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Li J, Xiang S, Song X. Screening Nonlinear miRNA Features of Breast Cancer by Using Ensemble Regularized Polynomial Logistic Regression. J Comput Biol 2024; 31:670-690. [PMID: 39017171 DOI: 10.1089/cmb.2023.0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024] Open
Abstract
Differentiating breast cancer subtypes based on miRNA data helps doctors provide more personalized treatment plans for patients. This paper explored the interaction between miRNA pairs and developed a novel ensemble regularized polynomial logistic regression method for screening nonlinear features of breast cancer. Three different types of second-order polynomial logistic regression with elastic network penalty (SOPLR-EN) in which each type contains 10 identical models were integrated to determine the most suitable sample set for feature screening by using bootstrap sampling strategy. A single feature and 39 nonlinear features were obtained by screening features that appeared at least 15 times in 30 integrations and were involved in the classification of at least 4 subtypes. The second-order polynomial logistic regression with ridge penalty (SOPLR-R) built on screened feature set achieved 82.30% classification accuracy for distinguishing breast cancer subtypes, surpassing the performance of other six methods. Further, 11 nonlinear miRNA biomarkers were identified, and their significant relevance to breast cancer was illustrated through six types of biological analysis.
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Affiliation(s)
- Juntao Li
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China
- Henan Engineering Laboratory for Big Data Statistical Analysis and Optimal Control, Xinxiang, China
| | - Shan Xiang
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China
- Henan Engineering Laboratory for Big Data Statistical Analysis and Optimal Control, Xinxiang, China
| | - Xuekun Song
- College of Information Technology, Henan University of Chinese Medicine, Zhengzhou, China
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2
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Shirani N, Mahdi‐Esferizi R, Eshraghi Samani R, Tahmasebian S, Yaghoobi H. In silico identification and in vitro evaluation of MRPS30-DT lncRNA and MRPS30 gene expression in breast cancer. Cancer Rep (Hoboken) 2024; 7:e2114. [PMID: 38886335 PMCID: PMC11182701 DOI: 10.1002/cnr2.2114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND It has been reported that long non-coding RNAs (lncRNAs) can play important roles in a variety of biological processes and cancer regulatory networks, including breast cancer. AIMS This study aimed to identify a novel upregulated lncRNA in breast cancer and its associated gene using bioinformatics analysis, and then evaluate their potential roles in breast cancer. METHODS AND RESULTS Extensive in silico studies were performed using various bioinformatics databases and tools to identify a potential upregulated breast cancer-associated lncRNA and its co-expressed gene, and to predict their potential roles, functions, and interactions. The expression level of MRPS30-DT lncRNA and MRPS30 was assessed in both BC tissues and cell lines using qRT-PCR technology. MRPS30-DT lncRNA and MRPS30 were selected as target genes using bioinformatics analysis. We found that MRPS30-DT and MRPS30 were significantly overexpressed in BC tissues compared with normal tissues. Also, MRPS30 showed upregulation in all three BC cell lines compared with HDF. On the other hand, MRPS30-DT significantly increased in MDA-MB-231 compared with HDF. While the expression of MRPS30-DT was significantly dropped in the resistance cell line MCF/MX compared to HDF and MCF7. Moreover, bioinformatics analysis suggested that MRPS30-DT and MRPS30 may play a potential role in BC through their involvement in some cancer signaling pathways and processes, as well as through their interaction with TFs, genes, miRNAs, and proteins related to carcinogenesis. CONCLUSIONS Overall, our findings showed the dysregulation of MRPS30-DT lncRNA and MRPS30 may provide clues for exploring new therapeutic targets or molecular biomarkers in BC.
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Affiliation(s)
- Nooshafarin Shirani
- Clinical Biochemistry Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
| | - Roohallah Mahdi‐Esferizi
- Clinical Biochemistry Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
- Department of Medical BiotechnologySchool of Advanced Technologies, Shahrekord University of Medical SciencesShahrekordIran
| | - Reza Eshraghi Samani
- Department of General SurgerySchool of Medicine, Isfahan University of Medical SciencesIsfahanIran
| | - Shahram Tahmasebian
- Department of Medical BiotechnologySchool of Advanced Technologies, Shahrekord University of Medical SciencesShahrekordIran
| | - Hajar Yaghoobi
- Clinical Biochemistry Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
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3
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Norouzi R, Mohamadzade Z, Norouzi R, Norouzi R, Esmaeili R, Soltani BM. In-silico and in-vitro evidence suggest LINC01405 as a sponge for miR-29b and miR-497-5p, and a potential regulator of Wnt, PI3K, and TGFB signaling pathways in breast carcinoma. Cancer Rep (Hoboken) 2024; 7:e1972. [PMID: 38225865 PMCID: PMC10849987 DOI: 10.1002/cnr2.1972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/09/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Carcinoma of the breast, a prevailing factor in female mortality worldwide, involves dysregulation of lncRNAs and microRNAs. AIM The main goal of this research was to predict and experimentally examine the LINC01405 expression status in breast cancer subtypes, along with investigation of its interaction with miR-29b and miR-497-5p that results in regulating PI3-Kinase, WNT, and TGF-beta signaling pathways. METHODS AND RESULTS We performed a meta-analysis of five GEO datasets, encompassing microarray and RNA-seq data, to identify differentially expressed genes. The Cancer Genome Atlas transcriptome dataset was also analyzed to determine essential gene modules, associated with different stages of breast cancer by weighted gene co-expression networks. In addition, networks of drug-gene interactions were constructed to explore potential treatment options. LINC01405 as a microRNA sponge was chosen and examined. furthermore, downstream target genes were discovered. Experimental validation consisted of plasmid constructs used in cell culture experiments, RT-qPCR for expression analysis, and cell cycle assays. Our bioinformatics findings showed higher LINC01405 expression in Basal-like triple-negative breast carcinoma. In contrast, lower expression in Luminal samples was observed compared with normal samples, which was consistently observed in both breast cancer tissues and cell lines. LINC01405 expression level was correlated with miR-29b and miR-497 levels. The MDA-MB-231 cell line demonstrated higher LINC01405 expression and lower miR-29b and miR-497 expression levels. However, SKBR3 and MCF7 cells had lower LINC01405 expression and higher miR-29b and miR-497 levels, suggesting a regulatory role for LINC01405 as a competing endogenous RNA. This was experimentally confirmed when LINC01405 was overexpressed in SKBR3 cells, and the common target genes of miR-29b and miR-497 were upregulated. Additionally, LINC01405 upregulation led to the increased cell populations, proliferation, and upregulation of critical cancer-related genes, including AKT1, AKT3, mTOR, WNT3A, SMAD3, CYCLIN D1, CYCLIN D2, BCL2, and GSK3B. CONCLUSION We revealed the differential expression of LINC01405 in several types of breast cancer and its role in regulating signaling pathways, potentially via scavenging miRNAs. These findings clarified the role of LINC01405 in breast cancer development and identified potential therapeutic targets.
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Affiliation(s)
- Romina Norouzi
- Molecular Genetics Department, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Zahra Mohamadzade
- Molecular Genetics Department, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Rambod Norouzi
- Molecular Biosciences DepartmentAutonomous University of MadridMadridSpain
| | | | - Rezvan Esmaeili
- Genetics Department, Center for Breast Cancer ResearchMotamed Cancer InstituteTehranIran
| | - Bahram M. Soltani
- Molecular Genetics Department, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
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Liang T, Cheng M, Lu L, Liu R. Competing endogenous RNA network characterization of lymph node metastases in Leuran gastric cancer subtypes. J Cancer Res Clin Oncol 2023; 149:16043-16053. [PMID: 37688630 DOI: 10.1007/s00432-023-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Gastric cancer is a kind of tumor with strong heterogeneity. Long noncoding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) play significant roles in the development of tumors. In this study, we divided all TCGA gastric cancer patients into the whole, intestinal and diffuse cohorts for further analysis, and constructed competitive endogenous RNA network and evaluated immune cells using CIBERSORTx. The support vector machines recursive feature elimination (SVM-RFE) was used for screening significant signatures and the support vector machines (SVM) for establishing model predicting the lymph node metastasis. The performance of SVM model was good in the intestinal and diffuse cohort, while the model in the whole cohort was relatively poor. Some important co-expression patterns between immune cells and ceRNAs network indicated significant correlation CD70 with dendritic cells and so on. Our research inferred competing endogenous RNA network of lymph node metastasis and built an excellent predicting model.
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Affiliation(s)
- Tianyu Liang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Minjun Cheng
- Intensive Care Unit, Chun'an First People's Hospital (Chun'an Branch of Zhejiang Provincial People's Hospital and Chun'an Hospital Affiliated to Hangzhou Medical College), Hangzhou, China
| | - Ling Lu
- Center for Rehabilitation Medicine, Department of Anesthesiology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Renyang Liu
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.
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Ratre P, Nazeer N, Bhargava A, Thareja S, Tiwari R, Raghuwanshi VS, Mishra PK. Design and Fabrication of a Nanobiosensor for the Detection of Cell-Free Circulating miRNAS-LncRNAS-mRNAS Triad Grid. ACS OMEGA 2023; 8:40677-40684. [PMID: 37953834 PMCID: PMC10637347 DOI: 10.1021/acsomega.3c05718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
The increased understanding of the competitive endogenous RNA (ceRNA) network in the onset and development of breast cancers has suggested their use as promising disease biomarkers. Keeping these RNAs as molecular targets, we designed and developed an optical nanobiosensor for specific detection of the miRNAs-LncRNAs-mRNAs triad grid in circulation. The sensor was formulated using three quantum dots (QDs), i.e., QD-705, QD-525, and GQDs. These QDs were surface-activated and modified with a target-specific probe. The results suggested the significant ability of the developed nanobiosensor to identify target RNAs in both isolated and plasma samples. Apart from the higher specificity and applicability, the assessment of the detection limit showed that the sensor could detect the target up to 1 fg concentration. After appropriate validation, the developed nanobiosensor might prove beneficial to characterizing and detecting aberrant disease-specific cell-free circulating miRNAs-lncRNAs-mRNAs.
