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Pokorná M, Černá M, Boussios S, Ovsepian SV, O’Leary VB. lncRNA Biomarkers of Glioblastoma Multiforme. Biomedicines 2024; 12:932. [PMID: 38790894 PMCID: PMC11117901 DOI: 10.3390/biomedicines12050932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules of 200 nucleotides or more in length that are not translated into proteins. Their expression is tissue-specific, with the vast majority involved in the regulation of cellular processes and functions. Many human diseases, including cancer, have been shown to be associated with deregulated lncRNAs, rendering them potential therapeutic targets and biomarkers for differential diagnosis. The expression of lncRNAs in the nervous system varies in different cell types, implicated in mechanisms of neurons and glia, with effects on the development and functioning of the brain. Reports have also shown a link between changes in lncRNA molecules and the etiopathogenesis of brain neoplasia, including glioblastoma multiforme (GBM). GBM is an aggressive variant of brain cancer with an unfavourable prognosis and a median survival of 14-16 months. It is considered a brain-specific disease with the highly invasive malignant cells spreading throughout the neural tissue, impeding the complete resection, and leading to post-surgery recurrences, which are the prime cause of mortality. The early diagnosis of GBM could improve the treatment and extend survival, with the lncRNA profiling of biological fluids promising the detection of neoplastic changes at their initial stages and more effective therapeutic interventions. This review presents a systematic overview of GBM-associated deregulation of lncRNAs with a focus on lncRNA fingerprints in patients' blood.
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Affiliation(s)
- Markéta Pokorná
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK;
- Faculty of Medicine, Health, and Social Care, Canterbury Christ Church University, Canterbury CT2 7PB, UK
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
- Kent Medway Medical School, University of Kent, Canterbury CT2 7LX, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
| | - Saak V. Ovsepian
- Faculty of Engineering and Science, University of Greenwich London, Chatham Maritime, Kent ME4 4TB, UK;
- Faculty of Medicine, Tbilisi State University, Tbilisi 0177, Georgia
| | - Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
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2
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Aguiar TFM, Rivas MP, de Andrade Silva EM, Pires SF, Dangoni GD, Macedo TC, Defelicibus A, Barros BDDF, Novak E, Cristofani LM, Odone V, Cypriano M, de Toledo SRC, da Cunha IW, da Costa CML, Carraro DM, Tojal I, de Oliveira Mendes TA, Krepischi ACV. First Transcriptome Analysis of Hepatoblastoma in Brazil: Unraveling the Pivotal Role of Noncoding RNAs and Metabolic Pathways. Biochem Genet 2024:10.1007/s10528-024-10764-y. [PMID: 38649558 DOI: 10.1007/s10528-024-10764-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues. The analysis unveiled 1,492 differentially expressed genes (1,031 upregulated and 461 downregulated), including 920 protein-coding genes (62%). Upregulated biological processes were linked to cell differentiation, signaling, morphogenesis, and development, involving known hepatoblastoma-associated genes (DLK1, MEG3, HDAC2, TET1, HMGA2, DKK1, DKK4), alongside with novel findings (GYNG4, CDH3, and TNFRSF19). Downregulated processes predominantly centered around oxidation and metabolism, affecting amines, nicotinamides, and lipids, featuring novel discoveries like the repression of SYT7, TTC36, THRSP, CCND1, GCK and CAMK2B. Two genes, which displayed a concordant pattern of DNA methylation alteration in their promoter regions and dysregulation in the transcriptome, were further validated by RT-qPCR: the upregulated TNFRSF19, a key gene in the embryonic development, and the repressed THRSP, connected to lipid metabolism. Furthermore, based on protein-protein interaction analysis, we identified genes holding central positions in the network, such as HDAC2, CCND1, GCK, and CAMK2B, among others, that emerged as prime candidates warranting functional validation in future studies. Notably, a significant dysregulation of non-coding RNAs (ncRNAs), predominantly upregulated transcripts, was observed, with 42% of the top 50 highly expressed genes being ncRNAs. An integrative miRNA-mRNA analysis revealed crucial biological processes associated with metabolism, oxidation reactions of lipids and carbohydrates, and methylation-dependent chromatin silencing. In particular, four upregulated miRNAs (miR-186, miR-214, miR-377, and miR-494) played a pivotal role in the network, potentially targeting multiple protein-coding transcripts, including CCND1 and CAMK2B. In summary, our transcriptome analysis highlighted disrupted embryonic development as well as metabolic pathways, particularly those involving lipids, emphasizing the emerging role of ncRNAs as epigenetic regulators in hepatoblastomas. These findings provide insights into the complexity of the hepatoblastoma transcriptome and identify potential targets for future therapeutic interventions.
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Affiliation(s)
- Talita Ferreira Marques Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, USA
| | - Maria Prates Rivas
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Edson Mario de Andrade Silva
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Minas Gerais, Brazil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
| | - Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Gustavo Dib Dangoni
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Taiany Curdulino Macedo
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Dirce Maria Carraro
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil.
