Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer
Gastric cancer (GC) is the fourth most common malignant tumor. The mechanism underlying GC occurrence and development remains unclear. Previous studies have indicated that long non-coding RNAs (lncRNAs) are significantly associated with gastric cancer, but a systematic understanding of the role of l...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Cell and Developmental Biology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fcell.2020.00557/full |
| _version_ | 1819145118008999936 |
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| author | Nan Xiao Nan Xiao Yang Hu Liran Juan |
| author_facet | Nan Xiao Nan Xiao Yang Hu Liran Juan |
| author_sort | Nan Xiao |
| collection | DOAJ |
| description | Gastric cancer (GC) is the fourth most common malignant tumor. The mechanism underlying GC occurrence and development remains unclear. Previous studies have indicated that long non-coding RNAs (lncRNAs) are significantly associated with gastric cancer, but a systematic understanding of the role of lncRNAs in gastric cancer is lacking. In recent years, with the development of next-generation sequencing technology, tens of thousands of lncRNAs have been discovered. However, a large number of unannotated lncRNAs remain unidentified in different tissues, including potential gastric cancer-related lncRNAs. In this study, RNA sequencing (RNA-seq) data from 16 samples of eight gastric cancer patients were obtained and analyzed. A total of 1,854 previously unannotated lncRNAs were identified by ab initio assembly, and 520 differentially expressed lncRNAs were validated in the TCGA expression dataset. Methylation and copy number variation (CNV) array data from the same sample were integrated in the analysis. Changes in DNA methylation levels and CNVs may be responsible for the differential expression of 91 lncRNAs. Differentially expressed lncRNAs were enriched in coexpressed clusters of genes related to functions such as cell signaling, cell cycle, immune response, metabolic processes, angiogenesis, and regulation of retinoic acid (RA) receptors. Finally, a differentially expressed lncRNA, AC004510.3, was identified as a potential biomarker for the prediction of the overall survival of gastric cancer patients. |
| first_indexed | 2024-12-22T12:52:56Z |
| format | Article |
| id | doaj.art-791979288f5844bda4a10060054ae1ca |
| institution | Directory Open Access Journal |
| issn | 2296-634X |
| language | English |
| last_indexed | 2024-12-22T12:52:56Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cell and Developmental Biology |
| spelling | doaj.art-791979288f5844bda4a10060054ae1ca2022-12-21T18:25:10ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2020-06-01810.3389/fcell.2020.00557551666Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric CancerNan Xiao0Nan Xiao1Yang Hu2Liran Juan3School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, ChinaSchool of Pharmaceutical Sciences, Tsinghua University, Beijing, ChinaSchool of Life Sciences and Technology, Harbin Institute of Technology, Harbin, ChinaSchool of Life Sciences and Technology, Harbin Institute of Technology, Harbin, ChinaGastric cancer (GC) is the fourth most common malignant tumor. The mechanism underlying GC occurrence and development remains unclear. Previous studies have indicated that long non-coding RNAs (lncRNAs) are significantly associated with gastric cancer, but a systematic understanding of the role of lncRNAs in gastric cancer is lacking. In recent years, with the development of next-generation sequencing technology, tens of thousands of lncRNAs have been discovered. However, a large number of unannotated lncRNAs remain unidentified in different tissues, including potential gastric cancer-related lncRNAs. In this study, RNA sequencing (RNA-seq) data from 16 samples of eight gastric cancer patients were obtained and analyzed. A total of 1,854 previously unannotated lncRNAs were identified by ab initio assembly, and 520 differentially expressed lncRNAs were validated in the TCGA expression dataset. Methylation and copy number variation (CNV) array data from the same sample were integrated in the analysis. Changes in DNA methylation levels and CNVs may be responsible for the differential expression of 91 lncRNAs. Differentially expressed lncRNAs were enriched in coexpressed clusters of genes related to functions such as cell signaling, cell cycle, immune response, metabolic processes, angiogenesis, and regulation of retinoic acid (RA) receptors. Finally, a differentially expressed lncRNA, AC004510.3, was identified as a potential biomarker for the prediction of the overall survival of gastric cancer patients.https://www.frontiersin.org/article/10.3389/fcell.2020.00557/fullgastric cancerlncRNAdifferential expressioncoexpression networksurvival biomarker |
| spellingShingle | Nan Xiao Nan Xiao Yang Hu Liran Juan Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer Frontiers in Cell and Developmental Biology gastric cancer lncRNA differential expression coexpression network survival biomarker |
| title | Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer |
| title_full | Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer |
| title_fullStr | Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer |
| title_full_unstemmed | Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer |
| title_short | Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer |
| title_sort | comprehensive analysis of differentially expressed lncrnas in gastric cancer |
| topic | gastric cancer lncRNA differential expression coexpression network survival biomarker |
| url | https://www.frontiersin.org/article/10.3389/fcell.2020.00557/full |
| work_keys_str_mv | AT nanxiao comprehensiveanalysisofdifferentiallyexpressedlncrnasingastriccancer AT nanxiao comprehensiveanalysisofdifferentiallyexpressedlncrnasingastriccancer AT yanghu comprehensiveanalysisofdifferentiallyexpressedlncrnasingastriccancer AT liranjuan comprehensiveanalysisofdifferentiallyexpressedlncrnasingastriccancer |