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Hong Z, Li Y, Chen M, Chen X, Deng X, Wu Y, Wang C, Qiu C. Protosappanin B enhances the chemosensitivity of 5-fluorouracil in colon adenocarcinoma by regulating the LINC00612/microRNA-590-3p/Golgi phosphoprotein 3 axis. Discov Oncol 2024; 15:193. [PMID: 38806777 PMCID: PMC11133243 DOI: 10.1007/s12672-024-01036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND 5-fluorouracil (5-FU) is conventionally used in chemotherapy for colon adenocarcinomas. Acquired resistance of 5-FU remains a clinical challenge in colon cancer, and efforts to develop targeted agents to reduce resistance have not yielded success. Protosappanin B (PSB), the main component of Lignum Sappan extract, is known to exhibit anti-tumor effects. However, whether and how PSB could improve 5-FU resistance in colon cancer have not yet been established. In this study, we aimed to explore the effects and underlying mechanisms of PSB in 5-FU-induced chemoresistance in colon adenocarcinoma. METHODS Forty-seven paired colon cancer tissue samples from patients who received 5-FU chemotherapy were collected as clinical samples. Two 5-FU resistant colon cancer cell lines were established for in vitro experiments. Reverse transcription-quantitative PCR (RT-qPCR) was performed to determine the mRNA and microRNA (miRNA) expression levels in colon adenocarcinoma tissues and cell lines. Cell Counting Kit-8 (CCK-8) and flow cytometry assays were performed to evaluate cell proliferation and apoptosis, respectively. RESULTS LINC00612 was highly expressed in colon adenocarcinoma samples and 5-FU resistant colon cancer cells. LINC00612 knockdown enhances 5-FU chemosensitivity in 5-FU resistant cells. Notably, PSB treatment attenuated LINC00612 expression in 5-FU resistant colon adenocarcinoma cells. Moreover, PSB treatment reversed the increase in LINC00612-induced 5-FU resistance. Mechanistically, LINC00612 specifically bound to miR-590-3p, which promoted 5-FU resistance in colon adenocarcinoma cells and attenuated the inhibitory effect of LINC00612 on GOLPH3 expression. CONCLUSION PSB attenuates 5-FU chemoresistance in colon adenocarcinoma by regulating the LINC00612/miRNA-590-3p/GOLPH3 axis.
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Affiliation(s)
- Zhongshi Hong
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Yachen Li
- Medical Department, The Second Affiliated Hospital of Fujian Medical University, No.34 Zhongshan North Road, Quanzhou, 362000, Fujian, China
| | - Mingliang Chen
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Xiaojing Chen
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Xian Deng
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Yuze Wu
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China
| | - Chunxiao Wang
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China.
| | - Chengzhi Qiu
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, No.34, Zhongshan North Road, Quanzhou, Fujian, 362000, China.
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Pan C, Wang Q, Wang H, Deng X, Chen L, Li Z. LncRNA CARD8-AS1 suppresses lung adenocarcinoma progression by enhancing TRIM25-mediated ubiquitination of TXNRD1. Carcinogenesis 2024; 45:311-323. [PMID: 38153696 DOI: 10.1093/carcin/bgad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/06/2023] [Accepted: 12/27/2023] [Indexed: 12/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in the tumorigenesis and progression of lung adenocarcinoma (LUAD). However, little was known about the role of lncRNAs in high-risk LUAD subtypes: micropapillary-predominant adenocarcinoma (MPA) and solid-predominant adenocarcinoma (SPA). In this study, we conducted a systematic screening of differentially expressed lncRNAs using RNA sequencing in 10 paired MPA/SPA tumor tissues and adjacent normal tissues. Consequently, 110 significantly up-regulated lncRNAs and 288 aberrantly down-regulated lncRNAs were identified (|Log2 Foldchange| ≥ 1 and corrected P < 0.05). The top 10 lncRNAs were further analyzed in 89 MPA/SPA tumor tissues and 59 normal tissues from The Cancer Genome Atlas database. Among them, CARD8-AS1 showed the most significant differential expression, and decreased expression of CARD8-AS1 was significantly associated with a poorer prognosis. Functionally, CARD8-AS1 overexpression remarkably suppressed the proliferation, migration and invasion of LUAD cells both in vitro and in vivo. Conversely, inhibition of CARD8-AS1 yielded opposite effects. Mechanistically, CARD8-AS1 acted as a scaffold to facilitate the interaction between TXNRD1 and E3 ubiquitin ligase TRIM25, thereby promoting the degradation of TXNRD1 through the ubiquitin-proteasome pathway. Additionally, TXNRD1 was found to promote LUAD cell proliferation, migration and invasion in vitro. Furthermore, the suppressed progression of LUAD cells resulting from CARD8-AS1 overexpression could be significantly reversed by simultaneous overexpression of TXNRD1. In conclusion, this study revealed that the lncRNA CARD8-AS1 played a suppressive role in the progression of LUAD by enhancing TRIM25-mediated ubiquitination of TXNRD1. The CARD8-AS1-TRIM25-TXNRD1 axis may represent a promising therapeutic target for LUAD.
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Affiliation(s)
- Cheng Pan
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Qi Wang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Hongshun Wang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xiaheng Deng
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Liang Chen
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Zhihua Li
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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E Y, Zhang X, Ma H, Dong F. Long Non-coding RNA Prader Willi/Angelman Region RNA 6 Suppresses Glioma Development by Modulating MicroRNA-106a-5p. Biochem Genet 2024; 62:1365-1378. [PMID: 37610693 DOI: 10.1007/s10528-023-10479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023]
Abstract
As one of the most frequent intracranial tumors, glioma showed invasive development and poor prognosis. lncRNAs have been illustrated to serve as biomarkers in various cancers. Whether the long non-coding RNA Prader Willi/Angelman region RNA 6 (PWAR6) was involved in glioma development and the underlying mechanism was investigated. PWAR6 in glioma was evaluated by polymerase chain reaction and its clinical significance was assessed with a series of statistical analyses. The biological function of PWAR6 was investigated with the cell counting kit 8 and Transwell assay. The potential underlying mechanism was studied with the luciferase reporter assay. The significant downregulation of PWAR6 was observed in glioma, which showed a close relationship with the major clinicopathological features and poor prognosis of patients. PWAR6 restrained cell growth, migration and invasion of glioma, which was alleviated by the overexpression of microRNA-106a-5p (miR-106a-5p). PWAR6 functioned as a prognostic biomarker and tumor suppressor of glioma through regulating miR-106a-5p.
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Affiliation(s)
- Yongjun E
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, 121000, Liaoning, China
| | - Xianglin Zhang
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, 121000, Liaoning, China.
| | - Heji Ma
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, 121000, Liaoning, China
| | - Furen Dong
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, 121000, Liaoning, China
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Wang P, Wang Z, Lin Y, Castellano L, Stebbing J, Zhu L, Peng L. Development of a Novel Pyroptosis-Associated lncRNA Biomarker Signature in Lung Adenocarcinoma. Mol Biotechnol 2024; 66:332-353. [PMID: 37154865 DOI: 10.1007/s12033-023-00757-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 04/15/2023] [Indexed: 05/10/2023]
Abstract
Pyroptosis is a novel type of cell death observed in various diseases. Our study aimed to investigate the relationship between pyroptosis-associated-long non-coding RNAs (lncRNAs), immune infiltration, and expression of immune checkpoints in the setting of lung adenocarcinoma and the prognostic value of pyroptosis-related lncRNAs. RNA-seq transcriptome data and clinical information from The Cancer Genome Atlas (TCGA) were downloaded, and consensus clustering analysis was used to separate the samples into two groups. Least absolute shrinkage and selection operator (LASSO) analyses were conducted to construct a risk signature. The association between pyroptosis-associated lncRNAs, immune infiltration, and expression of immune checkpoints were analysed. The cBioPortal tool was used to discover genomic alterations. Gene set enrichment analysis (GSEA) was utilized to investigate downstream pathways of the two clusters. Drug sensitivity was also examined. A total of 43 DEGs and 3643 differentially expressed lncRNAs were identified between 497 lung adenocarcinoma tissues and 54 normal samples. A signature consisting of 11 pyroptosis-related lncRNAs was established as prognostic for overall survival. Patients in the low-risk group have a significant overall survival advantage over those in the high-risk group in the training group. Immune checkpoints were expressed differently between the two risk groups. Risk scores were validated to develop an independent prognostic model based on multivariate Cox regression analysis. The area under time-dependent receiver operating characteristic curve (AUC of the ROC) at 1-, 3-, and 5-years measured0.778, 0.757, and 0.735, respectively. The high-risk group was more sensitive to chemotherapeutic drugs than the low-risk group. This study demonstrates the association between pyroptosis-associated lncRNAs and prognosis in lung adenocarcinoma and enables a robust predictive signature of 11 lncRNAs to inform overall survival.
