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Aranega AE, Franco D. Posttranscriptional Regulation by Proteins and Noncoding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:313-339. [PMID: 38884719 DOI: 10.1007/978-3-031-44087-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Posttranscriptional regulation comprises those mechanisms occurring after the initial copy of the DNA sequence is transcribed into an intermediate RNA molecule (i.e., messenger RNA) until such a molecule is used as a template to generate a protein. A subset of these posttranscriptional regulatory mechanisms essentially are destined to process the immature mRNA toward its mature form, conferring the adequate mRNA stability, providing the means for pertinent introns excision, and controlling mRNA turnover rate and quality control check. An additional layer of complexity is added in certain cases, since discrete nucleotide modifications in the mature RNA molecule are added by RNA editing, a process that provides large mature mRNA diversity. Moreover, a number of posttranscriptional regulatory mechanisms occur in a cell- and tissue-specific manner, such as alternative splicing and noncoding RNA-mediated regulation. In this chapter, we will briefly summarize current state-of-the-art knowledge of general posttranscriptional mechanisms, while major emphases will be devoted to those tissue-specific posttranscriptional modifications that impact on cardiac development and congenital heart disease.
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Affiliation(s)
- Amelia E Aranega
- Cardiovascular Research Group, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Diego Franco
- Cardiovascular Research Group, Department of Experimental Biology, University of Jaén, Jaén, Spain.
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Jha S, Thasma Loganathbabu VK, Kumaran K, Krishnasamy G, Aruljothi KN. Long Non-Coding RNAs (lncRNAs) in Heart Failure: A Comprehensive Review. Noncoding RNA 2023; 10:3. [PMID: 38250803 PMCID: PMC10801533 DOI: 10.3390/ncrna10010003] [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: 12/08/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/23/2024] Open
Abstract
Heart failure (HF) is a widespread cardiovascular condition that poses significant risks to a wide spectrum of age groups and leads to terminal illness. Although our understanding of the underlying mechanisms of HF has improved, the available treatments still remain inadequate. Recently, long non-coding RNAs (lncRNAs) have emerged as crucial players in cardiac function, showing possibilities as potential targets for HF therapy. These versatile molecules interact with chromatin, proteins, RNA, and DNA, influencing gene regulation. Notable lncRNAs like Fendrr, Trpm3, and Scarb2 have demonstrated therapeutic potential in HF cases. Additionally, utilizing lncRNAs to forecast survival rates in HF patients and distinguish various cardiac remodeling conditions holds great promise, offering significant benefits in managing cardiovascular disease and addressing its far-reaching societal and economic impacts. This underscores the pivotal role of lncRNAs in the context of HF research and treatment.
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Affiliation(s)
- Shambhavi Jha
- Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chengalpattu 603203, Tamilnadu, India; (S.J.); (V.K.T.L.); (K.K.)
| | - Vasanth Kanth Thasma Loganathbabu
- Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chengalpattu 603203, Tamilnadu, India; (S.J.); (V.K.T.L.); (K.K.)
| | - Kasinathan Kumaran
- Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chengalpattu 603203, Tamilnadu, India; (S.J.); (V.K.T.L.); (K.K.)
| | | | - Kandasamy Nagarajan Aruljothi
- Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chengalpattu 603203, Tamilnadu, India; (S.J.); (V.K.T.L.); (K.K.)
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3
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Li N, Zhou Y, Cai J, Wang Y, Zhou X, Hu M, Li Y, Zhang H, Li J, Cai B, Yuan X. A novel trans-acting lncRNA of ACTG1 that induces the remodeling of ovarian follicles. Int J Biol Macromol 2023:125170. [PMID: 37276900 DOI: 10.1016/j.ijbiomac.2023.125170] [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: 01/17/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Previous studies have implicated the attractive role of long noncoding RNAs (lncRNAs) in the remodeling of mammalian tissues. The migration of granulosa cells (GCs), which are the main supporting cells in ovarian follicles, stimulates the follicular remodeling. Here, with the cultured GCs as the follicular model, the actin gamma 1 (ACTG1) was observed to significantly promote the migration and proliferation while inhibit the apoptosis of GCs, suggesting that ACTG1 was required for ovarian remodeling. Moreover, we identified the trans-regulatory lncRNA of ACTG1 (TRLA), which was epigenetically targeted by histone H3 lysine 4 acetylation (H3K4ac). Mechanistically, the 2-375 nt of TRLA bound to ACTG1's mRNA to increase the expression of ACTG1. Furthermore, TRLA facilitated the migration and proliferation while inhibited the apoptosis of GCs, thereby accelerating follicular remodeling. Besides, TRLA acted as a ceRNA for miR-26a to increase the expression of high-mobility group AT-hook 1 (HMGA1). Collectively, TRLA induces the remodeling of ovarian follicles via complementary to ACTG1's mRNA and regulating miR-26a/HMGA1 axis in GCs. These observations revealed a novel and promising trans-acting lncRNA mechanism mediated by H3K4ac, and TRLA might be a new target to restore follicular remodeling and development.
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Affiliation(s)
- Nian Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yinqi Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jiali Cai
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yifei Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiaofeng Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Mengting Hu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yubin Li
- Reproductive Medical Center, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong 510080, China
| | - Hao Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Bing Cai
- Reproductive Medical Center, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong 510080, China.
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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Macvanin MT, Gluvic Z, Radovanovic J, Essack M, Gao X, Isenovic ER. Diabetic cardiomyopathy: The role of microRNAs and long non-coding RNAs. Front Endocrinol (Lausanne) 2023; 14:1124613. [PMID: 36950696 PMCID: PMC10025540 DOI: 10.3389/fendo.2023.1124613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Diabetes mellitus (DM) is on the rise, necessitating the development of novel therapeutic and preventive strategies to mitigate the disease's debilitating effects. Diabetic cardiomyopathy (DCMP) is among the leading causes of morbidity and mortality in diabetic patients globally. DCMP manifests as cardiomyocyte hypertrophy, apoptosis, and myocardial interstitial fibrosis before progressing to heart failure. Evidence suggests that non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), regulate diabetic cardiomyopathy-related processes such as insulin resistance, cardiomyocyte apoptosis and inflammation, emphasizing their heart-protective effects. This paper reviewed the literature data from animal and human studies on the non-trivial roles of miRNAs and lncRNAs in the context of DCMP in diabetes and demonstrated their future potential in DCMP treatment in diabetic patients.
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Affiliation(s)
- Mirjana T. Macvanin
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Zoran Gluvic
- University Clinical-Hospital Centre Zemun-Belgrade, Clinic of Internal Medicine, Department of Endocrinology and Diabetes, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Radovanovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Esma R. Isenovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Taliani V, Buonaiuto G, Desideri F, Setti A, Santini T, Galfrè S, Schirone L, Mariani D, Frati G, Valenti V, Sciarretta S, Perlas E, Nicoletti C, Musarò A, Ballarino M. The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart. eLife 2023; 12:81360. [PMID: 36877136 PMCID: PMC10023161 DOI: 10.7554/elife.81360] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/03/2023] [Indexed: 03/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes of action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodeling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing, and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the ventricular myocardium. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.
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Affiliation(s)
- Valeria Taliani
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Giulia Buonaiuto
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Fabio Desideri
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Adriano Setti
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Tiziana Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Silvia Galfrè
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Leonardo Schirone
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Davide Mariani
- Center for Human Technologies, Istituto Italiano di TecnologiaGenovaItaly
| | - Giacomo Frati
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Valentina Valenti
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Sebastiano Sciarretta
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL-RomeMonterotondoItaly
| | - Carmine Nicoletti
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Antonio Musarò
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
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Zhuo X, Yu Q, Russo R, Zhang Y, Wei X, Wang YZ, Holden PM, Gmitter FG. Role of long non-coding RNA in regulatory network response to Candidatus Liberibacter asiaticus in citrus. FRONTIERS IN PLANT SCIENCE 2023; 14:1090711. [PMID: 36890903 PMCID: PMC9986497 DOI: 10.3389/fpls.2023.1090711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) serve as crucial regulators in plant response to various diseases, while none have been systematically identified and characterized in response to citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) bacteria. Here, we comprehensively investigated the transcriptional and regulatory dynamics of the lncRNAs in response to CLas. Samples were collected from leaf midribs of CLas- and mock-inoculated HLB-tolerant rough lemon (Citrus jambhiri) and HLB-sensitive sweet orange (C. sinensis) at week 0, 7, 17, and 34 following inoculation using CLas+ budwood of three biological replicates in the greenhouse. A total of 8,742 lncRNAs, including 2,529 novel lncRNAs, were identified from RNA-seq data with rRNA-removed from strand-specific libraries. Genomic variation analyses of conserved lncRNAs from 38 citrus accessions showed that 26 single nucleotide polymorphisms (SNPs) were significantly correlated with HLB. In addition, lncRNA-mRNA weighted gene co-expression network analysis (WGCNA) showed a significant module correlated with CLas-inoculation in rough lemon. Notably, the most significant LNC_28805 and multiple co-expressed genes related to plant defense in the module were targeted by miRNA5021, suggesting that LNC28805 might compete with endogenous miR5021 to maintain the homeostasis of immune gene expression levels. Candidate WRKY33 and SYP121 genes targeted by miRNA5021 were identified as two key hub genes interacting with bacteria pathogen response genes based on the prediction of protein-protein interaction (PPI) network. These two genes were also found within HLB-associated QTL in linkage group 6. Overall, our findings provide a reference for a better understanding of the role of lncRNAs involved in citrus HLB regulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Fred G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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The Function and Therapeutic Potential of lncRNAs in Cardiac Fibrosis. BIOLOGY 2023; 12:biology12020154. [PMID: 36829433 PMCID: PMC9952806 DOI: 10.3390/biology12020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
Cardiac fibrosis remains an unresolved problem in cardiovascular diseases. Fibrosis of the myocardium plays a key role in the clinical outcomes of patients with heart injuries. Moderate fibrosis is favorable for cardiac structure maintaining and contractile force transmission, whereas adverse fibrosis generally progresses to ventricular remodeling and cardiac systolic or diastolic dysfunction. The molecular mechanisms involved in these processes are multifactorial and complex. Several molecular mechanisms, such as TGF-β signaling pathway, extracellular matrix (ECM) synthesis and degradation, and non-coding RNAs, positively or negatively regulate myocardial fibrosis. Long noncoding RNAs (lncRNAs) have emerged as significant mediators in gene regulation in cardiovascular diseases. Recent studies have demonstrated that lncRNAs are crucial in genetic programming and gene expression during myocardial fibrosis. We summarize the function of lncRNAs in cardiac fibrosis and their contributions to miRNA expression, TGF-β signaling, and ECMs synthesis, with a particular attention on the exosome-derived lncRNAs in the regulation of adverse fibrosis as well as the mode of action of lncRNAs secreted into exosomes. We also discuss how the current knowledge on lncRNAs can be applied to develop novel therapeutic strategies to prevent or reverse cardiac fibrosis.
