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Du J, Liu Y, Sun J, Yao E, Xu J, Wu X, Xu L, Zhou M, Yang G, Jiang X. ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis. Nat Commun 2024; 15:5994. [PMID: 39013863 PMCID: PMC11252270 DOI: 10.1038/s41467-024-50225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/02/2024] [Indexed: 07/18/2024] Open
Abstract
Chromatin remodeler ARID1A regulates gene transcription by modulating nucleosome positioning and chromatin accessibility. While ARID1A-mediated stage and lineage-restricted gene regulation during cell fate canalization remains unresolved. Using osteoclastogenesis as a model, we show that ARID1A transcriptionally safeguards the osteoclast (OC) fate canalization during proliferation-differentiation switching at single-cell resolution. Notably, ARID1A is indispensable for the transcriptional apparatus condensates formation with coactivator BRD4/lineage-specifying transcription factor (TF) PU.1 at Nfatc1 super-enhancer during safeguarding the OC fate canalization. Besides, the antagonist function between ARID1A-cBAF and BRD9-ncBAF complex during osteoclastogenesis has been validated with in vitro assay and compound mutant mouse model. Furthermore, the antagonistic function of ARID1A-"accelerator" and BRD9-"brake" both depend on coactivator BRD4-"clutch" during osteoclastogenesis. Overall, these results uncover sophisticated cooperation between chromatin remodeler ARID1A, coactivator, and lineage-specifying TF at super-enhancer of lineage master TF in a condensate manner, and antagonist between distinct BAF complexes in the proper and balanced cell fate canalization.
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Affiliation(s)
- Jiahui Du
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Yili Liu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Jinrui Sun
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Enhui Yao
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Jingyi Xu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Xiaolin Wu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Ling Xu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Mingliang Zhou
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Guangzheng Yang
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China.
| | - Xinquan Jiang
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China.
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Voutsadakis IA. Targeting super-enhancer activity for colorectal cancer therapy. Am J Transl Res 2024; 16:700-719. [PMID: 38586095 PMCID: PMC10994804 DOI: 10.62347/qkhb5897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/28/2024] [Indexed: 04/09/2024]
Abstract
In addition to genetic variants and copy number alterations, epigenetic deregulation of oncogenes and tumor suppressors is a major contributor in cancer development and propagation. Regulatory elements for gene transcription regulation can be found in promoters which are located in the vicinity of transcription start sites but also at a distance, in enhancer sites, brought to interact with proximal sites when occupied by enhancer protein complexes. These sites provide most of the specific regulatory sequences recognized by transcription factors. A sub-set of enhancers characterized by a longer structure and stronger activity, called super-enhancers, are critical for the expression of specific genes, usually associated with individual cell type identity and function. Super-enhancers show deregulation in cancer, which may have profound repercussions for cancer cell survival and response to therapy. Dysfunction of super-enhancers may result from multiple mechanisms that include changes in their sequence, alterations in the topological neighborhoods where they belong, and alterations in the proteins that mediate their function, such as transcription factors and epigenetic modifiers. These can become potential targets for therapeutic interventions. Genes that are targets of super-enhancers are cell and cancer type specific and could also be of interest for therapeutic targeting. In colorectal cancer, a super-enhancer regulated and over-expressed oncogene is MYC, under the influence of the WNT/β-catenin pathway. Identification and targeting of additional oncogenes regulated by super-enhancers in colorectal cancer may pave the way for combination therapies targeting the super-enhancer machinery and signal transduction pathways that regulate the specific transcription factors operative on them.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area HospitalSault Ste. Marie, ON, Canada
- Division of Clinical Sciences, Section of Internal Medicine, Northern Ontario School of MedicineSudbury, ON, Canada
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Cai H, Liang J, Jiang Y, Wang Z, Li H, Wang W, Wang C, Hou J. KLF7 regulates super-enhancer-driven IGF2BP2 overexpression to promote the progression of head and neck squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:69. [PMID: 38443991 PMCID: PMC10913600 DOI: 10.1186/s13046-024-02996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Head and neck squamous carcinoma (HNSCC) is known for its high aggressiveness and susceptibility to cervical lymph node metastasis, which greatly contributes to its poor prognosis. During tumorigenesis, many types of cancer cells acquire oncogenic super-enhancers (SEs) that drive the overexpression of oncogenes, thereby maintaining malignant progression. This study aimed to identify and validate the role of oncogenic SE-associated genes in the malignant progression of HNSCC. METHODS We identified HNSCC cell-specific SE-associated genes through H3K27Ac ChIP-seq and overlapped them with HNSCC-associated genes obtained from The Cancer Genome Atlas (TCGA) dataset and Gene Expression Omnibus (GEO) datasets using weighted gene coexpression network analysis (WGCNA) to identify hub genes. The expression of IGF2BP2 and KLF7 in HNSCC was detected using clinical samples. To determine the biological role of IGF2BP2, we performed CCK-8, colony formation assay, Transwell migration assay, invasion assay, and orthotopic xenograft model experiments. Furthermore, we utilized a CRISPR/Cas9 gene-editing system, small-molecule inhibitors, ChIP-qPCR, and dual-luciferase reporter assays to investigate the molecular mechanisms of IGF2BP2 and its upstream transcription factors. RESULTS Our study identified IGF2BP2 as a hub SE-associated gene that exhibited aberrant expression in HNSCC tissues. Increased expression of IGF2BP2 was observed to be linked with malignant progression and unfavorable prognosis in HNSCC patients. Both in vitro and in vivo experiments confirmed that IGF2BP2 promotes the tumorigenicity and metastasis of HNSCC by promoting cell proliferation, migration, and invasion. Mechanistically, the IGF2BP2-SE region displayed enrichment for H3K27Ac, BRD4, and MED1, which led to the inhibition of IGF2BP2 transcription and expression through deactivation of the SE-associated transcriptional program. Additionally, KLF7 was found to induce the transcription of IGF2BP2 and directly bind to its promoter and SE regions. Moreover, the abundance of KLF7 exhibited a positive correlation with the abundance of IGF2BP2 in HNSCC. Patients with high expression of both KLF7 and IGF2BP2 showed poorer prognosis. Lastly, we demonstrated that the small molecule inhibitor JQ1, targeting BRD4, attenuated the proliferation and metastatic abilities of HNSCC cells. CONCLUSIONS Our study reveals the critical role of IGF2BP2 overexpression mediated by SE and KLF7 in promoting HNSCC progression. Targeting SE-associated transcriptional programs may represent a potential therapeutic strategy in managing HNSCC.
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Affiliation(s)
- Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yaoqi Jiang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ziyi Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Hongyu Li
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wenjin Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Cheng Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China.
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China.
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China.
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Rojhannezhad M, Soltani BM, Vasei M, Ghorbanmehr N, Mowla SJ. Functional analysis of a putative HER2-associated expressed enhancer, Her2-Enhancer1, in breast cancer cells. Sci Rep 2023; 13:19516. [PMID: 37945744 PMCID: PMC10636096 DOI: 10.1038/s41598-023-46460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
HER-2/neu (HER2) is a member of the epidermal growth factor receptors family, encoding a protein with tyrosine kinase activity. Following the gene amplification or increased HER2 transcription, carcinogenesis has been observed in some cancers. Genetic and epigenetic changes occurring in enhancer sequences can deeply affect the expression and transcriptional regulation of downstream genes, which can cause some physiological and pathological changes, including tumor progression. A therapeutic approach that directly targets the genomic sequence alterations is of high importance, with low side effects on healthy cells. Here, we employed the CRISPR/Cas9 method to genetically knockout an expressed putative enhancer (GH17J039694; we coined it as Her2-Enhancer1) located within the HER2 gene, 17q12: 39,694,339-39,697,219 (UCSC-hg38). We then investigated the potential regulatory effect of Her2-Enhancer1 on HER2 and HER2-interacting genes. To evaluate the cis and trans effects of Her2-Enhancer1, genetic manipulation of this region was performed in HER2-positive and -negative breast cancer cells. Our bioinformatics and real-time PCR data revealed that this putative enhancer region is indeed expressed, and acts as an expressed enhancer. Further functional analysis on edited and unedited cells revealed a significant alteration in the expression of HER2 variants, as well as some other target genes of HER2. Moreover, the apoptosis rate was considerably elevated within the edited cells. As we expected, Western blot analysis confirmed a reduction in protein levels of HER2, GRB7, the gene interacting with HER2, and P-AKT in the PI3K/AKT pathway. Altogether, our findings revealed an enhancer regulatory role for Her2-Enhancer1 on HER2 and HER2-interacting genes; and that this region has a potential for targeted therapy of HER2-positive cancers.
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Affiliation(s)
- Mahdieh Rojhannezhad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahram M Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Vasei
- Cell-Based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nassim Ghorbanmehr
- Biotechnology Department, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Wu Q, Tao X, Luo Y, Zheng S, Lin N, Xie X. A novel super-enhancer-related gene signature predicts prognosis and immune microenvironment for breast cancer. BMC Cancer 2023; 23:776. [PMID: 37596527 PMCID: PMC10439574 DOI: 10.1186/s12885-023-11241-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND This study targeted at developing a robust, prognostic signature based on super-enhancer-related genes (SERGs) to reveal survival prognosis and immune microenvironment of breast cancer. METHODS RNA-sequencing data of breast cancer were retrieved from The Cancer Genome Atlas (TCGA), 1069 patients of which were randomly assigned into training or testing set in 1:1 ratio. SERGs were downloaded from Super-Enhancer Database (SEdb). After which, a SERGs signature was established based on the training set, with its prognostic value further validated in the testing set. Subsequently, we identified the potential function enrichment and tumor immune infiltration of the model. Moreover, in vitro experiments were completed to further explore the biological functions of ZIC2 gene (one of the risk genes in the prognostic model) in breast cancer. RESULTS A risk score system of prognostic value was constructed with 6 SERGs (ZIC2, NFE2, FOXJ1, KLF15, POU3F2 and SPIB) to find patients in high-risk group with significantly worse prognosis in both training and testing sets. In addition, a multivariate regression was established via integrating the 6 genes with age and N stage, indicating well performance by calibration, time-dependent receiver operating characteristic (ROC) analysis and decision curve analysis (DCA). Further analysis demonstrated that tumor-associated pathological processes and pathways were significantly enriched in the high-risk group. In general, the novel SERGs signature could be applied to screen breast cancer with immunosuppressive microenvironment for the risk score was negatively correlated with ESTIMATE score, tumor-infiltration lymphocytes (such as CD4 + and CD8 + T cell), immune checkpoints and chemotactic factors. Furthermore, down-regulation of ZIC2 gene expression inhibited the cell viability, cellular migration and cell cycle of breast cancer cells. CONCLUSIONS The novel SERGs signature could predict the prognosis of breast cancer; and SERGs might serve as potential therapeutic targets for breast cancer.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xuan Tao
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yang Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China
| | - Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, Fujian, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
- Department of Gastrointestinal Surgery, The 900th Hospital of Joint Logistics Support Forces of Chinese PLA, Fuzhou, Fujian, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China.