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Affiliation(s)
- Pooja Ratre
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Nazim Nazeer
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Arpit Bhargava
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
- Faculty
of Science, Ram Krishna Dharmarth Foundation
University, Bhopal 462030, India
| | - Suresh Thareja
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
| | - Rajnarayan Tiwari
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Vinay Singh Raghuwanshi
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Pradyumna Kumar Mishra
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
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6
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Kakati RT, Kim H, Whitman A, Spanheimer PM. High expression of the RET receptor tyrosine kinase and its ligand GDNF identifies a high-risk subset of estrogen receptor positive breast cancer. Breast Cancer Res Treat 2023; 199:589-601. [PMID: 37061618 PMCID: PMC10182256 DOI: 10.1007/s10549-023-06937-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
Abstract
PURPOSE Resistance to endocrine therapy is the primary cause of treatment failure and death in patients with ER-positive (ER +)/luminal breast cancer. Expression and activation of the RET receptor tyrosine kinase may be driving poor outcomes. We aim to identify high-risk patients and druggable pathways for biomarker-based clinical trials. METHODS We obtained batch-normalized mRNA expression data from Breast Invasive Carcinoma-The Cancer Genome Atlas, PanCancer Atlas (BRCA-TCGA). To determine clinically significant cutoffs for RET expression, patients were grouped at different thresholds for Kaplan-Meier plotting. Differential gene expression (DGE) analysis and enrichment for gene sets was performed. transcriptomic dataset of antiestrogen-treated ER + tumors stratified by clinical response was then analyzed. RESULTS High RET expression was associated with worse outcomes in patients with ER + tumors, and stratification was enhanced by incorporating GDNF expression. High RET/GDNF patients had significantly lower overall survival (HR = 2.04, p = 0.012), progression-free survival (HR = 2.87, p < 0.001), disease-free survival (HR = 2.67, p < 0.001), and disease-specific survival (HR = 3.53, p < 0.001) than all other ER + patients. High RET/GDNF tumors were enriched for estrogen-independent signaling and targetable pathways including NTRK, PI3K, and KRAS. Tumors with adaptive resistance to endocrine therapy were enriched for gene expression signatures of high RET/GDNF primary tumors. CONCLUSION Expression and activation of the RET receptor tyrosine kinase may be driving poor outcomes in some patients with ER + breast cancer. ER + patients above the 75th percentile may benefit from clinical trials with tyrosine kinase inhibitors.
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Affiliation(s)
- Rasha T Kakati
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA
| | - Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA
| | - Austin Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA
| | - Philip M Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Suite 1149, Chapel Hill, NC, 27599-7213, USA.
- Department of Surgery, University of North Carolina, Chapel Hill, NC, USA.
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7
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Yang S, Wang X, Zhou X, Hou L, Wu J, Zhang W, Li H, Gao C, Sun C. ncRNA-mediated ceRNA regulatory network: Transcriptomic insights into breast cancer progression and treatment strategies. Biomed Pharmacother 2023; 162:114698. [PMID: 37060661 DOI: 10.1016/j.biopha.2023.114698] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
With the rapid development of next-generation sequencing technology, several studies have shown that ncRNAs can act as competitive endogenous RNAs (ceRNAs) and are involved in various biological processes, such as proliferation, differentiation, apoptosis, and migration of breast cancer (BC) cells, and plays an important role in BC progression as a molecular target for its diagnosis, treatment, prognosis, and differentiation of subtypes and age groups of BC patients. Based on the description of ceRNA-related biological functions, this study screened and sorted the sequencing analysis and experimental verification conclusions of BC-related ceRNAs and found that the ncRNAs mediated ceRNA networks can promote the development of BC by promoting the expression of genes related to BC proliferation, drug resistance, and apoptosis, inducing the production of epithelial-mesenchymal transition (EMT) to promote metastasis and activating cancer-related signaling pathways.
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Affiliation(s)
- Shu Yang
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
| | - Xiaomin Wang
- Special Medicine Department, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xintong Zhou
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lin Hou
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
| | - Jibiao Wu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wenfeng Zhang
- School of Traditional Chinese Medicine, Macau University of Science and Technology, Macao Special Administrative Region, China
| | - Huayao Li
- College of Chinese Medicine, Weifang Medical University, Weifang, China
| | - Chundi Gao
- College of Chinese Medicine, Weifang Medical University, Weifang, China
| | - Changgang Sun
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China; College of Chinese Medicine, Weifang Medical University, Weifang, China.
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8
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Dhandapani H, Bose M, Kesavan S. The Immune-related ceRNA Network in Prognosis of Cervical Cancer. Asian Pac J Cancer Prev 2022; 23:3347-3354. [PMID: 36308358 PMCID: PMC9924325 DOI: 10.31557/apjcp.2022.23.10.3347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Immunotherapy is gaining attention and it is being included as one of the treatment strategies for cancer patients. However, the molecular mechanisms of immune-related genes and their affinity for cervical cancer progression remain unclear. In this study, we have developed an immune-related competing endogenous RNA [ceRNA] network and assessed the tumour infiltrating immune cells towards the prognosis of cervical cancer. METHODS Differential RNA expression pattern between stages I and II-IV of cervical cancer patients from The Cancer Genome Atlas [TCGA] was analyzed. Immune-related ceRNA network based on the immune gene signatures were retrieved and their targets were predicted using miRwalk 3.0. CIBERSORT was employed to identify the immune cell types based on their respective transcripts. The prognostic significance of RNAs in the ceRNA network and immune cell subsets was analyzed. RESULTS Significant differences in 22 long non-coding RNAs [lncRNAs], 15 microRNAs [miRNAs], and 252 messenger RNAs [mRNAs] between stages I and II-IV of cervical cancer were observed. Further, we shortlisted the 49 immune-related mRNAs based on immune gene signature and predicted their target miRNAs and lncRNAs. A potential ceRNA network of 4 lncRNAs, 10 miRNAs, and 11 mRNAs had a strong correlation for prognosis. Out of 11 protein-coding immune mRNAs, IRF4 and AZGP1 had high degrees of interaction. In addition, the evaluation of immune cell subsets showed increased infiltration of M1 macrophages had better survival outcome. CONCLUSIONS We have identified an immune-related ceRNA network based on differentially expressed transcripts between stages I and II-IV which may help predict the prognosis of cervical cancer.
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Wan X, Hao S, Hu C, Qu R. Identification of a novel lncRNA‐miRNA‐mRNA competing endogenous RNA network associated with prognosis of breast cancer. J Biochem Mol Toxicol 2022; 36:e23089. [PMID: 35532246 DOI: 10.1002/jbt.23089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 11/01/2021] [Accepted: 04/19/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaohui Wan
- Department of Hematology and Oncology The Second Hospital of Jilin University Changchun P. R. China
| | - Shuhong Hao
- Department of Hematology and Oncology The Second Hospital of Jilin University Changchun P. R. China
| | - Chunmei Hu
- Department of Hematology and Oncology The Second Hospital of Jilin University Changchun P. R. China
| | - Rongfeng Qu
- Department of Hematology and Oncology The Second Hospital of Jilin University Changchun P. R. China
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Hassani B, Mollanoori H, Pouresmaeili F, Asgari Y, Ghafouri-Fard S. Constructing mRNA, miRNA, circRNA and lncRNA regulatory network by Analysis of microarray data in breast cancer. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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11
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Identification of the Upregulation of MRPL13 as a Novel Prognostic Marker Associated with Overall Survival Time and Immunotherapy Response in Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:1498924. [PMID: 34868337 PMCID: PMC8639240 DOI: 10.1155/2021/1498924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022]
Abstract
Mitochondrial ribosomal protein (MRPL) genes have been reported to participate in many cellular processes, such as cell proliferation, apoptosis, and cell cycle. Meanwhile, the occurrence rate of breast cancer (BRCA) in China steadily increased. Exploring the prognostic value of MRPL genes in BRCA could provide novel biomarkers for BRCA. In this study, to identify prognosis-related genes in breast cancer, the P value and the hazard ratio (HR) of all genes are analyzed with TCGA database. We revealed higher expression level of CEL, PGK1, WNT3A, USP41, LINC02037, PCMT1, LRP11, MCTS1, TCP1, TMEM31, STK4-AS1, STXBP5, LOC100287036, SLC16A2, MRPL13, DERL1, and TARS was correlated to shorter OS time in BRCA. However, higher expression level of JCHAIN, KLRB1, and TNFRSF14 was correlated to longer OS time in BRCA. The further analysis demonstrated MRPL13 was overexpressed in BRCA. Subtype analysis showed that MRPL13 was overexpressed in luminal, HER2-positive BRCA, and TNBC samples and was highest in TNBC samples. Moreover, we revealed higher expression of MRPL13 was significantly correlated to shorter OS time and higher TMB levels in BRCA. Pan-cancer analysis further revealed the prognostic value of MRPL13 in human cancers. MRPL13 expression was significantly increased in multiple human cancers, such as bladder cancer, colon cancer, liver cancer, and prostate cancer. Pan-cancer TMB and overall survival time showed dysregulation of MRPL13 is significantly related to the OS and TMB levels in various cancers. These results further proved that MRPL13 may be a pan-cancer biomarker for predicting prognosis and the response to immunotherapy.
