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Jin W, Ou K, Li Y, Liu W, Zhao M. Metabolism-related long non-coding RNA in the stomach cancer associated with 11 AMMLs predictive nomograms for OS in STAD. Front Genet 2023; 14:1127132. [PMID: 36992704 PMCID: PMC10040790 DOI: 10.3389/fgene.2023.1127132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
Background: The metabolic processes involving amino acids are intimately linked to the onset and progression of cancer. Long non-coding RNAs (LncRNAs) perform an indispensable function in the modulation of metabolic processes as well as the advancement of tumors. Non-etheless, research into the role that amino acid metabolism-related LncRNAs (AMMLs) might play in predicting the prognosis of stomach adenocarcinoma (STAD) has not been done. Therefore, This study sought to design a model for AMMLs to predict STAD-related prognosis and elucidate their immune properties and molecular mechanisms.Methods: The STAD RNA-seq data in the TCGA-STAD dataset were randomized into the training and validation groups in a 1:1 ratio, and models were constructed and validated respectively. In the molecular signature database, This study screened for genes involved in amino acid metabolism. AMMLs were obtained by Pearson’s correlation analysis, and predictive risk characteristics were established using least absolute shrinkage and selection operator (LASSO) regression, univariate Cox analysis, and multivariate Cox analysis. Subsequently, the immune and molecular profiles of high- and low-risk patients and the benefit of the drug were examined.Results: Eleven AMMLs (LINC01697, LINC00460, LINC00592, MIR548XHG, LINC02728, RBAKDN, LINCOG, LINC00449, LINC01819, and UBE2R2-AS1) were used to develop a prognostic model. Moreover, high-risk individuals had worse overall survival (OS) than low-risk patients in the validation and comprehensive groups. A high-risk score was associated with cancer metastasis as well as angiogenic pathways and high infiltration of tumor-associated fibroblasts, Treg cells, and M2 macrophages; suppressed immune responses; and a more aggressive phenotype.Conclusion: This study identified a risk signal associated with 11 AMMLs and established predictive nomograms for OS in STAD. These findings will help us personalize treatment for gastric cancer patients.
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Affiliation(s)
- Wenjian Jin
- Department of Hepatopancreatobiliary Surgery, Changzhou First People’s Hospital, Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Kongbo Ou
- Department of Urinary Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People’s Hospital, Soochow University, Changzhou, China
| | - Yuanyuan Li
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People’s Hospital, Soochow University, Changzhou, China
| | - Wensong Liu
- Department of Hepatopancreatobiliary Surgery, Changzhou First People’s Hospital, Third Affiliated Hospital of Soochow University, Changzhou, China
- *Correspondence: Min Zhao, ; Wensong Liu,
| | - Min Zhao
- Department of Gastrointestinal Surgery, Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
- *Correspondence: Min Zhao, ; Wensong Liu,
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Examples of Inverse Comorbidity between Cancer and Neurodegenerative Diseases: A Possible Role for Noncoding RNA. Cells 2022; 11:cells11121930. [PMID: 35741059 PMCID: PMC9221903 DOI: 10.3390/cells11121930] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the most common causes of death; in parallel, the incidence and prevalence of central nervous system diseases are equally high. Among neurodegenerative diseases, Alzheimer’s dementia is the most common, while Parkinson’s disease (PD) is the second most frequent neurodegenerative disease. There is a significant amount of evidence on the complex biological connection between cancer and neurodegeneration. Noncoding RNAs (ncRNAs) are defined as transcribed nucleotides that perform a variety of regulatory functions. The mechanisms by which ncRNAs exert their functions are numerous and involve every aspect of cellular life. The same ncRNA can act in multiple ways, leading to different outcomes; in fact, a single ncRNA can participate in the pathogenesis of more than one disease—even if these seem very different, as cancer and neurodegenerative disorders are. The ncRNA activates specific pathways leading to one or the other clinical phenotype, sometimes with obvious mechanisms of inverse comorbidity. We aimed to collect from the existing literature examples of inverse comorbidity in which ncRNAs seem to play a key role. We also investigated the example of mir-519a-3p, and one of its target genes Poly (ADP-ribose) polymerase 1, for the inverse comorbidity mechanism between some cancers and PD. We believe it is very important to study the inverse comorbidity relationship between cancer and neurodegenerative diseases because it will help us to better assess these two major areas of human disease.
