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Wang T, Chen Y, Liu Z, Zhou J, Li N, Shan Y, He Y. Long noncoding RNA Glis2 regulates podocyte mitochondrial dysfunction and apoptosis in diabetic nephropathy via sponging miR-328-5p. J Cell Mol Med 2024; 28:e18204. [PMID: 38506068 PMCID: PMC10951868 DOI: 10.1111/jcmm.18204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Podocyte apoptosis exerts a crucial role in the pathogenesis of DN. Recently, long noncoding RNAs (lncRNAs) have been gradually identified to be functional in a variety of different mechanisms associated with podocyte apoptosis. This study aimed to investigate whether lncRNA Glis2 could regulate podocyte apoptosis in DN and uncover the underlying mechanism. The apoptosis rate was detected by flow cytometry. Mitochondrial membrane potential (ΔΨM) was measured using JC-1 staining. Mitochondrial morphology was detected by MitoTracker Deep Red staining. Then, the histopathological and ultrastructure changes of renal tissues in diabetic mice were observed using periodic acid-Schiff (PAS) staining and transmission electron microscopy. We found that lncRNA Glis2 was significantly downregulated in high-glucose cultured podocytes and renal tissues of db/db mice. LncRNA Glis2 overexpression was found to alleviate podocyte mitochondrial dysfunction and apoptosis. The direct interaction between lncRNA Glis2 and miR-328-5p was confirmed by dual luciferase reporter assay. Furthermore, lncRNA Glis2 overexpression alleviated podocyte apoptosis in diabetic mice. Taken together, this study demonstrated that lncRNA Glis2, acting as a competing endogenous RNA (ceRNA) of miRNA-328-5p, regulated Sirt1-mediated mitochondrial dysfunction and podocyte apoptosis in DN.
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Affiliation(s)
- Ting Wang
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Yanxia Chen
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Zhihong Liu
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Jing Zhou
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Na Li
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Yue Shan
- Department of EndocrinologySecond Hospital of Hebei Medical UniversityShijiazhuangHebeiP.R. China
| | - Yinxi He
- Department of Orthopaedic TraumaThe Third Hospital of ShijiazhuangShijiazhuangHebeiP.R. China
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Huang X, Huang J, Huang Q, Zhou S. A ten long noncoding RNA-based prognostic risk model construction and mechanism study in the basal-like immune-suppressed subtype of triple-negative breast cancer. Transl Cancer Res 2023; 12:3653-3671. [PMID: 38193005 PMCID: PMC10774046 DOI: 10.21037/tcr-23-147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/21/2023] [Indexed: 01/10/2024]
Abstract
Background According to the Fudan University Shanghai Cancer Center (FUSCC) system, triple-negative breast cancer (TNBC) is divided into four stable subtypes: (I) luminal androgen receptor, (II) immunomodulatory, (III) basal-like immune-suppressed (BLIS), and (IV) mesenchymal-like. However, the treatment outcomes of the corresponding targeted therapies are unsatisfactory, especially for the BLIS subtype. Therefore, we aimed to identify the key long noncoding RNAs (lncRNAs) to construct a prognostic model for BLIS subtype and discover potential targets to explore potential therapeutic strategies in this study. Methods The FUSCC cohort was used to establish a prognostic risk model via least absolute shrinkage and selection operator (LASSO) and Cox regression analysis. The Cancer Genome Atlas (TCGA) cohort was then used to evaluate and verify the model. To understand the functional aspects of the model, functional, immune landscape, mutation, and drug sensitivity analyses were performed between high- and low-risk groups. Results Ten prognostic-related lncRNAs identified, including C5ORF66-AS2, DIO3OS, FZD10-DT, LINC00393, LNC-ERI1-32, LNC-FOXO1-2, LNC-SPARCL1-1, HCG23, LNC-MMD-4 and LNC-TMEM106C-6, were selected for risk score system construction. The results showed that the model constructed could divide the patients with BLIS subtype into two groups of high and low risk, and patients with higher risk scores had shorter recurrence-free survival. In addition, drug sensitivity analysis identified 3 compounds, including BMS-754807, cytochalasin b, and linifanib, that could have a potential therapeutic effect on patients with the BLIS subtype. Conclusions The risk prognosis model showed good prognostic value for the BLIS subtype patients, and the ten lncRNAs may be potential therapeutic targets.
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Affiliation(s)
- Xiaoying Huang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jinlong Huang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qiuyan Huang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Shihao Zhou
- College of Life Science and Technology, Jinan University, Guangzhou, China
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Stacey VM, Kõks S. Genome-Wide Differential Transcription of Long Noncoding RNAs in Psoriatic Skin. Int J Mol Sci 2023; 24:16344. [PMID: 38003532 PMCID: PMC10671291 DOI: 10.3390/ijms242216344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) may contribute to the formation of psoriatic lesions. The present study's objective was to identify long lncRNA genes that are differentially expressed in patient samples of psoriasis through computational analysis techniques. By using previously published RNA sequencing data from psoriatic and healthy patients (n = 324), we analysed the differential expression of lncRNAs to determine transcripts of heightened expression. We computationally screened lncRNA transcripts as annotated by GENCODE across the human genome and compared transcription in psoriatic and healthy samples from two separate studies. We observed 54 differentially expressed genes as seen in two independent datasets collected from psoriasis and healthy patients. We also identified the differential expression of LINC01215 and LINC1206 associated with the cell cycle pathway and psoriasis pathogenesis. SH3PXD2A-AS1 was identified as a participant in the STAT3/SH3PXD2A-AS1/miR-125b/STAT3 positive feedback loop. Both the SH3PXD2A-AS1 and CERNA2 genes have already been recognised as part of the IFN-γ signalling pathway regulation. Additionally, EPHA1-AS1, CYP4Z2P and SNHG12 gene upregulation have all been previously linked to inflammatory skin diseases. Differential expression of various lncRNAs affects the pathogenesis of psoriasis. Further characterisation of lncRNAs and their functions are important for developing our understanding of psoriasis.
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Affiliation(s)
- Valerie M. Stacey
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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Kyrgiafini MA, Sarafidou T, Mamuris Z. The Role of Long Noncoding RNAs on Male Infertility: A Systematic Review and In Silico Analysis. Biology (Basel) 2022; 11:biology11101510. [PMID: 36290414 PMCID: PMC9598197 DOI: 10.3390/biology11101510] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022]
Abstract
Male infertility is a complex disorder affecting many couples worldwide. Long noncoding RNAs (lncRNAs) regulate important cellular processes; however, a comprehensive understanding of their role in male infertility is limited. This systematic review investigates the differential expressions of lncRNAs in male infertility or variations in lncRNA regions associated with it. The PRISMA guidelines were used to search Pubmed and Web of Science (1 June 2022). Inclusion criteria were human participants, patients diagnosed with male infertility, and English language speakers. We also performed an in silico analysis investigating lncRNAs that are reported in many subtypes of male infertility. A total of 625 articles were found, and after the screening and eligibility stages, 20 studies were included in the final sample. Many lncRNAs are deregulated in male infertility, and interactions between lncRNAs and miRNAs play an important role. However, there is a knowledge gap regarding the impact of variants found in lncRNA regions. Furthermore, eight lncRNAs were identified as differentially expressed in many subtypes of male infertility. After in silico analysis, gene ontology (GO) and KEGG enrichment analysis of the genes targeted by them revealed their association with bladder and prostate cancer. However, pathways involved in general in tumorigenesis and cancer development of all types, such as p53 pathways, apoptosis, and cell death, were also enriched, indicating a link between cancer and male infertility. This evidence, however, is preliminary. Future research is needed to explore the exact mechanism of action of the identified lncRNAs and investigate the association between male infertility and cancer.
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Liu Q. The Emerging Landscape of Long Non-Coding RNAs in Wilms Tumor. Front Oncol 2022; 11:780925. [PMID: 35127486 PMCID: PMC8807488 DOI: 10.3389/fonc.2021.780925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/29/2021] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) are transcripts of nucleic acid sequences with a length of more than 200 bp, which have only partial coding capabilities. Recent studies have shown that lncRNAs located in the nucleus or cytoplasm can be used as gene expression regulatory elements due to their important regulatory effects in a variety of biological processes. Wilms tumor (WT) is a common abdominal tumor in children whose pathogenesis remains unclear. In recent years, many specifically expressed lncRNAs have been found in WT, which affect the occurrence and development of WT. At the same time, lncRNAs may have the capacity to become novel biomarkers for the diagnosis and prognosis of WT. This article reviews related research progress on the relationship between lncRNAs and WT, to provide a new direction for clinical diagnosis and treatment of WT.
