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Stoeber S, Godin H, Xu C, Bai L. Pioneer factors: nature or nurture? Crit Rev Biochem Mol Biol 2024:1-15. [PMID: 38778580 DOI: 10.1080/10409238.2024.2355885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Chromatin is densely packed with nucleosomes, which limits the accessibility of many chromatin-associated proteins. Pioneer factors (PFs) are usually viewed as a special group of sequence-specific transcription factors (TFs) that can recognize nucleosome-embedded motifs, invade compact chromatin, and generate open chromatin regions. Through this process, PFs initiate a cascade of events that play key roles in gene regulation and cell differentiation. A current debate in the field is if PFs belong to a unique subset of TFs with intrinsic "pioneering activity", or if all TFs have the potential to function as PFs within certain cellular contexts. There are also different views regarding the key feature(s) that define pioneering activity. In this review, we present evidence from the literature related to these alternative views and discuss how to potentially reconcile them. It is possible that both intrinsic properties, like tight nucleosome binding and structural compatibility, and cellular conditions, like concentration and co-factor availability, are important for PF function.
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Affiliation(s)
- Shane Stoeber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Holly Godin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, USA
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2
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Won SJ, Zhang Y, Reinhardt CJ, MacRae NS, DeMeester KE, Njomen E, Hargis LM, Remsberg JR, Melillo B, Cravatt BF, Erb MA. Redirecting the pioneering function of FOXA1 with covalent small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586158. [PMID: 38562719 PMCID: PMC10983899 DOI: 10.1101/2024.03.21.586158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pioneer transcription factors (TFs) exhibit a specialized ability to bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report the chemical proteomic discovery of electrophilic small molecules that stereoselectively and site-specifically bind the pioneer TF, FOXA1, at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the covalent ligands relax the canonical DNA binding preference of FOXA1 by strengthening interactions with suboptimal ancillary sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.
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3
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Ji D, Shao C, Yu J, Hou Y, Gao X, Wu Y, Wang L, Chen P. FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor. Mol Cell 2024; 84:244-260.e7. [PMID: 38101414 DOI: 10.1016/j.molcel.2023.11.020] [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: 06/12/2023] [Revised: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
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Affiliation(s)
- Dengyu Ji
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Changrong Shao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyao Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiao Gao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Yichuan Wu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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4
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Mandatori S, Liu Y, Marturia-Navarro J, Hadi M, Henriksen K, Zheng J, Rasmussen LM, Rizza S, Kaestner KH, Issazadeh-Navikas S. PRKAG2.2 is essential for FoxA1 + regulatory T cell differentiation and metabolic rewiring distinct from FoxP3 + regulatory T cells. SCIENCE ADVANCES 2023; 9:eadj8442. [PMID: 38117896 PMCID: PMC10732530 DOI: 10.1126/sciadv.adj8442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/20/2023] [Indexed: 12/22/2023]
Abstract
Forkhead box A1 (FoxA1)+ regulatory T cells (Tregs) exhibit distinct characteristics from FoxP3+ Tregs while equally effective in exerting anti-inflammatory properties. The role of FoxP3+ Tregs in vivo has been challenged, motivating a better understanding of other Tregs in modulating hyperactive immune responses. FoxA1+ Tregs are generated on activation of the transcription factor FoxA1 by interferon-β (IFNβ), an anti-inflammatory cytokine. T cell activation, expansion, and function hinge on metabolic adaptability. We demonstrated that IFNβ promotes a metabolic rearrangement of FoxA1+ Tregs by enhancing oxidative phosphorylation and mitochondria clearance by mitophagy. In response to IFNβ, FoxA1 induces a specific transcription variant of adenosine 5'-monophosphate-activated protein kinase (AMPK) γ2 subunit, PRKAG2.2. This leads to the activation of AMPK signaling, thereby enhancing mitochondrial respiration and mitophagy by ULK1-BNIP3. This IFNβ-FoxA1-PRKAG2.2-BNIP3 axis is pivotal for their suppressive function. The involvement of PRKAG2.2 in FoxA1+ Treg, not FoxP3+ Treg differentiation, underscores the metabolic differences between Treg populations and suggests potential therapeutic targets for autoimmune diseases.
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Affiliation(s)
- Sara Mandatori
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yawei Liu
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joana Marturia-Navarro
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mahdieh Hadi
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Henriksen
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jin Zheng
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louise Munk Rasmussen
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Klaus H. Kaestner
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Dorso M, Patel PT, Pankov A, Boyer JA, Soni RK, Del Priore IS, Hayatt O, Kulick A, Hagen CJ, de Stanchina E, Junttila MR, Daemen A, Friedman LS, Hendrickson RC, Chandarlapaty S. A Druggable FOXA1-Glucocorticoid Receptor Transcriptional Axis Drives Tumor Growth in a Subset of Non-Small Cell Lung Cancer. CANCER RESEARCH COMMUNICATIONS 2023; 3:1788-1799. [PMID: 37691854 PMCID: PMC10484118 DOI: 10.1158/2767-9764.crc-23-0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
The FOXA1 pioneer factor is an essential mediator of steroid receptor function in multiple hormone-dependent cancers, including breast and prostate cancers, enabling nuclear receptors such as estrogen receptor (ER) and androgen receptor (AR) to activate lineage-specific growth programs. FOXA1 is also highly expressed in non-small cell lung cancer (NSCLC), but whether and how it regulates tumor growth in this context is not known. Analyzing data from loss-of-function screens, we identified a subset of NSCLC tumor lines where proliferation is FOXA1 dependent. Using rapid immunoprecipitation and mass spectrometry of endogenous protein, we identified chromatin-localized interactions between FOXA1 and glucocorticoid receptor (GR) in these tumor cells. Knockdown of GR inhibited proliferation of FOXA1-dependent, but not FOXA1-independent NSCLC cells. In these FOXA1-dependent models, FOXA1 and GR cooperate to regulate gene targets involved in EGF signaling and G1-S cell-cycle progression. To investigate the therapeutic potential for targeting this complex, we examined the effects of highly selective inhibitors of the GR ligand-binding pocket and found that GR antagonism with ORIC-101 suppressed FOXA1/GR target expression, activation of EGF signaling, entry into the S-phase, and attendant proliferation in vitro and in vivo. Taken together, our findings point to a subset of NSCLCs harboring a dependence on the FOXA1/GR growth program and provide rationale for its therapeutic targeting. Significance NSCLC is the leading cause of cancer deaths worldwide. There is a need to identify novel druggable dependencies. We identify a subset of NSCLCs dependent on FOXA1-GR and sensitive to GR antagonism.
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Affiliation(s)
- M. Dorso
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, New York
| | - Payal T. Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, New York
| | | | - Jacob A. Boyer
- Gerstner Sloan Kettering Graduate Program, Sloan Kettering Institute, New York, New York
| | - Rajesh K. Soni
- Microchemistry and Proteomics Core, Sloan Kettering Institute, New York, New York
| | - Isabella S. Del Priore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Hayatt
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amanda Kulick
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Connor J. Hagen
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Zhou M, Gan XL, Ren YX, Chen QX, Yang YZ, Weng ZJ, Zhang XF, Guan JX, Tang LY, Ren ZF. AGR2 and FOXA1 as prognostic markers in ER-positive breast cancer. BMC Cancer 2023; 23:743. [PMID: 37568077 PMCID: PMC10416444 DOI: 10.1186/s12885-023-10964-6] [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: 07/08/2022] [Accepted: 05/16/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND The prognostic role of either forkhead box A1 (FOXA1) or anterior gradient 2 (AGR2) in breast cancer has been found separately. Considering that there were interplays between them depending on ER status, we aimed to assess the statistical interaction between AGR2 and FOXA1 on breast cancer prognosis and examine the prognostic role of the combination of them by ER status. METHODS AGR2 and FOXA1 expression in tumor tissues were evaluated with tissue microarrays by immunohistochemistry in 915 breast cancer patients with follow up data. The expression levels of these two markers were treated as binary variables, and many different cutoff values were tried for each marker. Survival and Cox proportional hazard analyses were used to evaluate the relationship between AGR2, FOXA1 and prognosis, and the statistical interaction between them on the prognosis was assessed on multiplicative scale. RESULTS Statistical interaction between AGR2 and FOXA1 on the PFS was significant with all the cutoff points in ER-positive breast cancer patients but not ER-negative ones. Among ER-positive patients, the poor prognostic role of the high level of FOXA1 was significant only in patients with the low level of AGR2, and vice versa. When AGR2 and FOXA1 were considered together, patients with low levels of both markers had significantly longer PFS compared with all other groups. CONCLUSIONS There was a statistical interaction between AGR2 and FOXA1 on the prognosis of ER-positive breast cancer. The combination of AGR2 and FOXA1 was a more useful marker for the prognosis of ER-positive breast cancer patients.
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Affiliation(s)
- Meng Zhou
- School of Public Health, Sun Yat-Sen University, 74 Zhongshan 2Nd Rd, Guangzhou, 510080, China
| | - Xing-Li Gan
- School of Public Health, Sun Yat-Sen University, 74 Zhongshan 2Nd Rd, Guangzhou, 510080, China
| | - Yue-Xiang Ren
- The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Rd, Guangzhou, 510630, China.
| | - Qian-Xin Chen
- School of Public Health, Sun Yat-Sen University, 74 Zhongshan 2Nd Rd, Guangzhou, 510080, China
| | | | - Zi-Jin Weng
- The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Rd, Guangzhou, 510630, China
| | - Xiao-Fang Zhang
- The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Rd, Guangzhou, 510630, China
| | - Jie-Xia Guan
- The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Rd, Guangzhou, 510630, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Rd, Guangzhou, 510630, China.
| | - Ze-Fang Ren
- School of Public Health, Sun Yat-Sen University, 74 Zhongshan 2Nd Rd, Guangzhou, 510080, China.
