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
| | - Kate M Smith
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
| | - Ian D Waddell
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
- CRL, Chesterford Research Park, CB10 1XL, Alderley Park, UK
| | - Donald J Ogilvie
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
| | - Yuan Liu
- Department of Chemistry and Biochemistry, College of Arts, Sciences and Education, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Irina U Agoulnik
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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71
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Lee JH, Xiong F, Li W. Enhancer RNAs in cancer: regulation, mechanisms and therapeutic potential. RNA Biol 2020; 17:1550-1559. [PMID: 31916476 DOI: 10.1080/15476286.2020.1712895] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enhancers are distal genomic elements critical for gene regulation and cell identify control during development and diseases. Many human cancers were found to associate with enhancer malfunction, due to genetic and epigenetic alterations, which in some cases directly drive tumour growth. Conventionally, enhancers are known to provide DNA binding motifs to recruit transcription factors (TFs) and to control target genes. However, recent progress found that most, if not all, active enhancers pervasively transcribe noncoding RNAs that are referred to as enhancer RNAs (eRNAs). Increasing evidence points to functional roles of at least a subset of eRNAs in gene regulation in both normal and cancer cells, adding new insights into the action mechanisms of enhancers. eRNA expression was observed to be widespread but also specific to tumour types and individual patients, serving as opportunities to exploit them as potential diagnosis markers or therapeutic targets. In this review, we discuss the brief history of eRNA research, their functional mechanisms and importance in cancer gene regulation, as well as their therapeutic and diagnostic values in cancer. We propose that further studies of eRNAs in cancer will offer a promising 'eRNA targeted therapy' for human cancer intervention.
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Affiliation(s)
- Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA.,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth , Houston, TX, USA
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72
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Zhao Y, Zhou J, He L, Li Y, Yuan J, Sun K, Chen X, Bao X, Esteban MA, Sun H, Wang H. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nat Commun 2019; 10:5787. [PMID: 31857580 PMCID: PMC6923398 DOI: 10.1038/s41467-019-13598-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Emerging evidence supports roles of enhancer RNAs (eRNAs) in regulating target gene. Here, we study eRNA regulation and function during skeletal myoblast differentiation. We provide a panoramic view of enhancer transcription and categorization of eRNAs. Master transcription factor MyoD is crucial in activating eRNA production. Super enhancer (se) generated seRNA-1 and -2 promote myogenic differentiation in vitro and in vivo. seRNA-1 regulates expression levels of two nearby genes, myoglobin (Mb) and apolipoprotein L6 (Apol6), by binding to heterogeneous nuclear ribonucleoprotein L (hnRNPL). A CAAA tract on seRNA-1 is essential in mediating seRNA-1/hnRNPL binding and function. Disruption of seRNA-1-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the Mb locus, in coincidence with the reduction of its transcription. Furthermore, analyses of hnRNPL binding transcriptome-wide reveal its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction represents a mechanism contributing to target mRNA activation.
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Affiliation(s)
- Yu Zhao
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518000, China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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73
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Rahnamoun H, Orozco P, Lauberth SM. The role of enhancer RNAs in epigenetic regulation of gene expression. Transcription 2019; 11:19-25. [PMID: 31823686 DOI: 10.1080/21541264.2019.1698934] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Since the discovery that enhancers can support transcription, the roles of enhancer RNAs have remained largely elusive. We identified that enhancer RNAs interact with and augment bromodomain engagement with acetylated chromatin. Here, we discuss our recent findings and the potential mechanisms underlying the regulation and functions of enhancer RNA-bromodomain associations.
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Affiliation(s)
- Homa Rahnamoun
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Paola Orozco
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Shannon M Lauberth
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
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74
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Lewis MW, Li S, Franco HL. Transcriptional control by enhancers and enhancer RNAs. Transcription 2019; 10:171-186. [PMID: 31791217 PMCID: PMC6948965 DOI: 10.1080/21541264.2019.1695492] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/02/2022] Open
Abstract
The regulation of gene expression is a fundamental cellular process and its misregulation is a key component of disease. Enhancers are one of the most salient regulatory elements in the genome and help orchestrate proper spatiotemporal gene expression during development, in homeostasis, and in response to signaling. Notably, molecular aberrations at enhancers, such as translocations and single nucleotide polymorphisms, are emerging as an important source of human variation and susceptibility to disease. Herein we discuss emerging paradigms addressing how genes are regulated by enhancers, common features of active enhancers, and how non-coding enhancer RNAs (eRNAs) can direct gene expression programs that underlie cellular phenotypes. We survey the current evidence, which suggests that eRNAs can bind to transcription factors, mediate enhancer-promoter interactions, influence RNA Pol II elongation, and act as decoys for repressive cofactors. Furthermore, we discuss current methodologies for the identification of eRNAs and novel approaches to elucidate their functions.