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
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Wang M, Chen Q, Wang S, Xie H, Liu J, Huang R, Xiang Y, Jiang Y, Tian D, Bian E. Super-enhancers complexes zoom in transcription in cancer. J Exp Clin Cancer Res 2023; 42:183. [PMID: 37501079 PMCID: PMC10375641 DOI: 10.1186/s13046-023-02763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and noncoding regulatory element function. Therefore, they play central roles in the treatment of cancer. Here, we review the structural characteristics, organization, identification, and functions of SEs and the underlying molecular mechanism by which SEs drive oncogenic transcription in tumor cells. We then summarize abnormal SE complexes, SE-driven coding genes, and noncoding RNAs involved in tumor development. In summary, we believe that SEs show great potential as biomarkers and therapeutic targets.
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Affiliation(s)
- MengTing Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - QingYang Chen
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - ShuJie Wang
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - RuiXiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YuFei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YanYi Jiang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
| | - DaSheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - ErBao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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7
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Tang ZC, Qu Q, Teng XQ, Zhuang HH, Xu WX, Qu J. Bibliometric analysis of evolutionary trends and hotspots of super-enhancers in cancer. Front Pharmacol 2023; 14:1192855. [PMID: 37576806 PMCID: PMC10415222 DOI: 10.3389/fphar.2023.1192855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: In the past decade, super-enhancer (SE) has become a research hotspot with increasing attention on cancer occurrence, development, and prognosis. To illustrate the hotspots of SE in cancer research and its evolutionary tendency, bibliometric analysis was carried out for this topic. Methods: Literature published before Dec 31, 2022, in WOSCC, was systematically classified, and Citespace, bibliometric.com/app, and GraphPad Prism analyzed the data. Results: After screening out inappropriate documents and duplicate data, 911 publications were selected for further bibliometric analysis. The top five research areas were Oncology (257, 28.211%), Cell Biology (210, 23.052%), Biochemistry Molecular Biology (209, 22.942%), Science Technology Other Topics (138, 15.148%), and Genetics Heredity (132, 14.490%). The United States of America (United States) has the highest number of documents (462, 50.71%), followed by China (303, 33.26%). Among the most productive institutions, four of which are from the United States and one from Singapore, the National University of Singapore. Harvard Medical School (7.68%) has the highest percentage of articles. Young, Richard A, with 32 publications, ranks first in the number of articles. The top three authors came from Whitehead Institute for Biomedical Research as a research team. More than two-thirds of the research are supported by the National Institutes of Health of the United States (337, 37.654%) and the United States Department of Health Human Services (337, 37.654%). And "super enhancer" (525), "cell identity" (258), "expression" (223), "cancer" (205), and "transcription factor" (193) account for the top 5 occurrence keywords. Discussion: Since 2013, SE and cancer related publications have shown a rapid growth trend. The United States continues to play a leading role in this field, as the top literature numbers, affiliations, funding agencies, and authors were all from the United States, followed by China and European countries. A high degree of active cooperation is evident among a multitude of countries. The role of SEs in cell identity, gene transcription, expression, and inhibition, as well as the relationship between SEs and TFs, and the selective inhibition of SEs, have received much attention, suggesting that they are hot issues for research.
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Affiliation(s)
- Zhen-Chu Tang
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Hospital Management, Central South University, Changsha, China
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Xin-Qi Teng
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Hai-Hui Zhuang
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Wei-Xin Xu
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
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8
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Li G, Kang Y, Feng X, Wang G, Yuan Y, Li Z, Du L, Xu B. Dynamic changes of enhancer and super enhancer landscape in degenerated nucleus pulposus cells. Life Sci Alliance 2023; 6:e202201854. [PMID: 37012048 PMCID: PMC10070812 DOI: 10.26508/lsa.202201854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Inflammatory cascade and extracellular matrix remodeling have been identified as pivotal pathological factors in the progression of intervertebral disc degeneration (IDD), but the mechanisms underlying the aberrant activation of transcription during nucleus pulposus (NP) cell degeneration remain elusive. Super-enhancers (SEs) are large clusters of adjacent lone enhancers, which control expression modes of cellular fate and pathogenic genes. Here, we showed that SEs underwent tremendous remodeling during NP cell degeneration and that SE-related transcripts were most abundant in inflammatory cascade and extracellular matrix remodeling processes. Inhibition of cyclin-dependent kinase 7, a transcriptional kinase-mediated transcriptional initiation in trans-acting SE complex, constricted the transcription of inflammatory cascades, and extracellular matrix remodeling-related genes such as IL1β and MMP3 in NP cells, meanwhile, also restrained the transcription of Mmp16, Tnfrsf21, and Il11ra1 to retard IDD in rats. In summary, our findings clarify SEs control the transcription of genes associated with inflammatory cascade and extracellular matrix remodeling during NP cell degeneration and identify inhibition of the cyclin-dependent kinase 7, required for SE-mediated transcriptional activation, as a therapeutic option for IDD.
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Affiliation(s)
- Guowang Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Yuxiang Kang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Guohua Wang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Yue Yuan
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Zhenhua Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
| | - Lilong Du
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
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9
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Yang Z, Liu Y, Cheng Q, Chen T. Targeting super enhancers for liver disease: a review. PeerJ 2023; 11:e14780. [PMID: 36726725 PMCID: PMC9885865 DOI: 10.7717/peerj.14780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
Background Super enhancers (SEs) refer to the ultralong regions of a gene accompanied by multiple transcription factors and cofactors and strongly drive the expression of cell-type-related genes. Recent studies have demonstrated that SEs play crucial roles in regulating gene expression related to cell cycle progression and transcription. Aberrant activation of SEs is closely related to the occurrence and development of liver disease. Liver disease, especially liver failure and hepatocellular carcinoma (HCC), constitutes a major class of diseases that seriously endanger human health. Currently, therapeutic strategies targeting SEs can dramatically prevent disease progression and improve the prognosis of animal models. The associated new approaches to the treatment of related liver disease are relatively new and need systematic elaboration. Objectives In this review, we elaborate on the features of SEs and discuss their function in liver disease. Additionally, we review their application prospects in clinical practice in the future. The article would be of interest to hepatologists, molecular biologists, clinicians, and all those concerned with targeted therapy and prognosis of liver disease. Methodology We searched three bibliographic databases (Web of Science Core Collection, Embase, PubMed) from 01/1981 to 06/2022 for peer-reviewed scientific publications focused on (1) gene treatment of liver disease; (2) current status of SE research; and (3) targeting SEs for liver disease. We included English language original studies only. Results The number of published studies considering the role of enhancers in liver disease is considerable. Since SEs were just defined in 2013, the corresponding data on SEs are scarce: approximately 50 papers found in bibliographic databases on the correlation between enhancers (or SEs) and liver disease. Remarkably, half of these papers were published in the past three years, indicating the growing interest of the scientific community in this issue. Studies have shown that treatments targeting components of SEs can improve outcomes in liver disease in animal and clinical trials. Conclusions The treatment of liver disease is facing a bottleneck, and new treatments are needed. Therapeutic regimens targeting SEs have an important role in the treatment of liver disease. However, given the off-target effect of gene therapy and the lack of clinical trials, the available experimental data are still fragmented and controversial.
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10
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Bae S, Kim K, Kang K, Kim H, Lee M, Oh B, Kaneko K, Ma S, Choi JH, Kwak H, Lee EY, Park SH, Park-Min KH. RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts. Cell Mol Immunol 2023; 20:94-109. [PMID: 36513810 PMCID: PMC9794822 DOI: 10.1038/s41423-022-00959-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/03/2022] [Indexed: 12/15/2022] Open
Abstract
Monocyte/macrophage lineage cells are highly plastic and can differentiate into various cells under different environmental stimuli. Bone-resorbing osteoclasts are derived from the monocyte/macrophage lineage in response to receptor activator of NF-κB ligand (RANKL). However, the epigenetic signature contributing to the fate commitment of monocyte/macrophage lineage differentiation into human osteoclasts is largely unknown. In this study, we identified RANKL-responsive human osteoclast-specific superenhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) by integrating data obtained from ChIP-seq, ATAC-seq, nuclear RNA-seq and PRO-seq analyses. RANKL induced the formation of 200 SEs, which are large clusters of enhancers, while suppressing 148 SEs in macrophages. RANKL-responsive SEs were strongly correlated with genes in the osteoclastogenic program and were selectively increased in human osteoclasts but marginally presented in osteoblasts, CD4+ T cells, and CD34+ cells. In addition to the major transcription factors identified in osteoclasts, we found that BATF binding motifs were highly enriched in RANKL-responsive SEs. The depletion of BATF1/3 inhibited RANKL-induced osteoclast differentiation. Furthermore, we found increased chromatin accessibility in SE regions, where RNA polymerase II was significantly recruited to induce the extragenic transcription of SE-eRNAs, in human osteoclasts. Knocking down SE-eRNAs in the vicinity of the NFATc1 gene diminished the expression of NFATc1, a major regulator of osteoclasts, and osteoclast differentiation. Inhibiting BET proteins suppressed the formation of some RANKL-responsive SEs and NFATc1-associated SEs, and the expression of SE-eRNA:NFATc1. Moreover, SE-eRNA:NFATc1 was highly expressed in the synovial macrophages of rheumatoid arthritis patients exhibiting high-osteoclastogenic potential. Our genome-wide analysis revealed RANKL-inducible SEs and SE-eRNAs as osteoclast-specific signatures, which may contribute to the development of osteoclast-specific therapeutic interventions.
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Affiliation(s)
- Seyeon Bae
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kibyeong Kim
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 3116, Republic of Korea
| | - Haemin Kim
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Minjoon Lee
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Brian Oh
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Kaichi Kaneko
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA
| | - Sungkook Ma
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jae Hoon Choi
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Korea
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
| | - Eun Young Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Sung Ho Park
- Department of Biological Science, Ulsan National Institute of Science & Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
- BCMB Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10021, USA.
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11
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Li H, Muhetaer G, Xie Y, Yao K, Ma Q, Guan H, Xing S, Huang X, Zhou J. Identification of super-enhancer-driven peptidyl arginine deiminases as potential biomarkers and therapeutic targets for osimertinib-resistant non-small cell lung cancer. Front Pharmacol 2022; 13:1071365. [DOI: 10.3389/fphar.2022.1071365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Resistance to targeted drugs is now a challenging clinical problem in the treatment of non-small cell lung cancer (NSCLC). So far, there are no approved targeted therapeutic drugs for patients with disease progression after the third-generation epidermal growth factor receptor-tyrosine kinase inhibitor osimertinib resistance (OR). Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive gene expression. In this study, we aimed to explore the potential pathogenic SEs and their driven genes in OR NSCLC. OR cell line was established by exposure of H1975 cells to incremental dosing of osimertinib. RNA-sequencing and H3K27ac ChIP-sequencing were used to identify the differential expressed genes (DEGs) and SEs in parental and resistant cells. Gene ontology analysis for the OR-specific SEs-associated genes showed that histone citrullination, protein citrullination, and peptidyl-arginine modification are the top three biological processes, and the DEGs involved in these biological processes, including peptidyl arginine deiminase 1 (PADI1), PADI2, and PADI3. Realtime-PCR and western blot detections confirmed these genes were highly expressed in OR cells. SE inhibitor decreases their expression, ensuring that SEs regulate their transcriptional expressions. The PADI inhibitor inhibited OR cells’ proliferation, invasion, and colony formation. This study demonstrates that SE-driven PADI family genes are potential biomarkers and targets for OR NSCLC.
