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Dai Y, Ying Y, Zhu G, Xu Y, Ji K. STAT3 drives the expression of HIF1alpha in cancer cells through a novel super-enhancer. Biochem Biophys Res Commun 2024; 735:150483. [PMID: 39098275 DOI: 10.1016/j.bbrc.2024.150483] [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: 06/04/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
Aerobic glycolysis is one of the major hallmarks of malignant tumors. This metabolic reprogramming benefits the rapid proliferation of cancer cells, facilitates the formation of tumor microenvironment to support their growth and survival, and impairs the efficacy of various tumor therapies. Therefore, the elucidation of the mechanisms driving aerobic glycolysis in tumors represents a pivotal breakthrough in developing therapeutic strategies for solid tumors. HIF1α serves as a central regulator of aerobic glycolysis with elevated mRNA and protein expression across multiple tumor types. However, the mechanisms contributing to this upregulation remain elusive. This study reports the identification of a novel HIF1α super enhancer (HSE) in multiple cancer cells using bioinformatics analysis, chromosome conformation capture (3C), chromatin immunoprecipitation (ChIP), and CRISPR/Cas9 genome editing techniques. Deletion of HSE in cancer cells significantly reduces the expression of HIF1α, glycolysis, cell proliferation, colony and tumor formation ability, confirming the role of HSE as the enhancer of HIF1α in cancer cells. Particularly, we demonstrated that STAT3 promotes the expression of HIF1α by binding to HSE. The discovery of HSE will help elucidate the pathways driving tumor aerobic glycolysis, offering new therapeutic targets and potentially resolving the bottleneck in solid tumor treatment.
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Affiliation(s)
- Yonghui Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yue Ying
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Gaoyang Zhu
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Yang Xu
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China; Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0322, USA.
| | - Kaiyuan Ji
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China; Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China; Medical Research Center, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
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2
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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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Martella N, Pensabene D, Varone M, Colardo M, Petraroia M, Sergio W, La Rosa P, Moreno S, Segatto M. Bromodomain and Extra-Terminal Proteins in Brain Physiology and Pathology: BET-ing on Epigenetic Regulation. Biomedicines 2023; 11:biomedicines11030750. [PMID: 36979729 PMCID: PMC10045827 DOI: 10.3390/biomedicines11030750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
BET proteins function as histone code readers of acetylated lysins that determine the positive regulation in transcription of genes involved in cell cycle progression, differentiation, inflammation, and many other pathways. In recent years, thanks to the development of BET inhibitors, interest in this protein family has risen for its relevance in brain development and function. For example, experimental evidence has shown that BET modulation affects neuronal activity and the expression of genes involved in learning and memory. In addition, BET inhibition strongly suppresses molecular pathways related to neuroinflammation. These observations suggest that BET modulation may play a critical role in the onset and during the development of diverse neurodegenerative and neuropsychiatric disorders, such as Alzheimer’s disease, fragile X syndrome, and Rett syndrome. In this review article, we summarize the most recent evidence regarding the involvement of BET proteins in brain physiology and pathology, as well as their pharmacological potential as targets for therapeutic purposes.
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Affiliation(s)
- Noemi Martella
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Daniele Pensabene
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Michela Varone
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Mayra Colardo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Michele Petraroia
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - William Sergio
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, via dei Marsi 78, 00185 Rome, Italy
| | - Sandra Moreno
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Marco Segatto
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Correspondence:
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Zerio CJ, Sivinski J, Wijeratne EMK, Xu YM, Ngo DT, Ambrose AJ, Villa-Celis L, Ghadirian N, Clarkson MW, Zhang DD, Horton NC, Gunatilaka AAL, Fromme R, Chapman E. Physachenolide C is a Potent, Selective BET Inhibitor. J Med Chem 2023; 66:913-933. [PMID: 36577036 DOI: 10.1021/acs.jmedchem.2c01770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.
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Affiliation(s)
- Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - E M Kithsiri Wijeratne
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Ya-Ming Xu
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Duc T Ngo
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Luis Villa-Celis
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Michael W Clarkson
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85719, United States
| | - Donna D Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - A A Leslie Gunatilaka
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Raimund Fromme
- School of Molecular Sciences, Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, Arizona 85287, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
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Xiao Q, Xiao Y, Li LY, Chen MK, Wu M. Multifaceted regulation of enhancers in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194839. [PMID: 35750313 DOI: 10.1016/j.bbagrm.2022.194839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Enhancer is one kind of cis-elements regulating gene transcription, whose activity is tightly controlled by epigenetic enzymes and histone modifications. Active enhancers are classified into typical enhancers, super-enhancers and over-active enhancers, according to the enrichment and location of histone modifications. Epigenetic factors control the level of histone modifications on enhancers to determine their activity, such as histone methyltransferases and acetylases. Transcription factors, cofactors and mediators co-operate together and are required for enhancer functions. In turn, abnormalities in these trans-acting factors affect enhancer activity. Recent studies have revealed enhancer dysregulation as one of the important features for cancer. Variations in enhancer regions and mutations of enhancer regulatory genes are frequently observed in cancer cells, and altering the activity of onco-enhancers is able to repress oncogene expression, and suppress tumorigenesis and metastasis. Here we summarize the recent discoveries about enhancer regulation in cancer and discuss their potential application in diagnosis and treatment.