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Affiliation(s)
- Michael W. Lewis
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Shen Li
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hector L. Franco
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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75
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He Y, Lu J, Ye Z, Hao S, Wang L, Kohli M, Tindall DJ, Li B, Zhu R, Wang L, Huang H. Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer. Nucleic Acids Res 2019; 46:1895-1911. [PMID: 29309643 PMCID: PMC5829742 DOI: 10.1093/nar/gkx1306] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
Androgen receptor (AR) splice variants (ARVs) are implicated in development of castration-resistant prostate cancer (CRPC). Upregulation of ARVs often correlates with persistent AR activity after androgen deprivation therapy (ADT). However, the genomic and epigenomic characteristics of ARV-dependent cistrome and the disease relevance of ARV-mediated transcriptome remain elusive. Through integrated chromatin immunoprecipitation coupled sequencing (ChIP-seq) and RNA sequencing (RNA-seq) analysis, we identified ARV-preferential-binding sites (ARV-PBS) and a set of genes preferentially transactivated by ARVs in CRPC cells. ARVs preferentially bind to enhancers located in nucleosome-depleted regions harboring the full AR-response element (AREfull), while full-length AR (ARFL)-PBS are enhancers resided in closed chromatin regions containing the composite FOXA1-nnnn-AREhalf motif. ARV-PBS exclusively overlapped with AR binding sites in castration-resistant (CR) tumors in patients and ARV-preferentially activated genes were up-regulated in abiraterone-resistant patient specimens. Expression of ARV-PBS target genes, such as oncogene RAP2A and cell cycle gene E2F7, were significantly associated with castration resistance, poor survival and tumor progression. We uncover distinct genomic and epigenomic features of ARV-PBS, highlighting that ARVs are useful tools to depict AR-regulated oncogenic genome and epigenome landscapes in prostate cancer. Our data also suggest that the ARV-preferentially activated transcriptional program could be targeted for effective treatment of CRPC.
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Affiliation(s)
- Yundong He
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ji Lu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Siyuan Hao
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Manish Kohli
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Donald J Tindall
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Department of Urology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Benyi Li
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Runzhi Zhu
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA.,Center for Cell Therapy, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Department of Urology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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76
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Dysregulated Transcriptional Control in Prostate Cancer. Int J Mol Sci 2019; 20:ijms20122883. [PMID: 31200487 PMCID: PMC6627928 DOI: 10.3390/ijms20122883] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 12/24/2022] Open
Abstract
Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enhancer identified upstream of the androgen receptor (AR) gene. Super-enhancers are increasingly found to play important roles in aberrant oncogenic transcription. Several players involved in these processes are currently being evaluated as drug targets and may represent new vulnerabilities that can be exploited for prostate cancer treatment. They include factors involved in enhancer and super-enhancer function such as bromodomain proteins and cyclin-dependent kinases. In addition, non-coding RNAs with an important gene regulatory role are being explored. The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment paradigms for the benefit of patients.
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77
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Sharma NK. Exosomal packaging of trans-activation response element (TAR) RNA by HIV-1 infected cells: a pro-malignancy message delivery to cancer cells. Mol Biol Rep 2019; 46:3607-3612. [PMID: 30903574 DOI: 10.1007/s11033-019-04770-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/15/2019] [Indexed: 02/07/2023]
Abstract
Driven by the heterogeneous and complex nature of HIV-1 infection and tumors, the possibilities of viable cross-talk are facilitated by the intra-cellular and inter-cellular signaling regimens. There are evidences that support the clear role of exosomes containing TAR RNAs that are secreted by HIV-1 infected cells and these TAR RNA brings pro-growth and pro-survival effects upon cancer cells. Recently, the regulatory role of TAR RNAs in the intra-cellular signaling network is shown that augments cancer cells to achieve tremendous progression and malignancy. In this paper, author highlights the role of HIV-1 infected cells secreted exosomes containing TAR RNA in tumor hallmarks. Further, this paper provides future insights on new classes of cancer therapeutics centered on disrupting exosomes and TAR RNA.
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Affiliation(s)
- Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Department of Biotechnology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India.
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78
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Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023] Open
Abstract
Tight regulation of gene transcription is essential for normal development, tissue homeostasis, and disease-free survival. Enhancers are distal regulatory elements in the genome that provide specificity to gene expression programs and are frequently misregulated in cancer. Recent studies examined various enhancer-driven malignant dependencies and identified different approaches to specifically target these programs. In this review, we describe numerous features that make enhancers good transcriptional targets in cancer therapy and discuss different approaches to overcome enhancer perturbation. Interestingly, a number of approved therapeutic agents, such as cyclosporine, steroid hormones, and thiazolidinediones, actually function by affecting enhancer landscapes by directly targeting very specific transcription factor programs. More recently, a broader approach to targeting deregulated enhancer programs has been achieved via Bromodomain and Extraterminal (BET) inhibition or perturbation of transcription-related cyclin-dependent kinases (CDK). One challenge to enhancer-targeted therapy is proper patient stratification. We suggest that monitoring of enhancer RNA (eRNA) expression may serve as a unique biomarker of enhancer activity that can help to predict and monitor responsiveness to enhancer-targeted therapies. A more thorough investigation of cancer-specific enhancers and the underlying mechanisms of deregulation will pave the road for an effective utilization of enhancer modulators in a precision oncology approach to cancer treatment.
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Affiliation(s)
- Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
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79
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de Lara JCF, Arzate-Mejía RG, Recillas-Targa F. Enhancer RNAs: Insights Into Their Biological Role. Epigenet Insights 2019; 12:2516865719846093. [PMID: 31106290 PMCID: PMC6505235 DOI: 10.1177/2516865719846093] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/15/2022] Open
Abstract
Enhancers play a central role in the transcriptional regulation of metazoans. Almost a decade ago, the discovery of their pervasive transcription into noncoding RNAs, termed enhancer RNAs (eRNAs), opened a whole new field of study. The presence of eRNAs correlates with enhancer activity; however, whether they act as functional molecules remains controversial. Here we review direct experimental evidence supporting a functional role of eRNAs in transcription and provide a general pipeline that could help in the design of experimental approaches to investigate the function of eRNAs. We propose that induction of transcriptional activity at enhancers promotes an increase in its activity by an RNA-mediated titration of regulatory proteins that can impact different processes like chromatin accessibility or chromatin looping. In a few cases, transcripts originating from enhancers have acquired specific molecular functions to regulate gene expression. We speculate that these transcripts are either nonannotated long noncoding RNAs (lncRNAs) or are evolving toward functional lncRNAs. Further work will be needed to comprehend better the biological activity of these transcripts.