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Sadaf, Hazazi A, Alkhalil SS, Alsaiari AA, Gharib AF, Alhuthali HM, Rana S, Aloliqi AA, Eisa AA, Hasan MR, Dev K. Role of Fork-Head Box Genes in Breast Cancer: From Drug Resistance to Therapeutic Targets. Biomedicines 2023; 11:2159. [PMID: 37626655 PMCID: PMC10452497 DOI: 10.3390/biomedicines11082159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer has been acknowledged as one of the most notorious cancers, responsible for millions of deaths around the globe. Understanding the various factors, genetic mutations, comprehensive pathways, etc., that are involved in the development of breast cancer and how these affect the development of the disease is very important for improving and revitalizing the treatment of this global health issue. The forkhead-box gene family, comprising 19 subfamilies, is known to have a significant impact on the growth and progression of this cancer. The article looks into the various forkhead genes and how they play a role in different types of cancer. It also covers their impact on cancer drug resistance, interaction with microRNAs, explores their potential as targets for drug therapies, and their association with stem cells.
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Affiliation(s)
- Sadaf
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India;
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia;
| | - Samia S. Alkhalil
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 11961, Saudi Arabia;
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.F.G.); (H.M.A.)
| | - Amal F. Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.F.G.); (H.M.A.)
| | - Hayaa M. Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.F.G.); (H.M.A.)
| | - Shanika Rana
- School of Biosciences, Apeejay Stya University, Gurugram 122003, India;
| | - Abdulaziz A. Aloliqi
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Alaa Abdulaziz Eisa
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Medina 30002, Saudi Arabia;
| | - Mohammad Raghibul Hasan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 11961, Saudi Arabia;
| | - Kapil Dev
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India;
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8
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Kaddoura R, Alqutami F, Asbaita M, Hachim M. In Silico Analysis of Publicly Available Transcriptomic Data for the Identification of Triple-Negative Breast Cancer-Specific Biomarkers. Life (Basel) 2023; 13:life13020422. [PMID: 36836779 PMCID: PMC9965976 DOI: 10.3390/life13020422] [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: 01/02/2023] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Breast cancer is the most common type of cancer among women and is classified into multiple subtypes. Triple-negative breast cancer (TNBC) is the most aggressive subtype, with high mortality rates and limited treatment options such as chemotherapy and radiation. Due to the heterogeneity and complexity of TNBC, there is a lack of reliable biomarkers that can be used to aid in the early diagnosis and prognosis of TNBC in a non-invasive screening method. AIM This study aims to use in silico methods to identify potential biomarkers for TNBC screening and diagnosis, as well as potential therapeutic markers. METHODS Publicly available transcriptomic data of breast cancer patients published in the NCBI's GEO database were used in this analysis. Data were analyzed with the online tool GEO2R to identify differentially expressed genes (DEGs). Genes that were differentially expressed in more than 50% of the datasets were selected for further analysis. Metascape, Kaplan-Meier plotter, cBioPortal, and the online tool TIMER were used for functional pathway analysis to identify the biological role and functional pathways associated with these genes. Breast Cancer Gene-Expression Miner v4.7 was used to validify the obtained results in a larger cohort of datasets. RESULTS A total of 34 genes were identified as differentially expressed in more than half of the datasets. The DEG GATA3 had the highest degree of regulation, and it plays a role in regulating other genes. The estrogen-dependent pathway was the most enriched pathway, involving four crucial genes, including GATA3. The gene FOXA1 was consistently down-regulated in TNBC in all datasets. CONCLUSIONS The shortlisted 34 DEGs will aid clinicians in diagnosing TNBC more accurately as well as developing targeted therapies to improve patient prognosis. In vitro and in vivo studies are further recommended to validate the results of the current study.
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9
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Transcription networks in liver development and acute liver failure. LIVER RESEARCH 2022. [DOI: 10.1016/j.livres.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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10
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Sierra-Pagan JE, Garry DJ. The regulatory role of pioneer factors during cardiovascular lineage specification – A mini review. Front Cardiovasc Med 2022; 9:972591. [PMID: 36082116 PMCID: PMC9445115 DOI: 10.3389/fcvm.2022.972591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Cardiovascular disease (CVD) remains the number one cause of death worldwide. Ischemic heart disease contributes to heart failure and has considerable morbidity and mortality. Therefore, alternative therapeutic strategies are urgently needed. One class of epigenetic regulators known as pioneer factors has emerged as an important tool for the development of regenerative therapies for the treatment of CVD. Pioneer factors bind closed chromatin and remodel it to drive lineage specification. Here, we review pioneer factors within the cardiovascular lineage, particularly during development and reprogramming and highlight the implications this field of research has for the future development of cardiac specific regenerative therapies.
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Affiliation(s)
- Javier E. Sierra-Pagan
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Daniel J. Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Daniel J. Garry
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11
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Bartoloni S, Leone S, Pescatori S, Cipolletti M, Acconcia F. The antiviral drug telaprevir induces cell death by reducing
FOXA1
expression in estrogen receptor α (
ERα
)‐positive breast cancer cells. Mol Oncol 2022; 16:3568-3584. [PMID: 36056637 PMCID: PMC9533686 DOI: 10.1002/1878-0261.13303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/26/2022] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Previously, we found that telaprevir (Tel), the inhibitor of hepatitis C virus NS3/4A serine protease, reduces estrogen receptor α (ERα) content at the transcriptional level without binding to the receptor, prevents ERα transcriptional activity, and inhibits basal and 17β‐estradiol (E2)‐dependent cell proliferation in different breast cancer (BC) cell lines. Here, we further characterize the Tel action mechanisms on ERα levels and function, identify a possible molecular target of Tel in BC cells, and evaluate Tel as an antiproliferative agent for BC treatment. Tel‐dependent reduction in ERα levels and function depends on a Tel‐dependent decrease in FOXA1 levels and activity. The effect of Tel is transduced by the IGF1‐R/AKT/FOXA1 pathway, with the antiviral compound interacting with IGF1‐R. Tel prevents the proliferation of several BC cell lines, while it does not affect the proliferation of normal nontransformed cell lines, and its antiproliferative effect is correlated with the ratio of FOXA1/IGF1‐R expression. In conclusion, Tel interferes with the IGF1‐R/AKT/FOXA1 pathway and induces cell death in ERα‐expressing BC cells. Thus, we propose that this antiviral could be repurposed for the treatment of ERα‐expressing BC.
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Affiliation(s)
- Stefania Bartoloni
- Department of Sciences, Section Biomedical Sciences and Technology University Roma TRE, Viale Guglielmo Marconi, 446 I‐00146 Rome Italy
| | - Stefano Leone
- Department of Sciences, Section Biomedical Sciences and Technology University Roma TRE, Viale Guglielmo Marconi, 446 I‐00146 Rome Italy
| | - Sara Pescatori
- Department of Sciences, Section Biomedical Sciences and Technology University Roma TRE, Viale Guglielmo Marconi, 446 I‐00146 Rome Italy
| | - Manuela Cipolletti
- Department of Sciences, Section Biomedical Sciences and Technology University Roma TRE, Viale Guglielmo Marconi, 446 I‐00146 Rome Italy
| | - Filippo Acconcia
- Department of Sciences, Section Biomedical Sciences and Technology University Roma TRE, Viale Guglielmo Marconi, 446 I‐00146 Rome Italy
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12
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Scholtes C, Giguère V. Transcriptional control of energy metabolism by nuclear receptors. Nat Rev Mol Cell Biol 2022; 23:750-770. [DOI: 10.1038/s41580-022-00486-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 12/11/2022]
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13
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Jiang Z, Zhu H, Wang P, Que W, Zhong L, Li X, Du F. Different subpopulations of regulatory T cells in human autoimmune disease, transplantation, and tumor immunity. MedComm (Beijing) 2022; 3:e137. [PMID: 35474948 PMCID: PMC9023873 DOI: 10.1002/mco2.137] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022] Open
Abstract
CD4+CD25+ regulatory T cells (Tregs), a subpopulation of naturally CD4+ T cells that characteristically express transcription factor Forkhead box P3 (FOXP3), play a pivotal role in the maintenance of immune homeostasis and the prevention of autoimmunity. With the development of biological technology, the understanding of plasticity and stability of Tregs has been further developed. Recent studies have suggested that human Tregs are functionally and phenotypically diverse. The functions and mechanisms of different phenotypes of Tregs in different disease settings, such as tumor microenvironment, autoimmune diseases, and transplantation, have gradually become hot spots of immunology research that arouse extensive attention. Among the complex functions, CD4+CD25+FOXP3+ Tregs possess a potent immunosuppressive capacity and can produce various cytokines, such as IL‐2, IL‐10, and TGF‐β, to regulate immune homeostasis. They can alleviate the progression of diseases by resisting inflammatory immune responses, whereas promoting the poor prognosis of diseases by helping cells evade immune surveillance or suppressing effector T cells activity. Therefore, methods for targeting Tregs to regulate their functions in the immune microenvironment, such as depleting them to strengthen tumor immunity or expanding them to treat immunological diseases, need to be developed. Here, we discuss that different subpopulations of Tregs are essential for the development of immunotherapeutic strategies involving Tregs in human diseases.