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Xu J, Liao M. Long noncoding RNA SNHG6 promotes papillary thyroid cancer cells proliferation via regulating miR-186/CDK6 axis. Gland Surg 2021; 10:2935-2944. [PMID: 34804881 DOI: 10.21037/gs-21-586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/16/2021] [Indexed: 11/06/2022]
Abstract
Background Papillary thyroid cancer (PTC) is a common endocrine malignancy, and its incidence rate has been increasing in recent years. Long noncoding RNAs (lncRNAs) participate in cell biological processes through a variety of regulatory ways, and play an essential role in tumor development. Methods This study explored the expression of lncRNA small nucleolar RNA host gene 6 (SNHG6) in PTC by bioinformatics analysis, and quantitative real-time PCR (qRT-PCR). Cell counting kit-8 (CCK-8) assay, colony formation assay, and 5-ethynyl-2'-deoxyuridine (EdU) assay were used to study the effect of SNHG6 on the proliferation of PTC cells. Luciferase reporter gene assay and western blot were used to study the mechanism. Results SNHG6 was highly expressed in PTC tissue samples and cell lines. In vitro, overexpression of SNHG6 promoted the proliferation of PTC cells, while silencing SNHG6 inhibited the proliferation of PTC cells. miR-186 is the downstream target of SNHG6. SNHG6 regulates the proliferation of PTC cells through miR-186. In addition, CDK6 is the target gene of miR-186, which can inhibit the expression of CDK6 protein. SNHG6 can promote the expression of CDK6 by regulating miR-186. Conclusions SNHG6 is highly expressed in PTC and can promote the proliferation of PTC cells by regulating the miR-186/CDK6 axis, which is expected to become a potential therapeutic target for PTC.
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Affiliation(s)
- Jian Xu
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Miaomiao Liao
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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Chen M, Xie Y, Luo Y, Xie Y, Wu N, Peng S, Chen Q. Exosomes-a potential indicator and mediator of cleft lip and palate: a narrative review. Ann Transl Med 2021; 9:1485. [PMID: 34734037 PMCID: PMC8506753 DOI: 10.21037/atm-21-4198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/07/2021] [Indexed: 11/28/2022]
Abstract
Objective This article summarizes the recent literature on noncoding ribonucleic acids (ncRNAs) in relation to cleft lip with or without palate and exosomes and their usage in craniofacial diseases. Background Cleft lip with or without cleft palate (CL/P) is a common congenital malformation with genetic and environmental risk factors that affects numerous children and families. Surgical procedures can correct deformations; however, residual sequelae remain after surgery. Studies exploring the pathogenesis of CL/P are crucial for its early diagnosis and treatment and can inform treatment strategy decisions, etiology searches, and treatment during pregnancy. Recently, research has shown that most disease-related genes are ncRNAs, which are important transcripts in the human transcriptome. ncRNAs include microRNAs, long noncoding RNAs, and circular RNAs. These ncRNAs play essential roles in various pathophysiological processes, including cell proliferation, migration, apoptosis, and epithelial-mesenchymal transition. Previous studies on protein-coding genes have identified a number of genes related to CL/P; however, the pathogenesis of CL/P has not yet been thoroughly explained. Exosomes are vehicles that transfer various bioactive molecules between cells and represent a new method of intercellular communication. Research has shown that exosomes are related to some craniofacial diseases. Methods We searched the PubMed database for recently published English-language articles using the following keywords: “cleft lip with or without palate,” “noncoding RNA,” “exosomes,” and “craniofacial diseases”. We then reviewed the retrieved articles. Conclusions As exosomes serve as cellular communicators and the palate consists of epithelial and mesenchymal cells, communication between the two cell types may affect its formation. Thus, exosomes could represent a new indicator and mediator of CL/P.
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Affiliation(s)
- Meng Chen
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yue Xie
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yarui Luo
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China.,Department of Outpatient, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yimin Xie
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Na Wu
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Shulei Peng
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China.,Department of Sleep Medicine Centre, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Qiang Chen
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
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Ma W, Zhong M, Liu X. Identification of a glycolysis-related lncRNA prognostic signature for clear cell renal cell carcinoma. Biosci Rep 2021; 41:BSR20211451. [PMID: 34402862 DOI: 10.1042/BSR20211451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background: The present study investigated the independent prognostic value of glycolysis-related long noncoding (lnc)RNAs in clear cell renal cell carcinoma (ccRCC). Methods: A coexpression analysis of glycolysis-related mRNAs–long noncoding RNAs (lncRNAs) in ccRCC from The Cancer Genome Atlas (TCGA) was carried out. Clinical samples were randomly divided into training and validation sets. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were performed to establish a glycolysis risk model with prognostic value for ccRCC, which was validated in the training and validation sets and in the whole cohort by Kaplan–Meier, univariate and multivariate Cox regression, and receiver operating characteristic (ROC) curve analyses. Principal component analysis (PCA) and functional annotation by gene set enrichment analysis (GSEA) were performed to evaluate the risk model. Results: We identified 297 glycolysis-associated lncRNAs in ccRCC; of these, 7 were found to have prognostic value in ccRCC patients by Kaplan–Meier, univariate and multivariate Cox regression, and ROC curve analyses. The results of the GSEA suggested a close association between the 7-lncRNA signature and glycolysis-related biological processes and pathways. Conclusion: The seven identified glycolysis-related lncRNAs constitute an lncRNA signature with prognostic value for ccRCC and provide potential therapeutic targets for the treatment of ccRCC patients.
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Liang A, Zhong S, Xi B, Zhou C, Jiang X, Zhu R, Yang Y, Zhong L, Wan D. High expression of PYCARD is an independent predictor of unfavorable prognosis and chemotherapy resistance in glioma. Ann Transl Med 2021; 9:986. [PMID: 34277786 PMCID: PMC8267320 DOI: 10.21037/atm-21-2346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/28/2021] [Indexed: 11/06/2022]
Abstract
Background PYD and CARD domain-containing (PYCARD) was upregulated in TMZ-resistant cell lines and glioma tissue and was correlated with poor prognosis, its role in glioma is unclear known. The aim of this study was to elucidate the relationship between PYCARD and glioma based on Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and Chinese Glioma Genome Atlas (CGGA) databases. Methods Glioma-resistant cells were compared with parental cells based on the GSE53014 and GSE113510 data sets. The relationship between PYCARD, tumor microenvironment, and long noncoding RNAs (lncRNAs) was assessed using logistic regression. Moreover, Kaplan-Meier and Cox regression were used to analyze the relationship between PYCARD expression and survival rate. Gene set enrichment analysis (GSEA) was also used to determine the biological function of PYCARD and lncRNAs. Cell viability and cell migration assays were used to evaluate the ability of cells to migrate and proliferate. Finally, we analyzed the expression patterns of PYCARD genes in a wide range of cancers. Results Elevated expression of PYCARD promoted glioma cell proliferation and migration. PYCARD expression was significantly positively associated with gamma delta T cells but negatively correlated with M2 macrophages in glioblastoma multiforme (GBM). Likewise, PYCARD expression was significantly positively associated with monocytes but negatively associated with activated mast cells in low grade glioma (LGG). We also found that 3 PYCARD-related lncRNAs in GBM and 4 PYCARD-related lncRNAs in LGG had a predictive value for glioma patients. The pan-cancer analysis showed that PYCARD expression was higher in most cancer groups. Conclusions High expression of PYCARD is an independent predictor of unfavorable prognosis and chemotherapy resistance in glioma.
