Bioinformatics Analysis of Differentially Expressed Genes and miRNAs in Low-Grade Gliomas
Identifieur interne : 000747 ( Main/Exploration ); précédent : 000746; suivant : 000748Bioinformatics Analysis of Differentially Expressed Genes and miRNAs in Low-Grade Gliomas
Auteurs : Mohammed Amine Bendahou [Maroc] ; Azeddine Ibrahimi [Maroc] ; Mahjouba Boutarbouch [Maroc]Source :
- Cancer Informatics [ 1176-9351 ] ; 2020.
Abstract
Low-grade glioma is the most common type of primary intracranial tumor. In the last 3 years, new observations of molecular precursors in adults with gliomas have led to a modification in the histopathologic classification of these brain tumors. Among the biomarkers that have been highlighted, we have the micro RNAs (miRNAs) which play a crucial role in the regulation of gene expression and the long noncoding RNAs (lncRNAs) controlling various cellular and metabolic pathways. In our study, large-scale data on sequenced RNA and miRNAs from 516 patients were obtained from the Cancer Genome Atlas database by the TCGAbiolinks package. We identified the differential expression of miRNAs and genes using the Limma package and then we used the ClusterProfiler package for annotations of the biological pathways of the expressed genes, the survival package to estimate the survival analysis, and the GDCRNATools package to determine miRNAs-genes and miRNAs-lncRNAs interactions. We obtained a significant correlation between the miRNAs identified and the overall survival of the patients (log-rank
Url:
DOI: 10.1177/1176935120969692
PubMed: 33223819
PubMed Central: 7649870
Affiliations:
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Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco</nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Boutarbouch, Mahjouba" sort="Boutarbouch, Mahjouba" uniqKey="Boutarbouch M" first="Mahjouba" last="Boutarbouch">Mahjouba Boutarbouch</name><affiliation wicri:level="1"><nlm:aff id="aff2-1176935120969692">Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco</nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University in 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Mohammed V University in Rabat, Morocco</nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Ibrahimi, Azeddine" sort="Ibrahimi, Azeddine" uniqKey="Ibrahimi A" first="Azeddine" last="Ibrahimi">Azeddine Ibrahimi</name><affiliation wicri:level="1"><nlm:aff id="aff1-1176935120969692">Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco</nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University in Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Boutarbouch, Mahjouba" sort="Boutarbouch, Mahjouba" uniqKey="Boutarbouch M" first="Mahjouba" last="Boutarbouch">Mahjouba Boutarbouch</name><affiliation wicri:level="1"><nlm:aff id="aff2-1176935120969692">Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University in Rabat, Morocco</nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University in Rabat</wicri:regionArea></affiliation></author></analytic><series><title level="j">Cancer Informatics</title><idno type="eISSN">1176-9351</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Low-grade glioma is the most common type of primary intracranial tumor. In the last 3 years, new observations of molecular precursors in adults with gliomas have led to a modification in the histopathologic classification of these brain tumors. Among the biomarkers that have been highlighted, we have the micro RNAs (miRNAs) which play a crucial role in the regulation of gene expression and the long noncoding RNAs (lncRNAs) controlling various cellular and metabolic pathways. In our study, large-scale data on sequenced RNA and miRNAs from 516 patients were obtained from the Cancer Genome Atlas database by the TCGAbiolinks package. We identified the differential expression of miRNAs and genes using the Limma package and then we used the ClusterProfiler package for annotations of the biological pathways of the expressed genes, the survival package to estimate the survival analysis, and the GDCRNATools package to determine miRNAs-genes and miRNAs-lncRNAs interactions. We obtained a significant correlation between the miRNAs identified and the overall survival of the patients (log-rank <italic>P</italic> < .05) and we have theoretically proposed a novel network of miRNAs involved in low-grade gliomas, specifically astrocytomas and oligodendrogliomas, which combine both genes and lncRNAs.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wen, Py" uniqKey="Wen P">PY Wen</name></author><author><name sortKey="Huse, Jt" uniqKey="Huse J">JT. 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