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Yang Q, Dong YJ. LncRNA SNHG20 promotes migration and invasion of ovarian cancer via modulating the microRNA-148a/ROCK1 axis. J Ovarian Res 2021; 14:168. [PMID: 34836544 PMCID: PMC8626962 DOI: 10.1186/s13048-021-00889-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is characterized by early metastasis and poor prognosis, which threatens the health of women worldwide. Small nucleolar RNA host gene 20 (SNHG20), a long noncoding RNA (lncRNA), has been verified to be significantly up-regulated in several tumors, including OC. MicroRNA-148a (miR-148a)/rho-kinase1 (ROCK1) axis plays an important role in the modulation of tumor development. However, whether SNHG20 can regulate OC progression through miR-148a/ROCK1 axis remains unclear. Normal human ovarian epithelial cell line and four OC cell lines were adopted for in vitro experiments. Real-time PCR was performed to assess the levels of SNHG20 and miR-148a. OC cell proliferation, apoptosis, invasion and migration were detected using clone formation, flow cytometry, transwell, and wound healing assays, respectively. Tumor xenograft assay was applied to evaluate the effect of SNHG20 on tumor growth in vivo. RESULTS Significant higher expression of SNHG20 was observed in OC cell lines. SNHG20 markedly promoted the invasion, migration, proliferation and inhibited the apoptosis of OC cells. SNHG20 enhanced ROCK1 expression by sponging miR-148a, and the direct binding between SNHG20/ROCK1 and miR-148a was identified. CONCLUSION SNHG20 promoted invasion and migration of OC via targeting miR-148a/ROCK1 axis. The present research may provide a novel insight for the therapeutic strategies of OC.
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Affiliation(s)
- Qi Yang
- Department of Obstetrics and Gynecology, China-Japan Union Hospital of Jilin University, No. 126 Xiantai Street, Changchun, 130000, Jilin Province, P. R. China.
| | - Yu-Jie Dong
- Department of Emergency, China-Japan Union Hospital of Jilin University, Changchun, 130000, P. R. China
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13
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Lu C, Luo X, Xing C, Mao Y, Xu Y, Gao W, Wang W, Zhan T, Wang G, Liu Z, Yu C. Construction of a novel mRNA-miRNA-lncRNA network and identification of potential regulatory axis associated with prognosis in colorectal cancer liver metastases. Aging (Albany NY) 2021; 13:14968-14988. [PMID: 34081622 PMCID: PMC8221294 DOI: 10.18632/aging.203049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 04/29/2021] [Indexed: 12/24/2022]
Abstract
Liver metastasis is a leading cause of death in patients with colorectal cancer (CRC). Increasing evidence demonstrates that competing endogenous RNA (ceRNA) networks play important roles in malignant cancers. The purpose of this study was to identify molecular markers and build a ceRNA network as a significant predictor of colorectal liver metastases (CRLM). By integrated bioinformatics analysis, we found that apolipoprotein C1 (APOC1) was upregulated in CRLM and associated with prognosis in patients with CRC and thereby established an APOC1-dependent ceRNA network. By survival analysis, expression analysis, and correlation analysis of each element in the ceRNA network, we identified that ZEB1-AS1, miR-335-5p and APOC1 regulated each other. We further experimentally confirmed that ZEB1-AS1 promoted a CRC progression via regulating the expression of miR-335-5p that controlled the expression of APOC1. Our findings indicate that the ZEB1-AS1-miR-335-5p-APOC1 ceRNA regulatory network is significantly valuable for better prognosis of patients with CRC and as a new therapeutic target for the treatment of CRLM.
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Affiliation(s)
- Chen Lu
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Xiagang Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Cheng Xing
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Yonghuan Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Yuting Xu
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China
| | - Wenjie Gao
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Wulin Wang
- Department of Gastrointestinal Surgery, Jingzhou Central Hospital, Jingzhou 434000, Hubei, China
| | - Tian Zhan
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Guoguang Wang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Zhengxia Liu
- Department of Geriatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Chunzhao Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
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Zhang X, Zhang H, Li J, Ma X, He Z, Liu C, Gao C, Li H, Wang X, Wu J. 6-lncRNA Assessment Model for Monitoring and Prognosis of HER2-Positive Breast Cancer: Based on Transcriptome Data. Pathol Oncol Res 2021; 27:609083. [PMID: 34257572 PMCID: PMC8262145 DOI: 10.3389/pore.2021.609083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
Background: In view of the high malignancy and poor prognosis of human epidermal growth factor receptor 2 (HER2)-positive breast cancer, we analyzed the RNA expression profiles of HER2-positive breast cancer samples to identify the new prognostic biomarkers. Methods: The linear fitting method was used to identify the differentially expressed RNAs from the HER2-positive breast cancer RNA expression profiles in the Cancer Genome Atlas (TCGA). Then, a series of methods including univariate Cox, Kaplan-Meier, and random forests, were used to identify the core long non-coding RNAs (lncRNAs) with stable prognostic value for HER2-positive breast cancer. A clinical feature analysis was performed, and a competing endogenous RNA network was constructed to explore the role of these core lncRNAs in HER2-positive breast cancer. In addition, a functional analysis of differentially expressed messenger RNAs in HER-2 positive breast cancer also provided us with some enlightening insights. Results: The high expression of four core lncRNAs (AC010595.1, AC046168.1, AC069277.1, and AP000904.1) was associated with worse overall survival, while the low expression of LINC00528 and MIR762HG was associated with worse overall survival. The 6-lncRNA model has an especially good predictive power for overall survival (p < 0.0001) and 3-year survival (the area under the curve = 0.980) in HER2-positive breast cancer patients. Conclusion: This study provides a new efficient prognostic model and biomarkers of HER2-positive breast cancer. Meanwhile, it also provides a new perspective for elucidating the molecular mechanisms underlying HER2-positive breast cancer.
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Affiliation(s)
- Xiaoming Zhang
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Haiyan Zhang
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Li
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaoran Ma
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhengguo He
- Columbus Technical College, Columbus, GA, United States
| | - Cun Liu
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chundi Gao
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huayao Li
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xue Wang
- College of Basic Medicine, Qingdao University, Qingdao, China
| | - Jibiao Wu
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
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15
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Misir S, Hepokur C, Aliyazicioglu Y, Enguita FJ. Biomarker potentials of miRNA-associated circRNAs in breast cancer (MCF-7) cells: an in vitro and in silico study. Mol Biol Rep 2021; 48:2463-2471. [PMID: 33774752 DOI: 10.1007/s11033-021-06281-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/11/2021] [Indexed: 11/28/2022]
Abstract
Breast cancer is a heterogeneous disease, which is the most common malignancy in women. The incidence and mortality rates of breast cancer indicate that it is the leading cause of cancer-related with deaths. circRNAs operate as part of competing endogenous RNAs (ceRNAs) mechanisms, which play critical roles in the different biological processes of breast cancer such as proliferation, migration, and apoptosis. The goal of the present study is to identify the potential predictive biomarker for breast cancer diagnosis in the circRNA network by in vitro and in silico analyzes. 40 miRNAs were obtained from the miRWalk database and their combinatorial target genes (potential ceRNAs) were identified with ComiR. We stated that the cancer-specific circRNA genes in MCF-7 cells using the cancer-specific circRNA (CSDC) database, and obtained the ones showing potential ceRNA activity in our previous analysis among them. Identified genes with remarkable expression differences between BCa and normal breast tissue were determined by the GEPIA database. Moreover, the Spearman correlation test in the GEPIA database was used for the statistical analysis of the relationship between DCAF7 and SOGA1, SOGA1 and AVL 9, DCAF7 and AVL 9 gene pairs. And also, DCAF7, SOGA1, and AVL9 gene expression levels were detected in MCF-7 and MCF-10A cells by RT-qPCR method. DCAF7, SOGA1, and AVL9 gene were significantly more expressed to BCa tissue and MCF-7 cells than normal breast tissue and MCF-10 A cells. And also, DCAF7 and SOGA1, SOGA1 and AVL9, DCAF7 and AVL9 genes pairs were found to be significantly correlated with BCa. These genes may be considered as potential predictive biomarkers to discriminate BCa patients from healthy persons. Our preliminary results can supply a new perspective for in vitro and vivo studies in the future.
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Affiliation(s)
- Sema Misir
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, 58140, Sivas, Turkey.
| | - Ceylan Hepokur
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, 58140, Sivas, Turkey
| | - Yuksel Aliyazicioglu
- Department of Medical Biochemistry, Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
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16
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Li LJ, Chang WM, Hsiao M. Aberrant Expression of microRNA Clusters in Head and Neck Cancer Development and Progression: Current and Future Translational Impacts. Pharmaceuticals (Basel) 2021; 14:ph14030194. [PMID: 33673471 PMCID: PMC7997248 DOI: 10.3390/ph14030194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs are small non-coding RNAs known to negative regulate endogenous genes. Some microRNAs have high sequence conservation and localize as clusters in the genome. Their coordination is regulated by simple genetic and epigenetic events mechanism. In cells, single microRNAs can regulate multiple genes and microRNA clusters contain multiple microRNAs. MicroRNAs can be differentially expressed and act as oncogenic or tumor suppressor microRNAs, which are based on the roles of microRNA-regulated genes. It is vital to understand their effects, regulation, and various biological functions under both normal and disease conditions. Head and neck squamous cell carcinomas are some of the leading causes of cancer-related deaths worldwide and are regulated by many factors, including the dysregulation of microRNAs and their clusters. In disease stages, microRNA clusters can potentially control every field of oncogenic function, including growth, proliferation, apoptosis, migration, and intercellular commutation. Furthermore, microRNA clusters are regulated by genetic mutations or translocations, transcription factors, and epigenetic modifications. Additionally, microRNA clusters harbor the potential to act therapeutically against cancer in the future. Here, we review recent advances in microRNA cluster research, especially relative to head and neck cancers, and discuss their regulation and biological functions under pathological conditions as well as translational applications.