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12
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Mammary-Enriched Transcription Factors Synergize to Activate the Wap Super-Enhancer for Mammary Gland Development. Int J Mol Sci 2022; 23:ijms231911680. [PMID: 36232979 PMCID: PMC9569684 DOI: 10.3390/ijms231911680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Super-enhancers are large clusters of enhancers critical for cell-type-specific development. In a previous study, 440 mammary-specific super-enhancers, highly enriched for an active enhancer mark H3K27ac; a mediator MED1; and the mammary-enriched transcription factors ELF5, NFIB, STAT5A, and GR, were identified in the genome of the mammary epithelium of lactating mice. However, the triggering mechanism for mammary-specific super-enhancers and the molecular interactions between key transcription factors have not been clearly elucidated. In this study, we investigated in vivo protein-protein interactions between major transcription factors that activate mammary-specific super-enhancers. In mammary epithelial cells, ELF5 strongly interacted with NFIB while weakly interacting with STAT5A, and it showed modest interactions with MED1 and GR, a pattern unlike that in non-mammary cells. We further investigated the role of key transcription factors in the initial activation of the mammary-specific Wap super-enhancer, using CRISPR-Cas9 genome editing to introduce single or combined mutations at transcription factor binding sites in the pioneer enhancer of the Wap super-enhancer in mice. ELF5 and STAT5A played key roles in igniting Wap super-enhancer activity, but an intact transcription factor complex was required for the full function of the super-enhancer. Our study demonstrates that mammary-enriched transcription factors within a protein complex interact with different intensities and synergize to activate the Wap super-enhancer. These findings provide an important framework for understanding the regulation of cell-type-specific development.
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13
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Typical Enhancers, Super-Enhancers, and Cancers. Cancers (Basel) 2022; 14:cancers14184375. [PMID: 36139535 PMCID: PMC9496678 DOI: 10.3390/cancers14184375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary The cancer genome has been exhaustively studied upon the advent of Next-Generation Sequencing technologies. Coding and non-coding sequences have been defined as hotspots of genomic variations that affect the naïve gene expression programs established in normal cells, thus working as endogenous drivers of carcinogenesis. In this review, we comprehensively summarize fundamental aspects of gene expression regulation, with emphasis on the impact of sequence and structural variations mapped across non-coding cis-acting elements of genes encoding for tumor-related transcription factors. Chromatin architecture, epigenome reprogramming, transcriptional enhancers and Super-enhancers, oncogene regulation, cutting-edge technologies, and pharmacological treatment are substantially highlighted. Abstract Non-coding segments of the human genome are enriched in cis-regulatory modules that constitute functional elements, such as transcriptional enhancers and Super-enhancers. A hallmark of cancer pathogenesis is the dramatic dysregulation of the “archetype” gene expression profiles of normal human cells. Genomic variations can promote such deficiencies when occurring across enhancers and Super-enhancers, since they affect their mechanistic principles, their functional capacity and specificity, and the epigenomic features of the chromatin microenvironment across which these regulatory elements reside. Here, we comprehensively describe: fundamental mechanisms of gene expression dysregulation in cancers that involve genomic abnormalities within enhancers’ and Super-enhancers’ (SEs) sequences, which alter the expression of oncogenic transcription factors (TFs); cutting-edge technologies applied for the analysis of variation-enriched hotspots of the cancer genome; and pharmacological approaches for the treatment of Super-enhancers’ aberrant function. Finally, we provide an intratumor meta-analysis, which highlights that genomic variations in transcription-factor-driven tumors are accompanied overexpression of genes, a portion of which encodes for additional cancer-related transcription factors.
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14
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Sturmlechner I, Sine CC, Jeganathan KB, Zhang C, Fierro Velasco RO, Baker DJ, Li H, van Deursen JM. Senescent cells limit p53 activity via multiple mechanisms to remain viable. Nat Commun 2022; 13:3722. [PMID: 35764649 PMCID: PMC9240076 DOI: 10.1038/s41467-022-31239-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
Super-enhancers regulate genes with important functions in processes that are cell type-specific or define cell identity. Mouse embryonic fibroblasts establish 40 senescence-associated super-enhancers regardless of how they become senescent, with 50 activated genes located in the vicinity of these enhancers. Here we show, through gene knockdown and analysis of three core biological properties of senescent cells that a relatively large number of senescence-associated super-enhancer-regulated genes promote survival of senescent mouse embryonic fibroblasts. Of these, Mdm2, Rnase4, and Ang act by suppressing p53-mediated apoptosis through various mechanisms that are also engaged in response to DNA damage. MDM2 and RNASE4 transcription is also elevated in human senescent fibroblasts to restrain p53 and promote survival. These insights identify key survival mechanisms of senescent cells and provide molecular entry points for the development of targeted therapeutics that eliminate senescent cells at sites of pathology.
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Affiliation(s)
- Ines Sturmlechner
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Pediatrics, Molecular Genetics Section, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Chance C Sine
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Karthik B Jeganathan
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - Darren J Baker
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Jan M van Deursen
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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15
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Zhou T, Zhu X, Ye Z, Wang YF, Yao C, Xu N, Zhou M, Ma J, Qin Y, Shen Y, Tang Y, Yin Z, Xu H, Zhang Y, Zang X, Ding H, Yang W, Guo Y, Harley JB, Namjou B, Kaufman KM, Kottyan LC, Weirauch MT, Hou G, Shen N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nat Commun 2022; 13:1855. [PMID: 35388006 PMCID: PMC8987079 DOI: 10.1038/s41467-022-29514-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, epigenomic, and CRISPR activation approaches to screen for functional variants that regulate IRF8 expression. We demonstrate that the locus containing rs2280381 is a cell-type-specific enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter regulating IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to regulate AC092723.1 and IRF8 expression differentially. Our work illustrates an integrative strategy to define functional genetic variants that regulate the expression of critical genes in autoimmune diseases and decipher the mechanisms underlying the dysregulation of IRF8 expression mediated by lupus risk variants.
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Affiliation(s)
- Tian Zhou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Xinyi Zhu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Yong-Fei Wang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Chao Yao
- grid.9227.e0000000119573309Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031 China
| | - Ning Xu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Mi Zhou
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - Jianyang Ma
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuting Qin
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yiwei Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuanjia Tang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Hong Xu
- grid.16821.3c0000 0004 0368 8293Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China ,grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China
| | - Yutong Zhang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Xiaoli Zang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Huihua Ding
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Wanling Yang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Ya Guo
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - John B. Harley
- grid.413848.20000 0004 0420 2128US Department of Veterans Affairs Medical Center, Cincinnati, OH 45229 USA
| | - Bahram Namjou
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Kenneth M. Kaufman
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Leah C. Kottyan
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Matthew T. Weirauch
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Guojun Hou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Nan Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China ,grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
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BRD4 inhibitor GNE987 exerts anti-cancer effects by targeting super-enhancers in neuroblastoma. Cell Biosci 2022; 12:33. [PMID: 35303940 PMCID: PMC8932231 DOI: 10.1186/s13578-022-00769-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/26/2022] [Indexed: 12/14/2022] Open
Abstract
Background Neuroblastoma (NB) is a common extracranial malignancy with high mortality in children. Recently, super-enhancers (SEs) have been reported to play a critical role in the tumorigenesis and development of NB via regulating a wide range of oncogenes Thus, the synthesis and identification of chemical inhibitors specifically targeting SEs are of great urgency for the clinical therapy of NB. This study aimed to characterize the activity of the SEs inhibitor GNE987, which targets BRD4, in NB. Results In this study, we found that nanomolar concentrations of GNE987 markedly diminished NB cell proliferation and survival via degrading BRD4. Meanwhile, GNE987 significantly induced NB cell apoptosis and cell cycle arrest. Consistent with in vitro results, GNE987 administration (0.25 mg/kg) markedly decreased the tumor size in the xenograft model, with less toxicity, and induced similar BRD4 protein degradation to that observed in vitro. Mechanically, GNE987 led to significant downregulation of hallmark genes associated with MYC and the global disruption of the SEs landscape in NB cells. Moreover, a novel candidate oncogenic transcript, FAM163A, was identified through analysis of the RNA-seq and ChIP-seq data. FAM163A is abnormally transcribed by SEs, playing an important role in NB occurrence and development. Conclusion GNE987 destroyed the abnormal transcriptional regulation of oncogenes in NB by downregulating BRD4, which could be a potential therapeutic candidate for NB. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00769-8.
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ASCL1, NKX2-1, and PROX1 co-regulate subtype-specific genes in small-cell lung cancer. iScience 2021; 24:102953. [PMID: 34466783 PMCID: PMC8384902 DOI: 10.1016/j.isci.2021.102953] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 12/20/2022] Open
Abstract
Lineage-defining transcription factors (LTFs) play key roles in small-cell lung cancer (SCLC) pathophysiology. Delineating the LTF-regulated genes operative in SCLC could provide a road map to identify SCLC dependencies. We integrated chromatin landscape and transcriptome analyses of patient-derived SCLC preclinical models to identify super-enhancers (SEs) and their associated genes in the ASCL1-, NEUROD1-, and POU2F3-high SCLC subtypes. We find SE signatures predict LTF-based classification of SCLC, and the SE-associated genes are enriched with those defined as common essential genes in DepMap. In addition, in ASCL1-high SCLC, we show ASCL1 complexes with NKX2-1 and PROX1 to co-regulate genes functioning in NOTCH signaling, catecholamine biosynthesis, and cell-cycle processes. Depletion of ASCL1 demonstrates it is a key dependency factor in preclinical SCLC models and directly regulates multiple DepMap-defined essential genes. We provide LTF/SE-based subtype-specific gene sets for SCLC for further therapeutic investigation. Super-enhancers support lineage-defining transcription factor SCLC classification SCLC super-enhancer-associated genes represent essential and lineage-identity genes ASCL1, NKX2-1, and PROX1 proteins interact in a complex in SCLC-A ASCL1, NKX2-1, and PROX1 regulate Notch-signaling, NE-specific, and cell-cycle genes
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Li L, Wang N, Zhu M, Xiong Y, Wang F, Guo G, Wang X, Gu Y. Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma. Cell Death Dis 2021; 12:777. [PMID: 34362881 PMCID: PMC8346480 DOI: 10.1038/s41419-021-04060-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Poor response of tumors to radiotherapy is a major clinical obstacle. Because of the dynamic characteristics of the epigenome, identification of possible epigenetic modifiers may be beneficial to confer radio-sensitivity. This research was set to examine the modulation of ectodermal-neural cortex 1 (ENC1) in radio-resistance in breast carcinoma (BC). In silico identification and immunohistochemical staining revealed that overexpression of ENC1 promoted BC metastasis to the bone and brain. Moreover, its overexpression promoted the translocation of YAP1/TAZ into the nucleus and enhanced expression of GLI1, CTGF, and FGF1 through the Hippo pathway. ENC1 expression was controlled by a ~10-kb long SE. ENC1-SEdistal deletion reduced ENC1 expression and inhibited the malignant behavior of BC cells and their resistance to radiotherapy. The binding sites on the ENC1-SE region enriched the shared sequence between TCF4 and ENC1 promoter. Knocking-down TCF4 inhibited luciferase activity and H3K27ac-enriched binding of the ENC1-SE region. Additionally, SE-driven ENC1 overexpression mediated by TCF4 may have clinical implications in radio-resistance in BC patients. Our findings indicated that ENC1 overexpression is mediated by SE and the downstream TCF4 to potentiate the Hippo/YAP1/TAZ pathway. Targeting this axis might be a therapeutic strategy for overcoming BC radio-resistance.
