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Perumalsamy NK, Hemalatha C. Cis-regulatory elements (CREs) in spinal solitary fibrous tumours. Meta Gene 2022. [DOI: 10.1016/j.mgene.2022.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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2
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Kunc M, Popęda M, Biernat W, Senkus E. Lost but Not Least-Novel Insights into Progesterone Receptor Loss in Estrogen Receptor-Positive Breast Cancer. Cancers (Basel) 2021; 13:cancers13194755. [PMID: 34638241 PMCID: PMC8507533 DOI: 10.3390/cancers13194755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022] Open
Abstract
Estrogen receptor α (ERα) and progesterone receptor (PgR) are crucial prognostic and predictive biomarkers that are usually co-expressed in breast cancer (BC). However, 12-24% of BCs present ERα(+)/PgR(-) phenotype at immunohistochemical evaluation. In fact, BC may either show primary PgR(-) status (in chemonaïve tumor sample), lose PgR expression during neoadjuvant treatment, or acquire PgR(-) phenotype in local relapse or metastasis. The loss of PgR expression in ERα(+) breast cancer may signify resistance to endocrine therapy and poorer outcomes. On the other hand, ERα(+)/PgR(-) BCs may have a better response to neoadjuvant chemotherapy than double-positive tumors. Loss of PgR expression may be a result of pre-transcriptional alterations (copy number loss, mutation, epigenetic modifications), decreased transcription of the PGR gene (e.g., by microRNAs), and post-translational modifications (e.g., phosphorylation, sumoylation). Various processes involved in the down-regulation of PgR have distinct consequences on the biology of cancer cells. Occasionally, negative PgR status detected by immunohistochemical analysis is paradoxically associated with enhanced transcriptional activity of PgR that might be inhibited by antiprogestin treatment. Identification of the mechanism of PgR loss in each patient seems challenging, yet it may provide important information on the biology of the tumor and predict its responsiveness to the therapy.
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Affiliation(s)
- Michał Kunc
- Department of Pathomorphology, Medical University of Gdańsk, 80-214 Gdańsk, Poland; (M.K.); (W.B.)
| | - Marta Popęda
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland;
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, 80-214 Gdańsk, Poland; (M.K.); (W.B.)
| | - Elżbieta Senkus
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, 80-214 Gdańsk, Poland
- Correspondence: ; Tel.: +48-58-584-4481
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3
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Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana. Sci Rep 2018; 8:7577. [PMID: 29765071 PMCID: PMC5953924 DOI: 10.1038/s41598-018-25872-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/26/2018] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing, in which one gene produce multiple transcripts, may influence how adaptive genes respond to specific environments. A newly produced transcriptome of Drosophila montana shows the Gs1-like (Gs1l) gene to express multiple splice variants and to be down regulated in cold acclimated flies with increased cold tolerance. Gs1l’s effect on cold tolerance was further tested by injecting cold acclimated and non-acclimated flies from two distantly located northern and southern fly populations with double stranded RNA (dsRNA) targeting Gs1l. While both populations had similar cold acclimation responses, dsRNA injections only effected the northern population. The nature of splicing expression was then investigated in the northern population by confirming which Gs1l variants are present, by comparing the expression of different gene regions and by predicting the protein structures of splices using homology modelling. We find different splices of Gs1l not only appear to have independent impacts on cold acclimation but also elicit different effects in populations originating from two very different environments. Also, at the protein level, Gs1l appears homologous to the human HDHD1A protein and some splices might produce functionally different proteins though this needs to be verified in future studies by measuring the particular protein levels. Taken together, Gs1l appears to be an interesting new candidate to test how splicing influences adaptations.
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4
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Target-Recognition Mechanism and Specificity of RNA Activation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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5
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Foulds CE, Panigrahi AK, Coarfa C, Lanz RB, O'Malley BW. Long Noncoding RNAs as Targets and Regulators of Nuclear Receptors. Curr Top Microbiol Immunol 2016; 394:143-76. [PMID: 26362934 DOI: 10.1007/82_2015_465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Intensive research has been directed at the discovery, biogenesis, and expression patterns of long noncoding RNAs , yet their biochemical functions have remained elusive for the most part. Nuclear receptors that interpret signaling mediated by small molecule hormones play a role in regulating the expression of some long noncoding RNAs. More importantly, these RNAs have also been shown to effect hormone-affected gene transcription regulated by the nuclear receptors. In this chapter, we summarize the current knowledge that has been acquired on hormonal signaling inducing expression of long noncoding RNAs and how they then may act in trans or in cis to modulate gene transcription. We highlight a few of these noncoding RNA molecules in terms of how they may impact hormone-driven cancers. Future directions critical for moving this field forward are presented, with a clear emphasis on the need for better biochemical approaches to address the mechanism of action of these exciting RNAs.
