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Yang Y, Hou X, Wang C, Chen Q, Lu Y, Yu D, Wu K. The roles of non-coding RNAs in Hirschsprung's disease. Noncoding RNA Res 2024; 9:704-714. [PMID: 38577013 PMCID: PMC10990754 DOI: 10.1016/j.ncrna.2024.02.015] [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: 10/15/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 04/06/2024] Open
Abstract
Hirschsprung's disease (HSCR) is a congenital disorder characterized by the absence of ganglion cells in the colon, leading to various intestinal complications. The etiology of HSCR stems from complex genetic and environmental interactions, of which the intricate roles of non-coding RNAs (ncRNAs) are a key area of research. However, the roles of ncRNAs in the pathogenesis of HSCR have not been fully elucidated. In order to understand the variety of symptoms caused by HSCR and develop new therapeutic approaches, it is essential to understand the underlying biological genetic basis of HSCR. This review presents a comprehensive overview of the current understanding regarding the involvement of ncRNAs in HSCR, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, it provides a summary of the molecular mechanisms through which ncRNAs regulate the expression of genes related to the proliferation, migration, and differentiation of intestinal neural crest cells, thereby contributing to the advancement of HSCR research.
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Affiliation(s)
| | | | - Chen Wang
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Qinming Chen
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Yi Lu
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Daiyue Yu
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Kai Wu
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
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Chen J, Liu K, Vadas MA, Gamble JR, McCaughan GW. The Role of the MiR-181 Family in Hepatocellular Carcinoma. Cells 2024; 13:1289. [PMID: 39120319 PMCID: PMC11311592 DOI: 10.3390/cells13151289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth-leading cause of cancer-related death worldwide. Due to the high mortality rate in HCC patients, discovering and developing novel systemic treatment options for HCC is a vital unmet medical need. Among the numerous molecular alterations in HCCs, microRNAs (miRNAs) have been increasingly recognised to play critical roles in hepatocarcinogenesis. We and others have recently revealed that members of the microRNA-181 (miR-181) family were up-regulated in some, though not all, human cirrhotic and HCC tissues-this up-regulation induced epithelial-mesenchymal transition (EMT) in hepatocytes and tumour cells, promoting HCC progression. MiR-181s play crucial roles in governing the fate and function of various cells, such as endothelial cells, immune cells, and tumour cells. Previous reviews have extensively covered these aspects in detail. This review aims to give some insights into miR-181s, their targets and roles in modulating signal transduction pathways, factors regulating miR-181 expression and function, and their roles in HCC.
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Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Ken Liu
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| | - Mathew A. Vadas
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Jennifer R. Gamble
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Geoffrey W. McCaughan
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
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3
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Lucena-Padros H, Bravo-Gil N, Tous C, Rojano E, Seoane-Zonjic P, Fernández RM, Ranea JAG, Antiñolo G, Borrego S. Bioinformatics Prediction for Network-Based Integrative Multi-Omics Expression Data Analysis in Hirschsprung Disease. Biomolecules 2024; 14:164. [PMID: 38397401 PMCID: PMC10886964 DOI: 10.3390/biom14020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Hirschsprung's disease (HSCR) is a rare developmental disorder in which enteric ganglia are missing along a portion of the intestine. HSCR has a complex inheritance, with RET as the major disease-causing gene. However, the pathogenesis of HSCR is still not completely understood. Therefore, we applied a computational approach based on multi-omics network characterization and clustering analysis for HSCR-related gene/miRNA identification and biomarker discovery. Protein-protein interaction (PPI) and miRNA-target interaction (MTI) networks were analyzed by DPClusO and BiClusO, respectively, and finally, the biomarker potential of miRNAs was computationally screened by miRNA-BD. In this study, a total of 55 significant gene-disease modules were identified, allowing us to propose 178 new HSCR candidate genes and two biological pathways. Moreover, we identified 12 key miRNAs with biomarker potential among 137 predicted HSCR-associated miRNAs. Functional analysis of new candidates showed that enrichment terms related to gene ontology (GO) and pathways were associated with HSCR. In conclusion, this approach has allowed us to decipher new clues of the etiopathogenesis of HSCR, although molecular experiments are further needed for clinical validations.
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Affiliation(s)
- Helena Lucena-Padros
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Cristina Tous
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
| | - Pedro Seoane-Zonjic
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 29071 Malaga, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Juan A. G. Ranea
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 29071 Malaga, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
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Pai C, Sengupta R, Heuckeroth RO. Sequencing Reveals miRNAs Enriched in the Developing Mouse Enteric Nervous System. Noncoding RNA 2023; 10:1. [PMID: 38250801 PMCID: PMC10801555 DOI: 10.3390/ncrna10010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/01/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024] Open
Abstract
The enteric nervous system (ENS) is an essential network of neurons and glia in the bowel wall. Defects in ENS development can result in Hirschsprung disease (HSCR), a life-threatening condition characterized by severe constipation, abdominal distention, bilious vomiting, and failure to thrive. A growing body of literature connects HSCR to alterations in miRNA expression, but there are limited data on the normal miRNA landscape in the developing ENS. We sequenced small RNAs (smRNA-seq) and messenger RNAs (mRNA-seq) from ENS precursor cells of mid-gestation Ednrb-EGFP mice and compared them to aggregated RNA from all other cells in the developing bowel. Our smRNA-seq results identified 73 miRNAs that were significantly enriched and highly expressed in the developing ENS, with miR-9, miR-27b, miR-124, miR-137, and miR-488 as our top 5 miRNAs that are conserved in humans. However, contrary to prior reports, our follow-up analyses of miR-137 showed that loss of Mir137 in Nestin-cre, Wnt1-cre, Sox10-cre, or Baf53b-cre lineage cells had no effect on mouse survival or ENS development. Our data provide important context for future studies of miRNAs in HSCR and other ENS diseases and highlight open questions about facility-specific factors in development.