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Affiliation(s)
- Li-Jie Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - Wei-Min Chang
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-2-2789–8752
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17
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Zhao M, Shao Y, Xu J, Zhang B, Li C, Gong J. LINC00466 Impacts Cell Proliferation, Metastasis and Sensitivity to Temozolomide of Glioma by Sponging miR-137 to Regulate PPP1R14B Expression. Onco Targets Ther 2021; 14:1147-1159. [PMID: 33642868 PMCID: PMC7903952 DOI: 10.2147/ott.s273264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose LINC00466 is a newfound long non-coding RNA (lncRNA) that has been rarely explored in cancers. However, the specific role and molecular mechanism of LINC00466 in glioma remain to be further elucidated. Methods Bioinformatic analysis was used to screen differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was used to determine the expression of LINC00466, microRNA-137 (miR-137) and protein phosphatase 1 regulatory subunit 14B (PPP1R14B). Dual-luciferase reporter gene assay and RNA binding protein Immunoprecipitation (RIP) assays were employed to verify the binding relationship among LINC00466, miR-137 and PPP1R14B. The sensitivity of glioma cells to temozolomide (TMZ) was measured by cell counting kit-8 (CCK8) assay. The xenograft nude models were used to test the effects of LINC00466 on glioma tumor growth in vivo. Results Highly expressed LINC00466 and PPP1R14B and lowly expressed miR-137 were eventually revealed in glioma tissues. Overexpression of LINC00466 could promote proliferation, metastasis and drug sensitivity to TMZ of glioma cells. LINC00466 could bind to miR-137, and up-regulation of miR-137 could attenuate the enhancing effects caused by LINC00466 overexpression. We took a further step and found that miR-137 could bind to PPP1R14B. Besides, LINC00466 could function as a sponge to miR-137 to regulate PPP1R14B. In addition, overexpression of LINC00466 could promote tumor growth in vivo. Conclusion These findings validate LINC00466 could restrain the miR-137 expression to up-regulate PPP1R14B and therefore promote proliferation, metastasis and resistance to TMZ of glioma.
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Affiliation(s)
- Mingfei Zhao
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yijie Shao
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jinfang Xu
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Buyi Zhang
- Department of Pathology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Chenguang Li
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jie Gong
- Department of Neurointerventional, Zhejiang Hospital of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
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18
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Huaying C, Xing J, Luya J, Linhui N, Di S, Xianjun D. A Signature of Five Long Non-Coding RNAs for Predicting the Prognosis of Alzheimer's Disease Based on Competing Endogenous RNA Networks. Front Aging Neurosci 2021; 12:598606. [PMID: 33584243 PMCID: PMC7876075 DOI: 10.3389/fnagi.2020.598606] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in the pathogenesis of Alzheimer's disease (AD). However, the functions and regulatory mechanisms of lncRNA are largely unclear. Herein, we obtained 3,158 lncRNAs by microarray re-annotation. A global network of competing endogenous RNAs (ceRNAs) was developed for AD and normal samples were based on the gene expressions profiles. A total of 255 AD-deficient messenger RNA (mRNA)-lncRNAs were identified by the expression correlation analysis. Genes in the dysregulated ceRNAs were found to be mainly enriched in transcription factors and micro RNAs (miRNAs). Analysis of the disordered miRNA in the lncRNA-mRNA network revealed that 40 pairs of lncRNA shared more than one disordered miRNA. Among them, nine lncRNAs were closely associated with AD, Parkinson's disease, and other neurodegenerative diseases. Of note, five lncRNAs were found to be potential biomarkers for AD. Real-time quantitative reverse transcription PCR (qRT-PCR) assay revealed that PART1 was downregulated, while SNHG14 was upregulated in AD serum samples when compared to normal samples. This study elucidates the role of lncRNAs in the pathogenesis of AD and presents new lncRNAs that can be exploited to design diagnostic and therapeutic agents for AD.
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Affiliation(s)
- Cai Huaying
- Department of Neurology, Neuroscience Center, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jin Xing
- Department of Neurology, Neuroscience Center, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jin Luya
- Department of Neurology, Neuroscience Center, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Ni Linhui
- Department of Neurology, Neuroscience Center, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Sun Di
- Department of Neurology, Neuroscience Center, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Ding Xianjun
- Department of Orthopedic Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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19
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Liu W, Zhou X, Li Y, Jiang H, Chen A. Long Non-Coding RNA NORAD Inhibits Breast Cancer Cell Proliferation and Metastasis by Regulating miR-155-5p/SOCS1 Axis. J Breast Cancer 2021; 24:330-343. [PMID: 34190442 PMCID: PMC8250099 DOI: 10.4048/jbc.2021.24.e32] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/09/2021] [Accepted: 05/30/2021] [Indexed: 12/02/2022] Open
Abstract
Purpose Non-coding RNA activated by DNA damage (NORAD) has been reported to be a cancer-related long non-coding RNA (lncRNA) implicated in the progression of several cancers; however, its role in breast cancer (BC) has not yet been clarified. Methods Quantitative real-time polymerase chain reaction was used to examine NORAD, microRNA (miR)-155-5p, and suppressor of cytokine signaling 1 (SOCS1) mRNA expression levels. Western blotting was used to analyze SOCS1 protein expression. The malignancy of BC cells was assessed using the cell counting kit-8 (CCK-8), BrdU, and Transwell assays. Bioinformatics analysis, RNA immunoprecipitation assay, and dual-luciferase reporter gene assays were used to verify the targeted relationship between NORAD and miR-155-5p. Additionally, the regulatory effects of NORAD and miR-155-5p on SOCS1 expression were determined by western blotting. Results NORAD expression was significantly reduced in BC cell lines and tissues, and its low expression was associated with poor tumor tissue differentiation. NORAD overexpression repressed BC cell proliferation, migration, and invasion, whereas its knockdown produced the opposite effects. Additionally, miR-155-5p was found to be a target of NORAD, and the biological functions of miR-155-5p and NORAD were counteractive. MiR-155-5p was confirmed to target SOCS1, and SOCS1 was found to be positively regulated by NORAD. Conclusion NORAD suppresses miR-155-5p to upregulate SOCS1, thereby repressing the proliferation, migration, and invasion of BC cells.
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Affiliation(s)
- Weipeng Liu
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, China
| | - Xin Zhou
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, China
| | - Yuanqiang Li
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, China
| | - Hong Jiang
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, China
| | - Aijun Chen
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, China.
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20
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Li H, An X, Li Q, Yu H, Li Z. Construction and analysis of competing endogenous RNA network of MCF-7 breast cancer cells based on the inhibitory effect of 6-thioguanine on cell proliferation. Oncol Lett 2020; 21:104. [PMID: 33376537 PMCID: PMC7751352 DOI: 10.3892/ol.2020.12365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Previous research has proven that 6-thioguanine (6-TG) inhibits the growth of MCF-7 breast cancer cells. Accumulating evidence indicates that long non-coding (lnc)RNAs are involved in the development of various cancer types as competitive endogenous (ce)RNA molecules. The present study was conducted to investigate the regulatory mechanism underlying the function of lncRNAs as ceRNA molecules in MCF-7 cells and to identify more effective prognostic biomarkers for breast cancer treatment. The expression profiles of lncRNAs in untreated MCF-7 cells and 6-TG-treated MCF-7 cells were compared by RNA-seq. The regulatory associations among lncRNAs, micro (mi)RNAs and mRNAs were analyzed and verified by the TargetScan, miRDB and miRTarBas databases. The ceRNA networks were constructed by Cytoscape. The expression levels of two lncRNAs and two miRNAs in the ceRNA network were measured by reverse transcription-quantitative PCR. The OncoLnc and Kaplan-Meier plotter network databases were utilized to determine the effects of lncRNA and miRNA expression on the survival of patients with breast cancer. A ceRNA network was constructed for MCF-7 breast cancer cells treated with 6-TG, and this network may provide valuable information for further research elucidating the molecular mechanism underlying the effects of 6-TG on breast cancer. Moreover, LINC00324, MIR22HG, miR-370-3p and miR-424-5p were identified as potential prognostic and therapeutic biomarkers for breast cancer.
