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Chen C, Wan M, Peng X, Zhang Q, Liu Y. GPR37-centered ceRNA network contributes to metastatic potential in lung adenocarcinoma: Evidence from high-throughput sequencing. Transl Oncol 2024; 39:101819. [PMID: 37979558 PMCID: PMC10656721 DOI: 10.1016/j.tranon.2023.101819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023] Open
Abstract
The competing endogenous RNA (ceRNA)-based profiling has been extensively studied in carcinogenesis of lung adenocarcinoma (LUAD), while it has seldomly been applied to investigate the metastatic potential of LUAD. This study aims to examine the function and in-depth mechanism of GPR37-centered ceRNA network in LUAD. Cancer tissues and adjacent normal tissues from three LUAD patients were collected for high-throughput sequencing to screen for differentially expressed genes. A PPI network was constructed to screen the key gene GPR37, followed by analysis for the functions and pathways. Clinical data from LUAD patients were integrated with gene expression data in TCGA-LUAD dataset for survival analysis. Based on the miRNAs targeting_GPR37 and lncRNAs targeting_miRNAs, a lncRNA-miRNA-mRNA ceRNA network was established. GPR37 was up-regulated in LUAD tissue samples, and it may be a key gene involved in LUAD progression. GPR37 in LUAD was mainly enriched in the mitosis-related pathways. High GPR37 expression corresponded to poor prognosis in LUAD patients. Meanwhile, GPR37 could be used as an independent factor to predict the prognosis in LUAD patients. LncRNA DLEU1, up-regulated in LUAD tissue samples, may competitively bind to miR-4458 to up-regulate the expression of the miR-4458 downstream target GPR37. DLEU1 was associated with poor prognosis and tumor metastasis in LUAD patients. Altogether, our findings reveal a novel ceRNA network of DLEU1/miR-4458/GPR37 in LUAD growth and metastasis.
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Affiliation(s)
- Chuanhui Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Mengzhi Wan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Xiong Peng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Qing Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Yu Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China.
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2
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Ding Y, Wan S, Liu W, Lu Y, Xu Q, Gan Y, Yan L, Gu Y, Liu Z, Hu Y, Cao H, Shao F. Regulation Networks of Non-Coding RNA-Associated ceRNAs in Cisplatin-Induced Acute Kidney Injury. Cells 2022; 11:cells11192971. [PMID: 36230932 PMCID: PMC9563924 DOI: 10.3390/cells11192971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Cisplatin is widely used as a chemotherapeutic drug to treat various solid tumors. However, it often induces severe side effects, including nephrotoxicity, which limits its application in clinical settings. Furthermore, the underlying mechanisms of action are unclear. Here, we applied whole-transcriptome RNA sequencing to a cisplatin-induced acute kidney injury (CP-AKI) mouse model to evaluate competing endogenous RNA (ceRNA) networks. We found 4460 mRNAs, 1851 long non-coding RNAs, 101 circular RNAs, and 102 microRNAs significantly differentially expressed between CP-AKI and control mice. We performed gene set enrichment analysis to reveal the biological functions of the mRNAs and constructed non-coding RNA-associated ceRNA networks in CP-AKI mice. Two ceRNA regulatory pathways, Lhx1os-203/mmu-miR-21a-3p/Slc7a13 and circular RNA_3907/mmu-miR-185-3p/Ptprn, were validated using quantitative real-time PCR. The protein–protein interaction network indicated that Il6, Cxcl1, Cxcl2, and Plk1 serve as hub genes and are highly connected with the inflammatory response or DNA damage. Transcription factors, such as Stat3, Cebpb, and Foxm1, regulate gene expression levels in CP-AKI. Our study provides insight into non-coding RNA-associated ceRNA networks and mRNAs in CP-AKI and identifies potential treatment targets.
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Affiliation(s)
- Yun Ding
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Shengfeng Wan
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Wenna Liu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Yanfang Lu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Qin Xu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Yujin Gan
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Lei Yan
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Yue Gu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Ziyang Liu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Yifeng Hu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Huixia Cao
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Correspondence: (H.C.); (F.S.)
| | - Fengmin Shao
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Department of Nephrology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
- Correspondence: (H.C.); (F.S.)