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Affiliation(s)
- Lin Li
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Nan Wang
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Mingzhi Zhu
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Youyi Xiong
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Fang Wang
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Guangcheng Guo
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xinxing Wang
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yuanyan Gu
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China.
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19
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Liu M, Cao S, He L, Gao J, Arab JP, Cui H, Xuan W, Gao Y, Sehrawat TS, Hamdan FH, Ventura-Cots M, Argemi J, Pomerantz WCK, Johnsen SA, Lee JH, Gao F, Ordog T, Mathurin P, Revzin A, Bataller R, Yan H, Shah VH. Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis. Nat Commun 2021; 12:4560. [PMID: 34315876 PMCID: PMC8316465 DOI: 10.1038/s41467-021-24843-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
Alcoholic hepatitis (AH) is associated with liver neutrophil infiltration through activated cytokine pathways leading to elevated chemokine expression. Super-enhancers are expansive regulatory elements driving augmented gene expression. Here, we explore the mechanistic role of super-enhancers linking cytokine TNFα with chemokine amplification in AH. RNA-seq and histone modification ChIP-seq of human liver explants show upregulation of multiple CXCL chemokines in AH. Liver sinusoidal endothelial cells (LSEC) are identified as an important source of CXCL expression in human liver, regulated by TNFα/NF-κB signaling. A super-enhancer is identified for multiple CXCL genes by multiple approaches. dCas9-KRAB-mediated epigenome editing or pharmacologic inhibition of Bromodomain and Extraterminal (BET) proteins, transcriptional regulators vital to super-enhancer function, decreases chemokine expression in vitro and decreases neutrophil infiltration in murine models of AH. Our findings highlight the role of super-enhancer in propagating inflammatory signaling by inducing chemokine expression and the therapeutic potential of BET inhibition in AH treatment.
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Affiliation(s)
- Mengfei Liu
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Li He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinhang Gao
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
| | - Juan P Arab
- Department of Gastroenterology and Hepatology, School of Medicine of the Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Huarui Cui
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Weixia Xuan
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, China
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yandong Gao
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Tejasav S Sehrawat
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Meritxell Ventura-Cots
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josepmaria Argemi
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Steven A Johnsen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Fei Gao
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Ramon Bataller
- Department of Gastroenterology Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Huihuang Yan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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20
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Waddell AR, Huang H, Liao D. CBP/p300: Critical Co-Activators for Nuclear Steroid Hormone Receptors and Emerging Therapeutic Targets in Prostate and Breast Cancers. Cancers (Basel) 2021; 13:2872. [PMID: 34201346 PMCID: PMC8229436 DOI: 10.3390/cancers13122872] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/10/2023] Open
Abstract
The CREB-binding protein (CBP) and p300 are two paralogous lysine acetyltransferases (KATs) that were discovered in the 1980s-1990s. Since their discovery, CBP/p300 have emerged as important regulatory proteins due to their ability to acetylate histone and non-histone proteins to modulate transcription. Work in the last 20 years has firmly established CBP/p300 as critical regulators for nuclear hormone signaling pathways, which drive tumor growth in several cancer types. Indeed, CBP/p300 are critical co-activators for the androgen receptor (AR) and estrogen receptor (ER) signaling in prostate and breast cancer, respectively. The AR and ER are stimulated by sex hormones and function as transcription factors to regulate genes involved in cell cycle progression, metabolism, and other cellular functions that contribute to oncogenesis. Recent structural studies of the AR/p300 and ER/p300 complexes have provided critical insights into the mechanism by which p300 interacts with and activates AR- and ER-mediated transcription. Breast and prostate cancer rank the first and forth respectively in cancer diagnoses worldwide and effective treatments are urgently needed. Recent efforts have identified specific and potent CBP/p300 inhibitors that target the acetyltransferase activity and the acetytllysine-binding bromodomain (BD) of CBP/p300. These compounds inhibit AR signaling and tumor growth in prostate cancer. CBP/p300 inhibitors may also be applicable for treating breast and other hormone-dependent cancers. Here we provide an in-depth account of the critical roles of CBP/p300 in regulating the AR and ER signaling pathways and discuss the potential of CBP/p300 inhibitors for treating prostate and breast cancer.
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Affiliation(s)
- Aaron R. Waddell
- UF Health Cancer Center, Department of Anatomy and Cell Biology, University Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA;
| | - Haojie Huang
- Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA;
| | - Daiqing Liao
- UF Health Cancer Center, Department of Anatomy and Cell Biology, University Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA;
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21
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Li GH, Qu Q, Qi TT, Teng XQ, Zhu HH, Wang JJ, Lu Q, Qu J. Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance. J Exp Clin Cancer Res 2021; 40:174. [PMID: 34011395 PMCID: PMC8132395 DOI: 10.1186/s13046-021-01974-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Although new developments of surgery, chemotherapy, radiotherapy, and immunotherapy treatments for cancer have improved patient survival, the emergence of chemoresistance in cancer has significant impacts on treatment effects. The development of chemoresistance involves several polygenic, progressive mechanisms at the molecular and cellular levels, as well as both genetic and epigenetic heterogeneities. Chemotherapeutics induce epigenetic reprogramming in cancer cells, converting a transient transcriptional state into a stably resistant one. Super-enhancers (SEs) are central to the maintenance of identity of cancer cells and promote SE-driven-oncogenic transcriptions to which cancer cells become highly addicted. This dependence on SE-driven transcription to maintain chemoresistance offers an Achilles' heel for chemoresistance. Indeed, the inhibition of SE components dampens oncogenic transcription and inhibits tumor growth to ultimately achieve combined sensitization and reverse the effects of drug resistance. No reviews have been published on SE-related mechanisms in the cancer chemoresistance. In this review, we investigated the structure, function, and regulation of chemoresistance-related SEs and their contributions to the chemotherapy via regulation of the formation of cancer stem cells, cellular plasticity, the microenvironment, genes associated with chemoresistance, noncoding RNAs, and tumor immunity. The discovery of these mechanisms may aid in the development of new drugs to improve the sensitivity and specificity of cancer cells to chemotherapy drugs.
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Affiliation(s)
- Guo-Hua Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Ting-Ting Qi
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Hai-Hong Zhu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Jiao-Jiao Wang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiong Lu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
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22
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Li H, Zhao C, Li Z, Yao K, Zhang J, Si W, Liu X, Jiang Y, Zhu M. Identification of Potential Pathogenic Super-Enhancers-Driven Genes in Pulmonary Fibrosis. Front Genet 2021; 12:644143. [PMID: 34054916 PMCID: PMC8153712 DOI: 10.3389/fgene.2021.644143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Abnormal fibroblast differentiation into myofibroblast is a crucial pathological mechanism of pulmonary fibrosis (PF). Super-enhancers, a newly discovered cluster of regulatory elements, are regarded as the regulators of cell identity. We speculate that abnormal activation of super-enhancers must be involved in the pathological process of PF. This study aims to identify potential pathogenic super-enhancer-driven genes in PF. Differentially expressed genes (DEGs) in PF mouse lungs were identified from a GEO dataset (GDS1492). We collected super-enhancers and their associated genes in human lung fibroblasts and mouse embryonic fibroblasts from SEA version 3.0, a network database that provides comprehensive information on super-enhancers. We crosslinked upregulated DEGs and super-enhancer-associated genes in fibroblasts to predict potential super-enhancer-driven pathogenic genes in PF. A total of 25 genes formed an overlap, and the protein-protein interaction network of these genes was constructed by the STRING database. An interaction network of transcription factors (TFs), super-enhancers, and associated genes was constructed using the Cytoscape software. Gene enrichment analyses, including KEGG pathway and GO analysis, were performed for these genes. Latent transforming growth factor beta (TGF-β) binding protein 2 (LTBP2), one of the predicted super-enhancer-driven pathogenic genes, was used to verify the predicted network’s accuracy. LTBP2 was upregulated in the lungs of the bleomycin-induced PF mouse model and TGF-β1-stimulated mouse and human fibroblasts. Myc is one of the TFs binding to the LTBP2 super-enhancer. Knockout of super-enhancer sequences with a CRISPR/Cas9 plasmid or inhibition of Myc all decreased TGF-β1-induced LTBP2 expression in NIH/3 T3 cells. Identifying and interfering super-enhancers might be a new way to explore possible therapeutic methods for PF.
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Affiliation(s)
- Hang Li
- Central Lab, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Caiping Zhao
- Central Lab, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zeli Li
- Department of Respiratory, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Kainan Yao
- Department of Respiratory, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jingjing Zhang
- Department of Pathology, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Wenwen Si
- Central Lab, Shenzhen Bao'an Traditional Chinese Medicine Hospital (Group), Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xiaohong Liu
- Department of Respiratory, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Jiang
- Department of Respiratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Meiling Zhu
- Traditional Chinese Medicine Innovation Research Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
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23
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Ortutay Z, Grönholm A, Laitinen M, Keresztes-Andrei M, Hermelo I, Pesu M. Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells. Front Immunol 2021; 12:630389. [PMID: 33679774 PMCID: PMC7930619 DOI: 10.3389/fimmu.2021.630389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/22/2021] [Indexed: 12/30/2022] Open
Abstract
The proprotein convertase enzyme FURIN promotes the proteolytic maturation of pro-proteins and thereby it serves as an important factor for maintaining cellular homeostasis. In T cells, FURIN is critical for maintaining the T regulatory cell dependent peripheral immune tolerance and intact T helper cell polarization. The enzymatic activity of FURIN is directly associated with its expression levels, but genetic determinants for cell-type specific Furin gene regulation have remained elusive. By exploring the histone acetyltransferase p300 binding patterns in T helper cells, a putative regulatory region at ca. 20kB upstream of Furin gene was identified. When this region was deleted with CRISPR/Cas9 the production of Furin mRNA was significantly reduced in activated mouse T cells. Genome-wide RNA profiling by sequencing revealed that the novel Furin regulator region also impacted the expression of several genes that have previously been associated with the Th1 type hall mark cytokine IFNγ regulation or function. Finally, Furin genetic regulatory region was found to specifically promote the secretion of IFNγ by activated T cells. In sum, our data unravels the presence of Furin expression regulatory region in T cells that has characteristics of a super-enhancer for Th1 cell fate.
