Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma
PurposeColon adenocarcinoma (COAD) is the most common type of colorectal cancer (CRC) and is associated with poor prognosis. Emerging evidence has demonstrated that glycosylation by long noncoding RNAs (lncRNAs) was associated with COAD progression. To date, however, the prognostic values of glycosy...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Oncology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2022.954226/full |
| _version_ | 1811266364618309632 |
|---|---|
| author | Jiawei Zhang Jiawei Zhang Yinan Wu Yinan Wu Jiayi Mu Dijia Xin Luyao Wang Yili Fan Suzhan Zhang Yang Xu Yang Xu |
| author_facet | Jiawei Zhang Jiawei Zhang Yinan Wu Yinan Wu Jiayi Mu Dijia Xin Luyao Wang Yili Fan Suzhan Zhang Yang Xu Yang Xu |
| author_sort | Jiawei Zhang |
| collection | DOAJ |
| description | PurposeColon adenocarcinoma (COAD) is the most common type of colorectal cancer (CRC) and is associated with poor prognosis. Emerging evidence has demonstrated that glycosylation by long noncoding RNAs (lncRNAs) was associated with COAD progression. To date, however, the prognostic values of glycosyltransferase (GT)-related lncRNAs in COAD are still largely unknown.MethodsWe obtained the expression matrix of mRNAs and lncRNAs in COAD from The Cancer Genome Atlas (TCGA) database. Then, the univariate Cox regression analysis was conducted to identify 33 prognostic GT-related lncRNAs. Subsequently, LASSO and multivariate Cox regression analysis were performed, and 7 of 33 GT-related lncRNAs were selected to conduct a risk model. Gene set enrichment analysis (GSEA) was used to analyze gene signaling pathway enrichment of the risk model. ImmuCellAI, an online tool for estimating the abundance of immune cells, and correlation analysis were used to explore the tumor-infiltrating immune cells in COAD. Finally, the expression levels of seven lncRNAs were detected in colorectal cancer cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR).ResultsA total of 1,140 GT-related lncRNAs were identified, and 7 COAD-specific GT-related lncRNAs (LINC02381, MIR210HG, AC009237.14, AC105219.1, ZEB1-AS1, AC002310.1, and AC020558.2) were selected to conduct a risk model. Patients were divided into high- and low-risk groups based on the median of risk score. The prognosis of the high-risk group was worse than that of the low-risk group, indicating the good reliability and specificity of our risk model. Additionally, a nomogram based on the risk score and clinical traits was built to help clinical decisions. GSEA showed that the risk model was significantly enriched in metabolism-related pathways. Immune infiltration analysis revealed that five types of immune cells were significantly different between groups, and two types of immune cells were negatively correlated with the risk score. Besides, we found that the expression levels of these seven lncRNAs in tumor cells were significantly higher than those in normal cells, which verified the feasibility of the risk model.ConclusionThe efficient risk model based on seven GT-related lncRNAs has prognostic potential for COAD, which may be novel biomarkers and therapeutic targets for COAD patients. |
| first_indexed | 2024-04-12T20:41:45Z |
| format | Article |
| id | doaj.art-8b9ba47a46284c1f9cc0a4654ed0c6d7 |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-12T20:41:45Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-8b9ba47a46284c1f9cc0a4654ed0c6d72022-12-22T03:17:24ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2022-09-011210.3389/fonc.2022.954226954226Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinomaJiawei Zhang0Jiawei Zhang1Yinan Wu2Yinan Wu3Jiayi Mu4Dijia Xin5Luyao Wang6Yili Fan7Suzhan Zhang8Yang Xu9Yang Xu10Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaZhejiang University Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaZhejiang University Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaThe Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, ChinaZhejiang University Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaDepartment of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaDepartment of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaDepartment of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaZhejiang University Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaDepartment of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ChinaZhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, ChinaPurposeColon adenocarcinoma (COAD) is the most common type of colorectal cancer (CRC) and is associated with poor prognosis. Emerging evidence has demonstrated that glycosylation by long noncoding RNAs (lncRNAs) was associated with COAD progression. To date, however, the prognostic values of glycosyltransferase (GT)-related lncRNAs in COAD are still largely unknown.MethodsWe obtained the expression matrix of mRNAs and lncRNAs in COAD from The Cancer Genome Atlas (TCGA) database. Then, the univariate Cox regression analysis was conducted to identify 33 prognostic GT-related lncRNAs. Subsequently, LASSO and multivariate Cox regression analysis were performed, and 7 of 33 GT-related lncRNAs were selected to conduct a risk model. Gene set enrichment analysis (GSEA) was used to analyze gene signaling pathway enrichment of the risk model. ImmuCellAI, an online tool for estimating the abundance of immune cells, and correlation analysis were used to explore the tumor-infiltrating immune cells in COAD. Finally, the expression levels of seven lncRNAs were detected in colorectal cancer cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR).ResultsA total of 1,140 GT-related lncRNAs were identified, and 7 COAD-specific GT-related lncRNAs (LINC02381, MIR210HG, AC009237.14, AC105219.1, ZEB1-AS1, AC002310.1, and AC020558.2) were selected to conduct a risk model. Patients were divided into high- and low-risk groups based on the median of risk score. The prognosis of the high-risk group was worse than that of the low-risk group, indicating the good reliability and specificity of our risk model. Additionally, a nomogram based on the risk score and clinical traits was built to help clinical decisions. GSEA showed that the risk model was significantly enriched in metabolism-related pathways. Immune infiltration analysis revealed that five types of immune cells were significantly different between groups, and two types of immune cells were negatively correlated with the risk score. Besides, we found that the expression levels of these seven lncRNAs in tumor cells were significantly higher than those in normal cells, which verified the feasibility of the risk model.ConclusionThe efficient risk model based on seven GT-related lncRNAs has prognostic potential for COAD, which may be novel biomarkers and therapeutic targets for COAD patients.https://www.frontiersin.org/articles/10.3389/fonc.2022.954226/fullcolorectal cancerglycosyltransferaselncRNAsrisk modeloverall survival |
| spellingShingle | Jiawei Zhang Jiawei Zhang Yinan Wu Yinan Wu Jiayi Mu Dijia Xin Luyao Wang Yili Fan Suzhan Zhang Yang Xu Yang Xu Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma Frontiers in Oncology colorectal cancer glycosyltransferase lncRNAs risk model overall survival |
| title | Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma |
| title_full | Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma |
| title_fullStr | Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma |
| title_full_unstemmed | Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma |
| title_short | Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma |
| title_sort | glycosyltransferase related long non coding rna signature predicts the prognosis of colon adenocarcinoma |
| topic | colorectal cancer glycosyltransferase lncRNAs risk model overall survival |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2022.954226/full |
| work_keys_str_mv | AT jiaweizhang glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT jiaweizhang glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT yinanwu glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT yinanwu glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT jiayimu glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT dijiaxin glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT luyaowang glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT yilifan glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT suzhanzhang glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT yangxu glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma AT yangxu glycosyltransferaserelatedlongnoncodingrnasignaturepredictstheprognosisofcolonadenocarcinoma |