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Cacioppo R, Lindon C. Regulating the regulator: a survey of mechanisms from transcription to translation controlling expression of mammalian cell cycle kinase Aurora A. Open Biol 2022; 12:220134. [PMID: 36067794 PMCID: PMC9448500 DOI: 10.1098/rsob.220134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aurora Kinase A (AURKA) is a positive regulator of mitosis with a strict cell cycle-dependent expression pattern. Recently, novel oncogenic roles of AURKA have been uncovered that are independent of the kinase activity and act within multiple signalling pathways, including cell proliferation, survival and cancer stem cell phenotypes. For this, cellular abundance of AURKA protein is per se crucial and must be tightly fine-tuned. Indeed, AURKA is found overexpressed in different cancers, typically as a result of gene amplification or enhanced transcription. It has however become clear that impaired processing, decay and translation of AURKA mRNA can also offer the basis for altered AURKA levels. Accordingly, the involvement of gene expression mechanisms controlling AURKA expression in human diseases is increasingly recognized and calls for much more research. Here, we explore and create an integrated view of the molecular processes regulating AURKA expression at the level of transcription, post-transcription and translation, intercalating discussion on how impaired regulation underlies disease. Given that targeting AURKA levels might affect more functions compared to inhibiting the kinase activity, deeper understanding of its gene expression may aid the design of alternative and therapeutically more successful ways of suppressing the AURKA oncogene.
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Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
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2
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Del Moral-Morales A, González-Orozco JC, Hernández-Vega AM, Hernández-Ortega K, Peña-Gutiérrez KM, Camacho-Arroyo I. EZH2 Mediates Proliferation, Migration, and Invasion Promoted by Estradiol in Human Glioblastoma Cells. Front Endocrinol (Lausanne) 2022; 13:703733. [PMID: 35197928 PMCID: PMC8859835 DOI: 10.3389/fendo.2022.703733] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Glioblastomas (GBM) are the most frequent and aggressive brain tumors. 17β-estradiol (E2) increases proliferation, migration, and invasion of human GBM cells; however underlying mechanisms are no fully understood. Zeste 2 Enhancer Homologous enzyme (EZH2) is a methyltransferase part of Polycomb 2 repressor complex (PRC2). In GBM, EZH2 is overexpressed and involved in the cell cycle, migration, and invasion processes. We studied the role of EZH2 in the pro-oncogenic actions of E2 in human GBM cells. EZH2 gene silencing and pharmacological inhibition of EZH2 blocked proliferation, migration, and invasion of GBM cells induced by E2. We identified in silico additional putative estrogen response elements (EREs) at the EZH2 promoter, but E2 did not modify EZH2 expression. In silico analysis also revealed that among human GBM samples, EZH2 expression was homogeneous; in contrast, the heterogeneous expression of estrogen receptors (ERs) allowed the classification of the samples into groups. Even in the GBM cluster with high expression of ERs and those of their target genes, the expression of PCR2 target genes did not change. Overall, our data suggest that in GBM cells, pro-oncogenic actions of E2 are mediated by EZH2, without changes in EZH2 expression and by mechanisms that appear to be unrelated to the transcriptional activity of ERs.
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Affiliation(s)
- Aylin Del Moral-Morales
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Juan Carlos González-Orozco
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Ana María Hernández-Vega
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Karina Hernández-Ortega
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Karla Mariana Peña-Gutiérrez
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- *Correspondence: Ignacio Camacho-Arroyo,
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3
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The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13246261. [PMID: 34944881 PMCID: PMC8699117 DOI: 10.3390/cancers13246261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.