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Affiliation(s)
- Christopher Pai
- The Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA;
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajarshi Sengupta
- American Association for Cancer Research, Philadelphia, PA 19106, USA;
| | - Robert O. Heuckeroth
- The Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA;
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Overexpression of ST7-AS1 Enhances Apoptosis and Inhibits Proliferation of Papillary Thyroid Carcinoma Cells Via microRNA-181b-5p-Dependent Inhibition Tripartite Motif Containing 3. Mol Biotechnol 2023; 65:477-490. [PMID: 36030355 DOI: 10.1007/s12033-022-00536-7] [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: 03/22/2022] [Accepted: 07/19/2022] [Indexed: 10/15/2022]
Abstract
Long non-coding RNAs (lncRNAs) are of great significance in the pathogenesis and progression of papillary thyroid carcinoma (PTC). LncRNA tumorigenicity 7 antisense RNA 1 (ST7-AS1) is a newly identified lncRNA serving as an oncogene or tumor suppressor in different tumors; however, the role of ST7-AS1 in PTC remains completely unknown. In this study, ST7-AS1 was mainly distributed in the cytoplasm of PTC cells and presented reduced expression in THCA tumors and PTC cell lines. Functional experiments revealed that overexpressed ST7-AS1 inhibited the viability and proliferation of PTC cells, whereas accelerated the apoptosis of PTC cells. The expression of miR-181b-5p was upregulated and it bound with ST7-AS1 in PTC cells. Moreover, TRIM3 exhibited downregulated expression level in PTC cells and ST7-AS1 elevated TRIM3 expression via harboring miR-181b-5p. Rescue experiments illuminated that knockdown of TRIM3 reversed ST7-AS1 overexpression-induced promotion on PTC cell proliferation and suppression on PTC cell apoptosis. Overall, overexpression of ST7-AS1 enhances apoptosis and represses proliferation of PTC cells via targeting the miR-181b-5p/TRIM3 axis, which may help broaden the horizon and establish the foundation to develop therapeutic strategies for PTC in the future.
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Xu W, Yu H, Chen D, Pan W, Yang W, Miao J, Jia W, Zheng B, Liu Y, Chen X, Gao Y, Tian D. Identifying the potential transcriptional regulatory network in Hirschsprung disease by integrated analysis of microarray datasets. WORLD JOURNAL OF PEDIATRIC SURGERY 2023; 6:e000547. [PMID: 37082700 PMCID: PMC10111925 DOI: 10.1136/wjps-2022-000547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
Objective Hirschsprung disease (HSCR) is one of the common neurocristopathies in children, which is associated with at least 20 genes and involves a complex regulatory mechanism. Transcriptional regulatory network (TRN) has been commonly reported in regulating gene expression and enteric nervous system development but remains to be investigated in HSCR. This study aimed to identify the potential TRN implicated in the pathogenesis and diagnosis of HSCR. Methods Based on three microarray datasets from the Gene Expression Omnibus database, the multiMiR package was used to investigate the microRNA (miRNA)-target interactions, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we collected transcription factors (TFs) from the TransmiR database to construct the TF-miRNA-mRNA regulatory network and used cytoHubba to identify the key modules. Finally, the receiver operating characteristic (ROC) curve was determined and the integrated diagnostic models were established based on machine learning by the support vector machine method. Results We identified 58 hub differentially expressed microRNAs (DEMis) and 16 differentially expressed mRNAs (DEMs). The robust target genes of DEMis and DEMs mainly enriched in several GO/KEGG terms, including neurogenesis, cell-substrate adhesion, PI3K-Akt, Ras/mitogen-activated protein kinase and Rho/ROCK signaling. Moreover, 2 TFs (TP53 and TWIST1), 4 miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and 4 mRNAs (PIM3, CHUK, F2RL1, and CA1) were identified to construct the TF-miRNA-mRNA regulatory network. ROC analysis revealed a strong diagnostic value of the key TRN regulons (all area under the curve values were more than 0.8). Conclusion This study suggests a potential role of the TF-miRNA-mRNA network that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.
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Affiliation(s)
- Wenyao Xu
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Hui Yu
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Dian Chen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Peking University, Beijing, China
| | - Weikang Pan
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Weili Yang
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Jing Miao
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wanying Jia
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Baijun Zheng
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yong Liu
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Xinlin Chen
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Ya Gao
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Donghao Tian
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
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Fan M, Luo Y, Zhang B, Wang J, Chen T, Liu B, Sun Y, Nan Y, Hiscox JA, Zhao Q, Zhou EM. Cell Division Control Protein 42 Interacts With Hepatitis E Virus Capsid Protein and Participates in Hepatitis E Virus Infection. Front Microbiol 2021; 12:775083. [PMID: 34790187 PMCID: PMC8591454 DOI: 10.3389/fmicb.2021.775083] [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: 09/13/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022] Open
Abstract
Hepatitis E Virus (HEV) causes viral hepatitis in humans worldwide, while a subset of HEV species, avian HEV, causes hepatitis-splenomegaly syndrome in chickens. To date, there are few reports on the host proteins interacting with HEV and being involved in viral infection. Previous pull-down assay combining mass spectrometry indicated that cell division control protein 42 (CDC42), a member belonging to the Rho GTPase family, was pulled down by avian HEV capsid protein. We confirmed the direct interaction between CDC42 and avian and mammalian HEV capsid proteins. The interaction can increase the amount of active guanosine triphosphate binding CDC42 state (GTP-CDC42). Subsequently, we determined that the expression and activity of CDC42 were positively correlated with HEV infection in the host cells. Using the different inhibitors of CDC42 downstream signaling pathways, we found that CDC42-MRCK (a CDC42-binding kinase)-non-myosin IIA (NMIIA) pathway is involved in naked avian and mammalian HEV infection, CDC42-associated p21-activated kinase 1 (PAK1)-NMIIA/Cofilin pathway is involved in quasi-enveloped mammalian HEV infection and CDC42-neural Wiskott-Aldrich syndrome protein-actin-polymerizing protein Arp2/3 pathway (CDC42-(N-)WASP-Arp2/3) pathway participates in naked and quasi-enveloped mammalian HEV infection. Collectively, these results demonstrated for the first time that HEV capsid protein can directly bind to CDC42, and non- and quasi-enveloped HEV use different CDC42 downstream signaling pathways to participate in viral infection. The study provided some new insights to understand the life cycle of HEV in host cells and a new target of drug design for combating HEV infection.