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Wang Y, Zheng S, Han J, Li N, Ji R, Li X, Han C, Zhao W, Zhang L. LINC00629 protects osteosarcoma cell from ER stress-induced apoptosis and facilitates tumour progression by elevating KLF4 stability. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:354. [PMID: 36539799 PMCID: PMC9764730 DOI: 10.1186/s13046-022-02569-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Escaping from ER stress-induced apoptosis plays an important role in the progression of many tumours. However, its molecular mechanism in osteosarcoma remains incompletely understood. METHODS The molecular mechanism was investigated using RNA sequencing, qRT-PCR and Western blot assays. The relationship between LINC00629 and KLF4 was investigated using RNA pulldown and ubiquitylation assays. The transcriptional regulation of laminin subunit alpha 4 (LAMA4) by KLF4 was identified using bioinformatic analysis, a luciferase assay, and a chromatin immunoprecipitation assay. RESULTS Here, we demonstrated that LINC00629 was increased under ER stress treatment. Elevated LINC00629 inhibited ER stress-induced osteosarcoma cell apoptosis and promoted clonogenicity and migration in vitro and in vivo. Further mechanistic studies indicated that LINC00629 interacted with KLF4 and suppressed its degradation, which led to a KLF4 increase in osteosarcoma. In addition, we also found that KLF4 upregulated LAMA4 expression by directly binding to its promoter and that LINC00629 inhibited ER stress-induced apoptosis and facilitated osteosarcoma cell clonogenicity and metastasis by activating the KLF4-LAMA4 pathway. CONCLUSION Collectively, our data indicate that LINC00629 is a critical long noncoding RNA (lncRNA) induced by ER stress and plays an oncogenic role in osteosarcoma cell by activating the KLF4-LAMA4 axis.
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Affiliation(s)
- Yuan Wang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
| | - Shuo Zheng
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
| | - Jian Han
- grid.411971.b0000 0000 9558 1426Department of Orthopedics, The Third People’s Hospital of Dalian, Dalian Medical University, Dalian, Liaoning 116033 People’s Republic of China
| | - Na Li
- grid.411971.b0000 0000 9558 1426National-Local Joint Engineering Research Center for Drug-Research and Development (R&D) of Neurodegenerative Diseases, Dalian Medical University, Dalian, 116044 People’s Republic of China
| | - Renchen Ji
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
| | - Xiaodong Li
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
| | - Chuanchun Han
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
| | - Wenzhi Zhao
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
| | - Lu Zhang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China
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Chen S, Zhang C, Shen L, Hu J, Chen X, Yu Y. Noncoding RNAs in cataract formation: star molecules emerge in an endless stream. Pharmacol Res 2022; 184:106417. [PMID: 36038044 DOI: 10.1016/j.phrs.2022.106417] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
For decades, research on the pathological mechanism of cataracts has usually focused on the abnormal protein changes caused by a series of risk factors. However, an entire class of molecules, termed non-coding RNA (ncRNA), was discovered in recent years and proven to be heavily involved in cataract formation. Recent studies have recognized the key regulatory roles of ncRNAs in cataracts by shaping cellular activities such as proliferation, apoptosis, migration and epithelial-mesenchymal transition (EMT). This review summarizes our current insight into the biogenesis, properties and functions of ncRNAs and then discusses the development of research on ncRNAs in cataracts. Considering the significant role of ncRNA in cataract formation, research on novel associated regulatory mechanisms is urgently needed, and the development of therapeutic alternatives for the treatment of cataracts seems promising.
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Affiliation(s)
- Silong Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Chengshou Zhang
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Lifang Shen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Jianghua Hu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Department of Ophthalmology, Jiande Branch, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, China.
| | - Yibo Yu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China.
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Lu BH, Liu HB, Guo SX, Zhang J, Li DX, Chen ZG, Lin F, Zhao GA. Long non-coding RNAs: Modulators of phenotypic transformation in vascular smooth muscle cells. Front Cardiovasc Med 2022; 9:959955. [PMID: 36093159 PMCID: PMC9458932 DOI: 10.3389/fcvm.2022.959955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
Long non-coding RNA (lncRNAs) are longer than 200 nucleotides and cannot encode proteins but can regulate the expression of genes through epigenetic, transcriptional, and post-transcriptional modifications. The pathophysiology of smooth muscle cells can lead to many vascular diseases, and studies have shown that lncRNAs can regulate the phenotypic conversion of smooth muscle cells so that smooth muscle cells proliferate, migrate, and undergo apoptosis, thereby affecting the development and prognosis of vascular diseases. This review discusses the molecular mechanisms of lncRNA as a signal, bait, stent, guide, and other functions to regulate the phenotypic conversion of vascular smooth muscle cells, and summarizes the role of lncRNAs in regulating vascular smooth muscle cells in atherosclerosis, hypertension, aortic dissection, vascular restenosis, and aneurysms, providing new ideas for the diagnosis and treatment of vascular diseases.
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Affiliation(s)
- Bing-Han Lu
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
| | - Hui-Bing Liu
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
- Henan Normal University, Xinxiang, China
| | - Shu-Xun Guo
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
| | - Jie Zhang
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
| | - Dong-Xu Li
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
| | - Zhi-Gang Chen
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
| | - Fei Lin
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
| | - Guo-An Zhao
- Department of Cardiology, Life Science Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, China
- Key Laboratory of Cardiovascular Injury and Repair Medicine of Henan, Weihui, China
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Liu F, Cao L, Zhang Y, Xia X, Ji Y. LncRNA LIFR-AS1 overexpression suppressed the progression of serous ovarian carcinoma. J Clin Lab Anal 2022; 36:e25470. [PMID: 35778954 PMCID: PMC9396205 DOI: 10.1002/jcla.24570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Background Serous ovarian carcinoma (SOC) is a common malignant tumor in female reproductive system. Long noncoding RNA (lncRNA) LIFR‐AS1 is a tumor suppressor gene in colorectal cancer, but its effect and underlying mechanism in SOC are still unclear. Therefore, this study focuses on unveiling the regulatory mechanism of LIFR‐AS1 in SOC. Methods The relationship between LIFR‐AS1 expression and prognosis of SOC patients was analyzed by TCGA database and Starbase, and then, the LIFR‐AS1 expression in SOC tissues and cells was detected by quantitative real‐time PCR (qRT‐PCR) and in situ hybridization (ISH). Besides, the relationship between LIFR‐AS1 and clinical characteristics was analyzed. Also, the effects of LIFR‐AS1 on the biological behaviors of SOC cells were measured by Cell Counting Kit‐8, colony formation, and wound‐healing and Transwell assays, respectively. Western blot and qRT‐PCR were employed to determine the protein expressions of genes related to proliferation (PCNA), apoptosis (cleaved caspase‐3), epithelial‐mesenchymal transition (E‐cadherin, N‐cadherin, and Snail). Results LIFR‐AS1 was lowly expressed in SOC, which was correlated with the poor prognosis of SOC patients. Low expression of LIFR‐AS1 in SOC was associated with the tumor size, clinical stage, lymph node metastasis, and distant metastasis. LIFR‐AS1 overexpression promoted the expressions of cleaved caspase‐3 and E‐cadherin while suppressing the malignant behaviors (proliferation, migration, and invasion) of SOC cells, the expressions of PCNA, N‐cadherin, and Snail. Besides, silencing LIFR‐AS1 exerted the effects opposite to overexpressed LIFR‐AS1. Conclusion LIFR‐AS1 overexpression inhibits biological behaviors of SOC cells, which may be a new therapeutic method.
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Affiliation(s)
- Fang Liu
- Department of Gynecology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Linyan Cao
- Department of Gynecology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yufang Zhang
- Department of Gynecology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Xinyi Xia
- Department of Gynecology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yanhua Ji
- Department of Gynecology, The Fourth People's Hospital of Tongxiang, Jiaxing, China
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12
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Long Noncoding RNA SCIRT Promotes HUVEC Angiogenesis via Stabilizing VEGFA mRNA Induced by Hypoxia. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9102978. [PMID: 35698607 PMCID: PMC9187973 DOI: 10.1155/2022/9102978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/28/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022]
Abstract
Ischemia-reperfusion injury (IRI) is closely associated the abnormal expression of long noncoding RNAs (lncRNAs), especially for their regulatory roles in IRI-related angiogenesis. This study applied a hypoxia-reoxygenation (HR) cell model to simulate the IRI condition, as well as RNA sequencing and RNA pull-down experiments to reveal roles of the lncRNA and Stem Cell Inhibitory RNA Transcript (SCIRT), in endothelial angiogenesis. We found that SCIRT was increased under the HR condition and exhibited a high expression correlation with angiogenesis marker VEGFA. RNA-seq data analysis further revealed that VEGFA-related angiogenesis was regulated by SCIRT in HUVECs. Gain and loss of function experiments proved that SCIRT posttranscriptionally regulated VEGFA via affecting its mRNA stability. Furthermore, HuR (ELAVL1), an RNA binding protein (RBP), was identified as a SCIRT-binding partner, which bound and stabilized VEGFA. Moreover, SCIRT promoted HuR expression posttranslationally by inhibiting its ubiquitination under the HR condition. These findings reveal that lncRNA SCIRT can mediate endothelial angiogenesis by stabilizing the VEGFA mRNA via modulating RBP HuR stability under the HR condition.