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Affiliation(s)
- Aijun Liang
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Shupeng Zhong
- Department of Oncology, Zhongshan City People's Hospital, Zhongshan, China
| | - Bin Xi
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Chaoyang Zhou
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Xingxing Jiang
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Ronglan Zhu
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Yu Yang
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Liangchen Zhong
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Dengfeng Wan
- Department of Neurosurgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
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Shahmoradi M, Rezvani Z. Functional Prediction of Long Noncoding RNAs in Cutaneous Melanoma Using a Systems Biology Approach. Bioinform Biol Insights 2021; 15:1177932220988508. [PMID: 33613027 PMCID: PMC7868446 DOI: 10.1177/1177932220988508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/20/2020] [Indexed: 11/17/2022] Open
Abstract
Cutaneous melanoma is the most aggressive type of skin cancer which its incidence has significantly increased in recent years worldwide. Thus, more investigations are required to identify the underlying mechanisms of melanoma malignant transformation and metastasis. In this context, long noncoding RNAs (lncRNAs) are a new type of noncoding transcripts that their dysregulations are associated with almost all cancers including melanoma. However, the precise functional roles of most of the significantly altered lncRNAs in melanoma have not yet been fully inspected. In this study, a comprehensive list of lncRNAs was interrogated across cutaneous melanoma samples to identify the significantly altered/dysregulated lncRNAs. To this end, lncRNAs were filtered in several steps and the selected lncRNAs projected to a bioinformatic and systems biology analysis using several publicly available databases and tools such as GEPIA and cBioPortal. According to our results, 30 lncRNAs were notably altered/dysregulated in cutaneous melanoma most of which were co-expressed with each other. Also, co-expression/alteration and differential expression analyses led to the selection of 12 out of these 30 lncRNAs as cutaneous melanoma key lncRNAs. Furthermore, functional demonstrated that these 12 lncRNAs might be involved in melanoma-relevant biological processes and pathways. In addition, the end result of our analyses demonstrated that these lncRNAs are associated with the clinicopathological features of melanoma patients. These 12 lncRNAs need to be further investigated in future studies to characterize their exact roles in melanoma development and to identify their potential for being used as drug targets and/or biomarkers for cutaneous melanoma.
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Affiliation(s)
- Mozhdeh Shahmoradi
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Zahra Rezvani
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
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Li C, Liu Y, Qin J, Liu Y, Ma L, Zhang S, Wang J, Wang S. Profiles of differentially expressed long noncoding RNAs and messenger RNAs in the myocardium of septic mice. Ann Transl Med 2021; 9:199. [PMID: 33708826 PMCID: PMC7940873 DOI: 10.21037/atm-20-3830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Sepsis is the primary cause of mortality in the intensive care unit (ICU), mainly due to sepsis-induced dysfunction of essential organs such as the heart and lungs. This study investigated the myocardium's epigenetic characterization from septic mice to identify potential treatment targets for septic myocardial dysfunction. Methods Cecal ligation and puncture (CLP) was used to induce sepsis in male C57BL/6 mice. Hearts were collected 24 h after surgery to determine the expression profiles of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray. To validate the reliability of microarray results, we randomly chose six differentially expressed lncRNAs for qRT-PCR. Functional mapping of differentially expressed mRNAs was annotated with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses; lncRNA-mRNA co-expression network was constructed to reveal connections between lncRNAs and mRNAs. Results Microarray analysis indicated that 1,568 lncRNAs and 2,166 mRNAs were differentially expressed in the myocardium from septic mice, which was further confirmed by qRT-PCR. KEGG pathway analysis showed that numerous differentially expressed mRNAs were relevant to tumor necrosis factor (TNF) and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathways. Moreover, according to the lncRNA-mRNA co-expression network constructed by the above six lncRNAs and their interacting mRNAs, the co-expression network profiles had 57 network nodes and 134 connections, including 76 positive interactions and 58 negative interactions. Conclusions In mouse hearts, sepsis resulted in differential expression of lncRNAs and mRNAs related to TNF and PI3K-Akt signaling pathways, suggesting that lncRNAs and their interacting mRNAs may participate in the pathogenesis of septic myocardial dysfunction by regulating TNF and PI3K-Akt signaling pathways.
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Affiliation(s)
- Chengbao Li
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Yongchao Liu
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jing Qin
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Yuhao Liu
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Lijie Ma
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Shouqin Zhang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Junjie Wang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Sheng Wang
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
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Taniue K, Akimitsu N. The Functions and Unique Features of LncRNAs in Cancer Development and Tumorigenesis. Int J Mol Sci 2021; 22:E632. [PMID: 33435206 PMCID: PMC7826647 DOI: 10.3390/ijms22020632] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Over the past decades, research on cancer biology has focused on the involvement of protein-coding genes in cancer development. Long noncoding RNAs (lncRNAs), which are transcripts longer than 200 nucleotides that lack protein-coding potential, are an important class of RNA molecules that are involved in a variety of biological functions. Although the functions of a majority of lncRNAs have yet to be clarified, some lncRNAs have been shown to be associated with human diseases such as cancer. LncRNAs have been shown to contribute to many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein and RNA. Here we describe the literature regarding the biogenesis and features of lncRNAs. We also present an overview of the current knowledge regarding the roles of lncRNAs in cancer from the view of various aspects of cellular homeostasis, including proliferation, survival, migration and genomic stability. Furthermore, we discuss the methodologies used to identify the function of lncRNAs in cancer development and tumorigenesis. Better understanding of the molecular mechanisms involving lncRNA functions in cancer is critical for the development of diagnostic and therapeutic strategies against tumorigenesis.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Cancer Genomics and Precision Medicine, Division of Gastroenterology and Hematology-Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa 078-8510, Hokkaido, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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Wang J, Liu S, Shi J, Liu H, Li J, Zhao S, Yi Z. The Role of lncRNAs in Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells. Curr Stem Cell Res Ther 2020; 15:243-249. [PMID: 31880266 DOI: 10.2174/1574888x15666191227113742] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 02/01/2023]
Abstract
Bone Marrow Mesenchymal Stem Cells (BMSCs) are one of the primary cells found in the bone marrow, and they can differentiate into osteoblasts, chondrocytes, adipocytes and even myoblasts, and are, therefore, considered pluripotent cells. Because of their multipotential differentiation, selfrenewal capability, immunomodulation and other potential activities, BMSCs have become an important source of seed cells for gene therapy, tissue engineering, cell replacement therapy and regenerative medicine. Long non-coding RNA (lncRNA) is an RNA molecule greater than 200 nucleotides in length that is expressed in a variety of species, including animals, plants, yeast, prokaryotes, and viruses, but lacks an apparent open reading frame, and does not have the function of translation into proteins. Many studies have shown that lncRNAs play an important role in the osteogenic differentiation of BMSCs. Here, we describe the role of lncRNAs in the osteogenic differentiation of BMSCs, in order to provide a new theoretical and experimental basis for bone tissue engineering and clinical treatment.
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Affiliation(s)
- Jicheng Wang
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China.,Xi'an Medical University, Xi'an 710068, China
| | - Shizhang Liu
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Jiyuan Shi
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Huitong Liu
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Jingyuan Li
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Song Zhao
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China.,Xi'an Medical University, Xi'an 710068, China
| | - Zhi Yi
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
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14
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Park SA, Kim LK, Kim YT, Heo TH, Kim HJ. Long Noncoding RNA E2F4as Promotes Progression and Predicts Patient Prognosis in Human Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12123626. [PMID: 33287341 PMCID: PMC7761684 DOI: 10.3390/cancers12123626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary LncRNA is a promising biomarker that predicts the prognosis of a variety of cancers, but the important role of E2F4antisense lncRNA in cancer remains unclear. Therefore, we decided to explore the role of E2F4as lncRNA in the blood of an ovarian cancer patient. We found that E2F4as was highly expressed in ovarian cancer patients, and that the higher the expression of E2F4as, the worse the patient’s prognosis. In addition, we observed that downregulation of E2F4as in ovarian cancer cells reduced cell proliferation, invasion and migration, decreased expression of EMT-related genes, and increased apoptosis. These findings suggest that E2F4as may be a predictive biomarker in the blood of ovarian cancer patients, and have shown the potential to promote tumor aggression through EMT-related mechanisms. Abstract (1) Background: LncRNAs could be a promising biomarker to predict the prognosis of various cancers. The significance of E2F4antisense lncRNA remains unclear in cancer. In this study, we examined the expression level of E2F4as in the serum of ovarian cancer patients and the functional role of E2F4as. (2) Methods: Serum samples were obtained from 108 OC patients and 32 normal patients to measure the expression of E2F4as in the serum. Ovarian cancer cells were used to investigate the role of E2F4as in cell proliferation, invasion, migration and apoptosis, and the expression of E2F4as was knocked down using RNA interference. In addition, E2F4as knockdown cell lines were used in in vivo experiments. (3) Results: The expression of E2F4as was significantly higher in the serum of OC patients than in that of control patients (p < 0.05). The knockdown of E2F4as in ovarian cancer cells led to a decrease in cell proliferation, invasion and migration and an increase in apoptosis. E2F4as knockdown also reduced the expression of epithelium–mesenchymal metastasis (EMT) genes. (4) Conclusion: These findings highlight the clinical significance of E2F4as in predicting the prognosis of OC patients and suggest its potential in promoting tumour aggressiveness by the regulation of EMT-related mechanisms.
