Long Noncoding RNA and Cancer: a New Paradigm Arunoday Bhan, Milad Soleimani, and Subhrangsu S
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Genetic Characterization of Endometriosis Patients: Review of the Literature and a Prospective Cohort Study on a Mediterranean Population
International Journal of Molecular Sciences Article Genetic Characterization of Endometriosis Patients: Review of the Literature and a Prospective Cohort Study on a Mediterranean Population Stefano Angioni 1,*, Maurizio Nicola D’Alterio 1,* , Alessandra Coiana 2, Franco Anni 3, Stefano Gessa 4 and Danilo Deiana 1 1 Department of Surgical Science, University of Cagliari, Cittadella Universitaria Blocco I, Asse Didattico Medicna P2, Monserrato, 09042 Cagliari, Italy; [email protected] 2 Department of Medical Science and Public Health, University of Cagliari, Laboratory of Genetics and Genomics, Pediatric Hospital Microcitemico “A. Cao”, Via Edward Jenner, 09121 Cagliari, Italy; [email protected] 3 Department of Medical Science and Public Health, University of Cagliari, Cittadella Universitaria di Monserrato, Asse Didattico E, Monserrato, 09042 Cagliari, Italy; [email protected] 4 Laboratory of Molecular Genetics, Service of Forensic Medicine, AOU Cagliari, Via Ospedale 54, 09124 Cagliari, Italy; [email protected] * Correspondence: [email protected] (S.A.); [email protected] (M.N.D.); Tel.: +39-07051093399 (S.A.) Received: 31 January 2020; Accepted: 2 March 2020; Published: 4 March 2020 Abstract: The pathogenesis of endometriosis is unknown, but some evidence supports a genetic predisposition. The purpose of this study was to evaluate the recent literature on the genetic characterization of women affected by endometriosis and to evaluate the influence of polymorphisms of the wingless-type mammalian mouse tumour virus integration -
CDKN2A and CDKN2B Methylation in Coronary Heart Disease Cases and Controls
EXPERIMENTAL AND THERAPEUTIC MEDICINE 14: 6093-6098, 2016 CDKN2A and CDKN2B methylation in coronary heart disease cases and controls JINYAN ZHONG1,2*, XIAOYING CHEN3*, HUADAN YE3, NAN WU1,3, XIAOMIN CHEN1 and SHIWEI DUAN3 1Cardiology Center, Ningbo First Hospital, Ningbo University; 2Department of Cardiology, Ningbo Second Hospital, Ningbo, Zhejiang 315010; 3Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China Received May 27, 2016; Accepted March 24, 2017 DOI: 10.3892/etm.2017.5310 Abstract. The aim of the present study was to investigate frequencies were significantly associated with age, and there the association between cyclin-dependent kinase inhibitor was a gender dimorphism in CDKN2B methylation. 2A (CDKN2A) and cyclin-dependent kinase inhibitor 2B (CDKN2B) methylation, and coronary heart disease (CHD), Introduction and to explore the interaction between methylation status and CHD clinical characteristics in Han Chinese patients. A total Coronary heart disease (CHD) is a complex chronic disease of 189 CHD (96 males, 93 females) and 190 well-matched that is caused by an imbalance between blood supply and non-CHD controls (96 males, 94 females) were recruited for demand in myocardium. Various environmental and genetic the study. Methylation-specific polymerase chain reaction factors are known to contribute to onset and development of technology was used to examine gene promoter methylation CHD (1). As of 2010, CHD was the leading cause of mortality status. Comparisons of methylation frequencies between CHD globally, resulting in over 7 million cases of mortality (2). and non-CHD patients were carried out using the Chi-square Therefore, association studies for CHD biomarkers have been test. -
(12) United States Patent (10) Patent No.: US 7,807,373 B2 Srivastava Et Al
