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Hu Z, Liu C, Mei Z, Wang X, Ma Y, Liu X, Xu H, Fang G, Liu X, Li R, Wang J, Shi Z, Han C. A-to-I edited miR-154-p13-5p inhibited cell proliferation and migration and induced apoptosis by targeting LIX1L in the bladder cancer. J Cancer 2024; 15:3708-3723. [PMID: 38911375 PMCID: PMC11190776 DOI: 10.7150/jca.93388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/14/2024] [Indexed: 06/25/2024] Open
Abstract
With the advancement of RNA sequencing technology, there has been a drive to uncover and elucidate the pivotal role of A-to-I RNA editing events in tumorigenesis. However, A-to-I miRNA editing events have been clearly identified in bladder cancer, the molecular mechanisms underlying their role in bladder cancer remain unclear. In our investigation, we observed a notable under-expression of edited miR-154-p13-5p in bladder cancer (BC) tissues, in contrast to normal counterparts. Remarkably, heightened expression levels of edited miR-154-p13-5p correlated with improved survival outcomes. To assess the impact of modified miR-154-p13-5p, we conducted a string of cell phenotype assays through transfection of the corresponding miRNAs or siRNAs. The results unequivocally demonstrate that edited miR-154-p13-5p exerts a substantial inhibitory influence on proliferation, migration, and induces apoptosis by specifically targeting LIX1L in bladder cancer. Moreover, we observed that the editing of miR-154-p13-5p or LIX1L-siRNAs inhibits the expression of LIX1L, thereby suppressing EMT-related proteins and cell cycle protein CDK2. Simultaneously, an upregulation in the expression levels of Caspase-3 and Cleaved Caspase-3 were also detected. Our research findings suggest that the upregulation of edited miR-154-p13-5p could potentially enhance the prognosis of bladder cancer, thereby presenting molecular biology-based therapeutic strategies.
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Affiliation(s)
- Zhengxiang Hu
- Postgraduate Training Base of Jinzhou Medical University in The Central Hospital of Xuzhou, Jinzhou, Liaoning 121013, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu 221006, China
| | - Chunhui Liu
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Zujun Mei
- Department of Emergency, Jingzhou Central Hospital, Jingzhou, Hubei 434000, China
| | - Xinlei Wang
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Yuyang Ma
- Graduate School of Bengbu Medical College, Bengbu, Anhui 233060, China
| | - Xing Liu
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Hao Xu
- Graduate School of Bengbu Medical College, Bengbu, Anhui 233060, China
| | - Gaochuan Fang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xinyu Liu
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Rui Li
- Central Laboratory, Xuzhou Central Hospital, Jiangsu 221006, China
| | - Jie Wang
- Central Laboratory, Xuzhou Central Hospital, Jiangsu 221006, China
| | - Zhenduo Shi
- Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu 221006, China
| | - Conghui Han
- Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu 221006, China
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Shu WJ, Ma Z, Tian X, Wang F. Near-Infrared Fluorescence Imaging of miRNA Using a Transmembrane Polypeptide-Based Genetic Reporter. SMALL METHODS 2024; 8:e2300990. [PMID: 37882335 DOI: 10.1002/smtd.202300990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/29/2023] [Indexed: 10/27/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that play important regulatory roles in multiple biological processes. Many miRNAs exhibit unique expression patterns and are considered as theranostic biomarkers in a variety of human diseases. A reporter system that is capable of imaging miRNA in vivo is crucial for investigating miRNA biology. In the present study, an organic anion-transporting polypeptide 1B3 (OATP1B3)-based genetic switch system is designed and optimized to achieve near-infrared fluorescent imaging of miRNA by the uptake of indocyanine green (ICG) dye. The reporter system, named miR-ON-OB3, is shown to be efficient to regulate the expression of OATP1B3 in mammalian cells. Notably, the results indicate that the system is of high sensitivity for near-infrared fluorescence imaging of both exogenous and endogenous miRNA in mammalian cells. Moreover, the system is proved to be functional for real-time near-infrared fluorescence imaging of miRNA in living mice. This study establishes a novel genetic encoded reporter for near-infrared fluorescence imaging of miRNA, which may provide a potential tool for in vivo imaging of miRNA in clinical applications due to the clinical availability of ICG.