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Affiliation(s)
- Josué Cortés-Fernández de Lara
- Departamento de Genética Molecular, Instituto de
Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México,
México
| | - Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de
Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México,
México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de
Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México,
México
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80
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Stelloo S, Bergman AM, Zwart W. Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers. Endocr Relat Cancer 2019; 26:R267-R285. [PMID: 30865928 DOI: 10.1530/erc-19-0032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance. Genome-wide chromatin association studies revealed that transcriptional regulation by AR mainly depends on binding to distal regulatory enhancer elements that control gene expression through chromatin looping to gene promoters. Changes in the chromatin epigenetic landscape and DNA sequence can locally alter AR-DNA-binding capacity and consequently impact transcriptional output and disease outcome. The vast majority of reports describing AR chromatin interactions have been limited to cell lines, identifying numerous other factors and interacting transcription factors that impact AR chromatin interactions. Do these factors also impact AR cistromics - the genome-wide chromatin-binding landscape of AR - in vivo? Recent technological advances now enable researchers to identify AR chromatin-binding sites and their target genes in human specimens. In this review, we provide an overview of the different factors that influence AR chromatin binding in prostate cancer specimens, which is complemented with knowledge from cell line studies. Finally, we discuss novel perspectives on studying AR cistromics in clinical samples.
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Affiliation(s)
- Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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81
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Bunch H, Choe H, Kim J, Jo DS, Jeon S, Lee S, Cho DH, Kang K. P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes. Front Genet 2019; 10:342. [PMID: 31068966 PMCID: PMC6491683 DOI: 10.3389/fgene.2019.00342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/29/2019] [Indexed: 01/16/2023] Open
Abstract
Many non-coding RNAs (ncRNAs) serve as regulatory molecules in various physiological pathways, including gene expression in mammalian cells. Distinct from protein-coding RNA expression, ncRNA expression is regulated solely by transcription and RNA processing/stability. It is thus important to understand transcriptional regulation in ncRNA genes but is yet to be known completely. Previously, we identified that a subset of mammalian ncRNA genes is transcriptionally regulated by RNA polymerase II (Pol II) promoter-proximal pausing and in a tissue-specific manner. In this study, human ncRNA genes that are expressed in the early G1 phase, termed immediate early ncRNA genes, were monitored to assess the function of positive transcription elongation factor b (P-TEFb), a master Pol II pausing regulator for protein-coding genes, in ncRNA transcription. Our findings indicate that the expression of many ncRNA genes is induced in the G0–G1 transition and regulated by P-TEFb. Interestingly, a biphasic characteristic of P-TEFb-dependent transcription of serum responsive ncRNA genes was observed: Pol II carboxyl-terminal domain phosphorylated at serine 2 (S2) was largely increased in the transcription start site (TSS, -300 to +300) whereas overall, it was decreased in the gene body (GB, > +350) upon chemical inhibition of P-TEFb. In addition, the three representative, immediate early ncRNAs, whose expression is dependent on P-TEFb, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), nuclear enriched abundant transcript 1 (NEAT1), and X-inactive specific transcript (XIST), were further analyzed for determining P-TEFb association. Taken together, our data suggest that transcriptional activation of many human ncRNAs utilizes the pausing and releasing of Pol II, and that the regulatory mechanism of transcriptional elongation in these genes requires the function of P-TEFb. Furthermore, we propose that ncRNA and mRNA transcription are regulated by similar mechanisms while P-TEFb inhibition unexpectedly increases S2 Pol II phosphorylation in the TSSs in many ncRNA genes. One Sentence Summary: P-TEFb regulates Pol II phosphorylation for transcriptional activation in many stimulus-inducible ncRNA genes.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Hyeseung Choe
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Jongbum Kim
- Department of Transcriptome & Epigenome, Macrogen Incorporated, Seoul, South Korea
| | - Doo Sin Jo
- Institute of Life Science and Biotechnology, College of Natural Science, Kyungpook National University, Daegu, South Korea
| | - Soyeon Jeon
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Sanghwa Lee
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Dong-Hyung Cho
- Department of Life Science, College of Natural Science, Kyungpook National University, Daegu, South Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, South Korea
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82
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Bidaux G, Le Nézet C, Pisfil MG, Henry M, Furlan A, Bensaude O, Vandenbunder B, Héliot L. FRET Image Correlation Spectroscopy Reveals RNAPII-Independent P-TEFb Recruitment on Chromatin. Biophys J 2019; 114:522-533. [PMID: 29414698 DOI: 10.1016/j.bpj.2017.11.3783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/15/2022] Open
Abstract
Biochemical studies have revealed that the RNA Polymerase II (RNAPII) pause release is triggered by phosphorylation of the transcription machinery by the positive transcription elongation factor b (P-TEFb). However, there are no direct report that P-TEFb and RNA polymerase II interact in single living cells and the biophysical mechanisms mediating this association are still unclear. Förster resonance energy transfer (FRET) detects molecular interactions at the subcellular level. Time domain fluorescence lifetime imaging provides an accurate quantification of FRET efficiency, EFRET, because it is fluorochrome concentration-independent and insensitive to fluorescence bleed-through. However, the way FRET signal is usually analyzed does not provide information about the areas where protein-protein interactions take place. In this work, we developed a method, dubbed FRET image correlation spectroscopy (FICS), which relied on FRET fluorescence lifetime imaging image acquisition and image correlation spectroscopy of EFRET clusters to quantify the spatial distribution of interaction clusters in the nucleus. The combination of high content FRET microscopy with batch image analysis allowed a robust statistical analysis. By applying FICS, we characterized the area and density of interaction clusters between P-TEFb and RNAPII or histone H2A in single living cells. The FICS method applied to cells expressing genetically engineered mutated proteins confirmed that the histidine-rich domain of P-TEFb is required for its interaction with RNAPII. Furthermore, it demonstrated that P-TEFb was also located in close vicinity to histone H2A, independently of its interactions with RNAPII. These results support the hypothesis that P-TEFb dynamics on chromatin regulate its recruitment on RNAPII.