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Affiliation(s)
- Zsuzsanna Ortutay
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna Grönholm
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melina Laitinen
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melinda Keresztes-Andrei
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Ismail Hermelo
- Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marko Pesu
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
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24
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Liu Z, Chen SS, Clarke S, Veschi V, Thiele CJ. Targeting MYCN in Pediatric and Adult Cancers. Front Oncol 2021; 10:623679. [PMID: 33628735 PMCID: PMC7898977 DOI: 10.3389/fonc.2020.623679] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022] Open
Abstract
The deregulation of the MYC family of oncogenes, including c-MYC, MYCN and MYCL occurs in many types of cancers, and is frequently associated with a poor prognosis. The majority of functional studies have focused on c-MYC due to its broad expression profile in human cancers. The existence of highly conserved functional domains between MYCN and c-MYC suggests that MYCN participates in similar activities. MYC encodes a basic helix-loop-helix-leucine zipper (bHLH-LZ) transcription factor (TF) whose central oncogenic role in many human cancers makes it a highly desirable therapeutic target. Historically, as a TF, MYC has been regarded as “undruggable”. Thus, recent efforts focus on investigating methods to indirectly target MYC to achieve anti-tumor effects. This review will primarily summarize the recent progress in understanding the function of MYCN. It will explore efforts at targeting MYCN, including strategies aimed at suppression of MYCN transcription, destabilization of MYCN protein, inhibition of MYCN transcriptional activity, repression of MYCN targets and utilization of MYCN overexpression dependent synthetic lethality.
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Affiliation(s)
- Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Samuel S Chen
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Saki Clarke
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Veronica Veschi
- Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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25
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Zhang C, Chen L, Liu Y, Huang J, Liu A, Xu Y, Shen Y, He H, Xu D. Downregulated METTL14 accumulates BPTF that reinforces super-enhancers and distal lung metastasis via glycolytic reprogramming in renal cell carcinoma. Am J Cancer Res 2021; 11:3676-3693. [PMID: 33664855 PMCID: PMC7914369 DOI: 10.7150/thno.55424] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Methyltransferase-like 14 (METTL14) participates in tumorigenesis in several malignancies, but how METTL14 mediates the metastasis of renal cell carcinoma (RCC) has never been reported. Methods: Western blotting, quantitative real-time PCR, and immunohistochemistry were used to determine the mRNA and protein levels of relevant genes. Methylated RNA immunoprecipitation sequencing and RNA sequencing were utilized to screen potential targets of METTL14. Chromatin immunoprecipitation sequencing and assay for transposase-accessible chromatin sequencing were performed to investigate epigenetic alterations. The biological roles and mechanisms of METTL14/BPTF in promoting lung metastasis were confirmed in vitro and in vivo using cell lines, patient samples, xenograft models, and organoids. Results: Utilizing the TCGA-KIRC and Ruijin-RCC datasets, we found low expression of METTL14 in mRCC samples, which predicted poor prognosis. METTL14 deficiency promoted RCC metastasis in vitro and in vivo. Mechanistically, METTL14-mediated m6A modification negatively regulated the mRNA stability of bromodomain PHD finger transcription factor (BPTF) and depended on BPTF to drive lung metastasis. Accumulated BPTF in METTL14-deficient cells remodeled the enhancer landscape to reinforce several oncogenic crosstalk. Particularly, BPTF constituted super-enhancers that activate downstream targets like enolase 2 and SRC proto-oncogene nonreceptor tyrosine kinase, leading to glycolytic reprogramming of METTL14-/- cells. Finally, we determined the efficacy of the BPTF inhibitor AU1 in suppressing mRCC of patient-derived cells, mRCC-derived organoids (MDOs), and orthotopic xenograft models. Conclusions: Our study is the first to investigate the essential role of m6A modification and the METTL14/BPTF axis in the epigenetic and metabolic remodeling of mRCC, highlighting AU1 as a vital therapeutic candidate.
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26
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Skibba M, Drelich A, Poellmann M, Hong S, Brasier AR. Nanoapproaches to Modifying Epigenetics of Epithelial Mesenchymal Transition for Treatment of Pulmonary Fibrosis. Front Pharmacol 2020; 11:607689. [PMID: 33384604 PMCID: PMC7770469 DOI: 10.3389/fphar.2020.607689] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a chronically progressive interstitial lung that affects over 3 M people worldwide and rising in incidence. With a median survival of 2-3 years, IPF is consequently associated with high morbidity, mortality, and healthcare burden. Although two antifibrotic therapies, pirfenidone and nintedanib, are approved for human use, these agents reduce the rate of decline of pulmonary function but are not curative and do not reverse established fibrosis. In this review, we discuss the prevailing epithelial injury hypothesis, wherein pathogenic airway epithelial cell-state changes known as Epithelial Mesenchymal Transition (EMT) promotes the expansion of myofibroblast populations. Myofibroblasts are principal components of extracellular matrix production that result in airspace loss and mortality. We review the epigenetic transition driving EMT, a process produced by changes in histone acetylation regulating mesenchymal gene expression programs. This mechanistic work has focused on the central role of bromodomain-containing protein 4 in mediating EMT and myofibroblast transition and initial preclinical work has provided evidence of efficacy. As nanomedicine presents a promising approach to enhancing the efficacy of such anti-IPF agents, we then focus on the state of nanomedicine formulations for inhalable delivery in the treatment of pulmonary diseases, including liposomes, polymeric nanoparticles (NPs), inorganic NPs, and exosomes. These nanoscale agents potentially provide unique properties to existing pulmonary therapeutics, including controlled release, reduced systemic toxicity, and combination delivery. NP-based approaches for pulmonary delivery thus offer substantial promise to modify epigenetic regulators of EMT and advance treatments for IPF.
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Affiliation(s)
- Melissa Skibba
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
| | - Adam Drelich
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael Poellmann
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States
| | - Seungpyo Hong
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
- Yonsei Frontier Lab, Department of Pharmacy, Yonsei University, Seoul, South Korea
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI, United States
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27
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Chen H, Liang H. A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer. Cancer Cell 2020; 38:701-715.e5. [PMID: 33007258 PMCID: PMC7658066 DOI: 10.1016/j.ccell.2020.08.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/21/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical samples remains challenging, especially for super-enhancers. Enhancer activities can be inferred from enhancer RNA (eRNA) signals, which requires enhancer transcription loci definition. Only a small proportion of human eRNA loci has been precisely identified, limiting investigations of enhancer-mediated oncogenic mechanisms. Here, we characterize super-enhancer regions using aggregated RNA sequencing (RNA-seq) data from large cohorts. Super-enhancers usually contain discrete loci featuring sharp eRNA expression peaks. We identify >300,000 eRNA loci in ∼377 Mb super-enhancer regions that are regulated by evolutionarily conserved, well-positioned nucleosomes and are frequently dysregulated in cancer. The eRNAs provide explanatory power for cancer phenotypes beyond that provided by mRNA expression through resolving intratumoral heterogeneity with enhancer cell-type specificity. Our study provides a high-resolution map of eRNA loci through which super-enhancer activities can be quantified by RNA-seq and a user-friendly data portal, enabling a broad range of biomedical investigations.
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Affiliation(s)
- Han Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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28
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Shigeyasu K, Toden S, Ozawa T, Matsuyama T, Nagasaka T, Ishikawa T, Sahoo D, Ghosh P, Uetake H, Fujiwara T, Goel A. The PVT1 lncRNA is a novel epigenetic enhancer of MYC, and a promising risk-stratification biomarker in colorectal cancer. Mol Cancer 2020; 19:155. [PMID: 33148262 PMCID: PMC7643275 DOI: 10.1186/s12943-020-01277-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Accumulating evidence suggests that dysregulation of transcriptional enhancers plays a significant role in cancer pathogenesis. Herein, we performed a genome-wide discovery of enhancer elements in colorectal cancer (CRC). We identified PVT1 locus as a previously unrecognized transcriptional regulator in CRC with a significantly high enhancer activity, which ultimately was responsible for regulating the expression of MYC oncogene. High expression of the PVT1 long-non-coding RNA (lncRNA) transcribed from the PVT1 locus was associated with poor survival among patients with stage II and III CRCs (p < 0.05). Aberrant methylation of the PVT1 locus inversely correlated with the reduced expression of the corresponding the PVT1 lncRNA, as well as MYC gene expression. Bioinformatic analyses of CRC-transcriptomes revealed that the PVT1 locus may also broadly impact the expression and function of other key genes within two key CRC-associated signaling pathways - the TGFβ/SMAD and Wnt/β-Catenin pathways. We conclude that the PVT1 is a novel oncogenic enhancer of MYC and its activity is controlled through epigenetic regulation mediated through aberrant methylation in CRC. Our findings also suggest that the PVT1 lncRNA expression is a promising prognostic biomarker and a potential therapeutic target in CRC.
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Affiliation(s)
- Kunitoshi Shigeyasu
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Shusuke Toden
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Tsuyoshi Ozawa
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takatoshi Matsuyama
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Takeshi Nagasaka
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiaki Ishikawa
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Debashis Sahoo
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hiroyuki Uetake
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA.
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, 1218 S. Fifth Avenue, Suite 2226, Duarte, CA, USA.
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Wilson MR, Reske JJ, Holladay J, Neupane S, Ngo J, Cuthrell N, Wegener M, Rhodes M, Adams M, Sheridan R, Hostetter G, Alotaibi FT, Yong PJ, Anglesio MS, Lessey BA, Leach RE, Teixeira JM, Missmer SA, Fazleabas AT, Chandler RL. ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation. Cell Rep 2020; 33:108366. [PMID: 33176148 PMCID: PMC7682620 DOI: 10.1016/j.celrep.2020.108366] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/16/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Endometriosis affects 1 in 10 women and is characterized by the presence of abnormal endometrium at ectopic sites. ARID1A mutations are observed in deeply invasive forms of the disease, often correlating with malignancy. To identify epigenetic dependencies driving invasion, we use an unbiased approach to map chromatin state transitions accompanying ARID1A loss in the endometrium. We show that super-enhancers marked by high H3K27 acetylation are strongly associated with ARID1A binding. ARID1A loss leads to H3K27 hyperacetylation and increased chromatin accessibility and enhancer RNA transcription at super-enhancers, but not typical enhancers, indicating that ARID1A normally prevents super-enhancer hyperactivation. ARID1A co-localizes with P300 at super-enhancers, and genetic or pharmacological inhibition of P300 in ARID1A mutant endometrial epithelia suppresses invasion and induces anoikis through the rescue of super-enhancer hyperacetylation. Among hyperactivated super-enhancers, SERPINE1 (PAI-1) is identified as an essential target gene driving ARID1A mutant endometrial invasion. Broadly, our findings provide rationale for therapeutic strategies targeting super-enhancers in ARID1A mutant endometrium.