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Affiliation(s)
- Hao Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hao Yu
- College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
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21
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Qi X, Lin Y, Liu X, Chen J, Shen B. Biomarker Discovery for the Carcinogenic Heterogeneity Between Colon and Rectal Cancers Based on lncRNA-Associated ceRNA Network Analysis. Front Oncol 2020; 10:535985. [PMID: 33194594 PMCID: PMC7662689 DOI: 10.3389/fonc.2020.535985] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/05/2020] [Indexed: 02/05/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide. Emerging evidence has revealed that risk factors and metastatic patterns differ greatly between colon and rectal cancers. However, the molecular mechanism underlying their pathogenic differences remains unclear. Therefore, we here aimed to identify non-coding RNA biomarkers based on lncRNA-associated ceRNA network (LceNET) to elucidate the carcinogenic heterogeneity between colon and rectal cancers. Methods A global LceNET in human was constructed by employing experimental evidence-based miRNA-mRNA and miRNA-lncRNA interactions. Then, four context-specific ceRNA networks related to cancer initiation and metastasis were extracted by mapping differentially expressed lncRNAs, miRNAs and mRNAs to the global LceNET. Notably, a novel network-based bioinformatics model was proposed and applied to identify lncRNA/miRNA biomarkers and critical ceRNA triplets for understanding the carcinogenic heterogeneity between colon and rectal cancers. Moreover, the identified biomarkers were further validated by their diagnostic/prognostic performance, expression pattern and correlation analysis. Results Based on network modeling, lncRNA KCNQ1OT1 (AUC>0.85) and SNHG1 (AUC>0.94) were unveiled as common diagnostic biomarkers for the initiation and metastasis of colon and rectal cancers. qRT-PCR analysis uncovered that these lncRNAs had significantly higher expression level in CRC cell lines with high metastatic potential. In particular, KCNQ1OT1 and SNHG1 function in colon and rectal cancers via different ceRNA mechanisms. For example, KCNQ1OT1/miR-484/ANKRD36 axis was involved in the initiation of colon cancer, while KCNQ1OT1/miR-181a-5p/PCGF2 axis was implicated in the metastasis of rectal cancer; the SNHG1/miR-484/ORC6 axis played a role in colon cancer, while SNHG1/miR-423-5p/EZH2 and SNHG1/let-7b-5p/ATP6V1F axes participated in the initiation and metastasis of rectal cancer, respectively. In these ceRNA triplets, miR-484, miR-181a-5p, miR-423-5p and let-7b-5p were identified as miRNA biomarkers with excellent distinguishing ability between normal and tumor tissues, and ANKRD36, PCGF2, EZH2 and ATP6V1F were closely related to the prognosis of corresponding cancer. Conclusion The landscape of lncRNA-associated ceRNA network not only facilitates the exploration of non-coding RNA biomarkers, but also provides deep insights into the oncogenetic heterogeneity between colon and rectal cancers, thereby contributing to the optimization of diagnostic and therapeutic strategies of CRC.
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Affiliation(s)
- Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China.,Center for Systems Biology, Soochow University, Suzhou, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, China.,Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xingyun Liu
- Center for Systems Biology, Soochow University, Suzhou, China.,Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jiajia Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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22
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Ma E, Wang Q, Li J, Zhang X, Guo Z, Yang X. LINC01006 facilitates cell proliferation, migration and invasion in prostate cancer through targeting miR-34a-5p to up-regulate DAAM1. Cancer Cell Int 2020; 20:515. [PMID: 33088221 PMCID: PMC7574442 DOI: 10.1186/s12935-020-01577-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
Background Prostate cancer (PCa) is a kind of malignancy occurring in the prostate gland. Substantial researches have proved the major role of long noncoding RNAs (lncRNAs) in PCa. However, the role of long intergenic non-protein coding RNA 1006 (LINC01006) in PCa has not been investigated yet. Methods RT-qPCR was used to examine the expression levels of LINC01006 and its downstream targets. The function of LINC01006 in PCa was tested by in vitro and in vivo assays. With application of RNA pull down, RNA immunoprecipitation (RIP) and luciferase reporter assays, the interaction among LINC01006, miR-34a-5p and disheveled associated activator of morphogenesis 1 (DAAM1) were verified. Results LINC01006 expression presented high in PCa cell lines. LINC01006 silencing suppressed cell proliferative, migratory, invasive capacities while accelerated apoptotic rate. Besides, LINC01006 knockdown also suppressed tumor growth and metastasis in vivo. Furthermore, miR-34a-5p, a tumor suppressor in PCa, was sponged by LINC01006. Moreover, DAAM1 was targeted by miR-34a-5p and promoted PCa progression. More intriguingly, rescue assays suggested that the inhibitory effect of LINC01006 knockdown on PCa development was offset by DAAM1 overexpression. Conclusions LINC01006 promoted PCa progression by sponging miR-34a-5p to up-regulate DAAM1, providing a novel target for PCa therapy.
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Affiliation(s)
- Enhui Ma
- Department of Urology, Southwest Shandong Hospital Co., Ltd, Liaocheng, 252300 Shandong China
| | - Qianqian Wang
- Department of Nephrology, Zaozhuang Municipal Hospital, Zaozhuang, 277100 Shandong China
| | - Jinhua Li
- Orthopeadic Surgery, Southwest Shandong Hospital Co., Ltd, Liaocheng, 252300 Shandong China
| | - Xinqi Zhang
- Department of Urology, Shandong Zibo Mining Group Central Hospital, Zibo, 255120 Shandong China
| | - Zhenjia Guo
- Department of Urology, Southwest Shandong Hospital Co., Ltd, Liaocheng, 252300 Shandong China
| | - Xiaofeng Yang
- Department of Urology, Zaozhuang Municipal Hospital, NO.41 Longtou Road, Shizhong District, Zaozhuang, 277100 Shandong China
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23
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Li F, Shen ZZ, Xiao CM, Sha QK. YY1-mediated up-regulation of lncRNA LINC00466 facilitates glioma progression via miR-508/CHEK1. J Gene Med 2020; 23:e3287. [PMID: 33037684 DOI: 10.1002/jgm.3287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The abnormal expression of lncRNA LINC00466 (LINC00466) has been demonstrated in several tumor types. However, the expression pattern and functions of LINC00466 in glioma remain uninvestigated. METHODS A reverse transcriptase-polymerase chain reaction (RT-PCR) was utilized to analyze LINC00466 in human glioma tissues and cell lines. Luciferase reporter assays were performed to explore whether YY1 could bind to the promoter region of LINC00466. Cell counting kit-8, flow cytometry, colony-formation, transwell migration and invasion assays were carried out to determine the involvement of INC00466 in glioma. Luciferase assays and pulldown assays were conducted to verify the binding sites. RESULTS We report that LINC00466 expression is increased in glioma cells and tissues. YY1 transcription factor (YY1) can bind directly to the LINC00466 promoter region. Clinical studies revealed that the elevated expression of LINC00466 is closely correlated with an advanced World Health Organization grade (p = 0.008), Karnofsky Performance Status score (p = 0.004) and a short overall survival (p = 0.0035) of glioma patients. Functional assays revealed that LINC00466 knockdown distinctly suppresses glioma cell proliferation, migration, invasion and epithelial-mesenchymal progress, and also promotes apoptosis. Moreover, dual-luciferase reporter assays indicated that LINC00466 acts as an endogenous sponge via binding to miR-508 and decreasing its expression. Luciferase assays and RT-PCR assays demonstrated that checkpoint kinase 1 (CHEK1) is a target of miR-508, and LINC00466 modulates CHEK1 levels by competing for miR-508. LINC00466 may exhibit its anti-oncogenic roles through targeting the miR-508/CHEK1 axis. CONCLUSIONS Our findings identified a novel glioma-related long non-coding RNA, LINC00466, which may provide a potential novel prognostic and therapeutic target for glioma.
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Affiliation(s)
- Fei Li
- Department of Pharmacy, Qianjiang Central Hospital of Chongqing, Chongqing, China
| | - Zheng-Ze Shen
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Chao-Ming Xiao
- Department of Neurology, the Second People's Hospital of Chongqing Dazu District, Chongqing, China
| | - Qian-Kun Sha
- Department of Pharmacy, Chongqing Yangdu Biology Institute, Chongqing, China
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Song Y, Guo NH, Zheng JF. LncRNA-MALAT1 regulates proliferation and apoptosis of acute lymphoblastic leukemia cells via miR-205-PTK7 pathway. Pathol Int 2020; 70:724-732. [PMID: 32754978 DOI: 10.1111/pin.12993] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 11/28/2022]
Abstract
Long non-coding RNA (lncRNA) MALAT1 has been confirmed to function as an oncogene in various solid tumors. MALAT1 level has been shown to be upregulated in relapsed acute lymphoblastic leukemia (ALL) patients, but the mechanism is unclear. This study aims to investigate the functional roles and underlying mechanisms of MALAT1 in ALL. MALAT1 and miR-205 expression were assessed by real-time quantitative polymerase chain reaction (RT-qPCR). MTT assay and flow cytometry were performed to evaluate cell proliferation and apoptosis, respectively. Protein level of protein tyrosine kinase-7 (PTK7) was detected by Western blot assay. Dual luciferase reporter assay was conducted to confirm the binding of MALAT1 and miR-205, as well as miR-205 and PTK7. The levels of MALAT1 and PTK7 were upregulated in ALL samples. In contrast, miR-205 level was downregulated in ALL in ALL samples. Moreover, MALAT1 silencing or miR-205 overexpression restrained proliferation and promoted apoptosis of ALL cells. Mechanistically, MALAT1 sponged miR-205 to regulate PTK7 expression. In summary, MALAT1 affected ALL cell proliferation and apoptosis via regulating miR-205-PTK7 axis. Our results suggest that MALAT1-miR-205-PTK7 axis participates in the proliferation and apoptosis of ALL, which may provide a potential treatment target for ALL.