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Affiliation(s)
- Qiong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Yong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Ming-Kai Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
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El Hadi C, Ayoub G, Bachir Y, Haykal M, Jalkh N, Kourie HR. Polygenic and Network-Based Studies in Risk Identification and Demystification of cancer. Expert Rev Mol Diagn 2022; 22:427-438. [PMID: 35400274 DOI: 10.1080/14737159.2022.2065195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Diseases were initially thought to be the consequence of a single gene mutation. Advances in DNA sequencing tools and our understanding of gene behavior have revealed that complex diseases, such as cancer, are the product of genes cooperating with each other and with their environment in orchestrated communication networks. Seeing that the function of individual genes is still used to analyze cancer, the shift to using functionally interacting groups of genes as a new unit of study holds promise for demystifying cancer. AREAS COVERED The literature search focused on three types of cancer, namely breast, lung, and prostate, but arguments from other cancers were also included. The aim was to prove that multigene analyses can accurately predict and prognosticate cancer risk, subtype cancer for more personalized and effective treatments, and discover anti-cancer therapies. Computational intelligence is being harnessed to analyze this type of data and is proving indispensable to scientific progress. EXPERT OPINION In the future, comprehensive profiling of all kinds of patient data (e.g., serum molecules, environmental exposures) can be used to build universal networks that should help us elucidate the molecular mechanisms underlying diseases and provide appropriate preventive measures, ensuring lifelong health and longevity.
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Affiliation(s)
| | - George Ayoub
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Yara Bachir
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Michèle Haykal
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Technology and Health division, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Department of Hematology-Oncology, Hotel Dieu de France University Hospital, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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7
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Lelièvre SA. Can the epigenome contribute to risk stratification for cancer onset? NAR Cancer 2021; 3:zcab043. [PMID: 34734185 PMCID: PMC8559165 DOI: 10.1093/narcan/zcab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/10/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
The increasing burden of cancer requires identifying and protecting individuals at highest risk. The epigenome provides an indispensable complement to genetic alterations for a risk stratification approach for the following reasons: gene transcription necessary for cancer onset is directed by epigenetic modifications and many risk factors studied so far have been associated with alterations related to the epigenome. The risk level depends on the plasticity of the epigenome during phases of life particularly sensitive to environmental and dietary impacts. Modifications in the activity of DNA regulatory regions and altered chromatin compaction may accumulate, hence leading to the increase of cancer risk. Moreover, tissue architecture directs the unique organization of the epigenome for each tissue and cell type, which allows the epigenome to control cancer risk in specific organs. Investigations of epigenetic signatures of risk should help identify a continuum of alterations leading to a threshold beyond which the epigenome cannot maintain homeostasis. We propose that this threshold may be similar in the population for a given tissue, but the pace to reach this threshold will depend on the combination of germline inheritance and the risk and protective factors encountered, particularly during windows of epigenetic susceptibility, by individuals.