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Affiliation(s)
- Sun-Ae Park
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul 03722, Korea; (S.-A.P.); (L.K.K.)
| | - Lee Kyung Kim
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul 03722, Korea; (S.-A.P.); (L.K.K.)
| | - Young Tae Kim
- Institute of Women’s Life Medical Science, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Tae-Hwe Heo
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul 03722, Korea; (S.-A.P.); (L.K.K.)
- Correspondence: (T.-H.H.); (H.J.K.); Tel.: +82-2-2164-4088 (T.-H.H.); +82-2-2164-4088 (H.J.K.)
| | - Hee Jung Kim
- Laboratory of Pharmacoimmunology, Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Seoul 03722, Korea; (S.-A.P.); (L.K.K.)
- Correspondence: (T.-H.H.); (H.J.K.); Tel.: +82-2-2164-4088 (T.-H.H.); +82-2-2164-4088 (H.J.K.)
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15
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Abstract
Type 2 diabetes (T2D) is a metabolic disease characterized by disordered glucagon secretion, insulin resistance in target tissues, and decreased islet β-cell mass and function. The routine diagnosis was based on measurements of metabolic markers, while genetic risk factors have been considered to increase the probability of predicting the development of the disease. Recent evidence suggests that long noncoding RNAs (lncRNAs) regulate gene expression in various physiological and pathological processes. As increasing lncRNAs are identified in β cells, understanding the regulatory roles of lncRNAs in T2D becomes indispensable. In this review, we discuss the potential role of lncRNAs contributing to β-cell identity and T2D susceptibility, which provide a perspective insight into the development of novel diagnosis biomarkers for T2D.
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Affiliation(s)
- Han Zhu
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingru Gong
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
| | - Ping Yu
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huiping Lu
- Department of Pharmacy, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai 201399, China
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16
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Long L, Zeng C, Chen H, Zhou T, Wu L, Cai X. ADNCR modulates neural stem cell differentiation and proliferation through the regulation of TCF3 expression. Ann Transl Med 2020; 8:927. [PMID: 32953727 PMCID: PMC7475390 DOI: 10.21037/atm-20-1068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Background Neural stem cells (NSCs) are undifferentiated precursor cells that have the ability to self-renew and proliferate and have the capacity to become either glia (oligodendrocytes and astrocytes) or neurons. NSCs can act as beneficial adjuncts for many neurological disorders, such as cerebral infarction, spinal cord injuries, Alzheimer's disease, and Parkinson's disease. Long noncoding RNAs (lncRNAs) play essential roles during cell differentiation, proliferation, and metabolism. This study aimed to explore the role played by adipocyte differentiation-associated long noncoding RNA (ADNCR) in the self-renewal and multipotency of NSCs. Methods In this study, we identified NSCs and verified that these cells were able to regenerate and differentiate into both astrocytes and neurons. Then we studied the relation between expression of ADNCR and transcription factor 3 (TCF3) and proliferation of NSCs. Results ADNCR and TCF3 expression have been shown to decrease during the differentiation of NSCs into both neurons and astrocyte induction cells. However, the expression of the microRNA miR-204-5p increased over time during the differentiation of NSCs into both neurons and astrocyte induction cells. ADNCR acts as a competing endogenous RNA (ceRNA) for miR-204-5p, and the overexpression of ADNCR suppressed miR-204-5p expression and enhanced TCF3 expression in NSCs, which resulted in enhanced proliferation and suppressed neural differentiation. Conclusions These data suggested that the use of ADNCR may represent a new strategy for expanding the interventions used to treat neurological disorders.
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Affiliation(s)
- Ling Long
- Department of Neurology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chao Zeng
- Department of Pathology, the Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Honglei Chen
- Department of Gastrointestinal Endoscopy, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Taicheng Zhou
- Department of Gastroenterological Surgery and Hernia Center, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lili Wu
- Department of Ultrasound, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaodong Cai
- Department of Neurology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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17
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Kuang P, Chen P, Wang L, Li W, Chen B, Liu Y, Xu Y, Wang H, Zhao S, Ye L, Yu F, Ji H, He Y. RNA sequencing analysis of small cell lung cancer reveals candidate chemotherapy insensitivity long noncoding RNAs and microRNAs. Ann Transl Med 2020; 8:121. [PMID: 32175414 PMCID: PMC7049041 DOI: 10.21037/atm.2020.01.75] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The further progression of credible expression profiling analysis of genes continues to expand our understanding of the biological characteristics in lung cancer. In this study, RNA sequencing (RNA-Seq) was used to contrast the transcriptomics profiling of small cell lung cancer (SCLC) that acquired partial response (PR) and stable disease (SD)/progressive disease (PD) after first-line chemotherapy. We aimed to illuminate the underlying mechanisms of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in the efficacy of SCLC first-line chemotherapy. METHODS Six male patients (mean age, 64.2 years) with SCLC were enrolled in this study. RNA-Seq was executed on the tumor tissues from 3 patients with PR outcome and 3 patients with SD or PD therapeutic effect after first-line chemotherapy. RESULTS RNA-Seq generated 26.67×106 (±8.7×106) reads in SCLC tissues [mean (±standard deviation)]. Analysis revealed that 64 lncRNAs had higher expression and 194 had lower expression in the PR group ≥2-fold (P<0.05). Three downregulated genes in the PR group [HOXA-AS3, cancer susceptibility 9 (CASC9), and KEGG] could have a role in the insensitivity of SCLC. A total of 1,303 differential miRNAs were defined between PR and the SD or PD SCLC group, while 520 miRNAs had higher expression, and 783 had lower expression in the PR group. Two lower expressed miRNAs in the PR group (miRNA 601 and miRNA 596) might be the key genes in SCLC chemotherapy insensitivity. CONCLUSIONS The expression of 3 gene (HOXA-AS3, CASC9, and KEGG) and 2 miRNAs (miRNA 601 and miRNA 596) were markedly decreased in SCLC patients who achieved PR. They thus might be the promising candidate genes in SCLC chemotherapy insensitivity.
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Affiliation(s)
- Peng Kuang
- Department of Medical Oncology, The First Affiliated Hospital Of Nanchang University, Nanchang 330006, China
| | - Peixin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Yi Xu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Lingyun Ye
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Feng Yu
- Department of Medical Oncology, The First Affiliated Hospital Of Nanchang University, Nanchang 330006, China
| | - Hongbin Ji
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
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18
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Zhong B, Wang Q, He J, Xiong Y, Cao J. LncRNA LOC285194 modulates gastric carcinoma progression through activating Wnt/β-catenin signaling pathway. Cancer Med 2020; 9:2181-2189. [PMID: 31991056 PMCID: PMC7064030 DOI: 10.1002/cam4.2844] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/07/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022] Open
Abstract
Emerging evidences have revealed long noncoding RNAs (lncRNAs’) critical roles in diverse human carcinoma. Among these cancers, lncRNA LOC285194 has been extensively investigated in several types of carcinomas in the recent years. Nevertheless, the biological function, clinical relevance, and the influence of LOC285194 in gastric cancer (GC) are not fully understood. The present study aims to explore the biological function of LOC285194 in the progression and development of GC. First, LOC285194 expressions were detected in GC tissues and cell lines. The functional role of LOC285194 in GC was evaluated both in vitro and in vivo. Our data found that LOC285194 was lowly expressed both in human GC tissues and GC cell lines compared with corresponding normal controls. Moreover, LOC285194 was mitigated by transfection with LV‐LOC285194 in both HGC‐27 and MKN45 cell lines. Silencing of LOC285194 remarkably induced GC cell livability and cell proliferation. On the contrary, the LOC285194 overexpression suppressed MKN45 and HGC‐27 cell proliferation and promoted cell apoptosis. Additionally, silencing of LOC285194 increased the ability of colony formation, cell migration, and invasive capacities, together with blocking the apoptotic rates of GC cells. Correspondently, LOC285194 overexpression exerted the opposite effects. Mechanistically, silencing of LOC285194 promoted GC progression via inducing Wnt signaling activity. Moreover, in vivo xenografts nude mice model results showed that LOC285194 inhibited GC progression through targeting Wnt signaling. Taken together, LOC285194 is associated with GC progression by regulating the Wnt signaling transduction, potentiating LOC285194's promising role as a novel treatment biomarker in GC.