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Affiliation(s)
- Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Anil K Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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6
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Pendergraff HM, Debacker AJ, Watts JK. Single-Stranded Silencing RNAs: Hit Rate and Chemical Modification. Nucleic Acid Ther 2016; 26:216-22. [PMID: 27123752 DOI: 10.1089/nat.2015.0557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Single-stranded silencing RNAs (ss-siRNAs) are chemically modified single-stranded oligomers that engage the RNA interference machinery normally used by duplex RNAs to silence gene expression. ss-siRNAs have the potential to combine advantages of antisense oligonucleotides and siRNAs. Previous work has explored the chemistry of the phosphate and the oligonucleotide body. We now describe the process of attempting to develop and optimize ss-siRNAs based on five active siRNA duplexes. Three of the sequences failed to show any activity as ss-siRNAs, and in two of those cases the ss-siRNAs showed significantly increased toxicity relative to the parent duplexes. For the two sequences that did work well as ss-siRNAs, we show that the chemistry of the 3'-terminal dinucleotide also has a significant effect on the potency of ss-siRNAs. Previously published work on ss-siRNAs has been based on a 2'-O-methoxyethyl-RNA (MOE) dinucleotide at the 3'-terminus. To our surprise, oligomers containing 2'-O-Me-RNA modifications at the 3'-terminus showed significantly improved potency and activity relative to those modified with MOE at the same sites. Oligonucleotides with two locked nucleic acid units at the 3'-terminus showed improved activity over the MOE-modified analog for one sequence. Importantly, the fact that 2'-O-Me-RNA works so well makes the ss-siRNA approach accessible to a wider range of researchers since it can be achieved with inexpensive commercially available modifications.
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Affiliation(s)
- Hannah M Pendergraff
- 1 Department of Chemistry and Institute for Life Sciences, University of Southampton , United Kingdom
| | - Alexandre J Debacker
- 1 Department of Chemistry and Institute for Life Sciences, University of Southampton , United Kingdom .,2 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts
| | - Jonathan K Watts
- 1 Department of Chemistry and Institute for Life Sciences, University of Southampton , United Kingdom .,2 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts
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7
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Ioudinkova ES, Nefedochkina AV, Iarovaia OV, Razin SV. Detection of complementary transcripts for the intergenic region of the chicken α-globin gene domain. Mol Biol 2015. [DOI: 10.1134/s0026893315060229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Gellersen B, Brosens JJ. Cyclic decidualization of the human endometrium in reproductive health and failure. Endocr Rev 2014; 35:851-905. [PMID: 25141152 DOI: 10.1210/er.2014-1045] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Decidualization denotes the transformation of endometrial stromal fibroblasts into specialized secretory decidual cells that provide a nutritive and immunoprivileged matrix essential for embryo implantation and placental development. In contrast to most mammals, decidualization of the human endometrium does not require embryo implantation. Instead, this process is driven by the postovulatory rise in progesterone levels and increasing local cAMP production. In response to falling progesterone levels, spontaneous decidualization causes menstrual shedding and cyclic regeneration of the endometrium. A growing body of evidence indicates that the shift from embryonic to maternal control of the decidual process represents a pivotal evolutionary adaptation to the challenge posed by invasive and chromosomally diverse human embryos. This concept is predicated on the ability of decidualizing stromal cells to respond to individual embryos in a manner that either promotes implantation and further development or facilitates early rejection. Furthermore, menstruation and cyclic regeneration involves stem cell recruitment and renders the endometrium intrinsically capable of adapting its decidual response to maximize reproductive success. Here we review the endocrine, paracrine, and autocrine cues that tightly govern this differentiation process. In response to activation of various signaling pathways and genome-wide chromatin remodeling, evolutionarily conserved transcriptional factors gain access to the decidua-specific regulatory circuitry. Once initiated, the decidual process is poised to transit through distinct phenotypic phases that underpin endometrial receptivity, embryo selection, and, ultimately, resolution of pregnancy. We discuss how disorders that subvert the programming, initiation, or progression of decidualization compromise reproductive health and predispose for pregnancy failure.
