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Wang Z, Yin X, Yang P, Gong B, Liu H. miR-1202 regulates BPH-1 cell proliferation, apoptosis, and epithelial-to-mesenchymal transition through targeting HMGCL. Acta Biochim Biophys Sin (Shanghai) 2024; 56:675-687. [PMID: 38551020 PMCID: PMC11177111 DOI: 10.3724/abbs.2024001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/02/2023] [Indexed: 05/31/2024] Open
Abstract
Benign prostatic hyperplasia (BPH) is the expansion of the prostate gland that results in urinary symptoms. Both the epithelial-to-mesenchymal transition (EMT) and the Wnt signaling pathway are associated with BPH pathology. In this study, we find that miR-1202 is increased in BPH samples. Overexpression of miR-1202 in TGF-β-treated BPH-1 cells enhances cell survival and DNA synthesis and inhibits cell apoptosis, whereas miR-1202 inhibition partially abolishes the effects of TGF-β on BPH-1 cells. miR-1202 overexpression reduces E-cadherin level but elevates vimentin, N-cadherin, and snail levels, whereas miR-1202 inhibition partially attenuates the effects of TGF-β on EMT markers. Regarding the Wnt/β-catenin pathway, miR-1202 overexpression significantly enhances, whereas miR-1202 inhibition partially decreases, the promotive effects of TGF-β on Wnt1, c-Myc, and cyclin D1 proteins. 3-Hydroxy-3-methylglutaryl-CoA lyase (HMGCL) is a direct downstream target of miR-1202, and miR-1202 inhibits HMGCL expression through binding to its 3'UTR. Overexpression of HMGCL significantly reduces the effect of miR-1202 overexpression on the phenotypes of BPH-1 cells by inhibiting cell survival and promoting apoptosis. Similarly, HMGCL overexpression has the opposite effects on EMT markers and the Wnt/β-catenin signaling, and markedly alleviates the effects of miR-1202 overexpression. Finally, in the BPH rat model, Ki67 and vimentin levels are elevated, but E-cadherin and HMGCL levels are reduced. In conclusion, miR-1202 is upregulated in benign prostatic hyperplasia; miR-1202 enhances epithelial cell proliferation, suppresses cell apoptosis, and promotes EMT by targeting HMGCL. The Wnt/β-catenin pathway may participate in the miR-1202/HMGCL axis-mediated regulation of BPH-1 cell phenotypes.
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Affiliation(s)
- Zhenting Wang
- />Department of UrologyAffiliated Haikou Hospital of Xiangya Medical SchoolCentral South UniversityHaikou570208China
| | - Xianlai Yin
- />Department of UrologyAffiliated Haikou Hospital of Xiangya Medical SchoolCentral South UniversityHaikou570208China
| | - Peng Yang
- />Department of UrologyAffiliated Haikou Hospital of Xiangya Medical SchoolCentral South UniversityHaikou570208China
| | - Binghao Gong
- />Department of UrologyAffiliated Haikou Hospital of Xiangya Medical SchoolCentral South UniversityHaikou570208China
| | - Haifang Liu
- />Department of UrologyAffiliated Haikou Hospital of Xiangya Medical SchoolCentral South UniversityHaikou570208China
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Zhan C, Liu K, Zhang Y, Zhang Y, He M, Wu R, Bi C, Shen B. Myocardial infarction unveiled: Key miRNA players screened by a novel lncRNA-miRNA-mRNA network model. Comput Biol Med 2023; 160:106987. [PMID: 37141653 DOI: 10.1016/j.compbiomed.2023.106987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Myocardial infarction (MI) is a major contributor to global mortality, and microRNAs (miRNAs) are important in its pathogenesis. Identifying blood miRNAs with clinical application potential for the early detection and treatment of MI is crucial. METHODS We obtained MI-related miRNA and miRNA microarray datasets from MI Knowledge Base (MIKB) and Gene Expression Omnibus (GEO), respectively. A new feature called target regulatory score (TRS) was proposed to characterize the RNA interaction network. MI-related miRNAs were characterized using TRS, transcription factor (TF) gene proportion (TFP), and ageing-related gene (AG) proportion (AGP) via the lncRNA-miRNA-mRNA network. A bioinformatics model was then developed to predict MI-related miRNAs, which were verified by literature and pathway enrichment analysis. RESULTS The TRS-characterized model outperformed previous methods in identifying MI-related miRNAs. MI-related miRNAs had high TRS, TFP, and AGP values, and combining the three features improved prediction accuracy to 0.743. With this method, 31 candidate MI-related miRNAs were screened from the specific-MI lncRNA-miRNA-mRNA network, associated with key MI pathways like circulatory system processes, inflammatory response, and oxygen level adaptation. Most candidate miRNAs were directly associated with MI according to literature evidence, except hsa-miR-520c-3p and hsa-miR-190b-5p. Furthermore, CAV1, PPARA and VEGFA were identified as MI key genes, and were targeted by most of the candidate miRNAs. CONCLUSIONS This study proposed a novel bioinformatics model based on multivariate biomolecular network analysis to identify putative key miRNAs of MI, which deserve further experimental and clinical validation for translational applications.
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Affiliation(s)
- Chaoying Zhan
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China
| | - Kai Liu
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxin Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China
| | - Yingbo Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Mengqiao He
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China
| | - Rongrong Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China
| | - Cheng Bi
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China
| | - Bairong Shen
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, Sichuan, China.
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Xuan S, Zhang J, Guo Q, Zhao L, Yao X. A Diagnostic Classifier Based on Circulating miRNA Pairs for COPD Using a Machine Learning Approach. Diagnostics (Basel) 2023; 13:diagnostics13081440. [PMID: 37189541 DOI: 10.3390/diagnostics13081440] [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] [Revised: 03/29/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is highly underdiagnosed, and early detection is urgent to prevent advanced progression. Circulating microRNAs (miRNAs) have been diagnostic candidates for multiple diseases. However, their diagnostic value has not yet been fully established in COPD. The purpose of this study was to develop an effective model for the diagnosis of COPD based on circulating miRNAs. We included circulating miRNA expression profiles of two independent cohorts consisting of 63 COPD and 110 normal samples, and then we constructed a miRNA pair-based matrix. Diagnostic models were developed using several machine learning algorithms. The predictive performance of the optimal model was validated in our external cohort. In this study, the diagnostic values of miRNAs based on the expression levels were unsatisfactory. We identified five key miRNA pairs and further developed seven machine learning models. The classifier based on LightGBM was selected as the final model with the area under the curve (AUC) values of 0.883 and 0.794 in test and validation datasets, respectively. We also built a web tool to assist diagnosis for clinicians. Enriched signaling pathways indicated the potential biological functions of the model. Collectively, we developed a robust machine learning model based on circulating miRNAs for COPD screening.
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Affiliation(s)
- Shurui Xuan
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
| | - Jiayue Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
| | - Qinxing Guo
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
| | - Liang Zhao
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, 264 Guangzhou Road, Nanjing 210029, China
| | - Xin Yao
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
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Dinh P, Peng J, Tran T, Wu D, Tran C, Dinh T, Pan S. Identification of hsa_circ_0001445 of a novel circRNA-miRNA-mRNA regulatory network as potential biomarker for coronary heart disease. Front Cardiovasc Med 2023; 10:1104223. [PMID: 36998978 PMCID: PMC10043405 DOI: 10.3389/fcvm.2023.1104223] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/22/2023] [Indexed: 03/17/2023] Open
Abstract
ObjectsTo evaluate the hsa_circ_0001445 level in peripheral blood leukocytes of patients with coronary heart disease (CHD) and its related clinical factors, and predict its circRNA-miRNA-mRNA regulatory network in CHD pathogenesis via bioinformatics analysis.MethodsPeripheral blood leukocytes were isolated from the whole blood samples of 94 CHD patients (aged 65.96 ± 9.78 years old) and 126 healthy controls (aged 60.75 ± 8.81 years old). qRT-PCR was used to quantify the expression level of circRNA and subsequently analyze its association with CHD clinical parameters. Via bioinformatics algorithm and GEO datasets, differential miRNA expression was evaluated using the Limma package. A miRNA-mRNA regulatory network was predicted by cyTargetLinker. ClusterProfiler was employed to perform functional enrichment analysis of the circRNA network to investigate its role in CHD pathogenesis.ResultsThe expression of hsa_circ_0001445 in peripheral blood leukocytes of CHD patients was downregulated compared with that of healthy controls. Positive correlations were evident between hsa_circ_0001445 expression level and the levels of hemoglobin, triglycerides, high- and low-density lipoprotein cholesterol. A significant negative correlation was also found between hsa_circ_0001445 expression level and age and the neutrophil level. Low expression of hsa_circ_0001445 exhibited a discriminatory ability between CHD patients and healthy controls with a sensitivity of 67.5% and a specificity of 76.6% (p < 0.05). By bioinformatics analysis, 405 gene ontology terms were identified. The Kyoto Encyclopedia of Genes and Genomes terms focused principally on the PI3K-Akt signaling pathway. hsa_circ_0001445 was associated with the expression of three miRNAs that may regulate 18 genes involved in KEGG processes: hsa-miR-507, hsa-miR-375–3p, and hsa-miR-942–5p.ConclusionThe hsa_circ_0001445 level in peripheral blood leukocytes may serve as a biomarker for CHD diagnosis. Our work on circRNA-miRNA-mRNA networks suggests a potential role for hsa_circ_0001445 in CHD development.
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Affiliation(s)
- PhongSon Dinh
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- College of Medicine and Pharmacy, Duy Tan University, Danang, Vietnam
| | - JunHua Peng
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Center for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - ThanhLoan Tran
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- Department of Immunology and Pathophysiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - DongFeng Wu
- Department of the Geriatric Cardiology, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - ChauMyThanh Tran
- College of Medicine and Pharmacy, Duy Tan University, Danang, Vietnam
| | - ThiPhuongHoai Dinh
- Department of Neurosurgery, Hue University Hospital, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - ShangLing Pan
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Center for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, China
- Correspondence: ShangLing Pan
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Aparicio-Puerta E, Hirsch P, Schmartz GP, Fehlmann T, Keller V, Engel A, Kern F, Hackenberg M, Keller A. isomiRdb: microRNA expression at isoform resolution. Nucleic Acids Res 2022; 51:D179-D185. [PMID: 36243964 PMCID: PMC9825445 DOI: 10.1093/nar/gkac884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023] Open
Abstract
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.
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Affiliation(s)
| | | | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Rejuvenome, Astera Institute, Berkeley, CA 94705, USA
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Department for Internal Medicine II, Saarland University Hospital, 66421 Homburg, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, Universidad de Granada, 18071 Granada, Spain
| | - Andreas Keller
- To whom correspondence should be addressed. Tel: +49 681 30268611; Fax: +49 681 30268610;
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Shi ZE, Zhang MY, Liu JY, Zhang WD, Hu DM, Wang QX, Ji XL, Jiang YY, Qu YQ. Autophagy Induced by BCL2-Related ceRNA Network Participates in the Occurrence of COPD. Int J Chron Obstruct Pulmon Dis 2022; 17:791-808. [PMID: 35431545 PMCID: PMC9005473 DOI: 10.2147/copd.s347733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is a predominant cause of mortality worldwide. Autophagy, which depends on a lysosomal degradation pathway, plays an essential role in the occurrence of COPD. The aim of our study was to identify the potential function of autophagy and construct a BCL2-related competing endogenous RNA (ceRNA) network that induces autophagy in COPD. Methods Blood sample data from GSE31568, GSE24709, and GSE61741 were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs in COPD and controls were identified via GEO2R. Transcription factors were obtained from FunRich. DIANA, miRDB, miRTarBase, and TargetScan were used to predict target genes of miRNAs. Autophagy genes were collected from the Human Autophagy Database (HADb). The GSE151052 dataset was used to identify autophagy-related differentially expressed genes in tissues. Functional enrichment and protein–protein interaction (PPI) network analyses were conducted via Metascape and the STRING network. Spearman correlation analysis was used to analyze the relationship between autophagy-related differentially expressed genes and lung function. The BCL2-related ceRNA network was modeled by Cytoscape. Results We obtained 41 differentially expressed miRNAs and 10 significantly different transcription factors. We identified 19 autophagy-related differentially expressed genes that were significantly different (P<0.05) in tissue samples. The most significant enrichment in Metascape was an autophagy item, which further confirmed autophagy participation in the occurrence of COPD. PPI network analysis found four genes (BCL2, BECN1, MAPK8, and ITPR1), among which BCL2 was correlated with both FEV1/FVC and FEV1 prediction. Finally, the BCL2-related ceRNA network was constructed to clarify the interaction of RNAs and occurrence of autophagy, including 18 miRNAs and 65 lncRNAs. Conclusion We identified 19 autophagy-related differentially expressed genes that participated in COPD; among them, BCL2 was correlated with lung function, and a BCL2-related ceRNA network was constructed, which further revealed the potential mechanism of autophagy involvement in COPD.
