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Sargazi S, Mukhtar M, Rahdar A, Bilal M, Barani M, Díez-Pascual AM, Behzadmehr R, Pandey S. Opportunities and challenges of using high-sensitivity nanobiosensors to detect long noncoding RNAs: A preliminary review. Int J Biol Macromol 2022; 205:304-315. [PMID: 35182562 DOI: 10.1016/j.ijbiomac.2022.02.082] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022]
Abstract
The two types ofncRNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are responsible for several biological processes within cells, such as the immune responses, cell growth and invasion, and regulation of the cell cycle. Rapidly expanding class of ncRNAs, lncRNAsinteract with other molecules to form chromatin-remodeling complexes. These potential hallmarks of diseases contribute to transcriptional and post-transcriptional regulation of several genes, possibly via cross-talk with other RNAs. Aberrant expression of lncRNAshas drawn increasing attention to the pathophysiology of different diseases, includingcancer and cardiovasculardiseases. Unfortunately, circulating lncRNAs are presented in the bloodstream at very low levels, making sensitive detection difficult. Currently, there are few methods for detecting these ncRNAs from which quantitative real-time-polymerase chain reaction (qRT-PCR) is the most routinely used technique. These techniqueslack sensitivity for intracellular detection of lncRNAs. Moreover, they are tedious and require a large sample size. Currently, nanotechnology has taken over the diagnostic field because of the tunable properties and modification opportunities. Furthermore, these conventional techniques can be merged with nanotechnology to improve detection sensitivity.This review highlights some of the most recent findings on nanotechnology-based methods and possible obstacles intheir application for moreaccurate sensing of lncRNAs.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
| | - Mahwash Mukhtar
- Faculty of Pharmacy, Institute of Pharmaceutical Technology and Regulatory Affairs, University of Szeged, Eötvösutca 6, Szeged 6720, Hungary
| | - Abbas Rahdar
- Department of Physics, Faculty of Science, University of Zabol, 538-98615 Zabol, Iran.
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Mahmood Barani
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman 7616913555, Iran
| | - Ana M Díez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona, Km. 33.6, 28805 Alcalá de Henares, Madrid, Spain
| | - Razieh Behzadmehr
- Department of Radiology, Zabol university of medical sciences, Zabol, Iran
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Science, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
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Salehi S, Afzali S, Shahi A, Amirzargar AA, Mansoori Y. Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Organ Transplantation. Front Immunol 2022; 13:835746. [PMID: 35359941 PMCID: PMC8962195 DOI: 10.3389/fimmu.2022.835746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Organ transplantation is the most preferred treatment option for end-stage organ diseases; however, allograft rejection is the major hurdle in successful long-term transplant survival. In spite of developing better HLA matching and more effective immunosuppressive regimen, one-year graft survival has been increased by nearly 90% and the incidence of acute rejection by one-year post-transplantation has been decreased by 12.2% in the last decades, chronic allograft rejection has remained as one of the major obstacles to the long-lasting survival of the transplanted allograft. Therefore, seemingly preventing the allograft rejection and inducing immunological tolerance against transplanted allografts is one of the primary goals in transplantation research to enable long-lasting graft survival. Various mechanisms such as long noncoding RNAs (lncRNAs) have been proposed that induce immune tolerance by modulating the gene expression and regulating innate and adaptive immune responses during transplantation. Besides, because of involvement in regulating epigenetic, transcriptional, and post-translational mechanisms, lncRNAs could affect allograft status. Therefore, these molecules could be considered as the potential targets for prediction, prognosis, diagnosis, and treatment of graft rejection. It is suggested that the noninvasive predictive biomarkers hold promise to overcome the current limitations of conventional tissue biopsy in the diagnosis of rejection. Hence, this review aims to provide a comprehensive overview of lncRNAs and their function to facilitate diagnosis, prognosis, and prediction of the risk of graft rejection, and the suggestive therapeutic choices after transplantation.
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Affiliation(s)
- Saeedeh Salehi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Afzali
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shahi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Ali Akbar Amirzargar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
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Zhang Y, Du XK, Su X, Zou X, Zhang CY. Mismatched fluorescent probes with an enhanced strand displacement reaction rate for intracellular long noncoding RNA imaging. Chem Commun (Camb) 2022; 58:1760-1763. [PMID: 35037666 DOI: 10.1039/d1cc05270e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We design mismatched fluorescent probes to directly monitor the long noncoding RNA (lncRNA) in living cells. The introduction of mismatched bases in the fluorescent probe greatly enhances the strand displacement reaction rate toward the target lncRNA. These mismatched probes can monitor the intracellular lncRNA expression level in various cell lines and discriminate cancer cells from normal cells, holding great potential in fundamental biomedical research and clinical disease diagnosis.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Xue-Ke Du
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Xianwei Su
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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Sun D, Li F, Liu L, Yu S, Wang H, Gao X, Liu G, Zhao Y, Qiu G, Jiang X. PSMA3-AS1 induced by transcription factor PAX5 promotes cholangiocarcinoma proliferation, migration and invasion by sponging miR-376a-3p to up-regulate LAMC1. Aging (Albany NY) 2022; 14:509-525. [PMID: 35022330 PMCID: PMC8791211 DOI: 10.18632/aging.203828] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been reported to exhibit a crucial regulatory role in tumor progression, including cholangiocarcinoma (CCA). As a promising lncRNA, proteasome 20S subunit alpha 3 antisense RNA 1 (PSMA3-AS1) is involved in development of various tumors. However, the role and function of PSMA3-AS1 in CCA remain unclear. The aim of this study is to examine the expression, function, mechanism, and clinical significance of PSMA3-AS1 in CCA development. By TCGA database analysis, we found that PSMA3-AS1 was overexpressed in CCA. Consistent with the TCGA analysis, PSMA3-AS1 was significantly overexpressed in CCA tissues and cells by RT-qPCR. Upregulated PSMA3-AS1 was related to lymph node invasion, advanced TNM stage and poor survival, and was an independent risk factor of prognosis for CCA patients. Functionally, CCK-8, EdU and colony formation assays confirmed that upregulated PSMA3-AS1 promoted CCA cell proliferation, whereas downregulated PSMA3-AS1 inhibited proliferation. This result was further confirmed by subcutaneous tumor formation in nude mice. Wound healing and transwell assays confirmed that increased PSMA3-AS1 promoted CCA cell migration and invasion, whereas decreased PSMA3-AS1 inhibited these biological phenotypes. In addition, PSMA3-AS1 promoted the EMT process of CCA by downregulating E-cadherin and upregulating N-cadherin and vimentin. Mechanistically, transcription factor PAX5 bound to the promoter region of PSMA3-AS1 and promoted its transcription. Simultaneously, PSMA3-AS1 primarily localized in the cytoplasm could competitively bind miR-376a-3p to upregulate LAMC1, thereby accelerating CCA progression. This study uncovers that PSMA3-AS1 functions as a cancer-promoting gene in CCA, and PAX5/PSMA3-AS1/miR-376a-3p/LAMC1 axis plays a vital role in CCA development.
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Affiliation(s)
- Dongsheng Sun
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Fujun Li
- Department of General Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Lang Liu
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Shaobo Yu
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Haicun Wang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Xin Gao
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Guanglin Liu
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yuqiao Zhao
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Gongcai Qiu
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Xingming Jiang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
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Epigenetic modifications of histones during osteoblast differentiation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194780. [PMID: 34968769 DOI: 10.1016/j.bbagrm.2021.194780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/30/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022]
Abstract
In bone biology, epigenetics plays a key role in mesenchymal stem cells' (MSCs) commitment towards osteoblasts. It involves gene regulatory mechanisms governed by chromatin modulators. Predominant epigenetic mechanisms for efficient osteogenic differentiation include DNA methylation, histone modifications, and non-coding RNAs. Among these mechanisms, histone modifications critically contribute to altering chromatin configuration. Histone based epigenetic mechanisms are an essential mediator of gene expression during osteoblast differentiation as it directs the bivalency of the genome. Investigating the importance of histone modifications in osteogenesis may lead to the development of epigenetic-based remedies for genetic disorders of bone. Hence, in this review, we have highlighted the importance of epigenetic modifications such as post-translational modifications of histones, including methylation, acetylation, phosphorylation, ubiquitination, and their role in the activation or suppression of gene expression during osteoblast differentiation. Further, we have emphasized the future advancements in the field of epigenetics towards orthopaedical therapeutics.
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Yan H, Zhou Y, Chen Z, Yan X, Zhu L. Long non-coding RNA HCG11 enhances osteosarcoma phenotypes by sponging miR-1245b-5p that directly inhibits plakophilin 2. Bioengineered 2021; 13:140-154. [PMID: 34949159 PMCID: PMC8805843 DOI: 10.1080/21655979.2021.2010367] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Long non-coding RNA (lncRNA) HCG11 can regulate various cancers through the ceRNA network. However, its role in osteosarcoma (OS) remains unknown. The HOS and Saos-2 cell lines were used for in vitro analyses. HCG11 and plakophilin 2 (PKP2) silencers, a miR-1245b-5p mimic, and a miR-1245b-5p inhibitor were utilized for the regulation analysis of lncRNA HCG11, miR-1245b-5p, and PKP2. Cell Counting Kit-8, wound healing, and transwell assays were used for cell proliferation, migration, and invasion analyses, and caspase-3 activity assay was used to measure cell apoptosis. The expression levels of lncRNA HCG11, miR-1245b-5p, and PKP2 were evaluated by quantitative real-time PCR and Western blotting. The distribution of lncRNA HCG11 was assessed using the RNA-FISH assay. The sponging and targeting roles of HCG11 and PKP2 on miR-1245b-5p were confirmed by dual-luciferase reporter analysis. An RNA immunoprecipitation assay was used to assess the binding between lncRNA HCG11 and miRNA-1245b-5p. We found that the lncRNA HCG11 was significantly upregulated in OS. LncRNA HCG11 silencing inhibits OS progression by repressing cell proliferation, migration, and invasion, and promoting cell apoptosis. RNA-FISH analysis indicated that lncRNA HCG11 was located in the cytoplasm. Mechanistic experiments showed that lncRNA HCG11 sponges miR-1245b-5p and negatively regulates miR-1245b-5p expression. Upregulated lncRNA HCG11 promotes proliferation, migration, and invasion, and inhibits apoptosis by inhibiting miR-1245b-5p in OS cells. PKP2 was verified as a target gene of miR-1245b-5p. Upregulated PKP2 promotes proliferation, migration, and invasion, and inhibits apoptosis by inhibiting miR-1245b-5p in OS. In conclusion, the HCG11/miR-1245b-5p/PKP2 axis promotes OS expression by promoting cell proliferation, migration, and invasion, and inhibiting apoptosis.
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Affiliation(s)
- Hao Yan
- Department of Spinal Surgery, Hubei 672 Orthopaedics Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei, China
| | - Yong Zhou
- Department of Oncology, Hubei Provincial Hospital of TCM, Wuhan, Hubei, China
| | - Zhujiang Chen
- Department of Spinal Surgery, Hubei 672 Orthopaedics Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei, China
| | - Xiaokang Yan
- Department of Orthopaedics, Hubei 672 Orthopaedics Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei, China
| | - Ling Zhu
- Department of Spinal Surgery, Hubei 672 Orthopaedics Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei, China
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Klapproth C, Sen R, Stadler PF, Findeiß S, Fallmann J. Common Features in lncRNA Annotation and Classification: A Survey. Noncoding RNA 2021; 7:77. [PMID: 34940758 PMCID: PMC8708962 DOI: 10.3390/ncrna7040077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast majority is poorly described beyond the existence of their transcripts. In this review we survey common in silico approaches for lncRNA annotation. We focus on the well-established sets of features used for classification and discuss their specific advantages and weaknesses. While the available tools perform very well for the task of distinguishing coding sequence from other RNAs, we find that current methods are not well suited to distinguish lncRNAs or parts thereof from other non-protein-coding input sequences. We conclude that the distinction of lncRNAs from intronic sequences and untranslated regions of coding mRNAs remains a pressing research gap.