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13
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Zhang L, Zhang S, Wang R, Sun L. Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants. Int J Mol Sci 2022; 23:ijms23116247. [PMID: 35682924 PMCID: PMC9181106 DOI: 10.3390/ijms23116247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in chromatin remodeling remains unclear. In order to characterize the genome-wide lncRNA expression and their potential interacting factors during this process in Drosophila, we investigated the expression pattern of lncRNAs and mRNAs based on the transcriptome analyses and found significant differences between lncRNAs and mRNAs. Then, we performed TSA-FISH experiments of candidate lncRNAs and their potential interactors that have different functions in Drosophila embryos to determine their expression pattern. In addition, we also analyzed the expression of transposable elements (TEs) and their interactors to explore their expression in ISWI mutants. Our results provide a new perspective for understanding the possible regulatory mechanism of lncRNAs and TEs as well as their targets in chromatin remodeling.
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14
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Banerjee S, Prabhu Basrur N, Rai PS. Omics technologies in personalized combination therapy for cardiovascular diseases: challenges and opportunities. Per Med 2021; 18:595-611. [PMID: 34689602 DOI: 10.2217/pme-2021-0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The primary purpose of 'omics' technologies is to understand the intricacy of genomics, proteomics, metabolomics and other molecular mechanisms to reveal the complex traits of human diseases. The significant use of omics technologies and their applications in medicine gear up the study of the pathogenesis of several disorders. The detection of biomarkers in the early onset of diseases is challenging; still, omics can discover novel molecular mechanisms and biomarkers. In this review, the different types of omics and their technologies are explicated and aimed to provide their emerging applications in cardiovascular precision medicine. These technologies significantly impact optimizing medical treatment for individuals to reach a higher level in precision medicine.
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Affiliation(s)
- Saradindu Banerjee
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Navya Prabhu Basrur
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
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15
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Chen Y, Fan Z, Dong Q. LncRNA SNHG16 promotes Schwann cell proliferation and migration to repair sciatic nerve injury. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1349. [PMID: 34532486 PMCID: PMC8422103 DOI: 10.21037/atm-21-3971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/16/2021] [Indexed: 11/06/2022]
Abstract
Background To investigate the expression of long non-coding RNA (lncRNA) Snorna hostgene16 (SNHG16) in sciatic nerve injury tissues and cells. The molecular mechanism of SNHG16 regulating signal activator of transcription 3 (STAT3) expression through “sponge” adsorption of miR-93-5p was also studied. Methods A rat model of sciatic nerve injury was established, and primary Schwann cells (SCs) were extracted. The expression of SNHG16 in animal tissues with sciatic nerve injury and SCs treated with ischemia and hypoxia was detected by qPCR, and CCK-8 assay, cell scratch assay, and Transwell chamber assay were used to detect cell proliferation, migration, and invasion. The targeted binding of SNHG16 to miR-93-5p was verified by double luciferase reporter gene assay and miRNA immunoprecipitation assay. MiR-93-5p mimic, SNHG16 overexpression vector, and sh-STAT3 plasmid were transfected into cells, respectively, and the mRNA expressions of SNHG16, miR-93-5p, and STAT3 in the cells were detected by qPCR. Results The expression of lncRNA SNHG16 was decreased after sciatic nerve injury, while overexpression of SNHG16 promoted the proliferation, migration, and invasion of SCs. The results of dual luciferase reporter gene assay and miRNA immunoprecipitation reaction showed miR-93-5p interacted with SNHG16, and the overexpression of miR-93-5p reversed the promoting effects of SNHG16 on the proliferation and invasion of SCs. At the same time, the knockdown of STAT3, which is the target gene of miR-93-5p, reversed the proliferation and invasion promotion effect of SNHG16 on SCs. SNHG16 affected the expression of its downstream target gene STAT3 by adsorbing miR-93-5p via endogenous competitive sponge. Conclusions SNHG16 can regulate STAT3 expression by sponge adsorption of miR-93-5p in SCs, and SNHG16 and miR-93-5p can be used as potential targets for the diagnosis and treatment of sciatic nerve injury.
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Affiliation(s)
- Yujie Chen
- Department of Orthopaedics, the Second Affiliated Hospital of Soochow University, Suzhou, China.,Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Zhiying Fan
- Department of Orthopaedics, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qirong Dong
- Department of Orthopaedics, the Second Affiliated Hospital of Soochow University, Suzhou, China
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16
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Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts. PLoS Biol 2021; 19:e3001229. [PMID: 34003819 PMCID: PMC8130971 DOI: 10.1371/journal.pbio.3001229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/12/2021] [Indexed: 12/02/2022] Open
Abstract
DNA methylation, chromatin accessibility, and gene expression represent different levels information in biological process, but a comprehensive multiomics analysis of the mammalian heart is lacking. Here, we applied nucleosome occupancy and methylome sequencing, which detected DNA methylation and chromatin accessibility simultaneously, as well as RNA-seq, for multiomics analysis of the 4 chambers of adult and fetal human hearts, and adult mouse hearts. Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. Novel long noncoding RNAs were identified in the human heart, and the gene expression profiles of major cardiovascular diseases associated genes were displayed. Furthermore, cross-species comparisons revealed human-specific and mouse-specific differentially expressed genes between the atria and ventricles. We also reported the relationship among multiomics and found there was a bell-shaped relationship between gene-body methylation and expression in the human heart. In general, our study provided comprehensive spatiotemporal and evolutionary insights into the regulation of gene expression in the heart. Multi-omic analyses of the four chambers of the human and mouse heart, including transcriptome, DNA methylation and chromatin accessibility, reveals characteristic patterns of gene regulation at the level of heart regions.
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17
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Longenecker JZ, Gilbert CJ, Golubeva VA, Martens CR, Accornero F. Epitranscriptomics in the Heart: a Focus on m 6A. Curr Heart Fail Rep 2021; 17:205-212. [PMID: 32813261 DOI: 10.1007/s11897-020-00473-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Post-transcriptional modifications are key regulators of gene expression that allow the cell to respond to environmental stimuli. The most abundant internal mRNA modification is N6-methyladenosine (m6A), which has been shown to be involved in the regulation of RNA splicing, localization, translation, and decay. It has also been implicated in a wide range of diseases, and here, we review recent evidence of m6A's involvement in cardiac pathologies and processes. RECENT FINDINGS Studies have primarily relied on gain and loss of function models for the enzymes responsible for adding and removing the m6A modification. Results have revealed a multifaceted role for m6A in the heart's response to myocardial infarction, pressure overload, and ischemia/reperfusion injuries. Genome-wide analyses of mRNAs that are differentially methylated during cardiac stress have highlighted the importance of m6A in regulating the translation of specific categories of transcripts implicated in pathways such as calcium handling, cell growth, autophagy, and adrenergic signaling in cardiomyocytes. Regulation of gene expression by m6A is critical for cardiomyocyte homeostasis and stress responses, suggesting a key role for this modification in cardiac pathophysiology.
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Affiliation(s)
- Jacob Z Longenecker
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, 473 W 12th Ave, Columbus, OH, 43210, USA
| | - Christopher J Gilbert
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, 473 W 12th Ave, Columbus, OH, 43210, USA
| | - Volha A Golubeva
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, 473 W 12th Ave, Columbus, OH, 43210, USA
| | - Colton R Martens
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, 473 W 12th Ave, Columbus, OH, 43210, USA
| | - Federica Accornero
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, 473 W 12th Ave, Columbus, OH, 43210, USA.
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18
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Zhang X, Gao Y, Zhang X, Zhang X, Xiang Y, Fu Q, Wang B, Xu Z. FGD5-AS1 Is a Hub lncRNA ceRNA in Hearts With Tetralogy of Fallot Which Regulates Congenital Heart Disease Genes Transcriptionally and Epigenetically. Front Cell Dev Biol 2021; 9:630634. [PMID: 34046402 PMCID: PMC8144506 DOI: 10.3389/fcell.2021.630634] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/30/2021] [Indexed: 01/19/2023] Open
Abstract
Heart development requires robust gene regulation, and the related disruption could lead to congenital heart disease (CHD). To gain insights into the regulation of gene expression in CHD, we obtained the expression profiles of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in 22 heart tissue samples with tetralogy of Fallot (TOF) through strand-specific transcriptomic analysis. Using a causal inference framework based on the expression correlations and validated microRNA (miRNA)–lncRNA–mRNA evidences, we constructed the competing endogenous RNA (ceRNA)-mediated network driven by lncRNAs. Four lncRNAs (FGD5-AS1, lnc-GNB4-1, lnc-PDK3-1, and lnc-SAMD5-1) were identified as hub lncRNAs in the network. FGD5-AS1 was selected for further study since all its targets were CHD-related genes (NRAS, PTEN, and SMAD4). Both FGD5-AS1 and SMAD4 could bind with hsa-miR-421, which has been validated using dual-luciferase reporter assays. Knockdown of FGD5-AS1 not only significantly reduced PTEN and SMAD4 expression in HEK 293 and the fetal heart cell line (CCC-HEH-2) but also increased the transcription of its interacted miRNAs in a cell-specific way. Besides ceRNA mechanism, RNAseq and ATACseq results showed that FGD5-AS1 might play repression roles in heart development by transcriptionally regulating CHD-related genes. In conclusion, we identified a ceRNA network driven by lncRNAs in heart tissues of TOF patients. Furthermore, we proved that FGD5-AS1, one hub lncRNA in the TOF heart ceRNA network, regulates multiple genes transcriptionally and epigenetically.