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Affiliation(s)
- Bingzheng Zhong
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qiang Wang
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiali He
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yi Xiong
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jie Cao
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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19
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Xuan J, Xiong Y, Shi L, Aramini B, Wang H. Do lncRNAs and circRNAs expression profiles influence discoid lupus erythematosus progression?-a comprehensive analysis. Ann Transl Med 2019; 7:728. [PMID: 32042744 DOI: 10.21037/atm.2019.12.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs)are involved in the progression of discoid lupus erythematosus (DLE), but an understanding of their underlying mechanisms remains elusive. To explore the expression profiles of lncRNAs and circRNAs in DLE, we surveyed the lncRNA/circRNA and mRNA expression profiles in the epithelia of oral DLE and adjacent normal tissues. Methods The lesional and non-lesional lower lips of three DLE patients were analysed by RNA-sequencing (RNA-seq). The principal functions of the significantly deregulated genes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. And the correlated expression networks (coding-noncoding co-expression and lncRNAs-transcription factor-mRNA) were evaluated as well. Results Hundreds of significantly changed lncRNAs and mRNAs and dozens of significantly changed circRNAs were identified. lncRNA lnc-MIPOL1-6 and IncRNA IncDDX47-3 expressions were correlated with immune response-related genes, including IL19, CXCL1, CXCL11, and TNFSF15. Up-regulated IncRNA-TF network consists of 8 TFs and 74 related lncRNAs. The lncRNA-TF-gene trans-regulation consisting of 204 lncRNAs,39 TFs, and correlated 3 genes. Conclusions These results demonstrate that lncRNAs and circRNAs can influence the progression of DLE. Certain mRNAs/lncRNAs/circRNAs may have substantial value in DLE diagnosis and therapy.
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Affiliation(s)
- Jing Xuan
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, China
| | - Yaoyang Xiong
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China
| | - Linjun Shi
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China.,Department of Oral Mucosa Diseases, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Beatrice Aramini
- Division of Thoracic Surgery, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Haiyan Wang
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China.,Department of Oral Mucosa Diseases, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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20
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Gugnoni M, Ciarrocchi A. Long Noncoding RNA and Epithelial Mesenchymal Transition in Cancer. Int J Mol Sci 2019; 20:ijms20081924. [PMID: 31003545 PMCID: PMC6515529 DOI: 10.3390/ijms20081924] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a multistep process that allows epithelial cells to acquire mesenchymal properties. Fundamental in the early stages of embryonic development, this process is aberrantly activated in aggressive cancerous cells to gain motility and invasion capacity, thus promoting metastatic phenotypes. For this reason, EMT is a central topic in cancer research and its regulation by a plethora of mechanisms has been reported. Recently, genomic sequencing and functional genomic studies deepened our knowledge on the fundamental regulatory role of noncoding DNA. A large part of the genome is transcribed in an impressive number of noncoding RNAs. Among these, long noncoding RNAs (lncRNAs) have been reported to control several biological processes affecting gene expression at multiple levels from transcription to protein localization and stability. Up to now, more than 8000 lncRNAs were discovered as selectively expressed in cancer cells. Their elevated number and high expression specificity candidate these molecules as a valuable source of biomarkers and potential therapeutic targets. Rising evidence currently highlights a relevant function of lncRNAs on EMT regulation defining a new layer of involvement of these molecules in cancer biology. In this review we aim to summarize the findings on the role of lncRNAs on EMT regulation and to discuss their prospective potential value as biomarkers and therapeutic targets in cancer.
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Affiliation(s)
- Mila Gugnoni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy.
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy.
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21
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Cheshomi H, Matin MM. Exosomes and their importance in metastasis, diagnosis, and therapy of colorectal cancer. J Cell Biochem 2019; 120:2671-2686. [PMID: 30246315 DOI: 10.1002/jcb.27582] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/07/2018] [Indexed: 01/24/2023]
Abstract
Extracellular vesicles are known as actual intermediaries of intercellular communications, such as biological signals and cargo transfer between different cells. A variety of cells release the exosomes as nanovesicular bodies. Exosomes contain different compounds such as several types of nucleic acids and proteins. In this study, we focused on exosomes in colorectal cancer as good tools that can be involved in various cancer-related processes. Furthermore, we summarize the advantages and disadvantages of exosome extraction methods and review related studies on the role of exosomes in colorectal cancer. Finally, we focus on reports available on relations between mesenchymal stem cell-derived exosomes and colorectal cancer. Several cancer-related processes such as cancer progression, metastasis, and drug resistance of colorectal cancer are related to the cargoes of exosomes. A variety of molecules, especially proteins, microRNAs, and long noncoding RNAs, play important roles in these processes. The microenvironment features, such as hypoxia, also have very important effects on the properties of the origin cell-derived exosomes. On the other hand, exosomes derived from colorectal cancer cells also interfere with cancer chemoresistance. Furthermore, today it is known that exosomes and their contents can likely be very effective in noninvasive colorectal cancer diagnosis and therapy. Thus, exosomes, and especially their cargoes, play different key roles in various aspects of basic and clinical research related to both progression and therapy of colorectal cancer.
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Affiliation(s)
- Hamid Cheshomi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.,Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
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22
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Qian C, Li H, Chang D, Wei B, Wang Y. Identification of functional lncRNAs in atrial fibrillation by integrative analysis of the lncRNA-mRNA network based on competing endogenous RNAs hypothesis. J Cell Physiol 2018; 234:11620-11630. [PMID: 30478836 DOI: 10.1002/jcp.27819] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/06/2018] [Indexed: 12/14/2022]
Abstract
A mounting body of evidence has suggested that long noncoding RNAs (lncRNAs) play critical roles in human diseases by acting as competing endogenous RNAs (ceRNAs). However, the functions and ceRNA mechanisms of lncRNAs in atrial fibrillation (AF) remain to date unclear. In this study, we constructed an AF-related lncRNA-mRNA network (AFLMN) based on ceRNA theory, by integrating probe reannotation pipeline and microRNA (miRNA)-target regulatory interactions. Two lncRNAs with central topological properties in the AFLMN were first obtained. By using bidirectional hierarchical clustering, we identified two modules containing four lncRNAs, which were significantly enriched in many known pathways of AF. To elucidate the ceRNA interactions in certain disease or normal condition, the dysregulated lncRNA-mRNA crosstalks in AF were further analyzed, and six hub lncRNAs were obtained from the network. Furthermore, random walk analysis of the AFLMN suggested that lncRNA RP11-296O14.3 may function importantly in the pathological process of AF. All these eight lncRNAs that were identified from previous steps (RP11-363E7.4, GAS5, RP11-410L14.2, HAGLR, RP11-421L21.3, RP11-111K18.2, HOTAIRM1, and RP11-296O14.3) exhibited a strong diagnostic power for AF. The results of our study provide new insights into the functional roles and regulatory mechanisms of lncRNAs in AF, and facilitate the discovery of novel diagnostic biomarkers or therapeutic targets.
