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      Integrative analysis provides multi‐omics evidence for the pathogenesis of placenta percreta

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          Abstract

          Pernicious placenta previa with placenta percreta (PP) is a catastrophic condition during pregnancy. However, the underlying pathogenesis remains unclear. In the present study, the placental tissues of normal cases and PP tissues of pernicious placenta previa cases were collected to determine the expression profile of protein‐coding genes, miRNAs, and lncRNAs through sequencing. Weighted gene co‐expression network analysis (WGCNA), accompanied by miRNA target prediction and correlation analysis, were employed to select potential hub protein‐coding genes and lncRNAs. The expression levels of selected protein‐coding genes, Wnt5A and MAPK13, were determined by quantitative PCR and immunohistochemical staining, and lncRNA PTCHD1‐AS and PAPPA‐AS1 expression levels were determined by quantitative PCR and fluorescence in situ hybridization. The results indicated that 790 protein‐coding genes, 382 miRNAs, and 541 lncRNAs were dysregulated in PP tissues, compared with normal tissues. WGCNA identified coding genes in the module (ME) black and ME turquoise modules that may be involved in the pathogenesis of PP. The selected potential hub protein‐coding genes, Wnt5A and MAPK13, were down‐regulated in PP tissues, and their expression levels were positively correlated with the expression levels of PTCHD1‐AS and PAPPA‐AS1. Further analysis demonstrated that PTCHD1‐AS and PAPPA‐AS1 regulated Wnt5A and MAPK13 expression by interacting with specific miRNAs. Collectively, our results provided multi‐omics data to better understand the pathogenesis of PP and help identify predictive biomarkers and therapeutic targets for PP.

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          Most cited references53

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          WGCNA: an R package for weighted correlation network analysis

          Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at .
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            Long Noncoding RNA and Cancer: A New Paradigm.

            In addition to mutations or aberrant expression in the protein-coding genes, mutations and misregulation of noncoding RNAs, in particular long noncoding RNAs (lncRNA), appear to play major roles in cancer. Genome-wide association studies of tumor samples have identified a large number of lncRNAs associated with various types of cancer. Alterations in lncRNA expression and their mutations promote tumorigenesis and metastasis. LncRNAs may exhibit tumor-suppressive and -promoting (oncogenic) functions. Because of their genome-wide expression patterns in a variety of tissues and their tissue-specific expression characteristics, lncRNAs hold strong promise as novel biomarkers and therapeutic targets for cancer. In this article, we have reviewed the emerging functions and association of lncRNAs in different types of cancer and discussed their potential implications in cancer diagnosis and therapy. Cancer Res; 77(15); 3965-81. ©2017 AACR.
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              Emerging roles of long non‐coding RNA in cancer

              Since comprehensive analysis of the mammalian genome revealed that the majority of genomic products are transcribed in long non‐coding RNA (lncRNA), increasing attention has been paid to these transcripts. The applied next‐generation sequencing technologies have provided accumulating evidence of dysregulated lncRNA in cancer. The implication of this finding can be seen in many forms and at multiple levels. With impacts ranging from integrating chromatin remodeling complexes to regulating transcription and post‐transcriptional processes, aberrant expression of lncRNA may have repercussions in cell proliferation, tumor progression or metastasis. lncRNA may act as enhancers, scaffolds or decoys by physically interacting with other RNA species or proteins, resulting in a direct impact on cell signaling cascades. Even though their functional classification is well‐established in the context of cancer, clearer characterization in terms of their phenotypic outputs is needed to optimize and identify suitable candidates that enable the development of new therapeutic strategies and the design of novel diagnostic approaches. The present article aims to outline different cancer‐associated lncRNA according to their contribution to tumor suppression or tumor promotion based on their most current functional annotations.
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                Author and article information

                Contributors
                denghongx@scu.edu.cn
                wangxd_scu@sina.com
                Journal
                J Cell Mol Med
                J Cell Mol Med
                10.1111/(ISSN)1582-4934
                JCMM
                Journal of Cellular and Molecular Medicine
                John Wiley and Sons Inc. (Hoboken )
                1582-1838
                1582-4934
                21 October 2020
                December 2020
                : 24
                : 23 ( doiID: 10.1111/jcmm.v24.23 )
                : 13837-13852
                Affiliations
                [ 1 ] Department of Obstetrics and Gynecology West China Second University Hospital of Sichuan University and Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education Chengdu China
                [ 2 ] Department of Obstetrics Sichuan Provincial Hospital for Women and Children Chengdu China
                [ 3 ] State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University Chengdu China
                [ 4 ] Imaging Center Sichuan Provincial Hospital for Women and Children Chengdu China
                [ 5 ] Department of Laboratory Medicine Sichuan Provincial Hospital for Women and Children Chengdu China
                [ 6 ] Pathology Department Sichuan Provincial Hospital for Women and Children Chengdu China
                Author notes
                [*] [* ] Correspondence

                Xiaodong Wang, Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, No. 20, 3rd Section, South Renmin Road, Chengdu, Sichuan 610041, China.

                Email: wangxd_scu@ 123456sina.com

                Hongxin Deng, State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Ke‐yuan Road 4, No. 1, Gao‐peng Street, Chengdu, Sichuan 610041, China.

                Email: denghongx@ 123456scu.edu.cn

                Author information
                https://orcid.org/0000-0001-5094-1376
                https://orcid.org/0000-0002-5404-2017
                Article
                JCMM15973
                10.1111/jcmm.15973
                7754008
                33085209
                8eb8a728-afb5-409c-aef3-6c15ca469073
                © 2020 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 17 June 2020
                : 02 September 2020
                : 18 September 2020
                Page count
                Figures: 7, Tables: 3, Pages: 16, Words: 8300
                Funding
                Funded by: Science and Technology Program Key R&D Project of Sichuan Province
                Award ID: 2018SZ0265
                Funded by: Key R&D Program of Sichuan Province, China
                Award ID: 2020YFS0402
                Funded by: 1.3.5 project for disciplines of excellence, West China Hospital, Sichuan University
                Award ID: ZYGD20003
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                December 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.6 mode:remove_FC converted:22.12.2020

                Molecular medicine
                lncrna,mirna,pernicious placenta previa,placenta percreta,wnt5a
                Molecular medicine
                lncrna, mirna, pernicious placenta previa, placenta percreta, wnt5a

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