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Affiliation(s)
- Wen-Jie Shu
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhe Ma
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiaojie Tian
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Fu Wang
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang, Shaanxi, 712046, China
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3
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Liu Y, Guo S, Xie W, Yang H, Li W, Zhou N, Yang J, Zhou G, Mao C, Zheng Y. Identification of microRNA editing sites in clear cell renal cell carcinoma. Sci Rep 2023; 13:15117. [PMID: 37704698 PMCID: PMC10499803 DOI: 10.1038/s41598-023-42302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a malignant tumor originating from the renal tubular epithelium. Although the microRNAs (miRNAs) transcriptome of ccRCC has been extensively studied, the role of miRNAs editing in ccRCC is largely unknown. By analyzing small RNA sequencing profiles of renal tissues of 154 ccRCC patients and 22 normal controls, we identified 1025 miRNA editing sites from 246 pre-miRNAs. There were 122 editing events with significantly different editing levels in ccRCC compared to normal samples, which include two A-to-I editing events in the seed regions of hsa-mir-376a-3p and hsa-mir-376c-3p, respectively, and one C-to-U editing event in the seed region of hsa-mir-29c-3p. After comparing the targets of the original and edited miRNAs, we found that hsa-mir-376a-1_49g, hsa-mir-376c_48g and hsa-mir-29c_59u had many new targets, respectively. Many of these new targets were deregulated in ccRCC, which might be related to the different editing levels of hsa-mir-376a-3p, hsa-mir-376c-3p, hsa-mir-29c-3p in ccRCC compared to normal controls. Our study sheds new light on miRNA editing events and their potential biological functions in ccRCC.
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Affiliation(s)
- Yulong Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Huaide Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Nan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, 650223, Yunnan, China
| | - Guangchen Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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Hou X, Wong G. Nomogram for Early Prediction of Parkinson's Disease Based on microRNA Profiles and Clinical Variables. JOURNAL OF PARKINSON'S DISEASE 2023:JPD225080. [PMID: 37212072 DOI: 10.3233/jpd-225080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
BACKGROUND Few efficient and simple models for the early prediction of Parkinson's disease (PD) exists. OBJECTIVE To develop and validate a novel nomogram for early identification of PD by incorporating microRNA (miRNA) expression profiles and clinical indicators. METHODS Expression levels of blood-based miRNAs and clinical variables from 1,284 individuals were downloaded from the Parkinson's Progression Marker Initiative database on June 1, 2022. Initially, the generalized estimating equation was used to screen candidate biomarkers of PD progression in the discovery phase. Then, the elastic net model was utilized for variable selection and a logistics regression model was constructed to establish a nomogram. Additionally, the receiver operating characteristic (ROC) curves, decision curve analysis (DCA), and calibration curves were utilized to evaluate the performance of the nomogram. RESULTS An accurate and externally validated nomogram was constructed for predicting prodromal and early PD. The nomogram is easy to utilize in a clinical setting since it consists of age, gender, education level, and transcriptional score (calculated by 10 miRNA profiles). Compared with the independent clinical model or 10 miRNA panel separately, the nomogram was reliable and satisfactory because the area under the ROC curve achieved 0.72 (95% confidence interval, 0.68-0.77) and obtained a superior clinical net benefit in DCA based on external datasets. Moreover, calibration curves also revealed its excellent prediction power. CONCLUSION The constructed nomogram has potential for large-scale early screening of PD based upon its utility and precision.
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Affiliation(s)
- Xiangqing Hou
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
| | - Garry Wong
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
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Shu WJ, Lee K, Ma Z, Tian X, Kim JS, Wang F. A dual-regulation inducible switch system for microRNA detection and cell type-specific gene activation. Theranostics 2023; 13:2552-2561. [PMID: 37215565 PMCID: PMC10196832 DOI: 10.7150/thno.84111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Rationale: MicroRNAs (miRNAs) play key roles in multiple biological processes, many of which exhibit distinct cell type-specific expression patterns. A miRNA-inducible expression system can be adapted as a signal-on reporter for detecting miRNA activity or as a cell type-specific gene activation tool. However, due to the inhibitory properties of miRNAs on gene expression, few miRNA-inducible expression systems are available, and the available systems are only transcriptional or post-transcriptional regulatory system with obvious leaky expression. Methods: To address this limitation, a miRNA-inducible expression system that can tightly control target gene expression is desirable. Here, by taking advantage of an enhanced LacI repression system and the translational repressor L7Ae, a miRNA-inducible dual transcriptional-translational switch system was designed called the miR-ON-D system. Luciferase activity assay, western blotting, CCK-8 assay and flow cytometry analysis were performed to characterize and validate this system. Results: The results demonstrated that leakage expression was strongly suppressed in the miR-ON-D system. It was also validated that the miR-ON-D system could be used to detect exogenous and endogenous miRNAs in mammalian cells. Moreover, it was shown that the miR-ON-D system could be triggered by cell type-specific miRNAs to regulate the expression of biologically relevant proteins (e.g., p21 and Bax) to achieve cell type-specific reprogramming. Conclusion: This study established a tight miRNA-inducible expression switch system for miRNA detection and cell type-specific gene activation.