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Hansda AK, Goswami R. 17-β estradiol signalling affects cardiovascular and cancer pathogenesis by regulating the crosstalk between transcription factors and EC-miRNAs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Koedoot E, van Steijn E, Vermeer M, González-Prieto R, Vertegaal ACO, Martens JWM, Le Dévédec SE, van de Water B. Splicing factors control triple-negative breast cancer cell mitosis through SUN2 interaction and sororin intron retention. J Exp Clin Cancer Res 2021; 40:82. [PMID: 33648524 PMCID: PMC7919097 DOI: 10.1186/s13046-021-01863-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited therapeutic opportunities. Recently, splicing factors have gained attention as potential targets for cancer treatment. Here we systematically evaluated the role of RNA splicing factors in TNBC cell proliferation. METHODS In this study, we performed an RNAi screen targeting 244 individual splicing factors to systematically evaluate their role in TNBC cell proliferation. For top candidates, mechanistic insight was gained using amongst others western blot, PCR, FACS, molecular imaging and cloning. Pulldown followed by mass spectrometry were used to determine protein-protein interactions and patient-derived RNA sequencing data was used relate splicing factor expression levels to proliferation markers. RESULTS We identified nine splicing factors, including SNRPD2, SNRPD3 and NHP2L1, of which depletion inhibited proliferation in two TNBC cell lines by deregulation of sister chromatid cohesion (SCC) via increased sororin intron 1 retention and down-regulation of SMC1, MAU2 and ESPL1. Protein-protein interaction analysis of SNRPD2, SNRPD3 and NHP2L1 identified that seven out of the nine identified splicing factors belong to the same spliceosome complex including novel component SUN2 that was also critical for efficient sororin splicing. Finally, sororin transcript levels are highly correlated to various proliferation markers in BC patients. CONCLUSION We systematically determined splicing factors that control proliferation of breast cancer cells through a mechanism that involves effective sororin splicing and thereby appropriate sister chromatid cohesion. Moreover, we identified SUN2 as an important new spliceosome complex interacting protein that is critical in this process. We anticipate that deregulating sororin levels through targeting of the relevant splicing factors might be a potential strategy to treat TNBC.
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Affiliation(s)
- Esmee Koedoot
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Eline van Steijn
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marjolein Vermeer
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Mal R, Magner A, David J, Datta J, Vallabhaneni M, Kassem M, Manouchehri J, Willingham N, Stover D, Vandeusen J, Sardesai S, Williams N, Wesolowski R, Lustberg M, Ganju RK, Ramaswamy B, Cherian MA. Estrogen Receptor Beta (ERβ): A Ligand Activated Tumor Suppressor. Front Oncol 2020; 10:587386. [PMID: 33194742 PMCID: PMC7645238 DOI: 10.3389/fonc.2020.587386] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ) belong to a superfamily of nuclear receptors called steroid hormone receptors, which, upon binding ligand, dimerize and translocate to the nucleus where they activate or repress the transcription of a large number of genes, thus modulating critical physiologic processes. ERβ has multiple isoforms that show differing association with prognosis. Expression levels of the full length ERβ1 isoform are often lower in aggressive cancers as compared to normal tissue. High ERβ1 expression is associated with improved overall survival in women with breast cancer. The promise of ERβ activation, as a potential targeted therapy, is based on concurrent activation of multiple tumor suppressor pathways with few side effects compared to chemotherapy. Thus, ERβ is a nuclear receptor with broad-spectrum tumor suppressor activity, which could serve as a potential treatment target in a variety of human cancers including breast cancer. Further development of highly selective agonists that lack ERα agonist activity, will be necessary to fully harness the potential of ERβ.
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Affiliation(s)
- Rahul Mal
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Alexa Magner
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Joel David
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Jharna Datta
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Meghna Vallabhaneni
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Mahmoud Kassem
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Jasmine Manouchehri
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Natalie Willingham
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Daniel Stover
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Jeffery Vandeusen
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Sagar Sardesai
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Nicole Williams
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Robert Wesolowski
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Maryam Lustberg
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Ramesh K Ganju
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Bhuvaneswari Ramaswamy
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
| | - Mathew A Cherian
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, United States
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Abstract
Breast cancer, a malignant tumor originating from mammary epithelial tissue, is the most common cancer among women worldwide. Challenges facing the diagnosis and treatment of breast cancer necessitate the search for new mechanisms and drugs to improve outcomes. Estrogen receptor (ER) is considered to be important for determining the diagnosis and treatment strategy. The discovery of the second estrogen receptor, ERβ, provides an opportunity to understand estrogen action. The emergence of ERβ can be traced back to 1996. Over the past 20 years, an increasing body of evidence has implicated the vital effect of ERβ in breast cancer. Although there is controversy among scholars, ERβ is generally thought to have antiproliferative effects in disease progression. This review summarizes available evidence regarding the involvement of ERβ in the clinical treatment and prognosis of breast cancer and describes signaling pathways associated with ERβ. We hope to highlight the potential of ERβ as a therapeutic target.
