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Wang C, Zhao X, Wu Z, Huang G, Lin R, Chen H, Xu K, Sun K, Zhou H, Shu J. Identification of Differentially Expressed mRNAs and miRNAs and Related Regulatory Networks in Cumulus Oophorus Complexes Associated with Fertilization. Reprod Sci 2024:10.1007/s43032-023-01413-7. [PMID: 38216777 DOI: 10.1007/s43032-023-01413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/16/2023] [Indexed: 01/14/2024]
Abstract
Cumulus oophorus complexes (COCs) are the first extracellular barriers that sperm must pass through to fuse with oocytes, which have an important role in oocyte maturation and fertilization. However, little is known about the molecular mechanisms of COCs involved in fertilization. In this study, COCs were collected and then randomly divided into a test group that interacted with sperm and a control group that did not interact with sperm. Then, the total RNA was extracted; RNA transcriptome and small RNA libraries were prepared, sequenced, and analyzed. The results showed that 1283 differentially expressed genes (DEGs), including 560 upregulated and 723 downregulated genes. In addition, 57 differentially expressed miRNAs (DEMIs) with 35 upregulated and 22 downregulated were also detected. After the RNA-seq results were verified by RT-qPCR, 86 effective DEGs and 40 DEMIs were finally screened and a DEMI-DEG regulatory network was constructed. From this, the top ten hub target genes were HNF4A, SPN, WSCD1, TMEM239, SLC2A4, E2F2, SIAH3, ADORA3, PIK3R2, and GDNF, and they were all downregulated. The top ten hub DEMIs were miR-6876-5p, miR-877-3p, miR-6818-5p, miR-4690-3p, miR-6789-3p, miR-6837-5p, miR-6861-5p, miR-4421, miR-6501-5p, and miR-6875-3p, all of which were upregulated. The KEGG signaling pathway enrichment analysis showed that the effective DEGs were significantly enriched in the calcium, AMPK, and phospholipase D signaling pathways. Our study identified several DEGs and DEMIs and potential miRNA-mRNA regulatory pathways in COCs and these may contribute to fertilization. This study may provide novel insights into potential biomarkers for fertilization failure.
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Affiliation(s)
- Caizhu Wang
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Xin Zhao
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Zhulian Wu
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Guiting Huang
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Ruoyun Lin
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Huanhua Chen
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Kongrong Xu
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Kejian Sun
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China
| | - Hong Zhou
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China.
| | - Jinhui Shu
- Department of Reproductive Medicine, Guangxi Maternal and Child Health Hospital, Nanning, 530003, Guangxi, China.
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Xie L, Jian H, Dai H, Yang Y, Liu Y, Wei L, Tan M, Li J, Liu L. Screening of microRNAs and target genes involved in Sclerotinia sclerotiorum (Lib.) infection in Brassica napus L. BMC Plant Biol 2023; 23:479. [PMID: 37807039 PMCID: PMC10561407 DOI: 10.1186/s12870-023-04501-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) is the third largest source of vegetable oil in the world, and Sclerotinia sclerotiorum (Lib.) is a major soil-borne fungal plant pathogen that infects more than 400 plant species, including B. napus. Sclerotinia stem rot caused an annual loss of 10 - 20% in rapeseed yield. Exploring the molecular mechanisms in response to S. sclerotiorum infection in B. napus is beneficial for breeding and cultivation of resistant varieties. To gain a better understanding of the mechanisms regarding B. napus tolerance to Sclerotinia stem rot, we employed a miRNAome sequencing approach and comprehensively investigated global miRNA expression profile among five relatively resistant lines and five susceptible lines of oilseed at 0, 24, and 48 h post-inoculation. RESULTS In this study, a total of 40 known and 1105 novel miRNAs were differentially expressed after S. sclerotiorum infection, including miR156, miR6028, miR394, miR390, miR395, miR166, miR171, miR167, miR164, and miR172. Furthermore, 8,523 genes were predicted as targets for these differentially expressed miRNAs. These target genes were mainly associated with disease resistance (R) genes, signal transduction, transcription factors, and hormones. Constitutively expressing miR156b (OX156b) plants strengthened Arabidopsis resistance against S. sclerotiorum accompanied by smaller necrotic lesions, whereas blocking miR156 expression in Arabidopsis (MIM156) led to greater susceptibility to S. sclerotiorum disease, associated with extensive cell death of necrotic lesions. CONCLUSIONS This study reveals the distinct difference in miRNA profiling between the relatively resistant lines and susceptible lines of B. napus in response to S. sclerotiorum. The identified differentially expressed miRNAs related to sclerotinia stem rot resistance are involved in regulating resistance to S. sclerotiorum in rapeseed by targeting genes related to R genes, signal transduction, transcription factors, and hormones. miR156 positively modulates the resistance to S. sclerotiorum infection by restricting colonization of S. sclerotiorum mycelia. This study provides a broad view of miRNA expression changes after S. sclerotiorum infection in oilseed and is the first to elucidate the function and mechanism underlying the miR156 response to S. sclerotiorum infection in oilseed rape.
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Affiliation(s)
- Ling Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Haoxi Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Youhong Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yiling Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Lijuan Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Min Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
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Zhang L, Xu S, Zhang Z, Zhang X, Liu X. Transcriptomic profiling and characterization of microRNAs in Macrobrachium rosenbergii potentially involved in immune response to Enterobacter cloacae infection. Microb Pathog 2023; 183:106291. [PMID: 37557932 DOI: 10.1016/j.micpath.2023.106291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023]
Abstract
Enterobacter cloacae is a member of the Enterobacter family, which could prevent Macrobrachium rosenbergii from growing and cause mass mortality. However, no research has focused on microRNA immunity in M. rosenbergii infected with E. cloacae. To clarify the immune response mechanisms, transcriptomic analysis was performed on the miRNAs of M. rosenbergii infected with E. cloacae YZ3 strain. Following quality screening, 10,616,712 clean reads were obtained from the control group and 12,726,421 from the infected group. Among 899 known miRNAs, 446 differentially expressed miRNAs (DEMs) were identified. Meanwhile, 59 novel miRNAs were predicted, along with 39 DEMs. Target genes of DEMs have been predicted in order to gain a deeper understanding of the immune-related functions. GO and KEGG pathway analysis revealed the biological functions and signaling pathways of target genes. The results indicated that E. cloacae significantly affected the NOD-like receptor, RIG-I-like receptor and Toll-like receptor pathways. Ten DEMs were randomly selected, and their expression level was verified by Quantitative Real-time PCR technology. Overall, this study highlights the influential role of miRNAs in the innate immune system of M. rosenbergii, which has important implications for developing new strategies to prevent and treat related diseases in the future.
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Affiliation(s)
- Liwen Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Sunan Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zheling Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.
| | - Xiaodan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China; International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, China.