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Affiliation(s)
- Zhongyi Jiang
- Department of General Surgery Shanghai General Hospital Shanghai Jiao Tong University School of Medicine Shanghai P. R. China
| | - Haitao Zhu
- Department of Hepatobiliary Surgery The Affiliated Hospital of Guizhou Medical University Guizhou P. R. China
| | - Pusen Wang
- Department of General Surgery Shanghai General Hospital Shanghai Jiao Tong University School of Medicine Shanghai P. R. China
| | - Weitao Que
- Department of General Surgery Shanghai General Hospital Shanghai Jiao Tong University School of Medicine Shanghai P. R. China
| | - Lin Zhong
- Department of General Surgery Shanghai General Hospital Shanghai Jiao Tong University School of Medicine Shanghai P. R. China
| | - Xiao‐Kang Li
- Department of General Surgery Shanghai General Hospital Shanghai Jiao Tong University School of Medicine Shanghai P. R. China
- Division of Transplantation Immunology National Research Institute for Child Health and Development Tokyo Japan
| | - Futian Du
- Department of Hepatobiliary Surgery Weifang People's Hospital Shandong P. R. China
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14
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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15
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Shen M, Yang L, Lei T, Zhang P, Xiao L, Cao S, Chen F, Li L, Ye F, Bu H. Correlation between CA12 and TFF3 and their prediction value of neoadjuvant chemotherapy response in breast cancer. J Clin Pharm Ther 2022; 47:609-618. [PMID: 35229335 DOI: 10.1111/jcpt.13580] [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: 07/26/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023]
Abstract
WHAT IS KNOWN AND OBJECTIVE Compared with other molecular subtypes, hormone receptor-positive breast cancer often shows worse neoadjuvant chemotherapy efficacy. This study aims to explore the relationship between the oestrogen receptor (ER)-related genes carbonic anhydrase 12 (CA12) and trefoil factor 3 (TFF3) and their predictive value of neoadjuvant chemotherapy for breast cancer. METHODS We investigated the relationships between CA12, TFF3 and ER status and their predictive value of anthracycline-taxane neoadjuvant chemotherapy in 115 female breast cancer patients via real-time polymerase chain reaction (RT-PCR) and 4 GEO datasets: GSE41998, GSE25065, GSE20194 and GSE20271. Then, the effects of CA12 and TFF3 on the chemotherapy drugs doxorubicin and docetaxel were verified in vitro in the breast cancer cell lines MCF-7 and BT474. RESULTS AND DISCUSSION The GEO datasets and RT-PCR results showed that the relative expression of both CA12 and TFF3 was higher in oestrogen receptor-positive samples compared with the other samples (p < 0.05). CA12 was significantly correlated with TFF3 (p < 0.05). In MCF-7 cells, inhibition of TFF3 induced downregulation of CA12 and ESR1 (p < 0.05) at both the mRNA and the protein levels, while inhibition of CA12 also downregulated TFF3 and ESR1 (p < 0.05). In BT474 cells, inhibition of TFF3 downregulated CA12 and ESR1 (p < 0.05) at both the mRNA and the protein levels, while inhibition of CA12 led to slight upregulation of TFF3 and ESR1 (p > 0.05). Moreover, GEO datasets and RT-PCR results showed that CA12 and TFF3 were more highly expressed in nonpathological complete response (non-pCR) samples than in pCR samples (p < 0.05). Cell viability assays of MCF-7 and BT474 cells showed that inhibiting CA12 and TFF3 could enhance sensitivity to doxorubicin and docetaxel (p < 0.05). WHAT IS NEW AND CONCLUSION CA12 and TFF3 were correlated with each other, and their high expression might explain the worse efficacy of neoadjuvant chemotherapy in oestrogen receptor-positive breast cancer patients.
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Affiliation(s)
- Mengjia Shen
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Libo Yang
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Lei
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Peichuan Zhang
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Lab of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Xiao
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shiyu Cao
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fei Chen
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Li
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Ye
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Lab of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong Bu
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Lab of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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16
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Liu W, Ren D, Xiong W, Jin X, Zhu L. A novel FBW7/NFAT1 axis regulates cancer immunity in sunitinib-resistant renal cancer by inducing PD-L1 expression. J Exp Clin Cancer Res 2022; 41:38. [PMID: 35081978 PMCID: PMC8790872 DOI: 10.1186/s13046-022-02253-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/12/2022] [Indexed: 01/11/2023] Open
Abstract
Background Tyrosine kinase inhibitors (TKIs) alone and in combination with immune checkpoint inhibitors (ICIs) have been shown to be beneficial for the survival of metastatic renal cell carcinoma (mRCC) patients, but resistance to targeted therapy and ICIs is common in the clinic. Understanding the underlying mechanism is critical for further prolonging the survival of renal cancer patients. Nuclear factor of activated T cell 1 (NFAT1) is expressed in immune and nonimmune cells, and the dysregulation of NFAT1 contributes to the progression of various type of malignant tumors. However, the specific role of NFAT1 in RCC is elusive. As a regulator of the immune response, we would like to systemically study the role of NFAT1 in RCC. Methods TCGA-KIRC dataset analysis, Western blot analysis and RT-qPCR analysis was used to determine the clinic-pathological characteristic of NFAT1 in RCC. CCK-8 assays, colony formation assays and xenograft assays were performed to examine the biological role of NFAT1 in renal cancer cells. RNA-seq analysis was used to examine the pathways changed after NFAT1 silencing. ChIP-qPCR, coimmunoprecipitation analysis, Western blot analysis and RT-qPCR analysis were applied to explore the mechanism by NAFT1 was regulated in the renal cancer cells. Results In our study, we found that NFAT1 was abnormally overexpressed in RCC and that NFAT1 overexpression was associated with an unfavorable prognosis. Then, we showed that NFAT1 enhanced tumor growth and regulated the immune response by increasing PD-L1 expression in RCC. In addition, we demonstrated that NFAT1 was stabilized in sunitinib-resistant RCC via hyperactivation of the PI3K/AKT/GSK-3β signaling pathway. Furthermore, our study indicated that downregulation of the expression of FBW7, which promotes NFAT1 degradation, was induced by FOXA1 and SETD2 in sunitinib-resistant RCC. Finally, FBW7 was found to contribute to modulating the immune response in RCC. Conclusions Our data reveal a novel role for the FBW7/NFAT1 axis in the RCC response to TKIs and ICIs. NFAT1 and its associated signaling pathway might be therapeutic targets for RCC treatment, especially when combined with ICIs and/or TKIs. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02253-0.
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17
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Li J, Xin Y, Li J, Chen H, Li H. Phosphatidylethanolamine N-methyltransferase: from Functions to Diseases. Aging Dis 2022; 14:879-891. [PMID: 37191416 DOI: 10.14336/ad.2022.1025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Locating on endoplasmic reticulum and mitochondria associated membrane, Phosphatidylethanolamine N-methyltransferase (PEMT), catalyzes phosphatidylethanolamine methylation to phosphatidylcholine. As the only endogenous pathway for choline biosynthesis in mammals, the dysregulation of PEMT can lead to imbalance of phospholipid metabolism. Dysregulation of phospholipid metabolism in the liver or heart can lead to deposition of toxic lipid species that adversely result in dysfunction of hepatocyte/cardiomyocyte. Studies have shown that PEMT-/- mice increased susceptibility of diet-induced fatty liver and steatohepatitis. However, knockout of PEMT protects against diet-induced atherosclerosis, diet-induced obesity, and insulin resistance. Thus, novel insights to the function of PEMT in various organs should be summarized. Here, we reviewed the structural and functional properties of PEMT, highlighting its role in the pathogenesis of obesity, liver diseases, cardiovascular diseases, and other conditions.
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18
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Patel JM, Jeselsohn RM. Estrogen Receptor Alpha and ESR1 Mutations in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:171-194. [DOI: 10.1007/978-3-031-11836-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Porras L, Ismail H, Mader S. Positive Regulation of Estrogen Receptor Alpha in Breast Tumorigenesis. Cells 2021; 10:cells10112966. [PMID: 34831189 PMCID: PMC8616513 DOI: 10.3390/cells10112966] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor alpha (ERα, NR3A1) contributes through its expression in different tissues to a spectrum of physiological processes, including reproductive system development and physiology, bone mass maintenance, as well as cardiovascular and central nervous system functions. It is also one of the main drivers of tumorigenesis in breast and uterine cancer and can be targeted by several types of hormonal therapies. ERα is expressed in a subset of luminal cells corresponding to less than 10% of normal mammary epithelial cells and in over 70% of breast tumors (ER+ tumors), but the basis for its selective expression in normal or cancer tissues remains incompletely understood. The mapping of alternative promoters and regulatory elements has delineated the complex genomic structure of the ESR1 gene and shed light on the mechanistic basis for the tissue-specific regulation of ESR1 expression. However, much remains to be uncovered to better understand how ESR1 expression is regulated in breast cancer. This review recapitulates the current body of knowledge on the structure of the ESR1 gene and the complex mechanisms controlling its expression in breast tumors. In particular, we discuss the impact of genetic alterations, chromatin modifications, and enhanced expression of other luminal transcription regulators on ESR1 expression in tumor cells.
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20
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Seachrist DD, Anstine LJ, Keri RA. FOXA1: A Pioneer of Nuclear Receptor Action in Breast Cancer. Cancers (Basel) 2021; 13:cancers13205205. [PMID: 34680352 PMCID: PMC8533709 DOI: 10.3390/cancers13205205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
The pioneering function of FOXA1 establishes estrogen-responsive transcriptomes in luminal breast cancer. Dysregulated FOXA1 chromatin occupancy through focal amplification, mutation, or cofactor recruitment modulates estrogen receptor (ER) transcriptional programs and drives endocrine-resistant disease. However, ER is not the sole nuclear receptor (NR) expressed in breast cancers, nor is it the only NR for which FOXA1 serves as a licensing factor. Receptors for androgens, glucocorticoids, and progesterone are also found in the majority of breast cancers, and their functions are also impacted by FOXA1. These NRs interface with ER transcriptional programs and, depending on their activation level, can reprogram FOXA1-ER cistromes. Thus, NR interplay contributes to endocrine therapy response and resistance and may provide a vulnerability for future therapeutic benefit in patients. Herein, we review what is known regarding FOXA1 regulation of NR function in breast cancer in the context of cell identity, endocrine resistance, and NR crosstalk in breast cancer progression and treatment.
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Affiliation(s)
- Darcie D. Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Lindsey J. Anstine
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Department of Cancer Biology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence:
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21
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Rauner G, Kuperwasser C. Microenvironmental control of cell fate decisions in mammary gland development and cancer. Dev Cell 2021; 56:1875-1883. [PMID: 34256927 DOI: 10.1016/j.devcel.2021.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/28/2022]
Abstract
Cell fate decisions are critical for adequate tissue development, maintenance and regeneration. In the mammary gland, epithelial cell fates are tightly controlled by the microenvironment. Here, we review how cell fate decisions are regulated by components of the microenvironment during mammary gland development and how pathological changes in the microenvironment can alter cell fates, leading to malignancy. Specifically, we describe the current understanding of how mammary cell fate is controlled and directed by three elements: the extracellular matrix, the immune microenvironment, and hormones-and how these elements can converge to create microenvironments that promote a fourth element: DNA damage.
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Affiliation(s)
- Gat Rauner
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Charlotte Kuperwasser
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA; Laboratory for the Convergence of Biomedical, Physical, and Engineering Sciences, Tufts University School of Medicine, Boston, MA 02111, USA.