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Affiliation(s)
- Cheng Qian
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hang Li
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Danqi Chang
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Baozhu Wei
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yanggan Wang
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.,Medical Research Institute of Wuhan University, Wuhan University, Wuhan, China
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23
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Yuan LY, Qin X, Li L, Zhou J, Zhou M, Li X, Xu Y, Wang XJ, Xing H. The transcriptome profiles and methylation status revealed the potential cancer-related lncRNAs in patients with cervical cancer. J Cell Physiol 2018; 234:9756-9763. [PMID: 30362566 DOI: 10.1002/jcp.27661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022]
Abstract
Cervical cancer continues to be a major public health problem. Although long noncoding RNAs (lncRNAs) were involved in the initiation and progression of cancer, few studies focus on the lncRNAs in the cervical cancer. Here, we systematically studied the clinical information, transcriptome profiling, and methylation array data of cervical squamous cell carcinoma and endocervical adenocarcinoma that retrieved from genomic data commons (GDC). Compared with protein-coding genes, the expression levels of pseudogenes and lncRNAs were much lower. A total of 190 differentially expressed lncRNAs and 2,326 protein-coding genes were identified. Meanwhile, 269 differentially methylation regions (DMRs), where 16 lncRNAs were located, were figured out. Only one lncRNA, LINC00592, which was located in the DMRs, was also found differentially expressed. Several transcriptional regulation genes, such as ZNF20, ZNF441, ZNF573, and TMF1, were highly correlated with the expression of LINC00592, which illustrated its possible function on the transcription. Two microRNAs, which were both associated with tumor progression, can bind to LINC00592. Moreover, LINC00592 were also differentially expressed in other tumors. We proposed, with the help of various databases, that LINC00592 is a potential cancer-related lncRNA in cervical cancer and might activate the cancer progression through the regulation of transcription or structural integrity.
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Affiliation(s)
- Li-Yun Yuan
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Xiaomin Qin
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Lin Li
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Jinting Zhou
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Min Zhou
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Xianxian Li
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Ying Xu
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Xiao-Jun Wang
- Nursing and Midwifery College, Jiangsu College of Nursing, Huai'an, Jiangsu, China
| | - Hui Xing
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, Hubei, China
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Liang H, Zhang C, Guan H, Liu J, Cui Y. LncRNA DANCR promotes cervical cancer progression by upregulating ROCK1 via sponging miR-335-5p. J Cell Physiol 2018; 234:7266-7278. [PMID: 30362591 DOI: 10.1002/jcp.27484] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022]
Abstract
Emerging evidence highlights the key regulatory roles of long noncoding RNAs (lncRNAs) in the initiation and progression of numerous malignancies. The lncRNA identified as differentiation antagonizing nonprotein coding RNA (DANCR) is a novel lncRNA widely involved in the development of multiple human cancers. However, the function of DANCR and its potential molecular mechanism in cervical cancer remain unclear. In this study, we discovered that DANCR was significantly elevated in cervical cancer tissues and cells, and was closely correlated with poor prognosis of cervical cancer patients. In addition, knockdown of DANCR inhibited proliferation, migration, and invasion of cervical cancer cells in vitro, indicating that DANCR functioned as an oncogene in cervical cancer. Moreover, we verified that DANCR could directly bind to miR-335-5p, isolating miR-335-5p from its target gene Rho-associated coiled-coil containing protein kinase 1 (ROCK1). Functional analysis showed that DANCR regulated ROCK1 expression by competitively binding to miR-335-5p. Further cellular behavioral experiments revealed that miR-335-5p mimics and ROCK1 knockdown reversed the effects of upregulated DANCR on proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of cervical cancer cells by rescue assays. In summary, this study demonstrated that DANCR promoted cervical cancer progression by functioning as a competing endogenous RNA (ceRNA) to regulate ROCK1 expression via sponging miR-335-5p, suggesting a novel potential therapeutic target for cervical cancer.
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Affiliation(s)
- Huiling Liang
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunyan Zhang
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Hongya Guan
- Department of Translational Medicine Center, Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Jia Liu
- Department of Translational Medicine Center, Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Yuanbo Cui
- Department of Translational Medicine Center, Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China.,Department of Bioinformatics, School of Life Sciences, Zhengzhou University, Zhengzhou, China
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25
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Mou Y, Wang D, Xing R, Nie H, Mou Y, Zhang Y, Zhou X. Identification of long noncoding RNAs biomarkers in patients with hepatitis B virus-associated hepatocellular carcinoma. Cancer Biomark 2018; 23:95-106. [PMID: 29991128 DOI: 10.3233/cbm-181424] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancer worldwide and chronic infection of hepatitis B virus (HBV) serve as one of leading causes of HCC. OBJECTIVE This study aimed to identify the novel long noncoding RNAs (lncRNAs) biomarkers for HBV-associated HCC. METHODS The lncRNA and mRNA expression profiles of HCC patients with HBV infection were downloaded from The Cancer Genome Atlas. The differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between HCC and adjacent tissues were identified. The optimal diagnostic and prognostic lncRNA biomarkers for HCC were identified by using feature selection procedure and classification model. Functional annotation of DEmRNAs co-expressed with these lncRNAs biomarkers were performed. Receiver operating characteristic (ROC) curve and survival analysis of these lncRNAs biomarkers were performed. qRT-PCR validation was performed. RESULTS A total of 82 DElncRNAs and 805 DEmRNAs between HBV-associated HCC and normal tissues were identified. CAPN10-AS1, LINC01093, RP5-890E16.2, FENDRR and C17orf82 were selected as optimal diagnostic and prognostic lncRNA biomarkers for HBV-associated HCC that were co-expressed with 105, 86, 70, 30 and 1 DEmRNAs, respectively. Based on the DEmRNAs co-expressed with these five lncRNAs biomarkers, Jak-STAT signaling pathway and retinol metabolism were two significantly enriched pathways. The result in qRT-PCR validation were consistent with our analysis based on TCGA, generally. CONCLUSIONS This study identified five potential lncRNAs biomarkers for HBV-associated HCC with great diagnostic and prognostic value and provided clues for their functions in HBV-associated HCC.
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Affiliation(s)
- Yonghua Mou
- Department of Hepatobiliary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Dongguo Wang
- Department of Clinical Lab Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Renwei Xing
- Department of Hepatobiliary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Hanqiu Nie
- Department of Hepatobiliary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Yiping Mou
- Department of Gastrointestinal Surgery, Zhejiang People's Hospital, Hangzhou, Zhejiang, China
| | - Yang Zhang
- Department of Hepatobiliary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Xianfei Zhou
- Department of Hepatobiliary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
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26
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Qiu Z, Ye B, Yin L, Chen W, Xu Y, Chen X. Downregulation of AC061961.2, LING01-AS1, and RP11-13E1.5 is associated with dilated cardiomyopathy progression. J Cell Physiol 2018; 234:4460-4471. [PMID: 30203513 DOI: 10.1002/jcp.27247] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/19/2018] [Indexed: 01/16/2023]
Abstract
This study aimed to explore long noncoding RNAs (lncRNAs) implicated in dilated cardiomyopathy (DCM). Ten samples of failing hearts collected from the left ventricles of patients with DCM undergoing heart transplants, and ten control samples obtained from normal heart donors were included in this study. After sequencing, differentially expressed genes (DEGs) and lncRNAs between DCM and controls were screened, followed with functional enrichment analysis and weighted gene coexpression network analysis (WGCNA). Five key lncNRAs were validated through real-time polymerase chain reaction (PCR). Total 1,398 DEGs were identified, including 267 lncRNAs. WGCNA identified seven modules that were significantly correlated with DCM. The top 50 genes in the three modules (black, dark-green, and green-yellow) were significantly correlated with DCM disease state. Four core enrichment lncRNAs, such as AC061961.2, LING01-AS1, and RP11-557H15.4, in the green-yellow module were associated with neurotransmitter secretion. Five core enrichment lncRNAs, such as KB-1299A7.2 and RP11-13E1.5, in the black module were associated with the functions of blood circulation and heart contraction. AC061961.2, LING01-AS1, and RP11-13E1.5 were confirmed to be downregulated in DCM tissues by real-time PCR. The current study suggests that downregulation of AC061961.2, LING01-AS1, and RP11-13E1.5 may be associated with DCM progression, which may serve as key diagnostic biomarkers and therapeutic targets for DCM.
