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Kazemifard N, Farmani M, Baradaran Ghavami S, Kazemi M, Shahrokh S, Asadzadeh Aghdaei H, Zali M. A prediction of the CRNDE role by modulating NF-κB pathway in inflammatory bowel disease (IBD). Biochem Biophys Rep 2024; 38:101731. [PMID: 38766384 PMCID: PMC11101873 DOI: 10.1016/j.bbrep.2024.101731] [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: 03/06/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate multiple pathways and cellular mechanisms. Recent research has emphasized their involvement in the pathogenesis of complex diseases, such as Inflammatory Bowel Disease (IBD) which is characterized by chronic inflammation of the intestines. The two most common types of IBD are ulcerative colitis and Crohn's disease. CRNDE lncRNA was initially detected in colorectal cancer (CRC) and found to be involved in the tumorigenesis pathways. Further studies revealed the role of CRNDE in activating inflammation and promoting the release of inflammatory cytokines. This study utilizes the RNA-seq data analysis and bioinformatics tools to clarify the role of CRNDE in the IBD pathogenesis and confirms its expression in inflamed HT-29 and Caco-2 cell lines and also colonic and blood samples of UC patients and controls ex vivo. Based on our results, CRNDE was significantly upregulated in IBD samples compared to controls in RNA-seq data analysis and Real-time PCR of inflamed HT-29 cell line and colonic biopsies from UC patients. Additionally, predicted that its expression is positively correlated with the pro-inflammatory cytokines production. CRNDE interactions was investigated with several inflammation-related miRNAs and regulatory proteins computationally. Thus, CRNDE upregulation in the colon of IBD patients could be involved in IBD pathogenesis by promoting inflammatory pathways and targeting anti-inflammatory miRNAs.
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Affiliation(s)
- Nesa Kazemifard
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Farmani
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Baradaran Ghavami
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Reproductive Sciences and Sexual Health Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shabnam Shahrokh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Heydari R, Tavassolifar MJ, Fayazzadeh S, Sadatpour O, Meyfour A. Long non-coding RNAs in biomarking COVID-19: a machine learning-based approach. Virol J 2024; 21:134. [PMID: 38849961 PMCID: PMC11161961 DOI: 10.1186/s12985-024-02408-9] [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: 03/19/2024] [Accepted: 06/05/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The coronavirus pandemic that started in 2019 has caused the highest mortality and morbidity rates worldwide. Data on the role of long non-coding RNAs (lncRNAs) in coronavirus disease 2019 (COVID-19) is scarce. We aimed to elucidate the relationship of three important lncRNAs in the inflammatory states, H19, taurine upregulated gene 1 (TUG1), and colorectal neoplasia differentially expressed (CRNDE) with key factors in inflammation and fibrosis induction including signal transducer and activator of transcription3 (STAT3), alpha smooth muscle actin (α-SMA), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) in COVID-19 patients with moderate to severe symptoms. METHODS Peripheral blood mononuclear cells from 28 COVID-19 patients and 17 healthy controls were collected. The real-time quantitative polymerase chain reaction (RT-qPCR) was performed to evaluate the expression of RNAs and lncRNAs. Western blotting analysis was also performed to determine the expression levels of STAT3 and α-SMA proteins. Machine learning and receiver operating characteristic (ROC) curve analysis were carried out to evaluate the distinguishing ability of lncRNAs. RESULTS The expression levels of H19, TUG1, and CRNDE were significantly overexpressed in COVID-19 patients compared to healthy controls. Moreover, STAT3 and α-SMA expression levels were remarkedly increased at both transcript and protein levels in patients with COVID-19 compared to healthy subjects and were correlated with Three lncRNAs. Likewise, IL-6 and TNF-α were considerably upregulated in COVID-19 patients. Machine learning and ROC curve analysis showed that CRNDE-H19 panel has the proper ability to distinguish COVID-19 patients from healthy individuals (area under the curve (AUC) = 0.86). CONCLUSION The overexpression of three lncRNAs in COVID-19 patients observed in this study may align with significant manifestations of COVID-19. Furthermore, their co-expression with STAT3 and α-SMA, two critical factors implicated in inflammation and fibrosis induction, underscores their potential involvement in exacerbating cardiovascular, pulmonary and common symptoms and complications associated with COVID-19. The combination of CRNDE and H19 lncRNAs seems to be an impressive host-based biomarker panel for screening and diagnosis of COVID-19 patients from healthy controls. Research into lncRNAs can provide a robust platform to find new viral infection-related mediators and propose novel therapeutic strategies for viral infections and immune disorders.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Tavassolifar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Fayazzadeh
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Omid Sadatpour
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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lncRNA CRNDE Affects Th17/IL-17A and Inhibits Epithelial-Mesenchymal Transition in Lung Epithelial Cells Reducing Asthma Signs. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:2092184. [PMID: 36743692 PMCID: PMC9897922 DOI: 10.1155/2023/2092184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 01/28/2023]
Abstract
Background Asthma treatment is difficult due to disease heterogeneity and comorbidities. In addition, the development of drugs targeting the underlying mechanisms of asthma remains slow. We planned to identify the most upregulated differentially expressed long noncoding RNA in asthma to explore its regulatory patterns and pathways in asthma. Methods We sensitized mice using a mixture of ovalbumin, house dust mites, and lipopolysaccharide to establish an asthma mouse model. We also sensitized asthma cells with TGF-β1 in an in vitro model. We performed a microarray analysis to identify the lncRNA with the differential expression level in model mice. We applied hematoxylin and eosin and Masson's trichrome stainings to mouse tissues to quantify the tissue damage extent. Next, we assess the levels of lncRNA CRNDE, miR-29a-3p, TGF-β1, MCL-1, E-cadherin, vimentin, and snail. We counted the percentages of Th17 cells using flow cytometry. Finally, we performed a dual-luciferase reporter assay to assess the association between lncRNA CRNDE and miR-29a-3p. Results We successfully established asthma mouse/cell models and selected the lncRNA CRNDE for our study. Transfection of si-CRNDE reduced the degree of injury and inflammation in the mouse model and reversed the TGF-β1-induced epithelial-mesenchymal transition (EMT) in the cell model. Moreover, the E-cadherin level was upregulated, and the levels of IL-17A, vimentin, snail, and α-SMA were downregulated. We also discovered that lncRNA CRNDE negatively regulated miR-29a-3p and that this one in turn inhibited MCL-1 in mice. After lncRNA CRNDE expression downregulation, the level of miR-29a-3p was increased, and we detected reduced levels of MCL-1 and EMTs. Conclusions lncRNA CRNDE expression downregulation led to reduced inflammation and reduced lung damage in mice with induced asthma, it inhibited the EMTs of lung epithelial cells via the miR-29a-3p/MCL-1 pathway, and it reduced the levels of Th17/IL-17A cells to reduce asthma signs.