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22
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Oh C, Kim HR, Oh S, Ko JY, Kim Y, Kang K, Yang Y, Kim J, Park JH, Roe JS, Yoo KH. Epigenetic Upregulation of MAGE-A Isoforms Promotes Breast Cancer Cell Aggressiveness. Cancers (Basel) 2021; 13:cancers13133176. [PMID: 34202157 PMCID: PMC8268034 DOI: 10.3390/cancers13133176] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 01/28/2023] Open
Abstract
Simple Summary Breast cancer is a heterogeneous disease that has complex causes and mechanisms of development. Currently, patient treatment options depend on the breast cancer molecular subtype, which is classified based on the presence or absence of hormone receptors and HER2. However, this classification system has limitations in terms of predicting responsiveness to anticancer drugs and patient outcomes. In this study, we present a new approach to classifying molecular breast cancer subtypes: it is based on changes in histone modifications in the promoter region of the MAGEA12 locus, which we found related closely to MAGEA12 expression and MAGEA12-associated malignancy of breast cancer cells. Abstract After decades-long efforts to diagnose and treat breast cancer, the management strategy that has proved most successful to date is molecular-subtype-specific inhibition of the hormone receptors and HER2 that are expressed by individual cancers. Melanoma-associated antigen (MAGE) proteins comprise >40 highly conserved members that contain the MAGE homology domain. They are often overexpressed in multiple cancers and contribute to cancer progression and metastasis. However, it remains unclear whether the biological activity arising from MAGE gene expression is associated with breast cancer subtypes. In this study, we analyzed the RNA-sequencing (RNA-seq) data of 70 breast cancer cell lines and found that MAGEA12 and MAGEA3 were highly expressed in a subset of these lines. Significantly, MAGEA12 and MAGEA3 expression levels were independent of hormone receptor expression levels but were closely associated with markers of active histone modifications. This indicates that overexpression of these genes is attributable to epigenetic deregulation. RNA-seq of MAGEA12-depleted cells was then used to identify 382 candidate targets of MAGEA12 that were downregulated by MAGEA12 depletion. Furthermore, our gain-of-function experiments showed that MAGEA12 overexpression promoted aggressive behaviors of malignant breast cancer cells, including enhancing their cell migration and invasion. These changes were associated with increased epigenetic deregulation of the MAGEA12 signature genes. Thus, MAGEA12 may play an important role in breast cancer malignancy. Taken together, our findings suggest that MAGEA12 could be a promising therapeutic target in breast cancer, and its overexpression and epigenetic changes could serve as subtype classification biomarkers.
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Affiliation(s)
- Chaeun Oh
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (C.O.); (S.O.)
| | - Hwa-Ryeon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Sumin Oh
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (C.O.); (S.O.)
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea
| | - Je Yeong Ko
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (J.Y.K.); (Y.K.); (Y.Y.); (J.K.); (J.H.P.)
| | - Yesol Kim
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (J.Y.K.); (Y.K.); (Y.Y.); (J.K.); (J.H.P.)
| | - Keunsoo Kang
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea;
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (J.Y.K.); (Y.K.); (Y.Y.); (J.K.); (J.H.P.)
| | - Jongmin Kim
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (J.Y.K.); (Y.K.); (Y.Y.); (J.K.); (J.H.P.)
| | - Jong Hoon Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (J.Y.K.); (Y.K.); (Y.Y.); (J.K.); (J.H.P.)
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
- Correspondence: (J.-S.R.); (K.H.Y.); Tel.: +82-2-2123-2700 (J.-S.R.); +82-2-2077-7836 (K.H.Y.)
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; (C.O.); (S.O.)
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea
- Correspondence: (J.-S.R.); (K.H.Y.); Tel.: +82-2-2123-2700 (J.-S.R.); +82-2-2077-7836 (K.H.Y.)
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Islam Z, Ali AM, Naik A, Eldaw M, Decock J, Kolatkar PR. Transcription Factors: The Fulcrum Between Cell Development and Carcinogenesis. Front Oncol 2021; 11:681377. [PMID: 34195082 PMCID: PMC8236851 DOI: 10.3389/fonc.2021.681377] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Higher eukaryotic development is a complex and tightly regulated process, whereby transcription factors (TFs) play a key role in controlling the gene regulatory networks. Dysregulation of these regulatory networks has also been associated with carcinogenesis. Transcription factors are key enablers of cancer stemness, which support the maintenance and function of cancer stem cells that are believed to act as seeds for cancer initiation, progression and metastasis, and treatment resistance. One key area of research is to understand how these factors interact and collaborate to define cellular fate during embryogenesis as well as during tumor development. This review focuses on understanding the role of TFs in cell development and cancer. The molecular mechanisms of cell fate decision are of key importance in efforts towards developing better protocols for directed differentiation of cells in research and medicine. We also discuss the dysregulation of TFs and their role in cancer progression and metastasis, exploring TF networks as direct or indirect targets for therapeutic intervention, as well as specific TFs’ potential as biomarkers for predicting and monitoring treatment responses.
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Affiliation(s)
- Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ameena Mohamed Ali
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Adviti Naik
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Mohamed Eldaw
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Prasanna R Kolatkar
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
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Slepicka PF, Somasundara AVH, Dos Santos CO. The molecular basis of mammary gland development and epithelial differentiation. Semin Cell Dev Biol 2021; 114:93-112. [PMID: 33082117 PMCID: PMC8052380 DOI: 10.1016/j.semcdb.2020.09.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of the molecular events underpinning the development of mammalian organ systems has been increasing rapidly in recent years. With the advent of new and improved next-generation sequencing methods, we are now able to dig deeper than ever before into the genomic and epigenomic events that play critical roles in determining the fates of stem and progenitor cells during the development of an embryo into an adult. In this review, we detail and discuss the genes and pathways that are involved in mammary gland development, from embryogenesis, through maturation into an adult gland, to the role of pregnancy signals in directing the terminal maturation of the mammary gland into a milk producing organ that can nurture the offspring. We also provide an overview of the latest research in the single-cell genomics of mammary gland development, which may help us to understand the lineage commitment of mammary stem cells (MaSCs) into luminal or basal epithelial cells that constitute the mammary gland. Finally, we summarize the use of 3D organoid cultures as a model system to study the molecular events during mammary gland development. Our increased investigation of the molecular requirements for normal mammary gland development will advance the discovery of targets to predict breast cancer risk and the development of new breast cancer therapies.
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Affiliation(s)
- Priscila Ferreira Slepicka
- Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Hassani B, Taheri M, Asgari Y, Zekri A, Sattari A, Ghafouri-Fard S, Pouresmaeili F. Expression Analysis of Long Non-Coding RNAs Related With FOXM1, GATA3, FOXA1 and ESR1 in Breast Tissues. Front Oncol 2021; 11:671418. [PMID: 34094972 PMCID: PMC8171254 DOI: 10.3389/fonc.2021.671418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common neoplasm among females. Estrogen receptor (ESR) signaling has a prominent impact in the pathogenesis of breast cancer. Among the transcription factors associated with ESR signaling, FOXM1, GATA3, FOXA1 and ESR1 have been suggested as a candidate in the pathogenesis of this neoplasm. In the current project, we have designed an in silico approach to find long non-coding RNAs (lncRNAs) that regulate these transcription factors. Then, we used clinical samples to carry out validation of our in silico findings. Our systems biology method led to the identification of APTR, AC144450.1, linc00663, ZNF337.AS1, and RAMP2.AS1 lncRNAs. Subsequently, we assessed the expression of these genes in breast cancer tissues compared with the adjacent non-cancerous tissues (ANCTs). Expression of GATA3 was significantly higher in breast cancer tissues compared with ANCTs (Ratio of mean expressions (RME) = 4.99, P value = 3.12E−04). Moreover, expression levels of APTR, AC144450.1, and ZNF337.AS1 were elevated in breast cancer tissues compared with control tissues (RME = 2.27, P value = 5.40E−03; Ratio of mean expressions = 615.95, P value = 7.39E−19 and RME = 1.78, P value = 3.40E−02, respectively). On the other hand, the expression of RAMP2.AS1 was lower in breast cancer tissues than controls (RME = 0.31, P value = 1.87E−03). Expression levels of FOXA1, ESR1, and FOXM1 and linc00663 were not significantly different between the two sets of samples. Expression of GATA3 was significantly associated with stage (P value = 4.77E−02). Moreover, expressions of FOXA1 and RAMP2.AS1 were associated with the mitotic rate (P values = 2.18E−02 and 1.77E−02, respectively). Finally, expressions of FOXM1 and ZNF337.AS1 were associated with breastfeeding duration (P values = 3.88E−02 and 4.33E−02, respectively). Based on the area under receiver operating characteristics curves, AC144450.1 had the optimal diagnostic power in differentiating between cancerous and non-cancerous tissues (AUC = 0.95, Sensitivity = 0.90, Specificity = 0.96). The combination of expression levels of all genes slightly increased the diagnostic power (AUC = 0.96). While there were several significant pairwise correlations between expression levels of genes in non-tumoral tissues, the most robust correlation was identified between linc00663 and RAMP2.AS1 (r = 0.61, P value = 3.08E−8). In the breast cancer tissues, the strongest correlations were reported between FOXM1/ZNF337.AS1 and FOXM1/RAMP2.AS1 pairs (r = 0.51, P value = 4.79E−5 and r = 0.51, P value = 6.39E−5, respectively). The current investigation suggests future assessment of the functional role of APTR, AC144450.1 and ZNF337.AS1 in the development of breast neoplasms.
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Affiliation(s)
- Bita Hassani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yazdan Asgari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zekri
- Department of Medical Genetics and Molecular biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sattari
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Michmerhuizen AR, Spratt DE, Pierce LJ, Speers CW. ARe we there yet? Understanding androgen receptor signaling in breast cancer. NPJ Breast Cancer 2020; 6:47. [PMID: 33062889 PMCID: PMC7519666 DOI: 10.1038/s41523-020-00190-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
The role of androgen receptor (AR) activation and expression is well understood in prostate cancer. In breast cancer, expression and activation of AR is increasingly recognized for its role in cancer development and its importance in promoting cell growth in the presence or absence of estrogen. As both prostate and breast cancers often share a reliance on nuclear hormone signaling, there is increasing appreciation of the overlap between activated cellular pathways in these cancers in response to androgen signaling. Targeting of the androgen receptor as a monotherapy or in combination with other conventional therapies has proven to be an effective clinical strategy for the treatment of patients with prostate cancer, and these therapeutic strategies are increasingly being investigated in breast cancer. This overlap suggests that targeting androgens and AR signaling in other cancer types may also be effective. This manuscript will review the role of AR in various cellular processes that promote tumorigenesis and metastasis, first in prostate cancer and then in breast cancer, as well as discuss ongoing efforts to target AR for the more effective treatment and prevention of cancer, especially breast cancer.