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Affiliation(s)
- Zhuang-E Shi
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Meng-Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Jian-Yu Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Wen-Di Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Dong-Mei Hu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Qing-Xiang Wang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Jinan Traditional Chinese Medicine Hospital, Jinan, People’s Republic of China
| | - Yuan-Yuan Jiang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
- Correspondence: Yi-Qing Qu, Department of pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China, Tel +86 531 8216 9335, Fax +86 531 8296 7544, Email
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Zhang W, Zhang Q, Che L, Xie Z, Cai X, Gong L, Li Z, Liu D, Liu S. Using biological information to analyze potential miRNA-mRNA regulatory networks in the plasma of patients with non-small cell lung cancer. BMC Cancer 2022; 22:299. [PMID: 35313857 PMCID: PMC8939143 DOI: 10.1186/s12885-022-09281-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Background Lung cancer is the most common malignant tumor, and it has a high mortality rate. However, the study of miRNA-mRNA regulatory networks in the plasma of patients with non-small cell lung cancer (NSCLC) is insufficient. Therefore, this study explored the differential expression of mRNA and miRNA in the plasma of NSCLC patients. Methods The Gene Expression Omnibus (GEO) database was used to download microarray datasets, and the differentially expressed miRNAs (DEMs) were analyzed. We predicted transcription factors and target genes of the DEMs by using FunRich software and the TargetScanHuman database, respectively. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for GO annotation and KEGG enrichment analysis of downstream target genes. We constructed protein-protein interaction (PPI) and DEM-hub gene networks using the STRING database and Cytoscape software. The GSE20189 dataset was used to screen out the key hub gene. Using The Cancer Genome Atlas (TCGA) and UALCAN databases to analyze the expression and prognosis of the key hub gene and DEMs. Then, GSE17681 and GSE137140 datasets were used to validate DEMs expression. Finally, the receiver operating characteristic (ROC) curve was used to verify the ability of the DEMs to distinguish lung cancer patients from healthy patients. Results Four upregulated candidate DEMs (hsa-miR199a-5p, hsa-miR-186-5p, hsa-miR-328-3p, and hsa-let-7d-3p) were screened from 3 databases, and 6 upstream transcription factors and 2253 downstream target genes were predicted. These genes were mainly enriched in cancer pathways and PI3k-Akt pathways. Among the top 30 hub genes, the expression of KLHL3 was consistent with the GSE20189 dataset. Except for let-7d-3p, the expression of other DEMs and KLHL3 in tissues were consistent with those in plasma. LUSC patients with high let-7d-3p expression had poor overall survival rates (OS). External validation demonstrated that the expression of hsa-miR-199a-5p and hsa-miR-186-5p in peripheral blood of NSCLC patients was higher than the healthy controls. The ROC curve confirmed that the DEMs could better distinguish lung cancer patients from healthy people. Conclusion The results showed that miR-199a-5p and miR-186-5p may be noninvasive diagnostic biomarkers for NSCLC patients. MiR-199a-5p-KLHL3 may be involved in the occurrence and development of NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09281-1.
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Affiliation(s)
- Wei Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China.,Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China
| | - Qian Zhang
- Department of Renal Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Li Che
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Zhefan Xie
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Xingdong Cai
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Ling Gong
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China.,Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China
| | - Zhu Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China
| | - Daishun Liu
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China.
| | - Shengming Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China.
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Chen HH, Eteleeb A, Wang C, Fernandez MV, Budde JP, Bergmann K, Norton J, Wang F, Ebl C, Morris JC, Perrin RJ, Bateman RJ, McDade E, Xiong C, Goate A, Farlow M, Chhatwal J, Schofield PR, Chui H, Harari O, Cruchaga C, Ibanez L. Circular RNA detection identifies circPSEN1 alterations in brain specific to autosomal dominant Alzheimer's disease. Acta Neuropathol Commun 2022; 10:29. [PMID: 35246267 PMCID: PMC8895634 DOI: 10.1186/s40478-022-01328-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/07/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Autosomal-dominant Alzheimer's disease (ADAD) is caused by pathogenic mutations in APP, PSEN1, and PSEN2, which usually lead to an early age at onset (< 65). Circular RNAs are a family of non-coding RNAs highly expressed in the nervous system and especially in synapses. We aimed to investigate differences in brain gene expression of linear and circular transcripts from the three ADAD genes in controls, sporadic AD, and ADAD. METHODS We obtained and sequenced RNA from brain cortex using standard protocols. Linear counts were obtained using the TOPMed pipeline; circular counts, using python package DCC. After stringent quality control (QC), we obtained the counts for PSEN1, PSEN2 and APP genes. Only circPSEN1 passed QC. We used DESeq2 to compare the counts across groups, correcting for biological and technical variables. Finally, we performed in-silico functional analyses using the Circular RNA interactome website and DIANA mirPath software. RESULTS Our results show significant differences in gene counts of circPSEN1 in ADAD individuals, when compared to sporadic AD and controls (ADAD = 21, AD = 253, Controls = 23-ADADvsCO: log2FC = 0.794, p = 1.63 × 10-04, ADADvsAD: log2FC = 0.602, p = 8.22 × 10-04). The high gene counts are contributed by two circPSEN1 species (hsa_circ_0008521 and hsa_circ_0003848). No significant differences were observed in linear PSEN1 gene expression between cases and controls, indicating that this finding is specific to the circular forms. In addition, the high circPSEN1 levels do not seem to be specific to PSEN1 mutation carriers; the counts are also elevated in APP and PSEN2 mutation carriers. In-silico functional analyses suggest that circPSEN1 is involved in several pathways such as axon guidance (p = 3.39 × 10-07), hippo signaling pathway (p = 7.38 × 10-07), lysine degradation (p = 2.48 × 10-05) or Wnt signaling pathway (p = 5.58 × 10-04) among other KEGG pathways. Additionally, circPSEN1 counts were able to discriminate ADAD from sporadic AD and controls with an AUC above 0.70. CONCLUSIONS Our findings show the differential expression of circPSEN1 is increased in ADAD. Given the biological function previously ascribed to circular RNAs and the results of our in-silico analyses, we hypothesize that this finding might be related to neuroinflammatory events that lead or that are caused by the accumulation of amyloid-beta.
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Affiliation(s)
- Hsiang-Han Chen
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Abdallah Eteleeb
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Ciyang Wang
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - John P. Budde
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Curtis Ebl
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Richard J. Perrin
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Randall J. Bateman
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Eric McDade
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Jasmeer Chhatwal
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Peter R. Schofield
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Helena Chui
- Department of Neurology, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Dominantly Inherited Alzheimer Network
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Division of Biostatistics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
- Department of Neurology, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
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9
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Ogonowski N, Salcidua S, Leon T, Chamorro-Veloso N, Valls C, Avalos C, Bisquertt A, Rentería ME, Orellana P, Duran-Aniotz C. Systematic Review: microRNAs as Potential Biomarkers in Mild Cognitive Impairment Diagnosis. Front Aging Neurosci 2022; 13:807764. [PMID: 35095478 PMCID: PMC8790149 DOI: 10.3389/fnagi.2021.807764] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
The rate of progression from Mild Cognitive Impairment (MCI) to Alzheimer's disease (AD) is estimated at >10% per year, reaching up to 80-90% after 6 years. MCI is considered an indicator of early-stage AD. In this context, the diagnostic screening of MCI is crucial for detecting individuals at high risk of AD before they progress and manifest further severe symptoms. Typically, MCI has been determined using neuropsychological assessment tools such as the Montreal Cognitive Assessment (MoCA) or Mini-Mental Status Examination (MMSE). Unfortunately, other diagnostic methods are not available or are unable to identify MCI in its early stages. Therefore, identifying new biomarkers for MCI diagnosis and prognosis is a significant challenge. In this framework, miRNAs in serum, plasma, and other body fluids have emerged as a promising source of biomarkers for MCI and AD-related cognitive impairments. Interestingly, miRNAs can regulate several signaling pathways via multiple and diverse targets in response to pathophysiological stimuli. This systematic review aims to describe the current state of the art regarding AD-related target genes modulated by differentially expressed miRNAs in peripheral fluids samples in MCI subjects to identify potential miRNA biomarkers in the early stages of AD. We found 30 articles that described five miRNA expression profiles from peripheral fluid in MCI subjects, showing possible candidates for miRNA biomarkers that may be followed up as fluid biomarkers or therapeutic targets of early-stage AD. However, additional research is needed to validate these miRNAs and characterize the precise neuropathological mechanisms.
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Affiliation(s)
- Natalia Ogonowski
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Cognitive Neuroscience Center (CNC), National Scientific and Technical Research Council (CONICET), Universidad de San Andrés, Buenos Aires, Argentina
| | - Stefanny Salcidua
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Faculty of Engineering and Sciences, Universidad Adolfo Ibanez, Santiago, Chile
| | - Tomas Leon
- Global Brain Health Institute, Trinity College, Dublin, Ireland
- Memory and Neuropsychiatric Clinic (CMYN) Neurology Department, Hospital del Salvador, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | | | - Constanza Avalos
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
| | | | - Miguel E. Rentería
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paulina Orellana
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
| | - Claudia Duran-Aniotz
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
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10
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Zhou D, Bao Q, Fu S. Anticancer activity of ursolic acid on retinoblastoma cells determined by bioinformatics analysis and validation. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1548. [PMID: 34790754 PMCID: PMC8576664 DOI: 10.21037/atm-21-4617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 12/27/2022]
Abstract
Background This article aims to explore whether ursolic acid (UA) inhibits the progression of retinoblastoma (Rb) by regulating stearoyl-CoA desaturase (SCD). Methods The Gene Expression Omnibus (GEO) database was used to filter the chip, then the GEO2R software was used to analyze the microarray data (GSE97508, GSE24673, and GSE110811). Gene set enrichment analysis (GSEA) was used to analyze the relationship between the expression level of SCD and the proliferation, migration, invasion, and inflammation in Rb patients. SO-RB50 and Y79 cell proliferation, migration, and invasion were assessed by the CCK-8 assay, the colony formation assay, the Transwell assay, and the wound scratch test. The protein expression levels of SCD were measured by western blot. The mRNA expression levels of IL-8, IL-6, CXCL1, and CCL2 were measured by RT-qPCR. The protein expression levels of IL-8 and IL-6 were measured by ELISA. A xenograft nude mouse model was established to evaluate the effect of UA on tumor growth in male BALB/c mice. Results The expression levels of SCD were related to cell proliferation, migration, invasion, and inflammation. UA inhibited SO-RB50 and Y79 cell proliferation, migration, and invasion. At the same time, UA suppressed tumor growth in the xenograft nude mouse model. Overexpression of SCD promoted SO-RB50 and Y79 cell proliferation, migration, invasion, and inflammation, while SCD knockout inhibited SO-RB50 and Y79 cell proliferation, migration, invasion, and inflammation. Importantly, UA inhibited the proliferation, migration, and invasion of Rb cells through SCD inhibition. Conclusions UA inhibited the proliferation, migration, and invasion of Rb cells through SCD. This provides a new scientific basis for targeted therapy of Rb.