US007807373B2 (12) United States Patent (10) Patent No.: US 7,807,373 B2 Srivastava et al. (45) Date of Patent: Oct. 5, 2010 (54) PROSTATE SPECIFIC GENE, PCGEM1, AND GenBank. Accession No. ACO 13401, GI:8569780, 169700 bp DNA, METHODS OF USING PCEGM1 TO DETECT, Jul. 7, 2000. TREAT, AND PREVENT PROSTATE CANCER “AC003046.” EBI Database XPO02143197, Dec. 1, 2001. (75) Inventors: Shiv Srivastava, Potomac, MD (US); Srikantanet al., “Structure and Expression of a Novel Prostate Spe Judd W. Moul, Bethesda, MD (US); cific Gene: PCGEM1. Proc. American Assoc. Cancer Research Vasantha Srikantan, Rockville, MD Annual, XP000929230, vol. 40, p. 37 (Mar. 1999). (US); Zhiqiang Zou, Gaithersburg, MD Bussemakers et al., “A New Prostate-Specific Arker, Strongly (US) Overexpressed in Prostatic Tumors.” Urological Research, XP0020743.05, vol. 25, No. 1, p. 76 (Feb. 1997). (73) Assignee: Henry M. Jackson Foundation for the Wang et al., “Genes Regulated by Androgen in the Rat Ventral Pros Advancement of Military Medicine, tate.” Proc. Nat.1 Acad. Sci., U.S.A., vol. 94, pp. 12999-13004 (Nov. Rockville, MD (US) 1997). “ACO 13401, EBI Database XP002143200, Apr. 16, 2005. (*) Notice: Subject to any disclaimer, the term of this Srikantan et al., “PCGEM1, a Prostate-Specific Gene, Is Overex patent is extended or adjusted under 35 posed in Prostate Cancer.” Proc. Natl. Acad. Sci., vol.97, No. 22, pp. U.S.C. 154(b) by 285 days. 12216-12221 (Oct. 24, 2000). (21) Appl. No.: 12/166,723 Srikantan et al., Identification of Prostate Cancer Associated Novel Gene Expression Alterations, Proc. American Assoc. Cancer (22) Filed: Jul. -
Oncotarget-05-764.Pdf
Open Research Online The Open University’s repository of research publications and other research outputs Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer Journal Item How to cite: Crea, Francesco; Watahiki, Akira; Quagliata, Luca; Xue, Hui; Pikor, Larissa; Parolia, Abhijit; Wang, Yuwei; Lin, Dong; Lam, Wan L.; Farrar, William L.; Isogai, Takao; Morant, Rudolf; Castori-Eppenberger, Serenella; Chi, Kim N.; Wang, Yuzhuo and Helgason, Cheryl D. (2014). Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer. Oncotarget, 5(3) pp. 764–774. For guidance on citations see FAQs. c 2014 The Authors https://creativecommons.org/licenses/by/4.0/ Version: Version of Record Link(s) to article on publisher’s website: http://dx.doi.org/doi:10.18632/oncotarget.1769 Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online’s data policy on reuse of materials please consult the policies page. oro.open.ac.uk www.impactjournals.com/oncotarget/ Oncotarget, Vol. 5, No. 3 Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer Francesco Crea1, Akira Watahiki1,2, Luca Quagliata3, Hui Xue1, Larissa Pikor4, Abhijit Parolia1,5, Yuwei Wang1, Dong Lin1,2, Wan L. Lam4, William L. Farrar6, Takao Isogai7, Rudolf Morant8, Serenella Castori-Eppenberger3, Kim N. Chi2,9, Yuzhuo Wang1,2, and Cheryl D. Helgason1 1 Experimental Therapeutics, BC Cancer Agency Cancer Research Centre, Vancouver BC, Canada. -
With Coronary Heart Disease: a Case-Control Study and a Meta-Analysis
Int. J. Mol. Sci. 2014, 15, 17478-17492; doi:10.3390/ijms151017478 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422–0067 www.mdpi.com/journal/ijms Article Association of CDKN2BAS Polymorphism rs4977574 with Coronary Heart Disease: A Case-Control Study and a Meta-Analysis Yi Huang 1, Huadan Ye 2, Qingxiao Hong 2, Xuting Xu 2, Danjie Jiang 2, Limin Xu 2, Dongjun Dai 2, Jie Sun 1, Xiang Gao 1,* and Shiwei Duan 2,* 1 Department of Neurosurgery, Ningbo First Hospital, Ningbo 315010, China; E-Mails: [email protected] (Y.H.); [email protected] (J.S.) 2 Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China; E-Mails: [email protected] (H.Y.); [email protected] (Q.H.); [email protected] (X.X.); [email protected] (D.J.); [email protected] (L.X.); [email protected] (D.D.) * Authors to whom correspondence should be addressed; E-Mails: [email