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Lee S, Kang S, Heo J, Hong Y, Vu TH, Truong AD, Lillehoj HS, Hong YH. MicroRNA expression profiling in the lungs of genetically different Ri chicken lines against the highly pathogenic avian influenza H5N1 virus. J Anim Sci Technol 2023; 65:838-855. [PMID: 37970505 PMCID: PMC10640957 DOI: 10.5187/jast.2022.e127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/09/2022] [Accepted: 12/23/2022] [Indexed: 11/17/2023]
Abstract
The highly pathogenic avian influenza (HPAI) virus triggers infectious diseases, resulting in pulmonary damage and high mortality in domestic poultry worldwide. This study aimed to analyze miRNA expression profiles after infection with the HPAI H5N1 virus in resistant and susceptible lines of Ri chickens.For this purpose, resistant and susceptible lines of Vietnamese Ri chicken were used based on the A/G allele of Mx and BF2 genes. These genes are responsible for innate antiviral activity and were selected to determine differentially expressed (DE) miRNAs in HPAI-infected chicken lines using small RNA sequencing. A total of 44 miRNAs were DE after 3 days of infection with the H5N1 virus. Computational program analysis indicated the candidate target genes for DE miRNAs to possess significant functions related to cytokines, chemokines, MAPK signaling pathway, ErBb signaling pathway, and Wnt signaling pathway. Several DE miRNA-mRNA matches were suggested to play crucial roles in mediating immune functions against viral evasion. These results revealed the potential regulatory roles of miRNAs in the immune response of the two Ri chicken lines against HPAI H5N1 virus infection in the lungs.
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Affiliation(s)
- Sooyeon Lee
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Suyeon Kang
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Jubi Heo
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Yeojin Hong
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Thi Hao Vu
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Anh Duc Truong
- Department of Biochemistry and Immunology,
National Institute of Veterinary Research, Hanoi 100000, Viet
Nam
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology
Laboratory, Agricultural Research Services, United States Department of
Agriculture, Beltsville, MD 20705, USA
| | - Yeong Ho Hong
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
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Gholipour A, Zahedmehr A, Shakerian F, Irani S, Oveisee M, Mowla SJ, Malakootian M. Significance of microRNA-targeted ErbB signaling pathway genes in cardiomyocyte differentiation. Mol Cell Probes 2023; 69:101912. [PMID: 37019292 DOI: 10.1016/j.mcp.2023.101912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023]
Abstract
OBJECTIVE(S) Cardiomyocyte differentiation is a complex process that follows the progression of gene expression alterations. The ErbB signaling pathway is necessary for various stages of cardiac development. We aimed to identify potential microRNAs targeting the ErbB signaling pathway genes by in silico approaches. METHODS Small RNA-sequencing data were obtained from GSE108021 for cardiomyocyte differentiation. Differentially expressed miRNAs were acquired via the DESeq2 package. Signaling pathways and gene ontology processes for the identified miRNAs were determined and the targeted genes of those miRNAs affecting the ErbB signaling pathway were determined. RESULTS Results revealed highly differentially expressed miRNAs were common between the differentiation stages and they targeted the genes involved in the ErbB signaling pathway as follows: let-7g-5p targets both CDKN1A and NRAS, while let-7c-5p and let-7d-5p hit CDKN1A and NRAS exclusively. let-7 family members targeted MAPK8 and ABL2. GSK3B was targeted by miR-199a-5p and miR-214-3p, and ERBB4 was targeted by miR-199b-3p and miR-653-5p. miR-214-3p, miR-199b-3p, miR-1277-5p, miR-21-5p, and miR-21-3p targeted CBL, mTOR, Jun, JNKK, and GRB1, respectively. MAPK8 was targeted by miR-214-3p, and ABL2 was targeted by miR-125b-5p and miR-1277-5p, too. CONCLUSION We determined miRNAs and their target genes in the ErbB signaling pathway in cardiomyocyte development and consequently heart pathophysiology progression.
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Affiliation(s)
- Akram Gholipour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran; Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Zahedmehr
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Farshad Shakerian
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran; Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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Sun Z, Wang Y, Wei T, Liu L. Identification of key genes and miRNAs related to polycystic ovary syndrome by comprehensive analysis of microarray. BMC Med Genomics 2022; 15:267. [PMID: 36544152 PMCID: PMC9769000 DOI: 10.1186/s12920-022-01384-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/25/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND We aimed to explore mechanisms of development and progression of polycystic ovary syndrome (PCOS). METHODS The microRNA expression microarray GSE37914 and gene expression profiles GSE43264 and GSE98421 were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs (DEmiRNAs) and genes (DEGs) were screened using Limma package. Then, the DEGs and DEmiRNAs were combined to use for the subsequent analysis, including the functional enrichment analysis, protein-protein interaction (PPI) network and module analysis, drug-gene interaction network analysis, and DEmiRNAs-DEGs interactive network construction. RESULTS A total of 26 DEmiRNAs and 80 DEGs were screened. The PPI network contained 68 nodes and 259 interactions. A significant clustering module with 8 nodes and 25 interactions was obtained. Three PCOS-related overlapping pathways were obtained based on PPI-degree top10 and module genes, including prion diseases, Staphylococcus aureus infection, and Chagas disease (American trypanosomiasis). A total of 44 drug-gene interaction pairs were obtained, which included 2 up-regulated genes (LDLR and VCAM1), 4 down-regulated genes (C1QA, C1QB, IL6 and ACAN) and 26 small molecules drugs. A total of 52 nodes and 57 interactions were obtained in the DEmiRNA-DEGs regulatory network, LDLR was regulated by miR-152-3p, miR-1207-5p, miR-378a-5p and miR-150-5p. CONCLUSIONS Our research has identified several key genes and pathways related to PCOS. These results can improve our understanding of PCOS and provide new basis for drug target research.
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Affiliation(s)
- Ziqian Sun
- grid.415954.80000 0004 1771 3349Department of Gynecology and Obstetrics, China-Japan Union Hospital of Jilin University, Changchun, 130033 Jilin Province China
| | - Yang Wang
- Department of Dermatology, Bayi Hospital of Changchun, Changchun, 130021 Jilin Province China
| | - Tianshu Wei
- Department of Gynecology and Obstetrics, Jilin City Center Hospital, Jilin City, 132011 Jilin Province China
| | - Li Liu
- grid.415954.80000 0004 1771 3349Department of Gynecology and Obstetrics, China-Japan Union Hospital of Jilin University, Changchun, 130033 Jilin Province China ,grid.415954.80000 0004 1771 3349Reproductive Medical Center, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Road, Changchun, 130031 China
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Shu B, Lin Y, Qian G, Cai X, Liu L, Lin J. Integrated miRNA and transcriptome profiling to explore the molecular mechanism of Spodoptera frugiperda larval midgut in response to azadirachtin exposure. Pestic Biochem Physiol 2022; 187:105192. [PMID: 36127051 DOI: 10.1016/j.pestbp.2022.105192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
As a destructive agricultural pest, Spodoptera frugiperda has spread worldwide in the past few years. Azadirachtin, an environmentally friendly and most promising compound, showed adverse effects, including mortality and growth inhibition, against S. frugiperda. While the effects of azadirachtin on the midgut of this pest remain to be determined. In this study, structural damage was observed in the larval midguts of S. frugiperda with azadirachtin exposure. RNA-seq on the larval midguts with different azadirachtin treatments was performed. Compared to the control group, a total of 3344 and 4759 differentially expressed genes (DEGs) were identified in the midguts with 0.1 and 0.5 μg/g azadirachtin exposure, respectively. Among them, the DEGs encoding detoxification enzymes/proteins, immune-related proteins, digestion and absorption-related proteins, and transcript factors were further analyzed. High-throughput sequencing was also used for the identification of differentially expressed microRNAs in different treatments. A total of 153 conserved miRNAs and 147 novel miRNAs were identified, of which 11 and 29 miRNAs were affected by 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The integrated analysis found that 13 and 178 miRNA versus mRNA pairs were acquired in the samples with 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The results of high-throughput sequencing were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). These results provide useful information for revealing the molecular mechanism of S. frugiperda larval midgut in response to azadirachtin.