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Affiliation(s)
- Dan Zhou
- Department of Ophthalmology, Suzhou High Tech Zone People's Hospital, Suzhou, China
| | - Qi Bao
- Department of Ophthalmology, Suzhou High Tech Zone People's Hospital, Suzhou, China
| | - Songbin Fu
- Department of Ophthalmology, Harbin Medical University, Harbin, China
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11
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Shen Y, Sun C, Zhao B, Guo H, Li J, Xia Y, Liu M, Piao S, Saiyin W. miR-34c-5p mediates the cellular malignant behaviors of oral squamous cell carcinoma through targeted binding of TRIM29. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1537. [PMID: 34790743 PMCID: PMC8576676 DOI: 10.21037/atm-21-4679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022]
Abstract
Background This investigation examined the effects of the microRNA miR-34c-5p on the proliferation, migration, and invasion of oral squamous cell carcinoma (OSCC) and the mechanisms involved. Methods The Gene Expression Omnibus (GEO) database was used to filter the chips, and the GEO2R software (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to analyze the microarray data (GSE28100 and GSE45238). Gene set enrichment analysis (GSEA) was used to study the relationship between the expression of miR-34c-5p and the distant metastasis and pathological grade of OSCC. The correlation between TRIM29 (tripartite motif containing 29) expression and the malignant clinical phenotype of OSCC was also examined. The mRNA and protein expression levels of miR-34c-5p and TRIM29 were measured by real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot analysis. The proliferation, migration, invasion and apoptosis of the human oral squamous carcinoma cell lines CAL-27 and Tca8113 was assessed by performing cell-counting kit-8 (CCK-8) assays, colony formation assays, transwell tests, wound scratch tests and flow cytometry. Luciferase reporter assays were used to predict the relationship between miR-34c-5p and TRIM29. A xenograft nude model was established and used to evaluate the effect of miR-34c-5p on tumor growth in female BALB/c mice. Results The expression of miR-34c-5p was significantly correlated with the proliferation, migration, and metastasis of OSCC. Overexpression of miR-34c-5p promoted the proliferation, migration, and invasion of CAL-27 and Tca8113 cells, and suppressed their apoptosis. Inversely, low expression of miR-34c-5p suppressed the proliferation, migration, and invasion of CAL-27 and Tca8113 cells, and promoted their apoptosis. Overexpression of miR-34c-5p promoted tumor growth in the xenograft nude mice model. The expression of TRIM29 was related to malignant clinical phenotype of OSCC. Overexpression of TRIM29 inhibited the proliferation, migration and invasion of CAL-27 and Tca8113 cell, and induced their apoptosis. TRIM29 knockout had just the opposite effect. Importantly, miR-34c-5p binds to TRIM29 and inhibited TRIM29 expression. Conclusions MiR-34c-5p regulates the proliferation, migration, invasion, and apoptosis of OSCC through targeted binding of TRIM29. This may represent a novel therapeutic target for the treatment of patients with OSCC.
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Affiliation(s)
- Yuchen Shen
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Changsheng Sun
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Bowen Zhao
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Haobing Guo
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Jianhao Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Yanyun Xia
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Miaomiao Liu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Songlin Piao
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
| | - Wuliji Saiyin
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Stomatology, Harbin Medical University, Harbin, China
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12
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Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19. Viruses 2021; 13:v13081593. [PMID: 34452458 PMCID: PMC8402885 DOI: 10.3390/v13081593] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism for SARS-CoV-2-directed immune responses remains elusive. Herein, we used high throughput sequencing to profile the plasma of active and convalescent COVID-19 patients for the presence of small circulating RNAs. The existence of SARS-CoV-2 derived small RNAs in plasma samples of mild and severe COVID-19 cases is described. Clusters of high siRNA abundance were discovered, homologous to the nsp2 3′-end and nsp4 virus sequence. Four virus-derived small RNA sequences have the size of human miRNAs, and a target search revealed candidate genes associated with ageusia and long COVID symptoms. These virus-derived small RNAs were detectable also after recovery from the disease. The additional analysis of circulating human miRNAs revealed differentially abundant miRNAs, discriminating mild from severe cases. A total of 29 miRNAs were reduced or absent in severe cases. Several of these are associated with JAK-STAT response and cytokine storm.
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13
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Yang F, Wang H, Yan B, Li T, Min L, Chen E, Yang J. Decreased level of miR-1301 promotes colorectal cancer progression via activation of STAT3 pathway. Biol Chem 2021; 402:805-813. [PMID: 33984882 DOI: 10.1515/hsz-2020-0301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022]
Abstract
The molecular pathogenesis of colorectal cancer (CRC) has been widely investigated in recent years. Accumulating evidence has indicated that microRNA (miRNA) dysregulation participates in the processes of driving CRC initiation and progression. Aberrant expression of miR-1301 has been found in various tumor types. However, its role in CRC remains to be elucidated. In the present study, we identified miR-1301 was enriched in normal colorectal tissues and significantly down-regulated in CRC. Decreased level of miR-1301 strongly correlated with aggressive pathological characteristics, including advanced stage and metastasis. Bioinformatics and dual luciferase assay demonstrated that STAT3 is a direct target of miR-1301. Gain and loss-of-function assays showed that miR-1301 had no effect on cell proliferation. Overexpression of miR-1301 suppressed cell migration and invasion capacity of pSTAT3-positive LoVo cells, but not pSTAT3-negative SW480 cells, while inhibition of miR-1301 consistently promoted cell migration and invasion in both cell lines. Additionally, miR-1301 inhibition restored the suppressed migration and invasion of STAT3-knockdown LoVo cells. MiR-1301 functioned as a tumor suppressor to modulate the IL6/STAT3 signaling pathway. In summary, this study highlights the significant role of miR-1301/STAT3 axis in CRC metastasis.
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Affiliation(s)
- Fangfang Yang
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
| | - Hua Wang
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
| | - Bianbian Yan
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
| | - Tong Li
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
| | - Lulu Min
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
| | - Erfei Chen
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
| | - Jin Yang
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an710069, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an710069, China
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14
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Al-Shaheri FN, Alhamdani MSS, Bauer AS, Giese N, Büchler MW, Hackert T, Hoheisel JD. Blood biomarkers for differential diagnosis and early detection of pancreatic cancer. Cancer Treat Rev 2021; 96:102193. [PMID: 33865174 DOI: 10.1016/j.ctrv.2021.102193] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is currently the most lethal tumor entity and case numbers are rising. It will soon be the second most frequent cause of cancer-related death in the Western world. Mortality is close to incidence and patient survival after diagnosis stands at about five months. Blood-based diagnostics could be one crucial factor for improving this dismal situation and is at a stage that could make this possible. Here, we are reviewing the current state of affairs with its problems and promises, looking at various molecule types. Reported results are evaluated in the overall context. Also, we are proposing steps toward clinical utility that should advance the development toward clinical application by improving biomarker quality but also by defining distinct clinical objectives and the respective diagnostic accuracies required to achieve them. Many of the discussed points and conclusions are highly relevant to other solid tumors, too.
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Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany.
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Markus W Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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15
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Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson’s disease progression. ACTA ACUST UNITED AC 2021; 1:309-322. [PMID: 37118411 DOI: 10.1038/s43587-021-00042-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs have diagnostic and prognostic importance in Parkinson's disease (PD). We studied circulating small noncoding RNAs (sncRNAs) in two large-scale longitudinal PD cohorts (Parkinson's Progression Markers Initiative (PPMI) and Luxembourg Parkinson's Study (NCER-PD)) and modeled their impact on the transcriptome. Sequencing of sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI yielded 323 billion reads, most of which mapped to microRNAs but covered also other RNA classes such as piwi-interacting RNAs, ribosomal RNAs and small nucleolar RNAs. Dysregulated microRNAs associated with disease and disease progression occur in two distinct waves in the third and seventh decade of life. Originating predominantly from immune cells, they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. Profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort validated biomarkers and main findings by an independent technology. Finally, network analysis of sncRNA and transcriptome sequencing from PPMI identified regulatory modules emerging in patients with progressing PD.
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16
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Data Integration Reveals the Potential Biomarkers of Circulating MicroRNAs in Osteoarthritis. Diagnostics (Basel) 2021; 11:diagnostics11030412. [PMID: 33670901 PMCID: PMC7997238 DOI: 10.3390/diagnostics11030412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
The abnormal expression of circulating miRNAs (c-miRNAs) has become an emerging field in the development of miRNAs-based diagnostic and therapeutic tools for human diseases, including osteoarthritis (OA). OA is the most common form of arthritis leading to disability and a major socioeconomic burden. The abnormal expression of miRNAs plays important roles in the pathogenesis of OA. Unraveling the role of miRNAs in the pathogenesis of OA will throw light on the potential for the development of miRNAs-based diagnostic and therapeutic tools for OA. This article reviews and highlights recent advances in the study of miRNAs in OA, with specific demonstration of the functions of miRNA, especially c-miRNA, in OA pathogenesis as well as its potential implication in the treatment of OA. Based on a systematic literature search using online databases, we figured out the following main points: (1) the integrative systematic review of c-mRNAs and its target genes related to OA pathogenesis; (2) the potential use of c-miRNAs for OA diagnosis purposes as potential biomarkers; and (3) for therapeutic purposes, and we also highlight certain remedies that regulate microRNA expression based on its target genes.
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17
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Fehlmann T, Kahraman M, Ludwig N, Backes C, Galata V, Keller V, Geffers L, Mercaldo N, Hornung D, Weis T, Kayvanpour E, Abu-Halima M, Deuschle C, Schulte C, Suenkel U, von Thaler AK, Maetzler W, Herr C, Fähndrich S, Vogelmeier C, Guimaraes P, Hecksteden A, Meyer T, Metzger F, Diener C, Deutscher S, Abdul-Khaliq H, Stehle I, Haeusler S, Meiser A, Groesdonk HV, Volk T, Lenhof HP, Katus H, Balling R, Meder B, Kruger R, Huwer H, Bals R, Meese E, Keller A. Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients. JAMA Oncol 2021; 6:714-723. [PMID: 32134442 DOI: 10.1001/jamaoncol.2020.0001] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Importance The overall low survival rate of patients with lung cancer calls for improved detection tools to enable better treatment options and improved patient outcomes. Multivariable molecular signatures, such as blood-borne microRNA (miRNA) signatures, may have high rates of sensitivity and specificity but require additional studies with large cohorts and standardized measurements to confirm the generalizability of miRNA signatures. Objective To investigate the use of blood-borne miRNAs as potential circulating markers for detecting lung cancer in an extended cohort of symptomatic patients and control participants. Design, Setting, and Participants This multicenter, cohort study included patients from case-control and cohort studies (TREND and COSYCONET) with 3102 patients being enrolled by convenience sampling between March 3, 2009, and March 19, 2018. For the cohort study TREND, population sampling was performed. Clinical diagnoses were obtained for 3046 patients (606 patients with non-small cell and small cell lung cancer, 593 patients with nontumor lung diseases, 883 patients with diseases not affecting the lung, and 964 unaffected control participants). No samples were removed because of experimental issues. The collected data were analyzed between April 2018 and November 2019. Main Outcomes and Measures Sensitivity and specificity of liquid biopsy using miRNA signatures for detection of lung cancer. Results A total of 3102 patients with a mean (SD) age of 61.1 (16.2) years were enrolled. Data on the sex of the participants were available for 2856 participants; 1727 (60.5%) were men. Genome-wide miRNA profiles of blood samples from 3046 individuals were evaluated by machine-learning methods. Three classification scenarios were investigated by splitting the samples equally into training and validation sets. First, a 15-miRNA signature from the training set was used to distinguish patients diagnosed with lung cancer from all other individuals in the validation set with an accuracy of 91.4% (95% CI, 91.0%-91.9%), a sensitivity of 82.8% (95% CI, 81.5%-84.1%), and a specificity of 93.5% (95% CI, 93.2%-93.8%). Second, a 14-miRNA signature from the training set was used to distinguish patients with lung cancer from patients with nontumor lung diseases in the validation set with an accuracy of 92.5% (95% CI, 92.1%-92.9%), sensitivity of 96.4% (95% CI, 95.9%-96.9%), and specificity of 88.6% (95% CI, 88.1%-89.2%). Third, a 14-miRNA signature from the training set was used to distinguish patients with early-stage lung cancer from all individuals without lung cancer in the validation set with an accuracy of 95.9% (95% CI, 95.7%-96.2%), sensitivity of 76.3% (95% CI, 74.5%-78.0%), and specificity of 97.5% (95% CI, 97.2%-97.7%). Conclusions and Relevance The findings of the study suggest that the identified patterns of miRNAs may be used as a component of a minimally invasive lung cancer test, complementing imaging, sputum cytology, and biopsy tests.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Junior Research Group of Human Genetics, Saarland University, Homburg, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
| | - Lars Geffers
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathaniel Mercaldo
- Institute for Technology Assessment, Massachusetts General Hospital, Boston
| | | | - Tanja Weis
- Department of Internal Medicine, Heidelberg University, Heidelberg, Germany
| | - Elham Kayvanpour
- Department of Internal Medicine, Heidelberg University, Heidelberg, Germany
| | | | - Christian Deuschle
- Hertie Institute for Clinical Brain Research, Center of Neurology, Department of Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Claudia Schulte
- Hertie Institute for Clinical Brain Research, Center of Neurology, Department of Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Ulrike Suenkel
- Hertie Institute for Clinical Brain Research, Center of Neurology, Department of Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Anna-Katharina von Thaler
- Hertie Institute for Clinical Brain Research, Center of Neurology, Department of Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christian Herr
- Department of Internal Medicine V: Pulmonology, Allergology, Intensive Care Medicine, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Sebastian Fähndrich
- Department of Internal Medicine V: Pulmonology, Allergology, Intensive Care Medicine, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Claus Vogelmeier
- Department of Medicine, Pulmonary and Critical Care Medicine, Philipps-University of Marberg, Member of the German Centre for Lung Research (DZL), Marburg, Germany
| | - Pedro Guimaraes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Anne Hecksteden
- Institute of Sports and Preventive Medicine, Saarland University, Saarbrücken, Germany
| | - Tim Meyer
- Institute of Sports and Preventive Medicine, Saarland University, Saarbrücken, Germany
| | - Florian Metzger
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Tübingen, Germany.,Center for Geriatric Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Caroline Diener
- Institute of Human Genetics, Saarland University, Homburg, Germany
| | | | - Hashim Abdul-Khaliq
- Department of Pediatric Cardiology, Saarland University, Saarbrücken, Germany
| | - Ingo Stehle
- Schwerpunktpraxis Hämatologie und Onkologie, Kaiserslautern, Germany
| | - Sebastian Haeusler
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Andreas Meiser
- Department of Anaesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center and Faculty of Medicine, Saarland University, Homburg, Germany
| | - Heinrich V Groesdonk
- Department of Anaesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center and Faculty of Medicine, Saarland University, Homburg, Germany
| | - Thomas Volk
- Department of Anaesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center and Faculty of Medicine, Saarland University, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Hugo Katus
- Department of Internal Medicine, Heidelberg University, Heidelberg, Germany
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Benjamin Meder
- Department of Internal Medicine, Heidelberg University, Heidelberg, Germany
| | - Rejko Kruger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Parkinson's Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg
| | - Hanno Huwer
- Department of Cardiothoracic Surgery, Völklingen Heart Centre, Völklingen, Germany
| | - Robert Bals
- Department of Internal Medicine V: Pulmonology, Allergology, Intensive Care Medicine, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California
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Tang S, Zhong H, Xiong T, Yang X, Mao Y, Wang D. MiR-489 aggravates H2O2-induced apoptosis of cardiomyocytes via inhibiting IGF1. Biosci Rep 2020; 40:BSR20193995. [PMID: 32880387 PMCID: PMC7494985 DOI: 10.1042/bsr20193995] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 08/12/2020] [Accepted: 09/02/2020] [Indexed: 12/16/2022] Open
Abstract
Myocardial infarction (MI) is a major type of cardiovascular disorder worldwide. In the present study, we established a new microRNA (miRNA)-mRNA cross-talk network by integrating data obtained from The National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO). In addition, functional assays, including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analyses, were conducted using the Database for Annotation, Visualization, and Integration Discovery (DAVID). In our study, we generated a new differentially expressed miRNA (DEmiRNA)-differentially expressed gene (DEG) cross-talk network of MI composed of three miRNA (miR-489, miR-375, and miR-142-3p) nodes and 163 mRNA nodes. In vitro experiments demonstrated that miR-489 expression was increased in H2O2-treated H9c2 cardiomyocytes in vitro, mimicking myocardial injury. We observed that down-regulation of miR-489 reduced H2O2-induced apoptosis, while overexpression of miR-489 had the opposite effects, as revealed by flow cytometry and Western blot analyses. Furthermore, we confirmed the relationship between miR-489 and IGF1 through double luciferase reporter gene assays, which partly explains the antiapoptotic mechanism of miR-489. In conclusion, the experimental results of the present study could provide important clues for investigating the mechanism of MI.