protected] (X.G.); [email protected] (S.D.); Tel./Fax: +86-574-8708-5517 (X.G.); +86-574-8760-9950 (S.D.). External Editor: Camile S. Farah Received: 22 July 2014; in revised form: 12 September2014 / Accepted: 17 September 2014 / Published: 29 September 2014 Abstract: The goal of our study was to explore the significant association between a non-protein coding single nucleotide polymorphism (SNP) rs4977574 of CDKN2BAS gene and coronary heart disease (CHD). A total of 590 CHD cases and 482 non-CHD controls were involved in the present association study. A strong association of rs4977574 with CHD was observed in females (genotype: p = 0.002; allele: p = 0.002, odd ratio (OR) = 1.57, 95% confidential interval (CI) = 1.18–2.08). -
Novel Long Non-Coding Rnas Are Specific Diagnostic and Prognostic Markers for Prostate Cancer
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 6, No.6 Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer René Böttcher1,3, A. Marije Hoogland2, Natasja Dits1, Esther I. Verhoef2, Charlotte Kweldam2, Piotr Waranecki1, Chris H. Bangma1, Geert J.L.H. van Leenders2, Guido Jenster1 1Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands 2Dept. of Pathology, Erasmus MC, Rotterdam, The Netherlands 3Dept. of Bioinformatics, Technical University of Applied Sciences Wildau, Wildau, Germany Correspondence to: Guido Jenster, e-mail: [email protected] Keywords: Long non-coding RNA, prostate cancer, in situ hybridization, exon array, biomarkers Received: August 22, 2014 Accepted: December 08, 2014 Published: February 17, 2015 ABSTRACT Current prostate cancer (PCa) biomarkers such as PSA are not optimal in distinguishing cancer from benign prostate diseases and predicting disease outcome. To discover additional biomarkers, we investigated PCa-specific expression of novel unannotated transcripts. Using the unique probe design of Affymetrix Human Exon Arrays, we identified 334 candidates (EPCATs), of which 15 were validated by RT-PCR. Combined into a diagnostic panel, 11 EPCATs classified 80% of PCa samples correctly, while maintaining 100% specificity. High specificity was confirmed by in situ hybridization for EPCAT4R966 and EPCAT2F176 (SChLAP1) on extensive tissue microarrays. Besides being diagnostic, EPCAT2F176 and EPCAT4R966 showed significant association with pT-stage and were present in PIN lesions. We also found EPCAT2F176 and EPCAT2R709 to be associated with development of metastases and PCa-related death, and EPCAT2F176 to be enriched in lymph node metastases. Functional significance of expression of 9 EPCATs was investigated by siRNA transfection, revealing that knockdown of 5 different EPCATs impaired growth of LNCaP and 22RV1 PCa cells. -
Common Variants at 9P21 and 8Q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma
Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Wiggs, Janey L. et al. “Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma.” Ed. Gregory S. Barsh. PLoS Genetics 8.4 (2012): e1002654. Web. As Published http://dx.doi.org/10.1371/journal.pgen.1002654 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/71760 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.5/ Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma Janey L. Wiggs1.*, Brian L. Yaspan2., Michael A. Hauser3, Jae H. Kang4, R. Rand Allingham3, Lana M. Olson2, Wael Abdrabou1, Bao J. Fan1, Dan Y. Wang1, Wendy Brodeur5, Donald L. Budenz6, Joseph Caprioli7, Andrew Crenshaw5, Kristy Crooks3, Elizabeth DelBono1, Kimberly F. Doheny8, David S. Friedman9, Douglas Gaasterland10, Terry Gaasterland11, Cathy Laurie12, Richard K. Lee13, Paul R. Lichter14, Stephanie Loomis1,4, Yutao Liu3, Felipe A. Medeiros15, Cathy McCarty16, Daniel Mirel5, Sayoko E. Moroi14, David C. Musch14,17, Anthony Realini18, Frank W. Rozsa14, Joel S. Schuman19, Kathleen Scott14, Kuldev Singh20, Joshua D. Stein14, Edward H. Trager14, Paul VanVeldhuisen21, Douglas Vollrath22, Gadi Wollstein19, Sachiko Yoneyama14,17, Kang Zhang15, Robert N. Weinreb15, Jason Ernst5,23, Manolis Kellis5,23, Tomohiro Masuda9, Don Zack9, Julia E. Richards14,17, Margaret Pericak- Vance24, Louis R. Pasquale1,4", Jonathan L. -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