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Affiliation(s)
- Birgit Gellersen
- Endokrinologikum Hamburg (B.G.), 20251 Hamburg, Germany; and Division of Reproductive Health (J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
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Chu Y, Kalantari R, Dodd DW, Corey DR. Transcriptional silencing by hairpin RNAs complementary to a gene promoter. Nucleic Acid Ther 2012; 22:147-51. [PMID: 22703280 DOI: 10.1089/nat.2012.0360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Double-stranded RNAs can target gene promoters and inhibit transcription. To date, most research has focused on synthetic RNA duplexes. Transcriptional silencing by hairpin RNAs would facilitate a better understanding of endogenous RNA-mediated regulation of transcription within cells. Here we examine transcriptional silencing of progesterone receptor (PR) expression by hairpin RNAs. We identify the guide strand as the strand complementary to an antisense transcript at the PR promoter and that hairpin RNAs are active transcriptional silencing agents. The sequence of the hairpin loop affects activity, with the highest activity achieved when the loop has the potential for full complementarity to the antisense transcript target. Introduction of centrally mismatched bases relative to the target transcript does not prevent transcriptional silencing unless the mismatches are present on both the guide and passenger strands. These data demonstrate that hairpin RNAs can cause transcriptional silencing and offer insights into the mechanism of gene modulation by RNAs that target gene promoters.
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Affiliation(s)
- Yongjun Chu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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11
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Cochrane DR, Spoelstra NS, Richer JK. The role of miRNAs in progesterone action. Mol Cell Endocrinol 2012; 357:50-9. [PMID: 21952083 DOI: 10.1016/j.mce.2011.09.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 08/09/2011] [Accepted: 09/11/2011] [Indexed: 12/21/2022]
Abstract
Small non-coding RNAs termed microRNAs (miRNAs) are mediators of post-transcriptional gene silencing and are involved in all aspects of cell biology. Progesterone receptors (PR) are intimately involved in the normal physiology and diseases of hormone responsive tissues including the uterus and the breast. Recent evidence suggests that hormone regulated miRNAs play a substantial role in hormone receptor mediated gene regulation. However, relatively little is known regarding miRNAs regulated by PR or that target PR as compared to those regulated by or targeting estrogen receptors (ER). We summarize the state of current knowledge regarding miRNAs and PR action. We also delineate how progesterone regulated miRNAs might provide an additional level of control and fine tuning of gene regulation by hormone receptors and also facilitate cell- and tissue-specific gene regulation PR.
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Affiliation(s)
- Dawn R Cochrane
- Department of Pathology, University of Colorado, Anschutz Medical Campus, Denver 80045, USA
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12
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Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 2012; 5:1. [PMID: 22230046 PMCID: PMC3281776 DOI: 10.1186/1756-8935-5-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 01/09/2012] [Indexed: 12/27/2022] Open
Abstract
Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share specific properties. Herein we discuss some examples and a parsimonious model for their function is proposed. All are transcription units that tether their target promoters close to, or distant from, transcriptional hot spots (or 'factories').
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Affiliation(s)
- Petros Kolovos
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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Abstract
Improvements in the gene transfer vectors used in therapeutic trials have led to substantial clinical successes in patients with serious genetic conditions, such as immunodeficiency syndromes, blindness and some cancer types. Several barriers need to be overcome before this type of therapy becomes a widely accepted treatment for a broad group of medical diseases. However, recent progress in the field is finally realizing some of the promises made more than 20 years ago, providing optimism for additional successes in the near future.
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Affiliation(s)
- Mark A Kay
- Department of Pediatrics and Genetics, Stanford University, 269 Campus Drive, Room 2105, Stanford, California 94305, USA.
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Matsui M, Sakurai F, Elbashir S, Foster D, Manoharan M, Corey DR. Activation of LDL receptor expression by small RNAs complementary to a noncoding transcript that overlaps the LDLR promoter. CHEMISTRY & BIOLOGY 2010; 17:1344-55. [PMID: 21168770 PMCID: PMC3071588 DOI: 10.1016/j.chembiol.2010.10.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/30/2010] [Accepted: 10/12/2010] [Indexed: 11/15/2022]
Abstract
Low-density lipoprotein receptor (LDLR) is a cell-surface receptor that plays a central role in regulating cholesterol levels. Increased levels of LDLR would lead to reduced cholesterol levels and contribute to strategies designed to treat hypercholesterolemia. We have previously shown that duplex RNAs complementary to transcription start sites can associate with noncoding transcripts and activate gene expression. Here we show that duplex RNAs complementary to the promoter of LDLR activate expression of LDLR and increase the display of LDLR on the surface of liver cells. Activation requires complementarity to the LDLR promoter and can be achieved by chemically modified duplex RNAs. Promoter-targeted duplex RNAs can overcome repression of LDLR expression by 25-hydroxycholesterol and do not interfere with activation of LDLR expression by lovastatin. These data demonstrate that small RNAs can activate LDLR expression and affect LDLR function.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
| | - Fuminori Sakurai
- Department of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | | | | | | | - David R. Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
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