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Affiliation(s)
- Mengnan Fan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yuhang Luo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Beibei Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jiaxi Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Tianxiang Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Baoyuan Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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Xia M, Duan LJ, Lu BN, Pang YZ, Pang ZR. LncRNA AFAP1-AS1/miR-27b-3p/VEGF-C axis modulates stemness characteristics in cervical cancer cells. Chin Med J (Engl) 2021; 134:2091-2101. [PMID: 34334630 PMCID: PMC8440026 DOI: 10.1097/cm9.0000000000001665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: Long non-coding RNA (lncRNA) actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) functions as a competing endogenous RNA to regulate target genes expression by sponging microRNAs (miRs) to play cancer-promoting roles in cancer stem cells. However, the regulatory mechanism of AFAP1-AS1 in cervical cancer (CC) stem cells is unknown. The present study aimed to provide a new therapeutic target for the clinical treatment of CC. Methods: Hyaluronic acid receptor cluster of differentiation 44 variant exon 6 (CD44v6)(+) CC cells were isolated by flow cytometry (FCM). Small interfering RNAs of AFAP1-AS1 (siAFAP1-AS1) were transfected into the (CD44v6)(+) cells. The levels of AFAP1-AS1 were measured by quantitative real-time PCR (qRT-PCR). Sphere formation assay, cell cycle analysis, and Western blotting were used to detect the effect of siAFAP1-AS1. RNA pull-down and luciferase reporter assay were used to verify the relationship between miR-27b-3p and AFAP1-AS1 or vascular endothelial growth factor (VEGF)-C. Results: CD44v6(+) CC cells had remarkable stemness and a high level of AFAP1-AS1. However, AFAP1-AS1 knockdown with siAFAP1-AS1 suppressed the cell cycle transition of G(1)/S phase and inhibited self-renewal of CD44v6(+) CC cells, the levels of the stemness markers octamer-binding transcription factor 4 (OCT4), osteopontin (OPN), and cluster of differentiation 133 (CD133), and the epithelial-mesenchymal transition (EMT)-related proteins Twist1, matrix metalloprotease (MMP)-9, and VEGF-C. In the mechanism study, miR-27b-3p/VEGF-C signaling was demonstrated to be a key downstream of AFAP1-AS1 in the CD44v6(+) CC cells. Conclusions: LncRNA AFAP1-AS1 knockdown inhibits the CC cell stemness by upregulating miR-27b-3p to suppress VEGF-C.
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Affiliation(s)
- Meng Xia
- School of Pharmacy, Minzu University of China, Beijing 100081, China Department of Orthopedics, Bayannaoer City Hospital, Bayannaoer, Inner Mongolia 015000, China Guangxi Zhuang Yao Medicine Center of Engineering and Technology, Guangxi University of Chinese Medicine, Nanning, Guangxi 530200, China Key Laboratory of Ethnomedicine of Ministry of Education, Minzu University of China, Beijing 100081, China
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Xiong F, Zhu K, Deng S, Huang H, Yang L, Gong Z, Shi L, He Y, Tang Y, Liao Q, Yu J, Li X, Li Y, Li G, Zeng Z, Xiong W, Zhang S, Guo C. AFAP1-AS1: a rising star among oncogenic long non-coding RNAs. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1602-1611. [PMID: 33999309 DOI: 10.1007/s11427-020-1874-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/13/2020] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) have become a hotspot in biomedical research. This interest reflects their extensive involvement in the regulation of the expression of other genes, and their influence on the occurrence and development of a variety of human diseases. Actin filament associated protein 1-Antisense RNA 1(AFAP1-AS1) is a recently discovered oncogenic lncRNA. It is highly expressed in a variety of solid tumors, and regulates the expression of downstream genes and signaling pathways through adsorption and competing microRNAs, or by the direct binding to other proteins. Ultimately, AFAP1-AS1 promotes proliferation, chemotherapy resistance, and resistance to apoptosis, maintains stemness, and enhances invasion and migration of tumor cells. This paper summarizes the research concerning AFAP1-AS1 in malignant tumors, including the clinical application prospects of AFAP1-AS1 as a potential molecular marker and therapeutic target of malignant tumors. We also discuss the limitations in the knowledge of AFAP1-AS1 and directions of further research. AFAP1-AS1 is expected to provide an example for studies of other lncRNA molecules.
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Affiliation(s)
- Fang Xiong
- Science and Technology on Information System Engineering Laboratory, National University of Defense Technology, Changsha, 410000, China
- Department of Periodontology, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, 410078, China
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education of China, Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Kunjie Zhu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Su Deng
- Science and Technology on Information System Engineering Laboratory, National University of Defense Technology, Changsha, 410000, China
| | - Hongbin Huang
- Science and Technology on Information System Engineering Laboratory, National University of Defense Technology, Changsha, 410000, China
| | - Liting Yang
- Department of Periodontology, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital Central South University, Changsha, 410011, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital Central South University, Changsha, 410011, China
| | - Yi He
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Jianjun Yu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education of China, Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Yong Li
- Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education of China, Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education of China, Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education of China, Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Shanshan Zhang
- Department of Periodontology, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, 410078, China.
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education of China, Cancer Research Institute, Central South University, Changsha, 410078, China.