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Affiliation(s)
- Wen-Jie Shu
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Kyungwoo Lee
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Zhe Ma
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaojie Tian
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Fu Wang
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
- Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang 712046, Shaanxi, China
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6
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Characterizing Relevant MicroRNA Editing Sites in Parkinson's Disease. Cells 2022; 12:cells12010075. [PMID: 36611869 PMCID: PMC9818192 DOI: 10.3390/cells12010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are extensively edited in human brains. However, the functional relevance of the miRNA editome is largely unknown in Parkinson's disease (PD). By analyzing small RNA sequencing profiles of brain tissues of 43 PD patients and 88 normal controls, we found that the editing levels of five A-to-I and two C-to-U editing sites are significantly correlated with the ages of normal controls, which is disrupted in PD patients. We totally identified 362 miRNA editing sites with significantly different editing levels in prefrontal cortices of PD patients (PD-PC) compared to results of normal controls. We experimentally validated that A-to-I edited miR-497-5p, with significantly higher expression levels in PD-PC compared to normal controls, directly represses OPA1 and VAPB. Furthermore, overexpression of A-to-I edited miR-497-5p downregulates OPA1 and VAPB in two cell lines, and inhibits proliferation of glioma cells. These results suggest that the hyperediting of miR-497-5p in PD contributes to enhanced progressive neurodegeneration of PD patients. Our results provide new insights into the mechanistic understanding, novel diagnostics, and therapeutic clues of PD.
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Xie W, Yang J, Zhou N, Ding H, Zhou G, Wu S, Guo S, Li W, Zhang L, Yang H, Mao C, Zheng Y. Identification of microRNA editing sites in three subtypes of leukemia. Front Mol Biosci 2022; 9:1014288. [PMID: 36452459 PMCID: PMC9702332 DOI: 10.3389/fmolb.2022.1014288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/28/2022] [Indexed: 09/15/2023] Open
Abstract
Leukemia is an aberrant hyper-proliferation of immature blood cells that do not form solid tumors. The transcriptomes of microRNAs (miRNAs) of leukemia have been intensively explored. However, miRNA editing of leukemia has not been extensively studied. To identify miRNA editing patterns and explore their functional relevance in leukemia, we analyzed 200 small RNA sequencing profiles of three subtypes of leukemia and identified hundreds of miRNA editing sites in three subtypes of leukemia. Then, we compared the editing levels of identified miRNA editing sites in leukemia and normal controls. Many miRNAs were differential edited in different subtypes of leukemia. We also found the editing levels of 3'-A editing sites of hsa-mir-21-5p and hsa-mir-155-5p decreased in chronic lymphocytic leukemia patients with radiation treatments. By integrating PAR-CLIP sequencing profiles, we predicted the targets of original and edited miRNAs. One of the edited miRNA, hsa-let-7b_5c, with an additional cytosine at 5' end of hsa-let-7b-5p, potentially targeted VBP1 and CTDSP1. CTDSP1 was significantly downregulated in T-ALL compared to normal controls, which might be originated from the hyperediting of hsa-let-7b-5p in T-ALL. Our study provides a comprehensive view of miRNA editing in three different subtypes of leukemia.