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Affiliation(s)
- Christopher Klapproth
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
| | - Rituparno Sen
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), D-97080 Würzburg, Germany;
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, D-04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
- Facultad de Ciencias, Universidad National de Colombia, Bogotá CO-111321, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
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Zheng H, Zhao X, Wang H, Ding Y, Lu X, Zhang G, Yang J, Wang L, Zhang H, Bai Y, Li J, Wu J, Jiang Y, Xu L. Location deviations of DNA functional elements affected SNP mapping in the published databases and references. Brief Bioinform 2021; 21:1293-1301. [PMID: 31392334 DOI: 10.1093/bib/bbz073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022] Open
Abstract
The recent extensive application of next-generation sequencing has led to the rapid accumulation of multiple types of data for functional DNA elements. With the advent of precision medicine, the fine-mapping of risk loci based on these elements has become of paramount importance. In this study, we obtained the human reference genome (GRCh38) and the main DNA sequence elements, including protein-coding genes, miRNAs, lncRNAs and single nucleotide polymorphism flanking sequences, from different repositories. We then realigned these elements to identify their exact locations on the genome. Overall, 5%-20% of all sequence element locations deviated among databases, on the scale of kilobase-pair to megabase-pair. These deviations even affected the selection of genome-wide association study risk-associated genes. Our results implied that the location information for functional DNA elements may deviate among public databases. Researchers should take care when using cross-database sources and should perform pilot sequence alignments before element location-based studies.
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Affiliation(s)
- Hewei Zheng
- Harbin Medical University and Wenzhou Medical University
| | - Xueying Zhao
- Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences
| | - Hong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P R China
| | - Yu Ding
- Harbin Medical University and Wenzhou Medical University
| | - Xiaoyan Lu
- Harbin Medical University and Wenzhou Medical University
| | - Guosi Zhang
- Harbin Medical University and Wenzhou Medical University
| | - Jiaxin Yang
- Harbin Medical University and Wenzhou Medical University
| | - Lianzong Wang
- Harbin Medical University and Wenzhou Medical University
| | - Haotian Zhang
- Harbin Medical University and Wenzhou Medical University
| | - Yu Bai
- Harbin Medical University and Wenzhou Medical University
| | - Jing Li
- Harbin Medical University and Wenzhou Medical University
| | - Jingqi Wu
- Harbin Medical University and Wenzhou Medical University
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P. R. China
| | - Liangde Xu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, and Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, P. R. China
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Du Z, Shi X, Guan A. lncRNA H19 facilitates the proliferation and differentiation of human dental pulp stem cells via EZH2-dependent LATS1 methylation. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 25:116-126. [PMID: 34401209 PMCID: PMC8339349 DOI: 10.1016/j.omtn.2021.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 04/20/2021] [Indexed: 12/11/2022]
Abstract
Human dental pulp stem cells (hDPSCs) have been recognized as a candidate cell source for tissue engineering. Long non-coding RNAs (lncRNAs) are differentially expressed in inflamed human dental pulp tissues. The present study is aimed at investigating the role of lncRNA H19 in the differentiation potential of hDPSCs. hDPSCs were successfully isolated and cultured, followed by conducting gain and loss-of-function experiments on lncRNA H19 and large tumor suppressor 1 (LATS1) to elucidate their respective biological functions in hDPSCs. lncRNA H19 was able to promote, whereas LATS1 was found to inhibit the differentiation, proliferation, and migration capabilities of hDPSCs. LATS1 was found to activate the Hippo-Yes-associated protein (YAP) signaling pathway by decreasing levels of YAP and Tafazzin (TAZ). The effects of lncRNA H19 on hDPSCs were achieved by repressing LATS1 through enhancer of zeste homolog 2-induced trimethylation of histone 3 at lysine 27. Finally, hDPSCs overexpressing lncRNA H19 and/or LATS1 were transplanted into nude mice. It was shown that lncRNA H19 inhibited LATS1 to promote the production of odontoblasts in vivo. Taken together, lncRNA H19 serves as a contributor to the differentiation potential of hDPSCs via the inhibition of LATS1, therefore highlighting novel therapeutic targets for dental pulp repair.
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Affiliation(s)
- Zhen Du
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong Province, P.R. China
| | - Xiaoming Shi
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong Province, P.R. China
| | - Aizhong Guan
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong Province, P.R. China
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Bhattacharyya N, Pandey V, Bhattacharyya M, Dey A. Regulatory role of long non coding RNAs (lncRNAs) in neurological disorders: From novel biomarkers to promising therapeutic strategies. Asian J Pharm Sci 2021; 16:533-550. [PMID: 34849161 PMCID: PMC8609388 DOI: 10.1016/j.ajps.2021.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Long non coding RNAs (lncRNAs) are non-protein or low-protein coding transcripts that contain more than 200 nucleotides. They representing a large share of the cell's transcriptional output, demonstrate functional attributes viz. tissue-specific expression, determination of cell fate, controlled expression, RNA processing and editing, dosage compensation, genomic imprinting, conserved evolutionary traits etc. These long non coding variants are well associated with pathogenicity of various diseases including the neurological disorders like Alzheimer's disease, schizophrenia, Huntington's disease, Parkinson's disease etc. Neurological disorders are widespread and there knowing the underlying mechanisms become crucial. The lncRNAs take part in the pathogenesis by a plethora of mechanisms like decoy, scaffold, mi-RNA sequestrator, histone modifiers and in transcriptional interference. Detailed knowledge of the role of lncRNAs can help to use them further as novel biomarkers for therapeutic aspects. Here, in this review we discuss regulation and functional roles of lncRNAs in eight neurological diseases and psychiatric disorders, and the mechanisms by which they act. With these, we try to establish their roles as potential markers and viable diagnostic tools in these disorders.
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Affiliation(s)
| | - Vedansh Pandey
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, India
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lncRNA MSTRG.29039.1 Promotes Proliferation by Sponging hsa-miR-12119 via JAK2/STAT3 Pathway in Multiple Myeloma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9969449. [PMID: 34422217 PMCID: PMC8376436 DOI: 10.1155/2021/9969449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/12/2021] [Indexed: 12/27/2022]
Abstract
Noncoding RNA (ncRNA) is involved in the occurrence, development, metastasis, and drug resistance of tumors and involves a variety of biological functions. In addition, miRNA can regulate proliferation and migration and even regulate epigenetics to promote the development of multiple myeloma (MM). However, the mechanism of ncRNA involved in MM is still unclear, and there are many unknown ncRNAs to be explored. This research is aimed at discovering the unknown lncRNA in MM through high-throughput sequencing and to study the mechanism and role of competitive endogenous RNA (ceRNA) involved in the pathogenesis of MM for the development of novel molecular markers and potential new targeted drugs. We screened out 262 new lncRNAs with statistical differences by RNA sequencing and selected the lncRNA MSTRG.29039.1 according to the expression and function of lncRNAs and their target genes in MM. We verified that MSTRG.29039.1 and its target gene OSMR were highly expressed in MM. After knockdown of MSTRG.29039.1 in MM cell lines, the expression of OSMR was decreased, and the expression of hsa-miR-12119 was upregulated which can also promote cell apoptosis and inhibit proliferation. Then, we knocked down hsa-miR-12119 and MSTRG.29039.1, we found that apoptosis of MM cells was reduced, and cell proliferation was increased compared with just knocking down hsa-miR-12119. We further verified the direct binding relationship between MSTRG.29039.1 and OSMR by the dual-luciferase reporter assay system. Thus, MSTRG.29039.1 can competitively bind with miRNA to counteract the inhibitory effect of miRNA on OSMR, which regulates cell proliferation and apoptosis through the JAK2/STAT3 pathway. In a conclusion, lncRNA MSTRG.29039.1 could promote proliferation by sponging hsa-miR-12119 via the JAK2/STAT3 pathway in multiple myeloma. This may be a molecular marker and a potential therapeutic target for MM.
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Multifaceted roles of long non-coding RNAs in triple-negative breast cancer: biology and clinical applications. Biochem Soc Trans 2021; 48:2791-2810. [PMID: 33258920 DOI: 10.1042/bst20200666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer subtype that lacks targeted therapy due to the absence of estrogen, progesterone, and HER2 receptors. Moreover, TNBC was shown to have a poor prognosis, since it involves aggressive phenotypes that confer significant hindrance to therapeutic treatments. Recent state-of-the-art sequencing technologies have shed light on several long non-coding RNAs (lncRNAs), previously thought to have no biological function and were considered as genomic junk. LncRNAs are involved in various physiological as well as pathological conditions, and play a key role in drug resistance, gene expression, and epigenetic regulation. This review mainly focuses on exploring the multifunctional roles of candidate lncRNAs, and their strong association with TNBC development. We also summarise various emerging research findings that establish novel paradigms of lncRNAs function as oncogenes and/or tumor suppressors in TNBC development, suggesting their role as prospective therapeutic targets.
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Zhang XR, Shao JL, Li H, Wang L. Silencing of LINC00707 suppresses cell proliferation, migration, and invasion of osteosarcoma cells by modulating miR-338-3p/AHSA1 axis. Open Life Sci 2021; 16:728-736. [PMID: 34316513 PMCID: PMC8285991 DOI: 10.1515/biol-2021-0070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 04/23/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022] Open
Abstract
Osteosarcoma is the most common type of primary malignant tumor of the bone, with a high metastatic rate and poor prognosis. Therefore, it is important to further elucidate the molecular mechanisms involved in the development of osteosarcoma and explore new molecular therapeutic targets. Long intergenic nonprotein-coding RNA 707 (LINC00707) is an oncogenic gene in several cancers. In this study, we further clarified its role and regulatory mechanism in osteosarcoma. We found that LINC00707 levels are significantly higher in the osteosarcoma cell lines SW 1353, HOS, U-2 OS, MG-63, and Saos-2 compared to those in human fetal osteoblastic cell line hFOB1.19. LINC00707 silencing suppressed cell proliferation, migration, and invasion of MG-63 and Saos-2 cells. Moreover, LINC00707 can act as a competitive endogenous RNA of miR-338-3p, and miR-338-3p inhibitor and AHSA1 overexpression alleviated the effect of LINC00707 silencing. In conclusion, we demonstrated high expression of LINC00707 in osteosarcoma cell lines and that silencing LINC00707 suppresses cell proliferation, migration, and invasion by targeting the miR-338-3p/AHSA1 axis in MG-63 and Saos-2 cells. These findings suggest that LINC00707 may serve as a potential target for osteosarcoma treatment.