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Affiliation(s)
- Peng Wang
- Department of Medical Oncology, Yidu Central Hospital of Weifang, Weifang, Shandong Province, China
| | - Zhiqiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, Shandong Province, China
| | - Yanke Lin
- Guangdong TCRCure Biopharma Technology Co., Ltd, Guangzhou, China
| | - Leandro Castellano
- Department of Biochemistry, School of Life Sciences, University of Sussex, Brighton, UK
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Justin Stebbing
- Department of Biomedical Sciences, Anglia Ruskin University, Cambridge, UK
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, Shandong Province, China
| | - Liping Zhu
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, Shandong Province, China.
| | - Ling Peng
- Department of Respiratory Disease, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang Province, China.
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Tang W, Luo J, Lin S, Xu J, Yan Q. Mechanism of PWAR6 regulating cisplatin drug sensitivity in non-small cell lung cancer through miR-577/PHACTR1. Gene 2024; 893:147954. [PMID: 37923092 DOI: 10.1016/j.gene.2023.147954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
lncRNA Prader Willi/Angelman Region RNA 6 (PWAR6) is considered to play a protective lncRNA in glioma, but, the role of PWAR6 in the occurrence and cisplatin resistance of non-small cell lung cancer (NSCLC) is elusive. In the study, we aimed to assess the role of PWAR6 in the cisplatin resistance of NSCLC. Based on the oebiotech and TargetScanHuman database, we predicted the interaction between PWAR6, miR-577 and PHACTR1. We then used small interfering RNA (siRNA), miRNA mimics and dual-luciferase reporter assay to explore the regulatory role of PWAR6/miR-577PHACTR1. Based on the online database, miR-577 can interact with PWAR6 and PHACTR1. Soon afterwards, we observed that the expression of PWAR6 and PHACTR1 was increased, while miR-577 expression was decreased in A549/DDP cells. And the cell viability was decreased, while cell apoptosis was increased in A549/DDP cells. What's more, PWAR6 knockdown can promote the expression of miR-577 and inhibit the expression of PHACTR1. PWAR6 knockdown elevated cell proliferation and reduced cell apoptosis of A549/DDP cells. Interestingly, we found that miR-577 can interact with PHACTR1 to regulate the proliferation and apoptosis of A549/DDP cells. To conclude, we speculated that PWAR6 knockdown elevated cell proliferation and reduced cell apoptosis of A549/DDP cells via miR-577/PHACTR1, providing the theoretical basis for the clinical treatment of NSCLC patients.
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Affiliation(s)
- Wenjun Tang
- Department of Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou City, Hainan 570100, China.
| | - Jingru Luo
- Department of Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou City, Hainan 570100, China.
| | - Shu Lin
- Department of Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou City, Hainan 570100, China.
| | - Junnv Xu
- Department of Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou City, Hainan 570100, China.
| | - Qixing Yan
- Department of Pharmacy, The Second Affiliated Hospital of Hainan Medical University, Haikou City, Hainan 570100, China.
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Yang M, Zheng H, Su Y, Xu K, Yuan Q, Cai Y, Aihaiti Y, Xu P. Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures. Heliyon 2023; 9:e21503. [PMID: 38027935 PMCID: PMC10661155 DOI: 10.1016/j.heliyon.2023.e21503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Objective To study pyroptosis-related biomarkers that are associated with the prognosis and immune microenvironment characteristics of osteosarcoma (OS). The goal is to establish a foundation for the prognosis and treatment of OS. Methods We retrieved transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database for 88 OS patients. Using this data, we constructed a prognostic model to identify pyroptosis-related genes (PRGs) associated with OS prognosis. To further explore the biological function of these PRGs, we performed enrichment analysis. To identify pyroptosis-related long non-coding RNAs (PRLncs) associated with the prognosis of OS, we performed co-expression analysis. Subsequently, a risk prognostic model was constructed using these PRLncs to generate a risk score, termed as PRLncs-score, thereby obtaining PRLncs associated with the prognosis of OS. The accuracy of the prognostic model was verified through survival analysis, risk curve, independent prognostic analysis, receiver operating characteristic (ROC) curve, difference analysis between high- and low-risk groups, and clinical correlation analysis. And to determine whether PRLncs-score is independent prognostic factor for OS. In addition, we further conducted external and internal validation for the risk prognosis model. Further analyses of immune cell infiltration and tumor microenvironment were performed. A pyroptosis-related competitive endogenous RNA (PRceRNA) network was constructed to obtain PRceRNAs associated with the prognosis of OS and performed gene set enrichment analysis (GSEA) on PRceRNA genes. Results We obtained five PRGs (CHMP4C, BAK1, GSDMA, CASP1, and CASP6) that predicted OS prognosis and seven PRLncs (AC090559.1, AP003119.2, CARD8-AS1, AL390728.4, SATB2-AS1, AL133215.2, and AC009495.3) and one PRceRNA (CARD8-AS1-hsa-miR-21-5p-IL1B) that predicted OS prognosis and indicated characteristics of the OS immune microenvironment. The PRLncs-score, in combination with other clinical features, was established as an independent prognostic factor for OS patients. Subsequent scrutiny of the tumor microenvironment and immune infiltration indicated that patients with low-PRLncs-scores were associated with reduced metastatic risk, improved survival rates, heightened levels of immune cells and stroma, and increased immune activity compared to those with high-PRLncs-scores. Conclusion The study's findings offer insight into the prognosis of OS and its immune microenvironment, and hold promise for improving early diagnosis and immunotherapy.
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Affiliation(s)
- Mingyi Yang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Haishi Zheng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yani Su
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Qiling Yuan
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yongsong Cai
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yirixiati Aihaiti
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
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Lin X, Nie H, Tang R, Wang P, Jin X, Jiang Q, Han F, Chen N, Li Y. Network analysis between neuron dysfunction and neuroimmune response based on neural single-cell transcriptome of COVID-19 patients. Comput Biol Med 2022; 150:106055. [PMID: 36137317 PMCID: PMC9462930 DOI: 10.1016/j.compbiomed.2022.106055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022]
Abstract
Despite global vaccination efforts, COVID-19 breakthrough infections caused by variant virus continue to occur frequently, long-term sequelae of COVID-19 infection like neuronal dysfunction emerge as a noteworthy issue. Neuroimmune disorder induced by Inflammatory factor storm was considered as a possible reason, however, little was known about the functional factors affecting neuroimmune response to this virus. Here, using medial prefrontal cortex single cell data of COVID-19 patients, expression pattern analysis indicated that some immune-related pathway genes expressed specifically, including genes associated with T cell receptor, TNF signaling in microglia and Cytokine-cytokine receptor interaction and HIF-1 signaling pathway genes in astrocytes. Besides the well-known immune-related cell type microglia, we also observed immune-related factors like IL17D, TNFRSF1A and TLR4 expressed in Astrocytes. Based on the ligand-receptor relationship of immune-related factors, crosstalk landscape among cell clusters were analyzed. The findings indicated that astrocytes collaborated with microglia and affect excitatory neurons, participating in the process of immune response and neuronal dysfunction. Moreover, subset of astrocytes specific immune factors (hinged neuroimmune genes) were proved to correlate with Covid-19 infection and ventilator-associated pneumonia using multi-tissue RNA-seq and scRNA-seq data. Function characterization clarified that hinged neuroimmune genes were involved in activation of inflammation and hypoxia signaling pathways, which could lead to hyper-responses related neurological sequelae. Finally, a risk model was constructed and testified in RNA-seq and scRNA data of peripheral blood.
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Affiliation(s)
- Xiaoyu Lin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Ran Tang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
| | - Na Chen
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China; Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
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Ge X, Xu M, Cheng T, Hu N, Sun P, Lu B, Wang Z, Li J. TP53I13 promotes metastasis in glioma via macrophages, neutrophils, and fibroblasts and is a potential prognostic biomarker. Front Immunol 2022; 13:974346. [PMID: 36275718 PMCID: PMC9585303 DOI: 10.3389/fimmu.2022.974346] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background TP53I13 is a protein coding tumor suppression gene encoded by the tumor protein p53. Overexpression of TP53I13 impedes tumor cell proliferation. Nevertheless, TP53I13 role and expression in the emergence and progression of glioma (low-grade glioma and glioblastoma) are yet to be identified. Thus, we aim to use comprehensive bioinformatics analyses to investigate TP53I13 and its prognostic value in gliomas. Methods Multiple databases were consulted to evaluate and assess the expression of TP53I13, such as the Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), GeneMANIA, and Gene Expression Profiling Interactive. TP53I13 expression was further explored using immunohistochemistry (IHC) and multiplex immunohistochemistry (mIHC). Through Gene Set Enrichment Analysis (GSEA), the biological functions of TP53I13 and metastatic processes associated with it were studied. Results The expression of TP53I13 was higher in tumor samples compared to normal samples. In samples retrieved from the TCGA and CGGA databases, high TP53I13 expression was associated with poor survival outcomes. The analysis of multivariate Cox showed that TP53I13 might be an independent prognostic marker of glioma. It was also found that increased expression of TP53I13 was significantly correlated with PRS type, status, 1p/19q codeletion status, IDH mutation status, chemotherapy, age, and tumor grade. According to CIBERSORT (Cell-type Identification by Estimating Relative Subsets of RNA Transcript), the expression of TP53I13 correlates with macrophages, neutrophils, and dendritic cells. GSEA shows a close correlation between TP53I13 and p53 signaling pathways, DNA replication, and the pentose phosphate pathway. Conclusion Our results reveal a close correlation between TP53I13 and gliomas. Further, TP53I13 expression could affect the survival outcomes in glioma patients. In addition, TP53I13 was an independent marker that was crucial in regulating the infiltration of immune cells into tumors. As a result of these findings, TP53I13 might represent a new biomarker of immune infiltration and prognosis in patients with gliomas.