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Affiliation(s)
- Sophie A Lelièvre
- Institut de Cancérologie de l'Ouest (ICO)-Western Cancer Institute, Scientific Direction for Translational Research, Angers, France
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8
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Wengner AM, Scholz A, Haendler B. Targeting DNA Damage Response in Prostate and Breast Cancer. Int J Mol Sci 2020; 21:E8273. [PMID: 33158305 PMCID: PMC7663807 DOI: 10.3390/ijms21218273] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Steroid hormone signaling induces vast gene expression programs which necessitate the local formation of transcription factories at regulatory regions and large-scale alterations of the genome architecture to allow communication among distantly related cis-acting regions. This involves major stress at the genomic DNA level. Transcriptionally active regions are generally instable and prone to breakage due to the torsional stress and local depletion of nucleosomes that make DNA more accessible to damaging agents. A dedicated DNA damage response (DDR) is therefore essential to maintain genome integrity at these exposed regions. The DDR is a complex network involving DNA damage sensor proteins, such as the poly(ADP-ribose) polymerase 1 (PARP-1), the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the ataxia-telangiectasia-mutated (ATM) kinase and the ATM and Rad3-related (ATR) kinase, as central regulators. The tight interplay between the DDR and steroid hormone receptors has been unraveled recently. Several DNA repair factors interact with the androgen and estrogen receptors and support their transcriptional functions. Conversely, both receptors directly control the expression of agents involved in the DDR. Impaired DDR is also exploited by tumors to acquire advantageous mutations. Cancer cells often harbor germline or somatic alterations in DDR genes, and their association with disease outcome and treatment response led to intensive efforts towards identifying selective inhibitors targeting the major players in this process. The PARP-1 inhibitors are now approved for ovarian, breast, and prostate cancer with specific genomic alterations. Additional DDR-targeting agents are being evaluated in clinical studies either as single agents or in combination with treatments eliciting DNA damage (e.g., radiation therapy, including targeted radiotherapy, and chemotherapy) or addressing targets involved in maintenance of genome integrity. Recent preclinical and clinical findings made in addressing DNA repair dysfunction in hormone-dependent and -independent prostate and breast tumors are presented. Importantly, the combination of anti-hormonal therapy with DDR inhibition or with radiation has the potential to enhance efficacy but still needs further investigation.
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Affiliation(s)
| | | | - Bernard Haendler
- Preclinical Research, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (A.M.W.); (A.S.)
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Mbemi A, Khanna S, Njiki S, Yedjou CG, Tchounwou PB. Impact of Gene-Environment Interactions on Cancer Development. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E8089. [PMID: 33153024 PMCID: PMC7662361 DOI: 10.3390/ijerph17218089] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Several epidemiological and experimental studies have demonstrated that many human diseases are not only caused by specific genetic and environmental factors but also by gene-environment interactions. Although it has been widely reported that genetic polymorphisms play a critical role in human susceptibility to cancer and other chronic disease conditions, many single nucleotide polymorphisms (SNPs) are caused by somatic mutations resulting from human exposure to environmental stressors. Scientific evidence suggests that the etiology of many chronic illnesses is caused by the joint effect between genetics and the environment. Research has also pointed out that the interactions of environmental factors with specific allelic variants highly modulate the susceptibility to diseases. Hence, many scientific discoveries on gene-environment interactions have elucidated the impact of their combined effect on the incidence and/or prevalence rate of human diseases. In this review, we provide an overview of the nature of gene-environment interactions, and discuss their role in human cancers, with special emphases on lung, colorectal, bladder, breast, ovarian, and prostate cancers.
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Affiliation(s)
- Ariane Mbemi
- NIH/NIMHD RCMI-Center for Health Disparities Research, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, MS 39217, USA; (A.M.); (S.N.)
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18540, Jackson, MS 39217, USA
| | - Sunali Khanna
- Department of Oral Medicine and Radiology, Nair Hospital Dental College, Municipal Corporation of Greater Mumbai, Mumbai 400 008, India;
| | - Sylvianne Njiki
- NIH/NIMHD RCMI-Center for Health Disparities Research, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, MS 39217, USA; (A.M.); (S.N.)
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18540, Jackson, MS 39217, USA
| | - Clement G. Yedjou
- Department of Biological Sciences, College of Science and Technology, Florida Agricultural and Mechanical University, 1610 S. Martin Luther King Blvd., Tallahassee, FL 32307, USA;
| | - Paul B. Tchounwou
- NIH/NIMHD RCMI-Center for Health Disparities Research, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, MS 39217, USA; (A.M.); (S.N.)
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18540, Jackson, MS 39217, USA
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BET bromodomains as novel epigenetic targets for brain health and disease. Neuropharmacology 2020; 181:108306. [PMID: 32946883 DOI: 10.1016/j.neuropharm.2020.108306] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
Epigenetic pharmacotherapy for CNS-related diseases is a burgeoning area of research. In particular, members of the bromodomain and extra-terminal domain (BET) family of proteins have emerged as intriguing therapeutic targets due to their putative involvement in an array of brain diseases. With their ability to bind to acetylated histones and act as a scaffold for chromatin modifying complexes, BET proteins were originally thought of as passive epigenetic 'reader' proteins. However, new research depicts a more complex reality where BET proteins act as key nodes in lineage-specific and signal-dependent transcriptional mechanisms to influence disease-relevant functions. Amid a recent wave of drug development efforts from basic scientists and pharmaceutical companies, BET inhibitors are currently being studied in several CNS-related disease models, but safety and tolerability remain a concern. Here we review the progress in understanding the neurobiological mechanisms of BET proteins and the therapeutic potential of targeting BET proteins for brain health and disease.