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Affiliation(s)
- Xiao-Rong Zhang
- Department of Orthopedic and Traumatology, The First Affiliated Hospital of Jinan University, 601 West Huangpu Avenue, Tianhe District, Guangzhou 510630, China
| | - Jian-Li Shao
- Department of Orthopedic and Traumatology, The First Affiliated Hospital of Jinan University, 601 West Huangpu Avenue, Tianhe District, Guangzhou 510630, China
| | - Heng Li
- Department of Orthopedic, Center in Zhanjiang City People's Hospital, Zhanjiang 524045, China
| | - Liang Wang
- Department of Oncology, The First Affiliated Hospital of Jinan University, 601 West Huangpu Avenue, Tianhe District, Guangzhou 510630, China
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Kaleem M, Perwaiz M, Nur SM, Abdulrahman AO, Ahmad W, Al-Abbasi FA, Kumar V, Kamal MA, Anwar F. Epigenetics of Triple-negative breast cancer via natural compounds. Curr Med Chem 2021; 29:1436-1458. [PMID: 34238140 DOI: 10.2174/0929867328666210707165530] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 02/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is a highly resistant, lethal, and metastatic sub-division of breast carcinoma, characterized by the deficiency of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). In women, TNBC shows a higher aggressive behavior with poor patient prognosis and a higher recurrence rate during reproductive age. TNBC is defined by the presence of epithelial-to-mesenchymal-transition (EMT), which shows a significant role in cancer progression. At the epigenetic level, TNBC is characterized by epigenetic signatures, such as DNA methylation, histone remodeling, and a host of miRNA, MiR-193, LncRNA, HIF-2α, eEF2K, LIN9/NEK2, IMP3, LISCH7/TGF-β1, GD3s and KLK12 mediated regulation. These modifications either are silenced or activate the necessary genes that are prevalent in TNBC. The review is based on epigenetic mediated mechanistic changes in TNBC. Furthermore, Thymoquinone (TQ), Regorafenib, Fangjihuangqi decoction, Saikosaponin A, and Huaier, etc., are potent antitumor natural compounds extensively reported in the literature. Further, the review emphasizes the role of these natural compounds in TNBC and their possible epigenetic targets, which can be utilized as a potential therapeutic strategy in treatment of TNBC.
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Affiliation(s)
- Mohammed Kaleem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Maryam Perwaiz
- Department of Sciences, University of Toronto. Mississauga. Canada
| | - Suza Mohammad Nur
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | | | - Wasim Ahmad
- Department of Kuliyate Tib, National Institute of Unani Medicine, Kottigepalya, Bengaluru, India
| | - Fahad A Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Vikas Kumar
- Natural Product Discovery Laboratory, Department of Pharmaceutical Sciences, Shalom Institute of Health and Allied Sciences. SHUATS, Naini, Prayagraj, India
| | - Mohammad Amjad Kamal
- West China School of Nursing / Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Firoz Anwar
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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65
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Philip M, Chen T, Tyagi S. A Survey of Current Resources to Study lncRNA-Protein Interactions. Noncoding RNA 2021; 7:ncrna7020033. [PMID: 34201302 PMCID: PMC8293367 DOI: 10.3390/ncrna7020033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
Phenotypes are driven by regulated gene expression, which in turn are mediated by complex interactions between diverse biological molecules. Protein-DNA interactions such as histone and transcription factor binding are well studied, along with RNA-RNA interactions in short RNA silencing of genes. In contrast, lncRNA-protein interaction (LPI) mechanisms are comparatively unknown, likely directed by the difficulties in studying LPI. However, LPI are emerging as key interactions in epigenetic mechanisms, playing a role in development and disease. Their importance is further highlighted by their conservation across kingdoms. Hence, interest in LPI research is increasing. We therefore review the current state of the art in lncRNA-protein interactions. We specifically surveyed recent computational methods and databases which researchers can exploit for LPI investigation. We discovered that algorithm development is heavily reliant on a few generic databases containing curated LPI information. Additionally, these databases house information at gene-level as opposed to transcript-level annotations. We show that early methods predict LPI using molecular docking, have limited scope and are slow, creating a data processing bottleneck. Recently, machine learning has become the strategy of choice in LPI prediction, likely due to the rapid growth in machine learning infrastructure and expertise. While many of these methods have notable limitations, machine learning is expected to be the basis of modern LPI prediction algorithms.
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Affiliation(s)
- Melcy Philip
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC 3800, Australia; (M.P.); (T.C.)
| | - Tyrone Chen
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC 3800, Australia; (M.P.); (T.C.)
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC 3800, Australia; (M.P.); (T.C.)
- Monash eResearch Centre, Monash University, Clayton, VIC 3800, Australia
- Department of Infectious Disease, Monash University (Alfred Campus), 85 Commercial Road, Melbourne, VIC 3004, Australia
- Correspondence:
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66
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Yin T, Zhao D, Yao S. Identification of a Genome Instability-Associated LncRNA Signature for Prognosis Prediction in Colon Cancer. Front Genet 2021; 12:679150. [PMID: 34163531 PMCID: PMC8215581 DOI: 10.3389/fgene.2021.679150] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) were reported to have the potential in maintaining genome instability, but the identification of lncRNAs related to genome instability and their prognostic value have not been largely explored in colon cancer. In this study, we obtained 155 genome instability-associated lncRNAs based on somatic mutation profiles in colon cancer from The Cancer Genome Atlas (TCGA) database. Functional enrichment analysis revealed the possible roles of genes co-expressed with those lncRNAs involved in some cancer, genome instability and immune related biological processes. Combined with overall survival data, a seven-lncRNA signature was established for prognosis prediction. According to the risk score calculated by this signature, high-risk patients characterized by high somatic mutation count, high microsatellite instability, significantly poorer clinical outcomes and specific tumor immune infiltration status compared with low-risk patients. The lncRNA signature was validated to be an independent prognostic indicator with good predictive performance in TCGA cohort. Furthermore, the prognostic value of the ZNF503-AS1 in lncRNA signature was confirmed in another independent dataset from Gene Expression Omnibus database. In summary, the genome instability-associated lncRNA signature in this study could be a promising tool for effectively predicting survival outcomes in colon cancer.
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Affiliation(s)
- Tengfei Yin
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Dongyan Zhao
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Shukun Yao
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.,Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
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68
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Sun X, Zhou J, Wu X, Yu Y, Zhan X, Xue S, Zheng Y, Ju W. Expression and Clinical Significance of Long Non-Coding RNA RP4-669H2.1 in Glioblastoma. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Neuroglioma is the most common malignant tumor in the central nervous system and still has a poor prognosis. Here, we investigated the prognostic value of long non-coding RNAs(lncRNAs) in glioblastoma. We first analyzed the lncRNA expression profiles of glioblastoma (GBM) in The Cancer
Genome Atlas database and selected the most differential survival genes (lncRNA RP4-669H2.1) for further validation. We then performed qRT-PCR using samples of 88 glioblastoma patients treated in our department between January 2011 and December 2017 that were retrospectively selected to validate
the prognostic value of RP4-669H2.1expression in glioblastoma. Using a Cox multivariate analysis, we explored the prognostic value of RP4-669H2.1 and analyzed whether it was an independent prognostic factor. This analysis confirmed that the RP4-669H2.1 expression was significantly associated
with glioblastoma-associated mortality in this patient cohort (P =1.80E–05) in TCGA database. In fact, the overall survival (OS) of the RP4-669H2.1 high-expression group (78 cases) was lower than that of the low-expression group (49 cases) (P = 4.6E–06) in TCGA database.
Moreover, the TNM stage of the RP4-669H2.1 high-expression group was higher than that of the RP4-669H2.1 low-expression group (P = 0.001). A multivariate analysis further showed that a higher TNM stage (OR = 2.167, 95% CI: 1.349–3.479) and a higher RP4-669H2.1 expression (OR =
2.933, 95% CI: 1.122–7.663) were independent risk factors for the OS of glioblastoma patients. Finally, we predicted the target genes of RP4-669H2.1 using a Multi Experiment Matrix and annotated their biological functions. We observed that the target genes of RP4-669H2.1 were mainly
enriched in biological functions related to DNA-binding transcription factor activity. Among these, we selected SMAD6 because the expression of RP4-669H2.1 was positively correlated with that of SMAD6 in glioblastoma. Overall, we conclude that the upregulation of RP4-669H2.1 is an independent
poor prognosis factor for glioblastoma and that it can regulate the DNA-binding activity of transcription factors.
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Affiliation(s)
- Xinhu Sun
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Jingyu Zhou
- Department of Cardiology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Xijuan Wu
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Yongpeng Yu
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Xia Zhan
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Shuo Xue
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Yali Zheng
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
| | - Weiping Ju
- Department of Neurology, The Affiliated Weihai Central Hospital of Qingdao University, Qingdao 264400, Shandong, PR China
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Giordo R, Ahmed YMA, Allam H, Abusnana S, Pappalardo L, Nasrallah GK, Mangoni AA, Pintus G. EndMT Regulation by Small RNAs in Diabetes-Associated Fibrotic Conditions: Potential Link With Oxidative Stress. Front Cell Dev Biol 2021; 9:683594. [PMID: 34095153 PMCID: PMC8170089 DOI: 10.3389/fcell.2021.683594] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
Diabetes-associated complications, such as retinopathy, nephropathy, cardiomyopathy, and atherosclerosis, the main consequences of long-term hyperglycemia, often lead to organ dysfunction, disability, and increased mortality. A common denominator of these complications is the myofibroblast-driven excessive deposition of extracellular matrix proteins. Although fibroblast appears to be the primary source of myofibroblasts, other cells, including endothelial cells, can generate myofibroblasts through a process known as endothelial to mesenchymal transition (EndMT). During EndMT, endothelial cells lose their typical phenotype to acquire mesenchymal features, characterized by the development of invasive and migratory abilities as well as the expression of typical mesenchymal products such as α-smooth muscle actin and type I collagen. EndMT is involved in many chronic and fibrotic diseases and appears to be regulated by complex molecular mechanisms and different signaling pathways. Recent evidence suggests that small RNAs, in particular microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are crucial mediators of EndMT. Furthermore, EndMT and miRNAs are both affected by oxidative stress, another key player in the pathophysiology of diabetic fibrotic complications. In this review, we provide an overview of the primary redox signals underpinning the diabetic-associated fibrotic process. Then, we discuss the current knowledge on the role of small RNAs in the regulation of EndMT in diabetic retinopathy, nephropathy, cardiomyopathy, and atherosclerosis and highlight potential links between oxidative stress and the dyad small RNAs-EndMT in driving these pathological states.
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Affiliation(s)
- Roberta Giordo
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Yusra M. A. Ahmed
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hilda Allam
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Salah Abusnana
- Department of Diabetes and Endocrinology, University Hospital Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Lucia Pappalardo
- Department of Biology, Chemistry and Environmental Studies, American University of Sharjah, Sharjah, United Arab Emirates
| | - Gheyath K. Nasrallah
- Department of Biomedical Sciences, College of Health Sciences Member of QU Health, Qatar University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Arduino Aleksander Mangoni
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Flinders Medical Centre, Adelaide, SA, Australia
| | - Gianfranco Pintus
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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70
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Liu JX, Gao MM, Cui Z, Gao YL, Li F. DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization. BMC Bioinformatics 2021; 22:241. [PMID: 33980147 PMCID: PMC8114493 DOI: 10.1186/s12859-020-03868-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/09/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In the development of science and technology, there are increasing evidences that there are some associations between lncRNAs and human diseases. Therefore, finding these associations between them will have a huge impact on our treatment and prevention of some diseases. However, the process of finding the associations between them is very difficult and requires a lot of time and effort. Therefore, it is particularly important to find some good methods for predicting lncRNA-disease associations (LDAs). RESULTS In this paper, we propose a method based on dual sparse collaborative matrix factorization (DSCMF) to predict LDAs. The DSCMF method is improved on the traditional collaborative matrix factorization method. To increase the sparsity, the L2,1-norm is added in our method. At the same time, Gaussian interaction profile kernel is added to our method, which increase the network similarity between lncRNA and disease. Finally, the AUC value obtained by the experiment is used to evaluate the quality of our method, and the AUC value is obtained by the ten-fold cross-validation method. CONCLUSIONS The AUC value obtained by the DSCMF method is 0.8523. At the end of the paper, simulation experiment is carried out, and the experimental results of prostate cancer, breast cancer, ovarian cancer and colorectal cancer are analyzed in detail. The DSCMF method is expected to bring some help to lncRNA-disease associations research. The code can access the https://github.com/Ming-0113/DSCMF website.