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Salemi M, Lanza G, Mogavero MP, Cosentino FII, Borgione E, Iorio R, Ventola GM, Marchese G, Salluzzo MG, Ravo M, Ferri R. A Transcriptome Analysis of mRNAs and Long Non-Coding RNAs in Patients with Parkinson's Disease. Int J Mol Sci 2022; 23:ijms23031535. [PMID: 35163455 PMCID: PMC8836138 DOI: 10.3390/ijms23031535] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder. The number of cases of PD is expected to double by 2030, representing a heavy burden on the healthcare system. Clinical symptoms include the progressive loss of dopaminergic neurons in the substantia nigra of the midbrain, which leads to striatal dopamine deficiency and, subsequently, causes motor dysfunction. Certainly, the study of the transcriptome of the various RNAs plays a crucial role in the study of this neurodegenerative disease. In fact, the aim of this study was to evaluate the transcriptome in a cohort of subjects with PD compared with a control cohort. In particular we focused on mRNAs and long non-coding RNAs (lncRNA), using the Illumina NextSeq 550 DX System. Differential expression analysis revealed 716 transcripts with padj ≤ 0.05; among these, 630 were mRNA (coding protein), lncRNA, and MT_tRNA. Ingenuity pathway analysis (IPA, Qiagen) was used to perform the functional and pathway analysis. The highest statistically significant pathways were: IL-15 signaling, B cell receptor signaling, systemic lupus erythematosus in B cell signaling pathway, communication between innate and adaptive immune cells, and melatonin degradation II. Our findings further reinforce the important roles of mitochondria and lncRNA in PD and, in parallel, further support the concept of inverse comorbidity between PD and some cancers.
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Affiliation(s)
- Michele Salemi
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (G.L.); (F.I.I.C.); (E.B.); (M.G.S.); (R.F.)
- Correspondence: or
| | - Giuseppe Lanza
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (G.L.); (F.I.I.C.); (E.B.); (M.G.S.); (R.F.)
- Department of Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy
| | | | - Filomena I. I. Cosentino
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (G.L.); (F.I.I.C.); (E.B.); (M.G.S.); (R.F.)
| | - Eugenia Borgione
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (G.L.); (F.I.I.C.); (E.B.); (M.G.S.); (R.F.)
| | - Roberta Iorio
- Genomix4Life Srl, 84081 Baronissi, Italy; (R.I.); (G.M.V.); (G.M.); (M.R.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Giovanna Maria Ventola
- Genomix4Life Srl, 84081 Baronissi, Italy; (R.I.); (G.M.V.); (G.M.); (M.R.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Giovanna Marchese
- Genomix4Life Srl, 84081 Baronissi, Italy; (R.I.); (G.M.V.); (G.M.); (M.R.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Maria Grazia Salluzzo
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (G.L.); (F.I.I.C.); (E.B.); (M.G.S.); (R.F.)
| | - Maria Ravo
- Genomix4Life Srl, 84081 Baronissi, Italy; (R.I.); (G.M.V.); (G.M.); (M.R.)
- Genome Research Center for Health—CRGS, 84081 Baronissi, Italy
| | - Raffaele Ferri
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (G.L.); (F.I.I.C.); (E.B.); (M.G.S.); (R.F.)