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Aberrant activation of super enhancer and choline metabolism drive antiandrogen therapy resistance in prostate cancer. Oncogene 2020; 39:6556-6571. [PMID: 32917955 DOI: 10.1038/s41388-020-01456-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/20/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022]
Abstract
Next generation antiandrogens such as enzalutamide (Enz) are effective initially for the treatment of castration-resistant prostate cancer (CRPC). However, the disease often relapses and the underlying mechanisms remain elusive. By performing H3-lysine-27 acetylation (H3K27ac) ChIP-seq in Enz-resistant CRPC cells, we identified a group of super enhancers (SEs) that are abnormally activated in Enz-resistant CRPC cells and associated with enhanced transcription of a subset of tumor promoting genes such as CHPT1, which catalyzes phosphatidylcholine (PtdCho) synthesis and regulates choline metabolism. Increased CHPT1 conferred CRPC resistance to Enz in vitro and in mice. While androgen receptor (AR) primarily binds to a putative CHPT1 enhancer and mediates androgen-dependent expression of CHPT1 gene in Enz-sensitive prostate cancer cells, AR binds to a different enhancer within the CHPT1 SE locus and facilities androgen-independent expression of CHPT1 in Enz-resistant cells. We further identified a long-non coding RNA transcribed at CHPT1 enhancer (also known as enhancer RNA) that binds to the H3K27ac reader BRD4 and participates in regulating CHPT1 SE activity and CHPT1 gene expression. Our findings demonstrate that aberrantly activated SE upregulates CHPT1 expression and confers Enz resistance in CRPC, suggesting that SE-mediated expression of downstream effectors such as CHPT1 can be viable targets to overcome Enz resistance in PCa.
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12
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Baumgart SJ, Nevedomskaya E, Lesche R, Newman R, Mumberg D, Haendler B. Darolutamide antagonizes androgen signaling by blocking enhancer and super-enhancer activation. Mol Oncol 2020; 14:2022-2039. [PMID: 32333502 PMCID: PMC7463324 DOI: 10.1002/1878-0261.12693] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/03/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) is one of the most frequent tumor types in the male Western population. Early-stage PCa and late-stage PCa are dependent on androgen signaling, and inhibitors of the androgen receptor (AR) axis represent the standard therapy. Here, we studied in detail the global impact of darolutamide, a newly approved AR antagonist, on the transcriptome and AR-bound cistrome in two PCa cell models. Darolutamide strongly depleted the AR from gene regulatory regions and abolished AR-driven transcriptional signaling. Enhancer activation was blocked at the chromatin level as evaluated by H3K27 acetylation (H3K27ac), H3K4 monomethylation (H3K4me1), and FOXA1, MED1, and BRD4 binding. We identified genomic regions with high affinities for the AR in androgen-stimulated, but also in androgen-depleted conditions. A similar AR affinity pattern was observed in healthy and PCa tissue samples. High FOXA1, BRD4, H3K27ac, and H3K4me1 levels were found to mark regions showing AR binding in the hormone-depleted setting. Conversely, low FOXA1, BRD4, and H3K27ac levels were observed at regulatory sites that responded strongly to androgen stimulation, and AR interactions at these sites were blocked by darolutamide. Beside marked loss of AR occupancy, FOXA1 recruitment to chromatin was also clearly reduced after darolutamide treatment. We furthermore identified numerous androgen-regulated super-enhancers (SEs) that were associated with hallmark androgen and cell proliferation-associated gene sets. Importantly, these SEs are also active in PCa tissues and sensitive to darolutamide treatment in our models. Our findings demonstrate that darolutamide is a potent AR antagonist blocking genome-wide AR enhancer and SE activation, and downstream transcription. We also show the existence of a dynamic AR cistrome that depends on the androgen levels and on high AR affinity regions present in PCa cell lines and also in tissue samples.