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Affiliation(s)
- Gabriel Bidaux
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France.
| | - Corentin Le Nézet
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France
| | - Mariano Gonzalez Pisfil
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France
| | - Mélanie Henry
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France
| | - Alessandro Furlan
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France
| | - Oliver Bensaude
- S-2 Génomique Fonctionnelle, IBENS, CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, Paris, France
| | - Bernard Vandenbunder
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France
| | - Laurent Héliot
- CNRS UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, University Lille, Lille, France.
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83
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Mao R, Wu Y, Ming Y, Xu Y, Wang S, Chen X, Wang X, Fan Y. Enhancer RNAs: a missing regulatory layer in gene transcription. SCIENCE CHINA-LIFE SCIENCES 2018; 62:905-912. [PMID: 30593613 DOI: 10.1007/s11427-017-9370-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/01/2018] [Indexed: 01/12/2023]
Abstract
Enhancers and super-enhancers exert indispensable roles in maintaining cell identity through spatiotemporally regulating gene transcription. Meanwhile, active enhancers and super-enhancers also produce transcripts termed enhancer RNAs (eRNAs) from their DNA elements. Although enhancers have been identified for more than 30 years, widespread transcription from enhancers are just discovered by genome-wide sequencing and considered as the key to understand longstanding questions in gene transcription. RNA-transcribed enhancers are marked by histone modifications such as H3K4m1/2 and H3K27Ac, and enriched with transcription regulatory factors such as LDTFs, P300, CBP, BRD4 and MED1. Those regulatory factors might constitute a Mega-Trans-like complex to potently activate enhancers. Compared to mRNAs, eRNAs are quite unstable and play roles at local. Functionally, it has been shown that eRNAs promote formation of enhancer-promoter loops. Several studies also demonstrated that eRNAs help the binding of RNA polymerase II (RNAPII) or transition of paused RNAPII by de-association of the negative elongation factor (NELF) complex. Nevertheless, these proposed mechanisms are not universally accepted and still under controversy. Here, we comprehensively summarize the reported findings and make perspectives for future exploration. We also believe that super-enhancer derived RNAs (seRNAs) might be informative to understand the nature of super-enhancers.
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Affiliation(s)
- Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yuanyuan Wu
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yue Ming
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yuanpei Xu
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Shouyan Wang
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Xia Chen
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China.
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China.
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84
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Xiong W, Deng H, Huang C, Zen C, Jian C, Ye K, Zhong Z, Zhao X, Zhu L. MLL3 enhances the transcription of PD-L1 and regulates anti-tumor immunity. Biochim Biophys Acta Mol Basis Dis 2018; 1865:454-463. [PMID: 30385408 DOI: 10.1016/j.bbadis.2018.10.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/13/2018] [Accepted: 10/26/2018] [Indexed: 12/23/2022]
Abstract
Tumor cells utilize the overexpression of the programmed death-1 ligand 1(PD-L1) to escape T-cell controlled immune-surveillance. The clinical therapy that dilapidates PD1 or PD-L1-mediated cancer tolerance has pushed out the need to uncover the molecular regulation of PD-L1 overexpression in the tumor cell. In this study, we identify histone methyltransferase mixed-lineage leukemia protein 3 (MLL3) as a critical regulator of PD-L1 in prostate cancer cells. MLL3 and PD-L1 were highly expressed in the metastatic cancer tissues, compared to the primary cancer tissues. Furthermore, their expressions were highly correlated in the cancer tissues in the databases of TCGA and Xiangya Hospital. We found that MLL3 bound to the enhancer of PD-L1. Depletion of MLL3 decreased the binding level of H3K4me1 in the enhancer of PD-L1 and Pol II Ser-5p in the promoter of PD-L1. Importantly, MLL3 depletion impaired the mouse xenograft growth and decreased the response to PD-L1 antibody treatment in mice. The findings extend the understanding of the biology regulation of PD-L1 transcription and identify the histone writer MLL3 in an important immune checkpoint, and give prominence to a hidden therapeutic target to conquer immune evasion by tumor cells.
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Affiliation(s)
- Wei Xiong
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Huanghao Deng
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Changkun Huang
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Chong Zen
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Chengzhu Jian
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Kun Ye
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Zhaohui Zhong
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Xiaokun Zhao
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Liang Zhu
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China.