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Affiliation(s)
- Yuan Song
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ning-Hong Guo
- Institutional Office, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ji-Fu Zheng
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Construction and Analysis of Competing Endogenous RNA Networks for Breast Cancer Based on TCGA Dataset. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4078596. [PMID: 32775417 PMCID: PMC7396095 DOI: 10.1155/2020/4078596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) act as competing endogenous RNAs for microRNAs in cancer metastasis. However, the roles of lncRNA-mediated competing endogenous RNA (ceRNA) networks for breast cancer (BC) are still unclear. Material and Methods. The expression profiles of mRNAs, lncRNAs, and miRNAs with BC were extracted from The Cancer Genome Atlas database. Weighted gene coexpression network analysis was conducted to extract differentially expressed mRNAs (DEmRNAs) that might be core genes. Through miRWalk, TargetScan, and miRDB to predict the target genes, an abnormal lncRNA-miRNA-mRNA ceRNA network with BC was constructed. The survival possibilities of mRNAs, miRNAs, and lncRNAs for patients with BC were determined by Kaplan-Meier survival curves and Oncomine. Results We identified 2134 DEmRNAs, 1059 differentially expressed lncRNAs (DElncRNAs), and 86 differentially expressed miRNAs (DEmiRNAs). We then compose a ceRNA network for BC, including 72 DElncRNAs, 8 DEmiRNAs, and 12 DEmRNAs. After verification, 2 lncRNAs (LINC00466, LINC00460), 1 miRNA (Hsa-mir-204), and 5 mRNAs (TGFBR2, CDH2, CHRDL1, FGF2, and CHL1) were meaningful as prognostic biomarkers for BC patients. In the ceRNA network, we found that three axes were present in 10 RNAs related to the prognosis of BC, namely, LINC00466-Hsa-mir-204-TGFBR2, LINC00466-Hsa-mir-204-CDH2, and LINC00466-Hsa-mir-204-CHRDL1. Conclusion This study highlighted lncRNA-miRNA-mRNA ceRNA related to the pathogenesis of BC, which might be used for latent diagnostic biomarkers and therapeutic targets for BC.
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Coexpression Network Analysis of Genes Related to the Characteristics of Tumor Stemness in Triple-Negative Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7575862. [PMID: 32766313 PMCID: PMC7374213 DOI: 10.1155/2020/7575862] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023]
Abstract
Cancer stem cells (CSCs) are subsets of cells with the ability of self-renewal and differentiation in neoplasm, which are considered to be related to tumor heterogeneity. It has been reported that CSCs act on tumorigenesis and tumor biology of triple-negative breast cancer (TNBC). However, the key genes that cause TNBC showing stem cell characteristics are still unclear. We combined the RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) database and mRNA expression-based stemness index (mRNAsi) to further analyze mRNAsi with regard to molecular subtypes, tumor depth, and pathological staging characteristics of breast cancer (BC). Secondly, we extract the differential gene expression of tumor vs. normal group and TNBC vs. other subtypes of BC group, respectively, and intersect them to achieve precise results. We used a weighted gene coexpression network analysis (WGCNA) to screen significant gene modules and the functions of selected genes including BIRC5, CDC25A, KIF18B, KIF2C, ORC1, RAD54L, and TPX2 were carried out through gene ontology (GO) functional annotation. The Oncomine, bc-GenExMiner v4.4, GeneMANIA, Kaplan-Meier Plotter (KM-plotter), and GEPIA were used to verify the expression level and functions of key genes. In this study, we found that TNBC had the highest stem cell characteristics in BC compared with other subtypes. The lower the mRNAsi score, the better the overall survival and treatment outcome. Seven key genes of TNBC were screened and functional annotation indicated that there were strong correlations between them, relating to nuclear division, organelle fission, mitotic nuclear division, and other events that determine cell fate. Among these genes, we found four genes that were highly associated with adverse survival events. Seven key genes identified in this study were found to be closely related to the maintenance of TNBC stemness, and the overexpression of four showed earlier recurrence. The overall survival (OS) curves of all key genes between differential expression level crossed at around nine-year follow-up, which was consistent with the trend of the OS curve related to mRNAsi. These findings may provide new ideas for screening therapeutic targets in order to depress TNBC stemness.
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Dashti S, Taherian-Esfahani Z, Kholghi-Oskooei V, Noroozi R, Arsang-Jang S, Ghafouri-Fard S, Taheri M. In silico identification of MAPK14-related lncRNAs and assessment of their expression in breast cancer samples. Sci Rep 2020; 10:8316. [PMID: 32433496 PMCID: PMC7239855 DOI: 10.1038/s41598-020-65421-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/05/2020] [Indexed: 01/21/2023] Open
Abstract
Mitogen-activated protein kinase (MAP kinase) pathways participate in regulation of several cellular processes involved in breast carcinogenesis. A number of non-coding RNAs including both microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) regulate or being regulated by MAPKs. We performed an in-silico method for identification of MAPKs with high number of interactions with miRNAs and lncRNAs. Bioinformatics approaches revealed that MAPK14 ranked first among MAPKs. Subsequently, we identified miRNAs and lncRNAs that were predicted to be associated with MAPK14. Finally, we selected four lncRNAs with higher predicted scores (NORAD, HCG11, ZNRD1ASP and TTN-AS1) and assessed their expression in 80 breast cancer tissues and their adjacent non-cancerous tissues (ANCTs). Expressions of HCG11 and ZNRD1ASP were lower in tumoral tissues compared with ANCTs (P values < 0.0001). However, expression levels of MAPK14 and NORAD were not significantly different between breast cancer tissues and ANCTs. A significant association was detected between expression of HCG11 and estrogen receptor (ER) status in a way that tumors with up-regulation of this lncRNA were mostly ER negative (P value = 0.04). Expressions of ZNRD1ASP and HCG11 were associated with menopause age and breast feeding duration respectively (P values = 0.02 and 0.04 respectively). There was a trend towards association between ZNRD1ASP expression and patients' age of cancer diagnosis. Finally, we detected a trend toward association between expression of NORAD and history of hormone replacement therapy (P value = 0.06). Expression of MAPK14 was significantly higher in grade 1 tumors compared with grade 2 tumors (P value = 0.02). Consequently, the current study provides evidences for association between lncRNA expressions and reproductive factors or tumor features.
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Affiliation(s)
- Sepideh Dashti
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Taherian-Esfahani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi-Oskooei
- Department of Laboratory Sciences, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Sharam Arsang-Jang
- Department of Biostatistics and Epidemiology, Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Liu Z, Zhao W, Ren Y, Liu C, Liu X, Xiao J. Comprehensive analysis of the long non-coding RNA-associated competitive endogenous RNA network reveals novel prognostic biomarkers in Wilms' tumor. Oncol Lett 2020; 19:3731-3742. [PMID: 32382326 PMCID: PMC7202313 DOI: 10.3892/ol.2020.11500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/15/2020] [Indexed: 11/06/2022] Open
Abstract
Wilms' tumor (WT) is one of the most common types of renal carcinoma in children. The aim of the present study was to construct a competitive endogenous RNA (ceRNA) regulation network and explore novel prognostic biomarkers for WT. The expression profiles were downloaded from The Cancer Genome Atlas database to identify differentially expressed RNAs (DERNAs). Based on the interactions between microRNAs (miRNAs) and mRNAs/long non-coding RNAs (lncRNAs), a ceRNA network was constructed. Functional enrichment analyses were subsequently conducted to explore the functions of the ceRNA-associated DEmRNAs. Survival analysis was performed to screen for prognosis-associated RNAs and the χ2 test was used to assess the associations between prognosis-associated RNA expression and histology classification/clinical staging. The present study identified 1,784 lncRNAs, 114 miRNAs and 3,337 mRNAs, which were abnormally expressed in WT compared with that in normal samples. By prediction, pairing and network analysis, a ceRNA network consisting of 38 DElncRNAs, 18 DEmiRNAs and 99 DEmRNAs was established. These DEmRNAs were significantly enriched in pathways associated with the occurrence and development of WT. By combining the expression data with survival analysis, seven prognosis-associated RNAs were identified (P<0.05). Of these seven RNAs, two (zinc finger and BTB domain containing 4; and deleted in lymphocytic leukemia 2) were significantly associated with clinical staging and histology classification. Lastly, the expression levels of the seven RNAs were verified in the Gene Expression Omnibus database. The present study revealed that 7 RNAs might be considered as novel prognostic biomarkers and potential treatment targets for therapy in WT. In addition, the ceRNA regulation network could provide novel strategies for further studies on lncRNAs and miRNAs in WT.
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Affiliation(s)
- Zifeng Liu
- Department of Clinical Data Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Wenbo Zhao
- Department of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yuqing Ren
- Tianpeng Technology Co., Ltd, Guangzhou, Guangdong 510600, P.R. China
| | - Chang Liu
- Department of Clinical Data Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Xun Liu
- Department of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Jian Xiao
- Department of Medical Oncology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510655, P.R. China
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Zhao K, Zhang Q, Wang Y, Zhang J, Cong R, Song N, Wang Z. The construction and analysis of competitive endogenous RNA (ceRNA) networks in metastatic renal cell carcinoma: a study based on The Cancer Genome Atlas. Transl Androl Urol 2020; 9:303-311. [PMID: 32420136 PMCID: PMC7215020 DOI: 10.21037/tau.2020.02.17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The pathogenesis of metastatic renal cell carcinoma (mRCC), one of the most common malignant neoplasms, remains unknown. Studies on competitive endogenous RNAs (ceRNAs) have uncovered new interactions between RNAs, which suggest their roles in cancer pathogenesis. However, the role of ceRNA networks in mRCC has not yet been studied. Thus, this study aims to explore the role of ceRNA networks in mRCC development and identify potential prognostic indicators. Methods We analyzed RNA sequencing data of mRCC patients, which had been obtained from The Cancer Genome Atlas (TCGA) database. Next, differentially expressed long-noncoding RNAs (DElncRNAs), differentially expressed micro RNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in mRCC and clear cell RCC (ccRCC) samples were identified using the edgeR package that is available in R software. Moreover, based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID), enrichment analyses for biological processes and pathways functional were performed. As such, we built a ceRNA network and performed a survival analysis using the survival package in R. Results A total of 369 DElncRNAs, 12 DEmiRNAs, and 728 DEmRNAs were identified for further analysis. Of these, 11 lncRNAs, 20 mRNAs, and 2 miRNAs were included in the ceRNA network. Moreover, 7 of the 11 lncRNAs and 3 of the 20 mRNAs were associated with the overall survival of mRCC patients (P<0.05). Conclusions Collectively, our findings allow a deepened understanding of the molecular mechanism of the ceRNA network and its role in mRCC development, which can guide both mRCC therapy and related future research.