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Affiliation(s)
- Xingyu Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunqian Gao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoping Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Faculty of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Faculty of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuoming Xu
- Cardiac Intensive Care Unit, Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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19
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Li D, Li L, Chen X, Zhou C, Hao B, Cao Y. Dysregulation of lncRNA-CCRR contributes to brain metastasis of breast cancer by intercellular coupling via regulating connexin 43 expression. J Cell Mol Med 2021; 25:4826-4834. [PMID: 33793070 PMCID: PMC8107087 DOI: 10.1111/jcmm.16455] [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: 08/13/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 01/05/2023] Open
Abstract
Cardiac conduction regulatory RNA (CCRR) is down‐regulated in the pathogenesis of heart failure (HF), which accordingly suppresses cardiac conduction while promoting arrhythmogenicity. Meanwhile, CX43 was reported to play a role in the pathogenesis of metastatic breast cancer and melanoma brain colonization. In this study, we studied the role of long non‐coding RNA CCRR and its interaction with CX43 in brain metastasis of breast cancer. Breast cancer patients were grouped according to the metastasis status. Real‐time PCR and IHC assay were used to measure the expression of lncRNA‐CCRR and CX43 in patients. Western blot was conducted to observe the effect of lncRNA‐CCRR on the expression of CX43 in MDA‐MB‐231BR and BT‐474BR cells. Compared with the non‐metastasis group, the mRNA expression of tissue lncRNA‐CCRR, cerebrospinal fluid (CSF) lncRNA‐CCRR, tissue CX43 and tissue protein expression of CX43 were both evidently up‐regulated in metastasis patients, especially in patients with brain metastasis. The expression of lncRNA‐CCRR was positively correlated with the up‐regulated expression of CX43. Moreover, CX43 expression was significantly lower in MDA‐MB‐231WT cells compared with that in MDA‐MB‐231BR cells. Also, the overexpression of lncRNA‐CCRR evidently increased dye transfer rate from astrocytes to MDA‐MB‐231BR/BT‐474BR cells but reduced lncRNA‐CCRR expression and suppressed the transmigration of MDA‐MB‐231BR/BT‐474BR cells in a blood‐brain barrier (BBB) model. In this study, we demonstrated that the presence of lncRNA‐CCRR could up‐regulate the expression of CX43, which promoted gap junction formation in brain metastasis of breast cancer. Accordingly, the communication between breast cancer cells and astrocytes was also promoted.
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Affiliation(s)
- Deheng Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liangdong Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Changshuai Zhou
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bin Hao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiqun Cao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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20
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Kong Y, Han B, Zhang L, Liu Q, Zheng G, Guo K, Chen Q, Chen Z. Long noncoding RNA NONHSAT177112.1 aggravates inflammation and apoptosis in LPS-treated human cardiomyocytes. Epigenomics 2021; 13:411-422. [PMID: 33641342 DOI: 10.2217/epi-2020-0345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To explore the roles of lncRNA NONHSAT177112.1 in the inflammatory injury of human cardiomyocytes (HCMs) induced by lipopolysaccharide (LPS). Materials & methods: The sublocalization of NONHSAT177112.1 was detected by FISH. HCMs were stimulated with LPS to induce inflammatory injury. NONHSAT177112.1 expression was detected by quantitative real-time PCR. Cell apoptosis and viability were detected by flow cytometry and CCK-8 assays. The expression of inflammatory cytokines and myocardial enzymes were detected by PCR and ELISA. Results: NONHSAT177112.1 is expressed in the nucleus and cytoplasm. NONHSAT177112.1 showed dynamic expression that first increased and then decreased during LPS stimulation. NONHSAT177112.1 knockdown reversed the promotion effect of LPS on inflammatory injury. Conversely, NONHSAT177112.1 overexpression exerted the opposite effects. Conclusion: NONHSAT177112.1 aggravates inflammatory injury in LPS-treated HCMs.
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Affiliation(s)
- Yaru Kong
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Department of Midwifery, Taishan Vocational College of Nursing, Taian, Shandong 271000, China
| | - Bo Han
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.,Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Li Zhang
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Qingqing Liu
- Department of Pediatric Surgical Oncology, Children's Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Guanlin Zheng
- Department of Midwifery, Taishan Vocational College of Nursing, Taian, Shandong 271000, China
| | - Keying Guo
- Molecular, Cellular and Developmental Biology, Center for Integrative Biology, University of Toulouse, Toulouse, 31062, France
| | - Qing Chen
- Department of Midwifery, Taishan Vocational College of Nursing, Taian, Shandong 271000, China
| | - Zhongmei Chen
- Department of Midwifery, Taishan Vocational College of Nursing, Taian, Shandong 271000, China
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21
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Rong R, Wang M, You M, Li H, Xia X, Ji D. Pathogenesis and prospects for therapeutic clinical application of noncoding RNAs in glaucoma: Systematic perspectives. J Cell Physiol 2021; 236:7097-7116. [PMID: 33634475 PMCID: PMC8451868 DOI: 10.1002/jcp.30347] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/24/2021] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
Noncoding ribonucleic acids (ncRNAs) are an increasingly studied class of RNA molecules with extensive biological activities, including important roles in human development, health, and disease. Glaucoma is a neurodegenerative disease of the retina, and one of the leading causes of blindness worldwide. However, the specific roles of ncRNAs in the development and progression of glaucoma are unclear, and related reports are fragmented. An in‐depth understanding of ncRNAs participating in the pathogenesis and progression of glaucoma would be helpful for opening up new avenues to facilitate the early diagnosis and clinical treatment. Therefore, in this review, we aimed to discuss the current research progress, the potentialfuture clinical applications and the research limitations of three critical classes of ncRNAs in glaucoma, namely microRNAs, long noncoding RNAs, and circular RNAs.
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Affiliation(s)
- Rong Rong
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Mengxiao Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Mengling You
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Haibo Li
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Dan Ji
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
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22
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Szafranski P, Stankiewicz P. Long Non-Coding RNA FENDRR: Gene Structure, Expression, and Biological Relevance. Genes (Basel) 2021; 12:177. [PMID: 33513839 PMCID: PMC7911649 DOI: 10.3390/genes12020177] [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: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
The FOXF1 Adjacent Noncoding Developmental Regulatory RNA (Fendrr) plays an important role in the control of gene expression in mammals. It is transcribed in the opposite direction to the neighboring Foxf1 gene with which it shares a region containing promoters. In humans, FENDRR is located on chromosome 16q24.1, and is positively regulated both by the FOXF1 distant lung-specific cis-acting enhancer and by trans-acting FOXF1. Fendrr has been shown to function as a competing endogenous RNA, sponging microRNAs and protein factors that control stability of mRNAs, and as an epigenetic modifier of chromatin structure around gene promoters and other regulatory sites, targeting them with histone methyltrasferase complexes. In mice, Fendrr is essential for development of the heart, lungs, and gastrointestinal system; its homozygous loss causes embryonic or perinatal lethality. Importantly, deregulation of FENDRR expression has been causatively linked also to tumorigenesis, resistance to chemotherapy, fibrosis, and inflammatory diseases. Here, we review the current knowledge on the FENDRR structure, expression, and involvement in development and tissue maintenance.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
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23
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Zhao P, Wang Y, Zhang L, Zhang J, Liu N, Wang H. Mechanism of long non‑coding RNA metastasis‑associated lung adenocarcinoma transcript 1 in lipid metabolism and inflammation in heart failure. Int J Mol Med 2021; 47:5. [PMID: 33448307 PMCID: PMC7834958 DOI: 10.3892/ijmm.2020.4838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/21/2020] [Indexed: 01/02/2023] Open
Abstract
Heart failure (HF) is a serious threat to human health. Long noncoding RNAs (lncRNAs) are critical regulators of HF. The aim of the study was to investigate the molecular mechanism of MALAT1 in HF rats. MALAT1 expression was detected in serum of normal volunteers and HF patients, HF rats and isoproterenol (ISO)-induced H9C2 cells, and its diagnostic value was evaluated in HF patients. Indexes related to cardiac functions and hemodynamics, myocardial injury, lipid metabolism, lipid oxidation, and inflammation were detected. Moreover, the downstream mechanism of MALAT1 was predicted and verified and in vivo experiments were further performed in ISO-induced H9C2 cells to verify the effects of MALAT1 in HF. MALAT1 was highly expressed in serum of HF patients, HF rats and ISO-induced H9C2 cells and was valuable in predicting HF. Inhibition of MALAT1 increased cardiac function and anti-inflammation and alleviated myocardial injury, lipid metabolism, lipid oxidation and apoptosis rates. Inhibition of MALAT1 reduced H9C2 cell injury. MALAT1 competitively bound to microRNA (miR)-532-3p to upregulate LDLR protein. Inhibition of miR-532-3p weakened the protective effect of downregulated MALAT1 against H9C2 cell injury. We concluded that MALAT1 upregulated LDLR expression by competitively binding to miR-532-3p, thereby increasing pathological injury in HF.