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Xu Z, Wu S, Tu J, Wang M, Liang W, Cheng J, Guan J, Xu J. RACGAP1 promotes lung cancer cell proliferation through the PI3K/AKT signaling pathway. Sci Rep 2024; 14:8694. [PMID: 38622149 PMCID: PMC11018837 DOI: 10.1038/s41598-024-58539-0] [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: 02/08/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
We aimed to investigate the expression and clinic significance of Rac GTPase Activating Protein 1 (RACGAP1) in human lung adenocarcinoma (LUAD). Online database analysis revealed a significant increase in RACGAP1 mRNA expression among 26 types of tumor tissues, including LUAD tissues. Online database and tissue microarray analyses indicated that RACGAP1 expression was significantly upregulated in LUAD tissues. Genetic variation analysis identified four different genetic variations of RACGAPs in LUAD. Moreover, online database analysis showed that RACGAP1 upregulation was correlated with shorter survival in patients with LUAD. After silencing RACGAP1 expression in A549 cells using siRNA and assessing its protein levels via Western blotting, we found that RACGAP1 knockdown inhibited cell growth and induced apoptosis determined using the Cell Counting Kit-8 assay, colony formation assay, and flow cytometry. Mechanistically, western blot analysis indicated that Bax expression increased, whereas Bcl-2 expression decreased. Moreover, RACGAP1 knockdown attenuated PI3K/AKT pathway activation in lung cancer cells. Taken together, our findings showed that RACGAP1 was overexpressed in LUAD tissues and played an important role in lung cancer by increasing cell growth through the PI3K/AKT signaling pathway. This study suggests recommends evaluating RACGAP1 in clinical settings as a novel biomarker and potential therapeutic target for lung cancer.
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Affiliation(s)
- Zhiyang Xu
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China
| | - Shaohang Wu
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China
| | - Jiahua Tu
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China
| | - Mingyang Wang
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China
| | - Weicheng Liang
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China
| | - Jiangdong Cheng
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China
| | - Jun Guan
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China.
| | - Jianxin Xu
- Department of Thoracic Surgery, The First Hospital of Putian, The School of Clinical Medicine, Fujian Medical University Putian, Fujian, 351100, China.
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A review on the role of ADAMTS9-AS2 in different disorders. Pathol Res Pract 2023; 243:154346. [PMID: 36746036 DOI: 10.1016/j.prp.2023.154346] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Recent decade has seen a tremendous progress in identification of the role of different long non-coding RNAs (lncRNAs) in human pathologies. ADAMTS9-AS2 is an example of lncRNAs with different roles in human disorders. It is mostly acknowledged as a tumor suppressor lncRNA in different types of cancers. However, it has been reported to be up-regulated in tongue squamous cell carcinoma, salivary adenoid cystic carcinoma and glioblastoma. Moreover, ADAMTS9-AS2 is possibly involved in the pathoetiology of pulpitis, acute ischemic stroke, type 2 diabetes and its complications. This lncRNA sponges miR-196b-5p, miR-223-3p, miR-130a-5p, miR-600, miR-223-3p, miR-27a-3p, miR-32, miR-143-3p, miR-143-3p and miR-182-5p in order to regulate downstream mRNAs. This review aims at summarization of the role of ADAMTS9-AS2 in different disorders with a particular focus on its diagnostic and prognostic values.
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Cheng Y, Yao J, Fang Q, Chen B, Zang G. A circadian rhythm-related biomarker for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma. Aging (Albany NY) 2022; 14:9617-9631. [PMID: 36455876 PMCID: PMC9792196 DOI: 10.18632/aging.204411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Abstract
Lung adenocarcinoma (LUAD) remains a major reason of cancer-associated mortality globally, and there exists a lack of indicators for survival in LUAD patients. Therefore, it is clinically required to obtain a novel prognostically indicator for guiding clinical management. In this study, we established a circadian rhythm (CR) related signature by a combinative investigation of multiple datasets. The newly-established signature showed an acceptable ability to predict survival and could serve as an independent indicator for prognosis. Moreover, the newly-established signature was critically associated with tumor malignancy, including proliferation, invasion, EMT and metastasis. The newly-established signature was predictive of response to immune checkpoint blockade. Collectively, we established a CR-related gene signature that could forecast survival, tumor malignancy and therapeutic response; our findings could help guiding clinical management.