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Affiliation(s)
- Benshui Shu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Yanzheng Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Guozhao Qian
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Xueming Cai
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Luyang Liu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Jintian Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China.
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Ma Z, Zhong P, Yue P, Sun Z. Uncovering of Key Pathways and miRNAs for Intracranial Aneurysm Based on Weighted Gene Co-Expression Network Analysis. Eur Neurol 2022; 85:212-223. [PMID: 35034029 DOI: 10.1159/000521390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/03/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Intracranial aneurysm (IA) is a serious cerebrovascular disease. The identification of key regulatory genes can provide research directions for early diagnosis and treatment of IA. METHODS Initially, the miRNA and mRNA data were downloaded from the Gene Expression Omnibus database. Subsequently, the limma package in R was used to screen for differentially expressed genes. In order to investigate the function of the differentially expressed genes, a functional enrichment analysis was performed. Moreover, weighted gene co-expression network analysis (WGCNA) was performed to identify the hub module and hub miRNAs. The correlations between miRNAs and mRNAs were assessed by constructing miRNA-mRNA regulatory networks. In addition, in vitro validation was performed. Finally, diagnostic analysis and electronic expression verification were performed on the GSE122897 dataset. RESULTS In the present study, 955 differentially expressed mRNAs (DEmRNAs, 480 with increased and 475 with decreased expression) and 46 differentially expressed miRNAs (DEmiRNAs, 36 with increased and 10 with decreased expression) were identified. WGCNA demonstrated that the yellow module was the hub module. Moreover, 16 hub miRNAs were identified. A total of 1,124 negatively regulated miRNA-mRNA relationship pairs were identified. Functional analysis demonstrated that DEmRNAs in the targeted network were enriched in vascular smooth muscle contraction and focal adhesion pathways. In addition, the area under the curve of 16 hub miRNAs was >0.8. It is implied that 16 hub miRNAs may be used as potential diagnostic biomarkers of IA. CONCLUSION Hub miRNAs and key signaling pathways were identified by bioinformatics analysis. This evidence lays the foundation for understanding the underlying molecular mechanisms of IA and provided potential therapeutic targets for the treatment of this disease.
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Affiliation(s)
- Zhengfei Ma
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Neurology, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Ping Zhong
- Department of Neurology, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Peidong Yue
- Department of Neurosurgery, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Zhongwu Sun
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Wang J, Wang CY. Integrated miRNA and mRNA omics reveal the anti-cancerous mechanism of Licochalcone B on Human Hepatoma Cell HepG2. Food Chem Toxicol 2021; 150:112096. [PMID: 33647349 DOI: 10.1016/j.fct.2021.112096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022]
Abstract
To unravel the potential of Licochalcone B as an anti-tumour phytochemical agent and evaluate its underlying mechanisms, we analyzed the mRNAs and miRNAs expression profiles of HepG2 cells in response to Licochalcone B (120 μM). mRNA and miRNA expression libraries were conducted and functional analysis for differential expression mRNAs was carried out utilizing Clue GO. We found 763 Licochalcone B -responsive differently expressed genes, among them, 572 mRNAs were up-regulated and 191 mRNAs were down-regulated, many of which were related to the MAPK signaling pathway. A protein-protein interaction network was constructed to discover the hub genes, and IL6, FOS, JUN, NOTCH1, UBC, UBB, CXCL8, CDKN1A, IL1B, ATF3, and GATA3 genes were screened out. Additionally, miRNAs engaged in Licochalcone B -mediated regulation on HepG2 cells were also studied. 85 differential expression miRNAs were identified, including 39 up-regulated miRNAs and 46 down-regulated miRNAs. Co-expression of miRNA-mRNA network was created and two key miRNAs (hsa-miR-29b-3p and hsa-miR-96-5p) were identified. These recognized key genes, miRNA, and the miRNA-mRNA regulatory network may provide clues to understand the molecular mechanism of Licochalcone B as an apoptotic inducer which may offer hint for its application as a functional food component.
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Affiliation(s)
- Jun Wang
- School of Biological Food and Environment, Hefei University, Hefei, 230601, China.
| | - Chu-Yan Wang
- School of Biological Food and Environment, Hefei University, Hefei, 230601, China.
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Huang PY, Wu JG, Gu J, Zhang TQ, Li LF, Wang SQ, Wang M. Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis. J Orthop Surg Res 2021; 16:63. [PMID: 33468167 PMCID: PMC7814623 DOI: 10.1186/s13018-021-02201-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022] Open
Abstract
Background Osteoarthritis (OA) is a chronic degenerative joint disease and the most frequent type of arthritis. This study aimed to identify the key miRNAs and genes associated with OA progression. Methods The GSE105027 (microRNA [miRNA/miR] expression profile; 12 OA samples and 12 normal samples) and GSE48556 (messenger RNA [mRNA] expression profile; 106 OA samples and 33 normal samples) datasets were selected from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed using the limma and ROCR packages in R, respectively. The target genes that negatively correlated with the DEMs were predicted, followed by functional enrichment analysis and construction of the miRNA-gene and miRNA-transcription factor (TF)-gene regulatory networks. Additionally, key miRNAs and genes were screened, and their expression levels were verified by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results A total of 1696 DEGs (739 upregulated and 957 downregulated) and 108 DEMs (56 upregulated and 52 downregulated) were identified in the OA samples. Furthermore, 56 target genes that negatively correlated with the DEMs were predicted and found to be enriched in three functional terms (e.g., positive regulation of intracellular protein transport) and three pathways (e.g., human cytomegalovirus infection). In addition, three key miRNAs (miR-98-5p, miR-7-5p, and miR-182-5p) and six key genes (murine double minute 2, MDM2; glycogen synthase kinase 3-beta, GSK3B; transmembrane P24-trafficking protein 10, TMED10; DDB1 and CUL4-associated factor 12, DCAF12; caspase 3, CASP3; and ring finger protein 44, RNF44) were screened, among which the miR-7-5p → TMED10/DCAF12, miR-98-5p → CASP3/RNF44, and miR-182-5p → GSK3B pairs were observed in the regulatory network. Moreover, the expression levels of TMED10, miR-7-5p, CASP3, miR-98-5p, GSK3B, and miR-182-5p showed a negative correlation with qRT-PCR verification. Conclusion MiR-98-5p, miR-7-5p, miR-182-5p, MDM2, GSK3B, TMED10, DCAF12, CASP3, and RNF44 may play critical roles in OA progression. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-021-02201-2.