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A Transcriptome Analysis of mRNAs and Long Non-Coding RNAs in Patients with Parkinson's Disease. Int J Mol Sci 2022. [PMID: 35163455 DOI: 10.3390/ijms23031535.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder. The number of cases of PD is expected to double by 2030, representing a heavy burden on the healthcare system. Clinical symptoms include the progressive loss of dopaminergic neurons in the substantia nigra of the midbrain, which leads to striatal dopamine deficiency and, subsequently, causes motor dysfunction. Certainly, the study of the transcriptome of the various RNAs plays a crucial role in the study of this neurodegenerative disease. In fact, the aim of this study was to evaluate the transcriptome in a cohort of subjects with PD compared with a control cohort. In particular we focused on mRNAs and long non-coding RNAs (lncRNA), using the Illumina NextSeq 550 DX System. Differential expression analysis revealed 716 transcripts with padj ≤ 0.05; among these, 630 were mRNA (coding protein), lncRNA, and MT_tRNA. Ingenuity pathway analysis (IPA, Qiagen) was used to perform the functional and pathway analysis. The highest statistically significant pathways were: IL-15 signaling, B cell receptor signaling, systemic lupus erythematosus in B cell signaling pathway, communication between innate and adaptive immune cells, and melatonin degradation II. Our findings further reinforce the important roles of mitochondria and lncRNA in PD and, in parallel, further support the concept of inverse comorbidity between PD and some cancers.
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Liu B, Liu Z, Feng C, Li C, Zhang H, Li Z, Tu C, He S. Identification of cuproptosis-related lncRNA prognostic signature for osteosarcoma. Front Endocrinol (Lausanne) 2022; 13:987942. [PMID: 36313774 PMCID: PMC9606239 DOI: 10.3389/fendo.2022.987942] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Copper is an indispensably mineral element involved in various metabolic processes and functions in the active sites of many metalloproteins. Copper dysregulation is associated with cancers such as osteosarcoma (OS), the most common primary bone malignancy with invasiveness and metastasis. However, the causality between cuproptosis and OS remains elusive. We aim to identify cuproptosis-related long non-coding RNAs (lncRNAs) for osteosarcomatous prognosis, immune microenvironment response, and immunotherapy. METHODS The Person correlation and differential expression analysis were used to identify differentially expressed cuproptosis-related lncRNAs (CRLs). The univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were performed to construct the CRL signature. The Kaplan-Meier (K-M) survival analysis, receiver operating characteristic (ROC) curve, internal validation, independent prognostic analysis, and nomograph were used to evaluate the prognostic value. The functional enrichment, tumor microenvironment, immunotherapy and chemotherapy response between the two distinct groups were further explored using a series of algorithms. The expression of signature CRLs was verified by real-time quantitative polymerase chain reaction (RT-qPCR) in OS cell lines. RESULTS A novel CRL signature consisting of four CRLs were successfully identified. The K-M survival analysis indicated that the OS patients in the low-risk groups had a better prognosis than that in the high-risk group. Then, the ROC curve and subgroup survival analysis confirmed the prognostic evaluation performance of the signature. Equally, the independent prognostic analysis demonstrated that the CRL signature was an independently predicted factor for OS. Friends analysis determined the hub genes that played a critical role in differentially expressed genes between two distinct risk groups. In addition, the risk score was related to immunity status, immunotherapy response, and chemotherapeutic drug sensitivity. Finally, the expression of these signature CRLs detected by RT-qPCR was consistent with the bioinformatic analysis results. CONCLUSION In summary, our study confirmed that the novel CRL signature could effectively evaluate prognosis, tumor immune microenvironment, and immunotherapy response in OS. It may benefit for clinical decision-making and provide new insights for personalized therapeutics.
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Affiliation(s)
- Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Chao Tu, ; Shasha He,
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Chao Tu, ; Shasha He,
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Li M, Cheng WT, Li H, Zhang Z, Lu XL, Deng SS, Li J, Yang CH. Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values. Curr Med Sci 2021; 41:916-929. [PMID: 34671904 DOI: 10.1007/s11596-021-2430-2] [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: 09/15/2020] [Accepted: 12/29/2020] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge. METHODS A public data series (GSE87437) was downloaded to identify differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between osteosarcoma patients that do and do not respond to preoperative chemotherapy. Subsequently, functional analysis of the transcriptome expression profile, regulatory networks of DEGs and DElncRNAs, competing endogenous RNAs (ceRNA) and protein-protein interaction networks were performed. Furthermore, the function, pathway, and survival analysis of hub genes was performed and drug and disease relationship prediction of DElncRNA was carried out. RESULTS A total of 626 DEGs, 26 DElncRNAs, and 18 hub genes were identified. However, only one gene and two lncRNAs were found to be suitable as candidate gene and lncRNAs respectively. CONCLUSION The DEGs, hub genes, candidate gene, and candidate lncRNAs screened out in this context were considered as potential biomarkers for the response to neoadjuvant chemotherapy of osteosarcoma.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei-Ting Cheng
- Oncology Department, Wuhan No.1 Hospital, Wuhan, 430030, China
| | - Hao Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhi Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiao-Li Lu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Si-Si Deng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Jian Li
- Institute of Experimental Immunology, University Clinic of Rheinische Friedrich-Wilhelms-University, Bonn, D-53127, Germany.