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Affiliation(s)
- Wenping Xie
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jun Yang
- Yunnan Police College, Kunming, Yunnan, China
| | - Nan Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hao Ding
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Guangchen Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shuai Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Lei Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Huaide Yang
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
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8
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Hu F, Chen J, Zhang Y, Xu K, Sun Y, Liu Y, Cai H. MiR-219a-5p Inhibits Michigan Cancer Foundation-7 (MCF-7) Cell Migration by Regulating Zinc Finger E-Box Binding Homeobox 1 (ZEB1) Expression. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The potential role of miR-219a-5p in the migration of breast cancer has not been fully elucidated. In this study, bioinformatic analysis revealed that high miR-219a-5p expression in breast cancer tissue was associated with good survival of breast cancer patients. RT-qPCR analysis indicated
that miR-219a-5p expression is significantly lower in MDA-MB-231 triple-negative breast cancer (TNBC) cells. In addition, pre-miR-219a overexpression inhibited MCF-7 cell migration and inhibited ZEB1, Twist1 and vimentin expression but promoted the expression of E-cadherin. Moreover, miR-219a-5p
mimics inhibited MCF-7 cell migration, whereas MCF-7 cell migration was promoted by the miR-219a-5p inhibitor. Furthermore, miR-219a-5p was found to inhibit the translation of ZEB1 expression by targeting the 5′-ACAAUCA-3′ motif of the ZEB1 3′UTR, and the binding motif is
conserved in multiple species. ZEB1 overexpression rescued the inhibition of cell migration induced by miR-219a-5p. Finally, an inverse correlation of miR-219a-5p and ZEB1 expression was observed in four breast cancer cell lines. Thus, miR-219a-5p inhibits MCF-7 cell migration by regulating
ZEB1 expression, and ZEB1 is the target gene of miR-219a-5p.
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Affiliation(s)
- Fen Hu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, P. R. China
| | - Jiaxin Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, P. R. China
| | - Yunfeng Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, Hebei 063000, P. R. China
| | - Ke Xu
- Department of Life Sciences, Tangshan Normal University, Tangshan, Hebei 063000, P. R. China
| | - Yuxi Sun
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, P. R. China
| | - Yan Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, P. R. China
| | - Haifeng Cai
- The Second Department of Breast Surgery, Tangshan People’s Hospital, Tangshan, Hebei 063000, P. R. China
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Qin JX, Liu X, Wang XL, Wang GY, Liang Q, Dong Y, Pang K, Hao L, Xue L, Zhao Y, Hu ZX, Li R, Lv Q, Chao L, Meng FL, Shi ZD, Han CH. Identification and analysis of microRNA editing events in recurrent bladder cancer based on RNA sequencing: MicroRNA editing level is a potential novel biomarker. Front Genet 2022; 13:984279. [PMID: 36199571 PMCID: PMC9527279 DOI: 10.3389/fgene.2022.984279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: With the continued advancement of RNA-seq (RNA-sequencing), microRNA (miRNA) editing events have been demonstrated to play an important role in different malignancies. However, there is yet no description of the miRNA editing events in recurrent bladder cancer.Objective: To identify and compare miRNA editing events in primary and recurrent bladder cancer, as well as to investigate the potential molecular mechanism and its impact on patient prognosis.Methods: We examined the mRNA and miRNA transcriptomes of 12 recurrent bladder cancer cases and 13 primary bladder cancer cases. The differentially expressed mRNA sequences were analyzed. Furthermore, we identified the differentially expressed genes (DEGs) in recurrent bladder cancer. The Gene Ontology (GO) functional enrichment analyses on DEGs and gene set enrichment analysis were performed. The consensus molecular subtype (CMS) classification of bladder cancer was identified using the Consensus MIBC package in R (4.1.0); miRNA sequences were then further subjected to differentially expressed analysis and pathway enrichment analysis. MiRNA editing events were identified using miRge3.0. miRDB and TargetScanHuman were used to predict the downstream targets of specific differentially edited or expressed miRNAs. The expression levels of miR-154-5p and ADAR were validated by RT-qPCR. Finally, survival and co-expression studies were performed on the TCGA-BLCA cohort.Results: First, the mRNA expression levels in recurrent bladder cancer changed significantly, supporting progression via related molecular signal pathways. Second, significantly altered miRNAs in recurrent bladder cancer were identified, with miR-154-5p showing the highest level of editing in recurrent bladder cancer and may up-regulate the expression levels of downstream targets HS3ST3A1, AQP9, MYLK, and RAB23. The survival analysis results of TCGA data revealed that highly expressed HS3ST3A1 and RAB23 exhibited poor prognosis. In addition, miR-154 editing events were found to be significant to CMS classification.Conclusion: MiRNA editing in recurrent bladder cancer was detected and linked with poor patient prognosis, providing a reference for further uncovering the intricate molecular mechanism in recurrent bladder cancer. Therefore, inhibiting A-to-I editing of miRNA may be a viable target for bladder cancer treatment, allowing current treatment choices to be expanded and individualized.