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Affiliation(s)
- Pei-Yan Huang
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China
| | - Jun-Guo Wu
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China
| | - Jun Gu
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China
| | - Tie-Qi Zhang
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China
| | - Ling-Feng Li
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China
| | - Si-Qun Wang
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China
| | - Minghai Wang
- Department of Orthopaedic Surgery, Shanghai Fifth People's Hospital Affiliated to Fudan University, No. 128 Ruili Road, Minhang District, Shanghai, 200240, China.
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Abstract
BACKGROUND Endometrial cancer is a common gynecological cancer with annually increasing incidence worldwide. However, the biomarkers that provide prognosis and progression for this disease remain elusive. RESULTS Two eligible human endometrial cancer datasets (GSE17025 and GSE25405) were selected for the study. A total of 520 differentially expressed mRNAs and 30 differentially expressed miRNAs were identified. These mRNAs were mainly enriched in cell cycle, skeletal system development, vasculature development, oocyte maturation, and oocyte meiosis signalling pathways. A total of 160 pairs of differentially expressed miRNAs and mRNAs, including 22 differentially expressed miRNAs and 71 overlapping differentially expressed mRNAs, were validated in endometrial cancer samples using starBase v2.0 project. The prognosis analysis revealed that Cyclin E1 (CCNE1, one of the 82 hub genes, which correlated with hsa-miR-195 and hsa-miR-424) was significantly linked to a worse overall survival in endometrial cancer patients. CONCLUSIONS The hub genes and differentially expressed miRNAs identified in this study might be used as prognostic biomarkers for endometrial cancer and molecular targets for its treatment.
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Affiliation(s)
- Yaowei Li
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, 530021, People's Republic of China.,Department of Gynecology and obstetrics, Shangyu People's Hospital, Shangyu, Zhejiang, 312300, People's Republic of China
| | - Li Li
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, 530021, People's Republic of China.
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Zhu X, Liu X, Liu Y, Chang W, Song Y, Zhu S. Uncovering the Potential Differentially Expressed miRNAs and mRNAs in Ischemic Stroke Based on Integrated Analysis in the Gene Expression Omnibus Database. Eur Neurol 2020; 83:404-414. [PMID: 32906114 DOI: 10.1159/000507364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/19/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Ischemic stroke is the third leading cause of death. There is no known treatment or cure for the disease. Moreover, the pathological mechanism of ischemic stroke remains unclear. OBJECTIVE We aimed to identify potential microRNAs (miRNAs) and mRNAs, contributing to understanding the pathology of ischemic stroke. METHODS First, the data of miRNA and mRNA were downloaded for differential expression analysis. Then, the regulatory network between miRNA and mRNAs was constructed. Third, top 100 differentially expressed mRNAs were used to construct a protein-protein interaction network followed by the function annotation of mRNAs. In addition, in vitro experiment was used to validate the expression of mRNAs. Last, receiver operating characteristic diagnostic analysis of differentially methylated genes was performed. RESULTS Totally, up to 26 differentially expressed miRNAs and 1,345 differentially expressed mRNAs were identified. Several regulatory interaction pairs between miRNA and mRNAs were identified, such as hsa-miR-206-HMGCR/PICALM, hsa-miR-4491-TMEM97, hsa-miR-3622b-5p/hsa-miR-548k-KLF12, and hsa-miR-302a-3p/hsa-miR-3145-3p-CTSS. MAPK signaling pathway (involved DUSP1) and the Notch signaling pathway (involved NUMB and CREBBP) were identified. The expression validation of KLF12, ARG1, ITGAM, SIRT4, SERPINH1, and DUSP1 was consistent with the bioinformatics analysis. Interestingly, hsa-miR-206, hsa-miR-4491, hsa-miR-3622b-5p, hsa-miR-548k, hsa-miR-302a-3p, hsa-miR-3145-3p, KLF12, and ID3 had the potential diagnostic value of ischemic stroke. CONCLUSIONS The identified differentially expressed miRNAs and mRNAs may be associated with the development of ischemic stroke.
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Affiliation(s)
- Xiaotun Zhu
- Department of Neurology, Liaocheng Second Hospital Affiliated to Shandong First Medical University, Linqing City, China,
| | - Xiao Liu
- Department of Neurology, Liaocheng Second Hospital Affiliated to Shandong First Medical University, Linqing City, China
| | - Ying Liu
- Department of Neurology, Liaocheng Second Hospital Affiliated to Shandong First Medical University, Linqing City, China
| | - Wansheng Chang
- Department of Neurology, Liaocheng Second Hospital Affiliated to Shandong First Medical University, Linqing City, China
| | - Yanfeng Song
- Department of Neurology, Liaocheng Second Hospital Affiliated to Shandong First Medical University, Linqing City, China
| | - Shulai Zhu
- Department of Neurology, Liaocheng Second Hospital Affiliated to Shandong First Medical University, Linqing City, China
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Gu CL, Zhang Z, Fan WS, Li LA, Ye MX, Zhang Q, Zhang NN, Li Z, Meng YG. Identification of MicroRNAs as Potential Biomarkers in Ovarian Endometriosis. Reprod Sci 2020; 27:1715-1723. [PMID: 32651898 DOI: 10.1007/s43032-020-00148-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/02/2020] [Indexed: 12/16/2022]
Abstract
Endometriosis, as a prevalent gynecological disease, is characterized by the presence of endometrial-like tissue outside the uterus, causing infertility and considerable pain and affecting the quality of life of women. The pathogenic mechanism has not been fully elucidated, and there are no effective biomarkers for endometriosis. In our study, microRNA (miRNA) expression profiling of 10 ectopic endometrial plasma from patients with ovarian endometriosis and 10 normal plasma from healthy controls was analyzed using a microarray. As a result, 114 differentially expressed miRNAs were identified. Among them, 14 miRNAs were significantly downregulated in patients with ovarian endometriosis, which matched the microarray results. The diagnostic value of the 14 downregulated miRNAs in ovarian endometriosis was evaluated by receiver operating characteristic (ROC) curve analysis, and hsa-let-7i-5p showed the highest area under the ROC curve (AUC) with a value of 0.900. The target genes of the 14 miRNAs were predicted by miRWalk2.0, and the genes that were targeted by at least 2 of the 14 miRNAs were analyzed by function enrichment. The target genes were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as microRNAs in cancer, bladder cancer, and endocrine resistance pathways, and the Gene Ontology (GO) terms such as nucleobase-containing compound metabolic process, cellular nitrogen compound biosynthetic process, and heterocycle metabolic process. The identified 14 differentially expressed miRNAs could be potential biomarkers and therapeutic targets for the diagnosis and treatment of endometriosis.