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CRNDE: A valuable long noncoding RNA for diagnosis and therapy of solid and hematological malignancies. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:190-201. [PMID: 35402077 PMCID: PMC8961077 DOI: 10.1016/j.omtn.2022.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal neoplasia differentially expressed (CRNDE) is an oncogenic long noncoding RNA (lncRNA). Increased CRNDE expression was initially discovered in colorectal cancer and then in a variety of solid tumors and hematological malignancies. CRNDE participates in multiple biological processes, such as cell proliferation, differentiation, migration, and apoptosis. CRNDE has been shown to modulate target gene expression through multiple mechanisms, including transcriptional regulation, post-transcriptional regulation, and competition for microRNA (miRNA) binding. In this review, we summarize the evidence that supports CRNDE in the diagnosis and prognosis predicting of cancers. The functional roles and molecular mechanisms of CRNDE are further described for major types of solid tumors and hematological malignancies. The therapeutic potential of CRNDE as a target for research and development is also discussed.
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LncTRPM2-AS inhibits TRIM21-mediated TRPM2 ubiquitination and prevents autophagy-induced apoptosis of macrophages in asthma. Cell Death Dis 2021; 12:1153. [PMID: 34903714 PMCID: PMC8668916 DOI: 10.1038/s41419-021-04437-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/09/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) play a crucial role in macrophage development but little is known about their role in asthma. Here, we investigated the role of lncRNA lncTRPM2-AS in asthma and found that lncTRPM2-AS participates in the promotion of macrophage inflammation. Downregulation of lncTRPM2-AS promoted apoptosis and inhibited proliferation and production of cytokines including IL-1β, IL-4, IL-6, IL-10, TNF-α, and TGF-β. RNA-immunoprecipitation and mass spectrometry indicated that the protein TRPM2 interacted with both lncTRPM2-AS and the E3 ubiquitin ligase TRIM21. LncTRPM2-AS silencing enhanced the interaction between TRIM21 and TRPM2, resulting in elevated levels of ubiquitin-related degradation of TRPM2. Mutation analysis indicated that TRPM2 K1218 is a key site for TRIM21-dependent ubiquitination. Downregulation of lncTRPM2-AS significantly decreased intracellular calcium levels by restraining TRPM2 protein expression, which in turn decreased ROS levels and increased autophagy to promote macrophage apoptosis and reduce cytokine production, together inhibiting macrophage inflammation. Taken together, our findings demonstrate that lncTRPM2-AS blocks the ubiquitination of TRPM2 via TRIM21 and inhibits autophagy-induced apoptosis which may contribute to macrophage inflammation in asthma.
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6
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Feng Q, Qian C, Fan S. A Hypoxia-Related Long Non-Coding RNAs Signature Associated With Prognosis in Lower-Grade Glioma. Front Oncol 2021; 11:771512. [PMID: 34869006 PMCID: PMC8640178 DOI: 10.3389/fonc.2021.771512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Accumulating evidence suggests that hypoxia microenvironment and long non-coding lncRNAs (lncRNAs) exert critical roles in tumor development. Herein, we aim to develop a hypoxia-related lncRNA (HRL) model to predict the survival outcomes of patient with lower-grade glioma (LGG). The RNA-sequencing data of 505 LGG samples were acquired from The Cancer Genome Atlas (TCGA). Using consensus clustering based on the expression of hypoxia-related mRNAs, these samples were divided into three subsets that exhibit distinct hypoxia content, clinicopathologic features, and survival status. The differentially expressed lncRNAs across the subgroups were documented as candidate HRLs. With LASSO regression analysis, eight informative lncRNAs were selected for constructing the prognostic HRL model. This signature had a good performance in predicting LGG patients’ overall survival in the TCGA cohort, and similar results could be achieved in two validation cohorts from the Chinese Glioma Genome Atlas. The HRL model also showed correlations with important clinicopathologic characteristics such as patients’ age, tumor grade, IDH mutation, 1p/19q codeletion, MGMT methylation, and tumor progression risk. Functional enrichment analysis indicated that the HLR signature was mainly involved in regulation of inflammatory response, complement, hypoxia, Kras signaling, and apical junction. More importantly, the signature was related to immune cell infiltration, estimated immune score, tumor mutation burden, neoantigen load, and expressions of immune checkpoints and immunosuppressive cytokines. Finally, a nomogram was developed by integrating the HRL signature and clinicopathologic features, with a concordance index of 0.852 to estimate the survival probability of LGG patients. In conclusion, our study established an effective HRL model for prognosis assessment of LGG patients, which may provide insights for future research and facilitate the designing of individualized treatment.
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Affiliation(s)
- Qinglin Feng
- Department of Neurosurgery, Chongqing University Three Gorges Hospital & Chongqing Three Gorges Central Hospital, Chongqing, China
| | - Cheng Qian
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shibing Fan
- Department of Neurosurgery & Chongqing Municipality Clinical Research Center for Geriatric Diseases, Chongqing University Three Gorges Hospital, and School of Medicine Chongqing University, Chongqing, China
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7
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Zhang S, Li X, Tang C, Kuang W. Inflammation-Related Long Non-Coding RNA Signature Predicts the Prognosis of Gastric Carcinoma. Front Genet 2021; 12:736766. [PMID: 34819945 PMCID: PMC8607501 DOI: 10.3389/fgene.2021.736766] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Gastric carcinoma (GC) is a molecularly and phenotypically highly heterogeneous disease, making the prognostic prediction challenging. On the other hand, Inflammation as part of the active cross-talk between the tumor and the host in the tumor or its microenvironment could affect prognosis. Method: We established a prognostic multi lncRNAs signature that could better predict the prognosis of GC patients based on inflammation-related differentially expressed lncRNAs in GC. Results: We identified 10 differently expressed lncRNAs related to inflammation associated with GC prognosis. Kaplan-Meier survival analysis demonstrated that high-risk inflammation-related lncRNAs signature was related to poor prognosis of GC. Moreover, the inflammation-related lncRNAs signature had an AUC of 0.788, proving their utility in predicting GC prognosis. Indeed, our risk signature is more precise in predicting the prognosis of GC patients than traditional clinicopathological manifestations. Immune and tumor-related pathways for individuals in the low and high-risk groups were further revealed by GSEA. Moreover, TCGA based analysis revealed significant differences in HLA, MHC class-I, cytolytic activity, parainflammation, co-stimulation of APC, type II INF response, and type I INF response between the two risk groups. Immune checkpoints revealed CD86, TNFSF18, CD200, and LAIR1 were differently expressed between lowand high-risk groups. Conclusion: A novel inflammation-related lncRNAs (AC015660.1, LINC01094, AL512506.1, AC124067.2, AC016737.1, AL136115.1, AP000695.1, AC104695.3, LINC00449, AC090772.1) signature may provide insight into the new therapies and prognosis prediction for GC patients.