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Affiliation(s)
- Xinqi Ge
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Manyu Xu
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Tong Cheng
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Nan Hu
- Medical School of Nantong University, Nantong, China
| | - Pingping Sun
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Bing Lu
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ziheng Wang
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
- *Correspondence: Jian Li, ; Ziheng Wang,
| | - Jian Li
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- *Correspondence: Jian Li, ; Ziheng Wang,
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Chen H, Xu S, Hu Z, Wei Y, Zhu Y, Fang S, Pan Q, Liu K, Li N, Zhu L, Xu G. Bioinformatics algorithm for lung adenocarcinoma based on macropinocytosis-related long noncoding RNAs as a reliable indicator for predicting survival outcomes and selecting suitable anti-tumor drugs. Medicine (Baltimore) 2022; 101:e30543. [PMID: 36197217 PMCID: PMC9509037 DOI: 10.1097/md.0000000000030543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
As a highly conserved endocytic mechanism during evolution, macropinocytosis is enhanced in several malignant tumors, which promotes tumor growth by ingesting extracellular nutrients. Recent research has emphasized the crucial role of macropinocytosis in tumor immunity. In the present study, we established a new macropinocytosis-related algorithm comprising molecular subtypes and a prognostic signature, in which patients with lung adenocarcinoma (LUAD) were classified into different clusters and risk groups based on the expression of 16 macropinocytosis-related long noncoding RNAs. According to the molecular subtypes, we discovered that patients with LUAD in cluster1 had a higher content of stromal cells and immune cells, stronger intensity of immune activities, higher expression of PD1, PDL1, and HAVCR2, and a higher tumor mutational burden, while patients in cluster2 exhibited better survival advantages. Furthermore, the constructed prognostic signature revealed that low-risk patients showed better survival outcomes, earlier tumor stage, higher abundance of stromal cells and immune cells, higher immune activities, higher expression of PD1, PDL1, CTLA4, and HAVCR2, and more sensitivity to Paclitaxel and Erlotinib. By contrast, patients with high scores were more suitable for Gefitinib treatment. In conclusion, the novel algorithm that divided patients with LUAD into different groups according to their clusters and risk groups, which could provide theoretical support for predicting their survival outcomes and selecting drugs for chemotherapy, targeted therapy, and immunotherapy.
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Affiliation(s)
- Hang Chen
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Shuguang Xu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Zeyang Hu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Yiqing Wei
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Youjie Zhu
- Department of Respiratory Medicine, Ningbo Huamei Hospital, Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Shenzhe Fang
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Qiaoling Pan
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Kaitai Liu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Ni Li
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Linwen Zhu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Guodong Xu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China
- *Correspondence: Guodong Xu, Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, Zhejiang, China (e-mail: )
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Zhang N, Zhang H, Wu W, Zhou R, Li S, Wang Z, Dai Z, Zhang L, Liu F, Liu Z, Zhang J, Luo P, Liu Z, Cheng Q. Machine learning-based identification of tumor-infiltrating immune cell-associated lncRNAs for improving outcomes and immunotherapy responses in patients with low-grade glioma. Am J Cancer Res 2022; 12:5931-5948. [PMID: 35966587 PMCID: PMC9373811 DOI: 10.7150/thno.74281] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022] Open
Abstract
Rationale: Accumulating evidence demonstrated that long noncoding RNAs (lncRNAs) involved in the regulation of the immune system and displayed a cell-type-specific pattern in immune cell subsets. Given the vital role of tumor-infiltrating lymphocytes in effective immunotherapy, we explored the tumor-infiltrating immune cell-associated lncRNA (TIIClncRNA) in low-grade glioma (LGG), which has never been uncovered yet. Methods: This study utilized a novel computational framework and 10 machine learning algorithms (101 combinations) to screen out TIIClncRNAs by integratively analyzing the sequencing data of purified immune cells, LGG cell lines, and bulk LGG tissues. Results: The established TIIClnc signature based on the 16 most potent TIIClncRNAs could predict outcomes in public datasets and the Xiangya in-house dataset with decent efficiency and showed better performance when compared with 95 published signatures. The TIIClnc signature was strongly correlated to immune characteristics, including microsatellite instability, tumor mutation burden, and interferon γ, and exhibited a more active immunologic process. Furthermore, the TIIClnc signature predicted superior immunotherapy response in multiple datasets across cancer types. Notably, the positive correlation between the TIIClnc signature and CD8, PD-1, and PD-L1 was verified in the Xiangya in-house dataset. Conclusions: The TIIClnc signature enabled a more precise selection of the LGG population who were potential beneficiaries of immunotherapy.
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Affiliation(s)
- Nan Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,One-third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China.,Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, China
| | - Wantao Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,Department of Oncology, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Ran Zhou
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Shuyu Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
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11
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Yang M, Zheng H, Xu K, Yuan Q, Aihaiti Y, Cai Y, Xu P. A novel signature to guide osteosarcoma prognosis and immune microenvironment: Cuproptosis-related lncRNA. Front Immunol 2022; 13:919231. [PMID: 35967366 PMCID: PMC9373797 DOI: 10.3389/fimmu.2022.919231] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 01/08/2023] Open
Abstract
ObjectiveOsteosarcoma (OS) is a common bone malignancy with poor prognosis. We aimed to investigate the relationship between cuproptosis-related lncRNAs (CRLncs) and the survival outcomes of patients with OS.MethodsTranscriptome and clinical data of 86 patients with OS were downloaded from The Cancer Genome Atlas (TCGA). The GSE16088 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The 10 cuproptosis-related genes (CRGs) were obtained from a recently published article on cuproptosis in Science. Combined analysis of OS transcriptome data and the GSE16088 dataset identified differentially expressed CRGs related to OS. Next, pathway enrichment analysis was performed. Co-expression analysis obtained CRLncs related to OS. Univariate COX regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were used to construct the risk prognostic model of CRLncs. The samples were divided evenly into training and test groups to verify the accuracy of the model. Risk curve, survival, receiver operating characteristic (ROC) curve, and independent prognostic analyses were performed. Next, principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) analysis were performed. Single-sample gene set enrichment analysis (ssGSEA) was used to explore the correlation between the risk prognostic models and OS immune microenvironment. Drug sensitivity analysis identified drugs with potential efficacy in OS. Real-time quantitative PCR, Western blotting, and immunohistochemistry analyses verified the expression of CRGs in OS. Real-time quantitative PCR was used to verify the expression of CRLncs in OS.ResultsSix CRLncs that can guide OS prognosis and immune microenvironment were obtained, including three high-risk CRLncs (AL645608.6, AL591767.1, and UNC5B-AS1) and three low-risk CRLncs (CARD8-AS1, AC098487.1, and AC005041.3). Immune cells such as B cells, macrophages, T-helper type 2 (Th2) cells, regulatory T cells (Treg), and immune functions such as APC co-inhibition, checkpoint, and T-cell co-inhibition were significantly downregulated in high-risk groups. In addition, we obtained four drugs with potential efficacy for OS: AUY922, bortezomib, lenalidomide, and Z.LLNle.CHO. The expression of LIPT1, DLAT, and FDX1 at both mRNA and protein levels was significantly elevated in OS cell lines compared with normal osteoblast hFOB1.19. The mRNA expression level of AL591767.1 was decreased in OS, and that of AL645608.6, CARD8-AS1, AC005041.3, AC098487.1, and UNC5B-AS1 was upregulated in OS.ConclusionCRLncs that can guide OS prognosis and the immune microenvironment and drugs that may have a potential curative effect on OS obtained in this study provide a theoretical basis for OS survival research and clinical decision-making.
