Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate
Xiangpu Wang, Siyuan Guo, Xinli Zhou, Yupei Wang, Ting Zhang, Renji Chen Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People’s Republic of ChinaCorrespondence: Renji Ch...
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| Format: | Article |
| Language: | English |
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Dove Medical Press
2021-12-01
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| Series: | International Journal of General Medicine |
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| Online Access: | https://www.dovepress.com/exploring-the-molecular-mechanism-of-lncrnamirnamrna-networks-in-non-s-peer-reviewed-fulltext-article-IJGM |
| _version_ | 1818279890790645760 |
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| author | Wang X Guo S Zhou X Wang Y Zhang T Chen R |
| author_facet | Wang X Guo S Zhou X Wang Y Zhang T Chen R |
| author_sort | Wang X |
| collection | DOAJ |
| description | Xiangpu Wang, Siyuan Guo, Xinli Zhou, Yupei Wang, Ting Zhang, Renji Chen Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People’s Republic of ChinaCorrespondence: Renji ChenDepartment of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People’s Republic of ChinaFax +86-10-57099151Email chenrenji@126.comBackground: Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect. Growing evidence has demonstrated the competing endogenous RNA (ceRNA) hypothesis has played a role in the pathogenesis of NSCL/P. Here, we identified the important lncRNAs in NSCL/P and constructed a ceRNA regulatory network to predict their underlying functional mechanism.Methods: Total RNA isolated from the peripheral blood samples were analyzed by the Human Clariom D Affymetrix platform and differentially expressed genes (DEGs) were identified. Using the limma package in R software, DEGs in the expression profile of GSE42589 were identified from Gene Expression Omnibus (GEO) database. Co-differentially expressed lncRNAs (co-DElncRNAs) were used to predict the microRNAs that may bind to them. Co-differentially expressed mRNAs (co-DEmRNAs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The hub genes were screened using the cytohubba plug-in in Cytoscape. A ceRNA network was built to investigate the molecular mechanism underlying the etiology of NSCL/P. The expression levels of lncRNAs, miRNAs, and mRNAs in the network were assessed by quantitative real-time polymerase chain reaction (qRT-PCR).Results: We found 116 DElncRNAs and 2955 DEmRNAs from the GSE42589 dataset, and 2626 DElncRNAs and 2771 DEmRNAs from the Human Clariom D gene chip. A network of co-DEmRNAs containing 3712 edges and 621 nodes were identified by PPI analysis. A ceRNA regulatory network comprising lncRNA USP17L6P, hsa-miR-449c-5p, and MYC was established. qRT-PCR results revealed significantly lower expression levels of lncRNA USP17L6P and c-Myc in NSCL/P tissues, while the expression level of hsa-miR-449c-5p was higher as compared to control samples (p < 0.05).Conclusion: The identified lncRNAs and the established ceRNA regulatory network provide novel insight into the pathogenesis of NSCL/P, therefore hold great promise in NSCL/P management in clinical practice.Keywords: lncRNAs, ceRNAs, NSCL/P, bioinformatics |
| first_indexed | 2024-12-12T23:40:31Z |
| format | Article |
| id | doaj.art-a000542473bb4c028042b58f83fc6220 |
| institution | Directory Open Access Journal |
| issn | 1178-7074 |
| language | English |
| last_indexed | 2024-12-12T23:40:31Z |
| publishDate | 2021-12-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | International Journal of General Medicine |
| spelling | doaj.art-a000542473bb4c028042b58f83fc62202022-12-22T00:07:13ZengDove Medical PressInternational Journal of General Medicine1178-70742021-12-01Volume 149931994371564Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft PalateWang XGuo SZhou XWang YZhang TChen RXiangpu Wang, Siyuan Guo, Xinli Zhou, Yupei Wang, Ting Zhang, Renji Chen Department of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People’s Republic of ChinaCorrespondence: Renji ChenDepartment of Oral and Maxillofacial Plastic and Trauma Surgery, Center of Cleft Lip and Palate Treatment, Beijing Stomatological Hospital, Capital Medical University, Beijing, People’s Republic of ChinaFax +86-10-57099151Email chenrenji@126.comBackground: Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect. Growing evidence has demonstrated the competing endogenous RNA (ceRNA) hypothesis has played a role in the pathogenesis of NSCL/P. Here, we identified the important lncRNAs in NSCL/P and constructed a ceRNA regulatory network to predict their underlying functional mechanism.Methods: Total RNA isolated from the peripheral blood samples were analyzed by the Human Clariom D Affymetrix platform and differentially expressed genes (DEGs) were identified. Using the limma package in R software, DEGs in the expression profile of GSE42589 were identified from Gene Expression Omnibus (GEO) database. Co-differentially expressed lncRNAs (co-DElncRNAs) were used to predict the microRNAs that may bind to them. Co-differentially expressed mRNAs (co-DEmRNAs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The hub genes were screened using the cytohubba plug-in in Cytoscape. A ceRNA network was built to investigate the molecular mechanism underlying the etiology of NSCL/P. The expression levels of lncRNAs, miRNAs, and mRNAs in the network were assessed by quantitative real-time polymerase chain reaction (qRT-PCR).Results: We found 116 DElncRNAs and 2955 DEmRNAs from the GSE42589 dataset, and 2626 DElncRNAs and 2771 DEmRNAs from the Human Clariom D gene chip. A network of co-DEmRNAs containing 3712 edges and 621 nodes were identified by PPI analysis. A ceRNA regulatory network comprising lncRNA USP17L6P, hsa-miR-449c-5p, and MYC was established. qRT-PCR results revealed significantly lower expression levels of lncRNA USP17L6P and c-Myc in NSCL/P tissues, while the expression level of hsa-miR-449c-5p was higher as compared to control samples (p < 0.05).Conclusion: The identified lncRNAs and the established ceRNA regulatory network provide novel insight into the pathogenesis of NSCL/P, therefore hold great promise in NSCL/P management in clinical practice.Keywords: lncRNAs, ceRNAs, NSCL/P, bioinformaticshttps://www.dovepress.com/exploring-the-molecular-mechanism-of-lncrnamirnamrna-networks-in-non-s-peer-reviewed-fulltext-article-IJGMlncrnascernasnscl/pbioinformatics |
| spellingShingle | Wang X Guo S Zhou X Wang Y Zhang T Chen R Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate International Journal of General Medicine lncrnas cernas nscl/p bioinformatics |
| title | Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate |
| title_full | Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate |
| title_fullStr | Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate |
| title_full_unstemmed | Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate |
| title_short | Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate |
| title_sort | exploring the molecular mechanism of lncrna ndash mirna ndash mrna networks in non syndromic cleft lip with or without cleft palate |
| topic | lncrnas cernas nscl/p bioinformatics |
| url | https://www.dovepress.com/exploring-the-molecular-mechanism-of-lncrnamirnamrna-networks-in-non-s-peer-reviewed-fulltext-article-IJGM |
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