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3
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Xu J, Wen J, Li S, Shen X, You T, Huang Y, Xu C, Zhao Y. Immune-Related Nine-MicroRNA Signature for Predicting the Prognosis of Gastric Cancer. Front Genet 2021; 12:690598. [PMID: 34290743 PMCID: PMC8287335 DOI: 10.3389/fgene.2021.690598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/21/2021] [Indexed: 12/21/2022] Open
Abstract
Recent findings have demonstrated the superiority and utility of microRNAs (miRNAs) as new biomarkers for cancer diagnosis, therapy, and prognosis. In this study, to explore the prognostic value of immune-related miRNAs in gastric cancer (GC), we analyzed the miRNA-expression profiles of 389 patients with GC, using data deposited in The Cancer Genome Atlas database. Using a forward- and backward-variable selection and multivariate Cox regression analyses model, we identified a nine-miRNA signature (the “ImmiRSig,” consisting of miR-125b-5p, miR-99a-3p, miR-145-3p, miR-328-3p, miR-133a-5p, miR-1292-5p, miR-675-3p, miR-92b-5p, and miR-942-3p) in the training cohort that enabled the division of patients into high- and low-risk groups with significantly different survival rates. The ImmiRSig was successfully validated with an independent test cohort of 193 GC patients. Univariate and multivariate Cox regression analyses indicated that the ImmiRSig would serve as an independent prognostic factor after adjusting for other clinical covariates. Pending further prospective validation, the identified ImmiRSig appears to have significant clinical importance in terms of improving outcome predictions and guiding personalized treatment for patients with GC. Finally, significant associations between the ImmiRSig and the half-maximal inhibitory concentrations of chemotherapeutic agents were observed, suggesting that ImmiRSig may predict the clinical efficacy of chemotherapy.
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Affiliation(s)
- Jingxuan Xu
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jian Wen
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Shuangquan Li
- The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xian Shen
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tao You
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yingpeng Huang
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chongyong Xu
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaping Zhao
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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Fan F, Yin R, Wang L, Zhao S, Lv D, Yang K, Geng S, Yang N, Zhang X, Wang H. ALDH3A1 driving tumor metastasis is mediated by p53/BAG1 in lung adenocarcinoma. J Cancer 2021; 12:4780-4790. [PMID: 34234849 PMCID: PMC8247369 DOI: 10.7150/jca.58250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/22/2021] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a lethal malignancy with metastasis, a major tumor feature that predominantly correlated with progression, but the molecules that mediated tumor metastasis remain elusive. To declare the critical regulatory genes, RNA sequencing data in LUAD patients was acquired from The Cancer Genome Atlas (TCGA) and found that ALDH3A1 was distinctly highly expressed in LUAD patients with metastasis (M1) compared with those without metastasis (M0), linked to the property of cancer stem cell and epithelial-mesenchymal transition (EMT). Besides, high ALDH3A1 expression predicted a poor prognosis. Knockdown of ALDH3A1 showed decreased proliferation, migration, and invasion in A549 cell line. Furthermore, BAG1 was regulated by ALDH3A1 through p53, enhanced cell proliferation, and predicted clinical prognosis. Our findings collectively uncovered a novel mechanism that orchestrates tumor cells' metastasis, and decreasing ALDH3A1 represented a potential therapeutic target for reprogramming metastasis.