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Affiliation(s)
- Zhibing Qiu
- Department of Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bin Ye
- Department of Anesthesiology, Yangzhou Maternal and Child Health Hospital, Yangzhou, Jiangsu, China
| | - Li Yin
- Department of Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wen Chen
- Department of Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yueyue Xu
- Department of Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Chen
- Department of Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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27
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Wu Y, Wei J, Ming Y, Chen Z, Yu J, Mao R, Chen H, Zhou G, Fan Y. Orchestrating a biomarker panel with lncRNAs and mRNAs for predicting survival in pancreatic ductal adenocarcinoma. J Cell Biochem 2018; 119:7696-7706. [PMID: 29923223 DOI: 10.1002/jcb.27119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/04/2018] [Indexed: 12/15/2022]
Abstract
The low survival of patients with pancreatic ductal adenocarcinoma (PDAC) makes the treatment of this disease one of the most challenging task in modern medicine. Here, by mining a large-scale cancer genome atlas data set of pancreatic cancer tissues, we identified 21 long noncoding RNAs (lncRNAs) that significantly associated with overall survival in patients with PDAC (P < .01). Further analysis revealed that 8 lncRNAs turned out to be independently correlated with patients' overall survival, and the risk score could be calculated based on their expression. To obtain a better predicting power, we integrated lncRNA data with a total of 410 differently expressed messenger RNAs (mRNAs) screened from PDAC and normal tissues in gene expression omnibus (GEO) database. The integration resulted in a much better panel including 8 lncRNAs (RP3.470B24.5, CTA.941F9.9, RP11.557H15.3, LINC00960, AP000479.1, LINC00635, LINC00636, and AC073133.1) and 8 mRNAs (DHRS9, ONECUT1, OR8D4, MT1M, TCN1, MMP9, DPYSL3, and TTN) to predict prognosis. A functional evaluation showed that these lncRNAs might play roles in pancreatic secretion, cell adhesion, and proteolysis. Using normal and pancreatic cancer cell lines, we confirmed that a majority of identified lncRNAs and mRNAs showed altered expressions in pancreatic cancer cells. Especially, LINC01589, LINC00960, TCN1, and MT1M showed a profoundly increased expression in pancreatic cancer cells, which suggests their potentially important role in pancreatic cancer. The results of our work indicate that lncRNAs have vital roles in PADC and provide new insights to integrate multiple kinds of markers in clinical practices.
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Affiliation(s)
- Yingcheng Wu
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China
| | - Jinhuan Wei
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China
| | - Yue Ming
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Zhanghao Chen
- Department of Computer Science, New York University, New York, USA.,Department of Computer Science, New York University Shanghai, Shanghai, China
| | - Jinzhong Yu
- Department of Computer Science, New York University, New York, USA.,Department of Computer Science, New York University Shanghai, Shanghai, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, China
| | - Guoxiong Zhou
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, China.,Department of Immunology, School of Medicine, Nantong University, Nantong, China
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28
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Nardocci G, Carrasco ME, Acevedo E, Hodar C, Meneses C, Montecino M. Identification of a novel long noncoding RNA that promotes osteoblast differentiation. J Cell Biochem 2018; 119:7657-7666. [PMID: 29806713 DOI: 10.1002/jcb.27113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 12/30/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a heterogeneous class of transcripts, longer than 200 nucleotides, 5'-capped, polyadenylated, and poorly conserved among mammalian species. Several studies have shown the contribution of lncRNAs to different cellular processes, including regulation of the chromatin structure, control of messenger RNA translation, regulation of gene transcription, regulation of embryonic pluripotency, and differentiation. Although limited numbers of functional lncRNAs have been identified so far, the immense regulatory potential of these RNAs is already evident, indicating that a functional characterization of lncRNAs is needed. In this study, mouse preosteoblastic cells were induced to differentiate into osteoblasts. At 3 sequential differentiation stages, total RNA was isolated and libraries were constructed for Illumina sequencing. The resulting sequences were aligned and transcript abundances were determined. New lncRNA candidates that displayed differential expression patterns during osteoblast differentiation were identified by combining bioinformatics and reverse transcription polymerase chain reaction analyses. Among these, lncRNA-1 that exhibited increased expression during osteogenesis and was downregulated during myogenesis. Importantly, knockdown of lncRNA-1 expression in primary mouse preosteoblasts was found to inhibit osteogenic differentiation, reflected by a reduced transcription of the Runx2/p57 and Sp7 bone master genes. Together, our results indicate that lncRNA-1 represents a new regulatory RNA that plays a relevant role during the early stages of osteogenesis.
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Affiliation(s)
- Gino Nardocci
- Center for Biomedical Research, Faculty of Life Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Margarita E Carrasco
- Center for Biomedical Research, Faculty of Life Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Elvis Acevedo
- Center for Biomedical Research, Faculty of Life Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile
| | - Claudio Meneses
- FONDAP Center for Genome Regulation, Santiago, Chile.,Center of Plant Biotechnology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Martín Montecino
- Center for Biomedical Research, Faculty of Life Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
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29
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Liu XF, Hao JL, Xie T, Pant OP, Lu CB, Lu CW, Zhou DD. The BRAF activated non-coding RNA: A pivotal long non-coding RNA in human malignancies. Cell Prolif 2018; 51:e12449. [PMID: 29484737 DOI: 10.1111/cpr.12449] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) participate in the complex network of cancer and play an important role in tumourigenesis and progression. BRAF activated non-coding RNA (BANCR), a 4-exon transcript of 693-bp, was first discovered as an oncogenic long non-coding RNA in BRAFV600E melanomas cells in 2012 and was related to melanoma cell migration. Besides melanoma, increasing evidence has explored the potential role of BANCR in the development and progression of multiple other human malignancies, such as retinoblastoma, lung cancer, gastric cancer etc. since its discovery. The expression pattern of BANCR varies in different types of cancers, either as a tumour suppressor or as an accelerator. Functional BANCR may serve as a promising biomarker for cancer diagnosis as well as prognosis evaluation. BANCR-targeted intervention may also become a valuable novel therapeutic tool against human malignancies. This review summarized the advanced research progresses concerning the expression and role of BANCR in different human malignancies.
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Affiliation(s)
- Xiu-Fen Liu
- Department of Ophthalmology, The First Hospital of Jilin University, Jilin, China
| | - Ji-Long Hao
- Department of Ophthalmology, The First Hospital of Jilin University, Jilin, China
| | - Tian Xie
- Department of. Neurosurgery, The People's Hospital of Jilin Province, Jilin, China
| | - Om Prakash Pant
- Department of Ophthalmology, The First Hospital of Jilin University, Jilin, China
| | - Cheng-Bo Lu
- Department of Cardiology, The First Hospital of Jiamusi University, Heilongjiang, China
| | - Cheng-Wei Lu
- Department of Ophthalmology, The First Hospital of Jilin University, Jilin, China
| | - Dan-Dan Zhou
- Department of Radiology, The First Hospital of Jilin University, Jilin, China
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30
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Antonov I, Marakhonov A, Zamkova M, Medvedeva Y. ASSA: Fast identification of statistically significant interactions between long RNAs. J Bioinform Comput Biol 2018; 16:1840001. [PMID: 29375012 DOI: 10.1142/s0219720018400012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them are involved in post-transcriptional regulation of other RNAs and form inter-molecular duplexes with their targets. Sequence alignment tools have been used for transcriptome-wide prediction of RNA-RNA interactions. However, such approaches have poor prediction accuracy since they ignore RNA's secondary structure. Application of the thermodynamics-based algorithms to long transcripts is not computationally feasible on a large scale. Here, we describe a new computational pipeline ASSA that combines sequence alignment and thermodynamics-based tools for efficient prediction of RNA-RNA interactions between long transcripts. To measure the hybridization strength, the sum energy of all the putative duplexes is computed. The main novelty implemented in ASSA is the ability to quickly estimate the statistical significance of the observed interaction energies. Most of the functional hybridizations between long RNAs were classified as statistically significant. ASSA outperformed 11 other tools in terms of the Area Under the Curve on two out of four test sets. Additionally, our results emphasized a unique property of the [Formula: see text] repeats with respect to the RNA-RNA interactions in the human transcriptome. ASSA is available at https://sourceforge.net/projects/assa/.