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Affiliation(s)
- Kai Zhao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Qijie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yamin Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jiayi Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ninghong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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30
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Jia X, Meng W, Zhang L, Jia Y, Shi Y, Tong Z. Construction of differentially expressed Her-2 related lncRNA-mRNA-miRNA ceRNA network in Her-2 positive breast cancer. Transl Cancer Res 2020; 9:2527-2533. [PMID: 35117612 PMCID: PMC8798026 DOI: 10.21037/tcr.2020.03.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/21/2020] [Indexed: 12/19/2022]
Abstract
Background Her-2 positive subtype breast cancer is characterized as Her-2 gene amplification with poor survival and increased invasiveness accounting for 20–30% of invasive infiltrated breast cancer. A lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network is constructed to detect Her-2 specific RNAs in the development and progression of HER-2 positive breast cancer which may overcoming the anti-HER-2 therapy resistance of breast cancer cells. Methods One thousand one hundred and nine breast cancer samples obtained from The Cancer Genome Atlas (TCGA) database were classified into two cohorts including ER+/PR+ (n=461) and ER-/PR- breast cancer (n=152). Differently expressed mRNAs, lncRNAs and miRNAs were screened in ER+/PR+ and ER-/PR- breast cancer cohorts, respectively. lncRNA-miRNA interactions were preformed to predicted and verified by miRcode. miRNA-mRNA interactions were selected to predict targeted mRNAs of miRNAs by miRanda, Targetscan and miRTarBase. Results lncRNA-miRNA-mRNA ceRNA network was constructed by retained lncRNAs, miRNAs and mRNAs. Fifteen DEmiRNAs, 129 DElncRNAs and 269 DEmRNAs were retained in ER+/PR+ cohort after intersection with DEmiRNAs, DElncRNAs and DEmRNAs between breast cancer and normal tissues. Six hundred and ninety-three DEmRNAs, 25 DEmiRNAs and 364 DElncRNAs were retained in ER-/PR- cohort. ceRNA network in ER+/PR+ breast cancer cohort was constructed of the interactions of 4 DElncRNA–DEmiRNA pairs and 2 DEmiRNA–DEmRNA pairs included 4 DElncRNAs, 1 DEmiRNAs, and 2 DEmRNAs. ceRNA network in ER-/PR- breast cancer cohort was constructed of the interactions of 24 DElncRNA–DEmiRNA pairs and 1 DEmiRNA–DEmRNA pairs included 19 DElncRNAs, 4 DEmiRNAs, and 1 DEmRNA. MIR7-3HG- hsa-mir-204-NTRK2 axis was identified in both ER+/PR+ and ER-/PR- cohort in our study. Conclusions Based on the ceRNA hypothesis, a potential Her-2 related regulatory ceRNA networks are constructed which may provide novel insights into the mechanism underlying the biological processes of Her-2 positive breast cancer.
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Affiliation(s)
- Xiaochen Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
| | - Wenjing Meng
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
| | - Lu Zhang
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
| | - Yongsheng Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
| | - Yehui Shi
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
| | - Zhongsheng Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
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Zhang J, Cong R, Zhang Q, Zeng T, Song R, Meng X. Integrative analysis of ceRNA network and DNA methylation associated with gene expression in malignant pheochromocytomas: a study based on The Cancer Genome Atlas. Transl Androl Urol 2020; 9:344-354. [PMID: 32420140 PMCID: PMC7214974 DOI: 10.21037/tau.2020.01.29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Competitive endogenous RNAs (ceRNAs) have revealed a new mechanism of interaction between RNAs. Epigenetic regulation in the gene expression dynamics has become increasingly important in malignant pheochromocytomas (PCCs). We performed an integrative analysis of ceRNA networks and DNA methylation to identify key biomarkers and contribute to the understanding of the molecular biological mechanisms of malignant PCCs. Methods Differentially expressed genes in malignant PCCs and controls were identified from The Cancer Genome Atlas database by using the Limma package in R (v3.4.4). An abnormal lncRNA-miRNA-mRNA ceRNA network was constructed for malignant PCCs, and function enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery. For DNA methylation datasets, the methylation analysis package was used in identifying differential methylation genes, and potential prognostic genes were identified by Kaplan-Meier survival analysis. Results A total of 447 lncRNAs, 26 miRNAs, and 1,607 mRNAs were found to be differentially expressed in malignant PCCs as compared with those in normal samples. We then constructed an abnormal lncRNA-miRNA-mRNA ceRNA network for malignant PCCs. The network consisted of 12 lncRNAs, 6 miRNAs, and 220 mRNAs. Functional enrichment analysis showed that differentially expressed mRNAs were particularly enriched in the biological process, cellular component, and molecular function. Furthermore, four differentially expressed mRNAs from ceRNAs were identified through the cross-analysis of gene expression and DNA methylation profiles. LncRNA C9orf147 and 6 out of 220 mRNAs were indicated as prognostic biomarkers for patients with malignant PCCs (P<0.05). Conclusions Our research increases the understanding of the pathogenesis of malignant PCCs and offers potential genes as underlying therapeutic targets or prognostic biomarkers.
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Affiliation(s)
- Jiayi Zhang
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Rong Cong
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Qijie Zhang
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Tengyue Zeng
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Rijin Song
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xianghu Meng
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Candidate lncRNA-microRNA-mRNA networks in predicting non-small cell lung cancer and related prognosis analysis. J Cancer Res Clin Oncol 2020; 146:883-896. [PMID: 32124023 DOI: 10.1007/s00432-020-03161-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/17/2020] [Indexed: 12/29/2022]
Abstract
PURPOSE The role of non-coding RNA, once thought to be dark matter, is increasingly prominent in cancer. Our article explores the effect of non-coding RNA in lung adenocarcinoma and lung squamous cell carcinoma by mining TCGA public database. METHODS Download the data by applying the official TCGA software. The data were analyzed by R data analysis packages, 'edgeR', 'gplots' and 'survival'. We better illustrate the potential networks of lung cancer genes by constructing ceRNAs, using Cytoscape software. RESULTS We obtained genes which were differentially expressed in lung adenocarcinoma and lung squamous cell carcinoma analysis. Within these differentially expressed genes, we also conducted a survival analysis to find differentially expressed genes associated with prognosis in both lung adenocarcinoma and lung squamous cell carcinoma. Based on genes differentially expressed of both lung adenocarcinoma and lung squamous cell carcinoma, we constructed a ceRNA network to illustrate the mechanism of lung adenocarcinoma and lung squamous cell carcinoma. Our study analyzed genes which were differentially expressed in lung adenocarcinoma and lung squamous cell carcinoma using the TCGA database. CONCLUSION Based on this, the prognosis in both lung squamous cell carcinoma and lung adenocarcinoma was analyzed. We have also constructed a ceRNA network to provide a basis for the study of ceRNA in lung adenocarcinoma and lung squamous cell carcinoma.
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Dong Y, Xiao Y, Shi Q, Jiang C. Dysregulated lncRNA-miRNA-mRNA Network Reveals Patient Survival-Associated Modules and RNA Binding Proteins in Invasive Breast Carcinoma. Front Genet 2020; 10:1284. [PMID: 32010179 PMCID: PMC6975227 DOI: 10.3389/fgene.2019.01284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most common cancer in women, but few biomarkers are effective in clinic. Previous studies have shown the important roles of non-coding RNAs in diagnosis, prognosis, and therapy selection for breast cancer and have suggested the significance of integrating molecules at different levels to interpret the mechanism of breast cancer. Here, we collected transcriptome data including long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA for ~1,200 samples, including 1079 invasive breast carcinoma samples and 104 normal samples, from The Cancer Genome Atlas (TCGA) project. We identified differentially expressed lncRNAs, miRNAs, and mRNAs that distinguished invasive carcinoma samples from normal samples. We further constructed an integrated dysregulated network consisting of differentially expressed lncRNAs, miRNAs, and mRNAs and found housekeeping and cancer-related functions. Moreover, 58 RNA binding proteins (RBPs) involved in biological processes that are essential to maintain cell survival were found in the dysregulated network, and 10 were correlated with overall survival. In addition, we identified two modules that stratify patients into high- and low-risk subgroups. The expression patterns of these two modules were significantly different in invasive carcinoma versus normal samples, and some molecules were high-confidence biomarkers of breast cancer. Together, these data demonstrated an important clinical application for improving outcome prediction for invasive breast cancers.
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Affiliation(s)
- Yu Dong
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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Wang Z, Liu T, Li G, Cao Z. The exploration of new therapeutic targets for HPV-negative head and neck squamous cell cancer through the construction of a ceRNA network and immune microenvironment analysis. J Cell Biochem 2020; 121:3426-3437. [PMID: 31898341 DOI: 10.1002/jcb.29615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/11/2019] [Indexed: 01/11/2023]
Abstract
Previous studies have shown that human papillomavirus (HPV)-negative patients with head and neck squamous cell cancer (HNSCC) suffer from an unsatisfactory prognosis. Long noncoding RNAs (lncRNAs) have been verified to participate in many biological processes, including regulating gene expression as competing endogenous RNAs (ceRNAs), while few studies focused the ceRNA network regulation mechanism in patients with HPV-negative HNSCC tumor. Meanwhile, the immune microenvironment may be critical in the development and prognosis of HPV-negative tumors. Our study aimed to further investigate the pathogenesis and potential biomarkers for the diagnosis, therapy and prognosis of HPV-negative HNSCC through a ceRNA network. Comprehensively analyzing the sequencing data of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) in The Cancer Genome Atlas HNSCC dataset, we constructed a differentially expressed ceRNA network containing 131 lncRNAs, 35 miRNAs and 162 mRNAs. Then, survival analysis in the network was cited to explore the prognostic biomarkers. Eight mRNAs, nine lncRNAs, and one miRNA were identified to be associated with prognosis. Neuropilin (NRP) binding function, retinoid X receptor (RXR) binding, and the vascular endothelial growth factor (VEGF) signaling pathway were associated with the enrichment analysis, and they also related to the immune microenvironment. Combined with the analysis of the immune microenvironment differences, we obtained new targeted therapies using an RXR agonist, or a combination of the VEGF monoclonal antibody and an NRP antagonist, which may provide a promising future for HPV-negative HNSCC patients.