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Affiliation(s)
- Anna R Michmerhuizen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI USA
| | - Lori J Pierce
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI USA
| | - Corey W Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI USA
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Vohra M, Sharma AR, Prabhu B N, Rai PS. SNPs in Sites for DNA Methylation, Transcription Factor Binding, and miRNA Targets Leading to Allele-Specific Gene Expression and Contributing to Complex Disease Risk: A Systematic Review. Public Health Genomics 2020; 23:155-170. [PMID: 32966991 DOI: 10.1159/000510253] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/16/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The complex genetic diversity among human populations results from an assortment of factors acting at various sequential levels, including mutations, population migrations, genetic drift, and selection. Although there are a plethora of DNA sequence variations identified through genome-wide association studies (GWAS), the challenge remains to explain the mechanisms underlying interindividual phenotypic disparity accounting for disease susceptibility. Single nucleotide polymorphisms (SNPs) present in the sites for DNA methylation, transcription factor (TF) binding, or miRNA targets can alter the gene expression. The systematic review aimed to evaluate the complex crosstalk among SNPs, miRNAs, DNA methylation, and TFs for complex multifactorial disease risk. METHODS PubMed and Scopus databases were used from inception until May 15, 2019. Initially, screening of articles involved studies assessing the interaction of SNPs with TFs, DNA methylation, or miRNAs resulting in allele-specific gene expression in complex multifactorial diseases. We also included the studies which provided experimental validation of the interaction of SNPs with each of these factors. The results from various studies on multifactorial diseases were assessed. RESULTS A total of 11 articles for SNPs interacting with DNA methylation, 30 articles for SNPs interacting with TFs, and 11 articles for SNPs in miRNA binding sites were selected. The interactions of SNPs with epigenetic factors were found to be implicated in different types of cancers, autoimmune diseases, cardiovascular diseases, diabetes, and asthma. CONCLUSION The systematic review provides evidence for the interplay between genetic and epigenetic risk factors through allele-specific gene expression in various complex multifactorial diseases.
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Affiliation(s)
- Manik Vohra
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Anu Radha Sharma
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Navya Prabhu B
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India,
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Al-Bedairy I, Shamsa M, Salim SA, Mahdi M, Dawood K, Al Faisal AH. FOXA1 expression in Iraqi women with ER+ breast cancer. BAGHDAD JOURNAL OF BIOCHEMISTRY AND APPLIED BIOLOGICAL SCIENCES 2020. [DOI: 10.47419/bjbabs.v2i02.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: Breast cancer (BC) is a heterogeneous disease that can be classified into many subtypes according to histopathological and molecular characteristics. Forkhead box protein A1 (FOXA1) is a transcriptional pioneer factor that opens chromatin allowing estrogen receptor (α-ER) access to its genomic targets. FOXA1 expression is related to luminal BC with a good prognosis.
Objectives: The present study is sought to determine the FOXA1 expression in Iraqi women with ER+ BC.
Methods: Forty-eight fresh malignant breast tissues were analyzed by immunohistochemistry assay to choose ER+ samples, and then by RT-qPCR to evaluate FOXA1 gene expression.
Results: The ER-positive samples were (72.91%) of the total samples, and the molecular subtype of luminal A was the most common with a percentage of 56.25%. It was also noted that the high expression of the FOXA1 gene is highly significant (p<0.05) in Iraqi women with BC when compared with healthy controls.
Conclusions: Highly significant FOXA1 expression was found in Iraqi women with BC makes it eligible to be a good predictor or a biomarker for BC.
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Lin CL, Tan X, Chen M, Kusi M, Hung CN, Chou CW, Hsu YT, Wang CM, Kirma N, Chen CL, Lin CH, Lathrop KI, Elledge R, Kaklamani VG, Mitsuya K, Huang THM. ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer. BMC Med Genomics 2020; 13:69. [PMID: 32408897 PMCID: PMC7222439 DOI: 10.1186/s12920-020-0729-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote extensive translocations and copy-number alterations in proximal contact regions through inappropriate DNA stitching. Although studies have proposed models to explain the initiation of chromothripsis, few discussed how TFs influence this process for tumor progression. Methods This study focused on genomic alterations in amplification associated regions within chromosome 17. Inter−/intra-chromosomal rearrangements were analyzed using whole genome sequencing data of breast tumors in the Cancer Genome Atlas (TCGA) cohort. Common ERα binding sites were defined based on MCF-7, T47D, and MDA-MB-134 breast cancer cell lines using univariate K-means clustering methods. Nanopore sequencing technology was applied to validate frequent rearrangements detected between ATC loci on 17q23 and an ERα hub on 20q13. The efficacy of pharmacological inhibition of a potentially druggable target gene on 17q23 was evaluated using breast cancer cell lines and patient-derived circulating breast tumor cells. Results There are five adjoining regions from 17q11.1 to 17q24.1 being hotspots of chromothripsis. Inter−/intra-chromosomal rearrangements of these regions occurred more frequently in ERα-positive tumors than in ERα-negative tumors. In addition, the locations of the rearrangements were often mapped within or close to dense ERα binding sites localized on these five 17q regions or other chromosomes. This chromothriptic event was linked to concordant upregulation of 96 loci that predominantly regulate cell-cycle machineries in advanced luminal tumors. Genome-editing analysis confirmed that an ERα hub localized on 20q13 coordinately regulates a subset of these loci localized on 17q23 through long-range chromosome interactions. One of these loci, Tousled Like Kinase 2 (TLK2) known to participate in DNA damage checkpoint control, is an actionable target using phenothiazine antipsychotics (PTZs). The antiproliferative effect of PTZs was prominent in high TLK2-expressing cells, compared to low expressing cells. Conclusion This study demonstrates a new approach for identifying tumorigenic drivers from genomic regions highly susceptible to ERα-related chromothripsis. We found a group of luminal breast tumors displaying 17q-related chromothripsis for which antipsychotics can be repurposed as treatment adjuncts.
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Affiliation(s)
- Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Xi Tan
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chia-Nung Hung
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Nameer Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kate I Lathrop
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Richard Elledge
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Virginia G Kaklamani
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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30
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Hankey W, Chen Z, Wang Q. Shaping Chromatin States in Prostate Cancer by Pioneer Transcription Factors. Cancer Res 2020; 80:2427-2436. [PMID: 32094298 DOI: 10.1158/0008-5472.can-19-3447] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/14/2020] [Accepted: 02/19/2020] [Indexed: 01/28/2023]
Abstract
The androgen receptor (AR) is a critical therapeutic target in prostate cancer that responds to antagonists in primary disease, but inevitably becomes reactivated, signaling onset of the lethal castration-resistant prostate cancer (CRPC) stage. Epigenomic investigation of the chromatin environment and interacting partners required for AR transcriptional activity has uncovered three pioneer factors that open up chromatin and facilitate AR-driven transcriptional programs. FOXA1, HOXB13, and GATA2 are required for normal AR transcription in prostate epithelial development and for oncogenic AR transcription during prostate carcinogenesis. AR signaling is dependent upon these three pioneer factors both before and after the clinical transition from treatable androgen-dependent disease to untreatable CRPC. Agents targeting their respective DNA binding or downstream chromatin-remodeling events have shown promise in preclinical studies of CRPC. AR-independent functions of FOXA1, HOXB13, and GATA2 are emerging as well. While all three pioneer factors exert effects that promote carcinogenesis, some of their functions may inhibit certain stages of prostate cancer progression. In all, these pioneer factors represent some of the most promising potential therapeutic targets to emerge thus far from the study of the prostate cancer epigenome.
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Affiliation(s)
- William Hankey
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Zhong Chen
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina.
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina.
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31
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Giguère V. DNA-PK, Nuclear mTOR, and the Androgen Pathway in Prostate Cancer. Trends Cancer 2020; 6:337-347. [PMID: 32209447 DOI: 10.1016/j.trecan.2020.01.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 02/07/2023]
Abstract
Androgen and its receptor (AR) are major drivers of prostate cancer (PCa), a leading cause of mortality in aging men. Thus, understanding the numerous mechanisms by which AR can promote the growth and proliferation of PCa cells and enable their escape from hormone-dependent therapies, eventually leading to metastasis and death of the patient, is essential to discover alternative therapeutic approaches. Recently, two structurally related members of the phosphatidylinositol 3-kinase-like protein kinase (PIKK) family, DNA-dependent protein kinase (DNA-PK) and mammalian target of rapamycin (mTOR), were shown to have a direct role in modulating AR activity on chromatin of PCa cells. In this review, the common features of DNA-PK and mTOR and the similarities in their noncanonical roles as transcription coregulators of the AR are highlighted. An outlook on how these findings could be translated into new approaches to manage and treat PCa is provided.
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Affiliation(s)
- Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3G 1Y6, Canada.
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32
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Mangia A, Saponaro C, Vagheggini A, Opinto G, Centonze M, Vicenti C, Popescu O, Pastena M, Giotta F, Silvestris N. Should Tumor Infiltrating Lymphocytes, Androgen Receptor, and FOXA1 Expression Predict the Clinical Outcome in Triple Negative Breast Cancer Patients? Cancers (Basel) 2019; 11:cancers11091393. [PMID: 31540486 PMCID: PMC6769726 DOI: 10.3390/cancers11091393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor-infiltrating lymphocytes (TILs) are a valuable indicator of the immune microenvironment that plays the central role in new anticancer drugs. TILs have a strong prognostic role in triple negative breast cancer (TNBC). Little is known about the interaction with the androgen receptor (AR) and forkhead box A1 (FOXA1). We analyzed the relationships between TIL levels, AR, and FOXA1 expression and their clinical significance in TNBC patients. Further, we investigated their interaction with other biomarkers like programmed cell death ligand-1 (PD-L1), breast cancer type 1 susceptibility protein (BRCA1), poly (ADP-Ribose) polymerase 1 (PARP1), and Na+/H+ exchanger regulatory factor 1 (NHERF1). The expression of the proteins was evaluated by immunohistochemistry in 124 TNBC samples. TILs were performed adhering to International TILs Working Group 2014 criteria. Cox proportional hazards models were also used to identify risk factors associated with poor prognosis. Multivariate analysis identified TILs as independent prognostic factor of disease free survival (DFS; p = 0.045). A Kaplan-Meyer analysis revealed that the patients with high TILs had a better DFS compared to patients with low TILs (p = 0.037), and the phenotypes TILs-/AR+ and TILs-/FOXA1- had a worse DFS (p = 0.032, p = 0.001 respectively). AR was associated with FOXA1 expression (p = 0.007), and the tumors FOXA1+ presented low levels of TILs (p = 0.028). A poor DFS was observed for AR+/FOXA1+ tumors compared to other TNBCs (p = 0.0117). Low TILs score was associated with poor patients' survival, and TILs level in combination with AR or FOXA1 expression affected patient's clinical outcome. In addition, AR+/FOXA1+ phenotype identified a specific subgroup of TNBC patients with poor prognosis. These data may suggest new ways of therapeutic intervention to support current treatments.