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Silva JM, Wippel HH, Santos MDM, Verissimo DCA, Santos RM, Nogueira FCS, Passos GAR, Sprengel SL, Borba LAB, Carvalho PC, Fischer JDSDG. Proteomics pinpoints alterations in grade I meningiomas of male versus female patients. Sci Rep 2020; 10:10335. [PMID: 32587372 PMCID: PMC7316823 DOI: 10.1038/s41598-020-67113-3] [Citation(s) in RCA: 6] [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: 01/27/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
Meningiomas are among the most common primary tumors of the central nervous system (CNS) and originate from the arachnoid or meningothelial cells of the meninges. Surgery is the first option of treatment, but depending on the location and invasion patterns, complete removal of the tumor is not always feasible. Reports indicate many differences in meningiomas from male versus female patients; for example, incidence is higher in females, whereas males usually develop the malignant and more aggressive type. With this as motivation, we used shotgun proteomics to compare the proteomic profile of grade I meningioma biopsies of male and female patients. Our results listed several differentially abundant proteins between the two groups; some examples are S100-A4 and proteins involved in RNA splicing events. For males, we identified enriched pathways for cell-matrix organization and for females, pathways related to RNA transporting and processing. We believe our findings contribute to the understanding of the molecular differences between grade I meningiomas of female and male patients.
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Affiliation(s)
- Janaína M Silva
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Curitiba, Brazil
| | - Helisa H Wippel
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Curitiba, Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Curitiba, Brazil
| | - Denildo C A Verissimo
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Curitiba, Brazil
- Clinical Hospital of the Federal University of Paraná, Paraná, Brazil
| | - Renata M Santos
- Laboratory of Protein Chemistry, Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C S Nogueira
- Laboratory of Protein Chemistry, Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Sergio L Sprengel
- Clinical Hospital of the Federal University of Paraná, Paraná, Brazil
| | - Luis A B Borba
- Clinical Hospital of the Federal University of Paraná, Paraná, Brazil
- Hospital Universitário Evangélico Mackenzie, Paraná, Brazil
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Curitiba, Brazil.
| | - Juliana de S da G Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Curitiba, Brazil.
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9
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Chaurasiya S, Widmann S, Botero C, Lin CY, Gustafsson JÅ, Strom AM. Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity. PLoS One 2020; 15:e0226057. [PMID: 32413024 PMCID: PMC7228066 DOI: 10.1371/journal.pone.0226057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Estrogen receptor β (ERβ) was first identified in the rodent prostate and is abundantly expressed in human and rodent prostate epithelium, stroma, immune cells and endothelium of the blood vessels. In the prostates of mice with inactivated ERβ, mutant phenotypes include epithelial hyperplasia and increased expression of androgen receptor (AR)-regulated genes, most of which are also upregulated in prostate cancer (PCa). ERβ is expressed in both basal and luminal cells in the prostate while AR is expressed in luminal but not in the basal cell layer which harbors the prostate stem cells. To investigate the mechanisms of action of ERβ and its potential cross-talk with AR, we used RNA-seq to study the effects of estradiol or the synthetic ligand, LY3201, in AR-positive LNCaP PCa cells which had been engineered to express ERβ. Transcriptomic analysis indicated relatively few changes in gene expression with ERβ overexpression, but robust responses following ligand treatments. There is significant overlap of responsive genes between the two ligands, estradiol and LY3201 as well as ligand-specific alterations. Gene set analysis of down-regulated genes identified an enrichment of androgen-responsive genes, such as FKBP5, CAMKK2, and TBC1D4. Consistently, AR transcript, protein levels, and transcriptional activity were down-regulated following ERβ activation. In agreement with this, we find that the phosphorylation of the CAMKK2 target, AMPK, was repressed by ligand-activated ERβ. These findings suggest that ERβ-mediated signaling pathways are involved in the negative regulation of AR expression and activity, thus supporting a tumor suppressive role for ERβ in PCa.