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Affiliation(s)
- Yuanjun Cheng
- Department of Cardiothoracic Surgery, People’s Hospital of Chizhou, Chizhou, China
| | - Jie Yao
- Department of Cardiothoracic Surgery, People’s Hospital of Chizhou, Chizhou, China
| | - Qianru Fang
- Department of Obstetrics, People’s Hospital of Chizhou, Chizhou, China
| | - Bin Chen
- Department of Cardiothoracic Surgery, People’s Hospital of Chizhou, Chizhou, China
| | - Guohui Zang
- Department of Cardiothoracic Surgery, People’s Hospital of Chizhou, Chizhou, China
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Fu X, Liu H, Fan Y, Yuan J. Extracellular vesicle-mediated transfer of lncRNA CLDN10-AS1 aggravates low-density lipoprotein-induced vascular endothelial injury. Physiol Genomics 2022; 54:471-485. [PMID: 36250558 DOI: 10.1152/physiolgenomics.00094.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Oxidized low-density lipoprotein (ox-LDL) stimulation impairs the oxidation-reduction equilibrium in vascular endothelial cells (VECs) and contributes to atherosclerosis (AS). This study probed the mechanisms of extracellular vesicle (EV)-mediated transfer of lncRNA CLDN10 antisense RNA 1 (CLDN10-AS1) in ox-LDL-induced VEC injury. Initially, VEC injury models were established by treating human umbilical vein endothelial cells (HUVECs) with ox-LDL. EVs were isolated from HUVECs (HUVECs-EVs) and identified. CLDN10-AS1, microRNA (miR)-186, and Yin Yang 1 (YY1) expressions in ox-LDL-treated HUVECs and EVs derived from these cells (ox-EVs) were measured. HUVECs were incubated with EVs, after which the cell viability, apoptosis, and concentrations of proinflammatory cytokines and oxidative stress markers were measured. We discovered that CLDN10-AS1 and YY1 were upregulated in ox-LDL-treated HUVECs, whereas miR-186 was downregulated. ox-EVs treatment elevated CLDN10-AS1 expression in HUVECs and ox-EVs overexpressing CLDN10-AS1 promoted VEC injury. Besides, CLDN10-AS1 is competitively bound to miR-186 and promoted YY1 expression. Rescue experiments revealed that miR-186 overexpression or YY1 suppression partially reversed the roles of ox-EVs overexpressing CLDN10-AS1 in ox-LDL-induced VEC injury. Lastly, clinical serum samples were collected for verification. Overall, CLDN10-AS1 carried by HUVECs-EVs into HUVECs competitively bound to miR-186 to elevate YY1 expression, thereby aggravating ox-LDL-induced VEC injury.
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Affiliation(s)
- Xiaoyang Fu
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China.,People's Hospital of Zhengzhou University, Zhengzhou, China.,Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Heng Liu
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yulong Fan
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ji Yuan
- Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China.,School of Clinical Medicine, Henan University, Zhengzhou, China.,Department of Anaesthesia, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Anaesthesia, Central China Fuwai Hospital, Zhengzhou, China
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7
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Wei W, Xu T, Zhang Y, Huang Y, Wang X. Upregulation of long noncoding RNA linc02544 and its association with overall survival rate and the influence on cell proliferation and migration in lung squamous cell carcinoma. Discov Oncol 2022; 13:41. [PMID: 35635595 PMCID: PMC9151984 DOI: 10.1007/s12672-022-00501-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) exert crucial biological functions by regulating miRNAs, which are implicated in cancer progression and tumorigenesis. A previous study has indicated that lncRNA linc02544 expression is upregulated in lung adenocarcinoma, whereas, the role of linc02544 in LUSC is elusive. METHODS The differential linc02544 expression in LUSC tissues and adjacent non-tumor tissues were evaluated with RT-qPCR. Kaplan-Meier curve was conducted to evaluate the clinical prognostic significance of linc02544. Then cellular experiments were performed to assess the influence of linc02544 in LUSC proliferation, invasion, and migration, and a western blot assay was used to measure the metastasis-related protein levels. The downstream miRNAs were verified using the LncBase Experimental v.2 database and dual-luciferase reporter assay. RESULTS Linc02544 was overexpressed in LUSC tissues from positive lymph node metastasis-positive and TNM high-stage patients. Low linc02544 expression was associated with a longer survival rate. Downregulation of linc02544 by si-linc02544 restrained cell growth capacities, migration, and invasion abilities. Expression of MMP-2, MMP-9, and vimentin was decreased while E-cadherin was increased in si-linc02544 cells compared with that in untreated cells. Mechanistically, we identified that linc02544 acted as a sponge of miR-138-5p, which expression had a negative correlation. E2F3 was a potential target of miR-138-5p, CONCLUSIONS: Notably, high linc02544 expression was associated with severe clinical parameters and was a putative prognostic predictor for patients with LUSC. Downregulation of linc02544 may weaken the LUSC cell proliferation, migration, and invasion by regulating miR-138-5p/E2F3, which maybe serve as a biomarker for the prognosis and target treatment of LUSC.
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Affiliation(s)
- Wei Wei
- Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing University School of Medicine, Jiangsu, 210002, China
| | - Teng Xu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221000, China
| | - Ying Zhang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Yong Huang
- Department of Medical Oncology, Cancer Center of Jinling Hospital, No. 34, 34 Biao, Yanggongjing Street, Nanjing, 210002, Jiangsu, China.
| | - Xiang Wang
- Department of Medical Oncology, Xuzhou Central Hospital, 199 Jiefang South Road, Xuzhou, 221009, Jiangsu, China.