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Bian Q, Chen J, Wu J, Ding F, Li X, Ma Q, Zhang L, Zou X, Chen J. Bioinformatics analysis of a TF-miRNA-lncRNA regulatory network in major depressive disorder. Psychiatry Res 2021; 299:113842. [PMID: 33751989 DOI: 10.1016/j.psychres.2021.113842] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/25/2021] [Indexed: 12/28/2022]
Abstract
Major depressive disorder (MDD) is a highly prevalent disease and one of the main causes of disability worldwide. Although many studies have partially revealed the occurrence and development process of MDD, the pathogeny and molecular mechanisms are not fully understood. Weighted gene coexpression network analysis (WGCNA) was used to explore the co-expression modules and hub genes in MDD. A protein-protein interaction (PPI) network of the most significant module and a TF-miRNA-lncRNA regulatory network of MDD were constructed using bioinformatics analysis tools. A KEGG pathway and gene ontology (GO) functional enrichment analysis of the genes in the significant module was performed using DAVID. Five hub genes in the PPI network and 10 genes in the TF-miRNA-lncRNA regulatory network with high degree values were identified, which may provide new insights for the investigation of key pathways, diagnostic bio-markers, and therapeutic targets of MDD. This study brings a novel perspective and provides valuable information to explore the molecular mechanism of MDD.
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Affiliation(s)
- Qinglai Bian
- School of Basic Medical Science, Hubei University of Chinese Medicine, Wuhan, China
| | - Jianbei Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jiajia Wu
- School of Basic Medical Science, Hubei University of Chinese Medicine, Wuhan, China
| | - Fengmin Ding
- School of Basic Medical Science, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiaojuan Li
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
| | - Qingyu Ma
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Xiaojuan Zou
- School of Basic Medical Science, Hubei University of Chinese Medicine, Wuhan, China
| | - Jiaxu Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
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11
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Villalba-Benito L, López-López D, Torroglosa A, Casimiro-Soriguer CS, Luzón-Toro B, Fernández RM, Moya-Jiménez MJ, Antiñolo G, Dopazo J, Borrego S. Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development. Clin Epigenetics 2021; 13:51. [PMID: 33750457 PMCID: PMC7942176 DOI: 10.1186/s13148-021-01040-6] [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: 12/17/2020] [Accepted: 02/25/2021] [Indexed: 12/31/2022] Open
Abstract
Background Hirschsprung disease (HSCR, OMIM 142623) is a rare congenital disorder that results from a failure to fully colonize the gut by enteric precursor cells (EPCs) derived from the neural crest. Such incomplete gut colonization is due to alterations in EPCs proliferation, survival, migration and/or differentiation during enteric nervous system (ENS) development. This complex process is regulated by a network of signaling pathways that is orchestrated by genetic and epigenetic factors, and therefore alterations at these levels can lead to the onset of neurocristopathies such as HSCR. The goal of this study is to broaden our knowledge of the role of epigenetic mechanisms in the disease context, specifically in DNA methylation. Therefore, with this aim, a Whole-Genome Bisulfite Sequencing assay has been performed using EPCs from HSCR patients and human controls.
Results This is the first study to present a whole genome DNA methylation profile in HSCR and reveal a decrease of global DNA methylation in CpG context in HSCR patients compared with controls, which correlates with a greater hypomethylation of the differentially methylated regions (DMRs) identified. These results agree with the de novo Methyltransferase 3b downregulation in EPCs from HSCR patients compared to controls, and with the decrease in the global DNA methylation level previously described by our group. Through the comparative analysis of DMRs between HSCR patients and controls, a set of new genes has been identified as potential susceptibility genes for HSCR at an epigenetic level. Moreover, previous differentially methylated genes related to HSCR have been found, which validates our approach.
Conclusions This study highlights the relevance of an adequate methylation pattern for a proper ENS development. This is a research area that provides a novel approach to deepen our understanding of the etiopathogenesis of HSCR. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01040-6.
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Affiliation(s)
- Leticia Villalba-Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain
| | - Daniel López-López
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, University Hospital Virgen del Rocío, 41013, Sevilla, Spain.,Computational Systems Medicine, IBIS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain
| | - Carlos S Casimiro-Soriguer
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, University Hospital Virgen del Rocío, 41013, Sevilla, Spain.,Computational Systems Medicine, IBIS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, 41013, Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain
| | - Joaquín Dopazo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain.,Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, University Hospital Virgen del Rocío, 41013, Sevilla, Spain.,Computational Systems Medicine, IBIS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain. .,Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013, Seville, Spain.
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12
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Hu RH, Zhang ZT, Wei HX, Ning L, Ai JS, Li WH, Zhang H, Wang SQ. LncRNA ST7-AS1, by regulating miR-181b-5p/KPNA4 axis, promotes the malignancy of lung adenocarcinoma. Cancer Cell Int 2020; 20:568. [PMID: 33327962 PMCID: PMC7745379 DOI: 10.1186/s12935-020-01652-7] [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: 08/13/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Background Growing evidence suggests that suppressor of tumorigenicity 7 antisense RNA 1 (ST7-AS1) is an oncogenic long noncoding RNA (lncRNA). However, little is known on its clinical significance, biological functions, or molecular mechanisms in lung adenocarcinoma (LUAD). Methods The expression of ST7-AS1 and miR-181b-5p were examined by qRT-PCR. The correlations between ST7-AS1 level and different clinicopathological features were analysed. In vitro, LUAD cells were examined for cell viability, migration and invasion by MTT, wound healing and Transwell assay, respectively. Epithelial-mesenchymal transition (EMT) biomarkers were detected by Western blot. The regulations between ST7-AS1, miR-181b-5p, and KPNA4 were examined by luciferase assay, RNA immunoprecipitation, RNA pulldown. Both gain- and loss-of-function strategies were used to assess the importance of different signalling molecules in malignant phenotypes of LUAD cells. The in vivo effect was analysed using the xenograft and the experimental metastasis mouse models. Results ST7-AS1 was upregulated in LUAD tissues or cell lines, correlated with tumours of positive lymph node metastasis or higher TNM stages, and associated with shorter overall survival of LUAD patients. ST7-AS1 essentially maintained the viability, migration, invasion, and EMT of LUAD cells. The oncogenic activities of ST7-AS1 were accomplished by sponging miR-181b-5p and releasing the suppression of the latter on KPNA4. In LUAD tissues, ST7-AS1 level positively correlated with that of KPNA4 and negatively with miR-181b-5p level. In vivo, targeting ST7-AS1 significantly inhibited xenograft growth and metastasis. Conclusions ST7-AS1, by regulating miR-181b-5p/KPNA4 axis, promotes the malignancy of LUAD cells. Targeting ST7-AS1 and KPNA4 or up-regulating miR-181b-5p, therefore, may benefit the treatment of LUAD.