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Affiliation(s)
- Jia-Xin Qin
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Xing Liu
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Xin-Lei Wang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Guang-Yue Wang
- Graduate School of Bengbu Medical College, Bengbu, China
| | - Qing Liang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yang Dong
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Kun Pang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Liang Xue
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yan Zhao
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Zheng-Xiang Hu
- Graduate School of Jinzhou Medical College, Jinzhou, China
| | - Rui Li
- Central Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Qian Lv
- Central Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Liu Chao
- Department of Urology, The Suqian Affiliated Hospital of Xuzhou Medical University School, Suqian, China
| | - Fan-Lai Meng
- Department of Pathology, The Suqian Affiliated Hospital of Xuzhou Medical University School, Suqian, China
| | - Zhen-Duo Shi
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Zhen-Duo Shi, ; Cong-Hui Han,
| | - Cong-Hui Han
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Urology, Heilongjiang Provincial Hospital, Harbin, China
- *Correspondence: Zhen-Duo Shi, ; Cong-Hui Han,
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10
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Thakur A, Kumar M. AntiVIRmiR: A repository of host antiviral miRNAs and their expression along with experimentally validated viral miRNAs and their targets. Front Genet 2022; 13:971852. [PMID: 36159991 PMCID: PMC9493126 DOI: 10.3389/fgene.2022.971852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
miRNAs play an essential role in promoting viral infections as well as modulating the antiviral defense. Several miRNA repositories have been developed for different species, e.g., human, mouse, and plant. However, ‘VIRmiRNA’ is the only existing resource for experimentally validated viral miRNAs and their targets. We have developed a ‘AntiVIRmiR’ resource encompassing data on host/virus miRNA expression during viral infection. This resource with 22,741 entries is divided into four sub-databases viz., ‘DEmiRVIR’, ‘AntiVmiR’, ‘VIRmiRNA2’ and ‘VIRmiRTar2’. ‘DEmiRVIR’ has 10,033 differentially expressed host-viral miRNAs for 21 viruses. ‘AntiVmiR’ incorporates 1,642 entries for host miRNAs showing antiviral activity for 34 viruses. Additionally, ‘VIRmiRNA2’ includes 3,340 entries for experimentally validated viral miRNAs from 50 viruses along with 650 viral isomeric sequences for 14 viruses. Further, ‘VIRmiRTar2’ has 7,726 experimentally validated targets for viral miRNAs against 21 viruses. Furthermore, we have also performed network analysis for three sub-databases. Interactions between up/down-regulated human miRNAs and viruses are displayed for ‘AntiVmiR’ as well as ‘DEmiRVIR’. Moreover, ‘VIRmiRTar2’ interactions are shown among different viruses, miRNAs, and their targets. We have provided browse, search, external hyperlinks, data statistics, and useful analysis tools. The database available at https://bioinfo.imtech.res.in/manojk/antivirmir would be beneficial for understanding the host-virus interactions as well as viral pathogenesis.