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Affiliation(s)
- Mike R Wilson
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jake J Reske
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeanne Holladay
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Subechhya Neupane
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Julie Ngo
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nina Cuthrell
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mary Rhodes
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Rachael Sheridan
- Flow Cytometry Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Fahad T Alotaibi
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Physiology, College of Medicine, Al-Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Paul J Yong
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; British Columbia's Gynecological Cancer Research Team (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, BC, Canada
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA
| | - Richard E Leach
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Asgerally T Fazleabas
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Ronald L Chandler
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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30
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Zhou J, Wang D, Tang D, Huang W. Abnormal Activations of Super-Enhancers Enhance the Carcinogenicity in Lung Adenocarcinoma. Cancer Manag Res 2020; 12:8509-8518. [PMID: 32982443 PMCID: PMC7501973 DOI: 10.2147/cmar.s258497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
Background Lung tumors and normal lung tissues show large differences in epigenetic modification which can affect the chromosome structure and expression of genes. However, the epigenetic reprogramming in lung adenocarcinoma remains unclear. Methods and Results With the bioinformatics analysis, we found that some activated super-enhancers (SEs) only appear in lung adenocarcinoma cells, and 781 abnormal activated super-enhancers (AASEs) were found. Not only are the traditional oncogenes found to be activated by AASEs, such as MET and SLC2A1, but also some new genes were activated by AASEs, which probably contributes to the carcinogenic process in lung cancer. The enrichment analysis of the genes activated by AASEs shows that the glycolysis process and cell proliferation were enhanced and the apoptotic process was negatively regulated. Two AASEs were separately knockout by CRISPR/Cas9 in A549, PC-9, and H1299 cell lines and the expression of target genes decreased. The motif of CTCF, SMARCA1, SOX4, FOXM1, IRF3, IRF7, and STAT2 was enriched in AASEs, supporting that the chromosome structure changed and these transcription factors would be the master regulators on the formation of AASEs. Conclusion This study provided comprehensive insight into the mechanisms of SEs, as well as a potential therapeutic target for lung cancer.
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Affiliation(s)
- Jianlong Zhou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China.,Department of Oncology, The Affiliated Xinhui Hospital, Southern Medical University, Xinhui, People's Republic of China
| | - Dingxue Wang
- Department of Oncology, The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Dongxin Tang
- Department of Oncology, The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, People's Republic of China
| | - Wenhua Huang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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31
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Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer. Exp Mol Med 2020; 52:1550-1563. [PMID: 32879421 PMCID: PMC8080767 DOI: 10.1038/s12276-020-00493-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/22/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022] Open
Abstract
Although approved programmed cell death protein (PD)-1 inhibitors show durable responses, clinical benefits to these agents are only seen in one-third of patients in most cancer types. Therefore, strategies for improving the response to PD-1 inhibitor for treating various cancers including non-small cell lung cancer (NSCLC) are urgently needed. Compared with genome and transcriptome, tumor DNA methylome in anti-PD-1 response was relatively unexplored. We compared the pre-treatment methylation status of cis-regulatory elements between responders and non-responders to treatment with nivolumab or pembrolizumab using the Infinium Methylation EPIC Array, which can profile ~850,000 CpG sites, including ~350,000 CpG sites located in enhancer regions. Then, we analyzed differentially methylated regions overlapping promoters (pDMRs) or enhancers (eDMRs) between responders and non-responders to PD-1 inhibitors. We identified 1007 pDMRs and 607 eDMRs associated with the anti-PD-1 response. We also identified 1109 and 1173 target genes putatively regulated by these pDMRs and eDMRs, respectively. We found that eDMRs contribute to the epigenetic regulation of the anti-PD-1 response more than pDMRs. Hypomethylated pDMRs of Cytohesin 1 Interacting Protein (CYTIP) and TNF superfamily member 8 (TNFSF8) were more predictive than programmed cell death protein ligand 1 (PD-L1) expression for anti-PD-1 response and progression-free survival (PFS) and overall survival (OS) in a validation cohort, suggesting their potential as predictive biomarkers for anti-PD-1 immunotherapy. The catalog of promoters and enhancers differentially methylated between responders and non-responders to PD-1 inhibitors presented herein will guide the development of biomarkers and therapeutic strategies for improving anti-PD-1 immunotherapy in NSCLC.
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32
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Zhang Y, Huang YX, Wang DL, Yang B, Yan HY, Lin LH, Li Y, Chen J, Xie LM, Huang YS, Liao JY, Hu KS, He JH, Saw PE, Xu X, Yin D. LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network. Theranostics 2020; 10:10823-10837. [PMID: 32929382 PMCID: PMC7482804 DOI: 10.7150/thno.47830] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/15/2020] [Indexed: 12/21/2022] Open
Abstract
Rationale: The forkhead box A1 (FOXA1) is a crucial transcription factor in initiation and development of breast, lung and prostate cancer. Previous studies about the FOXA1 transcriptional network were mainly focused on protein-coding genes. Its regulatory network of long non-coding RNAs (lncRNAs) and their role in FOXA1 oncogenic activity remains unknown. Methods: The Cancer Genome Atlas (TCGA) data, RNA-seq and ChIP-seq data were used to analyze FOXA1 regulated lncRNAs. RT-qPCR was used to detect the expression of DSCAM-AS1, RT-qPCR and Western blotting were used to determine the expression of FOXA1, estrogen receptor α (ERα) and Y box binding protein 1 (YBX1). RNA pull-down and RIP-qPCR were employed to investigate the interaction between DSCAM-AS1 and YBX1. The effect of DSCAM-AS1 on malignant phenotypes was examined through in vitro and in vivo assays. Results: In this study, we conducted a global analysis of FOXA1 regulated lncRNAs. For detailed analysis, we chose lncRNA DSCAM-AS1, which is specifically expressed in lung adenocarcinoma, breast and prostate cancer. The expression level of DSCAM-AS1 is regulated by two super-enhancers (SEs) driven by FOXA1. High expression levels of DSCAM-AS1 was associated with poor prognosis. Knockout experiments showed DSCAM-AS1 was essential for the growth of xenograft tumors. Moreover, we demonstrated DSCAM-AS1 can regulate the expression of the master transcriptional factor FOXA1. In breast cancer, DSCAM-AS1 was also found to regulate ERα. Mechanistically, DSCAM-AS1 interacts with YBX1 and influences the recruitment of YBX1 in the promoter regions of FOXA1 and ERα. Conclusion: Our study demonstrated that lncRNA DSCAM-AS1 was transcriptionally activated by super-enhancers driven by FOXA1 and exhibited lineage-specific expression pattern. DSCAM-AS1 can promote cancer progression by interacting with YBX1 and regulating expression of FOXA1 and ERα.
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33
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Mi Z, Song Y, Cao X, Lu Y, Liu Z, Zhu X, Geng M, Sun Y, Lan B, He C, Xiong H, Zhang L, Chen Y. Super-enhancer-driven metabolic reprogramming promotes cystogenesis in autosomal dominant polycystic kidney disease. Nat Metab 2020; 2:717-731. [PMID: 32694829 DOI: 10.1038/s42255-020-0227-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/29/2020] [Indexed: 12/29/2022]
Abstract
Metabolic reprogramming is emerging as a key pathological contributor to the progression of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying dysregulated cellular metabolism in cystic cells remain elusive. Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive robust expression of cell identity and disease genes. Here, we show that SEs undergo extensive remodelling during cystogenesis and that SE-associated transcripts are most enriched for metabolic processes in cystic cells. Inhibition of cyclin-dependent kinase 7 (CDK7), a transcriptional kinase required for assembly and maintenance of SEs, or AMP deaminase 3 (AMPD3), one of the SE-driven and CDK7-controlled metabolic target genes, delays cyst growth in ADPKD mouse models. In a cohort of people with ADPKD, CDK7 expression was frequently elevated, and its expression was correlated with AMPD3 expression and disease severity. Together, our findings elucidate a mechanism by which SE controls transcription of metabolic genes during cystogenesis, and identify SE-driven metabolic reprogramming as a promising therapeutic target for ADPKD treatment.
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Affiliation(s)
- Zeyun Mi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yandong Song
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyi Cao
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yi Lu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhiheng Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xu Zhu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Meijuan Geng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yongzhan Sun
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bingxue Lan
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chaoran He
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hui Xiong
- Department of Urology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Lirong Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yupeng Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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Qu J, Ouyang Z, Wu W, Li G, Wang J, Lu Q, Li Z. Functions and Clinical Significance of Super-Enhancers in Bone-Related Diseases. Front Cell Dev Biol 2020; 8:534. [PMID: 32714929 PMCID: PMC7344144 DOI: 10.3389/fcell.2020.00534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
Super-enhancers (SEs) are a large cluster of cis-regulatory DNA elements that contain many binding motifs, which master transcription factors and cofactors bind to with high density. SEs usually regulate the expression of genes that can control the cell identity and fate, and SEs can be used to explain the patterns of the expression of cell-specific genes. Hence, it shows great potential for application in the treatment of diseases like cancer. At present, the clinical treatments for osteosarcoma, Ewing sarcoma, and other bone-related diseases remain challenging. The poor prognosis and difficult treatment of these diseases imposes heavy economic burden on patients and society. In recent years, research on SEs with respect to bone-related diseases has attracted increasing attention. In this paper, we first review the identification and functional mechanisms of SEs. Then, we integrate the findings of the emerging studies on SEs in bone-related diseases. Finally, we summarize recent strategies for targeting SEs for the treatment of bone-related diseases. This review aims to provide comprehensive insights into the roles of SEs in bone-related diseases.
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Affiliation(s)
- Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhanbo Ouyang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenqiang Wu
- Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guohua Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiaojiao Wang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiong Lu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhihong Li
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
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35
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Jones BG, Penkert RR, Surman SL, Sealy RE, Hurwitz JL. Nuclear Receptors, Ligands and the Mammalian B Cell. Int J Mol Sci 2020; 21:E4997. [PMID: 32679815 PMCID: PMC7404052 DOI: 10.3390/ijms21144997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022] Open
Abstract
Questions concerning the influences of nuclear receptors and their ligands on mammalian B cells are vast in number. Here, we briefly review the effects of nuclear receptor ligands, including estrogen and vitamins, on immunoglobulin production and protection from infectious diseases. We describe nuclear receptor interactions with the B cell genome and the potential mechanisms of gene regulation. Attention to the nuclear receptor/ligand regulation of B cell function may help optimize B cell responses, improve pathogen clearance, and prevent damaging responses toward inert- and self-antigens.
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Affiliation(s)
- Bart G. Jones
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.G.J.); (R.R.P.); (S.L.S.); (R.E.S.)
| | - Rhiannon R. Penkert
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.G.J.); (R.R.P.); (S.L.S.); (R.E.S.)
| | - Sherri L. Surman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.G.J.); (R.R.P.); (S.L.S.); (R.E.S.)
| | - Robert E. Sealy
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.G.J.); (R.R.P.); (S.L.S.); (R.E.S.)
| | - Julia L. Hurwitz
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.G.J.); (R.R.P.); (S.L.S.); (R.E.S.)