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Affiliation(s)
- Rong-Hang Hu
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, No. 89, GuHuai Road, Jining, 272029, Shandong, People's Republic of China
| | - Zi-Teng Zhang
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, No. 89, GuHuai Road, Jining, 272029, Shandong, People's Republic of China
| | - Hai-Xiang Wei
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, No. 89, GuHuai Road, Jining, 272029, Shandong, People's Republic of China
| | - Lu Ning
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, No. 89, GuHuai Road, Jining, 272029, Shandong, People's Republic of China
| | - Jiang-Shan Ai
- Medical College of Qingdao University, Qingdao, 266071, People's Republic of China
| | - Wen-Hui Li
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, No. 89, GuHuai Road, Jining, 272029, Shandong, People's Republic of China
| | - Heng Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, People's Republic of China.
| | - Shao-Qiang Wang
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, No. 89, GuHuai Road, Jining, 272029, Shandong, People's Republic of China.
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13
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Pan W, Wu A, Yu H, Yu Q, Zheng B, Yang W, Tian D, Li P, Gao Y. Involvement of the lncRNA AFAP1-AS1/microRNA-195/E2F3 axis in proliferation and migration of enteric neural crest stem cells of Hirschsprung's disease. Exp Physiol 2020; 105:1939-1949. [PMID: 32959905 DOI: 10.1113/ep088780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
NEW FINDINGS What is the central question of this study? Long non-coding RNAs (lncRNAs) are widely involved in the progression of Hirschsprung's disease (HSCR), but the role of actin filament associated protein 1 antisense RNA1 (AFAP1-AS1), an lncRNA, in HSCR has not been explored before. What is the main finding and its importance? Downregulation of AFAP1-AS1 blocks enteric neural crest stem cell proliferation, differentiation, migration and invasion and promotes the occurrence of HSCR via the miR-195/E2F3 axis, indicating thatAFAP1-AS might be a potential biomarker for HSCR patients. ABSTRACT Long non-coding RNAs (lncRNAs) are involved in several human disorders. Nevertheless, it remains unclear whether they are implicated in the phenotypes of enteric neural crest stem cells (ENCSCs) in Hirschsprung's disease (HSCR). Therefore, we designed this study to explore the pathogenicity of AFAP1-AS1 for HSCR. Microarray analysis and bioinformatic tools were used to screen out the differentially lncRNAs and microRNAs (miRNAs) in patients with HSCR. Small interference RNA transfection was applied to carry out functional experiments in ENCSCs. Cellular activities were detected by cell counting kit-8, 5-ethynyl-2'-deoxyuridine, Transwell assays and flow cytometry. Finally, rescue experiments were performed to examine the cofunction of AFAP1-AS1 and miR-195 and of miR-195 and E2F transcription factor 3 (E2F3). AFAP1-AS1 was reduced in HSCR patients. Meanwhile, knockdown of AFAP1-AS1 reduced the cell migratory and proliferative capacities and facilitated cell apoptosis along with G0/G1 phase arrest. E2F3 was diminished when miR-195 was upregulated, and AFAP1-AS1 inhibition reduced its ability to bind to miR-195. Altogether, AFAP1-AS1 silencing acts as an endogenous RNA by interacting with miR-195 to alter E2F3 expression, thus conferring repressive effects on ENCSC activity and promoting HSCR progression.
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Affiliation(s)
- Weikang Pan
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Ali Wu
- Department of Endoscopy, Shaanxi Nuclear Industry 215 Hospital, Xianyang, Shaanxi, PR China
| | - Hui Yu
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Qiang Yu
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Baijun Zheng
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Weili Yang
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Donghao Tian
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Peng Li
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Ya Gao
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
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14
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Torroglosa A, Villalba-Benito L, Fernández RM, Luzón-Toro B, Moya-Jiménez MJ, Antiñolo G, Borrego S. Identification of New Potential LncRNA Biomarkers in Hirschsprung Disease. Int J Mol Sci 2020; 21:ijms21155534. [PMID: 32748823 PMCID: PMC7432910 DOI: 10.3390/ijms21155534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy defined by intestinal aganglionosis due to alterations during the development of the Enteric Nervous System (ENS). A wide spectrum of molecules involved in different signaling pathways and mechanisms have been described in HSCR onset. Among them, epigenetic mechanisms are gaining increasing relevance. In an effort to better understand the epigenetic basis of HSCR, we have performed an analysis for the identification of long non-coding RNAs (lncRNAs) by qRT-PCR in enteric precursor cells (EPCs) from controls and HSCR patients. We aimed to test the presence of a set lncRNAs among 84 lncRNAs in human EPCs, which were previously related with crucial cellular processes for ENS development, as well as to identify the possible differences between HSCR patients and controls. As a result, we have determined a set of lncRNAs with positive expression in human EPCs that were screened for mutations using the exome data from our cohort of HSCR patients to identify possible variants related to this pathology. Interestingly, we identified three lncRNAs with different levels of their transcripts (SOCS2-AS, MEG3 and NEAT1) between HSCR patients and controls. We propose such lncRNAs as possible regulatory elements implicated in the onset of HSCR as well as potential biomarkers of this pathology.