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Affiliation(s)
- ShuQiao Zhang
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - XinYu Li
- Medical College of Acupuncture-Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - ChunZhi Tang
- Medical College of Acupuncture-Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - WeiHong Kuang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Dongguan, China
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8
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Momtazmanesh S, Rezaei N. Long Non-Coding RNAs in Diagnosis, Treatment, Prognosis, and Progression of Glioma: A State-of-the-Art Review. Front Oncol 2021; 11:712786. [PMID: 34322395 PMCID: PMC8311560 DOI: 10.3389/fonc.2021.712786] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Glioma is the most common malignant central nervous system tumor with significant mortality and morbidity. Despite considerable advances, the exact molecular pathways involved in tumor progression are not fully elucidated, and patients commonly face a poor prognosis. Long non-coding RNAs (lncRNAs) have recently drawn extra attention for their potential roles in different types of cancer as well as non-malignant diseases. More than 200 lncRNAs have been reported to be associated with glioma. We aimed to assess the roles of the most investigated lncRNAs in different stages of tumor progression and the mediating molecular pathways in addition to their clinical applications. lncRNAs are involved in different stages of tumor formation, invasion, and progression, including regulating the cell cycle, apoptosis, autophagy, epithelial-to-mesenchymal transition, tumor stemness, angiogenesis, the integrity of the blood-tumor-brain barrier, tumor metabolism, and immunological responses. The well-known oncogenic lncRNAs, which are upregulated in glioma, are H19, HOTAIR, PVT1, UCA1, XIST, CRNDE, FOXD2-AS1, ANRIL, HOXA11-AS, TP73-AS1, and DANCR. On the other hand, MEG3, GAS5, CCASC2, and TUSC7 are tumor suppressor lncRNAs, which are downregulated. While most studies reported oncogenic effects for MALAT1, TUG1, and NEAT1, there are some controversies regarding these lncRNAs. Expression levels of lncRNAs can be associated with tumor grade, survival, treatment response (chemotherapy drugs or radiotherapy), and overall prognosis. Moreover, circulatory levels of lncRNAs, such as MALAT1, H19, HOTAIR, NEAT1, TUG1, GAS5, LINK-A, and TUSC7, can provide non-invasive diagnostic and prognostic tools. Modulation of expression of lncRNAs using antisense oligonucleotides can lead to novel therapeutics. Notably, a profound understanding of the underlying molecular pathways involved in the function of lncRNAs is required to develop novel therapeutic targets. More investigations with large sample sizes and increased focus on in-vivo models are required to expand our understanding of the potential roles and application of lncRNAs in glioma.
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Affiliation(s)
- Sara Momtazmanesh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Sorokin M, Raevskiy M, Zottel A, Šamec N, Skoblar Vidmar M, Matjašič A, Zupan A, Mlakar J, Suntsova M, Kuzmin DV, Buzdin A, Jovčevska I. Large-Scale Transcriptomics-Driven Approach Revealed Overexpression of CRNDE as a Poor Survival Prognosis Biomarker in Glioblastoma. Cancers (Basel) 2021; 13:3419. [PMID: 34298634 PMCID: PMC8303503 DOI: 10.3390/cancers13143419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma is the most common and malignant brain malignancy worldwide, with a 10-year survival of only 0.7%. Aggressive multimodal treatment is not enough to increase life expectancy and provide good quality of life for glioblastoma patients. In addition, despite decades of research, there are no established biomarkers for early disease diagnosis and monitoring of patient response to treatment. High throughput sequencing technologies allow for the identification of unique molecules from large clinically annotated datasets. Thus, the aim of our study was to identify significant molecular changes between short- and long-term glioblastoma survivors by transcriptome RNA sequencing profiling, followed by differential pathway-activation-level analysis. We used data from the publicly available repositories The Cancer Genome Atlas (TCGA; number of annotated cases = 135) and Chinese Glioma Genome Atlas (CGGA; number of annotated cases = 218), and experimental clinically annotated glioblastoma tissue samples from the Institute of Pathology, Faculty of Medicine in Ljubljana corresponding to 2-58 months overall survival (n = 16). We found one differential gene for long noncoding RNA CRNDE whose overexpression showed correlation to poor patient OS. Moreover, we identified overlapping sets of congruently regulated differential genes involved in cell growth, division, and migration, structure and dynamics of extracellular matrix, DNA methylation, and regulation through noncoding RNAs. Gene ontology analysis can provide additional information about the function of protein- and nonprotein-coding genes of interest and the processes in which they are involved. In the future, this can shape the design of more targeted therapeutic approaches.
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Affiliation(s)
- Maxim Sorokin
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1000 Brussels, Belgium;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Mikhail Raevskiy
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Alja Zottel
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
| | - Neja Šamec
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
| | | | - Alenka Matjašič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Jernej Mlakar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Maria Suntsova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Denis V. Kuzmin
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Anton Buzdin
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1000 Brussels, Belgium;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- OmicsWay Corp., Walnut, CA 91789, USA
| | - Ivana Jovčevska
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
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Luo X, Tu T, Zhong Y, Xu S, Chen X, Chen L, Yang F. ceRNA Network Analysis Shows That lncRNA CRNDE Promotes Progression of Glioblastoma Through Sponge mir-9-5p. Front Genet 2021; 12:617350. [PMID: 33767729 PMCID: PMC7985093 DOI: 10.3389/fgene.2021.617350] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma accounts for 45.2% of central nervous system tumors. Despite the availability of multiple treatments (e.g., surgery, radiotherapy, chemotherapy, biological therapy, immunotherapy, and electric field therapy), glioblastoma has a poor prognosis, with a 5-year survival rate of approximately 5%. The pathogenesis and prognostic markers of this cancer are currently unclear. To this end, this study aimed to explore the pathogenesis of glioblastoma and identify potential prognostic markers. We used data from the GEO and TCGA databases and identified five genes (ITGA5, MMP9, PTPRN, PTX3, and STX1A) that could affect the survival rate of glioblastoma patients and that were differentially expressed between glioblastoma patients and non-tumors groups. Based on a variety of bioinformatics tools for reverse prediction of target genes associated with the prognosis of GBM, a ceRNA network of messenger RNA (STX1A, PTX3, MMP9)-microRNA (miR-9-5p)-long non-coding RNA (CRNDE) was constructed. Finally, we identified five potential therapeutic drugs (bacitracin, hecogenin, clemizole, chrysin, and gibberellic acid) that may be effective treatments for glioblastoma.
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Affiliation(s)
- Xiaobin Luo
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tianqi Tu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yali Zhong
- Graduate School of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Shangyi Xu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiangzhou Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ligang Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fubing Yang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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11
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Liu QM, Liu LL, Li XD, Tian P, Xu H, Li ZL, Wang LK. Silencing lncRNA TUG1 Alleviates LPS-Induced Mouse Hepatocyte Inflammation by Targeting miR-140/TNF. Front Cell Dev Biol 2021; 8:616416. [PMID: 33644034 PMCID: PMC7905057 DOI: 10.3389/fcell.2020.616416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis is a major public health problem that increases the risk of liver cirrhosis and liver cancer. Numerous studies have revealed that long non-coding RNAs (lncRNAs) exert essential function in the inflammatory response of multiple organs. Herein, we aimed to explore the effect of lncRNA TUG1 in LPS-induced hepatocyte inflammation response and further illuminate the underlying mechanisms. Mice were intraperitoneally injected with LPS, and the liver inflammation was evaluated. Microarray showed that lncRNA TUG1 was upregulated in LPS-induced hepatocyte inflammation. qRT-PCR and immunofluorescence assay indicated a significant increase of TUG1 in mice with LPS injection. Functional analysis showed that si-TUG1 inhibited LPS-induced inflammation response in mice liver, inhibited apoptosis level, and protected liver function. Then, we knock down TUG1 in normal human hepatocyte AML12. Consistent with in vivo results, si-TUG1 removed the injury of LPS on AML12 cells. Furthermore, TUG1 acted as a sponge of miR-140, and miR-140 directly targeted TNFα (TNF). MiR-140 or si-TNF remitted the beneficial effects of TUG1 on LPS-induced hepatocyte inflammation response both in vitro and in vivo. Our data revealed that deletion of TUG1 protected against LPS-induced hepatocyte inflammation via regulating miR-140/TNF, which might provide new insight for hepatitis treatment.