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Li R, Li JP, Liu TT, Huo C, Yao J, Ji XL, Qu YQ. Prognostic Value of Genomic Instability of m6A-Related lncRNAs in Lung Adenocarcinoma. Front Cell Dev Biol 2022; 10:707405. [PMID: 35309906 PMCID: PMC8928224 DOI: 10.3389/fcell.2022.707405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Genomic instability of N6-methyladenosine (m6A)–related long noncoding RNAs (lncRNAs) plays a pivotal role in the tumorigenesis of lung adenocarcinoma (LUAD). Our study identified a signature of genomic instability of m6A-associated lncRNA signature and revealed its prognostic role in LUAD. Methods: We downloaded RNA-sequencing data and somatic mutation data for LUAD from The Cancer Genome Atlas (TCGA) and the GSE102287 dataset from the Gene Expression Omnibus (GEO) database. The “Limma” R package was used to identify a network of regulatory m6A-related lncRNAs. We used the Wilcoxon test method to identify genomic-instability–derived m6A-related lncRNAs. A competing endogenous RNA (ceRNA) network was constructed to identify the mechanism of the genomic instability of m6A-related lncRNAs. Univariate and multivariate Cox regression analyses were performed to construct a prognostic model for internal testing and validation of the prognostic m6A-related lncRNAs using the GEO dataset. Performance analysis was conducted to compare our prognostic model with the previously published lncRNA models. The CIBERSORT algorithm was used to explore the relationship of m6A-related lncRNAs and the immune microenvironment. Prognostic m6A-related lncRNAs in prognosis, the tumor microenvironment, stemness scores, and anticancer drug sensitivity were analyzed to explore the role of prognostic m6A-related lncRNAs in LUAD. Results: A total of 42 genomic instability–derived m6A-related lncRNAs were differentially expressed between the GS (genomic stable) and GU (genomic unstable) groups of LUAD patients. Four differentially expressed lncRNAs, 17 differentially expressed microRNAs, and 75 differentially expressed mRNAs were involved in the genomic-instability–derived m6A-related lncRNA-mediated ceRNA network. A prediction model based on 17 prognostic m6A-associated lncRNAs was constructed based on three TCGA datasets (all, training, and testing) and validated in the GSE102287 dataset. Performance comparison analysis showed that our prediction model (area under the curve [AUC] = 0.746) could better predict the survival of LUAD patients than the previously published lncRNA models (AUC = 0.577, AUC = 0.681). Prognostic m6A-related-lncRNAs have pivotal roles in the tumor microenvironment, stemness scores, and anticancer drug sensitivity of LUAD. Conclusion: A signature of genomic instability of m6A-associated lncRNAs to predict the survival of LUAD patients was validated. The prognostic, immune microenvironment and anticancer drug sensitivity analysis shed new light on the potential novel therapeutic targets in LUAD.
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Affiliation(s)
- Rui Li
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jian-Ping Li
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ting-Ting Liu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chen Huo
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Yao
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Traditional Chinese Medicine Hospital of Jinan, Jinan, China
| | - Yi-Qing Qu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Yi-Qing Qu,
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Liu P, Li H, Liao C, Tang Y, Li M, Wang Z, Wu Q, Zhou Y. Identification of key genes and biological pathways in Chinese lung cancer population using bioinformatics analysis. PeerJ 2022; 10:e12731. [PMID: 35178291 PMCID: PMC8812315 DOI: 10.7717/peerj.12731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/11/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Identification of accurate prognostic biomarkers is still particularly urgent for improving the poor survival of lung cancer patients. In this study, we aimed to identity the potential biomarkers in Chinese lung cancer population via bioinformatics analysis. METHODS In this study, the differentially expressed genes (DEGs) in lung cancer were identified using six datasets from Gene Expression Omnibus (GEO) database. Subsequently, enrichment analysis was conducted to evaluate the underlying molecular mechanisms involved in progression of lung cancer. Protein-protein interaction (PPI) and CytoHubba analysis were performed to determine the hub genes. The GEPIA, Human Protein Atlas (HPA), Kaplan-Meier plotter, and TIMER databases were used to explore the hub genes. The receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic value of hub genes. Reverse transcription quantitative PCR (qRT-PCR) was used to validate the expression levels of hub genes in 10 pairs of lung cancer paired tissues. RESULTS A total of 499 overlapping DEGs (160 upregulated and 339 downregulated genes) were identified in the microarray datasets. DEGs were mainly associated with pathways in cancer, focal adhesion, and protein digestion and absorption. There were nine hub genes (CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A, UBE2C, CHEK1 and BIRC5) identified by PPI and module analysis. In GEPIA database, the expression levels of these genes in lung cancer tissues were significantly upregulated compared with normal lung tissues. The results of prognostic analysis showed that relatively higher expression of hub genes was associated with poor prognosis of lung cancer. In HPA database, most hub genes were highly expressed in lung cancer tissues. The hub genes have good diagnostic efficiency in lung cancer and normal tissues. The expression of any hub gene was associated with the infiltration of at least two immune cells. qRT-PCR confirmed that the expression level of CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A were highly expressed in lung cancer tissues. CONCLUSIONS The hub genes and functional pathways identified in this study may contribute to understand the molecular mechanisms of lung cancer. Our findings may provide new therapeutic targets for lung cancer patients.