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85
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Liu Y, Ding M, Liao X, Gao Q, He A, Liu B, Hu K, Xie H, Zhou Q, Zhan H, Liu Y, Huang W, Mei H. High expression of enhancer RNA MARC1 or its activation by DHT is associated with the malignant behavior in bladder cancer. Exp Cell Res 2018; 370:303-311. [PMID: 29964053 DOI: 10.1016/j.yexcr.2018.06.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/18/2018] [Accepted: 06/27/2018] [Indexed: 12/14/2022]
Abstract
Enhancer RNAs (eRNAs), a subclass of noncoding RNA from enhancers, have biological functions in gene expression. However, their potential role in bladder cancer (BCa) remains largely unknown. The present study investigated the functional role of androgen-associated androgen receptor (AR) mediated-eRNA MARC1 (eMARC1) in BCa progression. Cell proliferation, migration, and apoptosis of BCa cell lines (5637 and T24) with different eMARC1 expression levels or treated with 5α-dehydrotestosterone (DHT) were investigated. In the current study, we discovered that eMARC1 was highly expressed in BCa tissues and cell lines, and eMARC1 overexpression promoted the progression of BCa cells, while knockdown of eMARC1 suppressed tumorigenesis. DHT treatment significantly elevated eMARC1 expression levels, which also facilitated cell proliferation, motility, and inhibited cell apoptosis. We further found that eMARC1 silencing impaired the androgenic effect of DHT in BCa cells. These results suggested that eMARC1 exerted its effects on BCa cell progression, and DHT promoted bladder cancer progression by activating eMARC1.
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Affiliation(s)
- Yuhan Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Mengting Ding
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China; Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China
| | - Xinhui Liao
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Qunjun Gao
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China; Departmentof Urology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 511436, China
| | - Anbang He
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Baoer Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Kun Hu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China; Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China
| | - Haibiao Xie
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Qun Zhou
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China; Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China
| | - Hengji Zhan
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China.
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China.
| | - Hongbing Mei
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China.
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86
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Ding M, Liu Y, Li J, Yao L, Liao X, Xie H, Yang K, Zhou Q, Liu Y, Huang W, Cai Z. Oestrogen promotes tumorigenesis of bladder cancer by inducing the enhancer RNA-eGREB1. J Cell Mol Med 2018; 22:5919-5927. [PMID: 30252203 PMCID: PMC6237589 DOI: 10.1111/jcmm.13861] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/27/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
In recent years, studies have shown that enhancer RNAs (eRNAs) can be transcribed from enhancers. Increasing evidence has revealed that eRNAs play critical roles in the development of various cancers. Oestrogen‐associated eRNAs are closely related to breast cancer. In view of the gender differences in bladder cancer (BCa), we suppose that oestrogen‐associated eRNAs are also involved in tumorigenesis of BCa. In our study, we first demonstrated that eGREB1 derived from the enhancer of an oestrogen‐responsive gene—GREB1 was up‐regulated in BCa tissues, and the expression level of eGREB1 is positively associated with the histological grade and TNM stage of BCa. Knockdown of eGREB1 by CRISPR‐Cas13a could inhibit cell proliferation, migration and invasion and induce apoptosis in BCa cells T24 and 5637. Besides, we exhibited the promoting effect of oestrogen on BCa cells. What's more, down‐regulation of eGREB1 could improve the malignant biological characteristics of BCa cells induced by oestrogen. In conclusion, our data indicated that eGREB1 plays oncogenic role and oestrogen may promote the occurrence and progression of BCa by inducing eGREB1 production. Our findings provide new insights into the prevention of BCa and develop a novel therapeutic target for the treatment of BCa.
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Affiliation(s)
- Mengting Ding
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen, China.,Anhui Medical University, Hefei, China
| | - Yuhan Liu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jianfa Li
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Xinhui Liao
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Haibiao Xie
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Kang Yang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,University of South China, Hengyang, China
| | - Qun Zhou
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen, China.,Anhui Medical University, Hefei, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiming Cai
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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87
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Fagnocchi L, Poli V, Zippo A. Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity. Cell Mol Life Sci 2018; 75:2537-2555. [PMID: 29691590 PMCID: PMC11105402 DOI: 10.1007/s00018-018-2820-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022]
Abstract
Cancer heterogeneity arises during tumor progression as a consequence of genetic insults, environmental cues, and reversible changes in the epigenetic state, favoring tumor cell plasticity. The role of enhancer reprogramming is emerging as a relevant field in cancer biology as it supports adaptation of cancer cells to those environmental changes encountered during tumor progression and metastasis seeding. In this review, we describe the cancer-related alterations that drive oncogenic enhancer activity, leading to dysregulated transcriptional programs. We discuss the molecular mechanisms of both cis- and trans-factors in overriding the regulatory circuits that maintain cell-type specificity and imposing an alternative, de-regulated enhancer activity in cancer cells. We further comment on the increasing evidence which implicates stress response and aging-signaling pathways in the enhancer landscape reprogramming during tumorigenesis. Finally, we focus on the potential therapeutic implications of these enhancer-mediated subverted transcriptional programs, putting particular emphasis on the lack of information regarding tumor progression and the metastatic outgrowth, which still remain the major cause of mortality related to cancer.
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Affiliation(s)
- Luca Fagnocchi
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
| | - Vittoria Poli
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alessio Zippo
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, 20122, Milan, Italy.
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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88
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Ding M, Liu Y, Liao X, Zhan H, Liu Y, Huang W. Enhancer RNAs (eRNAs): New Insights into Gene Transcription and Disease Treatment. J Cancer 2018; 9:2334-2340. [PMID: 30026829 PMCID: PMC6036709 DOI: 10.7150/jca.25829] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/30/2018] [Indexed: 12/23/2022] Open
Abstract
Enhancers are cis-acting elements that have the ability to increase the expression of target genes. Recent studies have shown that enhancers can act as transcriptional units for the production of enhancer RNAs (eRNAs), which are hallmarks of activity enhancers and are involved in the regulation of gene transcription. The in-depth study of eRNAs is of great significance for us to better understand enhancer function and transcriptional regulation in various diseases. Therefore, eRNAs may be a potential therapeutic target for diseases. Here, we review the current knowledge of the characteristics of eRNAs, the molecular mechanisms of eRNAs action, as well as diseases related to dysregulation of eRNAs.