| | - Cai-Hong Yang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Integrated Analysis of lncRNA-Associated ceRNA Network Identifies Two lncRNA Signatures as a Prognostic Biomarker in Gastric Cancer. DISEASE MARKERS 2021; 2021:8886897. [PMID: 34603561 PMCID: PMC8479203 DOI: 10.1155/2021/8886897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 05/22/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
Background Gastric cancer (GC) is a malignant tumour that originates in the gastric mucosal epithelium and is associated with high mortality rates worldwide. Long noncoding RNAs (lncRNAs) have been identified to play an important role in the development of various tumours, including GC. Yet, lncRNA biomarkers in a competing endogenous RNA network (ceRNA network) that are used to predict survival prognosis remain lacking. The aim of this study was to construct a ceRNA network and identify the lncRNA signature as prognostic factors for survival prediction. Methods The lncRNAs with overall survival significance were used to construct the ceRNA network. Function enrichment, protein-protein interaction, and cluster analysis were performed for dysregulated mRNAs. Multivariate Cox proportional hazards regression was performed to screen the potential prognostic lncRNAs. RT-qPCR was used to measure the relative expression levels of lncRNAs in cell lines. CCK8 assay was used to assess the proliferation of GC cells transfected with sh-lncRNAs. Results Differentially expressed genes were identified including 585 lncRNAs, 144 miRNAs, and 2794 mRNAs. The ceRNA network was constructed using 35 DElncRNAs associated with overall survival of GC patients. Functional analysis revealed that these dysregulated mRNAs were enriched in cancer-related pathways, including TGF-beta, Rap 1, calcium, and the cGMP-PKG signalling pathway. A multivariate Cox regression analysis and cumulative risk score suggested that two of those lncRNAs (LINC01644 and LINC01697) had significant prognostic value. Furthermore, the results indicate that LINC01644 and LINC01697 were upregulated in GC cells. Knockdown of LINC01644 or LINC01697 suppressed the proliferation of GC cells. Conclusions The authors identified 2-lncRNA signature in ceRNA regulatory network as prognostic biomarkers for the prediction of GC patient survival and revealed that silencing LINC01644 or LINC01697 inhibited the proliferation of GC cells.
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Zhou L, Yang Y, Liu M, Gan Y, Liu R, Ren M, Zheng Y, Wang Y, Zhou Y. Identification of the RP11-21C4.1/SVEP1 gene pair associated with FAT2 mutations as a potential biomarker in gastric cancer. Bioengineered 2021; 12:4361-4373. [PMID: 34308747 PMCID: PMC8806586 DOI: 10.1080/21655979.2021.1953211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Gastric cancer (GC) is one of the most common malignancies worldwide. Despite rapid advances in systemic therapy, GC remains the third leading cause of cancer-related deaths. We aimed to identify a novel prognostic signature associated with FAT2 mutations in GC. We analyzed the expression levels of FAT2-mutant and FAT2-wildtype GC samples obtained from The Cancer Genome Atlas (TCGA). The Kaplan–Meier survival curve showed that patients with FAT2 mutations showed better prognosis than those without the mutation. Sixteen long non-coding RNAs (lncRNAs) and 62 messenger RNAs (mRNAs) associated with FAT2 mutations were correlated with the prognosis of GC. We then constructed a 4-mRNA signature and a 5-lncRNA signature for GC. Finally, we identified the most relevant RP11-21 C4.1/SVEP1 gene pair as a prognostic signature of GC that exhibited superior predictive performance in comparison with the 4-mRNA or 5-lncRNA signature by weighted gene correlation network analysis (WGCNA) and Cox proportional hazards regression analysis. In this study, we constructed a prognostic signature of GC by integrative genomics analysis, which also provided insights into the molecular mechanisms linked to FAT2 mutations in GC.