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Affiliation(s)
- Ping Liu
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Hui Li
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Chunfeng Liao
- Department of Cardiology, The First Hospital of Changsha, Changsha, China
| | - Yuling Tang
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Mengzhen Li
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Zhouyu Wang
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Qi Wu
- Department of Emergency, The First Hospital of Changsha, Changsha, China
| | - Yun Zhou
- Department of Spinal Surgery, The First Hospital of Changsha, Changsha, China
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10
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Identification of Differentially Expressed and Prognostic lncRNAs for the Construction of ceRNA Networks in Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2021:2659550. [PMID: 34987577 PMCID: PMC8723861 DOI: 10.1155/2021/2659550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/07/2021] [Indexed: 11/18/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) could function as competitive endogenous RNAs (ceRNAs) to competitively adsorb microRNAs (miRNAs), thereby regulating the expression of their target protein-coding mRNAs. In this study, we aim to identify more effective diagnostic and prognostic markers for lung adenocarcinoma (LUAD). Methods We obtained differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) for LUAD by using The Cancer Genomes Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) was performed to unveil core gene modules associated with LUAD. The Cox proportional hazards model was performed to determine the prognostic significance of DElncRNAs. The diagnostic and prognostic significance of DElncRNAs was further verified based on the receiver operating characteristic curve (ROC). Cytoscape was used to construct the ceRNA networks comprising the lncRNAs-miRNAs-mRNAs axis based on the correlation obtained from the miRcode, miRDB, and TargetScan. Results Compared with normal lung tissues, 2355 DElncRNAs, 820 DEmiRNAs, and 17289 DEmRNAs were identified in LUAD tissues. We generated 8 WGCNA core modules in the lncRNAs coexpression network, 5 modules in the miRNAs, and 12 modules in the mRNAs coexpression network, respectively. One lncRNA module (blue) consisting of 441 lncRNAs, two miRNA modules (blue and turquoise) containing 563 miRNAs, and one mRNA module (turquoise), which consisted of 15162 mRNAs, were mostly significantly related to LUAD status. Furthermore, 67 DEmRNAs were found to be tumor-associated as well as the target genes of the DElncRNAs-DEmiRNAs axis. Survival analyses showed that 6 lncRNAs (LINC01447, WWC2-AS2, OGFRP1, LINC00942, LINC01168, and AC005863.1) were significantly correlated with the prognosis of LUAD patients. Ultimately, the potential ceRNA networks including 6 DElncRNAs, 4 DEmiRNAs, and 22 DEmRNAs were constructed. Conclusion Our study indicated that 6 DElncRNAs had the possibilities as diagnostic and prognostic biomarkers for LUAD. The lncRNA-mediated ceRNA networks might provide novel insights into the molecular mechanisms of LUAD progression.
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Lin Z, Huang W, Yi Y, Li D, Xie Z, Li Z, Ye M. LncRNA ADAMTS9-AS2 is a Prognostic Biomarker and Correlated with Immune Infiltrates in Lung Adenocarcinoma. Int J Gen Med 2021; 14:8541-8555. [PMID: 34849000 PMCID: PMC8626860 DOI: 10.2147/ijgm.s340683] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background The role of long noncoding RNA (LncRNA) ADAMTS9 antisense RNA 2 (ADAMTS9-AS2) is unclear in lung adenocarcinoma (LUAD). The aim of this study was to explore the relationship between ADAMTS9-AS2 and LUAD, based on The Cancer Genome Atlas (TCGA) database and bioinformatics analysis. Methods Various statistical methods, Kaplan–Meier method, Cox regression analysis, GSEA, and immune infiltration analysis were used to evaluate the relationship between clinical features and ADAMTS9-AS2 expression, prognostic factors, and the significant involvement of ADAMTS9-AS2 in function. Results In LUAD patients, low expression of ADAMTS9-AS2 was associated with N stage (P=0.011), gender (P=0.002), number of packs smoked (P=0.024) and smoker (P<0.001). Low ADAMTS9-AS2 expression predicted a poorer overall survival (OS) (HR: 0.68; 95% CI: 0.51–0.91; P=0.01). And ADAMTS9-AS2 expression (HR: 0.626; 95% CI: 0.397–0.986; P=0.043) was independently correlated with OS in LUAD patients. Unwinding of DNA, extrinsic pathway, polo-like kinase-mediated events, cori cycle, MCM pathway, proteasome pathway, lagging strand synthesis and PCNA-dependent long patch base excision repair were differentially enriched in ADAMTS9-AS2 high expression phenotype. ADAMTS9-AS2 expression was correlated with certain immune infiltrating cells. Conclusion In LUAD patients, ADAMTS9-AS2 expression was significantly associated with poor survival and immune infiltration. ADAMTS9-AS2 may be a promising biomarker of prognosis and response to immunotherapy for LUAD.