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Affiliation(s)
- Anamika Thakur
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- *Correspondence: Manoj Kumar,
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11
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Jain CK, Srivastava P, Pandey AK, Singh N, Kumar RS. miRNA therapeutics in precision oncology: a natural premium to nurture. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:511-532. [PMID: 36071981 PMCID: PMC9446160 DOI: 10.37349/etat.2022.00098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamic spectrum of microRNA (miRNA) has grown significantly over the years with its identification and exploration in cancer therapeutics and is currently identified as an important resource for innovative strategies due to its functional behavior for gene regulation and modulation of complex biological networks. The progression of cancer is the consequence of uncontrolled, nonsynchronous procedural faults in the biological system. Diversified and variable cellular response of cancerous cells has always raised challenges in effective cancer therapy. miRNAs, a class of non-coding RNAs (ncRNAs), are the natural genetic gift, responsible to preserve the homeostasis of cell to nurture. The unprecedented significance of endogenous miRNAs has exhibited promising therapeutic potential in cancer therapeutics. Currently, miRNA mimic miR-34, and an antimiR aimed against miR-122 has entered the clinical trials for cancer treatments. This review, highlights the recent breakthroughs, challenges, clinical trials, and advanced delivery vehicles in the administration of miRNA therapies for precision oncology.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Poornima Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, GIFT city 382355, India
| | - R Suresh Kumar
- Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida 201307, India
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12
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Xie GY, Liu CJ, Guo AY. EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets. Brief Bioinform 2022; 23:6651306. [PMID: 35901462 DOI: 10.1093/bib/bbac310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular vesicles (EVs) carrying various small non-coding RNAs (sncRNAs) play a vital roles in cell communication and diseases. Correct quantification of multiple sncRNA biotypes simultaneously in EVs is a challenge due to the short reads (<30 bp) could be mapped to multiple sncRNA types. To address this question, we developed an optimized reads assignment algorithm (ORAA) to dynamically map multi-mapping reads to the sncRNA type with a higher proportion. We integrated ORAA with reads processing steps into EVAtool Python-package (http://bioinfo.life.hust.edu.cn/EVAtool) to quantify sncRNAs, especially for sncRNA-seq from EV samples. EVAtool allows users to specify interested sncRNA types in advanced mode or use default seven sncRNAs (microRNA, small nucleolar RNA, PIWI-interacting RNAs, small nuclear RNA, ribosomal RNA, transfer RNA and Y RNA). To prove the utilities of EVAtool, we quantified the sncRNA expression profiles for 200 samples from cognitive decline and multiple sclerosis. We found that more than 20% of short reads on average were mapped to multiple sncRNA biotypes in multiple sclerosis. In cognitive decline, the proportion of Y RNA is significantly higher than other sncRNA types. EVAtool is a flexible and extensible tool that would benefit to mine potential biomarkers and functional molecules in EVs.
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Affiliation(s)
- Gui-Yan Xie
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - Chun-Jie Liu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
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13
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Shin CH, Park SC, Park IG, Kim H, An B, Lee C, Kim SH, Lee J, Lee JM, Oh SJ. Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification. Nucleic Acids Res 2022; 50:5919-5933. [PMID: 35640600 PMCID: PMC9177975 DOI: 10.1093/nar/gkac431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA-dependent mRNA decay plays an important role in gene silencing by facilitating posttranscriptional and translational repression. Inspired by this intrinsic nature of microRNA-mediated mRNA cleavage, here, we describe a microRNA-targeting mRNA as a switch platform called mRNA bridge mimetics to regulate the translocation of proteins. We applied the mRNA bridge mimetics platform to Cas9 protein to confer it the ability to translocate into the nucleus via cleavage of the nuclear export signal. This system performed programmed gene editing in vitro and in vivo. Combinatorial treatment with cisplatin and miR-21-EZH2 axis-targeting CRISPR Self Check-In improved sensitivity to chemotherapeutic drugs in vivo. Using the endogenous microRNA-mediated mRNA decay mechanism, our platform is able to remodel a cell's natural biology to allow the entry of precise drugs into the nucleus, devoid of non-specific translocation. The mRNA bridge mimetics strategy is promising for applications in which the reaction must be controlled via intracellular stimuli and modulates Cas9 proteins to ensure safe genome modification in diseased conditions.
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Affiliation(s)
- Cheol-Hee Shin
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Su Chan Park
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Il-Geun Park
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyerim Kim
- Program in Nanoscience and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Byoungha An
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Choongil Lee
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sang-Heon Kim
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Juyong Lee
- Department of Chemistry, College of Natural Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ji Min Lee
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seung Ja Oh
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology (UST), Seoul, Republic of Korea
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14
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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15
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Guo S, Yang J, Jiang B, Zhou N, Ding H, Zhou G, Wu S, Suo A, Wu X, Xie W, Li W, Liu Y, Deng W, Zheng Y. MicroRNA editing patterns in Huntington's disease. Sci Rep 2022; 12:3173. [PMID: 35210471 PMCID: PMC8873361 DOI: 10.1038/s41598-022-06970-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/31/2022] [Indexed: 12/17/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disease. MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional regulation of target genes. Although miRNAs are extensively edited in human brains, the editome of miRNAs in brains of HD patients is largely unknown. By analyzing the small RNA sequencing profiles of brain tissues of 28 HD patients and 83 normal controls, 1182 miRNA editing sites with significant editing levels were identified. In addition to 27 A-to-I editing sites, we identified 3 conserved C-to-U editing sites in miRNAs of HD patients. 30 SNPs in the miRNAs of HD patients were also identified. Furthermore, 129 miRNA editing events demonstrated significantly different editing levels in prefrontal cortex samples of HD patients (HD-PC) when compared to those of healthy controls. We found that hsa-mir-10b-5p was edited to have an additional cytosine at 5'-end in HD-PC, and the edited hsa-mir-10b repressed GTPBP10 that was often downregulated in HD. The down-regulation of GTPBP10 might contribute to the progression of HD by causing gradual loss of function of mitochondrial. These results provide the first endeavor to characterize the miRNA editing events in HD and their potential functions.