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Affiliation(s)
| | | | - Ralf Lesche
- Research and Development, PharmaceuticalsBayer AGBerlinGermany
| | - Richard Newman
- Research and Development, PharmaceuticalsBayer AGBerlinGermany
| | - Dominik Mumberg
- Research and Development, PharmaceuticalsBayer AGBerlinGermany
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13
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Zheng C, Liu M, Fan H. Targeting complexes of super-enhancers is a promising strategy for cancer therapy. Oncol Lett 2020; 20:2557-2566. [PMID: 32782573 PMCID: PMC7400756 DOI: 10.3892/ol.2020.11855] [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: 12/28/2019] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
The hyperactivation and overexpression of critical oncogenes is a common occurrence in multiple types of malignant tumors. Recently, the abnormal activation mechanism of an oncogene by a super-enhancer (SE) has attracted significant attention. A series of changes (insertion, deletion, translocation and rearrangement) in the genome occurring in cancer cells may generate new SEs, leading to the overexpression of SE-driven oncogenes. SEs are composed of typical enhancers densely loaded with mediator complexes, transcription factors, and chromatin regulators, and drive the overexpression of oncogenes associated with cellular identity and disease. Cyclin-dependent kinase 7 (CDK7) and bromodomain protein 4 (BRD4) are critical mediator complexes associated with SE-mediated transcription. Clinical trials have shown that emerging small-molecule inhibitors (CDK7 and BRD4 inhibitor), targeting the SE exert a notable effect on cancer treatment. Increasing evidences has illustrated that the SE and its associated complexes play a critical role in the development of various types of cancer. The present review discusses the composition, function and regulation of SEs and their contribution to oncogenic transcription. In addition, creative therapeutic approaches that target SE, their advantages and disadvantages, as well as the problems with their clinical application are discussed. It was found that targeting SE may be used in conventional treatment and establish more access for patients with cancer.
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Affiliation(s)
- Chuqian Zheng
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Min Liu
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China.,School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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14
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Boedicker C, Hussong M, Grimm C, Dolgikh N, Meister MT, Enßle JC, Wanior M, Knapp S, Schweiger MR, Fulda S. Co-inhibition of BET proteins and PI3Kα triggers mitochondrial apoptosis in rhabdomyosarcoma cells. Oncogene 2020; 39:3837-3852. [PMID: 32161312 DOI: 10.1038/s41388-020-1229-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/14/2022]
Abstract
Remodeling transcription by targeting bromodomain and extraterminal (BET) proteins has emerged as promising anticancer strategy. Here, we identify a novel synergistic interaction of the BET inhibitor JQ1 with the PI3Kα-specific inhibitor BYL719 to trigger mitochondrial apoptosis and to suppress tumor growth in models of rhabdomyosarcoma (RMS). RNA-Seq revealed that JQ1/BYL719 co-treatment shifts the overall balance of BCL-2 family gene expression towards apoptosis and upregulates expression of BMF, BCL2L11 (BIM), and PMAIP1 (NOXA) while downregulating BCL2L1 (BCL-xL). These changes were confirmed by qRT-PCR and western blot analysis. Ingenuity pathway analysis (IPA) of RNA-Seq data followed by validation qRT-PCR and western blot identified MYC and FOXO3a as potential transcription factors (TFs) upstream of the observed gene expression pattern. Immunoprecipitation (IP) studies showed that JQ1/BYL719-stimulated increase in BIM expression enhances the neutralization of antiapoptotic BCL-2, BCL-xL, and MCL-1. This promotes the activation of BAK and BAX and caspase-dependent apoptosis, as (1) individual silencing of BMF, BIM, NOXA, BAK, or BAX, (2) overexpression of BCL-2 or MCL-1 or (3) the caspase inhibitor N-Benzyloxycarbonyl-Val-Ala-Asp(O-Me) fluoromethylketone (zVAD.fmk) all rescue JQ1/BYL719-induced cell death. In conclusion, co-inhibition of BET proteins and PI3Kα cooperatively induces mitochondrial apoptosis by proapoptotic re-balancing of BCL-2 family proteins. This discovery opens exciting perspectives for therapeutic exploitation of BET inhibitors in RMS.
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Affiliation(s)
- Cathinka Boedicker
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site, Frankfurt, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Hussong
- Laboratory for Epigenomics and Tumor genetics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christina Grimm
- Laboratory for Epigenomics and Tumor genetics, University Hospital Cologne, Cologne, Germany
| | - Nadezda Dolgikh
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
| | - Michael T Meister
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site, Frankfurt, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Julius C Enßle
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
| | - Marek Wanior
- Institute for Pharmaceutical Chemistry and BMLS (SGC), Frankfurt, Germany
| | - Stefan Knapp
- German Cancer Consortium (DKTK), Partner Site, Frankfurt, Germany
- Institute for Pharmaceutical Chemistry and BMLS (SGC), Frankfurt, Germany
| | - Michal R Schweiger
- Laboratory for Epigenomics and Tumor genetics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany.