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Affiliation(s)
- Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Leticia Villalba-Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, 41013 Seville, Spain;
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
- Correspondence:
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15
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Zhao J, Yang T, Ji J, Zhao F, Li C, Han X. RHPN1-AS1 promotes cell proliferation and migration via miR-665/Akt3 in ovarian cancer. Cancer Gene Ther 2020; 28:33-41. [PMID: 32457485 DOI: 10.1038/s41417-020-0180-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022]
Abstract
Recent efforts have revealed that long non-coding RNAs exert crucial roles in cancer initiation and progression. RHPN1-AS1 is a 2030 bp transcript from human chromosome 8q24, and involved in tumorigenesis in uveal melanoma and non-small cell lung cancer, but it remains unknown in ovarian cancer. This study focused on the role of RHPN1-AS1 in ovarian cancer and found that RHPN1-AS1 was up-regulated in ovarian cancer tissues and cell lines. Overexpression of RHPN1-AS1 promoted ovarian cancer cell proliferation, migration, and invasion. Mechanistically, overexpression of RHPN1-AS1 decreased the expression of miR-665 and subsequently promoted the expression of Akt3 at posttranscriptional level. Taken together, RHPN1-AS1 positively regulated the expression of Akt3 through sponging miR-665, and exerted an oncogenic role in ovarian cancer progression, and indicates that RHPN1-AS1 may be a potential therapeutic target in ovarian cancer.
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Affiliation(s)
- Juan Zhao
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Xi' an Jiaotong University, 710061, Xi' an, China
| | - Ting Yang
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Xi' an Jiaotong University, 710061, Xi' an, China
| | - Jing Ji
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Xi' an Jiaotong University, 710061, Xi' an, China
| | - Fan Zhao
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Xi' an Jiaotong University, 710061, Xi' an, China
| | - Chen Li
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Xi' an Jiaotong University, 710061, Xi' an, China
| | - Xiaobing Han
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Xi' an Jiaotong University, 710061, Xi' an, China.
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16
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Lv X, Li Y, Li H, Zhou L, Wang B, Zhi Z, Tang W. Molecular function predictions and diagnostic value analysis of plasma exosomal miRNAs in Hirschsprung's disease. Epigenomics 2020; 12:409-422. [PMID: 32297806 DOI: 10.2217/epi-2019-0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Aim: To discover the potential roles of plasma exosomal miRNAs in Hirschsprung's disease (HSCR) and identify potential noninvasive biomarkers for early diagnosis of HSCR. Materials & methods: Plasma samples were collected from HSCR patients and matched controls. Exosomes were isolated before high-throughput Illumina sequencing was utilized to gain a profile of dysregulated exosomal miRNAs, followed with further verification in two separate cohorts. Bioinformatics analyses were also adopted to explore the molecular functions of dysregulated miRNAs in Hirschsprung's disease. Results & conclusion: 31 dysregulated miRNAs were identified with five considered as promising HSCR signatures. Gene enrichment analysis disclosed that the upregulated miRNAs were most likely to participate in 'extracellular matrix-receptor interaction' and contribute to HSCR through interfering in cell junctions.
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Affiliation(s)
- Xiurui Lv
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Yuhan Li
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Hongxing Li
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Lingling Zhou
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Binyu Wang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Zhengke Zhi
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Weibing Tang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, PR China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, PR China
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17
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Profile analysis reveals endogenous RNAs regulate necrotizing enterocolitis progression. Biomed Pharmacother 2020; 125:109975. [PMID: 32036223 DOI: 10.1016/j.biopha.2020.109975] [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: 10/16/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 12/31/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is one of the most common and devastating gastrointestinal diseases in preterm newborns, and its underlying mechanisms remain unclear. Non-coding RNAs (ncRNAs) play critical roles in intestinal diseases; however, little is known about their roles in the development of NEC. To gain a deeper understanding of the pathophysiological mechanism of NEC, long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs were detected in an NEC rat model. In total, 1820 lncRNAs, 118 miRNAs and 929 mRNAs were differentially expressed in NEC group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these molecules were enriched in apoptosis, autophagic cell death, TLR4 signaling pathway, Notch signaling pathway, and mTOR signaling pathway. These pathways are thought to be closely associated with NEC. Furthermore, a lncRNA-miRNA interaction network was constructed, and four of the novel, differentially expressed lncRNAs with large changes were randomly verified using quantitative polymerase chain reaction (qPCR). The GO and KEGG pathway analysis of these four lncRNAs showed that they were associated with the negative regulation of TLR4 signaling pathway and Notch signaling pathway. In conclusion, our study revealed that these differentially expressed lncRNAs may participate in the development of NEC via interactions with miRNAs and may serve as possible biomarkers and target genes in NEC.
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18
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LncRNA AFAP1-AS1 promotes osteoblast differentiation of human aortic valve interstitial cells through regulating miR-155/SMAD5 axis. Mol Cell Probes 2020; 50:101509. [PMID: 31945413 DOI: 10.1016/j.mcp.2020.101509] [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: 10/09/2019] [Revised: 12/26/2019] [Accepted: 01/12/2020] [Indexed: 12/17/2022]
Abstract
AIM Degenerative calcific aortic valve disease (DCAVD) is a common valve disease characterized by massive calcium deposits in the aortic valve. Osteoblast differentiation of valve interstitial cells (VICs) is responsible for the formation of calcific nodules. This study aims to explore the function and underlying mechanism of long non-coding RNA (lncRNA) AFAP1-AS1 (actin filament-associated protein 1 antisense RNA 1) in the pathogenesis of DCAVD. METHODS AFAP1-AS1, miR-155 and mRNA levels were detected by qRT-PCR. Protein levels were measured by Western blot. Calcification deposition was examined by Alizarin Red staining. The interaction between AFAP1-AS1 and miR-155, as well as miR-155 and SMAD5 was evaluated using luciferase reporter assay. RESULTS AFAP1-AS1 expression was increased both in calcified aortic valves from DCAVD patients and after osteogenic induction in human VICs. Furthermore, AFAP1-AS1 overexpression promoted osteogenic differentiation of VICs, whereas AFAP1-AS1 knockdown inhibited osteogenic differentiation. Mechanistically, AFAP1-AS1 acted as a sponge for miR-155 to elevate SMAD5 expression. Further functional assays revealed that miR-155 mimic and SMAD5 silencing effectively reversed AFAP1-AS1-promoted osteogenic differentiation of VICs. CONCLUSION Collectively, AFAP1-AS1 promotes osteogenic differentiation of VICs, at least in part, by sponging miR-155 to upregulate SMAD5. This study sheds new light on lncRNA-directed therapeutics in DCAVD.