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Abstract
Pathological cardiac remodeling is induced through multiple mechanisms that include neurohumoral and biomechanical stress resulting in transcriptional alterations that ultimately become maladaptive and lead to the development of heart failure (HF). Although cardiac transcriptional remodeling is mediated by the activation of numerous signaling pathways that converge on a limited number of transcription factors (TFs) that promote hypertrophy (pro-hypertrophic TFs), the current therapeutic approach to prevent HF utilizes pharmacological inhibitors that largely target specific receptors that are activated in response to pathological stimuli. Thus, there is limited efficacy with the current pharmacological approaches to inhibit transcriptional remodeling associated with the development of HF. Recent evidence suggests that these pro-hypertrophic TFs co-localize at enhancers to cooperatively activate transcription associated with pathological cardiac remodeling. In disease states, including cancer and HF, evidence suggests that the general transcriptional machinery is disproportionately bound at enhancers. Therefore, pharmacological inhibition of transcriptional machinery that integrates pro-hypertrophic TFs may represent a promising alternative therapeutic approach to limit pathological remodeling associated with the development of HF.
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37
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Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2020; 47:11481-11496. [PMID: 31724731 PMCID: PMC7145697 DOI: 10.1093/nar/gkz1038] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/19/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression is precisely controlled in a stage and cell-type-specific manner, largely through the interaction between cis-regulatory elements and their associated trans-acting factors. Where these components aggregate in promoters and enhancers, they are able to cooperate to modulate chromatin structure and support the engagement in long-range 3D superstructures that shape the dynamics of a cell's genomic architecture. Recently, the term 'super-enhancer' has been introduced to describe a hyper-active regulatory domain comprising a complex array of sequence elements that work together to control the key gene networks involved in cell identity. Here, we survey the unique characteristics of super-enhancers compared to other enhancer types and summarize the recent advances in our understanding of their biological role in gene regulation. In particular, we discuss their capacity to attract the formation of phase-separated condensates, and capacity to generate three-dimensional genome structures that precisely activate their target genes. We also propose a multi-stage transition model to explain the evolutionary pressure driving the development of super-enhancers in complex organisms, and highlight the potential for involvement in tumorigenesis. Finally, we discuss more broadly the role of super-enhancers in human health disorders and related potential in therapeutic interventions.
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Affiliation(s)
- Xi Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Division of Theoretical Systems Biology, Germany Cancer Research Center, Heidelberg 69115, Germany.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia; and Hunter Medical Research Institute
| | - Jian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong S.A.R., China
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38
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Jones BG, Sealy RE, Penkert RR, Surman SL, Birshtein BK, Xu B, Neale G, Maul RW, Gearhart PJ, Hurwitz JL. From Influenza Virus Infections to Lupus: Synchronous Estrogen Receptor α and RNA Polymerase II Binding Within the Immunoglobulin Heavy Chain Locus. Viral Immunol 2020; 33:307-315. [PMID: 32105583 DOI: 10.1089/vim.2019.0144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Males and females respond to pathogens differently and exhibit significantly different frequencies of autoimmune disease. For example, vaccinated adult females control influenza virus better than males, but females suffer systemic lupus erythematosus at a 9:1 frequency compared to males. Numerous explanations have been offered for these sex differences, but most have involved indirect mechanisms by which estrogen, a nuclear hormone, modifies cell barriers or immunity. In search of a direct mechanism, we examined the binding of estrogen receptor α (ERα), a class I nuclear hormone receptor, to the immunoglobulin heavy chain locus. Here, we show that in purified murine B cells, ERα and RNA polymerase II (RNA Pol II) exhibit extraordinarily similar DNA binding patterns. We further demonstrate that ERα preferentially binds adenosine-cytidine (AC)-repeats in the immunoglobulin heavy chain locus when supplemental estrogen is added to purified, lipopolysaccharide-activated B cells. Based on these and previous data, we hypothesize that (i) estrogen guides the binding of ERα and its RNA Pol II partner within the locus, which in turn instructs sterile transcription and class switch recombination (CSR), (ii) ERα binding to AC-repeats modifies the DNA architecture and loops associated with CSR, and (iii) by these mechanisms, estrogen instructs antibody expression. By targeting ERα-DNA interactions in the immunoglobulin heavy chain locus, clinicians may ultimately enhance antibody responses in the context of infectious diseases and reduce antibody responses in the context of allergic or autoimmune reactions.
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Affiliation(s)
- Bart G Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert E Sealy
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rhiannon R Penkert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sherri L Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Barbara K Birshtein
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert W Maul
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Patricia J Gearhart
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Julia L Hurwitz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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39
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Bojcsuk D, Nagy G, Bálint BL. Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines. Int J Mol Sci 2020; 21:E1630. [PMID: 32120995 PMCID: PMC7084573 DOI: 10.3390/ijms21051630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 01/07/2023] Open
Abstract
Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators, which together establish a chromatin environment conducting to effective transcription. While cells with distinct TF profiles can have different functions, how different cells control overlapping genetic programs remains a question. In this paper, we show that the construction of estrogen receptor alpha-driven SEs is tissue-specific, both collaborating TFs and the active SE components greatly differ between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell lines have similar transcriptional outputs. These results delineate that despite the existence of a combinatorial code allowing alternative SE construction, a single master regulator might be able to determine the overall activity of SEs.
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Affiliation(s)
- Dóra Bojcsuk
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Bálint László Bálint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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40
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Huang M, Zeki J, Sumarsono N, Coles GL, Taylor JS, Danzer E, Bruzoni M, Hazard FK, Lacayo NJ, Sakamoto KM, Dunn JCY, Spunt SL, Chiu B. Epigenetic Targeting of TERT-Associated Gene Expression Signature in Human Neuroblastoma with TERT Overexpression. Cancer Res 2020; 80:1024-1035. [PMID: 31900258 DOI: 10.1158/0008-5472.can-19-2560] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/11/2019] [Accepted: 12/30/2019] [Indexed: 12/18/2022]
Abstract
Neuroblastoma is a deadly pediatric solid tumor with infrequent recurrent somatic mutations. Particularly, the pathophysiology of tumors without MYCN amplification remains poorly defined. Utilizing an unbiased approach, we performed gene set enrichment analysis of RNA-sequencing data from 498 patients with neuroblastoma and revealed a differentially overexpressed gene signature in MYCN nonamplified neuroblastomas with telomerase reverse transcriptase (TERT) gene overexpression and coordinated activation of oncogenic signaling pathways, including E2Fs, Wnt, Myc, and the DNA repair pathway. Promoter rearrangement of the TERT gene juxtaposes the coding sequence to strong enhancer elements, leading to TERT overexpression and poor prognosis in neuroblastoma, but TERT-associated oncogenic signaling remains unclear. ChIP-seq analysis of the human CLB-GA neuroblastoma cells harboring TERT rearrangement uncovered genome-wide chromatin co-occupancy of Brd4 and H3K27Ac and robust enrichment of H3K36me3 in TERT and multiple TERT-associated genes. Brd4 and cyclin-dependent kinases (CDK) had critical regulatory roles in the expression and chromatin activation of TERT and multiple TERT-associated genes. Epigenetically targeting Brd4 or CDKs with their respective inhibitors suppressed the expression of TERT and multiple TERT-associated genes in neuroblastoma with TERT overexpression or MYCN amplification. ChIP-seq and ChIP-qPCR provided evidence that the CDK inhibitor directly inhibited Brd4 recruitment to activate chromatin globally. Therefore, inhibiting Brd4 and CDK concurrently with AZD5153 and dinaciclib would be most effective in tumor growth suppression, which we demonstrated in neuroblastoma cell lines, primary human cells, and xenografts. In summary, we describe a unique mechanism in neuroblastoma with TERT overexpression and an epigenetically targeted novel therapeutic strategy. SIGNIFICANCE: Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks.
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Affiliation(s)
- Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Jasmine Zeki
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Nathan Sumarsono
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Garry L Coles
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Jordan S Taylor
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Enrico Danzer
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Matias Bruzoni
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Florette K Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Norman J Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Kathleen M Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - James C Y Dunn
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Sheri L Spunt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Bill Chiu
- Department of Surgery, Stanford University School of Medicine, Stanford, California.
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41
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Chang HC, Huang HC, Juan HF, Hsu CL. Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation. BMC Genomics 2019; 20:896. [PMID: 31888456 PMCID: PMC6936076 DOI: 10.1186/s12864-019-6293-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Super-enhancer RNAs (seRNAs) are a kind of noncoding RNA transcribed from super-enhancer regions. The regulation mechanism and functional role of seRNAs are still unclear. Although super-enhancers play a critical role in the core transcriptional regulatory circuity of embryonic stem cell (ESC) differentiation, whether seRNAs have similar properties should be further investigated. RESULTS We analyzed cap analysis gene expression sequencing (CAGE-seq) datasets collected during the differentiation of embryonic stem cells (ESCs) to cardiomyocytes to identify the seRNAs. A non-negative matrix factorization algorithm was applied to decompose the seRNA profiles and reveal two hidden stages during the ESC differentiation. We further identified 95 and 78 seRNAs associated with early- and late-stage ESC differentiation, respectively. We found that the binding sites of master regulators of ESC differentiation, including NANOG, FOXA2, and MYC, were significantly observed in the loci of the stage-specific seRNAs. Based on the investigation of genes coexpressed with seRNA, these stage-specific seRNAs might be involved in cardiac-related functions such as myofibril assembly and heart development and act in trans to regulate the co-expressed genes. CONCLUSIONS In this study, we used a computational approach to demonstrate the possible role of seRNAs during ESC differentiation.
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Affiliation(s)
- Hao-Chun Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Hsueh-Fen Juan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
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42
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Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington's disease. Proc Natl Acad Sci U S A 2019; 116:24840-24851. [PMID: 31744868 DOI: 10.1073/pnas.1908113116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder characterized by a late clinical onset despite ubiquitous expression of the mutant Huntingtin gene (HTT) from birth. Transcriptional dysregulation is a pivotal feature of HD. Yet, the genes that are altered in the prodromal period and their regulators, which present opportunities for therapeutic intervention, remain to be elucidated. Using transcriptional and chromatin profiling, we found aberrant transcription and changes in histone H3K27acetylation in the striatum of R6/1 mice during the presymptomatic disease stages. Integrating these data, we identified the Elk-1 transcription factor as a candidate regulator of prodromal changes in HD. Exogenous expression of Elk-1 exerted beneficial effects in a primary striatal cell culture model of HD, and adeno-associated virus-mediated Elk-1 overexpression alleviated transcriptional dysregulation in R6/1 mice. Collectively, our work demonstrates that aberrant gene expression precedes overt disease onset in HD, identifies the Elk-1 transcription factor as a key regulator linked to early epigenetic and transcriptional changes in HD, and presents evidence for Elk-1 as a target for alleviating molecular pathology in HD.
