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Li P, Ji W, Wei Z, Wang X, Qiao G, Gao C, Wang Y, Qi F. Comprehensive analysis to identify pseudogenes/lncRNAs-hsa-miR-200b-3p-COL5A2 network as a prognostic biomarker in gastric cancer. Hereditas 2022; 159:43. [PMID: 36447214 PMCID: PMC9706917 DOI: 10.1186/s41065-022-00257-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/12/2022] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE Gastric cancer is one of the most common and deadly types of cancer. The molecular mechanism of gastric cancer progression remains unclear. MATERIALS AND METHODS Four hub genes were identified through GEO and TCGA database screening and analysis. Prognostic analysis revealed that COL5A2 was the most likely to affect the prognosis of gastric cancer among the four hub genes. The relationships between COL5A2 and clinical variables and immune cell infiltration were analyzed. Then, COL5A2 was analyzed for single-gene differences and related functional enrichment. Using the starBase database for prediction and analysis, miRNAs and pseudogenes/lncRNAs that might combine with COL5A2 were identified; thus, the ceRNA network was constructed. Finally, the network was verified by Cox analysis and qPCR, and a nomogram was constructed. RESULTS First, we found that COL5A2, COL12A1, BGN and THBS2 were highly expressed in gastric cancer. COL5A2 had statistical significance in overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) analysis. Immune infiltration analysis suggested that COL5A2 might influence the changes in the tumor immune microenvironment. The StarBase database was used to predict that 3 pseudogenes and 7 lncRNAs might inhibit the hsa-miR-200b-3p-COL5A2 axis in gastric cancer. The pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 ceRNA network was identified and verified using Cox regression analysis and PCR. Finally, we constructed a nomogram. CONCLUSIONS We elucidated the regulatory role of the pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 network in gastric cancer progression and constructed a nomogram. These studies may provide effective treatments and potential prognostic biomarkers for gastric cancer.
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Affiliation(s)
- Peiyuan Li
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Wenbin Ji
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Zhiwang Wei
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Xiulan Wang
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Gangjie Qiao
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Chao Gao
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Yifan Wang
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
| | - Feng Qi
- grid.412645.00000 0004 1757 9434Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin, 300052 China
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Gan Y, Yang Y, Wu Y, Li T, Liu L, Liang F, Qi J, Liang P, Pan D. Comprehensive transcriptomic analysis of immune-related eRNAs associated with prognosis and immune microenvironment in melanoma. Front Surg 2022; 9:917061. [PMID: 36338651 PMCID: PMC9632973 DOI: 10.3389/fsurg.2022.917061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Recent evidence suggests that enhancer RNAs (eRNAs) play key roles in cancers. Identification of immune-related eRNAs (ireRNAs) in melanoma can provide novel insights into the mechanisms underlying its genesis and progression, along with potential therapeutic targets. Aim To establish an ireRNA-related prognostic signature for melanoma and identify potential drug candidates. Methods The ireRNAs associated with the overall survival (OS-ireRNAs) of melanoma patients were screened using data from The Cancer Genome Atlas (TCGA) via WGCNA and univariate Cox analysis. A prognostic signature based on these OS-ireRNAs was then constructed by performing the least absolute shrinkage and selection operator (LASSO) Cox regression analysis. The immune landscape associated with the prognostic model was evaluated by the ESTIMATE algorithm and CIBERSORT method. Finally, the potential drug candidates for melanoma were screened through the cMap database. Results A total of 24 OS-ireRNAs were obtained, of which 7 ireRNAs were used to construct a prognostic signature. The ireRNAs-related signature performed well in predicting the overall survival (OS) of melanoma patients. The risk score of the established signature was further verified as an independent risk factor, and was associated with the unique tumor microenvironment in melanoma. We also identified several potential anti-cancer drugs for melanoma, of which corticosterone ranked first. Conclusions The ireRNA-related signature is an effective prognostic predictor and provides reliable information to better understand the mechanism of ireRNAs in the progression of melanoma.
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Affiliation(s)
- Yuling Gan
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Yuan Yang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yajiao Wu
- Department of Ophthalmology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Tingdong Li
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Libing Liu
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Fudong Liang
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Jianghua Qi
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Peng Liang
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
- Correspondence: Dongsheng Pan Peng Liang
| | - Dongsheng Pan
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
- Correspondence: Dongsheng Pan Peng Liang
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