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Affiliation(s)
- Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Ming-Ming Gao
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Zhen Cui
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Ying-Lian Gao
- Qufu Normal University Library, Qufu Normal University, Rizhao, China
| | - Feng Li
- School of Computer Science, Qufu Normal University, Rizhao, China
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71
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Zhang X, Asllanaj E, Amiri M, Portilla-Fernandez E, Bramer WM, Nano J, Voortman T, Pan Q, Ghanbari M. Deciphering the role of epigenetic modifications in fatty liver disease: A systematic review. Eur J Clin Invest 2021; 51:e13479. [PMID: 33350463 PMCID: PMC8243926 DOI: 10.1111/eci.13479] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fatty liver disease (FLD), primarily nonalcoholic fatty liver disease (NAFLD), is the most common liver disorder that affects a quarter of the global population. NAFLD is a spectrum of disease ranging from simple steatosis to nonalcoholic steatohepatitis, which is associated with increased risk of developing liver cancer. Given that the pathogenic mechanisms of fatty liver remain largely elusive, it is important to further investigate potential underlying mechanisms including epigenetic modifications. Here, we performed a systematic review of human epigenetic studies on FLD presence. METHODS Five bibliographic databases were screened until 28 August 2020. We included cross-sectional, case-control and cohort studies in humans that examined the association of epigenetic modifications including global, candidate or epigenome-wide methylation of DNA, noncoding RNAs and histone modifications with FLD. RESULTS In total 36 articles, based on 33 unique studies, consisting of 12 112 participants met the inclusion criteria. Among these, two recent epigenome-wide association studies conducted among large population-based cohorts have reported the association between cg06690548 (SLC7A11) and FLD. Moreover, several studies have demonstrated the association between microRNAs (miRNAs) and FLD, in which miR-122, miR-34a and miR-192 were recognized as the most relevant miRNAs as biomarkers for FLD. We did not find any studies examining histone modifications in relation to FLD. CONCLUSIONS Cumulative evidence suggests a link between epigenetic mechanisms, specifically DNA methylation and miRNAs, and FLD. Further efforts should investigate the molecular pathways by which these epigenetic markers may regulate FLD and also the potential role of histone modifications in FLD.
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Affiliation(s)
- Xiaofang Zhang
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eralda Asllanaj
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Masoud Amiri
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eliana Portilla-Fernandez
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wichor M Bramer
- Medical Library, Erasmus MC, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Diabetes Center, München-Neuherberg, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
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LINC00200 contributes to the chemoresistance to oxaliplatin of gastric cancer cells via regulating E2F1/RAD51 axis. Hum Cell 2021; 34:1163-1173. [PMID: 33822325 DOI: 10.1007/s13577-021-00523-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/17/2021] [Indexed: 12/12/2022]
Abstract
The goal of this research was to decipher the biological functions and mechanism of long intergenic non-protein coding RNA 200 (LINC00200) in gastric cancer (GC). In this study, our data confirmed that LINC00200 expression was up-regulated in GC tissues and its high expression was correlated with the poor differentiation of GC tissues and lymph node metastasis of the patients. In vitro experiments indicated that, the overexpression of LINC00200 facilitated the proliferation of GC cells, constrained their apoptosis, and increased the IC50 of oxaliplatin (Oxa), whereas knockdown of LINC00200 exhibited the opposite effects. Additionally, we demonstrated that LINC00200 could bind to E2F transcription factor 1 (E2F1), and the up-regulation of LINC00200 expression enhanced the binding between E2F1 and RAD51 promoter, hence promoting RAD51 transcription, while knockdown of LINC00200 inhibited the transcription of RAD51. In conclusion, LINC00200 may recruit E2F1 to the RAD51 recombinase (RAD51) promoter region, thereby up-regulating the expression of RAD51 and enhancing the chemoresistance of GC cells to Oxa. Our data suggested that LINC00200 could probably be a promising target for treating GC.
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73
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Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLoS One 2021; 16:e0242530. [PMID: 33788851 PMCID: PMC8011741 DOI: 10.1371/journal.pone.0242530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/18/2021] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.
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Micallef I, Baron B. The Mechanistic Roles of ncRNAs in Promoting and Supporting Chemoresistance of Colorectal Cancer. Noncoding RNA 2021; 7:24. [PMID: 33807355 PMCID: PMC8103280 DOI: 10.3390/ncrna7020024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/03/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal Cancer (CRC) is one of the most common gastrointestinal malignancies which has quite a high mortality rate. Despite the advances made in CRC treatment, effective therapy is still quite challenging, particularly due to resistance arising throughout the treatment regimen. Several studies have been carried out to identify CRC chemoresistance mechanisms, with research showing different signalling pathways, certain ATP binding cassette (ABC) transporters and epithelial mesenchymal transition (EMT), among others to be responsible for the failure of CRC chemotherapies. In the last decade, it has become increasingly evident that certain non-coding RNA (ncRNA) families are involved in chemoresistance. Research investigations have demonstrated that dysregulation of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) contribute towards promoting resistance in CRC via different mechanisms. Considering the currently available data on this phenomenon, a better understanding of how these ncRNAs participate in chemoresistance can lead to suitable solutions to overcome this problem in CRC. This review will first focus on discussing the different mechanisms of CRC resistance identified so far. The focus will then shift onto the roles of miRNAs, lncRNAs and circRNAs in promoting 5-fluorouracil (5-FU), oxaliplatin (OXA), cisplatin and doxorubicin (DOX) resistance in CRC, specifically using ncRNAs which have been recently identified and validated under in vivo or in vitro conditions.
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Affiliation(s)
| | - Byron Baron
- Centre for Molecular Medicine and Biobanking, University of Malta, MSD2080 Msida, Malta;
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75
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Long non-coding RNA CIR inhibits chondrogenic differentiation of mesenchymal stem cells by epigenetically suppressing ATOH8 via methyltransferase EZH2. Mol Med 2021; 27:12. [PMID: 33546582 PMCID: PMC7866678 DOI: 10.1186/s10020-021-00272-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Background Osteoarthritis (OA) is the most common articular disorder, leading to joint malfunction and disability. Although the incidence of OA is increasing globally, the treatment of OA is very limited. LncRNA CIR has been implicated in OA through unclear mechanisms. Here, we investigated the role of lncRNA CIR in chondrogenic differentiation. Methods Human umbilical-cord-derived mesenchymal stem cells (hUC-MSCs) were obtained from human umbilical cords. Flow cytometry was used to analyze the surface markers of hUC-MSCs. Various culture conditions and corresponding staining assays were employed to assess the differentiation abilities of hUC-MSC. qRT-PCR, western blot, and immunostaining were used to measure expression levels of related genes and proteins such as lncRNA CIR, ATOH8, EZH2, and H3K27me3. RNA immunoprecipitation assay, biotin pull-down, and chromatin immunoprecipitaion assay were performed to analyze the interactions of lncRNA CIR, EZH2, H3K27me3 and ATOH8 promoter. Results hUC-MSCs exhibited MSCs features and could differentiate into chondrocytes under specific conditions. LncRNA CIR was downregulated while ATOH8 was upregulated during the chondrogenic differentiation of hUC-MSCs. Knockdown lncRNA CIR or overexpression of ATOH8 promoted chondrogenic differentiation. Further, lncRNA CIR bound to EZH2 and repressed ATOH8 expression via EZH2-mediated H3K27me3, which promotes the methylation of ATOH8. Inhibition of ATOH8 reversed the effects of knockdown lncRNA CIR on chondrogenic differentiation. Conclusion LncRNA CIR suppresses chondrogenic differentiation of hUC-MSCs. Mechanistically, lncRNA CIR could inhibit ATOH8 expression that functions to promote chondrogenic differentiation through EZH2-mediated epigenetic modifications.
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76
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Gnodi E, Mancuso C, Elli L, Ballarini E, Meneveri R, Beaulieu JF, Barisani D. Gliadin, through the Activation of Innate Immunity, Triggers lncRNA NEAT1 Expression in Celiac Disease Duodenal Mucosa. Int J Mol Sci 2021; 22:ijms22031289. [PMID: 33525473 PMCID: PMC7865487 DOI: 10.3390/ijms22031289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Celiac disease (CD) is an autoimmune enteropathy arising in genetically predisposed subjects exposed to gluten, which activates both innate and adaptive immunity. Although the pathogenesis is common to all patients, the clinical spectrum is quite variable, and differences could be explained by gene expression variations. Among the factors able to affect gene expression, there are lncRNAs. We evaluated the expression profile of 87 lncRNAs in CD vs. healthy control (HC) intestinal biopsies by RT-qPCR array. Nuclear enriched abundant transcript 1 (NEAT1) and taurine upregulated gene 1 (TUG1) were detected as downregulated in CD patients at diagnosis, but their expression increased in biopsies of patients on a gluten-free diet (GFD) exposed to gluten. The increase in NEAT1 expression after gluten exposure was mediated by IL-15 and STAT3 activation and binding to the NEAT1 promoter, as demonstrated by gel shift assay. NEAT1 is localized in the nucleus and can regulate gene expression by sequestering transcription factors, and it has been implicated in immune regulation and control of cell proliferation. The demonstration of its regulation by gluten thus also supports the role of lncRNAs in CD and prompts further research on these RNAs as gene expression regulators.
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Affiliation(s)
- Elisa Gnodi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (E.G.); (C.M.); (E.B.); (R.M.)
| | - Clara Mancuso
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (E.G.); (C.M.); (E.B.); (R.M.)
| | - Luca Elli
- Centre for the Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Elisa Ballarini
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (E.G.); (C.M.); (E.B.); (R.M.)
| | - Raffaella Meneveri
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (E.G.); (C.M.); (E.B.); (R.M.)
| | - Jean François Beaulieu
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
| | - Donatella Barisani
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (E.G.); (C.M.); (E.B.); (R.M.)
- Correspondence: ; Tel.: +39-0264488304
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Role of microRNA and long non-coding RNA in Marek's disease tumorigenesis in chicken. Res Vet Sci 2021; 135:134-142. [PMID: 33485054 DOI: 10.1016/j.rvsc.2021.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Marek's disease virus (MDV), the causative agent of Marek's disease (MD), results in highly infectious phymatosis, lymphatic tissue hyperplasia, and neoplasia. MD is associated with high morbidity and mortality rate. Non-coding RNAs (ncRNAs) entails long non-coding RNA (lncRNA) and microRNA (miRNA). Numerous studies have reported that specific miRNAs and lncRNAs participate in multiple cellular processes, such as proliferation, migration, and tumor cell invasion. Specialized miRNAs and lncRNAs militate a similar role in MD tumor oncogenesis. Despite its growing popularity, only a few reviews are available on ncRNA in MDV tumor oncogenes. Herein, we summarized the role of the miRNAs and lncRNAs in MD tumorigenesis. Altogether, we brought forth the research issues, such as MD prevention, screening, regulatory network formation, novel miRNAs, and lncRNAs analysis in MD that needs to be explored further. This review provides a theoretical platform for the further analysis of miRNAs and lncRNAs functions and the prevention and control of MD and malignancies in domestic animals.
