|
1
|
Wu B, Zhang X, Feng N, Guo Z, Gao L, Wan Z, Zhang W. Prognostic value and immune landscapes of anoikis-associated lncRNAs in lung adenocarcinoma. Aging (Albany NY) 2024; 16:2273-2298. [PMID: 38319706 PMCID: PMC10911388 DOI: 10.18632/aging.205481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Methods for predicting the outcome of lung adenocarcinoma (LUAD) in the clinic are limited. Anoikis is an important route to programmed cell death in LUAD, and the prognostic value of a model constructed with anoikis-related lncRNAs (ARlncRNAs) in LUAD is unclear. METHODS Transcriptome and basic information for LUAD patients was obtained from the Cancer Genome Atlas. Coexpression and Cox regression analyses were utilized to identify prognostically significant ARlncRNAs and construct a prognostic signature. Furthermore, the signature was combined with clinical characteristics to create a nomogram. Finally, we performed principal component, enrichment, tumor mutation burden (TMB), tumor microenvironment (TME) and drug sensitivity analyses to evaluate the basic research and clinical merit of the signature. RESULTS The prognostic signature developed with eleven ARlncRNAs can accurately predict that high-risk group patients have a worse prognosis, as proven by the receiver operating characteristic (ROC) curve (AUC: 0.718). Independent prognostic analyses indicated that the risk score is a significant independent prognostic element for LUAD (P<0.001). In the high-risk group, enrichment analysis demonstrated that glucose metabolism and DNA replication were the main enrichment pathways. TMB analysis indicated that the high-risk group had a high TMB (P<0.05). Drug sensitivity analyses can recognize drugs that are sensitive to different risk groups. Finally, 11 ARlncRNAs of this signature were verified by RT-qPCR analysis. CONCLUSIONS A novel prognostic signature developed with 11 ARlncRNAs can accurately predict the OS of LUAD patients and offer clinical guidance value for immunotherapy and chemotherapy treatment.
Collapse
Affiliation(s)
- Bo Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Xiang Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Nan Feng
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Zishun Guo
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Lu Gao
- Department of Thoracic Surgery, Baoding No.1 Central Hospital, Baoding 071000, China
| | - Zhihua Wan
- Department of Thoracic Surgery, Baoding No.1 Central Hospital, Baoding 071000, China
| | - Wenxiong Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| |
Collapse
|
|
2
|
Zhang Y, Lyu Y, Chen L, Cao K, Chen J, He C, Lyu X, Jiang Y, Xiang J, Liu B, Wu C. Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS. Int J Mol Sci 2023; 24:15259. [PMID: 37894938 PMCID: PMC10607287 DOI: 10.3390/ijms242015259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, VENTX, PCDH 7, JAKMIP1, MIR202HG, MIR378D1, LINC02472, and LINC02310. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis.
Collapse
Affiliation(s)
- Yuling Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yanping Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Liangping Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Kang Cao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jingwen Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chenzhou He
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Xuejie Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yu Jiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jianjun Xiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Baoying Liu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chuancheng Wu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| |
Collapse
|
|
3
|
Zhang Q, Sun Y, Wang C, Shao F. Circular RNA-microRNA-mRNA network identified circ_0007618 and circ_0029426 as new valuable biomarkers for lung adenocarcinoma. Bioengineered 2022; 13:6258-6271. [PMID: 35212617 PMCID: PMC8973644 DOI: 10.1080/21655979.2022.2027180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are involved in multiple physiological processes. However, whether circRNAs function as the indicators of lung adenocarcinoma (LUAD) remains unclear. Three LUAD-related microarray datasets were downloaded from the Gene Expression Omnibus database, and overlapping differentially expressed circRNAs (DECs) in LUAD were identified. circ_0007618 and circ_0029426 were revealed to be significantly dysregulated in LUAD and verified in LUAD tissues and serum obtained in this study. Subsequently, the overall survival curve and receiver operating characteristics curve analyses were performed to evaluate the prognosis, sensitivity, and specificity of circ_0007618 and circ_0029426 for LUAD diagnosis. The results indicate that the combination of circ_0007618 and circ_0029426 is a potential biomarker for LUAD diagnosis and prognosis. TargetScan and miRDB were used to predict interactions between microRNAs (miRNAs) and circRNAs/mRNAs. A circRNA–miRNA–mRNA network was established for LUAD diagnosis. The Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction network identified four hub genes. In conclusion, circ_0007618 and circ_0029426 may be novel biomarkers for LUAD diagnosis and prognosis. For LUAD diagnosis, PIK3CA and NRAS, and KRAS and ETS1, were targeted by circ_0007618 and circ_0029426, respectively.
Collapse
Affiliation(s)
- Qiang Zhang
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, China.,Department of Thoracic Surgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Pulmonary Nodule Diagnosis and Treatment Research Center, Nanjing Medical University, Nanjing, China
| | - Yungang Sun
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, China.,Department of Thoracic Surgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Pulmonary Nodule Diagnosis and Treatment Research Center, Nanjing Medical University, Nanjing, China
| | - Chao Wang
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, China.,Department of Thoracic Surgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Pulmonary Nodule Diagnosis and Treatment Research Center, Nanjing Medical University, Nanjing, China
| | - Feng Shao
- Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, China.,Department of Thoracic Surgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Pulmonary Nodule Diagnosis and Treatment Research Center, Nanjing Medical University, Nanjing, China
| |
Collapse
|
|
4
|
Gu S, Zhang G, Si Q, Dai J, Song Z, Wang Y. Web tools to perform long non-coding RNAs analysis in oncology research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6326500. [PMID: 34296748 PMCID: PMC8299716 DOI: 10.1093/database/baab047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/21/2021] [Accepted: 07/11/2021] [Indexed: 11/14/2022]
Abstract
Accumulated evidence suggests that the widely expressed long-non-coding RNAs (lncRNAs) are involved in biogenesis. Some aberrant lncRNAs are closely related to pathological changes, for instance, in cancer. Both in tumorigenesis and cancer progression, depending on the interplay with cellular molecules, lncRNAs can modulate transcriptional interference, chromatin remodeling, post-translational regulation and protein modification, and further interfere with signaling pathways. Aiming to the diagnosis/ prognosis markers or potential therapeutical targets, it is important to figure out the specific mechanism and the tissue-specific expressing patterns of lncRNAs. Generally, the bioinformatics analysis is the first step. More and more in silico databases are increasing. But the existing integrative online platforms’ functions are not only having their unique features but also share some common features, which may lead to a waste of time for researchers. Here, we reviewed these web tools according to the functions. For each database, we clarified the data source, analysis method and the evidence that the analysis result is derived from. This review also illustrated examples in practical use for a specific lncRNA by these web tools. It will provide convenience for researchers to quickly choose the appropriate bioinformatics web tools in oncology studies.
Collapse
Affiliation(s)
- Shixing Gu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Road, Chengdu, Sichuan 611137, China
| | - Guangjie Zhang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Road, Chengdu, Sichuan 611137, China.,Department of Clinical Laboratory, Chengdu Fifth People's Hospital, No.33 Mashi Street, Chengdu, Sichuan 611130, China
| | - Qin Si
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Road, Chengdu, Sichuan 611137, China
| | - Jiawen Dai
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Road, Chengdu, Sichuan 611137, China
| | - Zhen Song
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Road, Chengdu, Sichuan 611137, China
| | - Yingshuang Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, No.1166 Liutai Road, Chengdu, Sichuan 611137, China
| |
Collapse
|