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12
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El Khayari A, Bouchmaa N, Taib B, Wei Z, Zeng A, El Fatimy R. Metabolic Rewiring in Glioblastoma Cancer: EGFR, IDH and Beyond. Front Oncol 2022; 12:901951. [PMID: 35912242 PMCID: PMC9329787 DOI: 10.3389/fonc.2022.901951] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma multiforme (GBM), a highly invasive and incurable tumor, is the humans’ foremost, commonest, and deadliest brain cancer. As in other cancers, distinct combinations of genetic alterations (GA) in GBM induce a diversity of metabolic phenotypes resulting in enhanced malignancy and altered sensitivity to current therapies. Furthermore, GA as a hallmark of cancer, dysregulated cell metabolism in GBM has been recently linked to the acquired GA. Indeed, Numerous point mutations and copy number variations have been shown to drive glioma cells’ metabolic state, affecting tumor growth and patient outcomes. Among the most common, IDH mutations, EGFR amplification, mutation, PTEN loss, and MGMT promoter mutation have emerged as key patterns associated with upregulated glycolysis and OXPHOS glutamine addiction and altered lipid metabolism in GBM. Therefore, current Advances in cancer genetic and metabolic profiling have yielded mechanistic insights into the metabolism rewiring of GBM and provided potential avenues for improved therapeutic modalities. Accordingly, actionable metabolic dependencies are currently used to design new treatments for patients with glioblastoma. Herein, we capture the current knowledge of genetic alterations in GBM, provide a detailed understanding of the alterations in metabolic pathways, and discuss their relevance in GBM therapy.
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Affiliation(s)
- Abdellatif El Khayari
- Institute of Biological Sciences (ISSB-P), Mohammed VI Polytechnic University (UM6P), Ben-Guerir, Morocco
| | - Najat Bouchmaa
- Institute of Biological Sciences (ISSB-P), Mohammed VI Polytechnic University (UM6P), Ben-Guerir, Morocco
| | - Bouchra Taib
- Institute of Sport Professions (IMS), Ibn Tofail University, Avenida de l’Université, Kenitra, Morocco
- Research Unit on Metabolism, Physiology and Nutrition, Department of Biology, Faculty of Science, Ibn Tofail University, Kenitra, Morocco
| | - Zhiyun Wei
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ailiang Zeng
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rachid El Fatimy
- Institute of Biological Sciences (ISSB-P), Mohammed VI Polytechnic University (UM6P), Ben-Guerir, Morocco
- *Correspondence: Rachid El Fatimy,
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Liu H, Zong C, Sun J, Li H, Qin G, Wang X, Zhu J, Yang Y, Xue Q, Liu X. Bioinformatics analysis of lncRNAs in the occurrence and development of osteosarcoma. Transl Pediatr 2022; 11:1182-1198. [PMID: 35958002 PMCID: PMC9360822 DOI: 10.21037/tp-22-253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/04/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Osteosarcoma (OS) is a disease with high mortality in children and adolescents, and metastasis is one of its important clinical features. However, the molecular mechanism of OS occurrence is not completely clear. Thus, we screened potential biomarkers of OS and analyze their prognostic value. METHODS The Cancer Genome Atlas (TCGA) datasets were used to analyze the differential lncRNAs in patients with OS of different immune score and the lncRNAs expressed by immune cells. Cox regression was used to develop the prognosis prediction model and specify the prognosis outcomes. Risk-proportional regression model was constructed, and the samples were divided into high and low groups based on the risk scores for the survival analysis. The areas under the receiver operating characteristic (ROC) curve were calculated and the risk-score model was verified. Finally, using 4 gene sets (comprising chemokines, immune checkpoint blockades, immune activity-related genes, and immune cells), and 4 analysis tools (CIBERSORT, TIMER, XCELL and MCP) to evaluated tumor immune infiltration. RESULTS Twenty-nine long non-coding ribonucleic acids (lncRNAs) were obtained from the intersection of the screened lncRNAs. Caspase recruitment domain-containing protein 8-antisense RNA 1 (CARD8-AS1), lncRNA five prime to Xist (FTX), KAT8 regulatory NSL complex unit 1-antisense RNA 1 (KANSL1-AS1), Neuroplastin Intronic Transcript 1 (NPTN-IT1), oligodendrocyte maturation-associated long intervening non-coding RNA (OLMALINC) and RPARP Antisense RNA 1 (RPARP-AS1) were found to be correlated with survival. Univariate and multivariate regression analysis showed risk score [HR (hazard ratio) 3.5, P value 0.0043; HR 3.7, P value 0.0033] and metastasis (HR 4.7, P value 6.60E-05; HR 4.8, P value 8.36E-05) were the key factors of patients with OS. The areas under curves (AUCs) of the 1-, 3-, and 5-year ROC curves of the prognostic model were 0.715, 0.729, and 0.771. The low-risk patients tended to have a high abundance of immune cells. CONCLUSIONS This study showed that a risk score based on 6 lncRNAs has potential value in the prognosis of OS, and patients with low-risk scores have high immune cell infiltration and good prognosis. This study may enrich understandings of underlying mechanisms related to the occurrence and development of OS.
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Affiliation(s)
- Hua Liu
- Department of Radiation Oncology, Affiliated Hospital of Nantong University, Nantong, China.,Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Chenyu Zong
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiacheng Sun
- Xinglin College, Nantong University, Nantong, China
| | - Haiyang Li
- Department of Oncology, Binhai County People's Hospital, Yancheng, China
| | - Guangzhen Qin
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Xiaojian Wang
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Jianwei Zhu
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Yang Yang
- Department of Trauma Center, Affiliated Hospital of Nantong University, Nantong, China
| | - Qiang Xue
- Department of Radiation Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xianchen Liu
- Department of Radiation Oncology, Affiliated Hospital of Nantong University, Nantong, China
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14
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Ji Y, Zhang G, Zhang X. Identification of LncRNA CARD8-AS1 as a Potential Prognostic Biomarker Associated With Progression of Lung Adenocarcinoma. Br J Biomed Sci 2022; 79:10498. [PMID: 35996500 PMCID: PMC9302548 DOI: 10.3389/bjbs.2022.10498] [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: 03/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022]
Abstract
Introduction: Long non-coding RNAs (lncRNAs) exhibit crucial roles in human tumors. However, the role of lncRNA CARD8-AS1 in lung adenocarcinoma remains elusive. This study investigated the role of CARD8-AS1 in lung adenocarcinoma.Materials and Methods: The expression of CARD8-AS1 was detected by RT-qPCR analysis and confirmed using an online database. The clinical value of CARD8-AS1 was evaluated using the Kaplan-Meier curve and multivariate Cox regression analyses. The effects of CARD8-AS1 on cancer cell proliferation, migration, and invasion potential were assessed through several cellular experiments. Western blot assay was used to measure Bcl-2 and Bax protein levels. The interaction among CARD8-AS1, miR-650, and Bax, was assessed using a dual-luciferase reporter assay.Results: The expression of CARD8-AS1 was decreased in lung adenocarcinoma tissues and cell lines (p < 0.001). Low expression of CARD8-AS1 was related to tumor size (p = 0.042), TNM stage (p = 0.021), lymph node metastasis (p = 0.025), and poor overall survival (p < 0.05). Elevated expression of CARD8-AS1 could suppress cellular viability, migration potential, and invasion ability (p < 0.05). The Bcl-2 protein levels were decreased while Bax levels were increased by overexpression of CARD8-AS1 (p < 0.001). miR-650 may thus be a direct target of CARD8-AS1 and Bax may be a direct target of miR-650.Discussion: CARD8-AS1 expression was downregulated in lung adenocarcinoma and associated with several clinical parameters. CARD8-AS1 exerted tumor-suppressive effects by targeting the miR-650 and then regulating Bax expression. CARD8-AS1/miR-650 may serve as novel prognostic biomarkers and potential therapeutic targets for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Yong Ji
- Department of Respiratory, Shanghai General Hospital - Songjiang South Campus, Shanghai, China
| | - Guoqing Zhang
- Department of Respiratory, Shanghai General Hospital - Jiading Campus, Shanghai, China
- *Correspondence: Xingyi Zhang, ; Guoqing Zhang,
| | - Xingyi Zhang
- Department of Respiratory, Shanghai General Hospital - Songjiang South Campus, Shanghai, China
- *Correspondence: Xingyi Zhang, ; Guoqing Zhang,
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15
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Chen H, Zhou C, Hu Z, Sang M, Ni S, Wu J, Pan Q, Tong J, Liu K, Li N, Zhu L, Xu G. Construction of an algorithm based on oncosis-related LncRNAs comprising the molecular subtypes and a risk assessment model in lung adenocarcinoma. J Clin Lab Anal 2022; 36:e24461. [PMID: 35476781 PMCID: PMC9169186 DOI: 10.1002/jcla.24461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Background As an important non‐apoptotic cell death method, oncosis has been reported to be closely associated with tumors in recent years. However, few research reported the relationship between oncosis and lung cancer. Methods In this study, we established an oncosis‐based algorithm comprised of cluster grouping and a risk assessment model to predict the survival outcomes and related tumor immunity of patients with lung adenocarcinomas (LUAD). We selected 11 oncosis‐related lncRNAs associated with the prognosis (CARD8‐AS1, LINC00941, LINC01137, LINC01116, AC010980.2, LINC00324, AL365203.2, AL606489.1, AC004687.1, HLA‐DQB1‐AS1, and AL590226.1) to divide the LUAD patients into different clusters and different risk groups. Compared with patients in clsuter1, patients in cluster2 had a survival advantage and had a relatively more active tumor immunity. Subsequently, we constructed a risk assessment model to distinguish between patients into different risk groups, in which low‐risk patients tend to have a better prognosis. GO enrichment analysis revealed that the risk assessment model was closely related to immune activities. In addition, low‐risk patients tended to have a higher content of immune cells and stromal cells in tumor microenvironment, higher expression of PD‐1, CTLA‐4, HAVCR2, and were more sensitive to immune checkpoint inhibitors (ICIs), including PD‐1/CTLA‐4 inhibitors. The risk score had a significantly positive correlation with tumor mutation burden (TMB). The survival curve of the novel oncosis‐based algorithm suggested that low‐risk patients in cluster2 have the most obvious survival advantage. Conclusion The novel oncosis‐based algorithm investigated the prognosis and the related tumor immunity of patients with LUAD, which could provide theoretical support for customized individual treatment for LUAD patients.