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78
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Ameli Mojarad M, Ameli Mojarad M, Pourmahdian A. Long Non-coding RNA snaR Promotes Proliferation in EGFR Wild Type Non-Small Cell Lung Cancer Cells. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2021; 10:258-264. [PMID: 35875332 PMCID: PMC9273155 DOI: 10.22088/ijmcm.bums.10.4.258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022]
Abstract
Lung cancer is the second most common cancer and has high morbidity and mortality worldwide with non-small cell lung cancer (NSCLC) accounting for 85% of the cases. Over-expression of epidermal growth factor receptor (EGFR) has been clarified in different cancers, and has been shown to have a crucial role in tumor progression. In this study, we evaluated long non-coding RNA small NF90-associated RNA (snaR) expression in different EGFR-statue cell lines. Knockdown experiments were conducted to analyze snaR expression in selected cell lines. MTT and transwell assays were respectively employed to evaluate the proliferative and invasive abilities of NSCLC cells. The expression of snaR was remarkably up-regulated in SPC-A1 and A549 wild-type EGFR cell lines. Down regulation of snaR with small interfering RNA significantly inhibited cell invasion as well as proliferation of SPC-A1 and A549 cells. Our results indicate that snaR may be a potential therapeutic biomarker for NSCLC.
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Affiliation(s)
- Melika Ameli Mojarad
- Department of Biology, Faculty of Basic Sciences, Kharrazi University, Tehran, Iran.
| | - Mandana Ameli Mojarad
- Department of Biology, Faculty of Basic Sciences, Kharrazi University, Tehran, Iran.
| | - Alireza Pourmahdian
- Department of Molecular Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Corresponding author: Department of Molecular Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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79
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Shen JX, Bao ZD, Zhu W, Ma CL, Shen YQ, Kan Q, Zhou XG, Yang Y, Zhou XY. Expression profiles of long non-coding RNAs during fetal lung development. Exp Ther Med 2020; 20:144. [PMID: 33093882 DOI: 10.3892/etm.2020.9273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/29/2020] [Indexed: 11/05/2022] Open
Abstract
With advances in neonatology, a greater percentage of premature infants now survive and consequently, diseases of lung development, including bronchopulmonary dysplasia and neonatal respiratory distress syndrome, have become more common. However, few studies have addressed the association between fetal lung development and long non-coding RNA (lncRNA). In the present study, right lung tissue samples of fetuses at different gestational ages were collected within 2 h of the induction of labor in order to observe morphological discrepancies. An Affymetrix Human GeneChip was used to identify differentially expressed lncRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed. A total of 687 lncRNAs were identified to be differentially expressed among three groups of fetal lung tissue samples corresponding to the three embryonic periods. A total of 34 significantly upregulated and 12 significantly downregulated lncRNAs (fold-change, ≥1.5; P<0.05) were detected at different time points (embryonic weeks 7-16, 16-25 and 25-28) of fetal lung development and compared with healthy tissues Expression changes in lncRNAs n340848, n387037, n336823 and ENST00000445168 were validated by reverse transcription-quantitative PCR and the results were consistent with the GeneChip results. These novel identified lncRNAs may have roles in fetal lung development and the results of the present study may lay the foundation for subsequent in-depth studies into lncRNAs in fetal lung development and subsequent clarification of the pathogenesis of neonatal pulmonary diseases.
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Affiliation(s)
- Jin-Xin Shen
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Zhi-Dan Bao
- Department of Neonatology, The Affiliated Jiangyin Hospital of Southeast University Medical School, Jiangyin, Jiangsu 214400, P.R. China
| | - Wen Zhu
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Cheng-Ling Ma
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Yan-Qing Shen
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Qing Kan
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Xiao-Guang Zhou
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Yang Yang
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Xiao-Yu Zhou
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
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80
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Galvão MLTDC, Coimbra EC. Long noncoding RNAs (lncRNAs) in cervical carcinogenesis: New molecular targets, current prospects. Crit Rev Oncol Hematol 2020; 156:103111. [PMID: 33080526 DOI: 10.1016/j.critrevonc.2020.103111] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/15/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Aberrant expression of lncRNAs has been seen as a key factor in a wide range of diseases including cancer. The role of lncRNAs in cervical cancer has not been clearly explained, and has been the subject of recent studies. In this review, we have compiled an updated list of previously reported lncRNAs and established a general profile of these transcripts in accordance with the role they play in cervical carcinogenesis. Thus, information here includes the influence of lncRNAs on cervical tumorigenic process through a disturbance of cellular activities. Additionally, we described recent discoveries about how HPV contributes to lncRNAs expression in cervical cancer and we summarized exploratory studies of strategies adopted to modulate the expression levels of lncRNAs to treat cervical neoplasia, by drawing attention to radio and chemo-resistance. Finally, this paper provides a broad overview that sets out new research directions about the role of lncRNAs in cervical cancer.
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Affiliation(s)
- Maria Luiza Tabosa de Carvalho Galvão
- Faculty of Medical Sciences, University of Pernambuco, Brazil; Laboratory of Molecular Biology of Viruses, Biological Sciences Institute, University of Pernambuco, Brazil
| | - Eliane Campos Coimbra
- Laboratory of Molecular Biology of Viruses, Biological Sciences Institute, University of Pernambuco, Brazil.
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81
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Ren X, Yang R, Li L, Xu X, Liang S. Long non coding RNAs involved in MAPK pathway mechanism mediates diabetic neuropathic pain. Cell Biol Int 2020; 44:2372-2379. [PMID: 32844535 DOI: 10.1002/cbin.11457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Diabetes is the largest global epidemic of the 21st century, and the cost of diabetes and its complications comprise about 12% of global health expenditure. Diabetic neuropathy is the most common complication of diabetes, affecting up to 50% of patients over the course of their disease. Among them, 30%-50% develop neuropathic pain, which has typical symptoms that originate from the toes and progress to foot ulcers and seriously influence quality of life. The pathogenesis of diabetic neuropathic pain (DNP) is complicated and incompletely understood and there is no effective treatment except supportive treatment. Long noncoding RNAs (lncRNAs), a class of noncoding RNAs exceeding 200 nucleotides in length, have been shown to play key roles in fundamental cellular processes, and are considered to be potential targets for treatment. Recent research indicates that lncRNA is involved in the pathogenesis of DNP. Certain overexpressed lncRNAs can enhance the purinergic receptor-mediated neuropathic pain in peripheral ganglia and inflammatory cytokines are released due to receptors activated by adenosine triphosphate. In recent years, our laboratory also has been exploring the relationship and pathogenesis between lncRNAs and DNP. In this review, we focus on the recent progress in functional lncRNAs associated with DNP and investigate their roles related to respective receptors.
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Affiliation(s)
- Xinlu Ren
- Queen Mary University of London Joint Programme, Nanchang University, Nanchang, Jiangxi, China
| | - Runan Yang
- Neuropharmacology Laboratory of Physiology Department, Basic Medical School of Nanchang University, Nanchang, Jiangxi, 330006, China.,Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease, Nanchang, Jiangxi, 330006, China
| | - Lin Li
- Neuropharmacology Laboratory of Physiology Department, Basic Medical School of Nanchang University, Nanchang, Jiangxi, 330006, China.,Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease, Nanchang, Jiangxi, 330006, China
| | - Xiumei Xu
- Neuropharmacology Laboratory of Physiology Department, Basic Medical School of Nanchang University, Nanchang, Jiangxi, 330006, China.,Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease, Nanchang, Jiangxi, 330006, China
| | - Shangdong Liang
- Neuropharmacology Laboratory of Physiology Department, Basic Medical School of Nanchang University, Nanchang, Jiangxi, 330006, China.,Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease, Nanchang, Jiangxi, 330006, China
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82
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Gibbons A, Sundram S, Dean B. Changes in Non-Coding RNA in Depression and Bipolar Disorder: Can They Be Used as Diagnostic or Theranostic Biomarkers? Noncoding RNA 2020; 6:E33. [PMID: 32846922 PMCID: PMC7549354 DOI: 10.3390/ncrna6030033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
The similarities between the depressive symptoms of Major Depressive Disorders (MDD) and Bipolar Disorders (BD) suggest these disorders have some commonality in their molecular pathophysiologies, which is not apparent from the risk genes shared between MDD and BD. This is significant, given the growing literature suggesting that changes in non-coding RNA may be important in both MDD and BD, because they are causing dysfunctions in the control of biochemical pathways that are affected in both disorders. Therefore, understanding the changes in non-coding RNA in MDD and BD will lead to a better understanding of how and why these disorders develop. Furthermore, as a significant number of individuals suffering with MDD and BD do not respond to medication, identifying non-coding RNA that are altered by the drugs used to treat these disorders offer the potential to identify biomarkers that could predict medication response. Such biomarkers offer the potential to quickly identify patients who are unlikely to respond to traditional medications so clinicians can refocus treatment strategies to ensure more effective outcomes for the patient. This review will focus on the evidence supporting the involvement of non-coding RNA in MDD and BD and their potential use as biomarkers for treatment response.
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Affiliation(s)
- Andrew Gibbons
- The Florey Institute for Neuroscience and Mental Health, Parkville, The University of Melbourne, Melbourne, Victoria 3052, Australia; (S.S.); (B.D.)
- The Department of Psychiatry, Monash University, 27-31 Wright Street, Clayton, Victoria 3168, Australia
| | - Suresh Sundram
- The Florey Institute for Neuroscience and Mental Health, Parkville, The University of Melbourne, Melbourne, Victoria 3052, Australia; (S.S.); (B.D.)
- The Department of Psychiatry, Monash University, 27-31 Wright Street, Clayton, Victoria 3168, Australia
| | - Brian Dean
- The Florey Institute for Neuroscience and Mental Health, Parkville, The University of Melbourne, Melbourne, Victoria 3052, Australia; (S.S.); (B.D.)
- The Centre for Mental Health, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
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83
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Toraih EA, El-Wazir A, Ageeli EA, Hussein MH, Eltoukhy MM, Killackey MT, Kandil E, Fawzy MS. Unleash multifunctional role of long noncoding RNAs biomarker panel in breast cancer: a predictor classification model. Epigenomics 2020; 12:1215-1237. [PMID: 32812439 DOI: 10.2217/epi-2019-0291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aim: We aimed to explore the circulating expression profile of nine lncRNAs (MALAT1, HOTAIR, PVT1, H19, ROR, GAS5, ANRIL, BANCR, MIAT) in breast cancer (BC) patients relative to normal and risky individuals. Methods: Serum relative expressions of the specified long non-coding RNAs were quantified in 155 consecutive women, using quantitative reverse-transcription PCR. Random Forest (RF) and decision tree were also applied. Results: Significant MALAT1 upregulation and GAS5 downregulation could discriminate risky women from healthy controls. Overexpression of the other genes showed good diagnostic performances. Lower GAS5 levels were associated with metastasis and recurrence. RF model revealed a better performance when combining gene expression patterns with risk factors. Conclusion: The studied panel could be utilized as diagnostic/prognostic biomarkers in BC, providing promising epigenetic-based therapeutic targets.