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The importance of long non-coding RNAs in neuropsychiatric disorders. Mol Aspects Med 2019; 70:127-140. [DOI: 10.1016/j.mam.2019.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/10/2019] [Accepted: 07/14/2019] [Indexed: 12/20/2022]
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20
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Niu X, Xu Y, Gao N, Li A. Weighted Gene Coexpression Network Analysis Reveals the Critical lncRNAs and mRNAs in Development of Hirschsprung's Disease. J Comput Biol 2019; 27:1115-1129. [PMID: 31647312 DOI: 10.1089/cmb.2019.0261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hirschsprung's disease (HSCR) is a common newborn defect. This study aimed to identify critical genes involved in the development of HSCR. Differently expressed genes (DEGs) of public data set GSE98502 were analyzed using paired t-test. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) 6.8. Besides, Coexpression network of long noncoding RNAs (lncRNAs)-mRNAs (message RNA) were constructed using weighted gene coexpression network analysis. The key modules were filtered out by calculating the module-trait correlations. Then, hub genes were screened and the expression of these genes was further validated in an independent data set GSE96854. We identified 864 DEGs enriched in 19 GO biological functions such as negative regulation of growth and regulation of heart contraction; 11 KEGG pathways such as mineral absorption and protein digestion and absorption. lncRNAs-mRNAs coexpressed network was constructed, including 8 modules and 177 genes. Hub lncRNAs, including LINC00619, LINC00924, LINC00261, and DRAIC, were identified. Hub mRNAs, including CYCS, CCND1, BDKRB, ITGA6, and TNNC1, were mainly enriched in cancer pathways, p53 signaling pathway, and calcium signaling pathway. The expressions of the hub mRNAs were successfully validated by another independent GSE96854 data set. Our findings indicated the hub lncRNAs, including LINC00619, LINC00924, LINC00261, and DRAIC, as well as hub mRNAs, including CYCS, CCND1, BDKRB, ITGA6, and TNNC1, might involve in the progression of HSCR, and these genes might provide new clinical biomarkers for risk evaluation of HSCR.
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Affiliation(s)
- Xiaoguang Niu
- Department of Pediatric Surgery, Qilu Hospital, Shandong University, Jinan, China.,Department of Pediatric Surgery, Taian City Central Hospital, Taian, China
| | - Yongtao Xu
- Department of Pediatric Surgery, Taian City Central Hospital, Taian, China
| | - Ni Gao
- Department of Pediatric Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Aiwu Li
- Department of Pediatric Surgery, Qilu Hospital, Shandong University, Jinan, China
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21
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Torroglosa A, Villalba-Benito L, Luzón-Toro B, Fernández RM, Antiñolo G, Borrego S. Epigenetic Mechanisms in Hirschsprung Disease. Int J Mol Sci 2019; 20:ijms20133123. [PMID: 31247956 PMCID: PMC6650840 DOI: 10.3390/ijms20133123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
Hirschsprung disease (HSCR, OMIM 142623) is due to a failure of enteric precursor cells derived from neural crest (EPCs) to proliferate, migrate, survive or differentiate during Enteric Nervous System (ENS) formation. This is a complex process which requires a strict regulation that results in an ENS specific gene expression pattern. Alterations at this level lead to the onset of neurocristopathies such as HSCR. Gene expression is regulated by different mechanisms, such as DNA modifications (at the epigenetic level), transcriptional mechanisms (transcription factors, silencers, enhancers and repressors), postranscriptional mechanisms (3′UTR and ncRNA) and regulation of translation. All these mechanisms are finally implicated in cell signaling to determine the migration, proliferation, differentiation and survival processes for correct ENS development. In this review, we have performed an overview on the role of epigenetic mechanisms at transcriptional and posttranscriptional levels on these cellular events in neural crest cells (NCCs), ENS development, as well as in HSCR.
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Affiliation(s)
- Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.
| | - Leticia Villalba-Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain.
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22
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Wu L, Yuan W, Chen J, Zhou Z, Shu Y, Ji J, Liu Z, Tang Q, Zhang X, Shu X. Increased miR-214 expression suppresses cell migration and proliferation in Hirschsprung disease by interacting with PLAGL2. Pediatr Res 2019; 86:460-470. [PMID: 30822775 PMCID: PMC6768286 DOI: 10.1038/s41390-019-0324-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND The miR-214 has been reported to be associated with various diseases, but its involvement in the pathophysiology of Hirschsprung disease (HSCR) is almost completely unexplored. METHODS In our study, we conducted a series of experiments to unravel the biological role of miR-214 in the pathophysiology of HSCR. qRT-PCR and western blotting were utilized to investigate the relative expression levels of miR-214, mRNAs, and proteins of related genes in colon tissues from 20 controls without HSCR and 24 patients with HSCR. The potential biological role of miR-214 in two cell lines (SKN-SH and SH-SY5Y) was assessed using the CCK8 assay, EdU staining, transwell assay, and flow cytometry. The dual-luciferase reporter assay was used to confirm PLAGL2 as a common target gene of miR-214. RESULTS All results suggested that miR-214 is upregulated in HSCR tissue samples compared with controls. Additionally, we found that miR-214 could inhibit cell proliferation and migration by directly downregulating the expression of PLAGL2, and the extent of the miR-214-mediated inhibitory effects could be rescued by a PLAGL2 overexpression plasmid. CONCLUSION Our results revealed that miR-214 is indeed involved in the pathophysiology of HSCR and suppresses cell proliferation and migration by directly downregulating PLAGL2 in cell models.