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Affiliation(s)
- Qing-Min Liu
- Intensive Care Unit, Linyi People's Hospital, Linyi, China
| | - Li-Li Liu
- Department of Pathology, Linyi People's Hospital, Linyi, China
| | - Xi-Dong Li
- Department of Infection Control Center, Linyi People's Hospital, Linyi, China
| | - Ping Tian
- Department of Infection Control Center, Linyi People's Hospital, Linyi, China
| | - Hao Xu
- Department of Infection Control Center, Linyi People's Hospital, Linyi, China
| | - Zeng-Lian Li
- Department of Infection Control Center, Linyi People's Hospital, Linyi, China
| | - Li-Kun Wang
- Department of Infection Control Center, Linyi People's Hospital, Linyi, China
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12
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Khan MI, Nur SM, Adhami V, Mukhtar H. Epigenetic regulation of RNA sensors: Sentinels of immune response. Semin Cancer Biol 2021; 83:413-421. [PMID: 33484869 DOI: 10.1016/j.semcancer.2020.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
Living host system possess mechanisms like innate immune system to combat against inflammation, stress singling, and cancer. These mechanisms are initiated by PAMP and DAMP mediated recognition by PRR. PRR is consist of variety of nucleic acid sensors like-RNA sensors. They play crucial role in identifying exogenous and endogenous RNA molecules, which subsequently mediate pro/inflammatory cytokine, IFN and ISGs response in traumatized or tumorigenic conditions. The sensors can sensitize wide range of nucleic acid particle in term of size and structure, while each category sensors belongs subclasses with differentially expressed in cell and distinguished functioning mechanisms. They are also able to make comparison between self and non-self-nucleic acid molecules through specific mechanisms. Besides exhibiting anti-inflammatory and anti-tumorigenic responses, RNA sensors cover the broad spectrum of response mechanisms. Transcriptionally RNA sensors undergo with tight epigenetic regulations. In this review study, we will be going to discuss about the details of RNA sensors, their functional mechanisms and epi-transactional regulations.
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Affiliation(s)
- Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Suza Mohammad Nur
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vaqar Adhami
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Hasan Mukhtar
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, USA.
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13
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Yang J, Liu W, Xu M, Yu L. Long non-coding RNA CRNDE and toll-like receptor 3 correlate with disease severity, inflammation, and mortality in sepsis. J Clin Lab Anal 2020; 34:e23360. [PMID: 32696505 PMCID: PMC7521289 DOI: 10.1002/jcla.23360] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 01/02/2023] Open
Abstract
Objective This study aimed to assess the interaction between long non‐coding RNA colorectal neoplasia differentially expressed (lncRNA CRNDE) and toll‐like receptor 3 (TLR3), and assess their correlations with disease severity, inflammation, and 28‐days mortality in sepsis patients. Methods We consecutively enrolled 146 sepsis patients and 146 healthy controls (HCs), and collected their peripheral blood mononuclear cells to detect lncRNA CRNDE and TLR3 expressions using reverse transcription quantitative polymerase chain reaction. LncRNA CRNDE and TLR3 in sepsis patients were classified into four clusters according to quantile expressions (Quantile 1 (0%‐24%), Quantile 2 (25%‐50%), Quantile 3 (50%‐74%), and Quantile 4 (75%‐100%)) for correlation analysis. Results LncRNA CRNDE was upregulated in sepsis patients compared with HCs, and it showed good value in differentiating sepsis patients form HCs by receiver operating characteristic curve analysis. In sepsis patients, lncRNA CRNDE positively correlated with acute pathologic and chronic health evaluation II (APACHE II) score and sequential organ failure assessment (SOFA) score, as well as serum creatinine (Scr). As for inflammation, lncRNA CRNDE positively correlated with C‐reactive protein (CRP), tumor necrosis factor‐α (TNF‐α), interleukin (IL)‐1β, IL‐6, and IL‐8. Regarding mortality, lncRNA CRNDE positively correlated with 28‐days mortality. Furthermore, lncRNA CRNDE positively correlated with TLR3, and TLR3 positively associated with APACHE II score, SOFA score, Scr, albumin, CRP, TNF‐α, IL‐1β, IL‐6, IL‐8, and 28‐days mortality in sepsis patients. Conclusion LncRNA CRNDE interacts with TLR3, both of which correlate with advanced disease severity, inflammation, and higher 28‐days mortality in sepsis patients.
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Affiliation(s)
- Junhui Yang
- Department of Intensive Care Unit, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Liu
- Department of Intensive Care Unit, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Xu
- Department of Pain Clinic, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Yu
- Department of Intensive Care Unit, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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14
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Zottel A, Šamec N, Videtič Paska A, Jovčevska I. Coding of Glioblastoma Progression and Therapy Resistance through Long Noncoding RNAs. Cancers (Basel) 2020; 12:cancers12071842. [PMID: 32650527 PMCID: PMC7409010 DOI: 10.3390/cancers12071842] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma is the most aggressive and lethal primary brain malignancy, with an average patient survival from diagnosis of 14 months. Glioblastoma also usually progresses as a more invasive phenotype after initial treatment. A major step forward in our understanding of the nature of glioblastoma was achieved with large-scale expression analysis. However, due to genomic complexity and heterogeneity, transcriptomics alone is not enough to define the glioblastoma “fingerprint”, so epigenetic mechanisms are being examined, including the noncoding genome. On the basis of their tissue specificity, long noncoding RNAs (lncRNAs) are being explored as new diagnostic and therapeutic targets. In addition, growing evidence indicates that lncRNAs have various roles in resistance to glioblastoma therapies (e.g., MALAT1, H19) and in glioblastoma progression (e.g., CRNDE, HOTAIRM1, ASLNC22381, ASLNC20819). Investigations have also focused on the prognostic value of lncRNAs, as well as the definition of the molecular signatures of glioma, to provide more precise tumor classification. This review discusses the potential that lncRNAs hold for the development of novel diagnostic and, hopefully, therapeutic targets that can contribute to prolonged survival and improved quality of life for patients with glioblastoma.
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15
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Cheng L, Nan C, Kang L, Zhang N, Liu S, Chen H, Hong C, Chen Y, Liang Z, Liu X. Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis. J Transl Med 2020; 18:217. [PMID: 32471511 PMCID: PMC7257169 DOI: 10.1186/s12967-020-02372-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
Background Sepsis is a fatal disease referring to the presence of a known or strongly suspected infection coupled with systemic and uncontrolled immune activation causing multiple organ failure. However, current knowledge of the role of lncRNAs in sepsis is still extremely limited. Methods We performed an in silico investigation of the gene coexpression pattern for the patients response to all-cause sepsis in consecutive intensive care unit (ICU) admissions. Sepsis coexpression gene modules were identified using WGCNA and enrichment analysis. lncRNAs were determined as sepsis biomarkers based on the interactions among lncRNAs and the identified modules. Results Twenty-three sepsis modules, including both differentially expressed modules and prognostic modules, were identified from the whole blood RNA expression profiling of sepsis patients. Five lncRNAs, FENDRR, MALAT1, TUG1, CRNDE, and ANCR, were detected as sepsis regulators based on the interactions among lncRNAs and the identified coexpression modules. Furthermore, we found that CRNDE and MALAT1 may act as miRNA sponges of sepsis related miRNAs to regulate the expression of sepsis modules. Ultimately, FENDRR, MALAT1, TUG1, and CRNDE were reannotated using three independent lncRNA expression datasets and validated as differentially expressed lncRNAs. Conclusion The procedure facilitates the identification of prognostic biomarkers and novel therapeutic strategies of sepsis. Our findings highlight the importance of transcriptome modularity and regulatory lncRNAs in the progress of sepsis.