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Affiliation(s)
- Cheng-Lei Gu
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China.,Department of Gynecology and Obstetrics, The Eighth Medical Center of Chinese PLA General Hospital, 17 Heishanhu Road, Haidian District, Beijing, 100091, China
| | - Zhe Zhang
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Wen-Sheng Fan
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Li-An Li
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Ming-Xia Ye
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Qian Zhang
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Ni-Na Zhang
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhen Li
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Yuan-Guang Meng
- Department of Gynecology and Obstetrics, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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Liu C, Gao J, Su G, Xiang Y, Wan L. MicroRNA-1202 plays a vital role in osteoarthritis via KCNQ1OT1 has-miR-1202-ETS1 regulatory pathway. J Orthop Surg Res 2020; 15:130. [PMID: 32252801 PMCID: PMC7137223 DOI: 10.1186/s13018-020-01655-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/27/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND This study aimed to explore the molecular mechanism of osteoarthritis (OA) and provide information about new genes as potential targets for OA treatment. METHODS Gene expression profile of GSE105027, including 12 OA serum samples (OA group) and 12 healthy serum samples (ctrl group), was downloaded. The differentially expressed miRNAs (DEMs) as well as miRNA-mRNAs interactions were investigated, followed by function and pathway investigation. Then the protein-protein interaction (PPI) network was performed. Furthermore, the long non-coding RNA (lncRNA)-miRNA-mRNA interactions (competing endogenous RNAs, ceRNAs) were investigated. RESULTS A total of 17 downregulated miRNAs were revealed between OA and ctrl groups. These DEMs such as has-miR-1202 were mainly enriched in GO functions like histone acetyltransferase binding and KEGG pathways like cellular senescence. The integrated PPI network analysis showed that has-miR-1202, has-miR-33b-3p, has-miR-940, has-miR-4284, and has-miR-4281 were 5 downregulated miRNAs in this network. Furthermore, the lncRNA-miRNA-mRNA interactions such as KCNQ1OT1-has-miR-1202-ETS1 were revealed in the present ceRNA network. CONCLUSION Key DEMs such as miR-33b-3p, miR-940, and miR-1202 may be involved in OA. miR-1202 may regulate OA development via histone acetyltransferase pathway binding function and cellular senescence pathway. Furthermore, KCNQ1OT1-has-miR-1202-ETS1 might be vital for the process of OA.
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Affiliation(s)
- Changzeng Liu
- Department of Orthopaedics, No. 904th Hospital of the Joint Logistics Support Force of PLA, Liangxi District, Wuxi, 214044, Jiangsu, China.
| | - Jianming Gao
- Department of Orthopaedics, No. 904th Hospital of the Joint Logistics Support Force of PLA, Liangxi District, Wuxi, 214044, Jiangsu, China
| | - Guangyan Su
- Department of Orthopaedics, No. 904th Hospital of the Joint Logistics Support Force of PLA, Liangxi District, Wuxi, 214044, Jiangsu, China
| | - Yang Xiang
- Department of Orthopaedics, No. 904th Hospital of the Joint Logistics Support Force of PLA, Liangxi District, Wuxi, 214044, Jiangsu, China
| | - Le Wan
- Department of Orthopaedics, No. 904th Hospital of the Joint Logistics Support Force of PLA, Liangxi District, Wuxi, 214044, Jiangsu, China
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Hou G, Du C, Gao H, Liu S, Sun W, Lu H, Kang J, Xie Y, Ma D, Wang C. Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels. BMC Plant Biol 2020; 20:87. [PMID: 32103721 PMCID: PMC7045451 DOI: 10.1186/s12870-020-2296-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. RESULTS A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. CONCLUSIONS The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.
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Affiliation(s)
- Gege Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Du
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honghuan Gao
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sujun Liu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wan Sun
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongfang Lu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Kang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingxin Xie
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dongyun Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Chenyang Wang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
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Wei C, Gao JJ. Downregulated miR-383-5p contributes to the proliferation and migration of gastric cancer cells and is associated with poor prognosis. PeerJ 2019; 7:e7882. [PMID: 31637133 PMCID: PMC6798866 DOI: 10.7717/peerj.7882] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/12/2019] [Indexed: 12/24/2022] Open
Abstract
Aim The study aims to identify differentially expressed microRNAs (DEMs) in gastric cancer (GC) and explore the expression, prognosis and downstream regulation role of miR-383-5p in GC. Methods The GC miRNA-Seq and clinical information were downloaded from Firebrowse which stores integrated data sourced from The Cancer Genome Atlas database. The DEMs were identified with limma package in R software at the cut-off criteria of P < 0.05 and |log2 fold change| > 1.0 (|log2FC| > 1.0). The expression of miR-383-5p in GC cell lines and 54 paired GC tissues was measured by quantitative real-time polymerase chain reaction (qRT-PCR). The overall survival curve of miR-383-5p and the association between its expression and clinicopathological features were explored. Wound healing and cell counting kit-8 assays were performed to investigate the capacity of miR-383-5p in cell proliferation and migration. The downstream target genes were predicted by bioinformatics tools (miRDB, TargetScan and starBase). The consensus target genes were selected for gene functional enrichment analysis by FunRich v3.0 software. The luciferase reporter assay was performed to verify the potential targeting sites of miR-383-5p on lactate dehydrogenase A (LDHA). Results A total of 21 down-regulated miRNAs (including miR-383-5p) and 202 up-regulated miRNAs were identified by analyzing GC miRNA-Seq data. Survival analysis found that patients with low miR-383-5p expression had a shorter survival time (median survival time 21.1 months) than those with high expression (46.9 months). The results of qRT-PCR indicated that miR-383-5p was downregulated in GC cell lines and tissues, which was consistent with miRNA-Seq data. The expression of miR-383-5p was significantly associated with tumor size and differentiation grade. Besides, overexpression of miR-383-5p suppressed GC cells proliferation and migration. A total of 49 common target genes of miR-383-5p were obtained by bioinformatics tools and gene functional enrichment analysis showed that these predicted genes participated in PI3K, mTOR, c-MYC, TGF-beta receptor, VEGF/VEGFR and E-cadherin signaling pathways. The data showed that expression of miR-383-5p was negatively correlated with target LDHA (r = −0.203). Luciferase reporter assay suggested that LDHA was a target of miR-383-5p. Conclusion The present study concluded that miR-383-5p was downregulated and may act as a tumor suppressor in GC. Furthermore, its target genes were involved in important signaling pathways. It could be a prognostic biomarker and play a vital role in exploring the molecular mechanism of GC.