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Affiliation(s)
- Shan Tang
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hongyan Zhong
- Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Ting Xiong
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xinquan Yang
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yongqing Mao
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Daxin Wang
- Clinical Medical College, Yangzhou University, Yangzhou, China
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Keller A, Fehlmann T, Backes C, Kern F, Gislefoss R, Langseth H, Rounge TB, Ludwig N, Meese E. Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis. RNA Biol 2020; 17:1416-1426. [PMID: 32456538 DOI: 10.1080/15476286.2020.1771945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are regulators of gene expressionand may be key markers in liquid biopsy.Early diagnosis is an effective means to increase patients' overall survival. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analysed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom developed cancer. We selected 210 serum samples from patients with lung, colon or breast cancer at three time points prior to diagnosis (up to 32 years prior to diagnosis with median 5 years interval between TPs), one time-point after diagnosis and from individually matched controls. The controls were matched on age and year of all pre-diagnostic sampling time-points for the corresponding case. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 with adjusted p-values<10-10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p < 0.05). Self-organized maps (SOMs)indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. SOMsalsohighlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51% of all miRNAs were highly specific, either for a time-point or a cancer entity. Pathway analysis highlighted 12 pathways including Hipo signalling and ABC transporters.Our results indicate that tumours may be indicated by serum miRNAs decades prior the clinical manifestation.
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Affiliation(s)
- Andreas Keller
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine , Stanford, CA, USA
| | - Tobias Fehlmann
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Christina Backes
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Fabian Kern
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Randi Gislefoss
- Department of Research, Cancer Registry of Norway , Oslo, Norway
| | - Hilde Langseth
- Department of Research, Cancer Registry of Norway , Oslo, Norway.,Department of Epidemiology and Biostatistics, Imperial College London , London, UK
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway , Oslo, Norway.,Department of Informatics, University of Oslo , Oslo, Norway
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University , Homburg/Saar, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University , Homburg/Saar, Germany
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20
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Liang CY, Li ZY, Gan TQ, Fang YY, Gan BL, Chen WJ, Dang YW, Shi K, Feng ZB, Chen G. Downregulation of hsa-microRNA-204-5p and identification of its potential regulatory network in non-small cell lung cancer: RT-qPCR, bioinformatic- and meta-analyses. Respir Res 2020; 21:60. [PMID: 32102656 PMCID: PMC7045575 DOI: 10.1186/s12931-020-1274-9] [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: 04/06/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022] Open
Abstract
Background Pulmonary malignant neoplasms have a high worldwide morbidity and mortality, so the study of these malignancies using microRNAs (miRNAs) has attracted great interest and enthusiasm. The aim of this study was to determine the clinical effect of hsa-microRNA-204-5p (miR-204-5p) and its underlying molecular mechanisms in non-small cell lung cancer (NSCLC). Methods Expression of miR-204-5p was investigated by real-time quantitative PCR (RT-qPCR). After data mining from public online repositories, several integrative assessment methods, including receiver operating characteristic (ROC) curves, hazard ratios (HR) with 95% confidence intervals (95% CI), and comprehensive meta-analyses, were conducted to explore the expression and clinical utility of miR-204-5p. The potential objects regulated and controlled by miR-204-5p in the course of NSCLC were identified by estimated target prediction and analysis. The regulatory network of miR-204-5p, with its target genes and transcription factors (TFs), was structured from database evidence and literature references. Results The expression of miR-204-5p was downregulated in NSCLC, and the downtrend was related to gender, histological type, vascular invasion, tumor size, clinicopathologic grade and lymph node metastasis (P<0.05). MiR-204-5p was useful in prognosis, but was deemed unsuitable at present as an auxiliary diagnostic or prognostic risk factor for NSCLC due to the lack of statistical significance in meta-analyses and absence of large-scale investigations. Gene enrichment and annotation analyses identified miR-204-5p candidate targets that took part in various genetic activities and biological functions. The predicted TFs, like MAX, MYC, and RUNX1, interfered in regulatory networks involving miR-204-5p and its predicted hub genes, though a modulatory loop or axis of the miRNA-TF-gene that was out of range with shortage in database prediction, experimental proof and literature confirmation. Conclusions The frequently observed decrease in miR-204-5p was helpful for NSCLC diagnosis. The estimated target genes and TFs contributed to the anti-oncogene effects of miR-204-5p.
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Affiliation(s)
- Chang-Yu Liang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zu-Yun Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ting-Qing Gan
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ye-Ying Fang
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Bin-Liang Gan
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wen-Jie Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ke Shi
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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A novel circRNA-miRNA-mRNA network identifies circ-YOD1 as a biomarker for coronary artery disease. Sci Rep 2019; 9:18314. [PMID: 31797949 PMCID: PMC6892882 DOI: 10.1038/s41598-019-54603-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/12/2019] [Indexed: 01/07/2023] Open
Abstract
Circular RNAs (circRNAs) are involved in many physiological functions. Whether circulating circRNAs serve as markers for coronary artery disease (CAD) is unknown. Seven CAD-related microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database and were analyzed using clustering and functional enrichment to identify hub mRNAs and miRNAs. StarBase V3.0 and circinteractome databases were used to predict interactions between circRNAs and miRNAs whereas miRwalk and DIANA TOOLS were used to predict interactions between miRNAs and mRNAs. Altogether, this helped establish a circRNA-miRNA-mRNA triple network for diagnosis of CAD. Five non-coding RNAs (ncRNAs) were identified in our study population with the use of quantitative real-time PCR (RT-PCR). The prognostic values of circYOD1, hsa-miR-21-3p and hsa-miR-296-3p were evaluated using a receiver operating characteristic (ROC) curve. A CAD circRNA-miRNA-mRNA network was established from our analyses containing one circRNA, four miRNAs and thirteen mRNAs. After performing RT-PCR validation between CAD and non-CAD samples, only three ncRNAs of five ncRNAs showed significance for further analysis. The area under ROC curve (AUC) of circ-YOD1 was 0.824, the AUC of hsa-miR-21-3p was 0.731 and hsa-miR-296-3p was 0.776. The pairwise comparison results showed that circ-YOD1 had statistical significance (PYOD1-21 < 0.01 and PYOD1-296 < 0.05). The results of functional enrichment analysis of interacting genes and microRNAs showed that the shared circ-YOD1 may act as a new biomarker for CAD. Our investigation of the triple regulatory networks of circRNA-miRNA-mRNA in CAD revealed circ-YOD1 as a potential biomarker for CAD.
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A Circulating miRNA-Based Scoring System Established by WGCNA to Predict Colon Cancer. Anal Cell Pathol (Amst) 2019; 2019:1571045. [PMID: 31871878 PMCID: PMC6913280 DOI: 10.1155/2019/1571045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 01/22/2023] Open
Abstract
Introduction Circulation microRNAs (miRNAs) perform as potential diagnostic biomarkers of many kinds of cancers. This study is aimed at identifying circulation miRNAs as diagnostic biomarkers in colon cancer. Methods We conducted a weighted gene coexpression network analysis (WGCNA) in miRNAs to find out the expression pattern among circulation miRNAs by using a “WGCNA” package in R. Correlation analysis was performed to find cancer-related modules. Differentially expressed miRNAs (DEmiRs) in colon cancer were identified by a “limma” package in R. Hub gene analysis was conducted for these DEmiRs in the cancer-related modules by the “closeness” method in cytoscape software. Then, logistic regression was performed to identify the independent risk factors, and a scoring system was constructed based on these independent risk factors. Then, we use data from the GEO database to confirm the reliability of this scoring system. Results A total of 9 independent coexpression modules were constructed based on the expression levels of 848 miRNAs by WGCNA. After correlation analysis, green (cor = 0.77, p = 3 × 10‐25) and yellow (cor = 0.65, p = 6 × 10‐16) modules were strongly correlated with cancer development. 20 hub genes were found after hub gene analysis in these DEmiRs by cytoscape. Among all these hub genes, hsa-miR-23a-3p (OR = 2.6391, p = 6.23 × 10‐5) and hsa-miR-663a (OR = 1.4220, p = 0.0069) were identified as an independent risk factor of colon cancer by multivariate regression. Furthermore, a scoring system was built to predict the probability of colon cancer based on both of these miRNAs, the area under the curve (AUC) of which was 0.828. Data from GSE106817 and GSE112264 was used to confirm this scoring system. And the AUC of them was 0.980 and 0.917, respectively. Conclusion We built a scoring system based on circulation hub miRNAs found by WGCNA to predict the development of colon cancer.
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Carpi S, Polini B, Fogli S, Podestà A, Ylösmäki E, Cerullo V, Romanini A, Nieri P. Circulating microRNAs as biomarkers for early diagnosis of cutaneous melanoma. Expert Rev Mol Diagn 2019; 20:19-30. [PMID: 31747311 DOI: 10.1080/14737159.2020.1696194] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cutaneous melanoma is the deadliest form of skin cancer, with a dramatic increase in the incidence rate worldwide over the past decade. Early detection has been shown to improve the outcome of melanoma patients. The identification of noninvasive biomarkers able to identify melanoma at an early stage remains an unmet clinical need. Circulating miRNAs (c-miRNAs), small non-coding RNAs, appear as potential ideal candidate biomarkers due to their stability in biological fluids and easy detectability. Moreover, c-miRNAs are reported to be heavily deregulated in cancer patients.Areas covered: This review examines evidence of the specific c-miRNAs or panels of c-miRNAs reported to be useful in discriminating melanoma from benign cutaneous lesions.Expert opinion: Although the interesting reported by published studies, the non-homogeneity of detection and normalization methods prevents the individuation of single c-miRNA or panel of c-miRNAs that are specific for early detection of cutaneous melanoma. In the future, prospective wide and well-designed clinical trials will be needed to validate the diagnostic potential of some of the c-miRNA candidates in clinical practice.
