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Yuan Z, Yang X, Hu Z, Gao Y, Yan P, Zheng F, Guo Y, Wang X, Zhou J. Characterization of a predictive signature for tumor microenvironment and immunotherapy response in hepatocellular carcinoma involving neutrophil extracellular traps. Heliyon 2024; 10:e30827. [PMID: 38765048 PMCID: PMC11097059 DOI: 10.1016/j.heliyon.2024.e30827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/21/2024] Open
Abstract
Neutrophil extracellular traps (NETs) and other factors play a significant role in impacting the prognosis of patients with Hepatocellular carcinoma (HCC). Nevertheless, further research is warranted to fully elucidate the prognostic implications of NETs in patients with HCC. We employed a hierarchical clustering technique to examine the Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) data and identified subtypes associated with NETs. Subsequently, we utilized LASSO regression analysis to identify a distinct gene expression pattern within these subtypes. The strength of this signature was further validated through analysis of TCGA-LIHC and International Cancer Genome Consortium-Liver Cancer (ICGC-LIRI-JP) data. Our findings resulted in the construction of a six-gene signature related to NETs, which can predict survival outcomes in HCC patients. To enhance the predictive accuracy of our tool, we developed a nomogram that integrates the NETs signature with clinicopathological characteristics. We validated the significance of NETs in HCC patients using qRT-PCR and immunohistochemistry assays, along with in vitro experiments targeting high-risk genes. Furthermore, our exploration of the immune microenvironment uncovered augmented immune-specific metrics within the low-risk cohort, implying potential disparities in immune-related attributes between the high-risk and low-risk contingents. In summary, the NETs signature we discovered serves as a valuable biomarker and provides guidance for personalized therapy in HCC patients.
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Affiliation(s)
- Ziwei Yuan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Department of Endocrinology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Xuejia Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zujian Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yuanyuan Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Penghua Yan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Fan Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yangyang Guo
- Department of General Surgery, Ningbo First Hospital, Ningbo, 315000, China
| | - Xiaowu Wang
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Whenzhou Medical University, Ruian, 325200, Zhejiang Province, China
| | - Jingzong Zhou
- Department of Endocrinology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
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Zhong X, Wang H. LncRNA JHDM1D-AS1 promotes osteogenic differentiation of periodontal ligament cells by targeting miR-532-5p to activate IGF1R signaling. J Periodontal Res 2024; 59:220-230. [PMID: 37950511 DOI: 10.1111/jre.13209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
OBJECTIVE The aim of this study was to explore the mechanism underlying periodontal ligament cells (PDLCs) osteogenic differentiation. BACKGROUND Periodontitis causes damage to tooth-supporting apparatus and eventually leads to tooth loss. PDLCs hold great promise in periodontal regeneration due to their osteogenic features. METHODS The expression of osteogenic markers, lncRNA JHDM1D-AS1, miR-532-5p and IGF1R was examined. For osteogenic differentiation, primary human PDLCs (hPDLCs) were cultured in an osteogenic medium, and it was assessed by ALP activity and Alizarin Red staining. The interaction between JHDM1D-AS1, miR-532-5p and IGF1R was analyzed via dual luciferase, RIP and RNA pull-down assays. RESULTS JHDM1D-AS1 was up-regulated during osteogenic differentiation and its silencing inhibited hPDLC osteogenic differentiation. JHDM1D-AS1 worked as a miR-532-5p sponge in hPDLCs. miR-532-5p directly targeted IGF1R to suppress its expression, and miR-532-5p knockdown facilitated osteogenic differentiation of hPDLCs. Overexpression of IGF1R promoted osteogenic differentiation of hPDLCs via activating Notch/HES1 signaling in hPDLCs. CONCLUSION JHDM1D-AS1 promotes osteogenic differentiation of hPDLCs via sponging miR-532-5p to facilitate IGF1R expression and activate Notch/HES1 signaling.