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Affiliation(s)
- Anita Mangia
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Concetta Saponaro
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Alessandro Vagheggini
- Unit of Biostatistics and Clinical Trials, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
| | - Giuseppina Opinto
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Matteo Centonze
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Chiara Vicenti
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Ondina Popescu
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Maria Pastena
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Francesco Giotta
- Medical Oncology Unit, IRCCS-Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
| | - Nicola Silvestris
- Medical Oncology Unit, IRCCS-Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro' of Bari, 70124 Bari, Italy.
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Hata T, Rajabi H, Takahashi H, Yasumizu Y, Li W, Jin C, Long MD, Hu Q, Liu S, Fushimi A, Yamashita N, Kui L, Hong D, Yamamoto M, Miyo M, Hiraki M, Maeda T, Suzuki Y, Samur MK, Kufe D. MUC1-C Activates the NuRD Complex to Drive Dedifferentiation of Triple-Negative Breast Cancer Cells. Cancer Res 2019; 79:5711-5722. [PMID: 31519689 DOI: 10.1158/0008-5472.can-19-1034] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/25/2019] [Accepted: 09/09/2019] [Indexed: 01/04/2023]
Abstract
The NuRD chromatin remodeling and deacetylation complex, which includes MTA1, MBD3, CHD4, and HDAC1 among other components, is of importance for development and cancer progression. The oncogenic mucin 1 (MUC1) C-terminal subunit (MUC1-C) protein activates EZH2 and BMI1 in the epigenetic reprogramming of triple-negative breast cancer (TNBC). However, there is no known link between MUC1-C and chromatin remodeling complexes. Here, we showed that MUC1-C binds directly to the MYC HLH-LZ domain and identified a previously unrecognized MUC1-C→MYC pathway that regulates the NuRD complex. MUC1-C/MYC complexes selectively activated the MTA1 and MBD3 genes and posttranscriptionally induced CHD4 expression in basal- but not luminal-type BC cells. In turn, MUC1-C formed complexes with these NuRD components on the ESR1 promoter. Downregulating MUC1-C decreased MTA1/MBD3/CHD4/HDAC1 occupancy and increased H3K27 acetylation on the ESR1 promoter, with induction of ESR1 expression and downstream estrogen response pathways. Targeting MUC1-C and these NuRD components also induced expression of FOXA1, GATA3, and other markers associated with the luminal phenotype. These findings support a model in which MUC1-C activates the NuRD complex to drive dedifferentiation and reprogramming of TNBC cells. SIGNIFICANCE: MUC1-C directly interacts with MYC to activate the NuRD complex, mediating regulation of the estrogen receptor in triple-negative breast cancer cells.
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Affiliation(s)
- Tsuyoshi Hata
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Hasan Rajabi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Hidekazu Takahashi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Yota Yasumizu
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Wei Li
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Caining Jin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Nami Yamashita
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Deli Hong
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Masaaki Yamamoto
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Masaaki Miyo
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Masayuki Hiraki
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Takahiro Maeda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Yozo Suzuki
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mehmet K Samur
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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Mayran A, Sochodolsky K, Khetchoumian K, Harris J, Gauthier Y, Bemmo A, Balsalobre A, Drouin J. Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening. Nat Commun 2019; 10:3807. [PMID: 31444346 PMCID: PMC6707328 DOI: 10.1038/s41467-019-11791-9] [Citation(s) in RCA: 70] [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: 01/15/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Pioneer transcription factors are characterized by having the unique property of enabling the opening of closed chromatin sites, for implementation of cell fates. We previously found that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire, which allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigate the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes are defined by scRNAseq and chromatin accessibility profiling. We find that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.
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Affiliation(s)
- Alexandre Mayran
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Kevin Sochodolsky
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
| | - Konstantin Khetchoumian
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
| | - Juliette Harris
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
| | - Amandine Bemmo
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada.
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Département de Biochimie, Université de Montréal, Montreal, QC, Canada.
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Mopidevi B, Kaw MK, Sivankutty I, Jain S, Perla SK, Kumar A. A polymorphism in intron I of the human angiotensinogen gene ( hAGT) affects binding by HNF3 and hAGT expression and increases blood pressure in mice. J Biol Chem 2019; 294:11829-11839. [PMID: 31201268 DOI: 10.1074/jbc.ra119.007715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
Angiotensinogen (AGT) is the precursor of one of the most potent vasoconstrictors, peptide angiotensin II. Genome-wide association studies have shown that two A/G polymorphisms (rs2493134 and rs2004776), located at +507 and +1164 in intron I of the human AGT (hAGT) gene, are associated with hypertension. Polymorphisms of the AGT gene result in two main haplotypes. Hap-I contains the variants -217A, -6A, +507G, and +1164A and is pro-hypertensive, whereas Hap-II contains the variants -217G, -6G, +507A, and +1164G and does not affect blood pressure. The nucleotide sequence of intron I of the hAGT gene containing the +1164A variant has a stronger homology with the hepatocyte nuclear factor 3 (HNF3)-binding site than +1164G. Here we found that an oligonucleotide containing +1164A binds HNF3β more strongly than +1164G and that Hap-I-containing reporter gene constructs have increased basal and HNF3- and glucocorticoid-induced promoter activity in transiently transfected liver and kidney cells. Using a knock-in approach at the hypoxanthine-guanine phosphoribosyltransferase locus, we generated a transgenic mouse model containing the human renin (hREN) gene and either Hap-I or Hap-II. We show that transgenic animals containing Hap-I have increased blood pressure compared with those containing Hap-II. Moreover, the transcription factors glucocorticoid receptor, CCAAT enhancer-binding protein β, and HNF3β bound more strongly to chromatin obtained from the liver of transgenic animals containing Hap-I than to liver chromatin from Hap-II-containing animals. These findings suggest that, unlike Hap-II variants, Hap-I variants of the hAGT gene have increased transcription rates, resulting in elevated blood pressure.
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Affiliation(s)
| | - Meenakshi K Kaw
- Department of Physiology and Pharmacology, University of Toledo, Toledo, Ohio 43614
| | - Indu Sivankutty
- Department of Pathology, New York Medical College, Valhalla, New York 10595
| | - Sudhir Jain
- Department of Pathology, New York Medical College, Valhalla, New York 10595
| | - Sravan Kumar Perla
- Department of Pathology, New York Medical College, Valhalla, New York 10595
| | - Ashok Kumar
- Department of Pathology, New York Medical College, Valhalla, New York 10595
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36
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BenAyed-Guerfali D, Dabbèche-Bouricha E, Ayadi W, Trifa F, Charfi S, Khabir A, Sellami-Boudawara T, Mokdad-Gargouri R. Association of FOXA1 and EMT markers (Twist1 and E-cadherin) in breast cancer. Mol Biol Rep 2019; 46:3247-3255. [DOI: 10.1007/s11033-019-04784-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
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Meech R, Hu DG, McKinnon RA, Mubarokah SN, Haines AZ, Nair PC, Rowland A, Mackenzie PI. The UDP-Glycosyltransferase (UGT) Superfamily: New Members, New Functions, and Novel Paradigms. Physiol Rev 2019; 99:1153-1222. [DOI: 10.1152/physrev.00058.2017] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UDP-glycosyltransferases (UGTs) catalyze the covalent addition of sugars to a broad range of lipophilic molecules. This biotransformation plays a critical role in elimination of a broad range of exogenous chemicals and by-products of endogenous metabolism, and also controls the levels and distribution of many endogenous signaling molecules. In mammals, the superfamily comprises four families: UGT1, UGT2, UGT3, and UGT8. UGT1 and UGT2 enzymes have important roles in pharmacology and toxicology including contributing to interindividual differences in drug disposition as well as to cancer risk. These UGTs are highly expressed in organs of detoxification (e.g., liver, kidney, intestine) and can be induced by pathways that sense demand for detoxification and for modulation of endobiotic signaling molecules. The functions of the UGT3 and UGT8 family enzymes have only been characterized relatively recently; these enzymes show different UDP-sugar preferences to that of UGT1 and UGT2 enzymes, and to date, their contributions to drug metabolism appear to be relatively minor. This review summarizes and provides critical analysis of the current state of research into all four families of UGT enzymes. Key areas discussed include the roles of UGTs in drug metabolism, cancer risk, and regulation of signaling, as well as the transcriptional and posttranscriptional control of UGT expression and function. The latter part of this review provides an in-depth analysis of the known and predicted functions of UGT3 and UGT8 enzymes, focused on their likely roles in modulation of levels of endogenous signaling pathways.
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Affiliation(s)
- Robyn Meech
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Dong Gui Hu
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Ross A. McKinnon
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Siti Nurul Mubarokah
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Alex Z. Haines
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Pramod C. Nair
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Andrew Rowland
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Peter I. Mackenzie
- Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
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Glont SE, Chernukhin I, Carroll JS. Comprehensive Genomic Analysis Reveals that the Pioneering Function of FOXA1 Is Independent of Hormonal Signaling. Cell Rep 2019; 26:2558-2565.e3. [PMID: 30840881 PMCID: PMC6408623 DOI: 10.1016/j.celrep.2019.02.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/17/2018] [Accepted: 02/11/2019] [Indexed: 12/25/2022] Open
Abstract
Considerable work has linked hormone receptors, such as estrogen receptor-alpha (ER), with the pioneer factor FOXA1. Altered FOXA1 levels contribute to endocrine-resistant breast cancer, where it maintains ER-chromatin interactions, even in contexts in which cells are refractory to ER-targeted drugs. A recent study controversially suggests that FOXA1 binding can be induced by hormonal pathways, including the estrogen-ER complex. We now show that the vast majority (>99%) of FOXA1 binding events are unaffected by steroid activation. A small number (<1%) of FOXA1 binding sites appear to be induced by estrogen, but these are created from chromatin interactions between ER binding sites and adjacent FOXA1 binding sites and do not represent genuine new FOXA1-pioneering elements. FOXA1 is therefore not regulated by estrogen and remains a bone fide pioneer factor that is entirely upstream of the ER complex.