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Affiliation(s)
- Hang Chen
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Chongchang Zhou
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Zeyang Hu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Menglu Sang
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Saiqi Ni
- Department of Urology, Ningbo City First Hospital, Ningbo, China
| | - Jiacheng Wu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Qiaoling Pan
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Jingtao Tong
- Department of Radiation Oncology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Kaitai Liu
- Department of Radiation Oncology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Ni Li
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Linwen Zhu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Guodong Xu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
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16
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Du B, Gao W, Qin Y, Zhong J, Zhang Z. Study on the role of transcription factor SPI1 in the development of glioma. Chin Neurosurg J 2022; 8:7. [PMID: 35361282 PMCID: PMC8973577 DOI: 10.1186/s41016-022-00276-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/04/2022] [Indexed: 12/19/2022] Open
Abstract
Background Glioma is a common malignant brain tumor. The purpose of this study was to investigate the role of the transcription factor SPI1 in glioma. Methods SPI1 expression in glioma was identified using qRT-PCR and Western blotting. Cell proliferation was assessed using the CCK8 assay. Transwell and wound healing assays were utilized to evaluate cell migration. Additionally, cell cycle and apoptosis were detected using flow cytometry. Results We observed that the expression level of SPI1 was up-regulated in glioma tissues, compared to normal tissues. Furthermore, we found that SPI1 is able to promote proliferation and migration of glioma cells in vitro. Flow cytometry results demonstrate that, compared to si-NC cells, si-SPI1 cells stagnated in the G1 phase, and down-regulation of SPI1 expression is able to increase rates of apoptosis. Double luciferase activity and chromatin immunoprecipitation assay results indicated that SPI1 can bind to the promoter sites and promote the proliferation and migration of glioma cells by regulating the expression of oncogenic PAICS. Conclusions Our results suggest that SPI1 can promote proliferation and migration of glioma. Furthermore, SPI1 can be utilized as a potential diagnostic marker and therapeutic target for glioma. Supplementary Information The online version contains supplementary material available at 10.1186/s41016-022-00276-2.
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Chen Y, Guo Y, Li S, Xu J, Wang X, Ning W, Ma L, Qu Y, Zhang M, Zhang H. Identification of N6-Methyladenosine-Related lncRNAs as a Prognostic Signature in Glioma. Front Oncol 2022; 12:789283. [PMID: 35311131 PMCID: PMC8927984 DOI: 10.3389/fonc.2022.789283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most abundant modification in long noncoding RNAs (lncRNAs). Current studies have shown that the abnormal expression of m6A-related genes is closely associated with the tumorigenesis and progression of glioma. However, the role of m6A-related lncRNAs in glioma development is still unclear. Herein, we screened 566 m6A-related lncRNAs in glioma from The Cancer Genome Atlas (TCGA) database. The expression pattern of these lncRNAs could cluster samples into two groups, in which various classical tumor-related functions and the tumor immune microenvironment were significantly different. Subsequently, a nine-factor m6A-related lncRNA prognostic signature (MLPS) was constructed by using a LASSO regression analysis in the training set and was validated in the test set and independent datasets. The AUC values of the MLPS were 0.881, 0.918 and 0.887 for 1-, 3- and 5-year survival in the training set, respectively, and 0.856, 0.916 and 0.909 for 1-, 3-, and 5-year survival in the test set, respectively. Stratification analyses of the MLPS illustrated its prognostic performance in gliomas with different characteristics. Correlation analyses showed that the infiltrations of monocytes and tumor-associated macrophages (TAMs) were significantly relevant to the risk score in the MLPS. Moreover, we detected the expression of four MLPS factors with defined sequences in glioma and normal cells by using RT-PCR. Afterwards, we investigated the functions of LNCTAM34A (one of the MLPS factors) in glioma cells, which have rarely been reported. Via in vitro experiments, LNCTAM34A was demonstrated to promote the proliferation, migration and epithelial-mesenchymal transition (EMT) of glioma cells. Overall, our study revealed the critical role of m6A-related lncRNAs in glioma and elucidated that LNCTAM34A could promote glioma proliferation, migration and EMT.
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Affiliation(s)
- Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jiacheng Xu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Mingshan Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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18
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Chen H, Hu Z, Sang M, Ni S, Lin Y, Wu C, Mu Y, Liu K, Wu S, Li N, Xu G. Identification of an Autophagy-Related lncRNA Prognostic Signature and Related Tumor Immunity Research in Lung Adenocarcinoma. Front Genet 2021; 12:767694. [PMID: 34956321 PMCID: PMC8692741 DOI: 10.3389/fgene.2021.767694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/26/2021] [Indexed: 12/25/2022] Open
Abstract
Autophagy is closely associated with the tumor immune microenvironment (TIME) and prognosis of patients with lung adenocarcinoma (LUAD). In the present study, we established a signature on the basis of long noncoding RNAs (lncRNAs) related to autophagy (ARlncRNAs) to investigate the TIME and survival of patients with LUAD. We selected ARlncRNAs associated with prognosis to construct a model and divided each sample into different groups on the basis of risk score. The ARlncRNA signature could be recognized as an independent prognostic factor for patients with LUAD, and patients in the low-risk group had a greater survival advantage. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analysis suggested that several immune functions and pathways were enriched in different groups. A high-risk score correlated significantly negatively with high abundance of immune cells and stromal cells around the tumor and high tumor mutational burden. Low-risk patients had a higher PD-1, CTLA-4, and HAVCR2 expression and had a better efficacy of immune checkpoint inhibitors, including PD-1/CTLA-4 inhibitor. A reliable signature on the basis of ARlncRNAs was constructed to explore the TIME and prognosis of patients with LUAD, which could provide valuable information for individualized LUAD treatment.
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Affiliation(s)
- Hang Chen
- Medical School, Ningbo University, Ningbo, China
| | - Zeyang Hu
- Medical School, Ningbo University, Ningbo, China
| | - Menglu Sang
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Saiqi Ni
- Department of Urology, Ningbo City First Hospital, Ningbo, China
| | - Yao Lin
- Medical School, Ningbo University, Ningbo, China
| | - Chengfang Wu
- Medical School, Ningbo University, Ningbo, China
| | - Yinyu Mu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Kaitai Liu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Shibo Wu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Ni Li
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Guodong Xu
- Department of Cardiothoracic Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
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Xu S, Tang L, Liu Z, Luo C, Cheng Q. Hypoxia-Related lncRNA Correlates With Prognosis and Immune Microenvironment in Lower-Grade Glioma. Front Immunol 2021; 12:731048. [PMID: 34659218 PMCID: PMC8514865 DOI: 10.3389/fimmu.2021.731048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/09/2021] [Indexed: 01/12/2023] Open
Abstract
Background Hypoxia-related genes are demonstrated to correlate with the prognosis of various cancers. However, the role of hypoxia-related long non-coding RNAs (HRLs) in lower-grade glioma (LGG) remains unclear. Methods A total of 700 LGG samples were extracted from TCGA and CGGA databases. Pearson correlation analysis was used to identify HRLs. Lasso analysis was adopted to construct the HRL signature. TIDE algorithm was used to predict responses to immune checkpoint inhibitors. Cell proliferation was estimated by cell counting kit-8 assay, colony formation assay, and EdU assay. Results We identified 340 HRLs and constructed a novel risk signature composed of 19 HRLs. The risk score exhibited potent value in predicting the prognosis of LGG patients and was significantly associated with the prognosis of LGG patients. Moreover, HRL signature could distinguish patients with similar expression levels of immune checkpoints and might predict the efficacy of immune checkpoint inhibitors. Additionally, hypoxia-related pathways and immune pathways were enriched in high-risk group, and high risk score indicated low tumor purity and high immune infiltration. Two major HRLs, LINC00941 and BASP1-AS1, could significantly affect the proliferation of glioma cells. Conclusions Our study constructed a novel HRL signature that could predict the prognosis and immunotherapy response of LGG patients. HRLs could be novel biomarkers to predict the prognosis of LGG patients and potential targets for LGG treatment.
