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RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia.
Biosci Rep. 2020 Jul 31; 40(7)BR

Abstract

Asthenozoospermia is one of the major causes of human male infertility. Long noncoding RNAs (lncRNAs) play critical roles in the spermatogenesis processes. The present study aims to investigate the intricate regulatory network associated with asthenozoospermia. The lncRNAs expression profile was analyzed in the asthenozoospermia seminal plasma exosomes by RNA-sequencing, and the functions of differentially expressed genes (DEGs) were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and DO (Disease Ontology) enrichment analyses. Pearson's correlation test was utilized to calculate the correlation coefficients between lncRNA and mRNAs. Moreover, the lncRNA-miRNA-mRNA co-expression network was constructed with bioinformatics. From the co-expression analyses, we identified the cis regulated correlation pairs lncRNA-mRNA. To confirm sequencing results with five of the identified DElncRNAs were verified with quantitative reverse-transcription polymerase chain reaction (qRT-PCR). We identified 4228 significantly DEGs, 995 known DElncRNAs, 2338 DEmRNAs and 11,706 novel DElncRNAs between asthenozoospermia and normal group. GO and KEGG analyses showed that the DEGs were mainly associated with metabolism, transcription, ribosome and channel activity. We found 254,981 positive correlations lncRNA-mRNA pairs through correlation analysis. The detailed lncRNA-miRNA-mRNA regulatory network included 11 lncRNAs, 35 miRNAs and 59 mRNAs. From the co-expression analyses, we identified 7 cis-regulated correlation pairs lncRNA-mRNA. Additionally, the qRT-PCR analysis confirmed our sequencing results. Our study constructed the lncRNA-mRNA-miRNA regulation networks in asthenozoospermia. Therefore, the study findings provide a set of pivotal lncRNAs for future investigation into the molecular mechanisms of asthenozoospermia.

Authors+Show Affiliations

Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 570102, Hainan, China. Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China.Department of Emergency, Hainan General Hospital, Haikou 570311, Hainan, China.Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 570102, Hainan, China. Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China.Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 570102, Hainan, China. Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China.Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 570102, Hainan, China. Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China.Division of Biological Sciences, University of California, San Diego, California 92093, U.S.A.Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 570102, Hainan, China. Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China.Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China. Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 570102, Hainan, China. Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32614449

Citation

Lu, Hui, et al. "RNA-sequencing and Bioinformatics Analysis of Long Noncoding RNAs and mRNAs in the Asthenozoospermia." Bioscience Reports, vol. 40, no. 7, 2020.
Lu H, Xu D, Wang P, et al. RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia. Biosci Rep. 2020;40(7).
Lu, H., Xu, D., Wang, P., Sun, W., Xue, X., Hu, Y., Xie, C., & Ma, Y. (2020). RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia. Bioscience Reports, 40(7). https://doi.org/10.1042/BSR20194041
Lu H, et al. RNA-sequencing and Bioinformatics Analysis of Long Noncoding RNAs and mRNAs in the Asthenozoospermia. Biosci Rep. 2020 Jul 31;40(7) PubMed PMID: 32614449.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia. AU - Lu,Hui, AU - Xu,Dongchuan, AU - Wang,Ping, AU - Sun,Wenye, AU - Xue,Xinhuai, AU - Hu,Yuxin, AU - Xie,Chunli, AU - Ma,Yanlin, PY - 2019/11/20/received PY - 2020/05/15/revised PY - 2020/06/01/accepted PY - 2020/7/3/pubmed PY - 2020/7/3/medline PY - 2020/7/3/entrez KW - RNA sequencing KW - asthenozoospermia KW - exosomes KW - lncRNAs KW - mRNAs JF - Bioscience reports JO - Biosci. Rep. VL - 40 IS - 7 N2 - Asthenozoospermia is one of the major causes of human male infertility. Long noncoding RNAs (lncRNAs) play critical roles in the spermatogenesis processes. The present study aims to investigate the intricate regulatory network associated with asthenozoospermia. The lncRNAs expression profile was analyzed in the asthenozoospermia seminal plasma exosomes by RNA-sequencing, and the functions of differentially expressed genes (DEGs) were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and DO (Disease Ontology) enrichment analyses. Pearson's correlation test was utilized to calculate the correlation coefficients between lncRNA and mRNAs. Moreover, the lncRNA-miRNA-mRNA co-expression network was constructed with bioinformatics. From the co-expression analyses, we identified the cis regulated correlation pairs lncRNA-mRNA. To confirm sequencing results with five of the identified DElncRNAs were verified with quantitative reverse-transcription polymerase chain reaction (qRT-PCR). We identified 4228 significantly DEGs, 995 known DElncRNAs, 2338 DEmRNAs and 11,706 novel DElncRNAs between asthenozoospermia and normal group. GO and KEGG analyses showed that the DEGs were mainly associated with metabolism, transcription, ribosome and channel activity. We found 254,981 positive correlations lncRNA-mRNA pairs through correlation analysis. The detailed lncRNA-miRNA-mRNA regulatory network included 11 lncRNAs, 35 miRNAs and 59 mRNAs. From the co-expression analyses, we identified 7 cis-regulated correlation pairs lncRNA-mRNA. Additionally, the qRT-PCR analysis confirmed our sequencing results. Our study constructed the lncRNA-mRNA-miRNA regulation networks in asthenozoospermia. Therefore, the study findings provide a set of pivotal lncRNAs for future investigation into the molecular mechanisms of asthenozoospermia. SN - 1573-4935 UR - https://www.unboundmedicine.com/medline/citation/32614449/RNA-Sequencing_and_Bioinformatics_Analysis_of_Long_Noncoding_RNAs_and_mRNAs_in_the_asthenozoospermia L2 - https://portlandpress.com/bioscirep/article-lookup/doi/10.1042/BSR20194041 DB - PRIME DP - Unbound Medicine ER -
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