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Affiliation(s)
- Silvia-E Glont
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK.
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Baxter E, Windloch K, Kelly G, Lee JS, Gannon F, Brennan DJ. Molecular basis of distinct oestrogen responses in endometrial and breast cancer. Endocr Relat Cancer 2019; 26:31-46. [PMID: 30121621 DOI: 10.1530/erc-17-0563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022]
Abstract
Up to 80% of endometrial and breast cancers express oestrogen receptor alpha (ERα). Unlike breast cancer, anti-oestrogen therapy has had limited success in endometrial cancer, raising the possibility that oestrogen has different effects in both cancers. We investigated the role of oestrogen in endometrial and breast cancers using data from The Cancer Genome Atlas (TCGA) in conjunction with cell line studies. Using phosphorylation of ERα (ERα-pSer118) as a marker of transcriptional activation of ERα in TCGA datasets, we found that genes associated with ERα-pSer118 were predominantly unique between tumour types and have distinct regulators. We present data on the alternative and novel roles played by SMAD3, CREB-pSer133 and particularly XBP1 in oestrogen signalling in endometrial and breast cancer.
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Affiliation(s)
- Eva Baxter
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Karolina Windloch
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Greg Kelly
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jason S Lee
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Frank Gannon
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Donal J Brennan
- UCD School of Medicine, Catherine McAuley Research Centre, Mater Misericordiae University Hospital, Dublin, Ireland
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
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40
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Wang S, Singh SK, Katika MR, Lopez-Aviles S, Hurtado A. High Throughput Chemical Screening Reveals Multiple Regulatory Proteins on FOXA1 in Breast Cancer Cell Lines. Int J Mol Sci 2018; 19:ijms19124123. [PMID: 30572598 PMCID: PMC6321185 DOI: 10.3390/ijms19124123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022] Open
Abstract
Forkhead box A1 (FOXA1) belongs to the forkhead class transcription factor family, playing pioneering function for hormone receptors in breast and prostate cancers, and mediating activation of linage specific enhancers. Interplay between FOXA1 and breast cancer specific signaling pathways has been reported previously, indicating a regulation network on FOXA1 in breast cancer cells. Here in this study, we aimed to identify which are the proteins that could potentially control FOXA1 function in breast cancer cell lines expressing different molecular markers. We first established a luciferase reporter system reflecting FOXA1 binding to DNA. Then, we applied high throughput chemical screening of multiple protein targets and mass spectrometry in breast cancer cell lines expressing different molecular markers: ER positive/HER2 negative (MCF-7), ER positive/HER2 positive (BT474), and ER negative/HER2 positive (MDA-MB-453). Regardless of estrogen receptor status, HER2 (human epidermal growth factor receptor 2) enriched cell lines showed similar response to kinase inhibitors, indicating the control of FOXA1 by cell signaling kinases. Among these kinases, we identified additional receptor tyrosine kinases and cyclin-dependent kinases as regulators of FOXA1. Furthermore, we performed proteomics experiments from FOXA1 inmunoprecipitated protein complex to identify that FOXA1 interacts with several proteins. Among all the targets, we identified cyclin-dependent kinase 1 (CDK1) as a positive factor to interact with FOXA1 in BT474 cell line. In silico analyses confirmed that cyclin-dependent kinases might be the kinases responsible for FOXA1 phosphorylation at the Forkhead domain and the transactivation domain. These results reveal that FOXA1 is potentially regulated by multiple kinases. The cell cycle control kinase CDK1 might control directly FOXA1 by phosphorylation and other kinases indirectly by means of regulating other proteins.
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Affiliation(s)
- Shixiong Wang
- Breast Cancer Research group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, P.O. 1137 Blindern, 0318 Oslo, Norway.
| | - Sachin Kumar Singh
- Breast Cancer Research group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, P.O. 1137 Blindern, 0318 Oslo, Norway.
| | - Madhumohan R Katika
- Breast Cancer Research group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, P.O. 1137 Blindern, 0318 Oslo, Norway.
| | - Sandra Lopez-Aviles
- Cell Cycle Research group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, P.O. 1137 Blindern, 0318 Oslo, Norway.
| | - Antoni Hurtado
- Breast Cancer Research group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, P.O. 1137 Blindern, 0318 Oslo, Norway.
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41
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Zhang Y, Yang B, Cheng X, Liu L, Zhu Y, Gong Y, Yang Y, Tian J, Peng X, Zou D, Yang L, Mei S, Wang X, Lou J, Ke J, Li J, Gong J, Chang J, Yuan P, Zhong R. Integrative functional genomics identifies regulatory genetic variant modulating RAB31 expression and altering susceptibility to breast cancer. Mol Carcinog 2018; 57:1845-1854. [DOI: 10.1002/mc.22902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/14/2018] [Accepted: 08/31/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Yi Zhang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
- School of Public Health; Zunyi Medical University; Zunyi Guizhou China
| | - Beifang Yang
- Hubei Institute for Infectious Disease Control and Prevention; Hubei Provincial Center for Disease Control and Prevention; Wuhan China
| | - Xiang Cheng
- Department of Hepatobiliary Surgery; Union Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan China
| | - Li Liu
- Guangdong Key Lab of Molecular Epidemiology and Department of Epidemiology and Biostatistics; School of Public Health; Guangdong Pharmaceutical University; Guangzhou China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Yang Yang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Lan Yang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Shufang Mei
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Jiaoyuan Li
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Jing Gong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
| | - Peng Yuan
- Department of VIP Medical Services; National Cancer Center/Cancer Hospital; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health; School of Public Health; Tongji Medical College; Huazhong University of Science and Technology; Wuhan Hubei China
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42
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Zhao R, Liang X, Zhao B, Chen M, Liu R, Sun S, Yue X, Wang S. Ultrasound assisted gene and photodynamic synergistic therapy with multifunctional FOXA1-siRNA loaded porphyrin microbubbles for enhancing therapeutic efficacy for breast cancer. Biomaterials 2018; 173:58-70. [DOI: 10.1016/j.biomaterials.2018.04.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/29/2018] [Accepted: 04/30/2018] [Indexed: 12/20/2022]
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43
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Sartorelli V, Puri PL. Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master. Mol Cell 2018; 71:375-388. [PMID: 29887393 DOI: 10.1016/j.molcel.2018.04.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/05/2018] [Accepted: 04/27/2018] [Indexed: 01/14/2023]
Abstract
Since its discovery as a skeletal muscle-specific transcription factor able to reprogram somatic cells into differentiated myofibers, MyoD has provided an instructive model to understand how transcription factors regulate gene expression. Reciprocally, studies of other transcriptional regulators have provided testable hypotheses to further understand how MyoD activates transcription. Using MyoD as a reference, in this review, we discuss the similarities and differences in the regulatory mechanisms employed by tissue-specific transcription factors to access DNA and regulate gene expression by cooperatively shaping the chromatin landscape within the context of cellular differentiation.
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Affiliation(s)
- Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA 92037, USA; Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, Rome, Italy.
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44
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Hoffman JA, Trotter KW, Ward JM, Archer TK. BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome. eLife 2018; 7:35073. [PMID: 29792595 PMCID: PMC5967868 DOI: 10.7554/elife.35073] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/22/2018] [Indexed: 12/21/2022] Open
Abstract
The Glucocorticoid Receptor (GR) alters transcriptional activity in response to hormones by interacting with chromatin at GR binding sites (GBSs) throughout the genome. Our work in human breast cancer cells identifies three classes of GBSs with distinct epigenetic characteristics and reveals that BRG1 interacts with GBSs prior to hormone exposure. The GBSs pre-occupied by BRG1 are more accessible and transcriptionally active than other GBSs. BRG1 is required for a proper and robust transcriptional hormone response and knockdown of BRG1 blocks recruitment of the pioneer factors FOXA1 and GATA3 to GBSs. Finally, GR interaction with FOXA1 and GATA3 binding sites was restricted to sites pre-bound by BRG1. These findings demonstrate that BRG1 establishes specialized chromatin environments that define multiple classes of GBS. This in turn predicts that GR and other transcriptional activators function via multiple distinct chromatin-based mechanisms to modulate the transcriptional response. Steroid hormones play a number of roles in the body, including controlling the immune system and the body’s response to stress. Artificially produced steroid hormones may also be used as part of treatments for cancer. The hormones affect the behavior of cells by binding to and activating hormone receptor proteins. The receptors can then interact with the cell’s DNA to change the activity of nearby genes. Gaining access to particular sites on a strand of DNA is not always easy. Cells pack DNA into a structure called chromatin. In some regions the DNA is so tightly wrapped in the chromatin that the receptors cannot access it. The structure of the chromatin therefore affects how a cell responds to steroid hormones. Inaccessible regions of chromatin can be ‘opened up’ by two groups of proteins, known as remodeling proteins and pioneer factors. Hormone receptors can work with these proteins to access particular DNA regions, but exactly how all these proteins work together was not fully understood. Hoffman et al. have now used DNA and RNA sequencing technologies to examine the roles of a hormone receptor called the glucocorticoid receptor, a remodeling protein called BRG1, and various pioneer factors in human breast cancer cells. This revealed three ways in which the glucocorticoid receptors worked with the other proteins when binding to chromatin. These could be distinguished by the pattern of BRG1 molecules bound to the DNA. Further investigation showed that BRG1 controls how the glucocorticoid receptor affects the activity of genes. In addition, BRG1 influences how the receptor interacts with pioneer factors when it is bound to DNA. Future research into how these proteins work together could ultimately help us to improve how we use steroid hormones to treat diseases.