The Emergence of Lncrnas in Cancer Biology
Review The Emergence of lncRNAs in Cancer Biology John R. Prensner1,2 and Arul M. Chinnaiyan1–5 AbstAt R c The discovery of numerous noncoding RNA (ncRNA) transcripts in species from yeast to mammals has dramatically altered our understanding of cell biology, especially the biology of diseases such as cancer. In humans, the identification of abundant long ncRNA (lncRNA) >200 bp has catalyzed their characterization as critical components of cancer biology. Recently, roles for lncRNAs as drivers of tumor suppressive and oncogenic functions have appeared in prevalent cancer types, such as breast and prostate cancer. In this review, we highlight the emerging impact of ncRNAs in cancer research, with a particular focus on the mechanisms and functions of lncRNAs. Significance: lncRNAs represent the leading edge of cancer research. Their identity, function, and dysregulation in cancer are only beginning to be understood, and recent data suggest that they may serve as master drivers of carcinogenesis. Increased research on these RNAs will lead to a greater un- derstanding of cancer cell function and may lead to novel clinical applications in oncology. Cancer Discovery; 1(5):391–407. ©2011 AACR. intRoduction transcription reflects true biology or by-products of a leaky transcriptional system. Encompassed within these studies are A central question in biology has been, Which regions of the broad questions of what constitutes a human gene, what the human genome constitute its functional elements: those distinguishes a gene from a region that is simply transcribed, expressed as genes or those serving as regulatory elements? and how we interpret the biologic meaning of transcription. -
PCGEM1, a Prostate-Specific Gene, Is Overexpressed in Prostate Cancer
PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer Vasantha Srikantan*†, Zhiqiang Zou*†, Gyorgy Petrovics*, Linda Xu*, Meena Augustus*‡, Leland Davis*, Jeffrey R. Livezey*, Theresa Connell*, Isabell A. Sesterhenn§, Kiyoshi Yoshino¶, Gregory S. Buzard¶, F. K. Mostofi§, David G. McLeod*ሻ, Judd W. Moul*ሻ, and Shiv Srivastava*,** *Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799; ‡Genetics Department, Division of Clinical Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4470; §Armed Forces Institute of Pathology, Department of Genitourinary Pathology, Washington, DC 20307; ¶Laboratory of Comparative Carcinogenesis, Science Applications International Corporation, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, MD 21702-1201; and Urology Service, Department of Surgery, Walter Reed Army Medical Center, Washington, DC 20307-5001 Communicated by Bernhard Witkop, National Institutes of Health, Chevy Chase, MD, August 17, 2000 (received for review February 28, 2000) A prostate-specific gene, PCGEM1, was identified by differential anti-PSMA monoclonal antibodies (4). Furthermore, promising display analysis of paired normal and prostate cancer tissues. immunotherapy approaches are being pursued with PSMA Multiple tissue Northern blot analysis revealed that PCGEM1 was peptides (5). Recently described prostate-specific genes include expressed exclusively in human prostate tissue. Analysis of PC- an androgen-regulated homeobox gene, NKX3.1, which exhibits GEM1 expression in matched normal and primary tumor specimens function(s) in mouse prostate growth͞development (6, 7) and revealed tumor-associated overexpression in 84% of patients with shows overexpression in a subset of CaP (26). A prostate-specific prostate cancer by in situ hybridization assay and in 56% of gene, prostate stem cell antigen, has been shown to exhibit patients by reverse transcription–PCR assay. -