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Affiliation(s)
- Sara Carpi
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | - Stefano Fogli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Adriano Podestà
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Erkko Ylösmäki
- Drug Research program and IVTLab, University of Helsinki, Helsinki, Finland
| | - Vincenzo Cerullo
- Drug Research program and IVTLab, University of Helsinki, Helsinki, Finland
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Pisa, Italy
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Fehlmann T, Backes C, Pirritano M, Laufer T, Galata V, Kern F, Kahraman M, Gasparoni G, Ludwig N, Lenhof HP, Gregersen HA, Francke R, Meese E, Simon M, Keller A. The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals. Nucleic Acids Res 2019; 47:4431-4441. [PMID: 30937442 PMCID: PMC6511844 DOI: 10.1093/nar/gkz227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022] Open
Abstract
The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Marcello Pirritano
- Molecular Cell Dynamics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, 42097 Wuppertal, Germany
| | - Thomas Laufer
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Gilles Gasparoni
- Department of Genetics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | | | - Eckart Meese
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, 42097 Wuppertal, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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25
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Backes C, Fehlmann T, Kern F, Kehl T, Lenhof HP, Meese E, Keller A. miRCarta: a central repository for collecting miRNA candidates. Nucleic Acids Res 2019; 46:D160-D167. [PMID: 29036653 PMCID: PMC5753177 DOI: 10.1093/nar/gkx851] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022] Open
Abstract
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014. As a result, publications describing new miRNA candidates in the last three to five years might have a substantial overlap of candidates without noticing. With miRCarta we implemented a database to collect novel miRNA candidates and augment the information provided by miRBase. In the first stage, miRCarta is thought to be a highly sensitive collection of potential miRNA candidates with a high degree of analysis functionality, annotations and details on each miRNA. We added-besides the full content of the miRBase-12,857 human miRNA precursors to miRCarta. Users can match their own predictions to the entries of miRCarta to reduce potential redundancies in their studies. miRCarta provides the most comprehensive collection of human miRNAs and miRNA candidates to form a basis for further refinement and validation studies. The database is freely accessible at https://mircarta.cs.uni-saarland.de/.
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Affiliation(s)
- Christina Backes
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
| | - Eckart Meese
- Institute for Human Genetics, Medical School, Saarland University, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Germany
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Heinzelmann J, Arndt M, Pleyers R, Fehlmann T, Hoelters S, Zeuschner P, Vogt A, Pryalukhin A, Schaeffeler E, Bohle RM, Gajda M, Janssen M, Stoeckle M, Junker K. 4-miRNA Score Predicts the Individual Metastatic Risk of Renal Cell Carcinoma Patients. Ann Surg Oncol 2019; 26:3765-3773. [DOI: 10.1245/s10434-019-07578-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 12/24/2022]
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Han X, Li X, Zhao H, Zhou D, Sun B, Liu A, Zhang J, Cui Z, Ma X, Yuan L. Serum miR-515-3p, a potential new RNA biomarker, is involved in gastric carcinoma. J Cell Biochem 2019; 120:15834-15843. [PMID: 31081157 DOI: 10.1002/jcb.28854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/04/2019] [Accepted: 01/14/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVES microRNAs (miRNAs) have provided a new opportunity for developing diagnostic biomarkers and effective therapeutic targets in gastric cancer (GC). In this study, we aimed to investigate the relationship between miR-515-3p and GC development. EXPERIMENTAL DESIGN The Gene Expression Omnibus (GEO) database was used for screening genes and miRNA and for 2R analysis. miRNA prediction target genes and screening key genes were analyzed using protein interactions (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A network of miRNA-mRNA interactions was predicated by Cytoscape (v.3.5.1), Institute of Systems Biology & University of California, San Diego & Pasteur institute & University of California, San Francisco. Finally, miR-515-3p levels were detected by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in gastric cells and plasma levels. Then, the association between the expression level of miR-515-3p and the clinicopathological features of patients with GC was further analyzed. OBSERVATIONS AND CONCLUSIONS We found that miR-515-3p was markedly overexpressed in individuals with GC compared with that in normal gastric cells (NCs) and the surgery group (P < 0.0001). In addition, receiver operating characteristic (ROC) analysis yielded an area under the curve (AUC) value of 0.8555 for miR-515-3p. SIGNIFICANCE Our results present new information to the field of gastric cancer and has done a good job of creating an initial hypothesis using the database as well as validate their initial results. These results suggest that serum miR-515-3p is a novel potential biomarker for the detection of GC.
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Affiliation(s)
- Xue Han
- Department of Biochemistry and Molecular Biology, Daqing Campus, Harbin Medical University, Daqing, Heilongjiang, China
| | - Xing Li
- Department of Nephrology, Daqing People Hospital, Daqing, People's Republic of China
| | - Hengyu Zhao
- Imaging Department, Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China
| | - Danyang Zhou
- Department of Biochemistry and Molecular Biology, Daqing Campus, Harbin Medical University, Daqing, Heilongjiang, China
| | - Banghao Sun
- Department of Biochemistry and Molecular Biology, Daqing Campus, Harbin Medical University, Daqing, Heilongjiang, China
| | - Anqi Liu
- Department of Biochemistry and Molecular Biology, Daqing Campus, Harbin Medical University, Daqing, Heilongjiang, China
| | - Jianan Zhang
- Department of Biochemistry and Molecular Biology, Daqing Campus, Harbin Medical University, Daqing, Heilongjiang, China
| | - Zhongqi Cui
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Xiaoyu Ma
- Clinical Laboratory, Beijing Chaoyang District Taiyanggong Community Health Service Center, Beijing, China
| | - Lijie Yuan
- Department of Biochemistry and Molecular Biology, Daqing Campus, Harbin Medical University, Daqing, Heilongjiang, China.,Key Laboratory of Functional and Clinical, Transformation of Fujian Medical College in Xiamen Medical College, Xiamen, Fujian, China
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Huang ZS, Guo XW, Zhang G, Liang LX, Nong B. The Diagnostic and Prognostic Value of miR-200c in Gastric Cancer: A Meta-Analysis. DISEASE MARKERS 2019; 2019:8949618. [PMID: 31089400 PMCID: PMC6476052 DOI: 10.1155/2019/8949618] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 02/04/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The role of miR-200c in gastric cancer remains controversial. This study is aimed at clarifying the diagnostic and prognostic value of miR-200c in gastric cancer through a meta-analysis. METHODS A comprehensive literature search of PubMed, Embase, and Ovid library databases was conducted. The studies included were those conducted before December 2017. The sensitivity and specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under curve (AUC) were used to estimate the diagnostic value of miR-200c. Meanwhile, the pooled hazard ratio (HR) was used to estimate the prognostic value of miR-200c. RESULTS For the diagnostic value of miR-200c, six studies that included 202 patients with gastric cancer and 250 normal controls were analyzed. The sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.74, 0.66, 2.20, 0.40, 5.34, and 0.75, respectively. Subgroup analysis showed no significant difference in the type of the sample, method for testing miR-200c, and ethnicity among the patients. Meanwhile, for the prognostic value of miR-200c, seven studies comprising 935 patients with gastric cancer were analyzed. The pooled results showed that miR-200c expression was associated with overall survival (HR = 2.19) and disease-free survival (HR = 1.73), but not with progression-free survival (HR = 1.64) in patients with gastric cancer. There was no publication bias across the studies. CONCLUSIONS Both serum and tissue miR-200c have moderate diagnostic accuracy in gastric cancer. miR-200c could also be used as a valuable indicator for predicting the prognosis of gastric cancer patients.
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Affiliation(s)
- Zong-Sheng Huang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xian-Wen Guo
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guo Zhang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lie-Xin Liang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Bing Nong
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Kikuchi A, Naruse A, Sawamura T, Nonaka K. Evaluation of the efficacy of various reagents in improving microRNA extraction. Ann Clin Biochem 2019; 56:375-380. [PMID: 30813744 DOI: 10.1177/0004563219828405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND MicroRNA has received considerable attention in the clinical context, and attempts are being made to use microRNA in clinical diagnosis. However, adequate quantities of microRNA required for analysis are challenging to isolate. We tested the effect of various reagents in improving microRNA extraction and compared their efficacy to that of a commercially available extraction kit (HighPure miRNA isolation kit, Roche). METHODS We used the synthetic oligonucleotide miR-21 and formalin-fixed, paraffin-embedded (FFPE) tissue sections from colon cancer samples ( n = 10). We tested increasing volumes (100-600 μL) of 1,4-dioxane, 2-butanol, 2-propanol, acetonitrile, polyethylene glycol (PEG) 600, PEG 1000, PEG 1540, PEG 2000, tetraethylene glycol dimethyl ether (TDE), and tetrahydrofuran, instead of the binding enhancer solution provided in the kit. MiR-21 analysis was performed via stem-loop RT-qPCR using Universal ProbeLibrary probe (Roche). RESULTS The optimum amount of each enhancement solution was 200-500 μL. We obtained ΔCp values of optimum additional volume for each solution from 1.04 to 2.50 and compared these with those obtained using the commercially available kit. PEG 1540 and 2000 produced superior reactivity with minimal addition. For FFPE tissue samples, addition of the enhancement solutions PEG 1540 and 2000 resulted in mean crossing point values of 18.15 ± 2.26 and 17.73 ± 3.26, respectively. We obtained a crossing point value of 20.56 ± 4.26 (mean ± SD) using the commercially available kit. CONCLUSIONS The tested enhancer reagents, which are relatively readily available and easy to use, can improve microRNA extraction efficacy of a commercially available kit.
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Affiliation(s)
- Arizumi Kikuchi
- 1 Department of Research and Development, Daiyukai Research Institute for Medical Science, Ichinomiya, Aichi, Japan
| | - Azumi Naruse
- 1 Department of Research and Development, Daiyukai Research Institute for Medical Science, Ichinomiya, Aichi, Japan
| | - Takahiro Sawamura
- 1 Department of Research and Development, Daiyukai Research Institute for Medical Science, Ichinomiya, Aichi, Japan
| | - Kenichi Nonaka
- 2 Department of Surgery, Daiyukai General Hospital, Ichinomiya, Aichi, Japan
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30
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Khatri I, Ganguly K, Sharma S, Carmicheal J, Kaur S, Batra SK, Bhasin MK. Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis. Sci Rep 2019; 9:123. [PMID: 30644396 PMCID: PMC6333820 DOI: 10.1038/s41598-018-36328-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a 5-year survival rate of <8%. Its dismal prognosis stems from inefficient therapeutic modalities owing to the lack of understanding about pancreatic cancer pathogenesis. Considering the molecular complexity and heterogeneity of PDAC, identification of novel molecular contributors involved in PDAC onset and progression using global "omics" analysis will pave the way to improved strategies for disease prevention and therapeutic targeting. Meta-analysis of multiple miRNA microarray datasets containing healthy controls (HC), chronic pancreatitis (CP) and PDAC cases, identified 13 miRNAs involved in the progression of PDAC. These miRNAs showed dysregulation in both tissue as well as blood samples, along with progressive decrease in expression from HC to CP to PDAC. Gene-miRNA interaction analysis further elucidated 5 miRNAs (29a/b, 27a, 130b and 148a) that are significantly downregulated in conjunction with concomitant upregulation of their target genes throughout PDAC progression. Among these, miRNA-29a/b targeted genes were found to be most significantly altered in comparative profiling of HC, CP and PDAC, indicating its involvement in malignant evolution. Further, pathway analysis suggested direct involvement of miRNA-29a/b in downregulating the key pathways associated with PDAC development and metastasis including focal adhesion signaling and extracellular matrix organization. Our systems biology data analysis, in combination with real-time PCR validation indicates direct functional involvement of miRNA-29a in PDAC progression and is a potential prognostic marker and therapeutic candidate for patients with progressive disease.
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Affiliation(s)
- Indu Khatri
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Koelina Ganguly
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sunandini Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joseph Carmicheal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sukhwinder Kaur
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA.