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Affiliation(s)
- Chao Wei
- Department of General Surgery, The No.967 Hospital of PLA Joint Logistics Support Force, Postgraduate Culture Base of Jinzhou Medical University, Dalian, China
| | - Jian-Jun Gao
- Department of General Surgery, The No.967 Hospital of PLA Joint Logistics Support Force, Jinzhou Medical University, Dalian, China
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Zhang H, Mehmood K, Jiang X, Li Z, Yao W, Zhang J, Tong X, Wang Y, Li A, Waqas M, Iqbal M, Li J. Identification of differentially expressed MiRNAs profile in a thiram-induced tibial dyschondroplasia. Ecotoxicol Environ Saf 2019; 175:83-89. [PMID: 30889403 DOI: 10.1016/j.ecoenv.2019.03.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Tetramethyl thiuram disulfide (thiram) is a dithiocarbamate, which is widely used on seeds and storing food grains. The incorporation of thiram into the food chain could be a risk for both human beings and animals. Thiram-contaminated feed has been considered a common cause of tibial dyschondrolplasia (TD) in many avian species. The molecular mechanism of action of thiram on TD involving microRNA (miRNA) is not fully understood. For this purpose, the morbidity and pathologic changes were evaluated to understand the TD, and high-throughput RNA sequencing (RNA-Seq) was performed to explore the differentially expressed miRNAs (DEGs). RT-qPCR was used to confirm the validity as compared with sequencing data. The results showed that the marked alterations in the growth plate of the TD chickens were noticeable, with shrinking cells and irregular chondrocyte columns as compared with control group. In this study, we identified total 375 (p < 0.1), 340 (p < 0.05) and 266 (p < 0.01) significant DEGs between the TD and control groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that the target miRNAs were significantly enriched in different treatment groups, such as apoptosis, mRNA surveillance pathway, mitophagy-animal, etc. This study provides theoretical basis for in-depth understanding the pathogenesis of thiram-induced TD and explore the new insights towards the proposed molecular mechanism of specific miRNA as biomarkers for effective gene diagnosis and treatment of TD in broilers.
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Affiliation(s)
- Hui Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; College of Animals Husbandry and Veterinary Medicine, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, PR China; College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Khalid Mehmood
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; University College of Veterinary & Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Xiong Jiang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhixing Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Wangyuan Yao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jialu Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xiaole Tong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Muhammad Waqas
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Mujahid Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; Department of Pathology, Cholistan University of Veterinary & Animal Sciences (CUVAS), Bahawalpur, 63100, Pakistan
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; College of Animals Husbandry and Veterinary Medicine, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, PR China.
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Zong S, Liu X, Zhou N, Yue Y. E2F7, EREG, miR-451a and miR-106b-5p are associated with the cervical cancer development. Arch Gynecol Obstet 2019; 299:1089-1098. [PMID: 30607582 DOI: 10.1007/s00404-018-5007-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/07/2018] [Indexed: 01/15/2023]
Abstract
PURPOSE We aimed to seek the crucial genes or microRNAs (miRNA) correlated with the cervical cancer development. METHODS The miRNA profiling GSE30656 and gene expression profiling GSE63514 were obtained from Gene Expression Omnibus database. Differentially expressed microRNAs (DEMiRs) and differentially expressed genes (DEGs) were screened. Then target genes of DEMiRs were obtained and matched with DEGs to obtain interaction pairs between DEMiRs and DEGs. Gene Ontology-biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted for DEGs and DEMiRs in the DEMiRs-DEGs pairs. The DEMiRs-DEGs regulatory network, protein-protein interaction network and transcription factor (TF)-target regulatory network were constructed. Ultimately, long non-coding RNAs (lncRNAs) associated with DEMiRs were obtained, and then lncRNA-miRNA-target ceRNA network was established. RESULTS Total 18 DEMiRs and 620 DEGs were identified. DEMiRs were enriched in 35 KEGG pathways, such as PI3K-Akt signaling pathway (involving miR-451a). DEGs were enriched in various functions, such as DNA replication (involving E2F7) and angiogenesis (involving EREG). There were 120 nodes and 216 interaction pairs in the DEMIR-DEG regulatory network, and miR-106b-5p has the greatest degree. EREG and E2F7 were regulated by miR-451a and miR-148a-3p, respectively. Besides, E2F7 was identified in the TF-target regulatory network, regulating CDC6. There were 15 lncRNAs, 11 miRNAs and 90 DEGs in the ceRNA network. Specially, miR-148a-3p was interacted with lncRNA HOTAIR in the ceRNA network. CONCLUSION E2F7, EREG, miR-451a and miR-106b-5p were likely to be related to the cervical cancer development.
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Affiliation(s)
- Shan Zong
- Department of Gynecology Oncology, The First Hospital of Jilin University, 71th Xinmin Road, Chang Chun, 130021, Jilin, China
| | - Xiaoxia Liu
- Department of Gynecology Oncology, The First Hospital of Jilin University, 71th Xinmin Road, Chang Chun, 130021, Jilin, China
| | - Na Zhou
- Department of Gynecology and Obstetric, The First Hospital of Jilin University, Chang Chun, 130021, Jilin, China
| | - Ying Yue
- Department of Gynecology Oncology, The First Hospital of Jilin University, 71th Xinmin Road, Chang Chun, 130021, Jilin, China.
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Shi F, Zhou X, Yao MM, Tan Z, Zhou Q, Zhang L, Ji SJ. miRNAs play important roles in aroma weakening during the shelf life of 'Nanguo' pear after cold storage. Food Res Int 2018; 116:942-952. [PMID: 30717027 DOI: 10.1016/j.foodres.2018.09.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/05/2018] [Accepted: 09/09/2018] [Indexed: 10/28/2022]
Abstract
Cold storage is commonly employed to delay senescence in 'Nanguo' pear after harvest. However, this technique also causes fruit aroma weakening. MicroRNAs are regulators of gene expression at the post-transcriptional level that play important roles in plant development and in eliciting responses to abiotic environmental stressors. In this study, the miRNA transcript profiles of the fruit on the first day (C0, LT0) move in and out of cold storage and the optimum tasting period (COTP, LTOTP) during shelf life at room temperature and after cold storage were analyzed, respectively. 314 known miRNAs were identified in 'Nanguo' pear; 176 and 135 miRNAs were significantly differentially expressed on the C0 vs. LT0 and on the COTP vs. LTOTP, respectively. After prediction the target genes of these differentially expressed miRNAs, 9 s-lipoxygenase (LOX2S), 13 s-lipoxygenase (LOX1_5), hydroperoxide lyase (HPL), and alcohol dehydrogenase (ADH1) were found differentially expressed, which were the key genes during aroma formation. The expression pattern of these target genes and the related miRNAs were identified by RT-PCR. mdm-miR172a-h, mdm-miR159a/b, mdm-miR160a-e, mdm-miR395a-i, mdm-miR399a/b/c, mdm/ppe-miR535a/b, and mdm-miR7120a/b may negatively regulate the target genes expression. These results indicate that miRNAs may play key roles in aroma weakening in cold storage 'Nanguo' pear and provide valuable information for studying the molecular mechanisms of miRNAs in the aroma weakening of fruit due to low temperature.