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Affiliation(s)
- Lingshan Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Department of Geriatrics Ward 2, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuan Yang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Min Liu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuling Gan
- Department 1nd Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Rong Liu
- Department of Geriatrics Ward 2, The First Hospital of Lanzhou University, Lanzhou, China
| | - Man Ren
- Department of Geriatrics Ward 2, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
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Ji G, Ren R, Fang X. Identification and Characterization of Non-Coding RNAs in Thymoma. Med Sci Monit 2021; 27:e929727. [PMID: 34219124 PMCID: PMC8268976 DOI: 10.12659/msm.929727] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Thymoma is the most common tumor of the anterior mediastinum, and can be caused by infrequent malignancies arising from the epithelial cells of the thymus. Unfortunately, blood-based diagnostic markers are not currently available. High-throughput sequencing technologies, such as RNA-seq with next-generation sequencing, have facilitated the detection and characterization of both coding and non-coding RNAs (ncRNAs), which play significant roles in genomic regulation, transcriptional and post-transcriptional regulation, and imprinting and epigenetic modification. The knowledge about fusion genes and ncRNAs in thymomas is scarce. MATERIAL AND METHODS For this study, we gathered large-scale RNA-seq data belonging to samples from 25 thymomas and 25 healthy thymus specimens and analyzed them to identify fusion genes, lncRNAs, and miRNAs. RESULTS We found 21 fusion genes, including KMT2A-MAML2, HADHB-REEP1, COQ3-CGA, MCM4-SNTB1, and IFT140-ACTN4, as the most frequent and significant in thymomas. We also detected 65 differentially-expressed lncRNAs in thymomas, including AFAP1-AS1, LINC00324, ADAMTS9-AS1, VLDLR-AS1, LINC00968, and NEAT1, that have been validated with the TCGA database. Moreover, we identified 1695 miRNAs from small RNA-seq data that were overexpressed in thymomas. Our network analysis of the lncRNA-mRNA-miRNA regulation axes identified a cluster of miRNAs upregulated in thymomas, that can trigger the expression of target protein-coding genes, and lead to the disruption of several biological pathways, including the PI3K-Akt signaling pathway, FoxO signaling pathway, and HIF-1 signaling pathway. CONCLUSIONS Our results show that overexpression of this miRNA cluster activates PI3K-Akt, FoxO, HIF-1, and Rap-1 signaling pathways, suggesting pathway inhibitors may be therapeutic candidates against thymoma.
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Affiliation(s)
- Guanglei Ji
- First Department of Thoracic Surgery, Linyi Cancer Hospital, Linyi, Shandong, PR China
| | - Rongrong Ren
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
| | - Xichao Fang
- Second Department of Thoracic Surgery, Linyi Cancer Hospital, Linyi, Shandong, PR China
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Su Y, Chen Y, Tian Z, Lu C, Chen L, Ma X. lncRNAs classifier to accurately predict the recurrence of thymic epithelial tumors. Thorac Cancer 2020; 11:1773-1783. [PMID: 32374079 PMCID: PMC7327696 DOI: 10.1111/1759-7714.13439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Long non‐coding RNAs (lncRNAs), which have little or no ability to encode proteins, have attracted special attention due to their potential role in cancer disease. In this study we aimed to establish a lncRNAs classifier to improve the accuracy of recurrence prediction for thymic epithelial tumors (TETs). Methods TETs RNA sequencing (RNA‐seq) data set and the matched clinicopathologic information were downloaded from the Cancer Genome Atlas. Using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analysis, we developed a lncRNAs classifier related to recurrence. Functional analysis was conducted to investigate the potential biological processes of the lncRNAs target genes. The independent prognostic factors were identified by Cox regression model. Additionally, predictive ability and clinical application of the lncRNAs classifier were assessed, and compared with the Masaoka staging by receiver operating characteristic (ROC) analysis and decision curve analysis (DCA). Results Four recurrence‐free survival (RFS)‐related lncRNAs were identified, and the classifier consisting of the identified four lncRNAs was able to effectively divide the patients into high and low risk subgroups, with an area under curve (AUC) of 0.796 (three‐year RFS) and 0.788 (five‐year RFS), respectively. Multivariate analysis indicated that the lncRNAs classifier was an independent recurrence risk factor. The AUC of the lncRNAs classifier in predicting RFS was significantly higher than the Masaoka staging system. Decision curve analysis further demonstrated that the lncRNAs classifier had a larger net benefit than the Masaoka staging system. Conclusions A lncRNAs classifier for patients with TETs was an independent risk factor for RFS despite other clinicopathologic variables. It generated more accurate estimations of the recurrence probability when compared to the Masaoka staging system, but additional data is required before it can be used in clinical practice.