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Affiliation(s)
- Surendra Chaurasiya
- Department of Biology and Biochemistry, University of Houston, Center for Nuclear Receptors and Cell Signaling, Science & Engineering Research Center, Houston, Texas, United States of America
| | - Scott Widmann
- Department of Biology and Biochemistry, University of Houston, Center for Nuclear Receptors and Cell Signaling, Science & Engineering Research Center, Houston, Texas, United States of America
| | - Cindy Botero
- Department of Biology and Biochemistry, University of Houston, Center for Nuclear Receptors and Cell Signaling, Science & Engineering Research Center, Houston, Texas, United States of America
| | - Chin-Yo Lin
- Department of Biology and Biochemistry, University of Houston, Center for Nuclear Receptors and Cell Signaling, Science & Engineering Research Center, Houston, Texas, United States of America
| | - Jan-Åke Gustafsson
- Department of Biology and Biochemistry, University of Houston, Center for Nuclear Receptors and Cell Signaling, Science & Engineering Research Center, Houston, Texas, United States of America
- Department of BioSciences and Nutrition, Karolinska Institutet, Novum, Huddinge, Sweden
| | - Anders M. Strom
- Department of Biology and Biochemistry, University of Houston, Center for Nuclear Receptors and Cell Signaling, Science & Engineering Research Center, Houston, Texas, United States of America
- * E-mail:
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Alexandrova E, Giurato G, Saggese P, Pecoraro G, Lamberti J, Ravo M, Rizzo F, Rocco D, Tarallo R, Nyman TA, Collina F, Cantile M, Di Bonito M, Botti G, Nassa G, Weisz A. Interaction Proteomics Identifies ERbeta Association with Chromatin Repressive Complexes to Inhibit Cholesterol Biosynthesis and Exert An Oncosuppressive Role in Triple-negative Breast Cancer. Mol Cell Proteomics 2020; 19:245-260. [PMID: 31792072 PMCID: PMC7000115 DOI: 10.1074/mcp.ra119.001817] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/27/2019] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by poor response to therapy and low overall patient survival. Recently, Estrogen Receptor beta (ERβ) has been found to be expressed in a fraction of TNBCs where, because of its oncosuppressive actions on the genome, it represents a potential therapeutic target, provided a better understanding of its actions in these tumors becomes available. To this end, the cell lines Hs 578T, MDA-MB-468 and HCC1806, representing the claudin-low, basal-like 1 and 2 TNBC molecular subtypes respectively, were engineered to express ERβ under the control of a Tetracycline-inducible promoter and used to investigate the effects of this transcription factor on gene activity. The antiproliferative effects of ERβ in these cells were confirmed by multiple functional approaches, including transcriptome profiling and global mapping of receptor binding sites in the genome, that revealed direct negative regulation by ERβ of genes, encoding for key components of cellular pathways associated to TNBC aggressiveness representing novel therapeutic targets such as angiogenesis, invasion, metastasis and cholesterol biosynthesis. Supporting these results, interaction proteomics by immunoprecipitation coupled to nano LC-MS/MS mass spectrometry revealed ERβ association with several potential nuclear protein partners, including key components of regulatory complexes known to control chromatin remodeling, transcriptional and post-transcriptional gene regulation and RNA splicing. Among these, ERβ association with the Polycomb Repressor Complexes 1 and 2 (PRC1/2), known for their central role in gene regulation in cancer cells, was confirmed in all three TNBC subtypes investigated, suggesting its occurrence independently from the cellular context. These results demonstrate a significant impact of ERβ in TNBC genome activity mediated by its cooperation with regulatory multiprotein chromatin remodeling complexes, providing novel ground to devise new strategies for the treatment of these diseases based on ligands affecting the activity of this nuclear receptor or some of its protein partners.
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Affiliation(s)
- Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Genomix4Life Srl, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Genomix4Life Srl, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Pasquale Saggese
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, 90095
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy; Genomix4Life Srl, Spin-Off of the Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Domenico Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, 0424 Oslo, Norway
| | - Francesca Collina
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131 Italy
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131 Italy
| | - Maurizio Di Bonito
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131 Italy
| | - Gerardo Botti
- Scientific Direction, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples (NA), 80131, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (SA), 84081, Italy.
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11
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Splicing regulatory factors in breast cancer hallmarks and disease progression. Oncotarget 2019; 10:6021-6037. [PMID: 31666932 PMCID: PMC6800274 DOI: 10.18632/oncotarget.27215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. Moreover, we could relate expression of representative genes of four other hallmarks (enabling replicative mortality, genomic instability, avoiding immune destruction and evading growth suppression) to splice factor levels in human breast cancer tumors, suggesting that also these hallmarks could be regulated by splice factors. Since many splice factors are involved in multiple hallmarks of cancer, inhibiting splice factors might provide a new layer of oncogenic control and a powerful method to combat breast cancer progression.
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12
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Estrogen Receptors in Epithelial-Mesenchymal Transition of Prostate Cancer. Cancers (Basel) 2019; 11:cancers11101418. [PMID: 31548498 PMCID: PMC6826537 DOI: 10.3390/cancers11101418] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer (PC) remains a widespread malignancy in men. Since the androgen/androgen receptor (AR) axis is associated with the pathogenesis of prostate cancer, suppression of AR-dependent signaling by androgen deprivation therapy (ADT) still represents the primary intervention for this disease. Despite the initial response, prostate cancer frequently develops resistance to ADT and progresses. As such, the disease becomes metastatic and few therapeutic options are available at this stage. Although the majority of studies are focused on the role of AR signaling, compelling evidence has shown that estrogens and their receptors control prostate cancer initiation and progression through a still debated mechanism. Epithelial versus mesenchymal transition (EMT) is involved in metastatic spread as well as drug-resistance of human cancers, and many studies on the role of this process in prostate cancer progression have been reported. We discuss here the findings on the role of estrogen/estrogen receptor (ER) axis in epithelial versus mesenchymal transition of prostate cancer cells. The pending questions concerning this issue are presented, together with the impact of the available data in clinical management of prostate cancer patients.