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Affiliation(s)
- Lixin Cheng
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Chuanchuan Nan
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Lin Kang
- Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Ning Zhang
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Sheng Liu
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Huaisheng Chen
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Chengying Hong
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Youlian Chen
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Zhen Liang
- Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China.
| | - Xueyan Liu
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China.
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16
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Lu Y, Sha H, Sun X, Zhang Y, Wu Y, Zhang J, Zhang H, Wu J, Feng J. CRNDE: an oncogenic long non-coding RNA in cancers. Cancer Cell Int 2020; 20:162. [PMID: 32435153 PMCID: PMC7218640 DOI: 10.1186/s12935-020-01246-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal neoplasia differentially expressed (CRNDE) is a long non-coding RNA which has been proved upregulated in various cancers. Meanwhile, CRNDE has been demonstrated to be involved in multiple biological processes of different cancers according to previous study. Moreover, recent studies suggested CRNDE might be a potential diagnostic biomarker and prognostic predictor due to its high sensitivity and specificity in cancer tissues and plasma. In this review, we summarize the biological function of CRNDE and the relevant mechanisms in cancers to establish a molecular basis for the clinical use of CRNDE in the future.
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Affiliation(s)
- Ya Lu
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China.,2The Forth Clinical School of Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China.,2The Forth Clinical School of Nanjing Medical University, Nanjing, China
| | - Xun Sun
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China.,2The Forth Clinical School of Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China
| | - Yang Wu
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China
| | - Junying Zhang
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China
| | - Hui Zhang
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China.,2The Forth Clinical School of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China
| | - Jifeng Feng
- 1Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Baiziting42, 210009 Nanjing, China
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17
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Effects and Mechanism of lncRNA CRNDE on Sepsis-Induced Acute Kidney Injury. Anal Cell Pathol (Amst) 2020; 2020:8576234. [PMID: 32399391 PMCID: PMC7211233 DOI: 10.1155/2020/8576234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/19/2020] [Accepted: 03/14/2020] [Indexed: 11/26/2022] Open
Abstract
Objective To investigate the effects of lncRNA CRNDE on sepsis-associated acute kidney injury in the human kidney 2 cell line and explore the potential mechanisms. Methods HK-2 cells were treated with lipopolysaccharides to induce injuries. The expression of CRNDE and miR-146a in HK-2 cells were altered by a transient transfection assay. Cell apoptosis was detected by a flow cytometry assay, and the levels of inflammatory cytokines including TNF-α, IL-6, IL-8, and IL-1β were assessed by ELISA. Furthermore, western blot analysis was performed to detect the expression levels of TLR4/NF-κB pathway-related proteins. And a luciferase reporter gene assay was used to verify if miR-146a was the target of CRNDE. Results LPS treatment increased CRNDE expression in HK-2 cells. CRNDE overexpression enhanced cell injuries in HK-2 cells significantly increasing inflammatory cytokine levels, including TNF-α, IL-6, IL-8, and IL-1β, and cell apoptosis. In addition, CRNDE overexpression further activated the TLR4/NF-κB pathways in HK-2 cells. Inversely, opposite results were observed in the miR-146a mimic treatment group, and the miR-146a inhibitor could reverse the protein expression changes of TLR4/NF-κB in the si-CRNDE and LPS treatment group. Conclusion This study demonstrated that CRNDE overexpression could activate the TLR4/NF-κB signaling pathway by regulating miR-146a, which accelerated LPS-induced inflammation and apoptosis in HK-2 cells.
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18
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Tang X, Wang T, Qiu C, Zheng F, Xu J, Zhong B. Long Non-Coding RNA (lncRNA) CRNDE Regulated Lipopolysaccharides (LPS)-Induced MRC-5 Inflammation Injury Through Targeting MiR-141. Med Sci Monit 2020; 26:e920928. [PMID: 32317619 PMCID: PMC7191950 DOI: 10.12659/msm.920928] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background Pneumonia is a common disease with high morbidity and even death. In our country, pneumonia is the leading cause of child death. Therefore, research on the pathogenesis of pneumonia can help improve the treatment of pneumonia. Long non-coding RNA (lncRNA) is an important regulator of disease development, and its regulatory mechanism is closely related to cellular processes. However, the function and regulatory network of lncRNA is not fully elucidated in pneumonia. Material/Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to detect the expression of CRNDE and miR-141 in lipopolysaccharides (LPS)-induced MRC-5 cells and pneumonia tissues. MTT (3-(4,5-dimethylthiazol-2-yl)-2 5-diphenyl-2-tetrazolium) assay was used to assess cell proliferation. Flow cytometry assay was performed to detect cell apoptosis in LPS-induced MRC-5 cells. Enzyme-linked immunosorbent assay and western blot were used to measure the levels of interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α, respectively. In addition, luciferase reporter assay and RNA immunoprecipitation (RIP) assay were applied to prove the relationship between CRNDE and miR-141. Results In this study, we found that CRNDE expression was induced in LPS-induced MRC-5 cells and pneumonia tissues. Moreover, miR-141 expression was low in LPS-induced MRC-5 cells and was verified was a target miRNA of CRNDE by using luciferase reporter assay and RIP assay. The downregulation of CRNDE and upregulation of miR-141 promoted cell viability, inhibited cell apoptosis, as well as decreased the levels of IL-1β, IL-6, and TNF-α. Moreover, we demonstrated that si-CRNDE transfection increased cell viability and suppressed cell apoptosis and the levels of IL-1β, IL-6, and TNF-α, which were alleviated by anti-miR-141 transfection in LPS-induced MRC-5 cells. Conclusions In this study, we found that downregulation of CRNDE and upregulation of miR-141 inhibited cell apoptosis and inflammation response and promoted cell viability in LPS-induced MRC-5 cells. Low CRNDE expression increased cell growth and suppressed inflammation response, which was impaired by inhibition of miR-141. These results suggested that a novel therapeutic target was found in pneumonia treatment.