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Affiliation(s)
- Peng Zhao
- Department of Cardiology I, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Yunkai Wang
- Department of Cardiac Surgery ICU, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Luping Zhang
- Department of Reproductive Medicine, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Jinhua Zhang
- Department of Physical Examination, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Ning Liu
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Hongqiang Wang
- Department of Cardiology II, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
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24
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Byun Y, Choi YC, Jeong Y, Yoon J, Baek K. Long Noncoding RNA Expression Profiling Reveals Upregulation of Uroplakin 1A and Uroplakin 1A Antisense RNA 1 under Hypoxic Conditions in Lung Cancer Cells. Mol Cells 2020; 43:975-988. [PMID: 33273139 PMCID: PMC7772508 DOI: 10.14348/molcells.2020.0126] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Hypoxia plays important roles in cancer progression by inducing angiogenesis, metastasis, and drug resistance. However, the effects of hypoxia on long noncoding RNA (lncRNA) expression have not been clarified. Herein, we evaluated alterations in lncRNA expression in lung cancer cells under hypoxic conditions using lncRNA microarray analyses. Among 40,173 lncRNAs, 211 and 113 lncRNAs were up- and downregulated, respectively, in both A549 and NCI-H460 cells. Uroplakin 1A (UPK1A) and UPK1A-antisense RNA 1 (AS1), which showed the highest upregulation under hypoxic conditions, were selected to investigate the effects of UPK1AAS1 on the expression of UPK1A and the mechanisms of hypoxia-inducible expression. Following transfection of cells with small interfering RNA (siRNA) targeting hypoxiainducible factor 1α (HIF-1α), the hypoxia-induced expression of UPK1A and UPK1A-AS1 was significantly reduced, indicating that HIF-1α played important roles in the hypoxiainduced expression of these targets. After transfection of cells with UPK1A siRNA, UPK1A and UPK1A-AS1 levels were reduced. Moreover, transfection of cells with UPK1A-AS1 siRNA downregulated both UPK1A-AS1 and UPK1A. RNase protection assays demonstrated that UPK1A and UPK1A-AS1 formed a duplex; thus, transfection with UPK1A-AS1 siRNA decreased the RNA stability of UPK1A. Overall, these results indicated that UPK1A and UPK1A-AS1 expression increased under hypoxic conditions in a HIF-1α-dependent manner and that formation of a UPK1A/UPK1A-AS1 duplex affected RNA stability, enabling each molecule to regulate the expression of the other.
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MESH Headings
- Cell Hypoxia/genetics
- Cell Line, Tumor
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Lung Neoplasms/genetics
- Methylation
- RNA Stability/genetics
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Reproducibility of Results
- Ribonucleases/metabolism
- Up-Regulation/genetics
- Uroplakin Ia/genetics
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Affiliation(s)
- Yuree Byun
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Young-Chul Choi
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Yongsu Jeong
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Jaeseung Yoon
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Kwanghee Baek
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
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25
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Zhao Z, Liu D, Cui Y, Li S, Liang D, Sun D, Wang J, Liu Z. Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 2020; 21:853. [PMID: 33261549 PMCID: PMC7709324 DOI: 10.1186/s12864-020-07272-9] [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: 04/04/2020] [Accepted: 11/23/2020] [Indexed: 12/05/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07272-9.
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Affiliation(s)
- Zilong Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, China.,Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liang
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, China.
| | - Jianhe Wang
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China.
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, China.
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Miramontes-González JP, Usategui-Martín R, Martín-Vallejo J, Ziegler M, de Isla LL, O Connor D, González-Sarmiento R. VAV3 rs7528153 and VAV3-AS1 rs1185222 polymorphisms are associated with an increased risk of developing hypertension. Eur J Intern Med 2020; 80:60-65. [PMID: 32540412 DOI: 10.1016/j.ejim.2020.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 01/04/2023]
Abstract
The aetiology of essential hypertension is complex and involves both environmental and genetic factors. Approximately 30% of the inter-individual variability in blood pressure is genetically determined. It has been shown that numerous vasoconstrictors stimulate RhoA in local populations of vascular SMCs that, in turn, promote localised constriction of arterial blood vessels and elevations in blood pressure. The VAV3 gene encodes for VAV3 protein, a Rho GEF factor. VAV3-AS1 gene, a lncRNA, may regulate VAV3 expression. We performed an observational prospective case-control study, including patients attending in the Vascular Risk Unit from the University Hospital Salamanca for 6 months. A replication study was performed with data from The Kaiser Permanent database of the University of California. The results suggest that T allele of the VAV3 rs7528153 and G allele of the VAV3-AS1 rs11185222 polymorphisms are associated with an increased risk of developing hypertension. We hypothesise that these polymorphisms could modify blood pressure, likely through a modification in the Rho/Rac pathway. Our results suggest that those polymorphisms could be useful genetic markers of susceptibility to suffering hypertension.
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Affiliation(s)
- José Pablo Miramontes-González
- Department of Internal Medicine, Hospital Universitario de Salamanca, Valladolid, Spain; Molecular Medicine Unit, Department of Medicine, Universidad de Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain; Department of Medicine. University of California at San Diego, La Jolla, California-UCSD, United States.
| | - Ricardo Usategui-Martín
- Molecular Medicine Unit, Department of Medicine, Universidad de Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Javier Martín-Vallejo
- Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain; Department of Statistics, Universidad de Salamanca, Salamanca, Spain
| | - Michael Ziegler
- Department of Medicine. University of California at San Diego, La Jolla, California-UCSD, United States
| | - Leopoldo López de Isla
- Cardiac Image Unit. Hospital Clínico San Carlos. Madrid. Facultad de Medicina. Universidad Complutense de Madrid, Madrid, Spain
| | - Daniel O Connor
- Department of Medicine. University of California at San Diego, La Jolla, California-UCSD, United States
| | - Rogelio González-Sarmiento
- Molecular Medicine Unit, Department of Medicine, Universidad de Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain.
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27
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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28
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Zheng J, Peng B, Zhang Y, Ai F, Hu X. FOXD3-AS1 Knockdown Suppresses Hypoxia-Induced Cardiomyocyte Injury by Increasing Cell Survival and Inhibiting Apoptosis via Upregulating Cardioprotective Molecule miR-150-5p In Vitro. Front Pharmacol 2020; 11:1284. [PMID: 32973515 PMCID: PMC7469905 DOI: 10.3389/fphar.2020.01284] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 12/25/2022] Open
Abstract
Congenital heart disease (CHD) is the most common type of human innate malformation in fetuses. LncRNAs have been pointed to play critical regulatory roles in various types of cardiac development and diseases including CHD. Our study aimed to explore the effects of lncRNA forkhead box D3 antisense RNA 1 (FOXD3-AS1) on hypoxia-induced injury in AC16 cardiomyocytes and the related molecular mechanism. In vitro cell model of CHD was established by stimulating AC16 cells with hypoxia (1% O2). Expression of FOXD3-AS1 and miR-150-5p was detected by qRT-PCR. Hypoxia-induced injury was evaluated by detecting cell survival, lactate dehydrogenase (LDH) release, apoptosis, and caspase-3/7 activity using MTT, LDH assay, flow cytometry analysis, and caspase-3/7 activity assay, respectively. The regulatory relationship between FOXD3-AS1 and miR-150-5p was explored by luciferase reporter assay, RNA immunoprecipitation (RIP), and qRT-PCR. Results showed that hypoxia exposure caused an upregulation of FOXD3-AS1 and a downregulation of miR-150-5p in AC16 cells. Knockdown of FOXD3-AS1 attenuated reduction of cell survival and increase of LDH release, apoptosis, caspase-3/7 activity, and Bcl-2 associated X (Bax) expression induced by hypoxia in AC16 cells. Notably, we demonstrated that FOXD3-AS1 directly interacted with miR-150-5p to inhibit its expression. miR-150-5p knockdown reinforced the reduction of survival and induction of apoptosis by hypoxia and attenuated the effects of FOXD3-AS1 silencing on the same parameters in AC16 cells. In conclusion, FOXD3-AS1 knockdown protected AC16 cardiomyocytes from hypoxia-induced injury by increasing cell survival and inhibiting apoptosis through upregulating miR-150-5p.
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Affiliation(s)
- Jiayong Zheng
- Department of Children's Heart Center, Henan Province People's Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Bangtian Peng
- Department of Children's Heart Center, Henan Province People's Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Yanwei Zhang
- Department of Children's Heart Center, Henan Province People's Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Feng Ai
- Department of Children's Heart Center, Henan Province People's Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Xiaosong Hu
- Department of Children's Heart Center, Henan Province People's Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
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29
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Ma J, Chen S, Hao L, Sheng W, Chen W, Ma X, Zhang B, Ma D, Huang G. Long non-coding RNA SAP30-2:1 is downregulated in congenital heart disease and regulates cell proliferation by targeting HAND2. Front Med 2020; 15:91-100. [PMID: 32820380 DOI: 10.1007/s11684-020-0778-5] [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] [Received: 08/31/2019] [Accepted: 03/14/2020] [Indexed: 12/25/2022]
Abstract
Congenital heart disease (CHD) is the most common birth defect worldwide. Long non-coding RNAs (lncRNAs) have been implicated in many diseases. However, their involvement in CHD is not well understood. This study aimed to investigate the role of dysregulated lncRNAs in CHD. We used Gene Expression Omnibus data mining, bioinformatics analysis, and analysis of clinical tissue samples and observed that the novel lncRNA SAP30-2:1 with unknown function was significantly downregulated in damaged cardiac tissues from patients with CHD. Knockdown of lncRNA SAP30-2:1 inhibited the proliferation of human embryonic kidney and AC16 cells and decreased the expression of heart and neural crest derivatives expressed 2 (HAND2). Moreover, lncRNA SAP30-2:1 was associated with HAND2 by RNA immunoprecipitation. Overall, these results suggest that lncRNA SAP30-2:1 may be involved in heart development through affecting cell proliferation via targeting HAND2 and may thus represent a novel therapeutic target for CHD.
