Dataset Information

Co-expression network analysis of the lncRNAs and mRNAs associated with cervical cancer progression.

ABSTRACT: Introduction:Cervical cancer is the second most common type of cancer and the third leading cause of cancer deaths in females in developing countries. Recent studies showed that long non-coding RNAs play a key role in human cancers. However, the molecular mechanisms underlying the initiation and progression of cervical cancer remained to be further explored. Material and methods:In this study, we explored the differential expression of lncRNAs and mRNAs in cervical cancer progression by analyzing the public dataset GSE63514. Next, PPI and co-expression networks were constructed to reveal the potential roles of cervical cancer related mRNAs and lncRNAs. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed to explore functions of differentially expressed genes (DEGs) in cervical cancer. Results:In the present study, we observed that 3021 mRNAs were up-regulated and 1605 mRNAs were down-regulated in cervical cancer progression. Meanwhile, we for the first time found that 172 lncRNAs were up-regulated and 106 lncRNAs were down-regulated in cervical cancer progression. Co-expression network analysis showed that lncRNAs were widely co-expressed with cell cycle related genes in cervical cancer, implicating the important roles of these lncRNAs in cell proliferation regulation. Of note, we identified two hub lncRNA-mRNA networks involved in regulating various biological processes in cervical cancer progression. Conclusions:Our results identified key mRNAs and lncRNAs in cervical cancer progression. This study will provide novel insights to explore the potential mechanisms underlying cervical cancer progression.

SUBMITTER: Jiang L

PROVIDER: S-EPMC6524193 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Co-expression network analysis of the lncRNAs and mRNAs associated with cervical cancer progression.

Jiang Li L Hong Li L Yang Wenwu W Zhao Yuzi Y Tan Aili A Li Yang Y

Archives of medical science : AMS 20190430 3

<h4>Introduction</h4>Cervical cancer is the second most common type of cancer and the third leading cause of cancer deaths in females in developing countries. Recent studies showed that long non-coding RNAs play a key role in human cancers. However, the molecular mechanisms underlying the initiation and progression of cervical cancer remained to be further explored.<h4>Material and methods</h4>In this study, we explored the differential expression of lncRNAs and mRNAs in cervical cancer progress ...[more]

PMID: 31110543

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Project description:Although studies provide insights into the neurobiology of stress and depression, the exact molecular mechanisms underlying their pathologies remain largely unknown. Long non-coding RNA (lncRNA) has been implicated in brain functions and behavior. A potential link between lncRNA and psychiatric disorders has been proposed. However, it remains undetermined whether IncRNA regulation, in the brain, contributes to stress or depression pathologies. In this study, we used a valid animal model of depression-like symptoms; namely learned helplessness, RNA-seq, Gene Ontology and co-expression network analyses to profile the expression pattern of lncRNA and mRNA in the hippocampus of mice. We identified 6346 differentially expressed transcripts. Among them, 340 lncRNAs and 3559 protein coding mRNAs were differentially expressed in helpless mice in comparison with control and/or non-helpless mice (inescapable stress resilient mice). Gene Ontology and pathway enrichment analyses indicated that induction of helplessness altered expression of mRNAs enriched in fundamental biological functions implicated in stress/depression neurobiology such as synaptic, metabolic, cell survival and proliferation, developmental and chromatin modification functions. To explore the possible regulatory roles of the altered lncRNAs, we constructed co-expression networks composed of the lncRNAs and mRNAs. Among our differentially expressed lncRNAs, 17% showed significant correlation with genes. Functional co-expression analysis linked the identified lncRNAs to several cellular mechanisms implicated in stress/depression neurobiology. Importantly, 57% of the identified regulatory lncRNAs significantly correlated with 18 different synapse-related functions. Thus, the current study identifies for the first time distinct groups of lncRNAs regulated by induction of learned helplessness in the mouse brain. Our results suggest that lncRNA-directed regulatory mechanisms might contribute to stress-induced pathologies; in particular, to inescapable stress-induced synaptic modifications.

Project description:In dairy cattle, endometritis is a severe infectious disease that occurs following parturition. It is clear that genetic factors are involved in the etiology of endometritis, however, the molecular pathogenesis of endometritis is not entirely understood. In this study, a system biology approach was used to better understand the molecular mechanisms underlying the development of endometritis. Forty transcriptomic datasets comprising of 20 RNA-Seq (GSE66825) and 20 miRNA-Seq (GSE66826) were obtained from the GEO database. Next, the co-expressed modules were constructed based on RNA-Seq (Rb-modules) and miRNA-Seq (mb-modules) data, separately, using a weighted gene co-expression network analysis (WGCNA) approach. Preservation analysis was used to find the non-preserved Rb-modules in endometritis samples. Afterward, the non-preserved Rb-modules were assigned to the mb-modules to construct the integrated regulatory networks. Just highly connected genes (hubs) in the networks were considered and functional enrichment analysis was used to identify the biological pathways associated with the development of the disease. Furthermore, additional bioinformatic analysis including protein-protein interactions network and miRNA target prediction were applied to enhance the reliability of the results. Thirty-five Rb-modules and 10 mb-modules were identified and 19 and 10 modules were non-preserved, respectively, which were enriched in biological pathways related to endometritis like inflammation and ciliogenesis. Two non-preserved Rb-modules were significantly assigned to three mb-modules and three and two important sub-networks in the Rb-modules were identified, respectively, including important mRNAs, lncRNAs and miRNAs genes like IRAK1, CASP3, CCDC40, CCDC39, ZMYND10, FOXJ1, TLR4, IL10, STAT3, FN1, AKT1, CD68, ENSBTAG00000049936, ENSBTAG00000050527, ENSBTAG00000051242, ENSBTAG00000049287, bta-miR-449, bta-miR-484, bta-miR-149, bta-miR-30b and bta-miR-423. The potential roles of these genes have been previously demonstrated in endometritis or related pathways, which reinforced putative functions of the suggested integrated regulatory networks in the endometritis pathogenesis. These findings may help further elucidate the underlying mechanisms of bovine endometritis.

Dataset Information

Co-expression network analysis of the lncRNAs and mRNAs associated with cervical cancer progression.

Publications

Co-expression network analysis of the lncRNAs and mRNAs associated with cervical cancer progression.

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