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Affiliation(s)
- Mengting Ding
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China.,Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Yuhan Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China.,Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Xinhui Liao
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Hengji Zhan
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China.,Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
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89
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Current Advances on the Important Roles of Enhancer RNAs in Gene Regulation and Cancer. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2405351. [PMID: 29951530 PMCID: PMC5987348 DOI: 10.1155/2018/2405351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 12/27/2022]
Abstract
Revealing the gene regulation networks governing cancer initiation and development is necessary while it remains uncompleted. In recent years, enhancers have been reported to be widely transcribed, resulting in the generation of enhancer RNAs (eRNAs). Previous studies have reported that eRNAs are a subclass of long noncoding RNAs (lncRNAs), which play a critical role in gene regulation and cancer development. These eRNAs can promote enhancer-promoter (E-P) looping formation by binding to other protein factors or propel expression of downstream protein-coding gene. In this review, we have focused on the characteristics of eRNAs and illustrated the biological function and potential mechanism of eRNAs in regulating gene expression and cancer development.
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90
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Gao WW, Xiao RQ, Zhang WJ, Hu YR, Peng BL, Li WJ, He YH, Shen HF, Ding JC, Huang QX, Ye TY, Li Y, Liu ZY, Ding R, Rosenfeld MG, Liu W. JMJD6 Licenses ERα-Dependent Enhancer and Coding Gene Activation by Modulating the Recruitment of the CARM1/MED12 Co-activator Complex. Mol Cell 2018; 70:340-357.e8. [PMID: 29628309 PMCID: PMC6258263 DOI: 10.1016/j.molcel.2018.03.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 02/12/2018] [Accepted: 03/02/2018] [Indexed: 12/18/2022]
Abstract
Whereas the actions of enhancers in gene transcriptional regulation are well established, roles of JmjC-domain-containing proteins in mediating enhancer activation remain poorly understood. Here, we report that recruitment of the JmjC-domain-containing protein 6 (JMJD6) to estrogen receptor alpha (ERα)-bound active enhancers is required for RNA polymerase II recruitment and enhancer RNA production on enhancers, resulting in transcriptional pause release of cognate estrogen target genes. JMJD6 is found to interact with MED12 in the mediator complex to regulate its recruitment. Unexpectedly, JMJD6 is necessary for MED12 to interact with CARM1, which methylates MED12 at multiple arginine sites and regulates its chromatin binding. Consistent with its role in transcriptional activation, JMJD6 is required for estrogen/ERα-induced breast cancer cell growth and tumorigenesis. Our data have uncovered a critical regulator of estrogen/ERα-induced enhancer coding gene activation and breast cancer cell potency, providing a potential therapeutic target of ER-positive breast cancers.
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Affiliation(s)
- Wei-Wei Gao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Rong-Quan Xiao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Wen-Juan Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yi-Ren Hu
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing-Ling Peng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Wen-Juan Li
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yao-Hui He
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Hai-Feng Shen
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jian-Cheng Ding
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Qi-Xuan Huang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Tian-Yi Ye
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Ying Li
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Zhi-Ying Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Rong Ding
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
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91
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Zhao J, Zhao Y, Wang L, Zhang J, Karnes RJ, Kohli M, Wang G, Huang H. Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer. Oncotarget 2018; 7:38551-38565. [PMID: 27221037 PMCID: PMC5122410 DOI: 10.18632/oncotarget.9535] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/02/2016] [Indexed: 12/17/2022] Open
Abstract
Enzalutamide is a second-generation anti-androgen for treatment of castration-resistant prostate cancer (CPRC). It prolongs survival of CRPC patients, but its overall survival benefit is relatively modest (4.8 months) and by 24 months most patients progress on enzalutamide. To date, however, the molecular mechanisms underlying enzalutamide resistance remain elusive. Herein, we report enzalutamide treatment-induced alterations of androgen receptor (AR)-regulated enhancer RNAs (AR-eRNAs) and their roles in enzalutamide-resistant growth and survival of CRPC cells. AR chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) and RNA-seq analyses revealed that 188 and 227 AR-eRNAs were differentially expressed in enzalutamide-resistant LNCaP and C4-2 cells, respectively. The AR-eRNAs upregulated in C4-2 cells and downregulated in LNCaP cells were selected through meta-analysis. Expression of AR-eRNAs and related mRNAs in the loci of FTO, LUZP2, MARC1 and NCAM2 were further verified by real-time RT-PCR. Silencing of LUZP2 inhibited, but silencing of MARC1 increased the growth of enzalutamide-resistant C4-2 cells. Intriguingly, meta-analysis showed that expression of LUZP2 mRNA increased in primary tumors compared to normal prostate tissues, but decreased again in metastatic CRPC. Our findings suggest that eRNA alteration profiling is a viable new approach to identify functional gene loci that may not only contribute to enzalutamide-resistant growth of CRPC, but also serve as new targets for CRPC therapy.