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Affiliation(s)
- Jing Ma
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.,Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Shiyu Chen
- Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Lili Hao
- Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wei Sheng
- Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Weicheng Chen
- Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Bowen Zhang
- Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Duan Ma
- Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China. .,Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai, 201102, China.
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30
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Liu Y, Zhang H, Li Y, Yan L, Du W, Wang S, Zheng X, Zhang M, Zhang J, Qi J, Sun H, Zhang L, Li G, Zhu D. Long Noncoding RNA Rps4l Mediates the Proliferation of Hypoxic Pulmonary Artery Smooth Muscle Cells. Hypertension 2020; 76:1124-1133. [PMID: 32772647 DOI: 10.1161/hypertensionaha.120.14644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Pulmonary hypertension (PH) is a rare and fatal disorder involving the vascular remodeling of pulmonary arteries mediated by the enhanced proliferation of pulmonary artery smooth muscle cells (PASMCs). Long noncoding RNAs are a subclass of regulatory molecules with diverse cellular functions, but their role in PH remains largely unexplored. We aimed to identify and determine the functions of long noncoding RNAs involved in hypoxia-induced PH and PASMC proliferation. RNA sequencing in a hypoxic mouse model identified hypoxia-regulated long noncoding RNAs, including Rps4l. Rps4l expression was significantly reduced in PH-model mice and hypoxic PASMCs. The subcellular localization of Rps4l was detected by RNA fluorescence in situ hybridization and quantification of nuclear/cytoplasmic RNA. Rps4l overexpression rescued pulmonary arterial hypertension features, as demonstrated by right ventricle hypertrophy, right ventricular systolic pressure, hemodynamics, cardiac function, and vascular remodeling. At the cellular level, Rps4l overexpression weakened cell viability and proliferation and suppressed cell cycle progression. Potential Rps4l-binding proteins were identified via RNA pull-down followed by mass spectrometry, RNA immunoprecipitation, and microscale thermophoresis. These results indicated that Rps4l is associated with and affects the stabilization of ILF3 (interleukin enhancer-binding factor 3). Rps41 further regulates the levels of HIF-1α and consequently leads to hypoxia-induced PASMC proliferation and migration. Our results showed that in hypoxic PASMCs, Rps4l expression decreases due to regulation by hypoxia. This decrease affects the proliferation, migration, and cell cycle progression of PASMCs through ILF3/HIF-1α. These results provide a theoretical basis for further investigations into the pathological mechanism of hypoxic PH and may provide insight for the development of novel treatments.
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Affiliation(s)
- Ying Liu
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Hongyue Zhang
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Yiying Li
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Lixin Yan
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Wei Du
- College of Pharmacy, Harbin University of Commerce, Heilongjiang Province, China (W.D., S.W., D.Z.)
| | - Siqi Wang
- College of Pharmacy, Harbin University of Commerce, Heilongjiang Province, China (W.D., S.W., D.Z.)
| | - Xiaodong Zheng
- Department of Pathophysiology, College of Basic Medicine, Harbin Medical University, Daqing, China (X.Z.)
| | - Min Zhang
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Junting Zhang
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Jing Qi
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Hanliang Sun
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), P.R. China (L.Z.)
| | - Guangqun Li
- College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, Heilongjiang Province, China (G.L.)
| | - Daling Zhu
- From the Biopharmaceutical Key Laboratory of Heilongjiang Province, College of Pharmacy, Harbin Medical University, P.R. China (Y. Liu, H.Z., Y. Li, L. Yan, M.Z., J.Z., J.Q., H.S., D.Z.)
- College of Pharmacy, Harbin University of Commerce, Heilongjiang Province, China (W.D., S.W., D.Z.)
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31
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Murad MW, Khan MA, Islam MS, Islam ABMMK. A switch in bidirectional histone mark leads to differential modulation of lincRNAs involved in neuronal and hematopoietic cell differentiation from their progenitors. J Cell Biochem 2020; 121:3451-3462. [DOI: 10.1002/jcb.29619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Md. Wahid Murad
- Department of Genetic Engineering and BiotechnologyUniversity of Dhaka Dhaka Bangladesh
| | | | - Md. Sajedul Islam
- Department of Genetic Engineering and BiotechnologyUniversity of Dhaka Dhaka Bangladesh
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32
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Ahmadi S, Zobeiri M, Bradburn S. Molecular mechanisms underlying actions of certain long noncoding RNAs in Alzheimer's disease. Metab Brain Dis 2020; 35:681-693. [PMID: 32185592 DOI: 10.1007/s11011-020-00564-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/05/2020] [Indexed: 01/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a group of non-protein coding RNAs that have more than 200 nucleotides. LncRNAs play an important role in the regulation of protein-coding genes at the transcriptional and post-transcriptional levels. They are found in most organs, with a high prevalence in the central nervous system. Accumulating data suggests that lncRNAs are involved in various neurodegenerative disorders, including the onset and progression of Alzheimer's disease (AD). Recent insights suggest lncRNAs, such as BACE1-AS, 51A, 17A, NDM29 and AS-UCHL1, are dysregulated in AD tissues. Furthermore, there are ongoing efforts to explore the clinical usability of lncRNAs as biomarkers in the disease. In this review, we explore the mechanisms by which aberrant expressions of the most studied lncRNAs contribute to the neuropathologies associated with AD, including amyloid β plaques and neurofibrillary tangles. Understanding the molecular mechanisms of lncRNAs in patients with AD will reveal novel diagnosis strategies and more effective therapeutic targets.
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Affiliation(s)
- Shamseddin Ahmadi
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran.
| | - Mohammad Zobeiri
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Steven Bradburn
- Bioscience Research Centre, Manchester Metropolitan University, Manchester, UK
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Ma J, Chen S, Hao L, Sheng W, Chen W, Ma X, Zhang B, Ma D, Huang G. Hypermethylation-mediated down-regulation of lncRNA TBX5-AS1:2 in Tetralogy of Fallot inhibits cell proliferation by reducing TBX5 expression. J Cell Mol Med 2020; 24:6472-6484. [PMID: 32368852 PMCID: PMC7294119 DOI: 10.1111/jcmm.15298] [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: 05/29/2019] [Revised: 11/06/2019] [Accepted: 03/28/2020] [Indexed: 12/26/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common complex congenital heart disease (CHD) with uncertain cause. Although long non‐coding RNAs (lncRNAs) have been implicated in heart development and several CHDs, their role in TOF is not well understood. This study aimed to investigate how dysregulated lncRNAs contribute to TOF. Using Gene Expression Omnibus data mining, bioinformatics analysis and clinical heart tissue sample detecting, we identified a novel antisense lncRNA TBX5‐AS1:2 with unknown function that was significantly down‐regulated in injured cardiac tissues from TOF patients. LncRNA TBX5‐AS1:2 was mainly located in the nucleus of the human embryonic kidney 293 (HEK293T) cells and formed an RNA‐RNA double‐stranded structure in the overlapping region with its sense mRNA T‐box transcription factor 5 (TBX5), which is an important regulator in heart development. Knock‐down of lncRNA TBX5‐AS1:2 via promoter hypermethylation reduced TBX5 expression at both the mRNA and protein levels by affecting its mRNA stability through RNA‐RNA interaction. Moreover, lncRNA TBX5‐AS1:2 knock‐down inhibited the proliferation of HEK293T cells. In conclusion, these results indicated that lncRNA TBX5‐AS1:2 may be involved in TOF by affecting cell proliferation by targeting TBX5.
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Affiliation(s)
- Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital, Fudan University, Shanghai, China.,Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shiyu Chen
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lili Hao
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Sheng
- Children's Hospital of Fudan University, Shanghai, China
| | - WeiCheng Chen
- Children's Hospital of Fudan University, Shanghai, China
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai, China
| | - Bowen Zhang
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai, China
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Comprehensive Overview of Non-coding RNAs in Cardiac Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:197-211. [PMID: 32285413 DOI: 10.1007/978-981-15-1671-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cardiac development in the human embryo is characterized by the interactions of several transcription and growth factors leading the heart from a primordial linear tube into a synchronous contractile four-chamber organ. Studies on cardiogenesis showed that cell proliferation, differentiation, fate specification and morphogenesis are spatiotemporally coordinated by cell-cell interactions and intracellular signalling cross-talks. In recent years, research has focused on a class of inter- and intra-cellular modulators called non-coding RNAs (ncRNAs), transcribed from the noncoding portion of the DNA and involved in the proper formation of the heart. In this chapter, we will summarize the current state of the art on the roles of three major forms of ncRNAs [microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs)] in orchestrating the four sequential phases of cardiac organogenesis.
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Pereira IT, Spangenberg L, Cabrera G, Dallagiovanna B. Polysome-associated lncRNAs during cardiomyogenesis of hESCs. Mol Cell Biochem 2020; 468:35-45. [PMID: 32125578 DOI: 10.1007/s11010-020-03709-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.
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Affiliation(s)
- Isabela Tiemy Pereira
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Guillermo Cabrera
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Bruno Dallagiovanna
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil.
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Yang H, He X, Wang C, Zhang L, Yu J, Wang K. Knockdown of TUG 1 suppresses hypoxia-induced apoptosis of cardiomyocytes by up-regulating miR-133a. Arch Biochem Biophys 2020; 681:108262. [DOI: 10.1016/j.abb.2020.108262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/01/2020] [Accepted: 01/07/2020] [Indexed: 01/23/2023]
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Peters MM, Sampaio-Pinto V, da Costa Martins PA. Non-coding RNAs in endothelial cell signalling and hypoxia during cardiac regeneration. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118515. [DOI: 10.1016/j.bbamcr.2019.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/19/2019] [Accepted: 07/18/2019] [Indexed: 01/08/2023]
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Congenital heart diseases: genetics, non-inherited risk factors, and signaling pathways. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-0050-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
Congenital heart diseases (CHDs) are the most common congenital anomalies with an estimated prevalence of 8 in 1000 live births. CHDs occur as a result of abnormal embryogenesis of the heart. Congenital heart diseases are associated with significant mortality and morbidity. The damage of the heart is irreversible due to a lack of regeneration potential, and usually, the patients may require surgical intervention. Studying the developmental biology of the heart is essential not only in understanding the mechanisms and pathogenesis of congenital heart diseases but also in providing us with insight towards developing new preventive and treatment methods.