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Affiliation(s)
- Eman A Toraih
- Department of Histology & Cell Biology, Genetics Unit, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt.,Department of Surgery, Tulane University, School of Medicine, New Orleans, LA 70112, USA
| | - Aya El-Wazir
- Department of Histology & Cell Biology, Genetics Unit, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Essam Al Ageeli
- Department of Clinical Biochemistry (Medical Genetics), Faculty of Medicine, Jazan University, Jazan 82911, Saudi Arabia
| | - Mohammad H Hussein
- Department of Surgery, Tulane University, School of Medicine, New Orleans, LA 70112, USA
| | - Mohamed M Eltoukhy
- College of Computing and Information Technology, Khulais, University of Jeddah, Jeddah 21959, Saudi Arabia.,Department of Computer Science, Faculty of Computers and Informatics, Suez Canal University, Ismailia 41522, Egypt
| | - Mary T Killackey
- Department of Surgery, Tulane University, School of Medicine, New Orleans, LA 70112, USA
| | - Emad Kandil
- Department of Surgery, Division of Endocrine & Oncologic Surgery, Tulane University, School of Medicine, New Orleans, LA 70112, USA
| | - Manal S Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt.,Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
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84
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Outeiro-Pinho G, Barros-Silva D, Correia MP, Henrique R, Jerónimo C. Renal Cell Tumors: Uncovering the Biomarker Potential of ncRNAs. Cancers (Basel) 2020; 12:cancers12082214. [PMID: 32784737 PMCID: PMC7465320 DOI: 10.3390/cancers12082214] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022] Open
Abstract
Renal cell tumors (RCT) remain as one of the most common and lethal urological tumors worldwide. Discrimination between (1) benign and malignant disease, (2) indolent and aggressive tumors, and (3) patient responsiveness to a specific therapy is of major clinical importance, allowing for a more efficient patient management. Nonetheless, currently available tools provide limited information and novel strategies are needed. Over the years, a putative role of non-coding RNAs (ncRNAs) as disease biomarkers has gained relevance and is now one of the most prolific fields in biological sciences. Herein, we extensively sought the most significant reports on ncRNAs as potential RCTs' diagnostic, prognostic, predictive, and monitoring biomarkers. We could conclude that ncRNAs, either alone or in combination with currently used clinical and pathological parameters, might represent key elements to improve patient management, potentiating the implementation of precision medicine. Nevertheless, most ncRNA biomarkers require large-scale validation studies, prior to clinical implementation.
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Affiliation(s)
- Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Margareta P. Correia
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
- Correspondence: ; Tel.: +351-225084000; Fax: +351-225084199
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85
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Ghaderian S, Shomali N, Behravesh S, Danbaran GR, Hemmatzadeh M, Aslani S, Jadidi-Niaragh F, Hosseinzadeh R, Torkamandi S, Mohammadi H. The emerging role of lncRNAs in multiple sclerosis. J Neuroimmunol 2020; 347:577347. [PMID: 32745803 DOI: 10.1016/j.jneuroim.2020.577347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/05/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is the most common inflammatory demyelinating disease of the central nervous system (CNS) with various clinical manifestations. The characteristic of MS is that myelin is attacked by the body's immune system and increases the electrical capacity of axons, and is the primary pathophysiological mechanism of the transmission block. Studies have shown that epigenetic factors participate in the development of MS. LncRNAs are highly abundant and heterogeneous linear RNA transcripts with lengths exceeding 200 nucleotides and no protein-coding potential. Currently, pieces of evidence have demonstrated that lncRNAs have fundamental actions in multiple cellular pathways, including immune system regulation, epithelial-mesenchymal transition (EMT), cancer cell growth and metastasis, cellular homeostasis, and embryo development. It has been demonstrated that epigenetic mechanisms have an abundant role in the pathogenesis of MS in which the role of lncRNAs as epigenetic regulatory molecules in molecular processes has been proven. In this paper, we have focused on the correlation between MS and lncRNAs, the role of lncRNA in the pathogenesis of the disease, and the diagnostic and prognostic potential of lncRNA in MS.
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Affiliation(s)
- Samin Ghaderian
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Navid Shomali
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheil Behravesh
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Maryam Hemmatzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Aslani
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Hosseinzadeh
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahram Torkamandi
- Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran; Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
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86
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Huang M, Huang X, Jiang B, Zhang P, Guo L, Cui X, Zhou S, Ren L, Zhang M, Zeng J, Huang X, Liang P. linc00174-EZH2-ZNF24/Runx1-VEGFA Regulatory Mechanism Modulates Post-burn Wound Healing. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:824-836. [PMID: 32805486 PMCID: PMC7452087 DOI: 10.1016/j.omtn.2020.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022]
Abstract
Preservation of denatured dermis exerts promotive functions in wound healing and improves the appearance and function of skin. Angiogenesis is crucial for wound healing during burn injury. However, the potential molecular mechanism of angiogenesis in the recovery after burn injury remains to be elucidated. Herein, RNA chromatin immunoprecipitation (ChIP) sequencing analysis revealed upregulation of long intergenic non-coding RNA 00174 (linc00174) in the post-burn tissues. linc00174 overexpression promoted angiogenic activities of human umbilical vein endothelial cells (HUVECs) in the heat-denatured cell model, characterized by the promotion of cell proliferation, migration, and tube formation. Mechanistically, linc00174 directly bound to enhancer of zeste homolog 2 (EZH2), thus stimulating the protein level of trimethylation at lysine 27 of histone H3 (H3K27me3). Moreover, inhibition of EZH2 resulted in downregulation of ZNF24 and Runx1, as well as a decline of vascular endothelial growth factor A (VEGFA). Furthermore, EZH2 modulated epigenetic repression of ZNF24 and Runx1 through the promoter of H3K27me3. Additionally, ZNF24 and Runx1 both functioned as transcriptional inhibitors of VEGFA. Taken together, these findings uncover that linc00174 epigenetically inhibits ZNF24 and Runx1 expression through binding to EZH2, thus attenuating the suppression of VEGFA, contributing to the facilitation of angiogenesis during the recovery of heat-denatured endothelial cells.
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Affiliation(s)
- Mitao Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Xu Huang
- Department of Hyperbaric Oxygen, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Pihong Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Le Guo
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Xu Cui
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Situo Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Licheng Ren
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Minghua Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Jizhang Zeng
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Xiaoyuan Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, P.R. China.
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Li F, Chen ZH, Tan BB, Li Y. Long non-coding RNAs as potential markers for occurrence, progression, and prognosis of gastric cancer. Shijie Huaren Xiaohua Zazhi 2020; 28:544-552. [DOI: 10.11569/wcjd.v28.i13.544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In recent years, more and more attention has been paid to the relationship between long non-coding RNAs (lncRNAs) and tumor. Abnormal expression of lncRNAs plays an oncogenic or tumor-suppressing role in gastric cancer (GC) by participating in the biological behaviors of GC cells, such as proliferation, invasion, and migration. By summarizing the relevant literature, this paper discusses the research status, detection technology, and mechanism of action of lncRNAs in GC, as well as their potential as markers for occurrence, progression, prognosis, and drug resistance of GC. It is expected that lncRNAs can play an important role in early detection, early treatment, and effective improvement of chemotherapy resistance of GC to achieve personalized precise treatment of this malignancy.
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Affiliation(s)
- Fang Li
- Department of Pathology, Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei Province, China
| | - Zi-Hao Chen
- Third Department of Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei Province, China
| | - Bi-Bo Tan
- Third Department of Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei Province, China
| | - Yong Li
- Third Department of Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei Province, China
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88
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Han Z, He J, Zou M, Chen W, Lv Y, Li Y. Small interfering RNA target for long noncoding RNA PCGEM1 increases the sensitivity of LNCaP cells to baicalein. Anat Rec (Hoboken) 2020; 303:2077-2085. [PMID: 32445497 DOI: 10.1002/ar.24454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 12/16/2022]
Abstract
The objective of this study is to investigate the inhibitory effect and mechanism of long noncoding RNA PCGEM1 siRNA combined with baicalein on prostate cancer LNCaP cells. LNCaP cells transfected with small hairpin RNA lentiviral vector targeting PCGEM1 were constructed and their expression in LNCaP cells was absent. The stable cell line of LNCaP cells infected with LV3-shRNA-PCGEM1 was successfully constructed. In addition, LV3-shRNA-PCGEM1 was able to increase the baicalein-induced inhibitory effects on LNCaP cells, and the susceptibility was 2.3 fold higher than that of baicalein alone. LV3-shRNA-PCGEM1 combined with baicalein also inhibited the colony formation, increased G2 and S phase cells, inhibited the expression of PCGEM1, and induced autophagy of LNCaP cells. In summary, LV3-shRNA-PCGEM1 may improve the sensitivity of LNCaP cells to baicalein, and the molecular mechanism may be associated with the decrease of PCGEM1 expression and the induction of autophagy. Our findings provided an experimental basis for the combined treatment of Chinese traditional and Western medicine on prostate cancer in a clinical setting.
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Affiliation(s)
- Zeping Han
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong, People's Republic of China
| | - Jinhua He
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong, People's Republic of China
| | - Maoxian Zou
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong, People's Republic of China
| | - Weiming Chen
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong, People's Republic of China
| | - Yubing Lv
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong, People's Republic of China
| | - Yuguang Li
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong, People's Republic of China
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89
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Gao Y, Wang JW, Ren JY, Guo M, Guo CW, Ning SW, Yu S. Long noncoding RNAs in gastric cancer: From molecular dissection to clinical application. World J Gastroenterol 2020; 26:3401-3412. [PMID: 32655264 PMCID: PMC7327794 DOI: 10.3748/wjg.v26.i24.3401] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of cell processes that are usually dysregulated in gastric cancer (GC). Based on their high specificity and ease of detection in tissues and body fluids, increasing attention has spurred the study of the roles of lncRNAs in GC patients. Thus, it is necessary to elucidate the molecular mechanisms and further explore the clinical applications of lncRNAs in GC. In this review, we summarize current knowledge to examine dysregulated lncRNAs in GC and their underlying molecular mechanisms and activities in GC, which involve microRNA sponging, mRNA stability, genetic variants, alternative splicing, transcription factor binding, and epigenetic modification. More significantly, the potential of lncRNAs as prognostic, circulating, and drug-resistant biomarkers for GC is also described. This review highlights the method of dissecting molecular mechanisms to explore the clinical application of lncRNAs in GC. Overall, this review offers assistance in using lncRNAs as novel candidates for molecular mechanisms and for the identification of revolutionary biomarkers for GC.