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Affiliation(s)
- Jingwen Zhao
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Yu Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - R Jeffrey Karnes
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Manish Kohli
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Guixia Wang
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Department of Urology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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92
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Li Y, Liu M, Chen LF, Chen R. P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II. Transcription 2018; 9:88-94. [PMID: 28102758 PMCID: PMC5834220 DOI: 10.1080/21541264.2017.1281864] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 12/26/2022] Open
Abstract
The release of a paused Pol II depends on the recruitment of P-TEFb. Recent studies showed that both active P-TEFb and inactive P-TEFb (7SK snRNP) can be recruited to the promoter regions of global genes by different mechanisms. Here, we summarize the recent advances on these distinct recruitment mechanisms.
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Affiliation(s)
- You Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lin-Feng Chen
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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93
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Oncogenic non-coding RNA NEAT1 promotes the prostate cancer cell growth through the SRC3/IGF1R/AKT pathway. Int J Biochem Cell Biol 2018; 94:125-132. [DOI: 10.1016/j.biocel.2017.12.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/15/2022]
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94
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Madabhushi R, Kim TK. Emerging themes in neuronal activity-dependent gene expression. Mol Cell Neurosci 2017; 87:27-34. [PMID: 29254824 DOI: 10.1016/j.mcn.2017.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/23/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022] Open
Abstract
In this review, we attempt to discuss emerging themes in the regulation of neuronal activity-regulated genes, focusing primarily on an important subset of immediate-early genes. We first discuss earlier studies that have illuminated the role of cis-acting elements within the promoters of immediate-early genes, the corresponding transcription factors that bind these elements, and the roles of major activity-regulated signaling pathways. However, our emphasis is on new studies that have revealed an important role for epigenetic and topological mechanisms, including enhancer-promoter interactions, enhancer RNAs (eRNAs), and activity-induced DNA breaks, that have emerged as important factors that govern the temporal dynamics of activity-induced gene transcription.
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Affiliation(s)
- Ram Madabhushi
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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95
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RNA polymerase II pausing and transcriptional regulation of the HSP70 expression. Eur J Cell Biol 2017; 96:739-745. [DOI: 10.1016/j.ejcb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 08/16/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022] Open
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96
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Liu X, Gao Y, Ye H, Gerrin S, Ma F, Wu Y, Zhang T, Russo J, Cai C, Yuan X, Liu J, Chen S, Balk SP. Positive feedback loop mediated by protein phosphatase 1α mobilization of P-TEFb and basal CDK1 drives androgen receptor in prostate cancer. Nucleic Acids Res 2017; 45:3738-3751. [PMID: 28062857 PMCID: PMC5397168 DOI: 10.1093/nar/gkw1291] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/25/2016] [Indexed: 01/05/2023] Open
Abstract
P-TEFb (CDK9/cyclin T) plays a central role in androgen receptor (AR)-mediated transactivation by phosphorylating both RNA polymerase 2 complex proteins and AR at S81. CDK9 dephosphorylation mobilizes P-TEFb from an inhibitory 7SK ribonucleoprotein complex, but mechanisms targeting phosphatases to P-TEFb are unclear. We show that AR recruits protein phosphatase 1α (PP1α), resulting in P-TEFb mobilization and CDK9-mediated AR S81 phosphorylation. This increased pS81 enhances p300 recruitment, histone acetylation, BRD4 binding and subsequent further recruitment of P-TEFb, generating a positive feedback loop that sustains transcription. AR S81 is also phosphorylated by CDK1, and blocking basal CDK1-mediated S81 phosphorylation markedly suppresses AR activity and initiation of this positive feedback loop. Finally, androgen-independent AR activity in castration-resistant prostate cancer (CRPC) cells is driven by increased CDK1-mediated S81 phosphorylation. Collectively these findings reveal a mechanism involving PP1α, CDK9 and CDK1 that is used by AR to initiate and sustain P-TEFb activity, which may be exploited to drive AR in CRPC.
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Affiliation(s)
- Xiaming Liu
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yanfei Gao
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - HuiHui Ye
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sean Gerrin
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Fen Ma
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yiming Wu
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Tengfei Zhang
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Russo
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Changmeng Cai
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Xin Yuan
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shaoyong Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Steven P Balk
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
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97
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Angus SP, Zawistowski JS, Johnson GL. Epigenetic Mechanisms Regulating Adaptive Responses to Targeted Kinase Inhibitors in Cancer. Annu Rev Pharmacol Toxicol 2017; 58:209-229. [PMID: 28934561 DOI: 10.1146/annurev-pharmtox-010617-052954] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although targeted inhibition of oncogenic kinase drivers has achieved remarkable patient responses in many cancers, the development of resistance has remained a significant challenge. Numerous mechanisms have been identified, including the acquisition of gatekeeper mutations, activating pathway mutations, and copy number loss or gain of the driver or alternate nodes. These changes have prompted the development of kinase inhibitors with increased selectivity, use of second-line therapeutics to overcome primary resistance, and combination treatment to forestall resistance. In addition to genomic resistance mechanisms, adaptive transcriptional and signaling responses seen in tumors are gaining appreciation as alterations that lead to a phenotypic state change-often observed as an epithelial-to-mesenchymal shift or reversion to a cancer stem cell-like phenotype underpinned by remodeling of the epigenetic landscape. This epigenomic modulation driving cell state change is multifaceted and includes modulation of repressive and activating histone modifications, DNA methylation, enhancer remodeling, and noncoding RNA species. Consequently, the combination of kinase inhibitors with drugs targeting components of the transcriptional machinery and histone-modifying enzymes has shown promise in preclinical and clinical studies. Here, we review mechanisms of resistance to kinase inhibition in cancer, with special emphasis on the rewired kinome and transcriptional signaling networks and the potential vulnerabilities that may be exploited to overcome these adaptive signaling changes.