Main body
The etiology of congenital heart diseases is still elusive. Both genetic and environmental factors have been implicated to play a role in the pathogenesis of the diseases. Recently, cardiac transcription factors, cardiac-specific genes, and signaling pathways, which are responsible for early cardiac morphogenesis have been extensively studied in both human and animal experiments but leave much to be desired. The discovery of novel genetic methods such as next generation sequencing and chromosomal microarrays have led to further study the genes, non-coding RNAs and subtle chromosomal changes, elucidating their implications to the etiology of congenital heart diseases. Studies have also implicated non-hereditary risk factors such as rubella infection, teratogens, maternal age, diabetes mellitus, and abnormal hemodynamics in causing CHDs.
These etiological factors raise questions on multifactorial etiology of CHDs. It is therefore important to endeavor in research based on finding the causes of CHDs. Finding causative factors will enable us to plan intervention strategies and mitigate the consequences associated with CHDs. This review, therefore, puts forward the genetic and non-genetic causes of congenital heart diseases. Besides, it discusses crucial signaling pathways which are involved in early cardiac morphogenesis. Consequently, we aim to consolidate our knowledge on multifactorial causes of CHDs so as to pave a way for further research regarding CHDs.
Conclusion
The multifactorial etiology of congenital heart diseases gives us a challenge to explicitly establishing specific causative factors and therefore plan intervention strategies. More well-designed studies and the use of novel genetic technologies could be the way through the discovery of etiological factors implicated in the pathogenesis of congenital heart diseases.
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Lv Y, Liu Z, Huang J, Yu J, Dong Y, Wang J. LncRNA nuclear-enriched abundant transcript 1 regulates hypoxia-evoked apoptosis and autophagy via mediation of microRNA-181b. Mol Cell Biochem 2019; 464:193-203. [PMID: 31853799 DOI: 10.1007/s11010-019-03660-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/16/2019] [Indexed: 12/22/2022]
Abstract
Nuclear-enriched abundant transcript 1 (NEAT1), a vital long noncoding RNA (lncRNA), exhibits the functions in disparate cancers. Nevertheless, the influences of NEAT1 in congenital heart disease (CHD) remain unreported. The research delves into whether NEAT1 affects H9c2 cells apoptosis and autophagy under the hypoxia condition. Overexpressed NEAT1 vector was transfected into H9c2 cells; then, functions of NEAT1 in cell viability, apoptosis, autophagy, PI3K/AKT/mTOR and JAK1/STAT3 pathways were detected in H9c2 cells under hypoxia condition. Expression of NEAT1 and miR-181b in hypoxia and blood samples from CHD was evaluated. After miR-181b inhibitor transfection, functions of miR-181b repression in the above-mentioned cell behavior and PI3K/AKT/mTOR and JAK1/STAT3 pathways were reassessed. Overexpressed NEAT1 clearly allayed hypoxia-triggered H9c2 cells apoptosis and autophagy. The decreased NEAT1 and miR-181b were showcased in hypoxia and blood samples from CHD; meanwhile, elevated miR-181b evoked by overexpressed NEAT1 was observed in hypoxia-managed H9c2 cells. More importantly, miR-181b inhibition obviously overturned the influences of NEAT1 in hypoxia-affected H9c2 cells apoptosis and autophagy. Besides, overexpressed NEAT1 facilitated PI3K/AKT/mTOR and JAK1/STAT3 activations via enhancing miR-181b. The research exposed that NEAT1 eased hypoxia-triggered H9c2 cells apoptosis and autophagy by expediting PI3K/AKT/mTOR and JAK1/STAT3 pathways via elevating miR-181b.
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Affiliation(s)
- Ying Lv
- Department of Cardiovascular Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Road, Shijiazhuang, 050031, Hebei, China
| | - Zhaoming Liu
- Department of Pediatric Surgery, Shijiazhuang Maternity & Child Healthcare Hospital, No. 9 Jianguo Road, Shijiazhuang, 050051, Hebei, China
| | - Jiancheng Huang
- Department of Cardiovascular Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Road, Shijiazhuang, 050031, Hebei, China
| | - Jie Yu
- Department of Cardiovascular Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Road, Shijiazhuang, 050031, Hebei, China
| | - Yanbo Dong
- Department of Cardiovascular Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Road, Shijiazhuang, 050031, Hebei, China
| | - Jun Wang
- Department of Cardiovascular Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Road, Shijiazhuang, 050031, Hebei, China.
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40
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Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 2019; 21:102-117. [DOI: 10.1038/s41576-019-0184-5] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/14/2022]
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41
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Xue M, Shi D, Xu G, Wang W. The long noncoding RNA linc00858 promotes progress of lung cancer through miR-3182/MMP2 axis. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2091-2097. [PMID: 31131637 DOI: 10.1080/21691401.2019.1617728] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In previous studies, numerous dysregulated lncRNAs were identified using RNA-sequencing. Lung cancer is the most common malignant tumour worldwide and the second leading cause in cancer. The aim of this study is to investigate the function and mechanism of lincRNA00858 in the lung cancer. RT-PCR was used to detect the expression of lincRNA00858. Proliferation, invasion, and epithelial-mesenchymal transition (EMT) were examined by CCK8, transwell assay and western blot to evaluate the function of linc00858. Dual-luciferase reporter assay was used to identified the potential target of linc00858. Over-expression of linc00858 significantly promoted cell proliferation, invasion. We also found that linc00858 facilitated the EMT process. Dual-luciferase reporter assay revealed that linc00858 can bind with miR-3182 directly. Linc00858 can negatively regulate the expression of miR-3182. Further experiments demonstrated that MMP2 was the direct target of miR-3182. Rescue experiments revealed that linc00858 functioned through miR-3182/MMP2 axis. Taken together, we verified the role of an unknown linc00858 in lung cancer and provided its mechanism. Mechanistically, linc00858 acted as a competitive endogenous RNA to sponged miR-3182 and regulate MMP2 in lung cancer. Our study provided new clues for understanding the mechanism of lung cancer.
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Affiliation(s)
- Mingqiang Xue
- a Henan Provincial Chest Hospital , Zhengzhou , PR China
| | - Dongfeng Shi
- a Henan Provincial Chest Hospital , Zhengzhou , PR China
| | - Guanghui Xu
- b Department of Thoracic Oncology, Henan Provincial Chest Hospital , Zhengzhou , PR China
| | - Wenguang Wang
- b Department of Thoracic Oncology, Henan Provincial Chest Hospital , Zhengzhou , PR China
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42
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Ritter N, Ali T, Kopitchinski N, Schuster P, Beisaw A, Hendrix DA, Schulz MH, Müller-McNicoll M, Dimmeler S, Grote P. The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development. Dev Cell 2019; 50:644-657.e8. [PMID: 31422919 DOI: 10.1016/j.devcel.2019.07.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 05/10/2019] [Accepted: 07/10/2019] [Indexed: 11/29/2022]
Abstract
Precisely controlled gene regulatory networks are required during embryonic development to give rise to various structures, including those of the cardiovascular system. Long non-coding RNA (lncRNA) loci are known to be important regulators of these genetic programs. We have identified a novel and essential lncRNA locus Handsdown (Hdn), active in early heart cells, and show by genetic inactivation that it is essential for murine development. Hdn displays haploinsufficiency for cardiac development as Hdn-heterozygous adult mice exhibit hyperplasia in the right ventricular wall. Transcriptional activity of the Hdn locus, independent of its RNA, suppresses its neighboring gene Hand2. We reveal a switch in a topologically associated domain in differentiation of the cardiac lineage, allowing the Hdn locus to directly interact with regulatory elements of the Hand2 locus.
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Affiliation(s)
- Nicole Ritter
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Tamer Ali
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Faculty of Science, Benha University, Benha 13518, Egypt
| | - Nina Kopitchinski
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Peggy Schuster
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Arica Beisaw
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Marcel H Schulz
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; German Center for Cardiovascular Regeneration (DZHK), Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Institute of Cell Biology and Neuroscience, Goethe University, Max-von-Laue-Strasse 13, 60438 Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; German Center for Cardiovascular Regeneration (DZHK), Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
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43
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Ward MC, Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. eLife 2019; 8:42374. [PMID: 30958265 PMCID: PMC6538380 DOI: 10.7554/elife.42374] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/07/2019] [Indexed: 12/23/2022] Open
Abstract
Despite anatomical similarities, there are differences in susceptibility to cardiovascular disease (CVD) between primates; humans are prone to myocardial ischemia, while chimpanzees are prone to myocardial fibrosis. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) allow for direct inter-species comparisons of the gene regulatory response to CVD-relevant perturbations such as oxygen deprivation, a consequence of ischemia. To gain insight into the evolution of disease susceptibility, we characterized gene expression levels in iPSC-CMs in humans and chimpanzees, before and after hypoxia and re-oxygenation. The transcriptional response to hypoxia is generally conserved across species, yet we were able to identify hundreds of species-specific regulatory responses including in genes previously associated with CVD. The 1,920 genes that respond to hypoxia in both species are enriched for loss-of-function intolerant genes; but are depleted for expression quantitative trait loci and cardiovascular-related genes. Our results indicate that response to hypoxic stress is highly conserved in humans and chimpanzees.