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43
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Jones BG, Penkert RR, Surman SL, Sealy RE, Pelletier S, Xu B, Neale G, Maul RW, Gearhart PJ, Hurwitz JL. Matters of life and death: How estrogen and estrogen receptor binding to the immunoglobulin heavy chain locus may influence outcomes of infection, allergy, and autoimmune disease. Cell Immunol 2019; 346:103996. [PMID: 31703914 DOI: 10.1016/j.cellimm.2019.103996] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/20/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022]
Abstract
Sex hormones are best known for their influences on reproduction, but they also have profound influences on the immune response. Examples of sex-specific differences include: (i) the relatively poor control of influenza virus infections in males compared to females, (ii) allergic asthma, an IgE-associated hypersensitivity reaction that is exacerbated in adolescent females compared to males, and (iii) systemic lupus erythematosus, a life-threatening autoimmune disease with a 9:1 female:male bias. Here we consider how estrogen and estrogen receptor α (ERα) may influence the immune response by modifying class switch recombination (CSR) and immunoglobulin expression patterns. We focus on ERα binding to enhancers (Eμ and the 3' regulatory region) and switch sites (Sµ and Sε) in the immunoglobulin heavy chain locus. Our preliminary data from ChIP-seq analyses of purified, activated B cells show estrogen-mediated changes in the positioning of ERα binding within and near Sµ and Sε. In the presence of estrogen, ERα is bound not only to estrogen response elements (ERE), but also to adenosine-cytidine (AC)-repeats and poly adenosine (poly A) sequences, in some cases within constant region gene introns. We propose that by binding these sites, estrogen and ERα directly participate in the DNA loop formation required for CSR. We further suggest that estrogen regulates immunoglobulin expression patterns and can thereby influence life-and-death outcomes of infection, hypersensitivity, and autoimmune disease.
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Affiliation(s)
- Bart G Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Rhiannon R Penkert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sherri L Surman
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert E Sealy
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephane Pelletier
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Geoff Neale
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert W Maul
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Patricia J Gearhart
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - J L Hurwitz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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44
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Gowda C, Song C, Ding Y, Iyer S, Dhanyamraju PK, McGrath M, Bamme Y, Soliman M, Kane S, Payne JL, Dovat S. Cellular signaling and epigenetic regulation of gene expression in leukemia. Adv Biol Regul 2019; 75:100665. [PMID: 31623972 PMCID: PMC7239353 DOI: 10.1016/j.jbior.2019.100665] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
Alterations in normal regulation of gene expression is one of the key features of hematopoietic malignancies. In order to gain insight into the mechanisms that regulate gene expression in these diseases, we dissected the role of the Ikaros protein in leukemia. Ikaros is a DNA-binding, zinc finger protein that functions as a transcriptional regulator and a tumor suppressor in leukemia. The use of ChIP-seq, RNA-seq, and ATAC-seq—coupled with functional experiments—revealed that Ikaros regulates both the global epigenomic landscape and epigenetic signature at promoter regions of its target genes. Casein kinase II (CK2), an oncogenic kinase that is overexpressed in leukemia, directly phosphorylates Ikaros at multiple, evolutionarily-conserved residues. Phosphorylation of Ikaros impairs the protein's ability to regulate both the transcription of its target genes and global epigenetic landscape in leukemia. Treatment of leukemia cells with a specific inhibitor of CK2 restores Ikaros function, resulting in cytotoxicity of leukemia cells. Here, we review the mechanisms through which the CK2-Ikaros signaling axis regulates the global epigenomic landscape and expression of genes that control cellular proliferation in leukemia.
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Affiliation(s)
- Chandrika Gowda
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yali Ding
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mary McGrath
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yevgeniya Bamme
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mario Soliman
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Shriya Kane
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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45
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In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. Int J Mol Sci 2019; 20:ijms20143582. [PMID: 31336658 PMCID: PMC6679006 DOI: 10.3390/ijms20143582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/06/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
Understanding the gene regulatory network governing cancer initiation and progression is necessary, although it remains largely unexplored. Enhancer elements represent the center of this regulatory circuit. The study aims to identify the gene expression change driven by copy number variation in enhancer elements of pancreatic adenocarcinoma (PAAD). The pancreatic tissue specific enhancer and target gene data were taken from EnhancerAtlas. The gene expression and copy number data were taken from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) and copy number variations (CNVs) were identified between matched tumor-normal samples of PAAD. Significant CNVs were matched onto enhancer coordinates by using genomic intersection functionality from BEDTools. By combining the gene expression and CNV data, we identified 169 genes whose expression shows a positive correlation with the CNV of enhancers. We further identified 16 genes which are regulated by a super enhancer and 15 genes which have high prognostic potential (Z-score > 1.96). Cox proportional hazard analysis of these genes indicates that these are better predictors of survival. Taken together, our integrative analytical approach identifies enhancer CNV-driven gene expression change in PAAD, which could lead to better understanding of PAAD pathogenesis and to the design of enhancer-based cancer treatment strategies.
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46
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Li K, Xu C, Du Y, Junaid M, Kaushik AC, Wei DQ. Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer. J Cell Mol Med 2019; 23:5415-5431. [PMID: 31215771 PMCID: PMC6653217 DOI: 10.1111/jcmm.14424] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/30/2019] [Accepted: 05/12/2019] [Indexed: 01/02/2023] Open
Abstract
The lung metastasis of breast cancer involves complicated regulatory changes driven by chromatin remodelling. However, the epigenetic reprogramming and regulatory mechanisms in lung metastasis of breast cancer remain unclear. Here, we generated and analysed genome‐wide profiles of multiple histone modifications (H3K4me3, H3K27ac, H3K27me3, H3K4me1 and H3K9me3), as well as transcriptome data in lung‐metastatic and non‐lung‐metastatic breast cancer cells. Our results showed that the expression changes were correlated with the enrichment of specific histone modifications in promoters and enhancers. Promoter and enhancer reprogramming regulated gene expression in a synergetic way, and involved in multiple important biological processes and pathways. In addition, lots of gained super‐enhancers were identified in lung‐metastatic cells. We also identified master regulators driving differential gene expression during lung metastasis of breast cancer. We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover, regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. Functional studies motivated by our data analyses uncovered an important role of LMO4 in regulating metastasis. This study provided comprehensive insights into regulatory mechanisms, as well as potential prognostic markers for lung metastasis of breast cancer.
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Affiliation(s)
- Kening Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Congling Xu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Yuxin Du
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Aman-Chandra Kaushik
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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47
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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: 3.0] [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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48
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Chen CH, Yang N, Zhang Y, Ding J, Zhang W, Liu R, Liu W, Chen C. Inhibition of super enhancer downregulates the expression of KLF5 in basal-like breast cancers. Int J Biol Sci 2019; 15:1733-1742. [PMID: 31360115 PMCID: PMC6643226 DOI: 10.7150/ijbs.35138] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022] Open
Abstract
The transcription factor KLF5 (Krüpple-like factor 5) is highly expressed in basal-like breast cancer (BLBC), which promotes cell proliferation, survival, migration and stemness, serving as a potential therapeutic target. In the current study, a super-enhancer (SE) was identified to be located downstream of the KLF5 gene in BLBC cell lines, HCC1806 and HCC1937. JQ-1, a BRD4 inhibitor, inhibits the expression and activity of KLF5 in both HCC1806 and HCC1937 cells in a time- and dose-dependent manner. Compound 870, an in-house BRD4 inhibitor, exhibited higher potency than JQ-1 to inhibit KLF5 and BLBC growth by arresting cells in G1 phase. Additionally, THZ1, a CDK7 inhibitor, also inhibits KLF5 and BLBC growth in a similar manner. Our findings suggested that KLF5 is regulated by SE, and modulation of SE could be an effective therapeutic strategy for treating BLBC.
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Affiliation(s)
- Chuan-Huizi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.,School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Nong Yang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, Hunan, 410013, China
| | - Yongchang Zhang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, Hunan, 410013, China
| | - Jiancheng Ding
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian, 361102, China
| | - Wenjuan Zhang
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian, 361102, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Wen Liu
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian, 361102, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101, China.,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China, 510095
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Bao J, Li M, Liang S, Yang Y, Wu J, Zou Q, Fang S, Chen S, Guo L. Integrated high-throughput analysis identifies super enhancers associated with chemoresistance in SCLC. BMC Med Genomics 2019; 12:67. [PMID: 31118037 PMCID: PMC6532255 DOI: 10.1186/s12920-019-0520-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Chemoresistance is a primary clinical challenge for the management of small cell lung cancer. Additionally, transcriptional regulation by super enhancer (SE) has an important role in tumor evolution. The functions of SEs, a key class of noncoding DNA cis-regulatory elements, have been the subject of many recent studies in the field of cancer research. METHODS In this study, using chromatin immunoprecipitation-sequencing and RNA-sequencing (RNA-seq), we aimed to identify SEs associated with chemoresistance from H69AR cells. Through integrated bioinformatics analysis of the MEME chip, we predicted the master transcriptional factors (TFs) binding to SE sites and verified the relationships between TFs of SEs and drug resistance by RNA interference, cell counting kit 8 assays, quantitative real-time reverse transcription polymerase chain reaction. RESULTS In total, 108 SEs were screened from H69AR cells. When combining this analysis with RNA-seq data, 45 SEs were suggested to be closely related to drug resistance. Then, 12 master TFs were predicted to localize to regions of those SEs. Subsequently, we selected forkhead box P1 (FOXP1), interferon regulatory factor 1 (IRF1), and specificity protein 1 (SP1) to authenticate the functional relationships of master TFs with chemoresistance via SEs. CONCLUSIONS We screened out SEs involved with drug resistance and evaluated the functions of FOXP1, IRF1, and SP1 in chemoresistance. Our findings established a large group of SEs associated with drug resistance in small cell lung cancer, revealed the drug resistance mechanisms of SEs, and provided insights into the clinical applications of SEs.
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Affiliation(s)
- Jiarong Bao
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
- Department of Pathology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, 510900, People's Republic of China
| | - Man Li
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Shumei Liang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Yunchu Yang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Jingfang Wu
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Qingqing Zou
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Shun Fang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Size Chen
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China.
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China.
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Ding Y, Zhang B, Payne JL, Song C, Ge Z, Gowda C, Iyer S, Dhanyamraju PK, Dorsam G, Reeves ME, Desai D, Huang S, Payne KJ, Yue F, Dovat S. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia 2019; 33:2720-2731. [PMID: 31073152 PMCID: PMC6842075 DOI: 10.1038/s41375-019-0474-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Ikaros encodes a transcription factor that functions as a tumor suppressor in T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells resulted in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic, global, epigenomic and gene expression analyses to determine the mechanisms of Ikaros tumor suppressor activity. Our results identified novel Ikaros functions in the epigenetic regulation of gene expression: Ikaros directly regulates de novo formation and depletion of enhancers, de novo formation of active enhancers and activation of poised enhancers; Ikaros directly induces the formation of super-enhancers; and Ikaros demonstrates pioneering activity by directly regulating chromatin accessibility. Dynamic analyses demonstrate the long-lasting effects of Ikaros DNA binding on enhancer activation, de novo formation of enhancers and super-enhancers, and chromatin accessibility. Our results establish that Ikaros’ tumor suppressor function occurs via global regulation of the enhancer and super-enhancer landscape and through pioneering activity. Expression analysis identified a large number of novel signaling pathways that are directly regulated by Ikaros and Ikaros-induced enhancers, and that are responsible for the cessation of proliferation and induction of T-cell differentiation in T-ALL cells.
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Affiliation(s)
- Yali Ding
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chunhua Song
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital Southeast University, Institute of Hematology Southeast University, 210009, Nanjing, China
| | - Chandrika Gowda
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Glenn Dorsam
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Mark E Reeves
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Dhimant Desai
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suming Huang
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kimberly J Payne
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Sinisa Dovat
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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