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Affiliation(s)
- Ivan Antonov
- * Institute of Bioengineering, Federal Research Center Fundamentals of Biotechnology RAS, Moscow 117312, Russia.,† Department of Molecular and Biological Physics & Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Andrey Marakhonov
- ‡ Laboratory of Functional Analysis of the Genome, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.,§ Federal State Scientific Budgetary Institution, Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Maria Zamkova
- ¶ Russian N.N. Blokhin Cancer Research Center, Moscow 115478, Russia
| | - Yulia Medvedeva
- * Institute of Bioengineering, Federal Research Center Fundamentals of Biotechnology RAS, Moscow 117312, Russia.,† Department of Molecular and Biological Physics & Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.,∥ Vavilov Institute of General Genetics, RAS, Moscow 119333, Russia
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Abstract
The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.
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Affiliation(s)
- Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States.,Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Human Protein Science, University of Geneva , CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Emma K Lundberg
- SciLifeLab Stockholm and School of Biotechnology, KTH, Karolinska Institutet Science Park , Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Christopher M Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia , 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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Tian F, Xu J, Xue F, Guan E, Xu X. TINCR expression is associated with unfavorable prognosis in patients with hepatocellular carcinoma. Biosci Rep. 2017;37:pii: BSR20170301. [PMID: 28546230 PMCID: PMC5529205 DOI: 10.1042/bsr20170301] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
Emerging evidence are accumulating that long noncoding RNAs (lncRNAs) have recently been identified to participate in various cellular processes. Terminal differentiation induced ncRNA (TINCR) is a newly identified lncRNA with its functional roles not fully elucidated in human malignancy. The current study aims to identify the clinical significance of TINCR in prognosis and malignant progression of hepatocellular carcinoma (HCC). TINCR expression in HCC specimens at various stages of tumorigenesis were measured by quantitative real-time RT PCR (qRT-PCR). The matched para-carcinoma tissues were used as controls. The associations of TINCR with clinicopathological characteristics, disease-free survival (DFS) and overall survival (OS) of patients were further evaluated. Results revealed that high TINCR expression was significantly correlated with tumor size (P=0.005), tumor differentiation status (P=0.017), TNM stage (P=0.010), and vascular invasion (P=0.004). Moreover, Kaplan-Meier analysis demonstrated that TINCR was correlated to both DFS and OS in HCC cohorts. Patients with high TINCR expression tended to have worse prognosis. Multivariate Cox regression analysis indicated that TINCR was an independent poor prognostic indicator for DFS (HR =1.32, 95% CI: 1.00-1.57, P=0.000) and OS (HR =1.57, 95% CI: 1.30-1.86, P=0.004) in HCC. TINCR was demonstrated as a direct target of miR-137 and miR-133a, and was suppressed by miR-137/miR-133a These results provide the first evidence that the expression of TINCR in HCC may play an oncogenic role in HCC differentiation, invasion, and metastasis. miR-137/miR-133a-TINCR pathway may serve as a promising target for tumor recurrence and prognosis of patients with HCC.
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Deveson IW, Hardwick SA, Mercer TR, Mattick JS. The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome. Trends Genet 2017; 33:464-478. [PMID: 28535931 DOI: 10.1016/j.tig.2017.04.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 01/02/2023]
Abstract
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome.
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Affiliation(s)
- Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Simon A Hardwick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - John S Mattick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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Yang Z, Wang R, Zhang T, Dong X. Hypoxia/lncRNA-AK123072/EGFR pathway induced metastasis and invasion in gastric cancer. Int J Clin Exp Med 2015; 8:19954-19968. [PMID: 26884908 PMCID: PMC4723753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/09/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To investigate the role of long noncoding RNAs (lncRNAs) in hypoxia-induced gastric cancer (GC) metastasis and invasion. METHODS We investigated the differentially expressed lncRNAs resulting from hypoxia-induced GC and normoxia conditions using microarrays and validated our results through real-time quantitative polymerase chain reaction. The role of the targeting lncRNA was further detected by in vivo and in vitro assays. RESULTS We found an lncRNA, AK123072, which was up-regulated by hypoxia. AK123072 was frequently up-regulated in GC samples and promoted GC migration and invasion in vivo and in vitro. Furthermore, AK123072 could mediate the metastasis of hypoxia-induced GC cells. Next, we identified EGFR, which was a metastasis-related gene regulated by AK123072. In addition, we found that the expression of EGFR was positively correlated with that of AK123072 in the clinical GC samples used in our study. Furthermore, we found that the EGFR gene CpG island methylation was significantly increased in GC cells depleted of AK123072. Intriguingly, EGFR expression was also increased by hypoxia, and EGFR up-regulation by AK123072 mediated hypoxia-induced GC cell metastasis. CONCLUSION Our results identified hypoxia/lncRNA-AK123072/EGFR pathway in gastric cancer pathogenesis and this might help in the development of new therapeutics in clinics.
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Affiliation(s)
- Zhen Yang
- Department of Gastrointestinal Surgery, 1 Affiliated Hospital of Zhengzhou UniversityHenan Province, China
| | - Ruoming Wang
- Department of General Surgery, 1 Renmin Hospital of ShangqiuHenan Province, China
| | - Tengteng Zhang
- Department of Cancer, 1 Renmin Hospital of ShangqiuHenan Province, China
| | - Xinhua Dong
- Department of Gastrointestinal Surgery, 1 Affiliated Hospital of Zhengzhou UniversityHenan Province, China
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Wang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X. Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytol 2015; 207:1181-97. [PMID: 25919642 DOI: 10.1111/nph.13429] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 03/22/2015] [Indexed: 05/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts of at least 200 bp in length, possess no apparent coding capacity and are involved in various biological regulatory processes. Until now, no systematic identification of lncRNAs has been reported in cotton (Gossypium spp.). Here, we describe the identification of 30 550 long intergenic noncoding RNA (lincRNA) loci (50 566 transcripts) and 4718 long noncoding natural antisense transcript (lncNAT) loci (5826 transcripts). LncRNAs are rich in repetitive sequences and preferentially expressed in a tissue-specific manner. The detection of abundant genome-specific and/or lineage-specific lncRNAs indicated their weak evolutionary conservation. Approximately 76% of homoeologous lncRNAs exhibit biased expression patterns towards the At or Dt subgenomes. Compared with protein-coding genes, lncRNAs showed overall higher methylation levels and their expression was less affected by gene body methylation. Expression validation in different cotton accessions and coexpression network construction helped to identify several functional lncRNA candidates involved in cotton fibre initiation and elongation. Analysis of integrated expression from the subgenomes of lncRNAs generating miR397 and its targets as a result of genome polyploidization indicated their pivotal functions in regulating lignin metabolism in domesticated tetraploid cotton fibres. This study provides the first comprehensive identification of lncRNAs in Gossypium.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhui Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yonghui He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Keith Lindsey
- Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Li C, Yang L, Lin C. Long noncoding RNAs in prostate cancer: mechanisms and applications. Mol Cell Oncol 2014; 1:e963469. [PMID: 27308347 DOI: 10.4161/23723548.2014.963469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/04/2014] [Accepted: 08/12/2014] [Indexed: 12/26/2022]
Abstract
A large proportion of the control of gene expression in humans is mediated by noncoding elements in the genome. Long noncoding RNAs (lncRNAs) have emerged as a new class of pivotal regulatory components, orchestrating extensive cellular processes and connections. LncRNAs play various roles from chromatin modification to alternative splicing and post-transcriptional processing and are involved in almost all aspects of eukaryotic regulation. LncRNA-based mechanisms modulate cell fates during development, and their dysregulation underscores many human disorders, especially cancer, through chromosomal translocation, deletion, and nucleotide expansions. Recent studies demonstrate that multiple prostate cancer risk loci are associated with lncRNAs and that ectopic expression of these transcripts triggers a cascade of cellular events driving tumor initiation and progression. The recent increased rate of discovery of lncRNAs has been leveraged for application in clinical strategies such as novel biomarkers and therapeutic targets. Despite this potential, many issues remain to be addressed in this fast-growing field.
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Affiliation(s)
- Chunlai Li
- Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center ; Houston, TX, 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX, 77030, USA; Program in Cancer Biology; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX, 77030, USA; Program in Cancer Biology; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, 77030, USA
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