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Torella D, Iaconetti C, Tarallo R, Marino F, Giurato G, Veneziano C, Aquila I, Scalise M, Mancuso T, Cianflone E, Valeriano C, Marotta P, Tammè L, Vicinanza C, Sasso FC, Cozzolino D, Torella M, Weisz A, Indolfi C. miRNA Regulation of the Hyperproliferative Phenotype of Vascular Smooth Muscle Cells in Diabetes. Diabetes 2018; 67:2554-2568. [PMID: 30257973 DOI: 10.2337/db17-1434] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 09/14/2018] [Indexed: 02/05/2023]
Abstract
Harnessing the mechanisms underlying the exacerbated vascular remodeling in diabetes mellitus (DM) is pivotal to prevent the high toll of vascular diseases in patients with DM. miRNA regulates vascular smooth muscle cell (VSMC) phenotypic switch. However, miRNA modulation of the detrimental diabetic VSMC phenotype is underexplored. Streptozotocin-induced type 1 DM (T1DM) Wistar rats and type 2 DM (T2DM) Zucker rats underwent right carotid artery experimental angioplasty, and global miRNA/mRNA expression profiling was obtained by RNA sequencing (RNA-Seq). Two days after injury, a set of six miRNAs were found to be uniquely downregulated or upregulated in VSMCs both in T1DM and T2DM. Among these miRNAs, miR-29c and miR-204 were the most significantly misregulated in atherosclerotic plaques from patients with DM. miR-29c overexpression and miR-204 inhibition per se attenuated VSMC phenotypic switch in DM. Concomitant miR-29c overexpression and miR-204 inhibition fostered an additive reduction in VSMC proliferation. Epithelial membrane protein 2 (Emp2) and Caveolin-1 (Cav1) mRNAs were identified as direct targets of miR-29c and miR-204, respectively. Importantly, contemporary miR-29c overexpression and miR-204 inhibition in the injured artery robustly reduced arterial stenosis in DM rats. Thus, contemporaneous miR-29c activation and miR-204 inhibition in DM arterial tissues is necessary and sufficient to prevent the exaggerated VSMC growth upon injury.
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MESH Headings
- Animals
- Cell Proliferation/physiology
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/pathology
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Humans
- Male
- MicroRNAs/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Plaque, Atherosclerotic/metabolism
- Plaque, Atherosclerotic/pathology
- Rats
- Rats, Wistar
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Affiliation(s)
- Daniele Torella
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Claudio Iaconetti
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
| | - Fabiola Marino
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
| | - Claudia Veneziano
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Iolanda Aquila
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Mariangela Scalise
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Teresa Mancuso
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Eleonora Cianflone
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Chiara Valeriano
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Pina Marotta
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Laura Tammè
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Carla Vicinanza
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Ferdinando C Sasso
- Department of Internal and Experimental Medicine "Magrassi-Lanzara," University of Campania "L. Vanvitelli," Naples, Italy
| | - Domenico Cozzolino
- Department of Internal and Experimental Medicine "Magrassi-Lanzara," University of Campania "L. Vanvitelli," Naples, Italy
| | - Michele Torella
- Department of Cardiothoracic Sciences, University of Campania "L. Vanvitelli," Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
| | - Ciro Indolfi
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
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Baralle M, Baralle FE. The splicing code. Biosystems 2017; 164:39-48. [PMID: 29122587 DOI: 10.1016/j.biosystems.2017.11.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 01/09/2023]
Abstract
This issue dedicated to the code of life tackles very challenging and open questions in Biology. The genetic code, brilliantly uncovered over 50 years ago is an example of a univocal biological code. In fact, except for very few and marginal variations, it is the same from bacteria to man, the RNA stretch: 5' GUGUUC 3' reads as the dipeptide: Val-Phe in bacteria, in yeast, in Arabidopsis, in zebra fish, in mouse and in human. A degree of ambiguity is possible if mutations are introduced in the tRNAs in a way that the anticodon reads one amino acid but the aminoacyl-transferase attaches a different one onto the tRNA. These were the very useful suppressor genes that aided greatly the study of bacterial genetics. Other biological codes however, are more akin to social codes and are less amenable to an unambiguous deciphering. Legal and ethical codes, weather we like it or not, are flexible and depend on the structure and history of the society that has produced them, as well as a specific point in time. The codes that govern RNA splicing have similar characteristics. In fact, the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved. However a substantial amount of information towards the deciphering of the splicing code has been gathered and in this manuscript we summarize the point reached.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Italy.