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Affiliation(s)
- Shengchao Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chengke Luo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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20
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Noncoding RNAs link metabolic reprogramming to immune microenvironment in cancers. J Hematol Oncol 2021; 14:169. [PMID: 34654454 PMCID: PMC8518176 DOI: 10.1186/s13045-021-01179-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/27/2021] [Indexed: 02/08/2023] Open
Abstract
Altered metabolic patterns in tumor cells not only meet their own growth requirements but also shape an immunosuppressive microenvironment through multiple mechanisms. Noncoding RNAs constitute approximately 60% of the transcriptional output of human cells and have been shown to regulate numerous cellular processes under developmental and pathological conditions. Given their extensive action mechanisms based on motif recognition patterns, noncoding RNAs may serve as hinges bridging metabolic activity and immune responses. Indeed, recent studies have shown that microRNAs, long noncoding RNAs and circRNAs are widely involved in tumor metabolic rewiring, immune cell infiltration and function. Hence, we summarized existing knowledge of the role of noncoding RNAs in the remodeling of tumor metabolism and the immune microenvironment, and notably, we established the TIMELnc manual, which is a free and public manual for researchers to identify pivotal lncRNAs that are simultaneously correlated with tumor metabolism and immune cell infiltration based on a bioinformatic approach.
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21
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Lv D, Chang Z, Cai Y, Li J, Wang L, Jiang Q, Xu K, Ding N, Li X, Xu J, Li Y. TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome. Nucleic Acids Res 2021; 50:D413-D420. [PMID: 34570220 PMCID: PMC8728190 DOI: 10.1093/nar/gkab847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 01/10/2023] Open
Abstract
LncRNAs are not only well-known as non-coding elements, but also serve as templates for peptide translation, playing important roles in fundamental cellular processes and diseases. Here, we describe a database, TransLnc (http://bio-bigdata.hrbmu.edu.cn/TransLnc/), which aims to provide comprehensive experimentally supported and predicted lncRNA peptides in multiple species. TransLnc currently documents approximate 583 840 peptides encoded by 33 094 lncRNAs. Six types of direct and indirect evidences supporting the coding potential of lncRNAs were integrated, and 65.28% peptides entries were with at least one type of evidence. Considering the strong tissue-specific expression of lncRNAs, TransLnc allows users to access lncRNA peptides in any of the 34 tissues involved in. In addition, both the unique characteristic and homology relationship were also predicted and provided. Importantly, TransLnc provides computationally predicted tumour neoantigens from peptides encoded by lncRNAs, which would provide novel insights into cancer immunotherapy. There were 220 791 and 237 915 candidate neoantigens binding by major histocompatibility complex (MHC) class I or II molecules, respectively. Several flexible tools were developed to aid retrieve and analyse, particularly lncRNAs tissue expression patterns, clinical relevance across cancer types. TransLnc will serve as a valuable resource for investigating the translation capacity of lncRNAs and greatly extends the cancer immunopeptidome.
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Affiliation(s)
- Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Zhenghong Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yangyang Cai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Liping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qiushuang Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
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22
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Sun J, Zhang Z, Bao S, Yan C, Hou P, Wu N, Su J, Xu L, Zhou M. Identification of tumor immune infiltration-associated lncRNAs for improving prognosis and immunotherapy response of patients with non-small cell lung cancer. J Immunother Cancer 2021; 8:jitc-2019-000110. [PMID: 32041817 PMCID: PMC7057423 DOI: 10.1136/jitc-2019-000110] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Increasing evidence has demonstrated the functional relevance of long non-coding RNAs (lncRNAs) to immunity regulation and the tumor microenvironment in non-small cell lung cancer (NSCLC). However, tumor immune infiltration-associated lncRNAs and their value in improving clinical outcomes and immunotherapy remain largely unexplored. METHODS We developed a computational approach to identify an lncRNA signature (TILSig) as an indicator of immune cell infiltration in patients with NSCLC through integrative analysis for lncRNA, immune and clinical profiles of 115 immune cell lines, 187 NSCLC cell lines and 1533 patients with NSCLC. Then the influence of the TILSig on the prognosis and immunotherapy in NSCLC was comprehensively investigated. RESULTS Computational immune and lncRNA profiling analysis identified an lncRNA signature (TILSig) consisting of seven lncRNAs associated with tumor immune infiltration. The TILSig significantly stratified patients into the immune-cold group and immune-hot group in both training and validation cohorts. These immune-hot patients exhibit significantly improved survival outcome and greater immune cell infiltration compared with immune-cold patients. Multivariate analysis revealed that the TILSig is an independent predictive factor after adjusting for other clinical factors. Further analysis accounting for TILSig and immune checkpoint gene revealed that the TILSig has a discriminatory power in patients with similar expression levels of immune checkpoint genes and significantly prolonged survival was observed for patients with low TILSig and low immune checkpoint gene expression implying a better response to immune checkpoint inhibitor (ICI) immunotherapy. CONCLUSIONS Our finding demonstrated the importance and value of lncRNAs in evaluating the immune infiltrate of the tumor and highlighted the potential of lncRNA coupled with specific immune checkpoint factors as predictive biomarkers of ICI response to enable a more precise selection of patients.
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Affiliation(s)
- Jie Sun
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zicheng Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Siqi Bao
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Congcong Yan
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ping Hou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Liangde Xu
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
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23
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Zhu T, Yu Y, Liu J, Ren K. Identification of a Competing Endogenous RNA Network Related to Immune Signature in Lung Adenocarcinoma. Front Genet 2021; 12:665555. [PMID: 34149807 PMCID: PMC8209499 DOI: 10.3389/fgene.2021.665555] [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] [Received: 02/08/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Background The establishment of immunotherapy has led to a new era in oncotherapy. But the signature of immune-related genes (IRGs) in LUAD remains to be elucidated. Here we use integrated analysis to identify IRGs roles in immune signature and detect their relationship with competing endogenous RNA (ceRNA) networks in LUAD progression. Methods By analyzing the RNA-seq data from different platforms, we recognized the differentially expressed genes (DEGs) of each platform and screened out the top 20 hub IRGs related to immune responses. Then, we applied the CIBERSORT algorithm to explore the landscape of tumor-infiltrating immune cells (TILs) in LUAD and their connection with hub genes. Next, we predicted and validated the upstream miRNAs and lncRNAs according to their expression and prognostic roles. Finally, we constructed and validated an immune-related ceRNA network by co-expression analysis. Results A total of 71 IRGs were identified among 248 DEGs, which play key roles in immune responses. CIBERSORT analysis showed that six hub genes were closely related to TILs, such as SPP1 and naive B cells (R = −0.17), TEK and resting mast cells (R = 0.37). Stepwise prediction and validation from mRNA to lncRNA, including 6 hub genes, 5 miRNAs, and 9 lncRNAs, were applied to construct a ceRNA network. Ultimately, we confirmed the TMPO-AS1/miR-126-5p/SPP1 and CARD8-AS1/miR-21-5p/TEK as immune-related ceRNA networks in LUAD progression. Conclusion We elucidated two immune-related ceRNA networks in LUAD progression, which can be considered as immunotherapy targets for this disease.
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Affiliation(s)
- Ting Zhu
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Yong Yu
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Jun Liu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Kaiming Ren
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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24
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Huang S, Li Y, Hu J, Li L, Liu Z, Guo H, Jiang B, Chen J, Li J, Xiang X, Deng J, Xiong J. LncRNA PWAR6 regulates proliferation and migration by epigenetically silencing YAP1 in tumorigenesis of pancreatic ductal adenocarcinoma. J Cell Mol Med 2021; 25:4275-4286. [PMID: 33834618 PMCID: PMC8093982 DOI: 10.1111/jcmm.16480] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 12/24/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) are a novel class of regulators in multiple cancer biological processes. However, the functions of lncRNAs in pancreatic ductal adenocarcinoma (PDAC) remain largely unknown. In this study, we identified PWAR6 as a frequently down‐regulated lncRNA in PDAC samples as well as a panel of pancreatic cancer cell lines. Down‐regulated PWAR6 was associated with multiple clinical outcomes, including advanced tumour stage, distant metastasis, and overall survival of PDAC patients. In our cell‐based assays, ectopic expression of PWAR6 dramatically repressed PDAC cells proliferation, invasion and migration, accelerated apoptosis, and induced cell cycle arrest at G0/G1 phase. In contrast, depletion of PWAR6 mediated by siRNA exhibited opposite effects on PDAC cell behaviours. In vivo study further validated the anti‐tumour role of PWAR6 in PDAC. By taking advantage of available online sources, we also identified YAP1 as a potential PWAR6 target gene. Negative correlation between YAP1 and PWAR6 expressions were observed in both online database and our PDAC samples. Notably, rescue experiments further indicated that YAP1 is an important downstream effector involved in PWAR6‐mediated functions. Mechanistically, PWAR6 could bind to methyltransferase EZH2, a core component of Polycomb Repressive Complex 2 (PRC2) in regulating gene expression, and scaffold EZH2 to the promoter region of YAP1, resulting in epigenetic repression of YAP1. In conclusion, our data manifest the vital roles of PWAR6 in PDAC tumorigenesis and underscore the potential of PWAR6 as a promising target for PDAC diagnosis and therapy.