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Affiliation(s)
- Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Yongsheng Yi
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Dongbing Li
- MyGene Diagnostics Co., Ltd., Guangzhou, 510000, Guangdong, People's Republic of China
| | - Zehua Xie
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Zumei Li
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Min Ye
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
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12
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Li L, Wei H, Zhang YW, Zhao S, Che G, Wang Y, Chen L. Differential expression of long non-coding RNAs as diagnostic markers for lung cancer and other malignant tumors. Aging (Albany NY) 2021; 13:23842-23867. [PMID: 34670194 PMCID: PMC8580341 DOI: 10.18632/aging.203523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/02/2021] [Indexed: 02/05/2023]
Abstract
Due to advances in chip and sequencing technology, several types and numbers of long non-coding RNAs (lncRNAs) have been identified. LncRNAs are defined as non-protein-coding RNA molecules longer than 200 nucleotides, and are now thought as a new frontier in the study of human malignant diseases including NSCLC. Diagnosis of numerous malignant tumors has been closely linked to the differential expression of certain lncRNAs. LncRNAs are involved in gene expression regulation at multiple levels of epigenetics, transcriptional regulation, and post-transcriptional regulation. Mutations, deletions, or abnormal expression levels lead to physiological abnormalities, disease occurrence and are closely associated with human tumor diseases. LncRNAs play a crucial role in cancerous processes as either oncogenes or tumor suppressor genes. The expression of lncRNAs can regulate tumor cell in the proliferation, migration, apoptosis, cycle, invasion, and metastasis. As such, lncRNAs are potential diagnostic and treatment targets for cancer. And that, tumor biomarkers need to be detectable in easily accessible body samples, should be characterized by high specificity and sufficient sensitivity. Herein, it is significant clinical importance to screen and supplement new biomarkers for early diagnosis of lung cancer. This study aimed at systematically describing lncRNAs from five aspects based on recent studies: concepts, classification, structure, molecular mechanism, signal pathway, as well as review lncRNA implications in malignant tumor.
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Affiliation(s)
- Li Li
- College of Nursing and Health, Henan University, Kaifeng, Henan 475004, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haitao Wei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Department of Thoracic Surgery, Huaihe Hospital, Henan University, Kaifeng, Henan 475001, China
| | - Yi Wei Zhang
- College of Nursing and Health, Henan University, Kaifeng, Henan 475004, China
| | - Shizhe Zhao
- Basic Medical College of Henan University, Kaifeng, Henan 475004, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yun Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Longqi Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Kuo IY, Liu D, Lai WW, Wang YC, Loh YP. Carboxypeptidase E mRNA: Overexpression predicts recurrence and death in lung adenocarcinoma cancer patients. Cancer Biomark 2021; 33:369-377. [PMID: 34511486 DOI: 10.3233/cbm-210206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Effective biomarkers for prediction of recurrence of lung adenocarcinoma cancer (LADC) patients are needed to determine treatment strategies post-surgery to improve outcome. OBJECTIVE This study evaluates the efficacy of carboxypeptidase E (CPE) mRNA including its splice isoforms, CPE-ΔN, as a biomarker for predicting recurrence in adenocarcinoma patients. METHODS RNA was extracted from resected tumors from 86 patients with different stages of non-small cell LADC. cDNA was synthesized and qRT-PCR carried out to determine the copy numbers of CPE/CPE-ΔN mRNA. Patients were followed for 7 years post-tumor resection to determine recurrence and death. RESULTS ROC curve analysis showed the overall AUC for CPE/CPE-ΔN copy number was 0.563 in predicting recurrence and 0.563 in predicting death. Kaplan-Meier survival analysis showed statistical difference (p= 0.018), indicating that patients with high CPE/CPE-ΔN copy numbers had a shorter time of disease-free survival and also shorter time to death (p= 0.035). Subgroup analyses showed that association of disease-free survival time with CPE/CPE-ΔN copy number was stronger among stage I and II LADC patients (p= 0.047). CONCLUSIONS CPE/CPE-ΔN mRNA is a potentially useful biomarker for predicting recurrence and death in LADC patients, especially in identifying patients at high risk of recurrence at early stages I and II.