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15
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Tarallo R, Giurato G, Bruno G, Ravo M, Rizzo F, Salvati A, Ricciardi L, Marchese G, Cordella A, Rocco T, Gigantino V, Pierri B, Cimmino G, Milanesi L, Ambrosino C, Nyman TA, Nassa G, Weisz A. The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading. Genome Biol 2017; 18:189. [PMID: 29017520 PMCID: PMC5634881 DOI: 10.1186/s13059-017-1321-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/20/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities, antagonizing hormone-induced carcinogenesis and inhibiting growth and oncogenic functions in luminal-like breast cancers (BCs), where its expression correlates with a better prognosis of the disease. RESULTS Applying interaction proteomics coupled to mass spectrometry to characterize nuclear factors cooperating with ERβ in gene regulation, we identify AGO2 as a novel partner of ERβ in human BC cells. ERβ-AGO2 association was confirmed in vitro and in vivo in both the nucleus and cytoplasm and is shown to be RNA-mediated. ChIP-Seq demonstrates AGO2 association with a large number of ERβ binding sites, and total and nascent RNA-Seq in ERβ + vs ERβ - cells, and before and after AGO2 knock-down in ERβ + cells, reveals a widespread involvement of this factor in ERβ-mediated regulation of gene transcription rate and RNA splicing. Moreover, isolation and sequencing by RIP-Seq of ERβ-associated long and small RNAs in the cytoplasm suggests involvement of the nuclear receptor in RISC loading, indicating that it may also be able to directly control mRNA translation efficiency and stability. CONCLUSIONS These results demonstrate that AGO2 can act as a pleiotropic functional partner of ERβ, indicating that both factors are endowed with multiple roles in the control of key cellular functions.
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Affiliation(s)
- Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Giuseppina Bruno
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Luca Ricciardi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giovanna Marchese
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | | | - Teresa Rocco
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Valerio Gigantino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Biancamaria Pierri
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giovanni Cimmino
- Department of Cardiothoracic and Respiratory Sciences, University of Campania'L. Vanvitelli', Naples, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Segregate, MI, Italy
| | - Concetta Ambrosino
- Department of Science and Technology, University of Sannio, Benevento, Italy
- IRGS Biogem, Ariano Irpino, AV, Italy
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, via S. Allende, 1, 84081, Baronissi, SA, Italy.
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16
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Zhang Y, Wang DL, Yan HY, Liao JY, He JH, Hu KS, Deng WX, Wang YJ, Xing HT, Koeffler HP, Yin D. Genome-wide study of ER-regulated lncRNAs shows AP000439.3 may function as a key regulator of cell cycle in breast cancer. Oncol Rep 2017; 38:3227-3237. [PMID: 29048636 DOI: 10.3892/or.2017.5975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/12/2017] [Indexed: 11/06/2022] Open
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17
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Fiume G, Scialdone A, Rizzo F, De Filippo MR, Laudanna C, Albano F, Golino G, Vecchio E, Pontoriero M, Mimmi S, Ceglia S, Pisano A, Iaccino E, Palmieri C, Paduano S, Viglietto G, Weisz A, Scala G, Quinto I. IBTK Differently Modulates Gene Expression and RNA Splicing in HeLa and K562 Cells. Int J Mol Sci 2016; 17:ijms17111848. [PMID: 27827994 PMCID: PMC5133848 DOI: 10.3390/ijms17111848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/21/2016] [Accepted: 10/31/2016] [Indexed: 01/04/2023] Open
Abstract
The IBTK gene encodes the major protein isoform IBTKα that was recently characterized as substrate receptor of Cul3-dependent E3 ligase, regulating ubiquitination coupled to proteasomal degradation of Pdcd4, an inhibitor of translation. Due to the presence of Ankyrin-BTB-RCC1 domains that mediate several protein-protein interactions, IBTKα could exert expanded regulatory roles, including interaction with transcription regulators. To verify the effects of IBTKα on gene expression, we analyzed HeLa and K562 cell transcriptomes by RNA-Sequencing before and after IBTK knock-down by shRNA transduction. In HeLa cells, 1285 (2.03%) of 63,128 mapped transcripts were differentially expressed in IBTK-shRNA-transduced cells, as compared to cells treated with control-shRNA, with 587 upregulated (45.7%) and 698 downregulated (54.3%) RNAs. In K562 cells, 1959 (3.1%) of 63128 mapped RNAs were differentially expressed in IBTK-shRNA-transduced cells, including 1053 upregulated (53.7%) and 906 downregulated (46.3%). Only 137 transcripts (0.22%) were commonly deregulated by IBTK silencing in both HeLa and K562 cells, indicating that most IBTKα effects on gene expression are cell type-specific. Based on gene ontology classification, the genes responsive to IBTK are involved in different biological processes, including in particular chromatin and nucleosomal organization, gene expression regulation, and cellular traffic and migration. In addition, IBTK RNA interference affected RNA maturation in both cell lines, as shown by the evidence of alternative 3′- and 5′-splicing, mutually exclusive exons, retained introns, and skipped exons. Altogether, these results indicate that IBTK differently modulates gene expression and RNA splicing in HeLa and K562 cells, demonstrating a novel biological role of this protein.