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Affiliation(s)
- Xingping Tang
- Department of Respiratory Medicine, Yidu Central Hospital of Weifang, Qingzhou, Shandong, China (mainland)
| | - Ting Wang
- Department of Respiratory Medicine, Yidu Central Hospital of Weifang, Qingzhou, Shandong, China (mainland)
| | - Caihong Qiu
- Department of Respiratory Medicine, Yidu Central Hospital of Weifang, Qingzhou, Shandong, China (mainland)
| | - Fangfang Zheng
- Department of Pediatrics, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jiao Xu
- Department of Respiratory Medicine, Affiliated Wujin Hospital of Jiangsu University, Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China (mainland)
| | - Beilong Zhong
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
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19
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Li Y, Song J, Xie Z, Liu M, Sun K. Long noncoding RNA colorectal neoplasia differentially expressed alleviates sepsis-induced liver injury via regulating miR-126-5p. IUBMB Life 2020; 72:440-451. [PMID: 32031750 DOI: 10.1002/iub.2230] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/04/2020] [Indexed: 02/06/2023]
Abstract
In this study, we intended to determine the detailed function and mechanism of long noncoding RNA (lncRNA) colorectal neoplasia differentially expressed (CRNDE) in liver injury induced by sepsis. Cecal ligation and perforation (CLP) models were adopted to induce sepsis in vivo with rats, and hepatic epithelial cells L02 were treated with lipopolysaccharide (LPS) to mimic sepsis in vitro. Enzyme-linked immunosorbent assay was conducted to detect the levels of tumor necrosis factor (TNF-α), interleukin-6 (IL-6), interleukin-10 (IL-10), and interferon-γ (IFN-γ) in the serum of rats. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to measure the expressions of CRNDE and microRNA-126-5p (miR-126-5p). Flow cytometry analysis and Cell Counting Kit-8 (CCK-8) method were carried out followed by the up- or downregulation of CRNDE and miR-126-5p to monitor the proliferation and apoptosis of L02 cells, respectively. Western blot was then applied to determine the expressions of cysteinyl aspartate specific proteinase 3 (caspase 3), poly(ADP-ribose)polymerase (PARP), cytochrome c, and BCL2-like 2 (BCL2L2). The interactions between CRNDE with miR-126-5p and miR-126-5p with BCL2L2 were determined through bioinformatics, qRT-PCR, dual luciferase reporter assay, and RNA immunoprecipitation assay. CRNDE was significantly decreased in liver tissues and hepatic cells in sepsis models. Upregulation of CRNDE promoted the viability of L02 cells and inhibited their apoptosis, while downregulation of CRNDE had opposite effects. The expression of CRNDE in liver tissues of septic rats was correlated with the expression miR-126-5p. It was also demonstrated that the transfection of miR-126-5p mimics reversed the inhibitory effect induced by CRNDE on apoptosis of L02 cells. CRNDE could specifically bind to miR-126-5p and reduce its expression, in turn promote the expression of BCL2L2. Additionally, CRNDE overexpression in rats ameliorated liver injury induced by sepsis. Downregulated CRNDE aggravates hepatic injury via regulating miR-126-5p and BCL2L2 during sepsis.
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Affiliation(s)
- Yang Li
- Department of Emergency, Minhang Hospital, Fudan University, Shanghai, China
| | | | - Zichen Xie
- Department of Emergency, Minhang Hospital, Fudan University, Shanghai, China
| | - Mei Liu
- Department of Emergency, Minhang Hospital, Fudan University, Shanghai, China
| | - Keyu Sun
- Department of Emergency, Minhang Hospital, Fudan University, Shanghai, China
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20
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Guardia GDA, Correa BR, Araujo PR, Qiao M, Burns S, Penalva LOF, Galante PAF. Proneural and mesenchymal glioma stem cells display major differences in splicing and lncRNA profiles. NPJ Genom Med 2020; 5:2. [PMID: 31969990 PMCID: PMC6965107 DOI: 10.1038/s41525-019-0108-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Therapy resistance and recurrence in high-grade gliomas are driven by their populations of glioma stem cells (GSCs). Thus, detailed molecular characterization of GSCs is needed to develop more effective therapies. We conducted a study to identify differences in the splicing profile and expression of long non-coding RNAs in proneural and mesenchymal GSC cell lines. Genes related to cell cycle, DNA repair, cilium assembly, and splicing showed the most differences between GSC subgroups. We also identified genes distinctly associated with survival among patients of mesenchymal or proneural subgroups. We determined that multiple long non-coding RNAs with increased expression in mesenchymal GSCs are associated with poor survival of glioblastoma patients. In summary, our study established critical differences between proneural and mesenchymal GSCs in splicing profiles and expression of long non-coding RNA. These splicing isoforms and lncRNA signatures may contribute to the uniqueness of GSC subgroups, thus contributing to cancer phenotypes and explaining differences in therapeutic responses.
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Affiliation(s)
- Gabriela D A Guardia
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Bruna R Correa
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil.,4Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003 Catalonia Spain
| | - Patricia Rosa Araujo
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Mei Qiao
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Suzanne Burns
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA.,Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Pedro A F Galante
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
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21
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Wang Y, Xu Z, Yue D, Zeng Z, Yuan W, Xu K. Linkage of lncRNA CRNDE sponging miR-181a-5p with aggravated inflammation underlying sepsis. Innate Immun 2019; 26:152-161. [PMID: 31604377 PMCID: PMC7016407 DOI: 10.1177/1753425919880946] [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] [Indexed: 12/21/2022] Open
Abstract
This investigation was performed to verify whether lncRNA CRNDE sponging miR-181a-5p was involved with sepsis-relevant inflammatory dysfunctions. Aggregately 136 sepsis patients and 151 healthy people were recruited, and their fasting peripheral blood was gathered to detect expressions of CRNDE and miR-181a-5p. In addition, THP-1 cells were transfected with si-CRNDE, miR-181a-5p mimic, pcDNA3.1-TLR4 and si-TLR4, and then sepsis-specific inflammatory cytokines within the cells were quantified. The sponging relationships between CRNDE and miR-181a-5p, as well as between miR-181a-5p and TLR4, were ascertained by means of luciferase reporter gene assay. The experimental results revealed that over-expressed CRNDE and under-expressed miR-181a-5p were associated with shortened lifespan of sepsis patients. Mechanically, si-CRNDE-1 and miR-181a-5p mimic were able to reverse the promoting effects of LPS on production of NF-kB, TNF-α, IL-1β and IL-6 by THP-1 cells. Moreover, the expressional change of miR-181a-5p in THP-1 cells was in part owing to its being sponged by CRNDE. Lastly, TLR4, subjected to targeted modification of miR-181a-5p, was capable of disturbing the contribution of CRNDE and miR-181a-5p to THP-1 cells’ release of NF-kB, TNF-α, IL-1β and IL-6. Collectively, the CRNDE/miR-181a-5p/TLR4 axis seemed to have potential in modifying sepsis-related inflammatory pathogenesis, which offered a direction for sepsis diagnosis and treatment.