Lncrna‑P21 Promotes Chondrocyte Apoptosis in Osteoarthritis by Acting As a Sponge for Mir‑451
MOLECULAR MEDICINE REPORTS 18: 5295-5301, 2018 LncRNA‑p21 promotes chondrocyte apoptosis in osteoarthritis by acting as a sponge for miR‑451 LUPING TANG, JIANBO DING, GUANGJU ZHOU and ZHIHAI LIU Department of Emergency Medicine, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China Received December 20, 2017; Accepted September 11, 2018 DOI: 10.3892/mmr.2018.9506 Abstract. Osteoarthritis (OA) is the most common type of by the overexpression of lncRNA-p21 was abolished by the arthritis, and remains to be social and medical challenge. miR-451 mimic. Investigation into the underlying mechanism Thus, identifying novel molecular targets is important for revealed that lncRNA-p21 interacted with miRNA-451. In the prevention and treatment of OA. Long noncoding RNAs addition, lncRNA-p21 negatively regulated the expression of (lncRNAs) have been reported to modulate various biological miR-451. Furthermore, lncRNA-p21 promoted the apoptosis and pathological processes. The aim of the present study was of chondrocytes in OA by acting as a sponge for miR-451. to investigate the role of lncRNA-p21 in OA and its underlying Thus, lncRNA-p21 was proposed as a promising target for the mechanism, in order to better understand the development of OA treatment of OA. and its treatment. Chondrocytes were isolated from cartilage samples obtained from OA and normal patients. Chondrocytes Introduction were transfected with microRNA (miRNA/miR)-451 mimics, miR-451 inhibitor, pcDNA3.1(+)-p21 or small interfering Osteoarthritis (OA) is reported to afflict nearly 250 million RNA-p21. Flow cytometry was performed to analyze cell people in the whole world and is the most common apoptosis and reverse transcription-quantitative polymerase arthritis (1,2). -
Association Between Lncrna PCGEM1 Polymorphisms and Prostate Cancer Risk
Prostate Cancer and Prostatic Disease (2013) 16, 139–144 & 2013 Macmillan Publishers Limited All rights reserved 1365-7852/13 www.nature.com/pcan ORIGINAL ARTICLE Association between lncrna PCGEM1 polymorphisms and prostate cancer risk Y Xue1,2,5, M Wang2,3,5, M Kang2,3, Q Wang2,3,BWu2,3, H Chu1,2, D Zhong1,2, C Qin4, C Yin4, Z Zhang1,2,3 and D Wu2,3 BACKGROUND: Prostate cancer (PCa) gene expression marker 1 (PCGEM1), a long noncoding RNA, has drawn increasing attention for its important role in PCa. However, the association between genetic variations in the PCGEM1 gene and risk of PCa has not been investigated yet. METHODS: We investigated the effect of two tagging single-nucleotide polymorphism (tSNPs; rs6434568 and rs16834898) in PCGEM1 gene on PCa risk in the Chinese men. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association. RESULTS: We found a significantly decreased risk of PCa for rs6434568 AC and AC/AA genotype (adjusted OR ¼ 0.76, 95% CI ¼ 0.60–0.97 for AC; adjusted OR ¼ 0.76, 95% CI ¼ 0.61–0.96 for AC/AA), as well as rs16834898 AC and AC/CC genotype (adjusted OR ¼ 0.76, 95% CI ¼ 0.59–0.97 for AC; adjusted OR ¼ 0.79, 95% CI ¼ 0.62–0.99 for AC/CC), compared with the CC and AA genotypes, respectively. When we evaluated these two tSNPs together based on the risk alleles (that is, rs6434568 C and rs16834898 A), we found that the combined genotypes with four risk alleles were associated with an increased risk of PCa compared with those carrying 0–3 risk alleles (1.53, 1.19–1.97), and this increased risk was more pronounced among subjects ofp70 years (1.80, 1.24– 2.62), Gleason scorep7 (1.68, 1.28–2.22) and PSA levelX20 (1.64, 1.24–2.18).