- German Cancer Consortium (DKTK), Partner Site, Frankfurt, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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15
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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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16
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Stelloo S, Bergman AM, Zwart W. Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers. Endocr Relat Cancer 2019; 26:R267-R285. [PMID: 30865928 DOI: 10.1530/erc-19-0032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance. Genome-wide chromatin association studies revealed that transcriptional regulation by AR mainly depends on binding to distal regulatory enhancer elements that control gene expression through chromatin looping to gene promoters. Changes in the chromatin epigenetic landscape and DNA sequence can locally alter AR-DNA-binding capacity and consequently impact transcriptional output and disease outcome. The vast majority of reports describing AR chromatin interactions have been limited to cell lines, identifying numerous other factors and interacting transcription factors that impact AR chromatin interactions. Do these factors also impact AR cistromics - the genome-wide chromatin-binding landscape of AR - in vivo? Recent technological advances now enable researchers to identify AR chromatin-binding sites and their target genes in human specimens. In this review, we provide an overview of the different factors that influence AR chromatin binding in prostate cancer specimens, which is complemented with knowledge from cell line studies. Finally, we discuss novel perspectives on studying AR cistromics in clinical samples.
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Affiliation(s)
- Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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17
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Braadland PR, Urbanucci A. Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer. Endocr Relat Cancer 2019; 26:R211-R235. [PMID: 30844748 DOI: 10.1530/erc-18-0579] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Tumor evolution is based on the ability to constantly mutate and activate different pathways under the selective pressure of targeted therapies. Epigenetic alterations including those of the chromatin structure are associated with tumor initiation, progression and drug resistance. Many cancers, including prostate cancer, present enlarged nuclei, and chromatin appears altered and irregular. These phenotypic changes are likely to result from epigenetic dysregulation. High-throughput sequencing applied to bulk samples and now to single cells has made it possible to study these processes in unprecedented detail. It is therefore timely to review the impact of chromatin relaxation and increased DNA accessibility on prostate cancer growth and drug resistance, and their effects on gene expression. In particular, we focus on the contribution of chromatin-associated proteins such as the bromodomain-containing proteins to chromatin relaxation. We discuss the consequence of this for androgen receptor transcriptional activity and briefly summarize wider gain-of-function effects on other oncogenic transcription factors and implications for more effective prostate cancer treatment.
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Affiliation(s)
- Peder Rustøen Braadland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, Oslo, Norway
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18
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Yoo KH, Hennighausen L, Shin HY. Dissecting Tissue-Specific Super-Enhancers by Integrating Genome-Wide Analyses and CRISPR/Cas9 Genome Editing. J Mammary Gland Biol Neoplasia 2019; 24:47-59. [PMID: 30291498 DOI: 10.1007/s10911-018-9417-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022] Open
Abstract
Recent advances in genome-wide sequencing technologies have provided researchers with unprecedented opportunities to discover the genomic structures of gene regulatory units in living organisms. In particular, the integration of ChIP-seq, RNA-seq, and DNase-seq techniques has facilitated the mapping of a new class of regulatory elements. These elements, called super-enhancers, can regulate cell-type-specific gene sets and even fine-tune gene expression regulation in response to external stimuli, and have become a hot topic in genome biology. However, there is scant genetic evidence demonstrating their unique biological relevance and the mechanisms underlying these biological functions. In this review, we describe a robust genome-wide strategy for mapping cell-type-specific enhancers or super-enhancers in the mammary genome. In this strategy, genome-wide screening of active enhancer clusters that are co-occupied by mammary-enriched transcription factors, co-factors, and active enhancer marks is used to identify bona fide mammary tissue-specific super-enhancers. The in vivo function of these super-enhancers and their associated regulatory elements may then be investigated in various ways using the advanced CRISPR/Cas9 genome-editing technology. Based on our experience targeting various mammary genomic sites using CRISPR/Cas9 in mice, we comprehensively discuss the molecular consequences of the different targeting methods, such as the number of gRNAs and the dependence on their simultaneous or sequential injections. We also mention the considerations that are essential for obtaining accurate results and shed light on recent progress that has been made in developing modified CRISPR/Cas9 genome-editing techniques. In the future, the coupling of advanced genome-wide sequencing and genome-editing technologies could provide new insights into the complex genetic regulatory networks involved in mammary-gland development.