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Affiliation(s)
- Shanshan Huang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yaqi Li
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinhua Hu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Oncology, The Affiliated Xinyu Hospital, Nanchang University, Xinyu, China
| | - Li Li
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhen Liu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hui Guo
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bailing Jiang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Chen
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Junhe Li
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaojun Xiang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Deng
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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25
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Yadav B, Pal S, Rubstov Y, Goel A, Garg M, Pavlyukov M, Pandey AK. LncRNAs associated with glioblastoma: From transcriptional noise to novel regulators with a promising role in therapeutics. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:728-742. [PMID: 33996255 PMCID: PMC8099481 DOI: 10.1016/j.omtn.2021.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glioblastoma multiforme (GBM) is the most widespread and aggressive subtype of glioma in adult patients. Numerous long non-coding RNAs (lncRNAs) are deregulated or differentially expressed in GBM. These lncRNAs possess unique regulatory functions in GBM cells, ranging from high invasion/migration to recurrence. This review outlines the present status of specific involvement of lncRNAs in GBM pathogenesis, with a focus on their association with key molecular and cellular regulatory mechanisms. Also, we highlighted the potential of different novel RNA-based strategies that may be beneficial for therapeutic purposes.
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Affiliation(s)
- Bhupender Yadav
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Sonali Pal
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Yury Rubstov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russian Federation.,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Vavilova Street 7, 117312 Moscow, Russian Federation
| | - Akul Goel
- La Canada High School, La Canada Flintridge, CA 91011, USA
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Uttar Pradesh, Sector 125, Noida 201313, India
| | - Marat Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russian Federation
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
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26
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Zhang C, Liu H, Xu P, Tan Y, Xu Y, Wang L, Liu B, Chen Q, Tian D. Identification and validation of a five-lncRNA prognostic signature related to Glioma using bioinformatics analysis. BMC Cancer 2021; 21:251. [PMID: 33750353 PMCID: PMC7941710 DOI: 10.1186/s12885-021-07972-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/25/2021] [Indexed: 12/03/2022] Open
Abstract
Background To accurately predict the prognosis of glioma patients. Methods A total of 541 samples from the TCGA cohort, 181 observations from the CGGA database and 91 samples from our cohort were included in our study. Long non-coding RNAs (LncRNAs) associated with glioma WHO grade were evaluated by weighted gene co-expression network analysis (WGCNA). Five lncRNA features were selected out to construct prognostic signatures based on the Cox regression model. Results By weighted gene co-expression network analysis (WGCNA), 14 lncRNAs related to glioma grade were identified. Using univariate and multivariate Cox analysis, five lncRNAs (CYTOR, MIR155HG, LINC00641, AC120036.4 and PWAR6) were selected to develop the prognostic signature. The Kaplan-Meier curve depicted that the patients in high risk group had poor prognosis in all cohorts. The areas under the receiver operating characteristic curve of the signature in predicting the survival of glioma patients at 1, 3, and 5 years were 0.84, 0.92, 0.90 in the CGGA cohort; 0.8, 0.85 and 0.77 in the TCGA set and 0.72, 0.90 and 0.86 in our own cohort. Multivariate Cox analysis demonstrated that the five-lncRNA signature was an independent prognostic indicator in the three sets (CGGA set: HR = 2.002, p < 0.001; TCGA set: HR = 1.243, p = 0.007; Our cohort: HR = 4.457, p = 0.008, respectively). A nomogram including the lncRNAs signature and clinical covariates was constructed and demonstrated high predictive accuracy in predicting 1-, 3- and 5-year survival probability of glioma patients. Conclusion We established a five-lncRNA signature as a potentially reliable tool for survival prediction of glioma patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07972-9.
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Affiliation(s)
- Chunyu Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Haitao Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, Zhejiang Province, People's Republic of China
| | - Pengfei Xu
- Sun Yat-sen University, The Seventh Affiliated Hospital, Shenzhen, 518000, Guangdong Province, People's Republic of China
| | - Yinqiu Tan
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Yang Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Long Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Baohui Liu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China.
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Xiang J, Bian Y. PWAR6 interacts with miR‑106a‑5p to regulate the osteogenic differentiation of human periodontal ligament stem cells. Mol Med Rep 2021; 23:268. [PMID: 33576453 PMCID: PMC7893692 DOI: 10.3892/mmr.2021.11907] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Human periodontal ligament stem cells (hPDLSCs) associated with bone regeneration serve an important role in the treatment of periodontal disease. Long non-coding RNAs are involved in the osteogenesis of multiple stem cells and can act as a sponge of microRNAs (miRs). The present study aimed to investigate the interaction between Prader Willi/Angelman region RNA 6 (PWAR6) and miR-106a-5p, as well as their influences on the osteogenic differentiation of hPDLSCs. hPDLSCs were isolated and cultured in osteogenic medium (OM) or growth medium (GM) for 7 days prior to transfection with PWAR6 overexpression vector, short hairpin RNA PWAR6 or miR-106a-5p mimic. The expression levels of runt-related transcription factor 2, osteocalcin and bone morphogenetic protein 2 (BMP2) were detected by western blotting and reverse transcription-quantitative PCR (RT-qPCR), and the expression levels of PWAR6, miR-106a-5p and alkaline phosphatase (ALP) were determined by RT-qPCR. ALP activity assays and Alizarin red staining were performed to detect osteogenesis and mineralization, respectively. Luciferase activities of wild-type and mutant PWAR6 and BMP2 were assessed by conducting a dual-luciferase reporter assay. The results indicated that PWAR6 expression was upregulated in OM-incubated hPDLSCs compared with GM-incubated hPDLSCs, and PWAR6 overexpression increased the osteogenic differentiation and mineralization of hPDLSCs compared with the corresponding control group. By contrast, miR-106a-5p expression was downregulated in OM-incubated hPDLSCs compared with GM-incubated hPDLSCs. PWAR6 acted as a sponge of miR-106a-5p and PWAR6 overexpression promoted the osteogenesis of miR-106a-5p mimic-transfected hPDLSCs. BMP2 was predicted as a target gene of miR-106a-5p. Collectively, the results indicated that PWAR6 displayed a positive influence on the osteogenic differentiation of hPDLSCs. The results of the present study demonstrated that the PWAR6/miR-106a-5p interaction network may serve as a potential regulatory mechanism underlying hPDLSCs osteogenesis.
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Affiliation(s)
- Juan Xiang
- Department of Oral and Maxillofacial Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei 448000, P.R. China
| | - Ying Bian
- Department of Oral and Maxillofacial Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei 448000, P.R. China
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Guo J, Fang Q, Liu Y, Xie W, Zhang Y, Li C. Identifying critical protein-coding genes and long non-coding RNAs in non-functioning pituitary adenoma recurrence. Oncol Lett 2021; 21:264. [PMID: 33664827 PMCID: PMC7882882 DOI: 10.3892/ol.2021.12525] [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: 08/10/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022] Open
Abstract
Non-functioning pituitary adenoma (NFPA) is a very common type of intracranial tumor. Monitoring and predicting the postoperative recurrence of NFPAs is difficult, as these adenomas do not present with serum hormone hypersecretion. Long non-coding RNAs (lncRNAs) and protein-coding genes (PCGs) play critical roles in the development and progression of numerous tumors. However, the complex network of RNA interactions related to the mechanisms underlying the postoperative recurrence of NFPA is still unclear. In the present study, 73 patients with NFPA were investigated using high-throughput sequencing and follow-up investigations. In total, 6 of these patients with recurrence within 1 year after surgery were selected as the fast recurrence group, and 6 patients with recurrence 5 years after surgery were selected as the slow recurrence group. By performing differential expression analysis of the fast recurrence and slow recurrence groups, a set of differentially expressed PCGs and lncRNAs were obtained (t-test, P<0.05). Next, protein-protein interaction coregulatory networks and lncRNA-mRNA coexpression networks were identified. In addition, the hub lncRNA-mRNA modules related to NFPA recurrence were further screened and transcriptome expression markers for NFPA regression were identified (log-rank test, P<0.05). Finally, the ability of the hub and module genes to predict recurrence and progression-free survival in patients with NFPA was evaluated. To confirm the credibility of the bioinformatic analyses, nucleolar protein 6 and LL21NC02-21A1.1 were randomly selected from among the genes with prognostic significance for validation by reverse transcription-quantitative PCR in another set of NFPA samples (n=9). These results may be helpful for evaluating the slow and rapid recurrence of NFPA after surgery and exploring the mechanisms underlying NFPA recurrence. Future effective biomarkers and therapeutic targets may also be revealed.