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Affiliation(s)
- I-Ying Kuo
- Institute of Basic Medical Sciences and Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan
| | - Danping Liu
- Biostatistics and Bioinformatics Branch, Bethesda, MD, USA.,Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wu-Wei Lai
- Department of Surgery, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Wang
- Institute of Basic Medical Sciences and Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan
| | - Y Peng Loh
- Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Liu W, Luo W, Zhou P, Cheng Y, Qian L. Bioinformatics Analysis and Functional Verification of ADAMTS9-AS1/AS2 in Lung Adenocarcinoma. Front Oncol 2021; 11:681777. [PMID: 34395250 PMCID: PMC8358405 DOI: 10.3389/fonc.2021.681777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/29/2021] [Indexed: 01/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), as competitive endogenous RNAs (ceRNAs), play a critical role in biological processes of cancer. However, the roles of specific lncRNAs in ceRNA network of lung adenocarcinoma (LUAD) remains largely unclear. Herein, we identified the roles of lncRNA ADAMTS9-AS1/AS2 (ADAMTS-AS1/AS2) in lung adenocarcinoma by bioinformatics analyses and functional verification. First, differentially expressed genes ADAMTS9-AS1, ADAMTS9-AS2 and ADAMTS9 were screened out from GSE130779. Then the expression correlation of these three genes was analyzed. The results showed that ADAMTS9-AS1, ADAMTS9-AS2 and ADAMTS9 were down-regulated in LUAD, and were positively correlated with each other. After that, miRcode was used to find miR-150 which binds to ADAMTS9-AS1/ADAMTS9-AS2/ADAMTS9. Next, co-expression analysis and functional enrichment analyses were performed to further analyze differentially expressed genes. The results showed that the differentially expressed genes were mainly enriched in Beta3 integrin cell surface interactions and epithelial-to-mesenchymal transition. Finally, the cell functions of ADAMTS9-AS1 and ADAMTS9-AS2 in A549 and NCI-H1299 cell lines were verified. In vitro cell studies confirmed that ADAMTS9-AS1 and ADAMTS9-AS2 play an inhibitory role in LUAD cells.
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Affiliation(s)
- Wei Liu
- Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenguang Luo
- Department of Radiation Oncology, Anhui Provincial Hospital, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Peijie Zhou
- Department of Radiation Oncology, Anhui Provincial Hospital, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Yong Cheng
- Department of Radiation Oncology, Anhui Provincial Hospital, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Liting Qian
- Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Su L, Zhang G, Kong X. A Novel Five-Gene Signature for Prognosis Prediction in Hepatocellular Carcinoma. Front Oncol 2021; 11:642563. [PMID: 34336648 PMCID: PMC8322700 DOI: 10.3389/fonc.2021.642563] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has been a global health issue and attracted wide attention due to its high incidence and poor outcomes. In this study, our purpose was to explore an effective prognostic marker for HCC. Five cohort profile datasets from GEO (GSE25097, GSE36376, GSE62232, GSE76427 and GSE101685) were integrated with TCGA-LIHC and GTEx dataset to identify differentially expressed genes (DEGs) between normal and cancer tissues in HCC patients, then 5 upregulated differentially expressed genes and 32 downregulated DEGs were identified as common DEGs in total. Next, we systematically explored the relationship between the expression of 37 common DEGs in tumor tissues and overall survival (OS) rate of HCC patients in TCGA and constructed a novel prognostic model composed of five genes (AURKA, PZP, RACGAP1, ACOT12 and LCAT). Furthermore, the predicted performance of the five-gene signature was verified in ICGC and another independent clinical samples cohort, and the results demonstrated that the signature performed well in predicting the OS rate of patients with HCC. What is more, the signature was an independent hazard factor for HCC patients when considering other clinical factors in the three cohorts. Finally, we found the signature was significantly associated with HCC immune microenvironment. In conclusion, the prognostic five-gene signature identified in our present study could efficiently classify patients with HCC into subgroups with low and high risk of longer overall survival time and help clinicians make decisions for individualized treatment.
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Affiliation(s)
- Lisa Su
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Genhao Zhang
- Department of Blood Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zhao Y, Ma S, Cui Z, Li S, Chen Y, Yin Y, Yin Z. The relationship between LncRNAs and lung adenocarcinoma as well as their ceRNA network. Cancer Biomark 2021; 31:165-176. [PMID: 33896828 DOI: 10.3233/cbm-203078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND More and more studies have shown that long non-coding RNA (LncRNA) as a competing endogenous RNA (ceRNA) plays an important role in lung cancer. Therefore, we analyzed the RNA expression profiles of 82 lung cancer patients which were all from Gene Expression Omnibus (GEO). METHODS Firstly, we used BLASTN (evalue = 1e-10) to annotate the gene sets, performed in-group correction and batched normalization of the three data sets with R. Secondly, we used the limma and sva packages to compare tumor tissues with normal tissues. Then through WGCNA, we obtained the 4 gene modules most related to the trait. RESULTS We intersected the genes of above 4 modules with the differential expression genes: 28 LncRNAs (up: 5, down: 23) and 265 mRNAs (up:11, down: 254). Based on these genes, we picked up 6 LncRNAs (CCDC39, FAM182A, SRGAP3-AS2, ADAMTS9-AS2, AC020907.2, SFTA1P), then set and visualized the LncRNA-miRNA-mRNA ceRNA network with 12 miRNAs related to 12 mRNAs. Finally, we performed downstream analysis of 265 mRNAs by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Protein-Protein Interaction (PPI) network. CONCLUSION After analyzing, we think this study provides a new direction for basic and clinical research related to LAD, and is expected to provide new targets for early diagnosis, prognostic evaluation and clinical treatment of lung cancer.