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Affiliation(s)
- Kyung Hyun Yoo
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- BK21 Biological Science Visiting Professor, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Ha Youn Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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19
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Zhuo C, Wang D, Zhou C, Chen C, Li J, Tian H, Li S, Ji F, Liu C, Chen M, Zhang L. Double-Edged Sword of Tumour Suppressor Genes in Schizophrenia. Front Mol Neurosci 2019; 12:1. [PMID: 30809121 PMCID: PMC6379290 DOI: 10.3389/fnmol.2019.00001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
Schizophrenia (SCZ) is a common psychiatric disorder with polygenetic pathogenesis. Among the many identified candidate genes and loci, the group of tumour suppressor genes has drawn our interest. In this mini-review article, we describe evidence of a correlation between major tumour suppressor genes and SCZ development. Genetic mutations ranging from single nucleotide polymorphisms to large structural alterations have been found in tumour-related genes in patients with SCZ. Epigenetic mechanisms, including DNA methylation/acetylation and microRNA regulation of tumour suppressor genes, have also been implicated in SCZ. Beyond genetic correlations, we hope to establish causal relationships between tumour suppressor gene function and SCZ risk. Accumulating evidence shows that tumour suppressor genes may mediate cell survival and neural development, both of which contribute to SCZ aetiology. Moreover, converging intracellular signalling pathways indicate a role of tumour suppressor genes in SCZ pathogenesis. Tumour suppressor gene function may mediate a direct link between neural development and function and psychiatric disorders, including SCZ. A deeper understanding of how neural cell development is affected by tumour suppressors may lead to improved anti-psychotic drugs.
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Affiliation(s)
- Chuanjun Zhuo
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China.,Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China.,Department of Psychiatric Genetics, Tianjin Medical University, Tianjin, China.,Department of Psychiatry, Wenzhou Seventh People's Hospital, Wenzhou, China
| | - Dawei Wang
- Department of Neuroimaging Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Chunhua Zhou
- Department of Pharmacy, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ce Chen
- Department of Psychiatry, Wenzhou Seventh People's Hospital, Wenzhou, China
| | - Jie Li
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China
| | - Hongjun Tian
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China
| | - Shen Li
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China.,Department of Psychiatric Genetics, Tianjin Medical University, Tianjin, China
| | - Feng Ji
- Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China
| | - Chuanxin Liu
- Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China
| | - Min Chen
- Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China
| | - Li Zhang
- GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
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20
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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21
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Klein K. Bromodomain protein inhibition: a novel therapeutic strategy in rheumatic diseases. RMD Open 2018; 4:e000744. [PMID: 30564450 PMCID: PMC6269638 DOI: 10.1136/rmdopen-2018-000744] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/28/2018] [Accepted: 10/17/2018] [Indexed: 12/18/2022] Open
Abstract
The reading of acetylation marks on histones by bromodomain (BRD) proteins is a key event in transcriptional activation. Small molecule inhibitors targeting bromodomain and extra-terminal (BET) proteins compete for binding to acetylated histones. They have strong anti-inflammatory properties and exhibit encouraging effects in different cell types in vitro and in animal models resembling rheumatic diseases in vivo. Furthermore, recent studies that focus on BRD proteins beyond BET family members are discussed.
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Affiliation(s)
- Kerstin Klein
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
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22
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Nevedomskaya E, Baumgart SJ, Haendler B. Recent Advances in Prostate Cancer Treatment and Drug Discovery. Int J Mol Sci 2018; 19:ijms19051359. [PMID: 29734647 PMCID: PMC5983695 DOI: 10.3390/ijms19051359] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 02/08/2023] Open
Abstract
Novel drugs, drug sequences and combinations have improved the outcome of prostate cancer in recent years. The latest approvals include abiraterone acetate, enzalutamide and apalutamide which target androgen receptor (AR) signaling, radium-223 dichloride for reduction of bone metastases, sipuleucel-T immunotherapy and taxane-based chemotherapy. Adding abiraterone acetate to androgen deprivation therapy (ADT) in order to achieve complete androgen blockade has proven highly beneficial for treatment of locally advanced prostate cancer and metastatic hormone-sensitive prostate cancer (mHSPC). Also, ADT together with docetaxel treatment showed significant benefit in mHSPC. Ongoing clinical trials for different subgroups of prostate cancer patients include the evaluation of the second-generation AR antagonists enzalutamide, apalutamide and darolutamide, of inhibitors of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) pathway, of inhibitors of DNA damage response, of targeted alpha therapy and of prostate-specific membrane antigen (PSMA) targeting approaches. Advanced clinical studies with immune checkpoint inhibitors have shown limited benefits in prostate cancer and more trials are needed to demonstrate efficacy. The identification of improved, personalized treatments will be much supported by the major progress recently made in the molecular characterization of early- and late-stage prostate cancer using “omics” technologies. This has already led to novel classifications of prostate tumors based on gene expression profiles and mutation status, and should greatly help in the choice of novel targeted therapies best tailored to the needs of patients.
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Affiliation(s)
- Ekaterina Nevedomskaya
- Therapeutic Research Groups, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany.
| | - Simon J Baumgart
- Therapeutic Research Groups, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany.
| | - Bernard Haendler
- Therapeutic Research Groups, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany.