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Affiliation(s)
- Jing Guo
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Qiuyue Fang
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Yulou Liu
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Weiyan Xie
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Yazhuo Zhang
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Cell laboratory, Beijing Institute for Brain Disorders Brain Tumor Center, Beijing 100070, P.R. China.,Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing 100070, P.R. China
| | - Chuzhong Li
- Department of Cell Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Cell laboratory, Beijing Institute for Brain Disorders Brain Tumor Center, Beijing 100070, P.R. China.,Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing 100070, P.R. China
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Yang J, Yu D, Liu X, Changyong E, Yu S. LINC00641/miR-4262/NRGN axis confines cell proliferation in glioma. Cancer Biol Ther 2020; 21:758-766. [PMID: 32543324 DOI: 10.1080/15384047.2020.1776581] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Glioma is the most prevalent brain malignancy with high mortality. In recent decades, the regulatory role of long noncoding RNAs (lncRNAs) has been unmasked in glioma. In this study, we focused on the function and mechanism of LINC00641 in glioma. First of all, we found that LINC00641 was expressed at a low level in glioma cell lines. Importantly, overexpression of LINC00641 prevented cell proliferation but enhanced cell apoptosis. Meanwhile, NRGN, a previously-reported downregulated mRNA in GBM, was disclosed as a tumor suppressor in glioma cells. Besides, we verified that NRGN could be positively regulated by LINC00641 in glioma cells. Moreover, the cellular distribution of LINC00641 was identified to be cytoplasmic. Therefore, bioinformatics analysis and mechanism experiments were carried out and we determined that miR-4262 was the shared miRNA between LINC00641 and NRGN. In contrast to LINC00641 and NRGN, miR-4262 was dramatically upregulated in glioma cells. Furthermore, we confirmed that LINC00641 acted as a ceRNA in glioma cells via absorbing miR-4262 to upregulate NRGN. More importantly, silenced NRGN countervailed the repression on glioma cell proliferation caused by LINC00641 upregulation. Collectively, our findings unveiled that LINC00641 serves as a tumor inhibitor in glioma by targeting miR-4262/NRGN axis, providing a new potential therapeutic target for glioma patients.
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Affiliation(s)
- Jinghui Yang
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University , Changchun, Jilin, China
| | - Duo Yu
- Department of Radiotherapy, Second Hospital of Jilin University , Changchun, Jilin, China
| | - Xueshibojie Liu
- Department of Otolaryngology, Head and Neck Surgery, Second Hospital of Jilin University , Changchun, Jilin, China
| | - E Changyong
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University , Changchun, Jilin, China
| | - Shan Yu
- Department of Neurology, China-Japan Union Hospital of Jilin University , Changchun, Jilin, China
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Xu J, Shao T, Song M, Xie Y, Zhou J, Yin J, Ding N, Zou H, Li Y, Zhang J. MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer. Mol Cancer 2020; 19:51. [PMID: 32127004 PMCID: PMC7055097 DOI: 10.1186/s12943-020-01174-w] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/26/2020] [Indexed: 02/08/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are emerging as critical regulatory elements and play fundamental roles in the biology of various cancers. However, we are still lack of knowledge about their expression patterns and functions in human colorectal cancer (CRC). Methods Differentially expressed lncRNAs in CRC were identified by bioinformatics screen and the level of MIR22HG in CRC and control tissues were determined by qRT-PCR. Cell viability and migration capacities were examined by MTT and transwell assay. Mouse model was used to examine the function and rational immunotherapy of MIR22HG in vivo. Results We systematically investigated the expression pattern of lncRNAs and revealed MIR22HG acts as a tumor suppressor in CRC. The expression of MIR22HG was significantly decreased in CRC, which was mainly driven by copy number deletion. Reduced expression of MIR22HG was significantly associated with poor overall survival. Silencing of MIR22HG promoted cell survival, proliferation and tumor metastasis in vitro and in vivo. Mechanistically, MIR22HG exerts its tumor suppressive activity by competitively interacting with SMAD2 and modulating the activity of TGFβ pathway. Decreased MIR22HG promoted the epithelial-mesenchymal transition in CRC. Importantly, we found that MIR22HG expression is significantly correlated with CD8A and overexpression of MIR22HG triggers T cell infiltration, enhancing the clinical benefits of immunotherapy. Conclusion MIR22HG acts as a tumor suppressor in CRC. Our data provide mechanistic insights into the regulation of MIR22HG in TGFβ pathway and facilitates immunotherapy in cancer.
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Affiliation(s)
- Juan Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, 571199, China. .,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Mingxu Song
- Wuxi Oncology Institute, The Affiliated Hospital of Jiangnan University, Wuxi, 214062, China
| | - Yunjin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Jialiang Zhou
- Department of radiation oncology, The Affiliated Hospital of Jiangnan University, Wuxi, 214062, China
| | - Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Haozhe Zou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, 571199, China. .,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Jiwei Zhang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Zhou Q, Yu Q, Gong Y, Liu Z, Xu H, Wang Y, Shi Y. Construction of a lncRNA-miRNA-mRNA network to determine the regulatory roles of lncRNAs in psoriasis. Exp Ther Med 2019; 18:4011-4021. [PMID: 31611939 PMCID: PMC6781786 DOI: 10.3892/etm.2019.8035] [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: 02/17/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a chronic inflammatory skin disorder that impairs the quality of life of affected patients. Emerging studies indicate that certain long non-coding RNAs (lncRNAs) have important roles in psoriasis. However, the exact functions of lncRNAs and their regulatory mechanisms as competitive endogenous RNAs (ceRNAs) in psoriasis have remained to be fully elucidated. In the present study, differentially expressed lncRNAs, microRNAs (miRNAs) and mRNAs were identified by analyzing public datasets, and a psoriasis-associated lncRNA-miRNA-mRNA network was constructed based on the ceRNA theory. Furthermore, previously validated abnormally expressed miRNAs in psoriasis were identified by a systematic literature search in the PubMed and Web of Science databases, and a specific miRNA-associated lncRNA-miRNA-mRNA sub-network was extracted. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using DAVID 6.8. A total of 253 lncRNAs, 106 miRNAs and 1,156 mRNAs were identified as being differentially expressed between psoriasis skin and healthy control skin. The present study identified two key lncRNAs that may potentially have a role in the pathogenesis of psoriasis: AL035425.3 and Prader Willi/Angelman region RNA 6. This integrative analysis enhances the understanding of the molecular mechanism of psoriasis and may provide novel therapeutic targets for the treatment of psoriasis.
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Affiliation(s)
- Qianqian Zhou
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Qian Yu
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Yu Gong
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Zhicui Liu
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Hui Xu
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Yao Wang
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Yuling Shi
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai 200072, P.R. China
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Lei X, Yang S, Yang Y, Zhang J, Wang Y, Cao M. Long noncoding RNA DLX6-AS1 targets miR-124-3p/CDK4 to accelerate Ewing's sarcoma. Am J Transl Res 2019; 11:6569-6576. [PMID: 31737208 PMCID: PMC6834508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 04/15/2023]
Abstract
Ewing's sarcoma is one of leading cause of malignancy occurred in the children and adolescents worldwide. Given the emerging critical role of long noncoding RNA (lncRNA) in the human cancer, as well as Ewing's sarcoma, we aim to identify the biological role of DLX6-AS1 in the tumorigenesis. Results unveil that DLX6-AS1 expression was increased in the tissue sample and cells. Functionally, the silencing of DLX6-AS1 could repress the proliferation and accelerate the apoptosis of Ewing's sarcoma cells. Mechanically, DLX6-AS1 functioned as the sponge of miR-124-3p, and then miR-124-3p targeted the 3'-UTR of CDK4 mRNA, forming the DLX6-AS1/miR-124-3p/CDK4 regulatory pathway. In conclusion, the critical role of DLX6-AS1 might unveil a potential therapeutic target for Ewing's sarcoma.
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Affiliation(s)
- Xiaomei Lei
- Department of Child Health Care, The Second Affiliated Hospital, Xi’an Jiaotong UniversityXi’an 710004, Shaanxi, China
| | - Siping Yang
- Department of Medical Genetics, Xibei Maternal and Child Health HospitalXi’an 710061, Shaanxi, China
| | - Yuanyuan Yang
- Department of Child Health Care, The Second Affiliated Hospital, Xi’an Jiaotong UniversityXi’an 710004, Shaanxi, China
| | - Juan Zhang
- Department of Neonatal Paediatrics, Xibei Maternal and Child Health HospitalXi’an 710061, Shaanxi, China
| | - Yue Wang
- Department of Child Health Care, The Second Affiliated Hospital, Xi’an Jiaotong UniversityXi’an 710004, Shaanxi, China
| | - Minhui Cao
- Department of Child Health Care, Weinan Maternal and Child Health HospitalWeinan 714000, Shaanxi, China
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