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Affiliation(s)
- Yongchao Su
- Department of Thoracic Surgery, Sanya Central Hospital, Sanya, China
| | - Yongbing Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zuochun Tian
- Department of Thoracic Surgery, Sanya Central Hospital, Sanya, China
| | - Chuangang Lu
- Department of Thoracic Surgery, Sanya Central Hospital, Sanya, China
| | - Liang Chen
- Department of Respiratory Medicine, Sanya Central Hospital, Sanya, China
| | - Ximiao Ma
- Department of Thoracic Surgery, Haikou People's Hospital, Haikou, China
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Liu J, Yao Y, Hu Z, Zhou H, Zhong M. Transcriptional profiling of long-intergenic noncoding RNAs in lung squamous cell carcinoma and its value in diagnosis and prognosis. Mol Genet Genomic Med 2019; 7:e994. [PMID: 31617686 PMCID: PMC6900396 DOI: 10.1002/mgg3.994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 07/10/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Background Long intergenic noncoding RNAs (lincRNAs) are a series of novel transcribed regions expressed in cancers that may represent candidate biomarkers for lung squamous cell carcinoma (LSqCC) treatment. In this study, we evaluated the lincRNA profile in LSqCC patients and screened valuable lincRNAs for diagnosis and prognosis. Methods Transcriptome profiling of 549 samples derived from 501 LSqCC patients were identified in TCGA database. 48 patients had paired primary tumor (PT) and solid normal (SN) tissue samples, while 453 patients had only PT samples. 1,771 lincRNA candidates were evaluated. Paired test (Wilcoxon two‐sample paired signed rank tests) was performed in paired PT and SN samples. Logistic regression analysis were performed in independent 453 PT samples and 48 SN samples to screen the significant lincRNAs candidates for malignances. Independent 501 PT samples were further used to screen the significant lincRNAs candidates for prognosis. Results Among 1,771 lincRNAs, 10 lincRNAs were significant highly‐expressed risk candidates in PT samples, and 10 protective lincRNAs candidates were significant lowly‐expressed in PT samples. Among 10 highly‐expressed risk lincRNAs, a small panel of LINC00487, LINC01927, and C10orf143 (LINC00959) could effectively predict malignancies in paired samples (AUC = 0.7274, 95%CI = (0.6264, 0.8285)). When combined with protective lincRNA candidates LINC02315, LINC00491, and LINC01697, the predictive efficiency was greatly improved in both paired samples (AUC = 0.8030, 95%CI = (0.7250, 0.8810)) and independent samples (AUC = 0.7481, 95%CI= (0.6642, 0.8320)). Additionally, three highly‐expressed risk lincRNAs, LINC01031, LINC01088, and LINC01931, were significantly associated with poor prognosis in PT samples, suggesting potential targets for anti‐LSqCC treatment. Conclusion Therefore, lincRNAs could be promising biomarkers for predicting malignancies and potential anti‐LSqCC targets for drug development.
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Affiliation(s)
- Jieqiong Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China.,The First Hospital of Changsha City, Changsha, China
| | - Yali Yao
- The First Hospital of Changsha City, Changsha, China
| | - Zheyu Hu
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Hui Zhou
- Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Meizuo Zhong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
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