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Affiliation(s)
- Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun Yang
- Physical Evidence Spectral Technology Innovation Team, Yunnan Police College, Kunming, 650223, China
| | - Bingbing Jiang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Nan Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hao Ding
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, China
| | - Guangchen Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, China
| | - Shuai Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Angbaji Suo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xingwang Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Wenping Xie
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yulong Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Wei Deng
- Center of Statistical Research, Southwestern University of Finance and Economics, Chengdu, 611130, China
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China.
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16
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MicroRNA let-7 and viral infections: focus on mechanisms of action. Cell Mol Biol Lett 2022; 27:14. [PMID: 35164678 PMCID: PMC8853298 DOI: 10.1186/s11658-022-00317-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are fundamental post-transcriptional modulators of several critical cellular processes, a number of which are involved in host defense mechanisms. In particular, miRNA let-7 functions as an essential regulator of the function and differentiation of both innate and adaptive immune cells. Let-7 is involved in several human diseases, including cancer and viral infections. Several viral infections have found ways to dysregulate the expression of miRNAs. Extracellular vesicles (EV) are membrane-bound lipid structures released from many types of human cells that can transport proteins, lipids, mRNAs, and miRNAs, including let-7. After their release, EVs are taken up by the recipient cells and their contents released into the cytoplasm. Let-7-loaded EVs have been suggested to affect cellular pathways and biological targets in the recipient cells, and can modulate viral replication, the host antiviral response, and the action of cancer-related viruses. In the present review, we summarize the available knowledge concerning the expression of let-7 family members, functions, target genes, and mechanistic involvement in viral pathogenesis and host defense. This may provide insight into the development of new therapeutic strategies to manage viral infections.
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17
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Abstract
MicroRNAs (miRNAs) are considerably small yet highly important riboregulators involved in nearly all cellular processes. Due to their critical roles in posttranscriptional regulation of gene expression, they have the potential to be used as biomarkers in addition to their use as drug targets. Although computational approaches speed up the initial genomewide identification of putative miRNAs, experimental approaches are essential for further validation and functional analyses of differentially expressed miRNAs. Therefore, sensitive, specific, and cost-effective microRNA detection methods are imperative for both individual and multiplex analysis of miRNA expression in different tissues and during different developmental stages. There are a number of well-established miRNA detection methods that can be exploited depending on the comprehensiveness of the study (individual miRNA versus multiplex analysis), the availability of the sample and the location and intracellular concentration of miRNAs. This review aims to highlight not only traditional but also novel strategies that are widely used in experimental identification and quantification of microRNAs.