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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Lu HM, Yi WW, Ma YS, Wu W, Yu F, Fan HW, Lv ZW, Yang HQ, Chang ZY, Zhang C, Xie WT, Jiang JJ, Song YC, Chai L, Jia CY, Lu GX, Zhong XJ, Hou LK, Wu CY, Shi MX, Liu JB, Fu D. Prognostic implications of decreased microRNA-101-3p expression in patients with non-small cell lung cancer. Oncol Lett 2018; 16:7048-7056. [PMID: 30546438 PMCID: PMC6256371 DOI: 10.3892/ol.2018.9559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
To investigate the expression level of microRNA-101-3p (miR-101-3p) and its possible association with progression, prognosis and chemotherapy in patients with non-small cell lung cancer (NSCLC), the Gene Expression Omnibus (GEO) database was used. Quantitative polymerase chain reaction was used to verify the expression in 327 NSCLC and 42 adjacent normal lung tissues, of which 42 viable tissues were paired with nearby normal lung tissues. Based on the Cox regression model, univariate and multivariate analyses were used to address the factors that had effects on overall survival (OS) and disease-free survival (DFS) rate. Data from the GEO database demonstrated that the miR-101-3p expression in NSCLC was downregulated, compared with normal lung cancer. Survival analysis through univariate and multivariate models indicated that the miR-101-3p expression level was a crucial risk factor for OS and DFS in patients with NSCLC. A number of clinical parameters were determined to be associated with miR-101-3p expression, including tumor diameter, lymph node metastasis and tumor-node-metastasis stage. Adjuvant chemotherapy with high expression of miR-101-3p was determined to increase OS and DFS in patients with NSCLC, compared with patients with de novo or low expression of miR-101-3p. The present results demonstrated that miR-101-3p expression levels were associated with NSCLC progression and prognosis, which indicated that miR-101-3p may serve as a biomarker for patients with NSCLC who have received adjuvant chemotherapy.
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Affiliation(s)
- Hai-Min Lu
- Department of Thoracic Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226631, P.R. China
| | - Wan-Wan Yi
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P.R. China
| | - Wei Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Fei Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Heng-Wei Fan
- Department of Hepatic Surgery I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China
| | - Zhong-Wei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Hui-Qiong Yang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Zheng-Yan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Chao Zhang
- Department of Hepatic Surgery I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China
| | - Wen-Ting Xie
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Jun-Jian Jiang
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Ying-Chun Song
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Gai-Xia Lu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Xiao-Jun Zhong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangsu 330006, P.R. China
| | - Li-Kun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Chun-Yan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Min-Xin Shi
- Department of Thoracic Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226631, P.R. China
| | - Ji-Bin Liu
- Department of Thoracic Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226631, P.R. China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
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Magalhães M, Alvarez-Lorenzo C, Concheiro A, Figueiras A, Santos AC, Veiga F. RNAi-based therapeutics for lung cancer: biomarkers, microRNAs, and nanocarriers. Expert Opin Drug Deliv 2018; 15:965-982. [PMID: 30232915 DOI: 10.1080/17425247.2018.1517744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Despite the current advances in the discovery of the lung cancer biomarkers and, consequently, in the diagnosis, this pathology continues to be the primary cause of cancer-related death worldwide. In most cases, the illness is diagnosed in an advanced stage, which limits the current treatment options available and reduces the survival rate. Therefore, RNAi-based therapy arises as a promising option to treat lung cancer. AREAS COVERED This review provides an overview on the exploitation of lung cancer biology to develop RNAi-based therapeutics to be applied in the treatment of lung cancer. Furthermore, the review analyzes the main nanocarriers designed to deliver RNAi molecules and induce antitumoral effects in lung cancer, and provides updated information about current RNAi-based therapeutics for lung cancer in clinical trials. EXPERT OPINION RNAi-based therapy uses nanocarriers to perform a targeted and efficient delivery of therapeutic genes into lung cancer cells, by taking advantage of the known biomarkers in lung cancer. These therapeutic genes are key regulatory molecules of crucial cellular pathways involved in cell proliferation, migration, and apoptosis. Thereby, the characteristics and functionalization of the nanocarrier and the knowledge of lung cancer biology have direct influence in improving the therapeutic effect of this therapy.
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Affiliation(s)
- Mariana Magalhães
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
| | - Carmen Alvarez-Lorenzo
- c Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, R+D Pharma Group (GI-1645), Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS) , Universidade de Santiago de Compostela , Santiago de Compostela , Spain
| | - Angel Concheiro
- c Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, R+D Pharma Group (GI-1645), Facultad de Farmacia and Health Research Institute of Santiago de Compostela (IDIS) , Universidade de Santiago de Compostela , Santiago de Compostela , Spain
| | - Ana Figueiras
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
| | - Ana Cláudia Santos
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
| | - Francisco Veiga
- a Department of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal.,b REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy , University of Coimbra , Coimbra , Portugal
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Is miR-144 an effective inhibitor of PTEN mRNA: a controversy in breast cancer. In Vitro Cell Dev Biol Anim 2018; 54:621-628. [PMID: 30132256 DOI: 10.1007/s11626-018-0282-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
Abstract
Breast cancer is the first common cancer among women worldwide. One of the major signaling pathways playing a role in the onset and progression of this disease is PI3K/Akt/mTOR, which can be inhibited by PTEN. miRNAs are small non-coding molecules that regulate the expression of their targets by inhibition or suppression, and thus, their dysregulated expression results in the development of cancer. Using various software applications predicting miRNAs and evaluating GEO microarray data, miR-144 was selected as an inhibitor of PTEN. The expression of miR-144 and PTEN was evaluated in 18 triple negative breast cancer (TNBC) clinical samples and cell lines including 4T1, MDA-MB-231, MDA-MB-468, SK-BR-3, and MCF-7 in comparison with normal cells. PTEN and miR-144 expression analysis revealed their elevated expression in MCF-7 cells. MDA-MB-468, SK-BR-3, and MDA-MB-231 cells showed decreased levels of PTEN and increased levels of miR-144. In contrast, 4T1 cells had an increased expression of PTEN and decreased expression of miR-144. In clinical samples, miR-144 was up-regulated in 22% of the cases and PTEN was down-regulated in 78% of the cases. The results showed that the expression of PTEN and miR-144 was inversely correlated in metastatic breast cancer cell lines. However, in TNBC clinical samples, there was no correlation between the expression of miR-144 and PTEN. Literature shows that there are other influencing factors affecting the expression of miRNAs. Therefore, care should be taken in interpreting the results of gene expression studies and its relation with cancer diagnosis/prognosis.
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MicroRNA in diagnosis and therapy monitoring of early-stage triple-negative breast cancer. Sci Rep 2018; 8:11584. [PMID: 30072748 PMCID: PMC6072710 DOI: 10.1038/s41598-018-29917-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/09/2018] [Indexed: 11/12/2022] Open
Abstract
Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast cancer (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs of TNBC patients were assessed prior to and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases and 21 controls using microarrays, the identified signatures were verified independently in two laboratories on the same and a new cohort by RT-qPCR. We differentiated the blood of TNBC patients before NCT from controls with 84% sensitivity. The most significant miRNA for this diagnostic classification was miR-126-5p (two tailed t-test p-value of 1.4 × 10−5). Validation confirmed the microarray results for all tested miRNAs. Comparing cancer patients prior to and post NCT highlighted 321 significant miRNAs (among them miR-34a, p-value of 1.2 × 10−23). Our results also suggest that changes in miRNA expression during NCT may have predictive potential to predict pathological complete response (pCR). In conclusion we report that miRNA expression measured from blood facilitates early and minimally-invasive diagnosis of basal-like TNBC. We also demonstrate that NCT has a significant influence on miRNA expression. Finally, we show that blood-borne miRNA profiles monitored over time have potential to predict pCR.
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Xie ZC, Tang RX, Gao X, Xie QN, Lin JY, Chen G, Li ZY. A meta-analysis and bioinformatics exploration of the diagnostic value and molecular mechanism of miR-193a-5p in lung cancer. Oncol Lett 2018; 16:4114-4128. [PMID: 30250529 PMCID: PMC6144214 DOI: 10.3892/ol.2018.9174] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is a leading cause of mortality worldwide and despite recent improvements in lung cancer treatments patient mortality remains high. miR-193a-5p serves a crucial role in the initiation and development of cancer; it is necessary to understand the underlying molecular mechanisms of miR-193a-5p in lung cancer, which may enable the development of improved clinical diagnoses and therapies. The present study investigated the diagnostic value of peripheral blood and tissue miR-193a-5p expression using a microarray meta-analysis. Peripheral blood miR-193a-5p was revealed to be upregulated in patients with lung cancer. The pooled area under the curve (AUC) was 0.67, with a sensitivity and specificity of 0.74 and 0.56, respectively. Conversely, the peripheral tissue miR-193a-5p expression in patients with lung cancer was significantly downregulated. The pooled AUC was 0.83, and the sensitivity and specificity were 0.65 and 0.89, respectively. Through bioinformatics analysis, three Kyoto Encyclopedia of Genes and Genomes (KEGG) terms, pathways in cancer, prostate cancer and RIG-I-like receptor signaling pathway, were identified as associated with miR-193a-5p in lung cancer. In addition, in lung cancer, six key miR-193a-5p target genes, receptor tyrosine-protein kinase erbB-2 (ERBB2), nuclear cap-binding protein subunit 2 (NCBP2), collagen α-1(I) chain (COL1A1), roprotein convertase subtilisin/kexin type 9 (PCSK9), casein kinase II subunit α (CSNK2A1) and nucleolar transcription factor 1 (UBTF), were identified, five of which were significantly upregulated (ERBB2, NCBP2, COL1A1, CSNK2A1 and UBTF). The protein expression of ERBB2, NCBP2, COL1A1, CSNK2A1 and UBTF was also upregulated. NCBP2 and CSNK2A1 were negatively correlated with miR-193a-5p. The results demonstrated that miR-193a-5p exhibited opposite expression patterns in peripheral blood and tissue. Upregulated peripheral blood miR-193a-5p and downregulated tissue miR-193a-5p may be promising diagnostic biomarkers in lung cancer. In addition, the KEGG terms pathways in cancer, prostate cancer and RIG-I-like receptor signaling pathway may suggest which pathways serve vital roles in lung cancer by regulating miR-193a-5p. In addition, six genes, ERBB2, COL1A1, PCSK9, UBTF and particularly NCBP2 and CSNK2A1, may be key target genes of miR-193a-5p in lung cancer.
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Affiliation(s)
- Zu-Cheng Xie
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rui-Xue Tang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiang Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Qiong-Ni Xie
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jia-Ying Lin
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zu-Yun Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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36
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Keller A, Fehlmann T, Ludwig N, Kahraman M, Laufer T, Backes C, Vogelmeier C, Diener C, Biertz F, Herr C, Jörres RA, Lenhof HP, Meese E, Bals R. Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:162-171. [PMID: 29981854 PMCID: PMC6076380 DOI: 10.1016/j.gpb.2018.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 01/11/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) significantly increases the risk of developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development independent of the tumor type. From 2741 participants of COSYCONET diagnosed with COPD, we selected 534 individuals including 33 patients who developed cancer during the follow-up period of 54 months and 501 patients who did not develop cancer, but had similar age, gender and smoking history. Genome-wide miRNA profiles were generated and evaluated using machine learning techniques. For patients developing cancer we identified nine miRNAs with significantly decreased abundance (two-tailed unpaired t-test adjusted for multiple testing P < 0.05), including members of the miR-320 family. The identified miRNAs regulate different cancer-related pathways including the MAPK pathway (P = 2.3 × 10−5). We also observed the impact of confounding factors on the generated miRNA profiles, underlining the value of our matched analysis. For selected miRNAs, qRT-PCR analysis was applied to validate the results. In conclusion, we identified several miRNAs in blood of COPD patients, which could serve as candidates for biomarkers to help identify COPD patients at risk of developing cancer.
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Affiliation(s)
- Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Thomas Laufer
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany; Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Claus Vogelmeier
- Department of Internal Medicine, Division for Pulmonary Diseases, Philipps University of Marburg, 35043 Marburg, Germany
| | - Caroline Diener
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Frank Biertz
- Institute for Biostatistics, Hannover Medical School, 30625 Hanover, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University Hospital, 66421 Homburg, Germany
| | - Rudolf A Jörres
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Comprehensive Pneumology Center Munich (CPC-M), Ludwig-Maximilians-University Munich, Member of the German Center for Lung Research (DZL), 80539 Munich, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University Hospital, 66421 Homburg, Germany
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37
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Han B, Feng D, Yu X, Liu Y, Yang M, Luo F, Zhou L, Liu F. MicroRNA-144 mediates chronic inflammation and tumorigenesis in colorectal cancer progression via regulating C-X-C motif chemokine ligand 11. Exp Ther Med 2018; 16:1935-1943. [PMID: 30186421 PMCID: PMC6122338 DOI: 10.3892/etm.2018.6389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. The aim of the present study was to investigate the expression of microRNA-144 (miR-144) and C-X-C motif chemokine ligand 11 (CXCL11) in CRC and their association. Data from Gene Expression Omnibus (GEO) DataSets were analyzed to obtain the expression profile of CXCL11 in CRC. Subsequently, serum samples were collected from 65 subjects, including 39 patients with CRC and 26 controls; CRC and adjacent normal tissues were collected from all 39 CRC patients and the expression of CXCL11 was measured in these specimens. After searching for the potential regulator of CXCL11 through bioinformatics analysis, the levels of miR-144 in the clinical specimens were also detected. Finally, the regulatory association between miR-144 and CXCL11 was certified via the dual-luciferase reporter assay. Microarray data and bioinformatics analysis demonstrated that CXCL11 was significantly upregulated in CRC tissues and miR-144 was a potential regulator of CXCL11. In line with this finding, the expression of CXCL11 was significantly increased in the serum and tumor samples of patients with CRC, while that of miR-144 was downregulated. Dual-luciferase reporter assay revealed that miR-144 directly targets the 3′-untranslated region of CXCL11 mRNA to regulate its expression. These results demonstrated that enhanced CXCL11 expression in patients with CRC was associated with reduced miR-144 expression. The results of the present study may indicate a novel regulatory role of miR-144 in CRC through CXCL11 downregulation.