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Affiliation(s)
- Fei Shi
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Xin Zhou
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Miao-Miao Yao
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Zhuo Tan
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Qian Zhou
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Lei Zhang
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Shu-Juan Ji
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China.
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Yang C, Ren J, Li B, Zhang D, Ma C, Cheng C, Sun Y, Fu L, Shi X. Identification of clinical tumor stages related mRNAs and miRNAs in cervical squamous cell carcinoma. Pathol Res Pract 2018; 214:1638-1647. [PMID: 30149901 DOI: 10.1016/j.prp.2018.07.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/21/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023]
Abstract
OBJECTIVES The aim of this study is to identify the clinical tumor stage related mRNAs and miRNAs, shedding light on the potential molecular mechanisms of cervical squamous cell carcinoma (CSCC). METHODS Firstly, the mRNA and miRNA next-generation sequencing data were downloaded. Secondly, clinical tumor stage correlation analysis of mRNAs and miRNA was performed, followed by the functional enrichment analysis of all clinical tumor stage related mRNAs. Thirdly, differentially expression analysis of mRNAs and miRNA between different clinical tumor stages was performed, followed by target gene prediction of these differentially expressed miRNAs. RESULTS 3 mRNAs (PER1, PRKAB1 and PMM2) and 5 miRNAs (hsa-mir-486, hsa-mir-451, hsa-mir-424, hsa-mir-144 and hsa-mir-450a-2) were overlapped from stage 1, stage 2, stage 3 and stage 4. CONCLUSIONS Alterations of differentially expressed mRNAs and miRNAs may offer important insights into the molecular mechanisms in the pathology of CSCC.
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Affiliation(s)
- Chenggang Yang
- Gu'an Bojian Bio-Technology Co., LTD., Langfang, China; Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Jing Ren
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Bangling Li
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Dongmei Zhang
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Cui Ma
- Gu'an Bojian Bio-Technology Co., LTD., Langfang, China; Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Cheng Cheng
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Yaolan Sun
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Lina Fu
- Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China
| | - Xiaofeng Shi
- Gu'an Bojian Bio-Technology Co., LTD., Langfang, China; Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD., Beijing, China.
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Zhang C, Zhang CD, Ma MH, Dai DQ. Three-microRNA signature identified by bioinformatics analysis predicts prognosis of gastric cancer patients. World J Gastroenterol 2018; 24:1206-1215. [PMID: 29568201 PMCID: PMC5859223 DOI: 10.3748/wjg.v24.i11.1206] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 12/25/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To identify multiple microRNAs (miRNAs) for predicting the prognosis of gastric cancer (GC) patients by bioinformatics analysis.
METHODS The original microarray dataset GSE93415, which included 20 GC and 20 tumor adjacent normal gastric mucosal tissues, was downloaded from the Gene Expression Omnibus database and used for screening differentially expressed miRNAs (DEMs). The cut-off criteria were P < 0.05 and fold change > 2.0. In addition, we acquired the miRNA expression profiles and clinical information of 361 GC patients from The Cancer Genome Atlas database to assess the prognostic role of the DEMs. The target genes of miRNAs were predicted using TargetScan, miRDB, miRWalk, and DIANA, and then the common target genes were selected for functional enrichment analysis.
RESULTS A total of 110 DEMs including 19 up-regulated and 91 down-regulated miRNAs were identified between 20 pairs of GC and tumor adjacent normal tissues, and the Kaplan-Meier survival analysis found that a three-miRNA signature (miR-145-3p, miR-125b-5p, and miR-99a-5p) had an obvious correlation with the survival of GC patients. Furthermore, univariate and multivariate Cox regression analyses indicated that the three-miRNA signature could be a significant prognostic marker in GC patients. The common target genes of the three miRNAs are added up to 108 and used for Gene Functional Enrichment analysis. Biological Process and Molecular Function analyses showed that the target genes are involved in cell recognition, gene silencing and nucleic acid binding, transcription factor activity, and transmembrane receptor activity. Cellular Component analysis revealed that the genes are portion of nucleus, chromatin silencing complex, and TORC1/2 complex. Biological Pathway analysis indicated that the genes participate in several cancer-related pathways, such as the focal adhesion, PI3K, and mTOR signaling pathways.
CONCLUSION This study justified that a three-miRNA signature could play a role in predicting the survival of GC patients.
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Affiliation(s)
- Cheng Zhang
- Department of Gastroenterological Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Chun-Dong Zhang
- Department of Gastroenterological Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Ming-Hui Ma
- Department of Gastroenterological Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Dong-Qiu Dai
- Department of Gastroenterological Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
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Xin G, Chen R, Zhang X. Identification of key microRNAs, transcription factors and genes associated with congenital obstructive nephropathy in a mouse model of megabladder. Gene 2018; 650:77-85. [PMID: 29410288 DOI: 10.1016/j.gene.2018.01.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/21/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The present study aimed to investigate the molecular mechanism underlying congenital obstructive nephropathy (CON). METHODS The microarray dataset GSE70879 was downloaded from the Gene Expression Omnibus, including 3 kidney samples of megabladder mice and 4 control kidneys. Using this dataset, differentially expressed miRNAs (DEMs) were identified between the kidney samples from megabladder mice and controls, followed by identification of the target genes for these DEMs and construction of a DEM and target gene interaction network. Additionally, the target genes were subjected to Gene Ontology and pathway enrichment analyses, and were used for construction of a protein-protein interaction (PPI) network. Finally, regulatory networks were constructed to analyze transcription factors for the key miRNAs. RESULTS From 17 DEMs identified between kidney samples of megabladder mice and controls, 3 key miRNAs were screened, including mmu-miR-150-5p, mmu-miR-374b-5p and mmu-miR-126a-5p. The regulatory networks identified vascular endothelial growth factor A (Vegfa) as the common target gene of mmu-miR-150-5p and five transcription factors, including nuclear receptor subfamily 4, group A, member 2 (Nr4a2), Jun dimerisation protein 2 (Jdp2), Kruppel-like factor 6 (Klf6), Neurexophilin-3 (Nxph3) and RNA binding motif protein 17 (Rbm17). The gene encoding phosphatase and tensin homolog (Pten) was found to be co-regulated by mmu-miR-374b-5p and high mobility group protein A1 (Hmga1), whereas the kirsten rat sarcoma viral oncogene (Kras) was identified as a common target gene of mmu-miR-126a-5p and paired box 6 (Pax6). CONCLUSIONS In summary, the above-listed key miRNAs, transcription factors and key genes may be involved in the development of CON.
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Affiliation(s)
- Guangda Xin
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Rui Chen
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Xiaofei Zhang
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, China.