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Affiliation(s)
- Xiaohuan Zhong
- Center of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Huixin Wang
- Center of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
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Uzuner E, Ulu GT, Gürler SB, Baran Y. The Role of MiRNA in Cancer: Pathogenesis, Diagnosis, and Treatment. Methods Mol Biol 2022; 2257:375-422. [PMID: 34432288 DOI: 10.1007/978-1-0716-1170-8_18] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer is also determined by the alterations of oncogenes and tumor suppressor genes. These gene expressions can be regulated by microRNAs (miRNA). At this point, researchers focus on addressing two main questions: "How are oncogenes and/or tumor suppressor genes regulated by miRNAs?" and "Which other mechanisms in cancer cells are regulated by miRNAs?" In this work we focus on gathering the publications answering these questions. The expression of miRNAs is affected by amplification, deletion or mutation. These processes are controlled by oncogenes and tumor suppressor genes, which regulate different mechanisms of cancer initiation and progression including cell proliferation, cell growth, apoptosis, DNA repair, invasion, angiogenesis, metastasis, drug resistance, metabolic regulation, and immune response regulation in cancer cells. In addition, profiling of miRNA is an important step in developing a new therapeutic approach for cancer.
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Affiliation(s)
- Erez Uzuner
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Gizem Tugçe Ulu
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Sevim Beyza Gürler
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Yusuf Baran
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey.
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Mao Y, Chen R, Xia M, Guo P, Zeng F, Huang J, He M. Identification of an immune-based mRNA-lncRNA signature for overall survival in cervical squamous cell carcinoma. Future Oncol 2021; 17:2365-2380. [PMID: 33724869 DOI: 10.2217/fon-2020-1153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To better predict the survival of cervical squamous cell carcinoma (CESC) patients, we aimed to construct a signature according to different immune infiltration. Methods: We downloaded the RNA sequences of CESC patients from the Cancer Genome Atlas database. By using single-sample gene set enrichment analysis, we separated the samples into high- and low-immunity groups. Then we separated the samples into training and testing datasets and performed the following analyses: univariate, least absolute shrinkage and selection operator analysis, multivariate Cox regression analyses and weighted gene coexpression network analysis using R software. Gene ontology and Kyoto Encyclopedia of Genes and Genomes studies were performed using the Database for Annotation, Visualization and Integrated Discovery website. Results & conclusion: We finally identified a signature with three mRNAs and two lncRNAs: ADGRG5, HSH2D, ZMAT4, RBAKDN and LINC00200. In short, our study constructed an mRNA-lncRNA signature related to immune infiltration to better predict the survival of CESC patients.
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Affiliation(s)
- Yifang Mao
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
| | - Run Chen
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
| | - Meng Xia
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
| | - Peng Guo
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
| | - Feitianzhi Zeng
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
| | - Jiaming Huang
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
| | - Mian He
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, PR China
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Li W, Liu S, Su S, Chen Y, Sun G. Construction and validation of a novel prognostic signature of microRNAs in lung adenocarcinoma. PeerJ 2021; 9:e10470. [PMID: 33510968 PMCID: PMC7798616 DOI: 10.7717/peerj.10470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/11/2020] [Indexed: 11/20/2022] Open
Abstract
MicroRNA (miRNA, miR) has been reported to be highly implicated in a wide range of biological processes in lung cancer (LC), and identification of differentially expressed miRNAs between normal and LC samples has been widely used in the discovery of prognostic factors for overall survival (OS) and response to therapy. The present study was designed to develop and evaluate a miRNA-based signature with prognostic value for the OS of lung adenocarcinoma (LUAD), a common histologic subtype of LC. In brief, the miRNA expression profiles and clinicopathological factors of 499 LUAD patients were collected from The Cancer Genome Atlas (TCGA) database. Kaplan-Meier (K-M) survival analysis showed significant correlations between differentially expressed miRNAs and LUAD survival outcomes. Afterward, 1,000 resample LUAD training matrices based on the training set was applied to identify the potential prognostic miRNAs. The least absolute shrinkage and selection operator (LASSO) cox regression analysis was used to constructed a six-miRNA based prognostic signature for LUAD patients. Samples with different risk scores displayed distinct OS in K-M analysis, indicating considerable predictive accuracy of this signature in both training and validation sets. Furthermore, time-dependent receiver operating characteristic (ROC) analysis demonstrated the nomogram achieved higher predictive accuracy than any other clinical variables after incorporating the clinical information (age, sex, stage, and recurrence). In the stratification analysis, the prognostic value of this classifier in LUAD patients was validated to be independent of other clinicopathological variables, such as age, gender, tumor recurrence, and early stage. Gene set annotation analyses were also conducted through the Hallmark gene set and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, indicating target genes of the six miRNAs were positively related to various molecular pathways of cancer, such as hallmark UV response, Wnt signaling pathway and mTOR signaling pathway. In addition, fresh cancer tissue samples and matched adjacent tissue samples from 12 LUAD patients were collected to verify the expression of miR-582's target genes in the model, further revealing the potential relationship between SOX9, RASA1, CEP55, MAP4K4 and LUAD tumorigenesis, and validating the predictive value of the model. Taken together, the present study identified a robust signature for the OS prediction of LUAD patients, which could potentially aid in the individualized selection of therapeutic approaches for LUAD patients.