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Affiliation(s)
- Zuoyuan Wang
- Department of Forensic Pathology, School of Forensic Medicine China Medical University, Shenyang, Liaoning, China.,The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Tianyi Liu
- The Second Clinical College, China Medical University, Shenyang, Liaoning, China
| | - Guangqi Li
- The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Zhipeng Cao
- Department of Forensic Pathology, School of Forensic Medicine China Medical University, Shenyang, Liaoning, China
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35
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Feng W, Zhai C, Shi W, Zhang Q, Yan X, Wang J, Wang Q, Li M. Clinicopathological and prognostic value of LINC01296 in cancers: a meta-analysis. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:3315-3321. [PMID: 31385542 DOI: 10.1080/21691401.2019.1648284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Objective: The long intergenic non-coding RNA 01296 (LINC01296) has been reported to be overexpressed in multiple tumours. However, the role of LINC01296 in clinicopathologic and prognostic value in cancers remains completely unknown. The aim of the present meta-analysis was to comprehensively elucidate the correlation between LINC01296 with clinicopathological features and survival outcomes in tumours. Methods: Electronic databases of PubMed, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang Database were used to search relevant studies. The role of LINC01296 in cancers was evaluated by pooled hazard ratios (HRs), odds ratios (ORs) and 95% confidence intervals (CIs). Results: In total, nine studies compromising 720 participants were enrolled in this analysis. The pooled results showed increased LINC01296 expression could predict unfavourable overall survival (OS) (HR = 1.89, 95%CI = 1.47-2.43, p < .001). Additionally, elevated LINC01296 expression was correlated with clinical stage (OR = 2.95, 95%CI = 2.13-4.08, p < .001), lymph node metastasis (OR = 2.76, 95%CI = 2.00-3.81, p < .001), tumour size (OR = 2.80, 95%CI = 1.77-4.41, p < .001), and tumour differentiation (OR = 2.11, 95%CI = 1.36-3.27, p < .001) in patients with cancers. Conclusion: The results of this meta-analysis indicated LINC01296 was a novel biomarker for prognosis and clinicopathological parameters in cancers.
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Affiliation(s)
- Wei Feng
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Cui Zhai
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Wenhua Shi
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Qianqian Zhang
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Xin Yan
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Jian Wang
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Qingting Wang
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
| | - Manxiang Li
- a Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , Shaanxi , China
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36
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Li F. Expression of miR-221 and miR-489 in breast cancer patients and their relationship with prognosis. Oncol Lett 2019; 19:1523-1529. [PMID: 31966077 PMCID: PMC6956176 DOI: 10.3892/ol.2019.11196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Expression of miR-221 and miR-489 in breast cancer patients and their prognostic value were investigated. Sixty-two breast cancer patients admitted to the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine for tumor surgery, from July 2014 to January 2016, were selected as the research group (RG), and 27 female adults who underwent physical examination during the same period were selected as the control group (CG). miR-221 and miR-489 expression levels in the blood samples of the breast cancer patients and the healthy female adults were detected by fluorescence reverse transcription-quantitative PCR (RT-qPCR), and the relationship of the expression levels of miR-221 and miR-489 with the disease prognosis was analyzed. The expression levels of miR-221 and miR-489 in the blood samples of breast cancer patients were 7.13±1.19 and 0.88±0.09, respectively, and those in the blood samples of healthy individuals were 5.82±0.84 and 1.01±0.12, respectively. The expression level of miR-221 in the RG was significantly higher than that in the CG (P<0.01), while the expression level of miR-489 in the RG was significantly lower than that in the CG (P<0.01). The area under the curve (AUC) of miR-221 was 0.769, and the AUC of miR-489 was 0.805. When AUC was equal to 0.88, the combined detection of the two had higher sensitivity and specificity than the single detection. The 3-year survival rates of miR-221 low-expression group and miR-489 high-expression group were significantly higher than those of the miR-221 high-expression group and miR-489 low-expression group (P<0.05). miR-221 expression was upregulated and miR-489 expression was downregulated in blood samples of breast cancer patients, which had a certain impact on the patients survival. In the future, miR-221 can be used as an effective indicator for diagnosis, treatment and prognosis of breast cancer.
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Affiliation(s)
- Fanfan Li
- Department of Breast Surgery, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, P.R. China
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37
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Zhong G, Lou W, Yao M, Du C, Wei H, Fu P. Identification of novel mRNA-miRNA-lncRNA competing endogenous RNA network associated with prognosis of breast cancer. Epigenomics 2019; 11:1501-1518. [PMID: 31502865 DOI: 10.2217/epi-2019-0209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To identify novel competing endogenous RNA (ceRNA) network related to patients prognosis in breast cancer. Materials & methods: Dysregulated mRNA based on intersection of three Gene Expression Omnibus and The Cancer Genome Atlas datasets were analyzed by bioinformatics. Results: In total 72 upregulated and 208 downregulated genes were identified. Functional analysis showed that some pathways related to cancer were significantly enriched. By means of stepwise reverse prediction and validation from mRNA to lncRNA, 19 hub genes, nine key miRNA and four key lncRNAs were identified by expression and survival analysis. Ultimately, the coexpression analysis identified RRM2-let-7a-5p-SNHG16/MAL2 as key ceRNA subnetwork associated with prognosis of breast cancer. Conclusion: We successfully constructed a novel ceRNA network, among which each component was significantly associated with breast cancer prognosis.
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Affiliation(s)
- Guansheng Zhong
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, PR China
| | - Weiyang Lou
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Organ Transplantation, Zhejiang University, 79 Qingchun Road, Zhejiang Province, Hangzhou 310003, PR China
| | - Minya Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, PR China
| | - Chengyong Du
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, PR China
| | - Haiyan Wei
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, PR China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, PR China
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38
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LncRNA TRG-AS1 promotes glioblastoma cell proliferation by competitively binding with miR-877-5p to regulate SUZ12 expression. Pathol Res Pract 2019; 215:152476. [DOI: 10.1016/j.prp.2019.152476] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/13/2019] [Accepted: 05/25/2019] [Indexed: 01/10/2023]
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39
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Wang X, Xu Z, Chen X, Ren X, Wei J, Zhou S, Yang X, Zeng S, Qian L, Wu G, Gong Z, Yan Y. A tropomyosin receptor kinase family protein, NTRK2 is a potential predictive biomarker for lung adenocarcinoma. PeerJ 2019; 7:e7125. [PMID: 31245181 PMCID: PMC6585899 DOI: 10.7717/peerj.7125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/14/2019] [Indexed: 02/05/2023] Open
Abstract
Neurotrophic receptor tyrosine kinase 2 (NTRK2) is a member of the tropomyosin receptor kinase family associated with the tumor development. However, the detailed function of NTRK2 in lung cancer, especially in lung adenocarcinoma (LUAD), is still not fully understood. Here, we investigated the effects of NTRK2 on LUAD biology. Through analyzing bioinformatics data derived from several databases, such as Oncomine, Gene Expression Profiling Interactive Analysis and UALCAN, we found that NTRK2 expression was significantly decreased in LUAD tissues. Clinical data acquired from Wanderer database, which is linked to The Cancer Genome Atlas database, demonstrated that the expression and methylation site of NTRK2 were significantly related to the clinical characteristics and prognosis of LUAD. Furthermore, NTRK2 expression was increased remarkably after treatment with the protein kinase B (AKT) inhibitor MK2206 and the anticancer agent actinomycin D. Functional enrichment analysis of NTRK2-associated coexpression genes was further conducted. Together, our results suggested that downregulated NTRK2 might be used in the diagnostic and prognostic evaluation of LUAD patients, or as a potential therapeutic target for the treatment of LUAD.
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Affiliation(s)
- Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinxin Ren
- Center for Molecular Medicine, Xiangya Hospital, Key Laboratory of Molecular Radiation Oncology of Hunan Province, Central South University, Changsha, Hunan, China
| | - Jie Wei
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuyi Zhou
- Department of General Surgery, Hunan Provincial People's Hospital Xingsha Branch (People's Hospital of Changsha County), Changsha, Hunan, China
| | - Xue Yang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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40
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Zhang X, Gao C, Liu L, Zhou C, Liu C, Li J, Zhuang J, Sun C. DNA methylation‐based diagnostic and prognostic biomarkers of nonsmoking lung adenocarcinoma patients. J Cell Biochem 2019; 120:13520-13530. [PMID: 30920015 DOI: 10.1002/jcb.28627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaoming Zhang
- College of Traditional Chinese Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Chundi Gao
- College of First Clinical Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Lijuan Liu
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Chao Zhou
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Cun Liu
- College of First Clinical Medicine Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Jia Li
- School of Clinical Medicine Weifang Medical University Weifang Shandong PR China
| | - Jing Zhuang
- Department of Traditional Chinese Medicine Oncology Weifang Traditional Chinese Hospital Weifang Shandong PR China
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
| | - Changgang Sun
- Department of Oncology Affiliated Hospital of Weifang Medical University Weifang Shandong PR China
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