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Affiliation(s)
- Yijun Wang
- Department of Emergency Medicine, Chenzhou NO.1 People's Hospital, Chenzhou, Hunan Province, P. R. China
| | - Ziqiang Xu
- Department of Emergency Medicine, Chenzhou NO.1 People's Hospital, Chenzhou, Hunan Province, P. R. China
| | - Dongyou Yue
- Department of Emergency Medicine, Chenzhou NO.1 People's Hospital, Chenzhou, Hunan Province, P. R. China
| | - Zhenhua Zeng
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, P. R. China
| | - Weijie Yuan
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P. R. China
| | - Ke Xu
- Department of Critical Care Medicine, Chenzhou NO.1 People's Hospital, Chenzhou, Hunan Province, P. R. China
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Yi M, Dai X, Li Q, Xu X, Chen Y, Wang D. Downregulated lncRNA CRNDE contributes to the enhancement of nerve repair after traumatic brain injury in rats. Cell Cycle 2019; 18:2332-2343. [PMID: 31345079 PMCID: PMC6738523 DOI: 10.1080/15384101.2019.1647024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Objective: Long non-coding RNAs (lncRNAs) have recently been demonstrated to be involved in craniocerebral disease, but their expression in traumatic brain injury (TBI) is still unearthed. Therefore, we aimed to elucidate the effect of lncRNA CRNDE on TBI. Methods: Firstly, CRNDE expression was determined in serum of TBI patients and healthy controls. The TBI rat model was established based on Feeney’s freefall impact method. The modeled rats were injected with siRNA against CRNDE, and the rats’ neurobehavioral function were measured. Besides, expression of inflammatory factors, size, shape and number of hippocampal neurons, neuron apoptosis, Beclin I, LC3-I, LC3-II, glial fibrillary acidic protein (GFAP), BrdU, nerve growth factor (NGF), nestin, and neuronal nuclei (NeuN) expression were detected through different methods. Results: In TBI, CRNDE was found to be upregulated. Downregulated CRNDE improved neurobehavioral function, repressed expression of neuroinflammatory factors, elevated number of Nissl bodies, as well as restricted neuronal apoptosis and autophagy in TBI rats. Besides, downregulated CRNDE also promoted expression of GFAP, BrdU, NGF, nestin, and NeuN, thus induced the differentiation of neurons and the directional growth and regeneration of nerve fibers. Conclusion: Altogether, we found that silencing of CRNDE might be able to promote the nerve repair after TBI in rats.
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Affiliation(s)
- Min Yi
- Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University , Changsha , PR China
| | - Xingping Dai
- Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University , Changsha , PR China
| | - Qiuxia Li
- Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University , Changsha , PR China
| | - Xia Xu
- Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University , Changsha , PR China
| | - Yanyi Chen
- Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University , Changsha , PR China
| | - Dongsheng Wang
- Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University , Changsha , PR China
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23
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Yang F, Li XF, Cheng LN, Li XL. Long non-coding RNA CRNDE promotes cell apoptosis by suppressing miR-495 in inflammatory bowel disease. Exp Cell Res 2019; 382:111484. [PMID: 31251902 DOI: 10.1016/j.yexcr.2019.06.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/04/2019] [Accepted: 06/24/2019] [Indexed: 02/09/2023]
Abstract
OBJECTIVE This article aims to investigate the mechanism of microRNA-495 (miR-495) and long non-coding RNA CRNDE on the apoptosis of colonic epithelial cells in inflammatory bowel diseases (IBDs). METHODS The mouse model of IBD was induced by dextran sulfate sodium (DSS), and human colonic epithelial cell lines (HT-29, LOVO, and Caco-2) were treated with DSS, and received cell transfection. RNA interference was used to down-regulate CRNDE expression. RESULTS CRNDE and SOCS1 were highly expressed, but miR-495 was lowly expressed in the DSS-induced colitis tissues and colonic epithelial cell lines. Interference of CRNDE inhibited cell apoptosis of DSS-induced colonic epithelial cells. The interaction between CRNDE and miR-495 was confirmed by RNA immunoprecipitation and RNA pull-down assay. The target relationship between miR-495 and SOCS1 was confirmed by the luciferase reporter assay. CRNDE promoted DSS-induced colonic epithelial cell apoptosis via miR-495/SOCS1. CRNDE interference in DSS-induced colitis mouse model alleviated clinical manifestations of IBD. CONCLUSIONS Our findings demonstrated that CRNDE promoted DSS-induced colonic epithelial cell apoptosis via suppressing miR-495 and increasing SOCS1, indicating CRNDE as a novel target of treating IBD.
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Affiliation(s)
- Fan Yang
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Xiao-Fang Li
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Li-Na Cheng
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Xiu-Ling Li
- Department of Gastroenterology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
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24
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Zhou Y, Wang R, Xu T, Xie P, Zhang Y, Zhang A, Wang X, Yang C, Yang H, Zhu S. Prognostic Value of Long Noncoding RNA CRNDE as a Novel Biomarker in Solid Cancers: An Updated Systematic Review and Meta-Analysis. J Cancer 2019; 10:2386-2396. [PMID: 31258743 PMCID: PMC6584336 DOI: 10.7150/jca.31088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/13/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Long noncoding RNA colorectal neoplasia differentially expressed (CRNDE) has been reported to exhibit a potential oncogenic role in the development of human cancers. However, the clinical value of CRNDE expression in various cancers still remains unclear. Herein, we conducted a meta-analysis to investigate the association between CRNDE and clinical outcomes in solid cancers. Methods: A systematic search was performed though the PubMed, EMBASE, Web of Science, Ovid, Cochrane library, CNKI and WanFang databases for eligible studies on clinical values of CRNDE in solid cancers. The pooled hazard ratios (HRs) or odd ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate the link between CRNDE and clinical outcomes. Results: A total of 3690 patients from 20 studies (including 2 studies have 2 cohorts, respectively) were included. The results suggested that elevated CRNDE expression predicted a poor overall survival (OS) for in 13 types of solid cancers (HR=1.46, 95% CI: 1.33-1.58, P<0.001) with no heterogeneity (I2=21.8%, P=0.19). Subgroup analysis indicated a significant association between high CRNDE expression and shorter OS in the studies with digestive system cancers (HR=1.42, 95% CI: 1.28-1.55, P<0.001), qRT-PCR method (HR=1.45, 95% CI: 1.30-1.59, P<0.001), sample size >100 (HR=1.44, 95% CI: 1.32-1.57, P<0.001), and NOS>7 (HR= 1.50, 95% CI: 1.23-1.78, P<0.001). Furthermore, the pooled results showed that CRNDE was an independent prognostic factor for OS in cancer patients (HR=1.37, 95% CI: 1.22-1.52, P<0.001). In addition, we also revealed that CRNDE was positively related to tumor size (OR=2.10, 95%CI: 1.68-2.63, P<0.001), TNM stage (OR=2.86, 95%CI: 2.29-3.56, P<0.001), lymph node metastasis (LNM) (OR=3.21, 95%CI: 2.01-5.13, P<0.001), and distant metastasis (OR=4.36, 95%CI: 2.36-8.07, P<0.001). Although the probable evidences of publication bias were found in the studies with OS, tumor size, TNM stage or LNM, the trim and fill analysis confirmed the reliability of these results was not affected. Conclusion: Elevated CRNDE expression was associated with larger tumor size, advanced TNM stage, worse LNM and distant metastasis, and shorter OS, suggesting that CRNDE may act as an independent prognostic biomarker in solid cancers.
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Affiliation(s)
- Yu Zhou
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Institute of Laboratory Medicine, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Rui Wang
- Organ Transplant Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Tian Xu
- Organ Transplant Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Ping Xie
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Institute of Laboratory Medicine, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Yun Zhang
- Organ Transplant Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Aifeng Zhang
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaojie Wang
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chong Yang
- Organ Transplant Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Hongji Yang
- Organ Transplant Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Shikai Zhu
- Organ Transplant Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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25
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Dai M, Li S, Qin X. Colorectal neoplasia differentially expressed: a long noncoding RNA with an imperative role in cancer. Onco Targets Ther 2018; 11:3755-3763. [PMID: 29988699 PMCID: PMC6029599 DOI: 10.2147/ott.s162754] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Colorectal neoplasia differentially expressed (CRNDE), as a long noncoding RNA (lncRNA), has attracted increasing attention in recent years and has been documented to be at abnormally high expression in various types of cancer, such as colorectal cancer, glioma, hepatocellular carcinoma, lung cancer, and breast cancer. It could not only be used as a clinical biomarker for the early diagnosis and prognosis evaluation in a variety of cancers but also promote the development and progress of various tumor cells. Moreover, it is involved in the targeting regulation of multiple microRNAs and the activation/inhibition of multiple signaling pathways. In this review, we presented a systematic summary of the potential carcinogenicity and clinical value of CRNDE in the current evidence, so as to provide reference for early diagnosis, prognosis evaluation, and targeted therapy of various clinical cancers.