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Affiliation(s)
- Bin Han
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China.,Department of Pharmacology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Dan Feng
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Xin Yu
- Health Service Center of Southeast Community, Nanchong, Sichuan 637000, P.R. China
| | - Yuanqi Liu
- Department of Pharmacology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ming Yang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Fei Luo
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Liming Zhou
- Department of Pharmacology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Fu Liu
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
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38
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Hart M, Kern F, Backes C, Rheinheimer S, Fehlmann T, Keller A, Meese E. The deterministic role of 5-mers in microRNA-gene targeting. RNA Biol 2018; 15:819-825. [PMID: 29749304 DOI: 10.1080/15476286.2018.1462652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
MiRNAs play a central role in physiological and pathological processes. Both for the biological understanding and for their clinical application, it is essential to understand the interaction of miRNAs and their targets. Target identification largely hinges on in-silico prediction, which requires a complete consideration of miRNA binding sites within the UTRs of target genes. Here, we show that 5-mer sites might also play an essential role for human miRNA-target binding. We implemented and employed an algorithm to all pairs of 2,588 human miRNAs annotated in miRBase and the 3' UTRs of 16725 genes (>43 million combinations). Our in-silico analysis showed a highly significant enrichment (p = 1.4 × 10-69) of 5-mer binding sites in 3' UTRs across all experimentally validated miRNA-target gene pairs. We next confirmed the central role of 5-mer binding sites by reporter assays and demonstrated that two non-canonical 5-mer sites of miR-34a in the 3' UTR of T-cell receptor alpha (TCRA) have a significantly stronger influence on its posttranscriptional regulation than the canonical binding sites. These observations indicate an essential role of 5-mer binding sites for the miRNA targeting in human cells.
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Affiliation(s)
- Martin Hart
- a Institute of Human Genetics, Saarland University , Homburg , Germany
| | - Fabian Kern
- b Chair for Clinical Bioinformatics, Saarland University , Saarbrücken , Germany
| | - Christina Backes
- b Chair for Clinical Bioinformatics, Saarland University , Saarbrücken , Germany
| | | | - Tobias Fehlmann
- b Chair for Clinical Bioinformatics, Saarland University , Saarbrücken , Germany
| | - Andreas Keller
- b Chair for Clinical Bioinformatics, Saarland University , Saarbrücken , Germany
| | - Eckart Meese
- a Institute of Human Genetics, Saarland University , Homburg , Germany
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39
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Yin Y, Cai J, Meng F, Sui C, Jiang Y. MiR-144 suppresses proliferation, invasion, and migration of breast cancer cells through inhibiting CEP55. Cancer Biol Ther 2018; 19:306-315. [PMID: 29561704 PMCID: PMC5902245 DOI: 10.1080/15384047.2017.1416934] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The study aimed to investigate the molecular mechanism of miR-144 and CEP55 as well as the influence of their interaction on the cell proliferation, migration, invasion, cell cycle and cell apoptosis in breast cancer. METHODS In this study, The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/ ) database was used for microarray analysis. The expressions of miR-144 and CEP55 in 40 adjacent tissues and 36 tumor tissues were examined by western blot, qRT-PCR and immunohistochemistry. The target relationship between miR-144 and CEP55 was predicted and confirmed by TargetScan and luciferase reporter assay. The cell proliferation, cell cycle and cell apoptosis in different groups were detected by MTT and flow cytometry assays, while wound healing and transwell assays were used for the cell migration and invasion tests. The regulatory effects of miR-144 and CEP55 on breast tumor were verified through nude mouse model in vivo experiment. RESULTS MiR-144 was down-regulated in breast cancerous tissues and cells, whereas CEP55 expression was up-regulated in breast cancerous tissues. Moreover, there existed a target relationship between miR-144 and CEP55 and negative correlation on their expressions. MiR-144 could down-regulate CEP55 expression, thereby inhibiting proliferation, invasion, migration, retarding cell cycle and accelerating cell apoptosis. MiR-144 could inhibit cell progression through down-regulating CEP55 in vivo. CONCLUSION MiR-144 suppressed cell proliferation, migration, invasion and induced cell cycle arrest and cell apoptosis by repressing CEP55. This might provide a promising therapy for clinical treatment.
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Affiliation(s)
- Yuanqin Yin
- Biotherapy Laboratory, Cancer Institute, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jingjing Cai
- Department of Medicine, General Hospital of Fushun Mining Bureau, Fushun, Liaoning, China
| | - Fandong Meng
- Biotherapy Laboratory, Cancer Institute, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chengguang Sui
- Biotherapy Laboratory, Cancer Institute, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Youhong Jiang
- Biotherapy Laboratory, Cancer Institute, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
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40
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Van Laar R, Lincoln M, Van Laar B. Development and validation of a plasma-based melanoma biomarker suitable for clinical use. Br J Cancer 2018; 118:857-866. [PMID: 29360813 PMCID: PMC5886119 DOI: 10.1038/bjc.2017.477] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
This corrects the article DOI: 10.1038/bjc.2017.85.
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Affiliation(s)
- Ryan Van Laar
- Geneseq Biosciences Pty Ltd, PO Box 309, Balaclava, VIC 3183, Victoria, Australia
| | - Mitchel Lincoln
- Geneseq Biosciences Pty Ltd, PO Box 309, Balaclava, VIC 3183, Victoria, Australia
| | - Barton Van Laar
- Geneseq Biosciences Pty Ltd, PO Box 309, Balaclava, VIC 3183, Victoria, Australia
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41
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Bauer AS, Nazarov PV, Giese NA, Beghelli S, Heller A, Greenhalf W, Costello E, Muller A, Bier M, Strobel O, Hackert T, Vallar L, Scarpa A, Büchler MW, Neoptolemos JP, Kreis S, Hoheisel JD. Transcriptional variations in the wider peritumoral tissue environment of pancreatic cancer. Int J Cancer 2018; 142:1010-1021. [PMID: 28983920 PMCID: PMC5813190 DOI: 10.1002/ijc.31087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 08/10/2017] [Accepted: 08/30/2017] [Indexed: 01/23/2023]
Abstract
Transcriptional profiling was performed on 452 RNA preparations isolated from various types of pancreatic tissue from tumour patients and healthy donors, with a particular focus on peritumoral samples. Pancreatic ductal adenocarcinomas (PDAC) and cystic tumours were most different in these non-tumorous tissues surrounding them, whereas the actual tumours exhibited rather similar transcript patterns. The environment of cystic tumours was transcriptionally nearly identical to normal pancreas tissue. In contrast, the tissue around PDAC behaved a lot like the tumour, indicating some kind of field defect, while showing far less molecular resemblance to both chronic pancreatitis and healthy tissue. This suggests that the major pathogenic difference between cystic and ductal tumours may be due to their cellular environment rather than the few variations between the tumours. Lack of correlation between DNA methylation and transcript levels makes it unlikely that the observed field defect in the peritumoral tissue of PDAC is controlled to a large extent by such epigenetic regulation. Functionally, a strikingly large number of autophagy-related transcripts was changed in both PDAC and its peritumoral tissue, but not in other pancreatic tumours. A transcription signature of 15 autophagy-related genes was established that permits a prognosis of survival with high accuracy and indicates the role of autophagy in tumour biology.
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Affiliation(s)
- Andrea S. Bauer
- Division of Functional Genome AnalysisGerman Cancer Research Centre (DKFZ)HeidelbergGermany
| | - Petr V. Nazarov
- Genomics and Proteomics Research Unit, Luxembourg Institute of HealthLuxembourg CityLuxembourg
| | - Nathalia A. Giese
- Department of General SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - Stefania Beghelli
- Department of Pathology and DiagnosticsUniversità di VeronaVeronaItaly
| | - Anette Heller
- Department of General SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - William Greenhalf
- National Institute for Health Research, Pancreas Biomedical Research Unit and the Liverpool Experimental Cancer Medicine CentreLiverpoolUnited Kingdom
| | - Eithne Costello
- National Institute for Health Research, Pancreas Biomedical Research Unit and the Liverpool Experimental Cancer Medicine CentreLiverpoolUnited Kingdom
| | - Arnaud Muller
- Genomics and Proteomics Research Unit, Luxembourg Institute of HealthLuxembourg CityLuxembourg
| | - Melanie Bier
- Division of Functional Genome AnalysisGerman Cancer Research Centre (DKFZ)HeidelbergGermany
| | - Oliver Strobel
- Department of General SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - Thilo Hackert
- Department of General SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - Laurent Vallar
- Genomics and Proteomics Research Unit, Luxembourg Institute of HealthLuxembourg CityLuxembourg
| | - Aldo Scarpa
- Department of Pathology and DiagnosticsUniversità di VeronaVeronaItaly
| | - Markus W. Büchler
- Department of General SurgeryUniversity Hospital HeidelbergHeidelbergGermany
| | - John P. Neoptolemos
- National Institute for Health Research, Pancreas Biomedical Research Unit and the Liverpool Experimental Cancer Medicine CentreLiverpoolUnited Kingdom
| | - Stephanie Kreis
- Life Sciences Research Unit, University of LuxembourgLuxembourg CityLuxembourg
| | - Jörg D. Hoheisel
- Division of Functional Genome AnalysisGerman Cancer Research Centre (DKFZ)HeidelbergGermany
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42
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ElSharawy A, Röder C, Becker T, Habermann JK, Schreiber S, Rosenstiel P, Kalthoff H. Concentration of circulating miRNA-containing particles in serum enhances miRNA detection and reflects CRC tissue-related deregulations. Oncotarget 2018; 7:75353-75365. [PMID: 27683108 PMCID: PMC5342746 DOI: 10.18632/oncotarget.12205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/12/2016] [Indexed: 01/02/2023] Open
Abstract
The emerging potential of miRNAs as biomarkers for cancer detection demands parallel evaluation of strategies for reliable identification of disease-related signatures from easily accessible and pertinent body compartments. Here, we addressed whether efficient concentration of circulating miRNA-carrying particles is a rationale for miRNA biomarker discovery. We systematically compared miRNA signatures in 93 RNA preparations from three serum entities (whole serum, particle-concentrated, and particle-depleted fractions) and corresponding tissue samples from patients with colorectal cancer (CRC) as a model disease. Significant differences between whole sera and particle-concentrated serum fractions of CRC patients emerged for 45 of 742 tested miRNAs. Twenty-eight of these 45 miRNAs were differentially expressed between particle-concentrated serum fractions of metastatic CRC- and healthy individuals. Over half of these candidates (15 of 28) showed deregulations only in concentrated serum fractions, but not in whole sera, compared to the respective controls.Our results also provided evidence of a consistent downregulation of miR-486 and miR-92a, and further showed a possible "strand-specific" deregulation of extracellular miRNAs in CRC. More importantly, most of the identified miRNAs in the enriched sera reflected the patterns of the corresponding tumor tissues and showed links to cancer-related inflammation. Further investigation of seven serum pools revealed a subset of potential extracellular miRNA candidates to be implicated in both neoplastic and inflammatory bowel disease.Our findings demonstrate that enrichment and sensitive detection of miRNA carriers is a promising approach to detect CRC-related pathological changes in liquid biopsies, and has potential for clinical diagnostics.