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Affiliation(s)
- Liang Wu
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Wenzheng Yuan
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,0000 0004 1758 2270grid.412632.0Present Address: Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060 China
| | - Jinhuang Chen
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Zili Zhou
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yan Shu
- 0000 0004 4677 3586grid.470508.eCollege of Clinical Medicine, Hubei University of Science and Technology, Xianning, 437100 China
| | - Jintong Ji
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Zhengyi Liu
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Qiang Tang
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xudan Zhang
- 0000 0004 0368 7223grid.33199.31Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xiaogang Shu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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23
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Li X, Li B, Ran P, Wang L. Identification of ceRNA network based on a RNA-seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma. Oncol Lett 2018; 16:5697-5708. [PMID: 30344725 PMCID: PMC6176255 DOI: 10.3892/ol.2018.9336] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 07/05/2018] [Indexed: 02/06/2023] Open
Abstract
Previous studies have emphasized the significant functions of long non-coding RNAs (lncRNAs) as competing endogenous RNAs (ceRNAs) in tumor biology. However, the functions of certain cancer lncRNAs in the lncRNA-related ceRNA network in lung adenocarcinoma (LUAD) are unknown. A systematic and integrative survey of RNA-seq data from The Cancer Genome Atlas (TCGA) was performed to identify candidate lncRNAs for the prognosis of LUAD. In total, 20,502 genes that contain 181 lncRNAs were evaluated in a cohort of 570 LUAD cases. Initially, 6,280 differentially expressed genes (fold-change >2, P<0.05) were obtained using R package, which includes 75 lncRNAs. Next, by univariate regression and multivariate Cox proportional hazards analysis, 32 genes were associated with survival in LUAD. Using these 29 mRNAs and 3 lncRNAs, a prognosis index (PI) was calculated to accurately estimate the survival in LUAD: PI=∑exprisk gene × HRrisk gene. Furthermore, the 32-gene signature was an independent prognostic indicator for LUAD (HR >1; P<0.05, by multivariate analysis). Weighted gene co-expression network analysis (WGCNA) of three risk lncRNAs-FAM138B, NHEG1 and TLX1NB-was performed, based on the P-values of the associated genes, and the top 27 miRNAs that bound to these lncRNAs were predicted by Miranda as target miRNAs. Next, these target miRNAs were transferred to the TarBase, miRTarBase, miRecards and starBase v2.0 databases to obtain their target genes. According to the previous miRNA-mRNA and miRNA-lncRNA data, three lncRNA-miRNA-mRNA ceRNA networks were established, based on the 29 prognostic mRNAs, forming a regulatory network in LUAD. The present study provided insight into the lncRNA-related ceRNA network in LUAD and has identified potential diagnostic and prognostic biomarkers.
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Affiliation(s)
- Xing Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511400, P.R. China.,Oncology Department, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, Gansu 730050, P.R. China
| | - Bing Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511400, P.R. China
| | - Pixin Ran
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510030, P.R. China
| | - Lanying Wang
- Oncology Department, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, Gansu 730050, P.R. China
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24
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Li Y, Zhou L, Lu C, Shen Q, Su Y, Zhi Z, Wu F, Zhang H, Wen Z, Chen G, Li H, Xia Y, Tang W. Long non-coding RNA FAL1 functions as a ceRNA to antagonize the effect of miR-637 on the down-regulation of AKT1 in Hirschsprung's disease. Cell Prolif 2018; 51:e12489. [PMID: 30062828 DOI: 10.1111/cpr.12489] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/29/2018] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Emerged evidence demonstrates that long non-coding RNAs (lncRNAs) may play quintessential regulatory roles in the cellular processes, tumourigenesis and the development of disease. Though focally amplified lncRNA on chromosome 1 (FAL1) has been identified to have crucial functions in many diseases, its biological mechanism in the development of Hirschsprung's disease (HSCR) still remains unknown. MATERIALS AND METHODS The expression levels of FAL1 in HSCR aganglionic tissues and matched normal specimens were detected by quantitative real-time PCR (qRT-PCR). Cell proliferation and migration were detected by Cell Counting Kit-8 (CCK-8) assay, Ethynyl-deoxyuridine (EdU) assay and transwell assay relatively. Cell cycle and apoptosis were assessed using flow cytometer analysis. Moreover, the novel targets of FAL1 were confirmed with the help of bioinformatics analysis and dual-luciferase reporter assay. Western blot assay as well as RNA immunoprecipitation (RIP) assay was conducted to investigate the potential mechanism. RESULTS FAL1 expression was markedly down-regulated in HSCR aganglionic tissues and decreased FAL1 expression was associated with the diagnosis of HSCR. Cell functional analyses indicated that FAL1 overexpressing notably promoted cell proliferation and migration, while down-regulation of FAL1 suppressed cell proliferation and migration. Additionally, Flow cytometry assay demonstrated that knockdown of FAL1 induced markedly cell cycle stalled in the G0/G1 phase. Furthermore, FAL1 could positively regulate AKT1 expression by competitively binding to miR-637. CONCLUSIONS These results illuminated that FAL1 may work as a ceRNA to modulate AKT1 expression via competitively binding to miR-637 in HSCR, suggesting that it may be clinically valuable as a biomarker of HSCR.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Lingling Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Changgui Lu
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Qiyang Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Su
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengke Zhi
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hua Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zechao Wen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Guanglin Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hongxing Li
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Nanjing Medical University, Nanjing, China
| | - Weibing Tang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
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25
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Chen G, Peng L, Zhu Z, Du C, Shen Z, Zang R, Su Y, Xia Y, Tang W. Erratum: LncRNA AFAP1-AS Functions as a Competing Endogenous RNA to Regulate RAP1B Expression by sponging miR-181a in the HSCR: Erratum. Int J Med Sci 2018; 15:1472. [PMID: 30443167 PMCID: PMC6216066 DOI: 10.7150/ijms.29742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.7150/ijms.18392.].
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Affiliation(s)
- Guanglin Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Lei Peng
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Zhongxian Zhu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Chunxia Du
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Ziyang Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Rujin Zang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Yang Su
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Key Laboratory of Modern Toxicology (Nanjing Medical University), Ministry of Education, China
| | - Weibing Tang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University
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