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Affiliation(s)
- Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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Cardoso C, Serafim RB, Kawakami A, Gonçalves Pereira C, Vazquez VL, Valente V, Fisher DE, Espreafico EM. The lncRNA RMEL3 protects immortalized cells from serum withdrawal-induced growth arrest and promotes melanoma cell proliferation and tumor growth. Pigment Cell Melanoma Res 2019; 32:303-314. [PMID: 30457212 PMCID: PMC6613776 DOI: 10.1111/pcmr.12751] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022]
Abstract
RMEL3 is a recently identified lncRNA associated with BRAFV600E mutation and melanoma cell survival. Here, we demonstrate strong and moderate RMEL3 upregulation in BRAF and NRAS mutant melanoma cells, respectively, compared to melanocytes. High expression is also more frequent in cutaneous than in acral/mucosal melanomas, and analysis of an ICGC melanoma dataset showed that mutations in RMEL3 locus are preponderantly C > T substitutions at dipyrimidine sites including CC > TT, typical of UV signature. RMEL3 mutation does not correlate with RMEL3 levels, but does with poor patient survival, in TCGA melanoma dataset. Accordingly, RMEL3 lncRNA levels were significantly reduced in BRAFV600E melanoma cells upon treatment with BRAF or MEK inhibitors, supporting the notion that BRAF-MEK-ERK pathway plays a role to activate RMEL3 gene transcription. RMEL3 overexpression, in immortalized fibroblasts and melanoma cells, increased proliferation and survival under serum starvation, clonogenic ability, and xenografted melanoma tumor growth. Although future studies will be needed to elucidate the mechanistic activities of RMEL3, our data demonstrate that its overexpression bypasses the need of mitogen activation to sustain proliferation/survival of non-transformed cells and suggest an oncogenic role for RMEL3.
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Affiliation(s)
- Cibele Cardoso
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rodolfo B. Serafim
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristiano Gonçalves Pereira
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Vinicius L. Vazquez
- Molecular Oncology Research Center (CPOM) and Melanoma/sarcoma Surgery Department, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Valeria Valente
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, SP, 14800-903, Brazil; Center for Cell-Based Therapy CEPID/FAPESP, Ribeirão Preto, Brazil
| | - David E. Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Enilza M. Espreafico
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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45
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Barman P, Reddy D, Bhaumik SR. Mechanisms of Antisense Transcription Initiation with Implications in Gene Expression, Genomic Integrity and Disease Pathogenesis. Noncoding RNA 2019; 5:ncrna5010011. [PMID: 30669611 PMCID: PMC6468509 DOI: 10.3390/ncrna5010011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/01/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Non-coding antisense transcripts arise from the strand opposite the sense strand. Over 70% of the human genome generates non-coding antisense transcripts while less than 2% of the genome codes for proteins. Antisense transcripts and/or the act of antisense transcription regulate gene expression and genome integrity by interfering with sense transcription and modulating histone modifications or DNA methylation. Hence, they have significant pathological and physiological relevance. Indeed, antisense transcripts were found to be associated with various diseases including cancer, diabetes, cardiac and neurodegenerative disorders, and, thus, have promising potentials for prognostic and diagnostic markers and therapeutic development. However, it is not clearly understood how antisense transcription is initiated and epigenetically regulated. Such knowledge would provide new insights into the regulation of antisense transcription, and hence disease pathogenesis with therapeutic development. The recent studies on antisense transcription initiation and its epigenetic regulation, which are limited, are discussed here. Furthermore, we concisely describe how antisense transcription/transcripts regulate gene expression and genome integrity with implications in disease pathogenesis and therapeutic development.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Divya Reddy
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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46
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Ma C, Luo H, Liu B, Li F, Tschöpe C, Fa X. Long noncoding RNAs: A new player in the prevention and treatment of diabetic cardiomyopathy? Diabetes Metab Res Rev 2018; 34:e3056. [PMID: 30160026 DOI: 10.1002/dmrr.3056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/12/2018] [Accepted: 08/01/2018] [Indexed: 12/20/2022]
Abstract
Diabetic cardiomyopathy (DCM) can cause extensive necrosis of the heart muscle by metabolic disorders and microangiopathy, with subclinical cardiac dysfunction, and eventually progress to heart failure, arrhythmia, and cardiogenic shock; severe patients may even die suddenly. Long noncoding RNAs (lncRNAs) are a class of nonprotein-coding RNAs longer than 200 nucleotides. They have critical roles in various biological processes, including gene expression regulation, genomic imprinting, nuclear-cytoplasmic trafficking, RNA splicing, and translational control. Recent studies indicated that lncRNAs extensively participate in the development of diverse cardiac diseases, such as cardiac ischaemia, hypertrophy, and heart failure. Little is known about lncRNA in DCM. In this review, we summarize the current literature on lncRNAs in DCM studies, aiming to provide new methods for DCM's future prevention and treatment strategies.
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Affiliation(s)
- Chao Ma
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Cardiology, Campus Virchow, Charité-Universitätsmedizin Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Huan Luo
- Department of Ophthalmology, Campus Virchow, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bing Liu
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Li
- Department of Thoracic Surgery, Campus Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Tschöpe
- Department of Cardiology, Campus Virchow, Charité-Universitätsmedizin Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Xianen Fa
- Department of Cardiovascular Surgery, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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47
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Long non-coding RNA CCRR controls cardiac conduction via regulating intercellular coupling. Nat Commun 2018; 9:4176. [PMID: 30301979 PMCID: PMC6177441 DOI: 10.1038/s41467-018-06637-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 09/10/2018] [Indexed: 12/31/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as a new class of gene expression regulators playing key roles in many biological and pathophysiological processes. Here, we identify cardiac conduction regulatory RNA (CCRR) as an antiarrhythmic lncRNA. CCRR is downregulated in a mouse model of heart failure (HF) and in patients with HF, and this downregulation slows cardiac conduction and enhances arrhythmogenicity. Moreover, CCRR silencing induces arrhythmias in healthy mice. CCRR overexpression eliminates these detrimental alterations. HF or CCRR knockdown causes destruction of intercalated discs and gap junctions to slow longitudinal cardiac conduction. CCRR overexpression improves cardiac conduction by blocking endocytic trafficking of connexin43 (Cx43) to prevent its degradation via binding to Cx43-interacting protein CIP85, whereas CCRR silence does the opposite. We identified the functional domain of CCRR, which can reproduce the functional roles and pertinent molecular events of full-length CCRR. Our study suggests CCRR replacement a potential therapeutic approach for pathological arrhythmias.
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Shen C, Kong B, Liu Y, Xiong L, Shuai W, Wang G, Quan D, Huang H. YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiotensin II-induced atrial fibrillation by modulating miR-384b/CACNA1C axis. Biochem Biophys Res Commun 2018; 505:134-140. [DOI: 10.1016/j.bbrc.2018.09.064] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/10/2018] [Indexed: 12/16/2022]
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Biró O, Rigó J, Nagy B. Noninvasive prenatal testing for congenital heart disease - cell-free nucleic acid and protein biomarkers in maternal blood. J Matern Fetal Neonatal Med 2018; 33:1044-1050. [PMID: 30078353 DOI: 10.1080/14767058.2018.1508437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Context: Congenital heart disease (CHD) is the most common fetal malformation. Prenatal ultrasonography is routinely applied for the screening of CHD but many factors influence its diagnostic accuracy. The introduction of new biomarkers could facilitate the identification of high-risk pregnancies.Objective: In our review, our aim was to collect expression studies of cell-free nucleic acids and proteins in maternal circulation. Syndromic CHDs which can be detected by noninvasive prenatal testing (NIPT) techniques were also discussed.Methods: PubMed and Web of Science databases were screened for studies where the levels of potential CHD biomarkers were measured in maternal blood samples. Available NIPT tests were collected from the providers' resources.Results: There are nine CHD-associated chromosomal abnormalities, five aneuploidies, and four microdeletions, which are included in NIPT panels. We found eight articles from which five included the analysis of specific cell-free RNA expression and three measurements of protein levels.Conclusions: Most of the common heart-related chromosomal aberrations can be diagnosed by NIPT. Specific cell-free RNAs and circulating proteins seem to be potential biomarkers for fetal CHDs. The application of these new biomarkers could improve the detection rate at early pregnancy, making it possible to provide optimal perinatal and perioperative management.
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Affiliation(s)
- Orsolya Biró
- First Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - János Rigó
- First Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Bálint Nagy
- Department of Human Genetics, University of Debrecen, Debrecen, Hungary
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Biró O, Hajas O, Nagy-Baló E, Soltész B, Csanádi Z, Nagy B. Relationship between cardiovascular diseases and circulating cell-free nucleic acids in human plasma. Biomark Med 2018; 12:891-905. [DOI: 10.2217/bmm-2017-0386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the main cause of human morbidity and mortality worldwide. Early diagnosis could improve the efficiency of treatments. New biomarkers are needed for the identification of high-risk populations in order to make accurate diagnosis and therapy monitoring. Circulating cell-free nucleic acids (cf-NAs) offer a promising new noninvasive tool. These have a role in the regulation of normal physiological functions and in the development of pathological alterations. There is extended research on the clinical application and utilization of cell-free genomic DNA, mtDNA, mRNA, miRNA and long noncoding RNA in CVDs. These molecules could serve as components of new generation therapeutics. Our review focuses on the role of cf-NAs in the pathogenesis of CVDs and we are discussing also possible diagnostic applications and therapeutic implications.
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Affiliation(s)
- Orsolya Biró
- Department of Obstetrics & Gynecology, Semmelweis University, Budapest, Hungary
| | - Orsolya Hajas
- Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Edina Nagy-Baló
- Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltán Csanádi
- Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bálint Nagy
- Department of Obstetrics & Gynecology, Semmelweis University, Budapest, Hungary
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