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Affiliation(s)
- Abdou ElSharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,Faculty of Sciences, Division of Biochemistry, Department of Chemistry, Damietta University, New Damietta City, Egypt
| | - Christian Röder
- Institute for Experimental Cancer Research, Christian-Albrechts-University, Kiel, Germany
| | - Thomas Becker
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,Clinic for Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Holger Kalthoff
- Institute for Experimental Cancer Research, Christian-Albrechts-University, Kiel, Germany
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43
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Keller A, Rounge T, Backes C, Ludwig N, Gislefoss R, Leidinger P, Langseth H, Meese E. Sources to variability in circulating human miRNA signatures. RNA Biol 2017; 14:1791-1798. [PMID: 28820329 PMCID: PMC5731815 DOI: 10.1080/15476286.2017.1367888] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/07/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
An increasing number of studies propose circulating microRNAs (miRNAs) as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurologic pathologies and others. To further validate miRNA as biomarkers it is indispensable to understand the variability of circulating miRNAs in healthy individuals. We determined the longitudinal miRNomes of 90 serum samples from the Janus Serum Bank in Norway, which have been stored between 23 and 40 y at -25 °Celsius. We profiled 3 serum samples with microarrays for 30 individuals, each. For each individual the samples were collected with a time interval of approximately 5 y. This design allowed insights into inter-individual variability, age dependent miRNA variability and the impact of storage length and pre-processing. A significant proportion of the miRNome was affected by the age of the blood donor and a not negligible, albeit small, part of the miRNome by the storage time. A substantial part of miRNAs was differentially abundant between individuals, independent of the time when samples were collected. Stepwise filtering of the 529 miRNAs that were detected in the serum samples showed 168 miRNAs with differential abundance depending on the time point analyzed, 56 miRNAs differentially abundant between individuals, and 169 miRNAs with an abundance depending on the sampling procedure. While these groups of miRNAs contain generally interesting and biologically important miRNAs, the remaining 135 miRNAs constitute very promising biomarker candidates as they show an overall low variability between healthy individuals, a likewise overall low variability across a longer life span, and a high independence of the sampling process and the storage length.
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Affiliation(s)
- Andreas Keller
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Trine Rounge
- b Cancer Registry of Norway , Institute of Population-based Cancer Research , Oslo , Norway
| | - Christina Backes
- a Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Nicole Ludwig
- c Department of Human Genetics , Saarland University , Homburg , Germany
| | - Randi Gislefoss
- b Cancer Registry of Norway , Institute of Population-based Cancer Research , Oslo , Norway
| | - Petra Leidinger
- c Department of Human Genetics , Saarland University , Homburg , Germany
| | - Hilde Langseth
- b Cancer Registry of Norway , Institute of Population-based Cancer Research , Oslo , Norway
| | - Eckart Meese
- c Department of Human Genetics , Saarland University , Homburg , Germany
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44
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Fehlmann T, Backes C, Kahraman M, Haas J, Ludwig N, Posch AE, Würstle ML, Hübenthal M, Franke A, Meder B, Meese E, Keller A. Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. Nucleic Acids Res 2017; 45:8731-8744. [PMID: 28911107 PMCID: PMC5587802 DOI: 10.1093/nar/gkx595] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2023] Open
Abstract
The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | - Jan Haas
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | | | | | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
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45
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Mustafa S, Pan L, Marzoq A, Fawaz M, Sander L, Rückert F, Schrenk A, Hartl C, Uhler R, Yildirim A, Strobel O, Hackert T, Giese N, Büchler MW, Hoheisel JD, Alhamdani MSS. Comparison of the tumor cell secretome and patient sera for an accurate serum-based diagnosis of pancreatic ductal adenocarcinoma. Oncotarget 2017; 8:11963-11976. [PMID: 28060763 PMCID: PMC5355318 DOI: 10.18632/oncotarget.14449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 12/25/2016] [Indexed: 01/05/2023] Open
Abstract
Pancreatic cancer is the currently most lethal malignancy. Toward an accurate diagnosis of the disease in body liquids, we studied the protein composition of the secretomes of 16 primary and established cell lines of pancreatic ductal adenocarcinoma (PDAC). Compared to the secretome of non-tumorous cells, 112 proteins exhibited significantly different abundances. Functionally, the proteins were associated with PDAC features, such as decreased apoptosis, better cell survival and immune cell regulation. The result was compared to profiles obtained from 164 serum samples from two independent cohorts - a training and a test set - of patients with PDAC or chronic pancreatitis and healthy donors. Eight of the 112 secretome proteins exhibited similar variations in their abundance in the serum profile specific for PDAC patients, which was composed of altogether 189 proteins. The 8 markers shared by secretome and serum yielded a 95.1% accuracy of distinguishing PDAC from healthy in a Receiver Operating Characteristic curve analysis, while any number of serum-only markers produced substantially less accurate results. Utility of the identified markers was confirmed by classical enzyme linked immunosorbent assays (ELISAs). The study highlights the value of cell secretome analysis as a means of defining reliable serum biomarkers.
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Affiliation(s)
- Shakhawan Mustafa
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.,Kurdistan Institution for Strategic Studies and Scientific Research, Kurdistan Region, Iraq
| | - Longqiang Pan
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Aseel Marzoq
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Malak Fawaz
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Laureen Sander
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Felix Rückert
- Chirurgische Klinik, Universitätsmedizin Mannheim, Theodor-Kutzer-Ufer 1-3, Mannheim, Germany
| | - Andrea Schrenk
- Chirurgische Klinik, Universitätsmedizin Mannheim, Theodor-Kutzer-Ufer 1-3, Mannheim, Germany
| | - Christina Hartl
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Rico Uhler
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Adem Yildirim
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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46
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Kahraman M, Laufer T, Backes C, Schrörs H, Fehlmann T, Ludwig N, Kohlhaas J, Meese E, Wehler T, Bals R, Keller A. Technical Stability and Biological Variability in MicroRNAs from Dried Blood Spots: A Lung Cancer Therapy-Monitoring Showcase. Clin Chem 2017; 63:1476-1488. [DOI: 10.1373/clinchem.2017.271619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/27/2017] [Indexed: 02/02/2023]
Abstract
Abstract
BACKGROUND
Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results.
METHODS
We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions. Second, we investigated technical reproducibility by performing 7 replicates of DBS again from 1 person. Third, we investigated DBS samples from 53 patients with lung cancer undergoing different therapies. Across these 3 stages, 108 genome-wide miRNA profiles from DBS were generated and evaluated biostatistically.
RESULTS
In the stability analysis, we observed that temperature and humidity had an overall limited influence on the miRNomes (average correlation between the different conditions of 0.993). Usage of a silica gel slightly diminished DBS' technical reproducibility. The 7 technical replicates had an average correlation of 0.996. The correlation with whole-blood PAXGene miRNomes of the same individual was remarkable (correlation of 0.88). Finally, evaluation of the samples from the 53 patients with lung cancer exposed to different therapies showed that the biological variations exceeded the technical variability significantly (P < 0.0001), yielding 51 dysregulated miRNAs.
CONCLUSIONS
We present a stable work flow for profiling of whole miRNomes on the basis of samples collected from DBS. Biological variations exceeded technical variations significantly. DBS-based miRNA profiles will potentially further the translational character of miRNA biomarker studies.
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Affiliation(s)
- Mustafa Kahraman
- Clinical Bioinformatics, Saarland University, Homburg, Germany
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | | | | | | | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Homburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | | | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Thomas Wehler
- Department of Internal Medicine V – Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V – Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Homburg, Germany
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47
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Li J, Sun P, Yue Z, Zhang D, You K, Wang J. miR-144-3p Induces Cell Cycle Arrest and Apoptosis in Pancreatic Cancer Cells by Targeting Proline-Rich Protein 11 Expression via the Mitogen-Activated Protein Kinase Signaling Pathway. DNA Cell Biol 2017; 36:619-626. [PMID: 28574724 DOI: 10.1089/dna.2017.3656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jian Li
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Peisheng Sun
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Zhongyi Yue
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Dezhong Zhang
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Kun You
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Jianguo Wang
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
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48
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MicroRNA-Mediated Rescue of Fear Extinction Memory by miR-144-3p in Extinction-Impaired Mice. Biol Psychiatry 2017; 81:979-989. [PMID: 28104225 DOI: 10.1016/j.biopsych.2016.12.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/06/2016] [Accepted: 12/13/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND MicroRNA (miRNA)-mediated control of gene expression suggests that miRNAs are interesting targets and/or biomarkers in the treatment of anxiety- and trauma-related disorders, where often memory-associated gene expression is adversely affected. METHODS The role of miRNAs in the rescue of impaired fear extinction was assessed using the 129S1/SvlmJ (S1) mouse model of impaired fear extinction. miRNA microarray analysis, reverse transcription polymerase chain reaction, fluorescent in situ hybridization, lentiviral overexpression, and Luciferase reporter assays were used to gain insight into the mechanisms underlying miRNA-mediated normalization of deficient fear extinction. RESULTS Rescuing impaired fear extinction via dietary zinc restriction was associated with differential expression of miRNAs in the amygdala. One candidate, miR-144-3p, robustly expressed in the basolateral amygdala, showed specific extinction-induced, but not fear-induced, increased expression in both extinction-rescued S1 mice and extinction-intact C57BL/6 (BL6) mice. miR-144-3p upregulation and effects on subsequent behavioral adaption was assessed in S1 and BL6 mice. miR-144-3p overexpression in the basolateral amygdala rescued impaired fear extinction in S1 mice, led to enhanced fear extinction acquisition in BL6 mice, and furthermore protected against fear renewal in BL6 mice. miR-144-3p targets a number of genes implicated in the control of plasticity-associated signaling cascades, including Pten, Spred1, and Notch1. In functional interaction studies, we revealed that the miR-144-3p target, PTEN, colocalized with miR-144-3p in the basolateral amygdala and showed functional downregulation following successful fear extinction in S1 mice. CONCLUSIONS These findings identify a fundamental role of miR-144-3p in the rescue of impaired fear extinction and suggest this miRNA as a viable target in developing novel treatments for posttraumatic stress disorder and related disorders.
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49
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Luo P, Yang Q, Cong LL, Wang XF, Li YS, Zhong XM, Xie RT, Jia CY, Yang HQ, Li WP, Cong XL, Xia Q, Fu D, Zeng QH, Ma YS. Identification of miR‑124a as a novel diagnostic and prognostic biomarker in non‑small cell lung cancer for chemotherapy. Mol Med Rep 2017; 16:238-246. [PMID: 28534972 PMCID: PMC5482144 DOI: 10.3892/mmr.2017.6595] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/20/2017] [Indexed: 01/18/2023] Open
Abstract
Previous studies have suggested that dysregulation of microRNA (miR) −124a is associated with various types of human cancer. However, there are few studies reporting the level of miR-124a expression in non-small cell lung cancer (NSCLC). The present study investigated the association between miR-124a and NSCLC by analyzing the differential expression of miR-124a in NSCLC using the GEO database, as well as subsequently performing reverse transcription-quantitative polymerase chain reaction analysis on 160 NSCLC biopsies, 32 of which were paired with adjacent normal tissues. The results indicated that mir-124a expression levels were decreased in NSCLC tumor biopsies compared with adjacent normal tissues. The overall survival (OS) in patients with a high expression of miR-124a was prolonged relative to patients with low expression of miR-124a. The expression levels of miR-124a were associated with clinical characteristics, including lymph-node metastasis, tumor differentiation, tumor node metastasis (TNM) stage and diameter. Frequently, lymph-node metastasis, TNM stage, diameter and lack of chemotherapy have been associated with a worse prognosis in patients. In addition, the present study identified that high expression of miR-124awith chemotherapy may increase OS. In conclusion, the current study demonstrated that miR-124a was downregulated in NSCLC, and miR-124a was a potential prognostic tumor biomarker response to chemotherapy.
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Affiliation(s)
- Pei Luo
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Qing Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Le-Le Cong
- Department of Neurology, China Japan Union Hospital, Jilin University, Changchun, Jilin 130031, P.R. China
| | - Xiao-Feng Wang
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Sheng Li
- Department of Orthopedics, Xiangya Hospital, Central‑South University, Changsha, Hunan 410008, P.R. China
| | - Xiao-Ming Zhong
- Department of Radiology, Jiangxi Provincial Tumor Hospital, Nanchang, Jiangxi 330029, P.R. China
| | - Ru-Ting Xie
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Hui-Qiong Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Wen-Ping Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Xian-Ling Cong
- Tissue Bank, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Qing Xia
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Da Fu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Qing-Hua Zeng
- Department of Respiratory, The First Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
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50
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Alles J, Ludwig N, Rheinheimer S, Leidinger P, Grässer FA, Keller A, Meese E. MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins. Oncotarget 2017; 8:56417-56427. [PMID: 28915601 PMCID: PMC5593572 DOI: 10.18632/oncotarget.17662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022] Open
Abstract
Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3′UTR of either SOS1 or SOS2. Each of the 3′UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.
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Affiliation(s)
- Julia Alles
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Petra Leidinger
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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