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Affiliation(s)
- Meiyu Dai
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China,
| | - Shan Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China,
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China,
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26
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Knockdown CRNDE alleviates LPS-induced inflammation injury via FOXM1 in WI-38 cells. Biomed Pharmacother 2018; 103:1678-1687. [PMID: 29864958 DOI: 10.1016/j.biopha.2018.04.192] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 04/25/2018] [Accepted: 04/29/2018] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Pneumonia is the leading global cause of mortality and morbidity in children and elderly people worldwide. The lncRNA colorectal neoplasia differentially expressed (CRNDE) plays an important role in the human development and disease progression. The present study was aimed to investigate the effect of CRNDE on LPS-induced injuries in WI-38 cells and explore the potential mechanism. METHODS WI-38 cells were treated with LPS to induce injuries. The expression of CRNDE and FOXM1 in WI-38 cells were altered by transient transfection assay. Cell viability was measured by CCK-8 assay and cell apoptosis was detected by flow cytometry assay and western blot. The levels of inflammatory cytokines were assessed by ELISA and western blot. Furthermore, western blot analysis was performed to detect the expression levels of NF-κB and JAK/STAT pathway-related proteins. RESULTS LPS exposure induced cell injuries and increased CRNDE expression in WI-38 cells. CRNDE overexpression enhanced cell injuries in WI-38 cells with significantly reducing cell viability, increasing cell apoptosis and inflammatory cytokines levels. In addition, CRNDE overexpression further activated the NF-κB and JAK/STAT pathways in LPS-injured WI-38 cells. Inversely, opposite results were observed in CRNDE inhibition treatment group. Interestingly, FOXM1 was up-regulated by CRNDE and FOXM1 silence blocked the effect of CRNDE overexpression in cell apoptosis, inflammation and activation of NF-κB and JAK/STAT signaling pathways. CONCLUSION This study demonstrated that CRNDE overexpression accelerated LPS-induced apoptosis and inflammation via up-regulation of FOXM1 in WI-38 cells.
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27
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Kim T, Croce CM. Long noncoding RNAs: Undeciphered cellular codes encrypting keys of colorectal cancer pathogenesis. Cancer Lett 2018; 417:89-95. [PMID: 29306015 PMCID: PMC5825189 DOI: 10.1016/j.canlet.2017.12.033] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs are non-protein coding transcripts longer than 200 nucleotides in length. By the advance in genetic and bioinformatic technologies, the new genomic landscape including noncoding transcripts has been revealed. Despite their non-capacity to be translated into proteins, lncRNAs have a versatile functions through various mechanisms interacting with other cellular molecules including DNA, protein, and RNA. Recent research interest and endeavor have identified the functional role of lncRNAs in various diseases including cancer. Colorectal cancer (CRC) is not only one of the most frequent cancer but also one of the cancer types with remarkable achievements in lncRNA research. Of the numerous notable lncRNAs identified and characterized in CRC, we will focus on key lncRNAs with the high potential as CRC-specific biomarkers in this review.
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Affiliation(s)
- Taewan Kim
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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28
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Zhang J, Yin M, Peng G, Zhao Y. CRNDE: An important oncogenic long non-coding RNA in human cancers. Cell Prolif 2018; 51:e12440. [PMID: 29405523 DOI: 10.1111/cpr.12440] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/12/2017] [Indexed: 01/03/2023] Open
Abstract
Aberrant overexpression of long non-coding RNA CRNDE (Colorectal Neoplasia Differentially Expressed) is confirmed in various human cancers, which is correlated with advanced clinicopathological features and poor prognosis. CRNDE promotes cancer cell proliferation, migration and invasion, and suppresses apoptosis in complicated mechanisms, which result in the initialization and development of human cancers. In this review, we provide an overview of the oncogenic role and potential clinical applications of CRNDE.
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Affiliation(s)
- Jiaming Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minuo Yin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Peng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchao Zhao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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29
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Li XQ, Chen FS, Tan WF, Fang B, Zhang ZL, Ma H. Elevated microRNA-129-5p level ameliorates neuroinflammation and blood-spinal cord barrier damage after ischemia-reperfusion by inhibiting HMGB1 and the TLR3-cytokine pathway. J Neuroinflammation 2017; 14:205. [PMID: 29061187 PMCID: PMC5654055 DOI: 10.1186/s12974-017-0977-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/03/2017] [Indexed: 02/06/2023] Open
Abstract
Background Ischemia-reperfusion (IR) affects microRNA (miR) expression and causes substantial inflammation. Multiple roles of the tumor suppressor miR-129-5p in cerebral IR have recently been reported, but its functions in the spinal cord are unclear. Here, we investigated the role of miR-129-5p after spinal cord IR, particularly in regulating high-mobility group box-1 (HMGB1) and the Toll-like receptor (TLR)-3 pathway. Methods Ischemia was induced via 5-min occlusion of the aortic arch. The relationship between miR-129-5p and HMGB1 was elucidated via RT-PCR, western blotting, and luciferase assays. The cellular distribution of HMGB1 was determined via double immunofluorescence. The effect of miR-129-5p on the expression of HMGB1, TLR3, and downstream cytokines was evaluated using synthetic miRs, rHMGB1, and the TLR3 agonist Poly(I:C). Blood-spinal cord barrier (BSCB) permeability was examined by measuring Evans blue (EB) dye extravasation and the water content. Results The temporal miR-129-5p and HMGB1 expression profiles and luciferase assay results indicated that miR-129-5p targeted HMGB1. Compared with the Sham group, the IR group had higher HMGB1 immunoreactivity, which was primarily distributed in neurons and microglia. Intrathecal injection of the miR-129-5p mimic significantly decreased the HMGB1, TLR3, interleukin (IL)-1β and tumor necrosis factor (TNF)-α levels and the double-labeled cell count 48 h post-surgery, whereas rHMGB1 and Poly(I:C) reversed these effects. Injection of miR-129-5p mimic preserved motor function and prevented BSCB leakage based on increased Basso Mouse Scale scores and decreased EB extravasation and water content, whereas injection rHMGB1 and Poly(I:C) aggravated these injuries. Conclusions Increasing miR-129-5p levels protect against IR by ameliorating inflammation-induced neuronal and BCSB damage by inhibiting HMGB1 and TLR3-associated cytokines.
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Affiliation(s)
- Xiao-Qian Li
- Department of Anesthesiology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, 110001, China
| | - Feng-Shou Chen
- Department of Anesthesiology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, 110001, China
| | - Wen-Fei Tan
- Department of Anesthesiology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, 110001, China
| | - Bo Fang
- Department of Anesthesiology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, 110001, China
| | - Zai-Li Zhang
- Department of Anesthesiology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, 110001, China
| | - Hong Ma
- Department of Anesthesiology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, 110001, China.
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