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Affiliation(s)
- Feifei Fan
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ruxue Yin
- Department of rheumatism and immunology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Liuya Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shunxin Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Dan Lv
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Kangli Yang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shen Geng
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ningning Yang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaohong Zhang
- Department of Respiratory Medicine, Zhengzhou Central Hospital, Zhengzhou 450052, China
| | - Hongmin Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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5
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Li R, Han K, Xu D, Chen X, Lan S, Liao Y, Sun S, Rao S. A Seven-Long Non-coding RNA Signature Improves Prognosis Prediction of Lung Adenocarcinoma: An Integrated Competing Endogenous RNA Network Analysis. Front Genet 2021; 11:625977. [PMID: 33584817 PMCID: PMC7876394 DOI: 10.3389/fgene.2020.625977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Early and precise prediction is an important way to reduce the poor prognosis of lung adenocarcinoma (LUAD) patients. Nevertheless, the widely used tumor, node, and metastasis (TNM) staging system based on anatomical information only often could not achieve adequate performance on foreseeing the prognosis of LUAD patients. This study thus aimed to examine whether the long non-coding RNAs (lncRNAs), known highly involved in the tumorigenesis of LUAD through the competing endogenous RNAs (ceRNAs) mechanism, could provide additional information to improve prognosis prediction of LUAD patients. To prove the hypothesis, a dataset consisting of both RNA sequencing data and clinical pathological data, obtained from The Cancer Genome Atlas (TCGA) database, was analyzed. Then, differentially expressed RNAs (DElncRNAs, DEmiRNAs, and DEmRNAs) were identified and a lncRNA-miRNA-mRNA ceRNA network was constructed based on those differentially expressed RNAs. Functional enrichment analysis revealed that this ceRNA network was highly enriched in some cancer-associated signaling pathways. Next, lasso-Cox model was run 1,000 times to recognize the potential survival-related combinations of the candidate lncRNAs in the ceRNA network, followed by the "best subset selection" to further optimize these lncRNA-based combinations, and a seven-lncRNA prognostic signature with the best performance was determined. Based on the median risk score, LUAD patients could be well distinguished into high-/low-risk subgroups. The Kaplan-Meier survival curve showed that LUAD patients in the high-risk group had significantly shorter overall survival than those in the low-risk group (log-rank test P = 4.52 × 10-9). The ROC curve indicated that the clinical genomic model including both the TNM staging system and the signature had a superior performance in predicting the patients' overall survival compared to the clinical model with the TNM staging system only. Further stratification analysis suggested that the signature could work well in the different strata of the stage, gender, or age, rendering it to be a wide application. Finally, a ceRNA subnetwork related to the signature was extracted, demonstrating its high involvement in the tumorigenesis mechanism of LUAD. In conclusion, the present study established a lncRNA-based molecular signature, which can significantly improve prognosis prediction for LUAD patients.
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Affiliation(s)
- Rang Li
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Kedong Han
- Department of Cardiology, Maoming People's Hospital, Maoming, China
| | - Dehua Xu
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Xiaolin Chen
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Shujin Lan
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yuanjun Liao
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Shengnan Sun
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Shaoqi Rao
- Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, China
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6
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Fan F, Ping Y, Yang L, Duan X, Resegofetse Maimela N, Li B, Li X, Chen J, Zhang K, Wang L, Liu S, Zhao X, Wang H, Zhang Y. Characterization of a non-coding RNA-associated ceRNA network in metastatic lung adenocarcinoma. J Cell Mol Med 2020; 24:11680-11690. [PMID: 32860342 PMCID: PMC7579711 DOI: 10.1111/jcmm.15778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 04/11/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a highly malignant cancer. Although competing endogenous RNA (ceRNA)-based profiling has been investigated in patients with LUAD, it has not been specifically used to study metastasis in LUAD. We found 130 differentially expressed (DE) lncRNAs, 32 DE miRNAs and 981 DE mRNAs from patients with LUAD in The Cancer Genome Atlas (TCGA) database. We analysed the functions and pathways of 981 DE mRNAs using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Based on the target DE mRNAs and DE lncRNAs of DE miRNAs, we established an lncRNA-miRNA-mRNA ceRNA network, comprising 37 DE lncRNAs, 22 DE miRNAs and 212 DE mRNAs. Subsequently, we constructed a protein-protein interaction network of DE mRNAs in the ceRNA network. Among all, DE RNAs, 5 DE lncRNAs, 5 DE miRNAs and 45 DE mRNAs were confirmed found to be associated with clinical prognosis. Moreover, 3 DE lncRNAs, 4 DE miRNAs and 9 DE mRNAs in the ceRNA network were associated with clinical prognosis. We further screened 3 DE lncRNAs, 3 DE miRNAs and 3 DE mRNAs using clinical samples. These DE lncRNAs, DE miRNAs and DE mRNAs in ceRNA network may serve as independent biomarkers of LUAD metastasis.
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Affiliation(s)
- Feifei Fan
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Ping
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoran Duan
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Bingjie Li
- Cancer Center, The First Affiliated of Zhengzhou University, Zhengzhou, China
| | - Xiangnan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Chen
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kai Zhang
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liping Wang
- Cancer Center, The First Affiliated of Zhengzhou University, Zhengzhou, China
| | - Shasha Liu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuan Zhao
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongmin Wang
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated of Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, China
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