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Affiliation(s)
- Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Annarita Scialdone
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, via S. Allende 1, 84081 Baronissi, Italy.
| | - Maria Rosaria De Filippo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, via S. Allende 1, 84081 Baronissi, Italy.
| | - Carmelo Laudanna
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, via S. Allende 1, 84081 Baronissi, Italy.
| | - Francesco Albano
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Gaetanina Golino
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Eleonora Vecchio
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Marilena Pontoriero
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Selena Mimmi
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Simona Ceglia
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Antonio Pisano
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Enrico Iaccino
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Sergio Paduano
- Department of Health Sciences, University "Magna Graecia", 88100 Catanzaro, Italy.
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, via S. Allende 1, 84081 Baronissi, Italy.
| | - Giuseppe Scala
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
| | - Ileana Quinto
- Department of Experimental and Clinical Medicine, University 'Magna Graecia' of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy.
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Epigenetic alterations of CYP19A1 gene in Cumulus cells and its relevance to infertility in endometriosis. J Assist Reprod Genet 2016; 33:1105-13. [PMID: 27167072 DOI: 10.1007/s10815-016-0727-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/02/2016] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The purpose of the present study was to investigate the epigenetic mechanisms responsible for the aberrant aromatase expression (CYP19A1) in Cumulus Cells (CCs) of infertile endometriosis patients. METHOD Cumulus cells were obtained from 24 infertile patients with and without endometriosis who underwent ovarian stimulation for intracytoplasmic sperm injection. Expression of CYP19A1 gene was quantified using Reverse Transcription Q-PCR. DNA methylation, histone modifications, and binding of Estrogen Receptor, ERβ to regulatory DNA sequences of CYP19A1 gene were evaluated by Chromatin ImmunoPrecipitation (ChIP) assay. RESULTS CYP19A1 gene expression in CCs of endometriosis patients was significantly lower than the control group (P = 0.04). Higher incorporation of MeCP2 (as a marker of DNA methylation) on PII and PI.4 promoters, and hypoacetylation at H3K9 in PII and hypermethylation at H3K9 in PI.4 were observed in CYP19A1 gene in endometriosis patients (P < 0.05). Moreover, a decreased level of ERβ binding to PII and an increased level of its binding to PI.3 and PI.4 promoters of CYP19A1 were observed in endometriosis patients when compared to control. CONCLUSION Significant reduction of CYP19A1 gene expression in CCs of endometriosis patients may be the result of epigenetic alterations in its regulatory regions, either by DNA methylation or histone modifications. These epigenetic changes along with differential binding of ERβ (as a transcription factor) in CYP19A1 promoters may impair follicular steroidogenesis, leading to poor Oocyte and embryo condition in endometriosis patients.
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Tao S, Liu YB, Zhou ZW, Lian B, Li H, Li JP, Zhou SF. miR-3646 promotes cell proliferation, migration, and invasion via regulating G2/M transition in human breast cancer cells. Am J Transl Res 2016; 8:1659-1677. [PMID: 27186291 PMCID: PMC4859896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are often located in genomic breakpoint regions and play a critical role in regulating a variety of the cellular processes in human cancer. miR-3646 has been reported to take part in tumorigenic progression in breast and bladder cancer, but its potential functions and exact mechanistic roles in breast cancer are still unclear. The objective of this study was to investigate the role of miR-3646 in breast cancer growth and metastasis using both bioinformatic and experimental approaches. Before starting the bench work, we conducted a bioinformatic study to predict the target genes regulated by miR-3646 using a panel of different algorithms. The results showed that miR-3646 might regulate a large number of genes that are related to cell growth, proliferation, metabolis, transport, and apoptosis and some were cancer-related genes. We found that the expression level of miR-3646 was significantly upregulated in breast cancer cells and tissues compared with normal breast cells and no tumor tissues. Subsequently, the MTT and colony formation assay results showed that up-regulation of miR-3646 promoted the cell viability and proliferation. Our results also showed that down-regulation of miR-3646 arrested the cells in G2/M phase in MCF7 and MDA-MB-231 cells which was accompanied by the down-regulation of CDK1/CDC2 and cyclin B1 and upregulation of p21Waf1/Cip1, p27 Kip1, and p53, suggesting that down-regulation of miR-3646 induces G2/M arrest through activation of the p53/p21/CDC2/cyclin B1 pathway. In addition, overexpression of miR-3646 promoted migration and invasion of MCF7 and MDA-MB-231 cells. Taken together, miR-3646 is a potential oncogene in breast cancer and it may represent a new niomarker in the diagnosis and prediction of prognosis and therapeutic response.