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Sun H, Zhou Z, Dong Y, Yang A, Jiang J, Chen Z, Guan X, Wang B, Gao S, Jiang B. Expression analysis of microRNAs related to the skin ulceration syndrome of sea cucumber Apostichopus japonicus. Fish Shellfish Immunol 2016; 49:205-212. [PMID: 26723265 DOI: 10.1016/j.fsi.2015.12.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/20/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in many biological processes. To investigate the miRNAs related to skin ulceration syndrome (SUS) of Apostichopus japonicus, small RNA libraries of body wall, intestine, respiratory tree and coelomocytes from healthy and diseased A. japonicus were sequenced on Illumina Hiseq 2000 platform. A total of 247 conserved and 10 novel miRNAs were identified across all libraries. After pair-wise comparisons, 215 miRNAs in body wall, 36 in intestine, 2 in respiratory tree and 38 in coelomocytes showed significant expression differences. Further analyses were conducted on some tissue-specific differentially expressed miRNAs: miR-8 and miR-486-5p in body wall, miR-200-3p, let-7-5p and miR-125 in intestine, miR-278a-3p and bantam in respiratory, miR-10a and miR-184 in coelomocytes. Notably, these miRNAs in some species were reported to function in various physiological or pathological processes associated with immune regulations. Using stem-loop quantitative real time PCR, six representative miRNAs in four tissues were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the six miRNAs ranged from 0.777 to 0.948, which confirmed the consistency and accuracy between these two approaches. This study provides comprehensive expression and regulation patterns of functional miRNAs in different tissues and gives insights into the tissue-specific immune response mechanisms in SUS-infected A. japonicus.
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Affiliation(s)
- Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
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Luo Y, Zhang C, Tang F, Zhao J, Shen C, Wang C, Yu P, Wang M, Li Y, Di JI, Chen R, Rili G. Bioinformatics identification of potentially involved microRNAs in Tibetan with gastric cancer based on microRNA profiling. Cancer Cell Int 2015; 15:115. [PMID: 26692821 PMCID: PMC4676900 DOI: 10.1186/s12935-015-0266-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE The incidence of gastric cancer is high in Chinese Tibetan. This study aimed to identify the differentially expressed microRNAs (miRNAs) and further explore their potential roles in Tibetan with gastric cancer so as to predict potential therapeutic targets. METHODS A total of 10 Tibetan patients (male:female = 6:4) with gastric cancer were enrolled for isolation of matched gastric cancer and adjacent non-cancerous tissue samples. Affymetrix GeneChip microRNA 3.0 Array was employed for detection of miRNA expression in samples. Differential expression analysis between two sample groups was analyzed using Limma package. Then, MultiMiR package was used to predict targets for miRNAs. Following, the target genes were put into DAVID (Database for Annotation, Visualization and Integrated Discovery) to identify the significant pathways of miRNAs. RESULTS Using Limma package in R, a total of 27 differentially expressed miRNAs were screened out in gastric cancer, including 25 down-regulated (e.g. hsa-miR-148a-3p, hsa-miR-148b-3p and hsa-miR-363-3p) and 2 up-regulated miRNAs. According to multiMiR package, a number of 1445 target genes (e.g. Wnt1, KLF4 and S1PR1) of 13 differentially expressed miRNAs were screened out. Among those miRNAs, hsa-miR-148a-3p, hsa-miR-148b-3p and hsa-miR-363-3p were identified with the most target genes. Furthermore, three miRNAs were significantly enriched in numerous common cancer-related pathways, including "Wnt signaling pathway", "MAPK signaling pathway" and "Jak-STAT signaling pathway". CONCLUSIONS The present study identified a downregulation and enrichment in cancer-related pathways of hsa-miR-148a-3p, hsa-miR-148b-3p and hsa-miR-363-3p in Tibetan with gastric cancer, which can be suggested as therapeutic targets.
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Affiliation(s)
- Yushuang Luo
- Research Center for High Altitude Medicine, Qinghai University of Medical School, Kunlong Road 16, Xining, 810001 China.,Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Chengwu Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Feng Tang
- Research Center for High Altitude Medicine, Qinghai University of Medical School, Kunlong Road 16, Xining, 810001 China
| | - Junhui Zhao
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Cunfang Shen
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Cheng Wang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Pengjie Yu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Miaozhou Wang
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Yan Li
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - J I Di
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Rong Chen
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, 810001 China
| | - Ge Rili
- Research Center for High Altitude Medicine, Qinghai University of Medical School, Kunlong Road 16, Xining, 810001 China
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Abstract
Neuroglioma is a complex neuroglial tumor involving dysregulation of many biological pathways at multiple levels. Here, we aim to screen differentially expressed miRNAs (DEMs) as well as the functions and pathways of their target genes in neuroglioma. miRNA high-throughput sequencing data were downloaded from The Cancer Genome Atlas (TCGA), and then the DEMs were subjected to perform principal component analysis (PCA) based on their expression values. Following that, Targetscan software was used to predict the target genes, and enrichment analysis and pathway annotation of these target genes were done by DAVID and KEGG, respectively. Finally, survival analysis between the DEMs and patients' survival time was done, and the miRNAs with prediction potential were obtained. A total of 33 DEMs were obtained, among which 25 miRNAs were upregulated including hsa-mir-675, hsa-mir-196a-1, and hsa-mir-196a-2, while eight miRNAs were downregulated including hsa-mir-1911, hsa-mir-1264, and hsa-mir-1298. Five miRNAs with diagnostic and preventive potentials were significantly correlated with survival time, including has-mir-155, has-mir-199b, has-mi-10a, has-mir-1274b, and has-mir-455. The target genes of miRNA identified in this study played important roles in tumor signaling pathways, and their detailed functions could be further studied so as to explore novel neuroglioma therapies.
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Affiliation(s)
- Haiyuan Yang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, 140# Hanzhong Road, Nanjing, Jiangsu, 210029, China
| | - Ying Wang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, 140# Hanzhong Road, Nanjing, Jiangsu, 210029, China.
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Li B, Rao N, Liu D, Yang Y, Liu D, Li Y, Liu H, Gan T, Ding H, Lin H. Analysis of connection networks among miRNAs differentially expressed in early gastric cancer for disclosing some biological features of disease development. Gene 2014; 548:159-65. [PMID: 25014139 DOI: 10.1016/j.gene.2014.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 05/20/2014] [Accepted: 07/08/2014] [Indexed: 02/05/2023]
Abstract
This paper first identified differentially expressed miRNAs associated with early gastric cancer and then respectively constructed relevant connection networks among the identified differentially expressed miRNAs that corresponded to early gastric cancer and control tissues. Twenty-three differentially expressed miRNAs were identified, 18 of which were different with the related results on the same data, and they provide great discriminatory power between patients and controls. There are not only conserved unchangeable sub-networks but also different sub-networks between the two connection networks. From the consistency and differences between two connection networks, we disclosed several new biological features that promote early gastric cancer development. This study shows 23 miRNAs that are early gastric cancer-specific and are worthy to do further experimental studies. The revealed biological features for early gastric cancer will provide new insights into improved understanding of the molecular mechanisms of this disease.
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Affiliation(s)
- Boyu Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Nini Rao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
| | - Dingyu Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yang Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dingyun Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yi Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hanming Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Tao Gan
- Digestive Endoscopic Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Ding
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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