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23
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Ruggero K, Farran-Matas S, Martinez-Tebar A, Aytes A. Epigenetic Regulation in Prostate Cancer Progression. ACTA ACUST UNITED AC 2018; 4:101-115. [PMID: 29888169 PMCID: PMC5976687 DOI: 10.1007/s40610-018-0095-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Purpose of Review An important number of newly identified molecular alterations in prostate cancer affect gene encoding master regulators of chromatin biology epigenetic regulation. This review will provide an updated view of the key epigenetic mechanisms underlying prostate cancer progression, therapy resistance, and potential actionable mechanisms and biomarkers. Recent Findings Key players in chromatin biology and epigenetic master regulators has been recently described to be crucially altered in metastatic CRPC and tumors that progress to AR independency. As such, epigenetic dysregulation represents a driving mechanism in the reprograming of prostate cancer cells as they lose AR-imposed identity. Summary Chromatin integrity and accessibility for transcriptional regulation are key features altered in cancer progression, and particularly relevant in nuclear hormone receptor-driven tumors like prostate cancer. Understanding how chromatin remodeling dictates prostate development and how its deregulation contributes to prostate cancer onset and progression may improve risk stratification and treatment selection for prostate cancer patients.
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Affiliation(s)
- Katia Ruggero
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Sonia Farran-Matas
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Adrian Martinez-Tebar
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Alvaro Aytes
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain.,Programs of Cancer Therapeutics Resistance (ProCURE), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
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24
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Abstract
Several oncogenic factors have been involved in prostate cancer progression. However, therapeutic approaches still focus on suppression of androgen receptor (AR) signaling. In fact, whereas the full-length AR incorporates a ligand-binding domain, which has become a drug target for competitive inhibitors, other transcription factors often do not have tractable binding pockets that aid drug development. Consequently drug development efforts have turned to transcription co-regulators, often chromatin-modifying enzymes or factors that bind to epigenetic modifications to chromatin. Bromodomain (BRD)-containing proteins fall into the latter category and significant progress has been made in developing small molecule inhibitors that target a particular subgroup of BRD-containing proteins known as the Bromodomain and extra-terminal (BET) family proteins. These inhibitors have proven particularly effective in inactivating c-Myc in lymphoma but more recently members of the BET family have also been identified as AR-interacting proteins raising the prospect of using these inhibitors as an alternative strategy for targeting AR-driven cancers. In this review we will provide an overview of BRD-containing proteins and the potential for exploiting them as biomarkers and drug targets in prostate cancer.
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Affiliation(s)
- Alfonso Urbanucci
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, University of Oslo, Forskningsparken, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| | - Ian G Mills
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, University of Oslo, Forskningsparken, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer, Centre for Cancer Research and Cell Biology, Queen's University of Belfast, BT9 7AE Belfast, UK
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25
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Hamdan FH, Johnsen SA. Super enhancers - new analyses and perspectives on the low hanging fruit. Transcription 2017; 9:123-130. [PMID: 28980882 DOI: 10.1080/21541264.2017.1372044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Significant attention has recently been given to a class of enhancers termed "super enhancers", while implying that "typical enhancers" are less important. In this report, we examine criteria for identification of super enhancers and address the need to evaluate the differences between BRD4-occupied "typical" and "super" enhancers.
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Affiliation(s)
- Feda H Hamdan
- a Department of General, Visceral and Pediatric Surgery , University Medical Center Göttingen , Göttingen , Germany
| | - Steven A Johnsen
- a Department of General, Visceral and Pediatric Surgery , University Medical Center Göttingen , Göttingen , Germany
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26
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Baumgart SJ, Haendler B. Exploiting Epigenetic Alterations in Prostate Cancer. Int J Mol Sci 2017; 18:ijms18051017. [PMID: 28486411 PMCID: PMC5454930 DOI: 10.3390/ijms18051017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer affects an increasing number of men worldwide and is a leading cause of cancer-associated deaths. Beside genetic mutations, many epigenetic alterations including DNA and histone modifications have been identified in clinical prostate tumor samples. They have been linked to aberrant activity of enzymes and reader proteins involved in these epigenetic processes, leading to the search for dedicated inhibitory compounds. In the wake of encouraging anti-tumor efficacy results in preclinical models, epigenetic modulators addressing different targets are now being tested in prostate cancer patients. In addition, the assessment of microRNAs as stratification biomarkers, and early clinical trials evaluating suppressor microRNAs as potential prostate cancer treatment are being discussed.
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Affiliation(s)
- Simon J Baumgart
- Drug Discovery, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany.
| | - Bernard Haendler
- Drug Discovery, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany.
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