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Affiliation(s)
- Shuang Tao
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Yao-Bang Liu
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Zhi-Wei Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, Texas Tech University, Health Sciences CenterAmarillo, Texas, USA
| | - Bin Lian
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Hong Li
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Jin-Ping Li
- Ningxia Medical UniversityYinchuan, Ningxia 750004, China
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South FloridaTampa, Florida, USA
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Li H, Yuan Z, Ji J, Xu J, Zhang T, Zhang X, Xue F. A novel Markov Blanket-based repeated-fishing strategy for capturing phenotype-related biomarkers in big omics data. BMC Genet 2016; 17:51. [PMID: 26957081 PMCID: PMC4784463 DOI: 10.1186/s12863-016-0358-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
Background We propose a novel Markov Blanket-based repeated-fishing strategy (MBRFS) in attempt to increase the power of existing Markov Blanket method (DASSO-MB) and maintain its advantages in omic data analysis. Results Both simulation and real data analysis were conducted to assess its performances by comparing with other methods including χ2 test with Bonferroni and B-H adjustment, least absolute shrinkage and selection operator (LASSO) and DASSO-MB. A serious of simulation studies showed that the true discovery rate (TDR) of proposed MBRFS was always close to zero under null hypothesis (odds ratio = 1 for each SNPs) with excellent stability in all three scenarios of independent phenotype-related SNPs without linkage disequilibrium (LD) around them, correlated phenotype-related SNPs without LD around them, and phenotype-related SNPs with strong LD around them. As expected, under different odds ratio and minor allel frequency (MAFs), MBRFS always had the best performances in capturing the true phenotype-related biomarkers with higher matthews correlation coefficience (MCC) for all three scenarios above. More importantly, since proposed MBRFS using the repeated fishing strategy, it still captures more phenotype-related SNPs with minor effects when non-significant phenotype-related SNPs emerged under χ2 test after Bonferroni multiple correction. The various real omics data analysis, including GWAS data, DNA methylation data, gene expression data and metabolites data, indicated that the proposed MBRFS always detected relatively reasonable biomarkers. Conclusions Our proposed MBRFS can exactly capture the true phenotype-related biomarkers with the reduction of false negative rate when the phenotype-related biomarkers are independent or correlated, as well as the circumstance that phenotype-related biomarkers are associated with non-phenotype-related ones. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0358-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongkai Li
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
| | - Zhongshang Yuan
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
| | - Jiadong Ji
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
| | - Jing Xu
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
| | - Tao Zhang
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
| | - Xiaoshuai Zhang
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
| | - Fuzhong Xue
- Department of biostatistics, School of Public Health, Shandong University, Jinan City, Shandong Province, P. R. China.
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Menazza S, Murphy E. The Expanding Complexity of Estrogen Receptor Signaling in the Cardiovascular System. Circ Res 2016; 118:994-1007. [PMID: 26838792 DOI: 10.1161/circresaha.115.305376] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/28/2015] [Indexed: 12/21/2022]
Abstract
Estrogen has important effects on cardiovascular function including regulation of vascular function, blood pressure, endothelial relaxation, and the development of hypertrophy and cardioprotection. However, the mechanisms by which estrogen mediates these effects are still poorly understood. As detailed in this review, estrogen can regulate transcription by binding to 2 nuclear receptors, ERα and ERβ, which differentially regulate gene transcription. ERα and ERβ regulation of gene transcription is further modulated by tissue-specific coactivators and corepressors. Estrogen can bind to ERα and ERβ localized at the plasma membrane as well as G-protein-coupled estrogen receptor to initiate membrane delimited signaling, which enhances kinase signaling pathways that can have acute and long-term effects. The kinase signaling pathways can also mediate transcriptional changes and can synergize with the ER to regulate cell function. This review will summarize the beneficial effects of estrogen in protecting the cardiovascular system through ER-dependent mechanisms with an emphasis on the role of the recently described ER membrane signaling mechanisms.
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Affiliation(s)
- Sara Menazza
- From the Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD.
| | - Elizabeth Murphy
- From the Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD
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