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Affiliation(s)
- Wanzhen Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shiqing Liu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China.,Key cite of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China.,Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, China
| | - Shihong Su
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Gengyun Sun
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Wang Q, Zhang L, Yan Z, Xie L, An Y, Li H, Han Y, Zhang G, Dong H, Zheng H, Zhu W, Li Y, Wang Y, Guo X. OScc: an online survival analysis web server to evaluate the prognostic value of biomarkers in cervical cancer. Future Oncol 2019; 15:3693-3699. [DOI: 10.2217/fon-2019-0412] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: To establish a web server that can mutually validate prognostic biomarkers of cervical cancer. Methods: Four datasets including expression profiling and relative clinical follow-up data were collected from Gene Expression Omnibus and The Cancer Genome Atlas. The web server was developed by R software. Results: The web server was named OScc including 690 patients and can be accessed at http://bioinfo.henu.edu.cn/CESC/CESCList.jsp . The Kaplan–Meier survival curves with log-rank p-value and hazard ratio will be generated of interested gene in OScc. Compared with previous predictive tools, OScc had the advantages of registration-free, larger sample size and subgroup analysis. Conclusion: The OScc is highly valuable to perform the preliminary assessment and validation of new or interested prognostic biomarkers for cervical cancer.
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Affiliation(s)
- Qiang Wang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Lu Zhang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Zhongyi Yan
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Longxiang Xie
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Yang An
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Huimin Li
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Yali Han
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Guosen Zhang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Huan Dong
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Hong Zheng
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Wan Zhu
- Department of Anesthesia, Stanford University, Stanford, CA 94305, USA
| | - Yongqiang Li
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
| | - Yunlong Wang
- Henan Bioengineering Research Center, Zhengzhou 450046, PR China
| | - Xiangqian Guo
- Department of Preventive Medicine, Institute of Biomedical Informatics, Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Bioinformatics Center, Henan Provincial Engineering Centre for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng 475004, PR China
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Xiong J, Bing Z, Guo S. Observed Survival Interval: A Supplement to TCGA Pan-Cancer Clinical Data Resource. Cancers (Basel) 2019; 11:E280. [PMID: 30813652 PMCID: PMC6468755 DOI: 10.3390/cancers11030280] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/16/2019] [Accepted: 02/22/2019] [Indexed: 12/17/2022] Open
Abstract
To drive high-quality omics translational research using The Cancer Genome Atlas (TCGA) data, a TCGA Pan-Cancer Clinical Data Resource was proposed. However, there is an out-of-step issue between clinical outcomes and the omics data of TCGA for skin cutaneous melanoma (SKCM), due to the majority of metastatic samples. In clinical cases, the survival time started from the initial SKCM diagnosis, while the omics data were characterized at TCGA sampling. This study aimed to address this issue by proposing an observed survival interval (OBS), which was defined as the time interval from TCGA sampling to patient death or last follow-up. We compared the OBS with the usual recommended overall survival (OS) by associating them with both clinical data and microRNA sequencing data of TCGA-SKCM. We found that the OS of primary SKCM was significantly shorter than that of metastatic SKCM, while the opposite happened if OBS was compared. OS was associated with the pathological stage of both primary and metastatic SKCM, while OBS was associated with the pathological stage of primary SKCM but not that of metastatic SKCM. Five previously cross-validated survival-associated microRNAs were found to be associated with the OBS rather than OS in metastatic SKCM. Thus, the OBS was more appropriate for associating microRNA-omics data of TCGA-SKCM than OS, and it is a timely supplement to TCGA Pan-Cancer Clinical Data Resource.
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Affiliation(s)
- Jie Xiong
- Department of Epidemiology and Health Statistics, XiangYa School of Public Health, Central South University, Changsha 410078, China.
| | - Zhitong Bing
- Department of Computational Physics, Institute of Modern Physics of Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Shengyu Guo
- Department of Epidemiology and Health Statistics, XiangYa School of Public Health, Central South University, Changsha 410078, China.
- Department of Public Management, College of Economic Management, Changsha University, Changsha 410022, China.
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