Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer
Background: Long non-coding RNAs (lncRNAs) are importantly involved in the initiation and progression of non-small cell lung cancer (NSCLC). However, the classification and mechanisms of lncRNAs remain largely elusive. Aim: Hence, we addressed this through bioinformatics analysis. Methods and result...
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Elsevier
2024-12-01
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| Series: | Biochemistry and Biophysics Reports |
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| author | Yinqiang Liu Hongjv Yang Guoli Lv Jin Duan Wei Zhao Yunfei Shi Youming Lei |
| author_facet | Yinqiang Liu Hongjv Yang Guoli Lv Jin Duan Wei Zhao Yunfei Shi Youming Lei |
| author_sort | Yinqiang Liu |
| collection | DOAJ |
| description | Background: Long non-coding RNAs (lncRNAs) are importantly involved in the initiation and progression of non-small cell lung cancer (NSCLC). However, the classification and mechanisms of lncRNAs remain largely elusive. Aim: Hence, we addressed this through bioinformatics analysis. Methods and results: We utilized microarray technology to analyze lncRNAs and mRNAs in twenty paired NSCLC tumor tissues and adjacent normal tissues. Gene set enrichment analysis, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology were conducted to discern the biological functions of identified differentially expressed transcripts. Additionally, networks of lncRNA-mRNA co-expression, including cis-regulation, lncRNA-transcription factor (TF)-mRNA, trans-regulation, and lncRNA-miRNA-mRNA interactions were explored. Furthermore, the study examined differentially expressed transcripts and their prognostic values in a large RNA-seq dataset of 1016 NSCLC tumors and normal tissues extracted from the Cancer Genome Atlas (TCGA). The analysis revealed 391 lncRNAs and 344 mRNAs with differential expression in NSCLC tumor tissues compared to adjacent normal tissues. Subsequently, 43,557 co-expressed lncRNA-mRNA pairs were identified, including 27 lncRNA-mRNA pairs in cis, 9 lncRNA-TF-mRNA networks, 34 lncRNA-mRNA pairs in trans, and 8701 lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks. Notably, these lncRNAs were found to be involved in immune-related pathways. Six significant transcripts, including NTF4, PTPRD-AS, ITGA11, HID1-AS1, RASGRF2-AS1, and TBX2-AS1, were identified within the ceRNA network and trans-regulation. Conclusion: This study brings important insights into the regulatory roles of lncRNAs in NSCLC, providing a fresh perspective on lncRNA research in tumor biology. |
| format | Article |
| id | doaj-art-7aa86472fbbe40498b718aed58e522a6 |
| institution | OA Journals |
| issn | 2405-5808 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biochemistry and Biophysics Reports |
| spelling | doaj-art-7aa86472fbbe40498b718aed58e522a62025-08-20T02:19:54ZengElsevierBiochemistry and Biophysics Reports2405-58082024-12-014010183210.1016/j.bbrep.2024.101832Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancerYinqiang Liu0Hongjv Yang1Guoli Lv2Jin Duan3Wei Zhao4Yunfei Shi5Youming Lei6Department of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaDepartment of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaDepartment of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaDepartment of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaDepartment of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaCorresponding author.; Department of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaCorresponding author.; Department of Geriatric Thoracic Surgery, the First Hospital of Kunming Medical University, Kunming, ChinaBackground: Long non-coding RNAs (lncRNAs) are importantly involved in the initiation and progression of non-small cell lung cancer (NSCLC). However, the classification and mechanisms of lncRNAs remain largely elusive. Aim: Hence, we addressed this through bioinformatics analysis. Methods and results: We utilized microarray technology to analyze lncRNAs and mRNAs in twenty paired NSCLC tumor tissues and adjacent normal tissues. Gene set enrichment analysis, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology were conducted to discern the biological functions of identified differentially expressed transcripts. Additionally, networks of lncRNA-mRNA co-expression, including cis-regulation, lncRNA-transcription factor (TF)-mRNA, trans-regulation, and lncRNA-miRNA-mRNA interactions were explored. Furthermore, the study examined differentially expressed transcripts and their prognostic values in a large RNA-seq dataset of 1016 NSCLC tumors and normal tissues extracted from the Cancer Genome Atlas (TCGA). The analysis revealed 391 lncRNAs and 344 mRNAs with differential expression in NSCLC tumor tissues compared to adjacent normal tissues. Subsequently, 43,557 co-expressed lncRNA-mRNA pairs were identified, including 27 lncRNA-mRNA pairs in cis, 9 lncRNA-TF-mRNA networks, 34 lncRNA-mRNA pairs in trans, and 8701 lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks. Notably, these lncRNAs were found to be involved in immune-related pathways. Six significant transcripts, including NTF4, PTPRD-AS, ITGA11, HID1-AS1, RASGRF2-AS1, and TBX2-AS1, were identified within the ceRNA network and trans-regulation. Conclusion: This study brings important insights into the regulatory roles of lncRNAs in NSCLC, providing a fresh perspective on lncRNA research in tumor biology.http://www.sciencedirect.com/science/article/pii/S2405580824001961Non-small cell lung cancerLong non-coding RNAscis-Regulationtrans-RegulationTumorigenesis |
| spellingShingle | Yinqiang Liu Hongjv Yang Guoli Lv Jin Duan Wei Zhao Yunfei Shi Youming Lei Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer Biochemistry and Biophysics Reports Non-small cell lung cancer Long non-coding RNAs cis-Regulation trans-Regulation Tumorigenesis |
| title | Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer |
| title_full | Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer |
| title_fullStr | Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer |
| title_full_unstemmed | Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer |
| title_short | Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer |
| title_sort | integration analysis of cis and trans regulatory long non coding rnas associated with immune related pathways in non small cell lung cancer |
| topic | Non-small cell lung cancer Long non-coding RNAs cis-Regulation trans-Regulation Tumorigenesis |
| url | http://www.sciencedirect.com/science/article/pii/S2405580824001961 |
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