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Affiliation(s)
- Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Jun-Wei Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Jia-Yi Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Mian Guo
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Cheng-Wang Guo
- Department of Gastroenterology and Gastrosurgery, Gansu Wuwei Tumor Hospital, Wuwei 733000, Gansu Province, China
| | - Shang-Wei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Shan Yu
- Department of Pathology, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, China
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90
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Xu C, Zhou X, Xie T, Zhou Y, Zhang Q, Jiang S, Zhang R, Liao L, Dong J. Renal tubular Bim mediates the tubule-podocyte crosstalk via NFAT2 to induce podocyte cytoskeletal dysfunction. Theranostics 2020; 10:6806-6824. [PMID: 32550905 PMCID: PMC7295056 DOI: 10.7150/thno.43145] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/03/2020] [Indexed: 12/17/2022] Open
Abstract
Diabetic nephropathy (DN) is mainly regarded as diabetic glomerulopathy, and its progression is tightly correlated with tubular epithelial lesions. However, the underlying molecular mechanisms linking tubular damage and glomerulopathy are poorly understood. Methods: We previously reported that the upregulation of Bim mediated proximal tubular epithelial cell (PTEC) apoptosis and was crucial in the early stages of DN. Herein we modulated Bim expression in PTECs and subsequently determined podocyte (PC) cytoskeletal arrangement by building a Transwell co-culture system in high glucose (HG). Results: Compared to normal glucose, exposure to 40 mM of HG for 48 h induced significant expression of Bim in PTECs and disorganization in the PC cytoskeleton. When cocultured with PTECs in HG, exacerbated filamentous actin (F-actin) rearrangement and reduced synaptopodin levels were detected in PCs. In contrast, gene knockdown of Bim in PTECs was correlated with the absence of PC cytoskeletal disorganization. NFAT2 level and its nuclear translocation in PTECs were decreased by suppressing Bim expression. Upregulating NFAT2 disrupted the beneficial effects on F-actin organization in PCs obtained by inhibiting Bim. LncRNA microarray analysis identified NONHSAT179542.1, which was implicated in Bim-mediated PC cytoskeletal disorder. Conclusion: Our study clarified the functional role of Bim, a pro-apoptotic factor, which is involved in the crosstalk between PTECs and PCs. Bim promotes NFAT2 activation in PTECs, inducing the downregulation of lncRNA NONHSAT179542.1 in PCs, contributing to the cytoskeletal damage. Identification of the role of the Bim/NFAT2 pathway may represent a promising research direction for a better understanding of DN development.
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91
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Wu H, Qin W, Lu S, Wang X, Zhang J, Sun T, Hu X, Li Y, Chen Q, Wang Y, Zhao H, Piao H, Zhang R, Wei M. Long noncoding RNA ZFAS1 promoting small nucleolar RNA-mediated 2'-O-methylation via NOP58 recruitment in colorectal cancer. Mol Cancer 2020; 19:95. [PMID: 32443980 PMCID: PMC7243338 DOI: 10.1186/s12943-020-01201-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/15/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Increasing evidence supports the role of small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs) as master gene regulators at the epigenetic modification level. However, the underlying mechanism of these functional ncRNAs in colorectal cancer (CRC) has not been well investigated. METHODS The dysregulated expression profiling of lncRNAs-snoRNAs-mRNAs and their correlations and co-expression enrichment were assessed by GeneChip microarray analysis. The candidate lncRNAs, snoRNAs, and target genes were detected by in situ hybridization (ISH), RT-PCR, qPCR and immunofluorescence (IF) assays. The biological functions of these factors were investigated using in vitro and in vivo studies that included CCK8, trans-well, cell apoptosis, IF assay, western blot method, and the xenograft mice models. rRNA 2'-O-methylation (Me) activities were determined by the RTL-P assay and a novel double-stranded primer based on the single-stranded toehold (DPBST) assay. The underlying molecular mechanisms were explored by bioinformatics and RNA stability, RNA fluorescence ISH, RNA pull-down and translation inhibition assays. RESULTS To demonstrate the involvement of lncRNA and snoRNAs in 2'-O-Me modification during tumorigenesis, we uncovered a previously unreported mechanism linking the snoRNPs NOP58 regulated by ZFAS1 in control of SNORD12C, SNORD78 mediated rRNA 2'-O-Me activities in CRC initiation and development. Specifically, ZFAS1 exerts its oncogenic functions and significantly up-regulated accompanied by elevated NOP58, SNORD12C/78 expression in CRC cells and tissues. ZFAS1 knockdown suppressed CRC cell proliferation, migration, and increased cell apoptosis, and this inhibitory effect could be reversed by NOP58 overexpression in vitro and in vivo. Mechanistically, the NOP58 protein could be recognized by the specific motif (AAGA or CAGA) of ZFAS1. This event accelerates the assembly of SNORD12C/78 to allow for further guiding of 2'-O-Me at the corresponding Gm3878 and Gm4593 sites. Importantly, silencing SNORD12C or 78 reduced the rRNAs 2'-O-Me activities, which could be rescued by overexpression ZFAS1, and this subsequently inhibits the RNA stability and translation activity of their downstream targets (e.g., EIF4A3 and LAMC2). CONCLUSION The novel ZFAS1-NOP58-SNORD12C/78-EIF4A3/LAMC2 signaling axis that functions in CRC tumorigenesis provides a better understanding regarding the role of lncRNA-snoRNP-mediated rRNAs 2'-O-Me activities for the prevention and treatment of CRC.
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Affiliation(s)
- Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Wenyan Qin
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Senxu Lu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xiufang Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Jing Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Tong Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yalun Li
- Department of Anorectal Surgery, First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Qiuchen Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yuanhe Wang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, 110042, People's Republic of China
| | - Haishan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Haiyan Piao
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, 110042, People's Republic of China
| | - Rui Zhang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, 110042, People's Republic of China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China. .,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China.
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Shi J, Huang Y, Wen C, He S, Wu L, Zhou H. Genome-wide identification and characterization of long non-coding RNAs involved in acquired resistance to gefitinib in non-small-cell lung cancer. Comput Biol Chem 2020; 87:107288. [PMID: 32521497 DOI: 10.1016/j.compbiolchem.2020.107288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Acquired resistance is a major obstacle to the therapeutic efficacy of gefitinib in non-small-cell lung cancer (NSCLC). Current knowledge about the role of long non-coding RNAs (lncRNAs) in this phenomenon is insufficient. In this study, we searched RNA sequencing data for lncRNAs associated with acquired resistance to gefitinib in NSCLC, and constructed a functional lncRNA-mRNA co-expression network and protein-protein interaction (PPI) network to analyze their putative target genes and biological functions. The expression levels of 14 outstanding dysregulated lncRNAs and mRNA were verified using real-time PCR. Changes in the expression levels of 39 lncRNAs and 121 mRNAs showed common patterns in our two pairs of gefitinib-sensitive and gefitinib-resistant NSCLC cell lines. The co-expression network included 1235 connections among these common differentially expressed lncRNAs and mRNAs. The significantly enriched signaling pathways based on dysregulated mRNAs were mainly involved in the Hippo signaling pathway; proteoglycans in cancer; and valine, leucine, and isoleucine biosynthesis. The results show that LncRNAs play an important part in acquired gefitinib resistance in NSCLC by regulating mRNA expression and function, and may represent potential new molecular biomarkers and therapeutic targets for gefitinib-resistant NSCLC.
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Affiliation(s)
- Jingjing Shi
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yutang Huang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Chunjie Wen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Shuai He
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Lanxiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China.
| | - Honghao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China; Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
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93
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Maroñas O, García-Quintanilla L, Luaces-Rodríguez A, Fernández-Ferreiro A, Latorre-Pellicer A, Abraldes MJ, Lamas MJ, Carracedo A. Anti-VEGF Treatment and Response in Age-related Macular Degeneration: Disease's Susceptibility, Pharmacogenetics and Pharmacokinetics. Curr Med Chem 2020; 27:549-569. [PMID: 31296152 DOI: 10.2174/0929867326666190711105325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/03/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
The current review is focussing different factors that contribute and directly correlate to the onset and progression of Age-related Macular Degeneration (AMD). In particular, the susceptibility to AMD due to genetic and non-genetic factors and the establishment of risk scores, based on the analysis of different genes to measure the risk of developing the disease. A correlation with the actual therapeutic landscape to treat AMD patients from the point of view of pharmacokinetics and pharmacogenetics is also exposed. Treatments commonly used, as well as different regimes of administration, will be especially important in trying to classify individuals as "responders" and "non-responders". Analysis of different genes correlated with drug response and also the emerging field of microRNAs (miRNAs) as possible biomarkers for early AMD detection and response will be also reviewed. This article aims to provide the reader a review of different publications correlated with AMD from the molecular and kinetic point of view as well as its commonly used treatments, major pitfalls and future directions that, to our knowledge, could be interesting to assess and follow in order to develop a personalized medicine model for AMD.
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Affiliation(s)
- Olalla Maroñas
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura García-Quintanilla
- Servicio de Farmacia, Xerencia de Xestión Integrada de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Andrea Luaces-Rodríguez
- Departamento de Farmacia e Tecnoloxia Farmaceutica e Instituto de Farmacia Industrial, Facultade de Farmacia, Universidade de Santiago de Compostela, Spain.,Grupo de Farmacoloxia Clínica, Instituto de Investigacion en Salud de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Anxo Fernández-Ferreiro
- Departamento de Farmacia e Tecnoloxia Farmaceutica e Instituto de Farmacia Industrial, Facultade de Farmacia, Universidade de Santiago de Compostela, Spain.,Grupo de Farmacoloxia Clínica, Instituto de Investigacion en Salud de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.,Departamento de Farmacia, Hospital Clínico Universitario de Santiago de Compostela (SERGAS) (CHUS), Santiago de Compostela, Spain
| | - Ana Latorre-Pellicer
- Unidad de Genetica Clínica y Genomica Funcional, Departamento de Farmacologia-Fisiología, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Maximino J Abraldes
- Servicio de Oftalmoloxía, Xerencia de Xestion Integrada de Santiago de Compostela, Santiago de Compostela, Spain.,Departamento de Ciruxía e Especialidades Médico- Quirúrxicas, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María J Lamas
- Grupo de Farmacoloxia Clínica, Instituto de Investigacion en Salud de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado (CEGEN-PRB3), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
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94
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Tsai CY, Hsieh SC, Wu TH, Li KJ, Shen CY, Liao HT, Wu CH, Kuo YM, Lu CS, Yu CL. Pathogenic Roles of Autoantibodies and Aberrant Epigenetic Regulation of Immune and Connective Tissue Cells in the Tissue Fibrosis of Patients with Systemic Sclerosis. Int J Mol Sci 2020; 21:ijms21093069. [PMID: 32349208 PMCID: PMC7246753 DOI: 10.3390/ijms21093069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Systemic sclerosis (SSc) is a multi-system autoimmune disease with tissue fibrosis prominent in the skin and lung. In this review, we briefly describe the autoimmune features (mainly autoantibody production and cytokine profiles) and the potential pathogenic contributors including genetic/epigenetic predisposition, and environmental factors. We look in detail at the cellular and molecular bases underlying tissue-fibrosis which include trans-differentiation of fibroblasts (FBs) to myofibroblasts (MFBs). We also state comprehensively the pro-inflammatory and pro-fibrotic cytokines relevant to MFB trans-differentiation, vasculopathy-associated autoantibodies, and fibrosis-regulating microRNAs in SSc. It is conceivable that tissue fibrosis is mainly mediated by an excessive production of TGF-β, the master regulator, from the skewed Th2 cells, macrophages, fibroblasts, myofibroblasts, and keratinocytes. After binding with TGF-β receptors on MFB, the downstream Wnt/β-catenin triggers canonical Smad 2/3 and non-canonical Smad 4 signaling pathways to transcribe collagen genes. Subsequently, excessive collagen fiber synthesis and accumulation as well as tissue fibrosis ensue. In the later part of this review, we discuss limited data relevant to the role of long non-coding RNAs (lncRNAs) in tissue-fibrosis in SSc. It is expected that these lncRNAs may become the useful biomarkers and therapeutic targets for SSc in the future. The prospective investigations in the development of novel epigenetic modifiers are also suggested.