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Affiliation(s)
- Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
| | - Kevin W Trotter
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
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45
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Xu Z, Yang Y, Li B, Li Y, Xia K, Yang Y, Li X, Wang M, Li S, Wu H. Checkpoint suppressor 1 suppresses transcriptional activity of ERα and breast cancer cell proliferation via deacetylase SIRT1. Cell Death Dis 2018; 9:559. [PMID: 29752474 PMCID: PMC5948204 DOI: 10.1038/s41419-018-0629-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 02/08/2023]
Abstract
Breast cancer is a highly heterogeneous carcinoma in women worldwide, but the underlying mechanisms that account for breast cancer initiation and development have not been fully established. Mounting evidence indicates that Checkpoint suppressor 1 (CHES1) is tightly associated with tumorigenesis and prognosis in many types of cancer. However, the definitive function of CHES1 in breast cancer remains to be explored. Here we showed that CHES1 had a physical interaction with estrogen receptor-α (ERα) and repressed the transactivation of ERα in breast cancer cells. Mechanistically, the interaction between CHES1 and ERα enhanced the recruitment of nicotinamide adenine dinucleotide (NAD+) deacetylase Sirtuin 1 (SIRT1), and it further induced SIRT1-mediated ERα deacetylation and repression on the promoter-binding enrichment of ERα. In addition, we also found that the expression of CHES1 was repressed by estrogen-ERα signaling and the expression level of CHES1 was significantly downregulated in ERα-positive breast cancer. The detailed mechanism was that ERα may directly bind to CHES1 potential promoter via recognizing the conserved estrogen response element (ERE) motif in response to estrogen stimulation. Functionally, CHES1 inhibited ERα-mediated proliferation and tumorigenesis of breast cancer cells in vivo and in vitro. Totally, these results identified a negative cross-regulatory loop between ERα and CHES1 that was required for growth of breast cancer cells, it might uncover novel insight into molecular mechanism of CHES1 involved in breast cancer and provide new avenues for molecular-targeted therapy in hormone-regulated breast cancer.
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Affiliation(s)
- Zhaowei Xu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yangyang Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Bowen Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yanan Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Kangkai Xia
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yuxi Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xiahui Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Miao Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Shujing Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Huijian Wu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
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46
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Joseph C, Macnamara O, Craze M, Russell R, Provenzano E, Nolan CC, Diez-Rodriguez M, Sonbul SN, Aleskandarany MA, Green AR, Rakha EA, Ellis IO, Mukherjee A. Mediator complex (MED) 7: a biomarker associated with good prognosis in invasive breast cancer, especially ER+ luminal subtypes. Br J Cancer 2018; 118:1142-1151. [PMID: 29588513 PMCID: PMC5931067 DOI: 10.1038/s41416-018-0041-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/19/2018] [Accepted: 01/30/2018] [Indexed: 01/08/2023] Open
Abstract
Background Mediator complex (MED) proteins have a key role in transcriptional regulation, some interacting with the oestrogen receptor (ER). Interrogation of the METABRIC cohort suggested that MED7 may regulate lymphovascular invasion (LVI). Thus MED7 expression was assessed in large breast cancer (BC) cohorts to determine clinicopathological significance. Methods MED7 gene expression was investigated in the METABRIC cohort (n = 1980) and externally validated using bc-GenExMiner v4.0. Immunohistochemical expression was assessed in the Nottingham primary BC series (n = 1280). Associations with clinicopathological variables and patient outcome were evaluated. Results High MED7 mRNA and protein expression was associated with good prognostic factors: low grade, smaller tumour size, good NPI, positive hormone receptor status (p < 0.001), and negative LVI (p = 0.04) status. Higher MED7 protein expression was associated with improved BC-specific survival within the whole cohort and ER+/luminal subgroup. Pooled MED7 gene expression data in the external validation cohort confirmed association with better survival, corroborating with the protein expression. On multivariate analysis, MED7 protein was independently predictive of longer BC-specific survival in the whole cohort and Luminal A subtype (p < 0.001). Conclusions MED7 is an important prognostic marker in BC, particularly in ER+luminal subtypes, associated with improved survival and warrants future functional analysis.
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Affiliation(s)
- Chitra Joseph
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Olivia Macnamara
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Madeleine Craze
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | | | - Elena Provenzano
- Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Christopher C Nolan
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Maria Diez-Rodriguez
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Sultan N Sonbul
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Mohammed A Aleskandarany
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Andrew R Green
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Emad A Rakha
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Ian O Ellis
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Abhik Mukherjee
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK.
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Abstract
Pioneer transcription factors have the unique and important role of unmasking chromatin domains during development to allow the implementation of new cellular programs. Compared with those of other transcription factors, this activity implies that pioneer factors can recognize their target DNA sequences in so-called compacted or "closed" heterochromatin and can trigger remodeling of the adjoining chromatin landscape to provide accessibility to nonpioneer transcription factors. Recent studies identified several steps of pioneer action, namely rapid but weak initial binding to heterochromatin and stabilization of binding followed by chromatin opening and loss of cytosine-phosphate-guanine (CpG) methylation that provides epigenetic memory. Whereas CpG demethylation depends on replication, chromatin opening does not. In this Minireview, we highlight the unique properties of this transcription factor class and the challenges of understanding their mechanism of action.
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Affiliation(s)
- Alexandre Mayran
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
| | - Jacques Drouin
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
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48
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Ye W, Wang Y, Mei B, Hou S, Liu X, Wu G, Qin L, Zhao K, Huang Q. Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis. Bone 2018; 108:132-144. [PMID: 29307778 DOI: 10.1016/j.bone.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 01/19/2023]
Abstract
The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Numerous single nucleotide polymorphisms (SNPs) in the SOST locus are firmly associated with bone mineral density (BMD) and fracture in genome-wide association studies (GWAS) and candidate gene association studies. However, the validation and mechanistic elucidation of causal genetic variants, especially for SNPs located beyond the promoter-proximal region, remain largely unresolved. By employing computational and experimental approaches, here we identify four SNPs rs1230399, rs7220711, rs1107748 and rs75901553 as functional variants which display allelic variation in SOST gene expression. The osteoporosis associated SNP rs1230399 in the SOST distal upstream regulatory region shows FOXA1 binding activity with subsequent transinactivation in a T allele-specific manner. The BMD GWAS lead SNPs rs7220711 and rs1107748 both reside in the 52-kb regulatory element deletion 35-kb downstream of the SOST gene which leads to Van Buchem disease. The rs7220711-A has a higher affinity for the transcriptional repressors MAFF or MAFK homodimers than rs7220711-G, while rs1107748 confers C allele specific transcriptional enhancer activity via a CTCF binding element. The variant rs75901553 C>T located in a conserved site of the SOST 3' UTR abolishes a target binding site for miR-98-5p which is negatively responsive to parathyroid hormone or 17β-estradiol in osteoblastic cell lines. Our findings uncover the biological consequences of four independent genetic variants in the SOST region and their important roles in SOST expression via diverse mechanisms, providing new insights into the genetics and molecular pathogenesis of osteoporosis.
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Affiliation(s)
- Weiyuan Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Bing Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Sasa Hou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xinhong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Guiju Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Longjuan Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Kehui Zhao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.
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49
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Zhang Y, Li Y, Jiang S, Chen W, Lou J, Ke J, Li J, Zhu Y, Gong Y, Yang Y, Tian J, Peng X, Zou D, Gong J, Chang J, Miao X, Zhong R. A functional variant rs4442975 modulating FOXA1-binding affinity does not influence the risk or progression of breast cancer in Chinese Han population. Oncotarget 2018; 7:81691-81697. [PMID: 27835577 PMCID: PMC5348423 DOI: 10.18632/oncotarget.13168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/19/2016] [Indexed: 11/25/2022] Open
Abstract
The DNA-binding protein FOXA1 has been shown to regulate nearly all estrogen receptor-chromatin interactions, thereby influencing target gene expression levels in breast cancer (BC) cells. Recently, the rs4442975 T-allele, which disrupts the recruitment of FOXA1 and interacts with the IGFBP5 promoter, was associated to BC susceptibility in a European population. We conducted a hospital-based case-control study that included 1227 cases and 1285 controls to explore the potential association between rs4442975 and BC risk in Chinese Han population, and the effect of this SNP on BC progression was also observed in cases. No significant associations between rs4442975 and BC risk were observed under any genetic models, with an odds ratio of 0.96 (95% confidence interval = 0.81-1.15) under the additive model. When stratified based on estrogen or progesterone receptor expression, smoking or drinking habits, or menopausal status, similar negative associations were observed for all subgroups. No significant associations were observed between rs4442975 and traditional progression factors such as tumor size, nodal status, distant metastasis, or TNM staging. These results reveal that rs4442975 may not confer a risk of BC occurrence or progression in the Chinese Han population, which indicates a distinct association related to genetic heterogeneity across ethnic populations.
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Affiliation(s)
- Yi Zhang
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Department of Preventive Medicine, School of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yan Li
- Department of Preventive Medicine, School of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
| | - Shaojie Jiang
- Department of Gastroenterology, Jing Zhou Central Hospital, Jingzhou, China
| | - Wei Chen
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.,Zhuhai Center for Chronic Disease Control, Zhuhai, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Jiaoyuan Li
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Yang Yang
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Jing Gong
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and State Key Laboratory of Environment Health (Incubation), Ministry of Education Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
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50
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Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer. Nat Commun 2018; 9:482. [PMID: 29396493 PMCID: PMC5797120 DOI: 10.1038/s41467-018-02856-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/04/2018] [Indexed: 11/09/2022] Open
Abstract
Male breast cancer (MBC) is rare and poorly characterized. Like the female counterpart, most MBCs are hormonally driven, but relapse after hormonal treatment is also noted. The pan-hormonal action of steroid hormonal receptors, including estrogen receptor alpha (ERα), androgen receptor (AR), progesterone receptor (PR), and glucocorticoid receptor (GR) in this understudied tumor type remains wholly unexamined. This study reveals genomic cross-talk of steroid hormone receptor action and interplay in human tumors, here in the context of MBC, in relation to the female disease and patient outcome. Here we report the characterization of human breast tumors of both genders for cistromic make-up of hormonal regulation in human tumors, revealing genome-wide chromatin binding landscapes of ERα, AR, PR, GR, FOXA1, and GATA3 and enhancer-enriched histone mark H3K4me1. We integrate these data with transcriptomics to reveal gender-selective and genomic location-specific hormone receptor actions, which associate with survival in MBC patients.
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