Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia
Sarah Albogami Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi ArabiaCorrespondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email dr.sarah@tu.edu.saPurpose: According to the Wor...
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| Format: | Article |
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Dove Medical Press
2023-09-01
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| Series: | Pharmacogenomics and Personalized Medicine |
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| Online Access: | https://www.dovepress.com/genome-wide-identification-of-lncrna-and-mrna-for-diagnosing-type-2-di-peer-reviewed-fulltext-article-PGPM |
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| author | Albogami S |
| author_facet | Albogami S |
| author_sort | Albogami S |
| collection | DOAJ |
| description | Sarah Albogami Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi ArabiaCorrespondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email dr.sarah@tu.edu.saPurpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with diabetes mellitus. To our knowledge, no research has addressed the potential of noncoding RNA as a diagnostic and/or management biomarker for patients with type 2 diabetes mellitus (T2DM) living in high-altitude areas. This study aimed to identify molecular biomarkers influencing patients with T2DM living in high-altitude areas by analyzing lncRNA and mRNA.Patients and Methods: RNA sequencing and bioinformatics analyses were used to identify significantly expressed lncRNAs and mRNAs in T2DM and healthy control groups. Coding potential was analyzed using coding–noncoding indices, the coding potential calculator, and PFAM, and the lncRNA function was predicted using Pearson’s correlation. Differentially expressed transcripts between the groups were identified, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify the biological functions of both lncRNAs and mRNAs.Results: We assembled 1766 lncRNAs in the T2DM group, of which 582 were novel. This study identified three lncRNA target genes (KLF2, CREBBP, and REL) and seven mRNAs (PIK3CD, PIK3R5, IL6R, TYK2, ZAP70, LAMTOR4, and SSH2) significantly enriched in important pathways, playing a role in the progression of T2DM.Conclusion: To the best of our knowledge, this comprehensive study is the first to explore the applicability of certain lncRNAs as diagnostic or management biomarkers for T2DM in females in Taif City, Saudi Arabia through the genome-wide identification of lncRNA and mRNA profiling using RNA seq and bioinformatics analysis. Our findings could help in the early diagnosis of T2DM and in designing effective therapeutic targets.Keywords: T2DM, long noncoding RNA, high altitude, bioinformatic analyses |
| first_indexed | 2024-03-12T00:01:31Z |
| format | Article |
| id | doaj.art-d3f16ca8256346c4a05b1e2972d3f9aa |
| institution | Directory Open Access Journal |
| issn | 1178-7066 |
| language | English |
| last_indexed | 2024-03-12T00:01:31Z |
| publishDate | 2023-09-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | Pharmacogenomics and Personalized Medicine |
| spelling | doaj.art-d3f16ca8256346c4a05b1e2972d3f9aa2023-09-17T16:39:52ZengDove Medical PressPharmacogenomics and Personalized Medicine1178-70662023-09-01Volume 1685988286719Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi ArabiaAlbogami SSarah Albogami Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi ArabiaCorrespondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email dr.sarah@tu.edu.saPurpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with diabetes mellitus. To our knowledge, no research has addressed the potential of noncoding RNA as a diagnostic and/or management biomarker for patients with type 2 diabetes mellitus (T2DM) living in high-altitude areas. This study aimed to identify molecular biomarkers influencing patients with T2DM living in high-altitude areas by analyzing lncRNA and mRNA.Patients and Methods: RNA sequencing and bioinformatics analyses were used to identify significantly expressed lncRNAs and mRNAs in T2DM and healthy control groups. Coding potential was analyzed using coding–noncoding indices, the coding potential calculator, and PFAM, and the lncRNA function was predicted using Pearson’s correlation. Differentially expressed transcripts between the groups were identified, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify the biological functions of both lncRNAs and mRNAs.Results: We assembled 1766 lncRNAs in the T2DM group, of which 582 were novel. This study identified three lncRNA target genes (KLF2, CREBBP, and REL) and seven mRNAs (PIK3CD, PIK3R5, IL6R, TYK2, ZAP70, LAMTOR4, and SSH2) significantly enriched in important pathways, playing a role in the progression of T2DM.Conclusion: To the best of our knowledge, this comprehensive study is the first to explore the applicability of certain lncRNAs as diagnostic or management biomarkers for T2DM in females in Taif City, Saudi Arabia through the genome-wide identification of lncRNA and mRNA profiling using RNA seq and bioinformatics analysis. Our findings could help in the early diagnosis of T2DM and in designing effective therapeutic targets.Keywords: T2DM, long noncoding RNA, high altitude, bioinformatic analyseshttps://www.dovepress.com/genome-wide-identification-of-lncrna-and-mrna-for-diagnosing-type-2-di-peer-reviewed-fulltext-article-PGPMt2dmlong noncoding rnahigh altitudebioinformatic analyses |
| spellingShingle | Albogami S Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia Pharmacogenomics and Personalized Medicine t2dm long noncoding rna high altitude bioinformatic analyses |
| title | Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia |
| title_full | Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia |
| title_fullStr | Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia |
| title_full_unstemmed | Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia |
| title_short | Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia |
| title_sort | genome wide identification of lncrna and mrna for diagnosing type 2 diabetes in saudi arabia |
| topic | t2dm long noncoding rna high altitude bioinformatic analyses |
| url | https://www.dovepress.com/genome-wide-identification-of-lncrna-and-mrna-for-diagnosing-type-2-di-peer-reviewed-fulltext-article-PGPM |
| work_keys_str_mv | AT albogamis genomewideidentificationoflncrnaandmrnafordiagnosingtype2diabetesinsaudiarabia |