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Affiliation(s)
- Steven P Angus
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; , ,
| | - Jon S Zawistowski
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; , ,
| | - Gary L Johnson
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; , ,
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98
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Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT-mTORC1 activation. Nat Med 2017; 23:1055-1062. [PMID: 28805822 PMCID: PMC5653288 DOI: 10.1038/nm.4379] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/29/2017] [Indexed: 12/19/2022]
Abstract
Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising anticancer therapies. The gene encoding the E3 ubiquitin ligase substrate-binding adaptor speckle-type POZ protein (SPOP) is the most frequently mutated in primary prostate cancer. Here we demonstrate that wild-type SPOP binds to and induces ubiquitination and proteasomal degradation of BET proteins (BRD2, BRD3 and BRD4) by recognizing a degron motif common among them. In contrast, prostate cancer-associated SPOP mutants show impaired binding to BET proteins, resulting in decreased proteasomal degradation and accumulation of these proteins in prostate cancer cell lines and patient specimens and causing resistance to BET inhibitors. Transcriptome and BRD4 cistrome analyses reveal enhanced expression of the GTPase RAC1 and cholesterol-biosynthesis-associated genes together with activation of AKT-mTORC1 signaling as a consequence of BRD4 stabilization. Our data show that resistance to BET inhibitors in SPOP-mutant prostate cancer can be overcome by combination with AKT inhibitors and further support the evaluation of SPOP mutations as biomarkers to guide BET-inhibitor-oriented therapy in patients with prostate cancer.
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99
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Tosetti V, Sassone J, Ferri ALM, Taiana M, Bedini G, Nava S, Brenna G, Di Resta C, Pareyson D, Di Giulio AM, Carelli S, Parati EA, Gorio A. Transcriptional role of androgen receptor in the expression of long non-coding RNA Sox2OT in neurogenesis. PLoS One 2017; 12:e0180579. [PMID: 28704421 PMCID: PMC5507538 DOI: 10.1371/journal.pone.0180579] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/16/2017] [Indexed: 11/19/2022] Open
Abstract
The complex architecture of adult brain derives from tightly regulated migration and differentiation of precursor cells generated during embryonic neurogenesis. Changes at transcriptional level of genes that regulate migration and differentiation may lead to neurodevelopmental disorders. Androgen receptor (AR) is a transcription factor that is already expressed during early embryonic days. However, AR role in the regulation of gene expression at early embryonic stage is yet to be determinate. Long non-coding RNA (lncRNA) Sox2 overlapping transcript (Sox2OT) plays a crucial role in gene expression control during development but its transcriptional regulation is still to be clearly defined. Here, using Bicalutamide in order to pharmacologically inactivated AR, we investigated whether AR participates in the regulation of the transcription of the lncRNASox2OTat early embryonic stage. We identified a new DNA binding region upstream of Sox2 locus containing three androgen response elements (ARE), and found that AR binds such a sequence in embryonic neural stem cells and in mouse embryonic brain. Our data suggest that through this binding, AR can promote the RNA polymerase II dependent transcription of Sox2OT. Our findings also suggest that AR participates in embryonic neurogenesis through transcriptional control of the long non-coding RNA Sox2OT.
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Affiliation(s)
- Valentina Tosetti
- Department of Cerebrovascular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Jenny Sassone
- Vita-Salute University and San Raffaele Scientific Institute, Division of Neuroscience, Milan, Italy
| | - Anna L. M. Ferri
- Department of Cerebrovascular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Michela Taiana
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Gloria Bedini
- Department of Cerebrovascular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Sara Nava
- Cell Therapy Production Unit, Laboratory of Cellular Neurobiology, Cerebrovascular Unit, and Unit of Molecular Neuro-Oncology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Greta Brenna
- Biostatistician Service Clinical Research—Scientific Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Di Resta
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Pareyson
- Neurological Rare Diseases of Adulthood Unit, Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Anna Maria Di Giulio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
- Pediatric Clinical Research Center Fondazione Romeo e Enrica Invernizzi, University of Milan, Milan, Italy
| | - Stephana Carelli
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Eugenio A. Parati
- Department of Cerebrovascular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Alfredo Gorio
- Laboratory of Pharmacology, Department of Health Sciences, University of Milan, Milan, Italy
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Ko JY, Oh S, Yoo KH. Functional Enhancers As Master Regulators of Tissue-Specific Gene Regulation and Cancer Development. Mol Cells 2017; 40:169-177. [PMID: 28359147 PMCID: PMC5386954 DOI: 10.14348/molcells.2017.0033] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
Tissue-specific transcription is critical for normal development, and abnormalities causing undesirable gene expression may lead to diseases such as cancer. Such highly organized transcription is controlled by enhancers with specific DNA sequences recognized by transcription factors. Enhancers are associated with chromatin modifications that are distinct epigenetic features in a tissue-specific manner. Recently, super-enhancers comprising enhancer clusters co-occupied by lineage-specific factors have been identified in diverse cell types such as adipocytes, hair follicle stem cells, and mammary epithelial cells. In addition, noncoding RNAs, named eRNAs, are synthesized at super-enhancer regions before their target genes are transcribed. Many functional studies revealed that super-enhancers and eRNAs are essential for the regulation of tissue-specific gene expression. In this review, we summarize recent findings concerning enhancer function in tissue-specific gene regulation and cancer development.
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Affiliation(s)
- Je Yeong Ko
- Molecular Medicine Laboratory, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Sumin Oh
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
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