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Affiliation(s)
- Chang-Youh Tsai
- Division of Allergy, Immunology & Rheumatology, Taipei Veterans General Hospital & National Yang-Ming University, #201 Sec. 2, Shih-Pai Road, Taipei 11217, Taiwan;
- Correspondence: (C.-Y.T.); (C.-L.Y.); Fax: +886-2-28717483 (C.-Y.T.); +886-2-23957801 (C.-L.Y.)
| | - Song-Chou Hsieh
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
| | - Tsai-Hung Wu
- Division of Nephrology, Taipei Veterans General Hospital & National Yang-Ming University, #201 Sec. 2, Shih-Pai Road, Taipei 11217, Taiwan;
| | - Ko-Jen Li
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
| | - Chieh-Yu Shen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
- Institute of Clinical Medicine, National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Hsien-Tzung Liao
- Division of Allergy, Immunology & Rheumatology, Taipei Veterans General Hospital & National Yang-Ming University, #201 Sec. 2, Shih-Pai Road, Taipei 11217, Taiwan;
| | - Cheng-Han Wu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
- Institute of Clinical Medicine, National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Yu-Min Kuo
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
- Institute of Clinical Medicine, National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Cheng-Shiun Lu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
- Institute of Clinical Medicine, National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan
| | - Chia-Li Yu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, #7 Chung-Shan South Road, Taipei 10002, Taiwan; (S.-C.H.); (K.-J.L.); (C.-Y.S.); (C.-H.W.); (Y.-M.K.); (C.-S.L.)
- Correspondence: (C.-Y.T.); (C.-L.Y.); Fax: +886-2-28717483 (C.-Y.T.); +886-2-23957801 (C.-L.Y.)
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95
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Zhang Y, Liu H, Liu X, Guo Y, Wang Y, Dai Y, Zhuo J, Wu B, Wang H, Zhang X. Identification of an exosomal long non-coding RNAs panel for predicting recurrence risk in patients with colorectal cancer. Aging (Albany NY) 2020; 12:6067-6088. [PMID: 32246818 PMCID: PMC7185113 DOI: 10.18632/aging.103006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Recurrence is a major cause of cancer-related deaths in colorectal cancer (CRC) patients, but the current strategies are limited to predict this clinical behavior. Our aim is to develop a recurrence prediction model based on long non-coding RNAs (lncRNAs) in exosomes of serum to improve the prediction accuracy. In discovery phase, 11 lncRNAs were found to be associated with CRC recurrence in tissues using high-throughput lncRNAs microarray and reverse transcription quantitative real-time PCR. And, 9 of them were correlated with their expression levels of serum exosomes. In training phase, a model based on 5-exosomal lncRNAs (exolncRNAs) panel was constructed, and showed high distinguish capability for recurrent CRC patients. ROC showed the panel was superior to serum CEA and CA19-9 in prediction of CRC recurrence. In both training and test sets, high-risk patients defined by the 5-exolncRNAs panel had poor recurrence free and overall survival. And, COX model showed it was an independent factor for CRC prognosis. Moreover, there was a significant relationship in detection of 5-exolncRNAs between plasma samples and paired serum samples. In summary, the 5-exolncRNAs panel robustly stratifies CRC patients’ risk of recurrence, enabling more accurate prediction of prognosis.
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Affiliation(s)
- Yanli Zhang
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250031, Shandong Province, China
| | - Hui Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Xinfeng Liu
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250031, Shandong Province, China
| | - Yulian Guo
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yanlei Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yonggang Dai
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250031, Shandong Province, China
| | - Jinhua Zhuo
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250031, Shandong Province, China
| | - Bing Wu
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250031, Shandong Province, China
| | - Hongchun Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
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96
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Chen Z, Zhang K, Qiu W, Luo Y, Pan Y, Li J, Yang Y, Wu B, Fang F. Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells. Stem Cell Res Ther 2020; 11:114. [PMID: 32169113 PMCID: PMC7071724 DOI: 10.1186/s13287-020-01622-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/03/2020] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) play an important role in the multiple differentiations of mesenchymal stem cells (MSCs). However, few studies have focused on the regulatory mechanism of lncRNAs in the odontogenic differentiation of human dental pulp stem cells (hDPSCs). METHODS hDPSCs were induced to differentiate into odontoblasts in vitro, and the expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) in differentiated and undifferentiated cells were obtained by microarray. Bioinformatics analyses including Gene Ontology (GO) analysis, pathway analysis, and binding site prediction were performed for functional annotation of lncRNA. miRNA/odontogenesis-related gene networks and lncRNA-associated ceRNA networks were constructed. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was used to verify the expression of selected genes. RNA fluorescence in situ hybridization (FISH), qRT-PCR, and western blot analysis were used to explore the location and function of lncRNA-G043225. Dual-luciferase reporter assay was performed to confirm the binding sites of miR-588 with G043225 and Fibrillin 1 (FBN1). RESULTS We identified 132 lncRNAs, 114 miRNAs, and 172 mRNAs were differentially expressed. GO analysis demonstrated that regulation of the neurogenic locus notch homolog (Notch), Wnt, and epidermal growth factor receptor (ERBB) signaling pathways and activation of mitogen-activated protein kinase (MAPK) activity were related to odontogenic differentiation. Pathway analysis indicated that the most significant pathway was the forkhead box O (FoxO) signaling pathway, which is related to odontogenic differentiation. Two odontogenesis-related gene-centered lncRNA-associated ceRNA networks were successfully constructed. The qRT-PCR validation results were consistent with the microarray analysis. G043225 mainly locating in cytoplasm was proved to promote the odontogenic differentiation of hDPSCs via miR-588 and FBN1. CONCLUSION This is the first study revealing lncRNA-associated ceRNA network during odontogenic differentiation of hDPSCs using microarray, and it could provide clues to explore the mechanism of action at the RNA-RNA level as well as novel treatments for dentin regeneration based on stem cells.
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Affiliation(s)
- Zhao Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Kaiying Zhang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Wei Qiu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Yifei Luo
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Yuhua Pan
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jianjia Li
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Yeqing Yang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Buling Wu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China. .,College of Stomatology, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China. .,College of Stomatology, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
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97
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Al-Attar R, Storey KB. Suspended in time: Molecular responses to hibernation also promote longevity. Exp Gerontol 2020; 134:110889. [PMID: 32114078 DOI: 10.1016/j.exger.2020.110889] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022]
Abstract
Aging in most animals is an inevitable process that causes or is a result of physiological, biochemical, and molecular changes in the body, and has a strong influence on an organism's lifespan. Although advancement in medicine has allowed humans to live longer, the prevalence of age-associated medical complications is continuously burdening older adults worldwide. Current animal models used in research to study aging have provided novel information that has helped investigators understand the aging process; however, these models are limiting. Aging is a complex process that is regulated at multiple biological levels, and while a single manipulation in these models can provide information on a process, it is not enough to understand the global regulation of aging. Some mammalian hibernators live up to 9.8-times higher than their expected average lifespan, and new research attributes this increase to their ability to hibernate. A common theme amongst these mammalian hibernators is their ability to greatly reduce their metabolic rate to a fraction of their normal rate and initiate cytoprotective responses that enable their survival. Metabolic rate depression is strictly regulated at different biological levels in order to enable the animal to not only survive, but to also do so by relying mainly on their limited internal fuels. As such, understanding both the global and specific regulatory mechanisms used to promote survival during hibernation could, in theory, allow investigators to have a better understanding of the aging process. This can also allow pharmaceutical industries to find therapeutics that could delay or reverse age-associated medical complications and promote healthy aging and longevity in humans.
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Affiliation(s)
- Rasha Al-Attar
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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98
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Rahmani Z, Mojarrad M, Moghbeli M. Long non-coding RNAs as the critical factors during tumor progressions among Iranian population: an overview. Cell Biosci 2020; 10:6. [PMID: 31956395 PMCID: PMC6961246 DOI: 10.1186/s13578-020-0373-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cancer is associated with various genetic and environmental risk factors. Beside the mutations or aberrant expression of protein-coding genes, the genetic deregulation of non-coding RNAs has also an important role during tumor progression and metastasis. Long non-coding RNAs (lncRNAs) are a class of ncRNAs larger than 200 nucleotides that may function as tumor-suppressor or oncogene. MAIN BODY There is a raising trend of cancer incidence among Iranian population during the last decades. Therefore, it is required to prepare a general population specific panel of genetic markers for the early detection of cancer in this population. The tissue-specific expression characteristics and high stability in body fluids highlight the lncRNAs as efficient diagnostic and prognostic noninvasive biomarkers in cancer. In present review we summarized all of the lncRNAs which have been reported until now in different tumors among Iranian patients. CONCLUSIONS This review paves the way of introducing a population based noninvasive diagnostic panel of lncRNAs for the early detection of tumor cells among Iranian population.
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Affiliation(s)
- Zahra Rahmani
- Department of Medical Genetics, Golestan University of Medical Sciences, Gorgan, Iran
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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99
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Kim DN, Thiel BC, Mrozowich T, Hennelly SP, Hofacker IL, Patel TR, Sanbonmatsu KY. Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nat Commun 2020; 11:148. [PMID: 31919376 PMCID: PMC6952434 DOI: 10.1038/s41467-019-13942-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/09/2019] [Indexed: 02/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.
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Affiliation(s)
- Doo Nam Kim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Bernhard C Thiel
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Tyler Mrozowich
- Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Scott P Hennelly
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Trushar R Patel
- Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
- New Mexico Consortium, Los Alamos, New Mexico, USA.
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100
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LncRNA CAR10 Upregulates PDPK1 to Promote Cervical Cancer Development by Sponging miR-125b-5p. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4351671. [PMID: 32025520 PMCID: PMC6984746 DOI: 10.1155/2020/4351671] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/18/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023]
Abstract
Cervical cancer is one of the malignant tumors that seriously threaten women's health. The mechanism of development needs to be deeply studied. In recent years, lncRNA has been identified as one of the important factors affecting the malignant progression of tumors. In this study, we illustrated the important mechanism of lncRNA CAR10 in the development of cervical cancer. We found that CAR10 is significantly increased in4 cervical cancer tissues and cells, which can promote the proliferation of cervical cancer cells in vitro and in vivo, indicating that CAR10 is involved in the progression of cervical cancer as an oncogene. Further studies showed that CAR10 is a target gene of miR-125b-5p, and miR-125b-5p can inhibit the effect of CAR10 on the proliferation of cervical cancer cells. In addition, we also found that 3-phosphoinositide-dependent protein kinase 1 (PDPK1) is also a target gene of miR-125b-5p, and CAR10 can upregulate the expression level of PDPK1. The results showed that CAR10 acts as a ceRNA to upregulate the expression of PDPK1 by sponging miR-125b-5p. Knockdown of PDPK1 can inhibit the effect of CAR10 on cervical cancer cells. Our study demonstrates that, based on ceRNA mechanism, CAR10/miR-125b-5p/PDPK1 network can regulate the proliferation of cervical cancer cells and play an important role in the development of cervical cancer. In addition, our study also suggests that intervention of CAR10/miR-125b-5p/PDPK1 network may be a new strategy for targeted therapy of cervical cancer.
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