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Affiliation(s)
- Yuxin Zhao
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Shuwen Ma
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Zhigang Cui
- School of Nursing, China Medical University, Shenyang, Liaoning, China
| | - Sixuan Li
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yao Chen
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Yu Yin
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China
| | - Zhihua Yin
- China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China.,Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang North New Area, Shenyang, Liaoning, China
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Xu Y, Lin L, Lv D, Yan S, He S, Ge H. LncRNA-LINC01089 inhibits lung adenocarcinoma cell proliferation and promotes apoptosis via sponging miR-543. Tissue Cell 2021; 72:101535. [PMID: 33892399 DOI: 10.1016/j.tice.2021.101535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 01/22/2023]
Abstract
LINC01089, a newly discovered long non-coding RNA (lncRNA), has been reported to inhibit the progression of various types of cancers. This study aimed to characterize LINC01089 in the pathogenesis of lung adenocarcinoma (LUAD). LINC01089 expression in LUAD tissues or/and cells and its association with the overall survival of LUAD patients was analyzed in The Cancer Genome Atlas (TCGA)-LUAD database, by qRT-PCR or by Kaplan-Meier's curve. Databases of StarBase, LncBase, and DEmiRNA were used to predict and confirm the interaction between LINC01089 and potential LINC01089-targeted microRNAs (miRNAs). The expressions of these miRNAs in LUAD tissues or/and cells were determined by qRT-PCR, and dual-luciferase reporter assay was performed to validate lncRNA-miRNA interaction. The expressions of B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein (Bax) and Cleaved caspase-3 in LUAD cells were analyzed by Western blot. LINC01089 improved overall survival of LUAD patients and was low-expressed in LUAD. Upregulating LINC01089 expression reduced LUAD cell viability, inhibited colony formation, enhanced apoptosis, accompanied by downregulated Bcl-2 and miR-543 and upregulated Bax and Cleaved caspase-3. MiR-543 was determined as a target gene of LINC01089, and was high-expressed in LUAD tissues. Upregulating miR-543 expression induced the opposite effects to LINC01089 upregulation on these cellular biological behaviors and the expressions of Bcl-2, Bax and Cleaved caspase-3. Moreover, the effects of miR-543 upregulation and LINC01089 upregulation were mutually counteracted by each other. LINC01089 inhibited lung adenocarcinoma cell proliferation and promoted apoptosis via sponging miR-543.
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Affiliation(s)
- Youwen Xu
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), China
| | - Ling Lin
- Department of Respiratory Medicine, Taizhou Hospital of Wenzhou Medical University, China
| | - Dongqing Lv
- Department of Respiratory Medicine, Taizhou Hospital of Wenzhou Medical University, China
| | - Shuangquan Yan
- Department of Respiratory Medicine, Taizhou Hospital of Wenzhou Medical University, China
| | - Susu He
- Department of Respiratory Medicine, Taizhou Hospital of Wenzhou Medical University, China
| | - Hongfei Ge
- Department of Thoracic Surgery, Taizhou Hospital of Wenzhou Medical University, China.
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Wang J, Li J. LncRNA MIR155HG functions as a ceRNA for inhibition of lung adenocarcinoma growth and prediction of prognosis. Arch Med Sci 2021; 20:539-556. [PMID: 38757039 PMCID: PMC11094835 DOI: 10.5114/aoms/131198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/04/2020] [Indexed: 05/18/2024] Open
Abstract
Introduction Long non-coding RNAs (lncRNAs) functioning as competing endogenous RNAs (ceRNAs) play critical roles in tumour progression. However, prognosis-related ceRNA networks in lung adenocarcinoma (LUAD) have not been well characterised. Material and methods LUAD datasets were downloaded from the TCGA database, and the patients were divided into metastasis and non-metastasis groups. The differential expression of lncRNAs (DELs), miRNAs (DEMs), and mRNAs (DEGs) was analysed using the Limma package. Next, interactions between miRNA, lncRNA, and mRNA were predicted by miRcode, miRTar-Base, miRDB, and TargetScan. The ceRNA network was constructed based on these interactions using Cytoscape software. DEG enrichment analysis was performed by GO and KEGG. After the prognosis analysis, we further screened molecules and constructed the prognosis-related ceRNA network. Moreover, the interactions between lncRNA, miRNA, and mRNA were validated by biological experiments. Results 854 DELs, 150 DEMs, and 2211 DEGs between metastasis and non-metastasis LUAD patients were identified. Functional enrichment analysis suggested that DEGs were closely related to key biological processes involved in LUAD progression. The prognosis-related ceRNA network included 1 miRNA, 2 lncRNAs, and 4 mRNAs. In this network, MIR155HG and ADAMTS9-AS2 can function as ceRNAs of miR-212 to regulate EPM2AIP1, LAX1, PRICKLE2, and CD226. Moreover, our study confirmed that MIR155HG inhibited the proliferation, migration, and invasion of LUAD cells by sponging miR-212-3p to regulate CD226. Conclusions This ceRNA network contributes to understanding the pathogenesis of LUAD. Furthermore, the molecules in the network are valuable predictive factors for LUAD prognosis as well as potential therapeutic biomarkers.
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Affiliation(s)
- Jing Wang
- Department of Thoracic Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jie Li
- Department of Thoracic Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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