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18
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Sonehara K, Sakaue S, Maeda Y, Hirata J, Kishikawa T, Yamamoto K, Matsuoka H, Yoshimura M, Nii T, Ohshima S, Kumanogoh A, Okada Y. Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population. Hum Mol Genet 2021; 31:1806-1820. [PMID: 34919704 PMCID: PMC9169454 DOI: 10.1093/hmg/ddab361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic effects on non-coding RNA (ncRNA) expression facilitates functional characterization of disease-associated genetic loci. Among several classes of ncRNAs, microRNAs (miRNAs) are key post-transcriptional gene regulators. Despite its biological importance, previous studies on the genetic architecture of miRNA expression focused mostly on the European individuals, underrepresented in other populations. Here, we mapped miRNA expression quantitative trait loci (miRNA-eQTL) for 343 miRNAs in 141 Japanese using small RNA sequencing (sRNA-seq) and whole-genome sequencing (WGS), identifying 1275 cis-miRNA-eQTL variants for 40 miRNAs (false discovery rate < 0.2). Of these, 25 miRNAs having eQTL were unreported in the European studies, including 5 miRNAs with their lead variant monomorphic in the European populations, which demonstrates the value of miRNA-eQTL analysis in diverse ancestral populations. MiRNAs with eQTL effect showed allele-specific expression (ASE) (e.g. miR-146a-3p), and ASE analysis further detected cis-regulatory variants not captured by the conventional miRNA-eQTL mapping (e.g. miR-933). We identified a copy number variation (CNV) associated with miRNA expression (e.g. miR-570-3p, P = 7.2 × 10-6), which contributes to a more comprehensive landscape of miRNA-eQTLs. To elucidate a post-transcriptional modification in miRNAs, we created a catalog of miRNA-editing sites, including ten canonical and six non-canonical sites. Finally, by integrating the miRNA-eQTLs and Japanese genome-wide association studies of 25 complex traits (mean n = 192 833), we conducted a transcriptome-wide association study (TWAS), identifying miR-1908-5p as a potential mediator for adult height, colorectal cancer, and type 2 diabetes (P < 9.1 × 10-5). Our study broadens the population diversity in ncRNA-eQTL studies and contributes to functional annotation of disease-associated loci found in non-European populations.
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Affiliation(s)
- Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan
| | - Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Center for Data Sciences, Harvard Medical School, Boston, MA, 02114, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Hino, 191-8512, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Otorhinolaryngology - Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, 464-8681, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan
| | - Hidetoshi Matsuoka
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, 586-8521, Japan
| | - Maiko Yoshimura
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, 586-8521, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shiro Ohshima
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, 586-8521, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, 565-0871, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan.,The Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, 565-0871, Japan.,Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
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19
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Chen J, Liu HF, Qiao LB, Wang FB, Wang L, Lin Y, Liu J. Global RNA editing identification and characterization during human pluripotent-to-cardiomyocyte differentiation. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:879-891. [PMID: 34760335 PMCID: PMC8551472 DOI: 10.1016/j.omtn.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
Abstract
RNA editing is widely involved in stem cell differentiation and development; however, RNA editing events during human cardiomyocyte differentiation have not yet been characterized and elucidated. Here, we identified genome-wide RNA editing sites and systemically characterized their genomic distribution during four stages of human cardiomyocyte differentiation. It was found that the expression level of ADAR1 affected the global number of adenosine to inosine (A-to-I) editing sites but not the editing degree. Next, we identified 43, 163, 544, and 141 RNA editing sites that contribute to changes in amino acid sequences, variation in alternative splicing, alterations in miRNA-target binding, and changes in gene expression, respectively. Generally, RNA editing showed a stage-specific pattern with 211 stage-shared editing sites. Interestingly, cardiac muscle contraction and heart-disease-related pathways were enriched by cardio-specific editing genes, emphasizing the connection between cardiomyocyte differentiation and heart diseases from the perspective of RNA editing. Finally, it was found that these RNA editing sites are also related to several congenital and noncongenital heart diseases. Together, our study provides a new perspective on cardiomyocyte differentiation and offers more opportunities to understand the mechanisms underlying cell fate determination, which can promote the development of cardiac regenerative medicine and therapies for human heart diseases.
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Affiliation(s)
- Juan Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Hui-Fang Liu
- Department of Endocrinology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Li-Bo Qiao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Fang-Bin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yan Lin
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.,Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui 230009, China
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20
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Soler M, Davalos V, Sánchez-Castillo A, Mora-Martinez C, Setién F, Siqueira E, Castro de Moura M, Esteller M, Guil S. The transcribed ultraconserved region uc.160+ enhances processing and A-to-I editing of the miR-376 cluster: hypermethylation improves glioma prognosis. Mol Oncol 2021; 16:648-664. [PMID: 34665919 PMCID: PMC8807354 DOI: 10.1002/1878-0261.13121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 11/11/2022] Open
Abstract
Transcribed ultraconserved regions (T‐UCRs) are noncoding RNAs derived from DNA sequences that are entirely conserved across species. Their expression is altered in many tumor types, and, although a role for T‐UCRs as regulators of gene expression has been proposed, their functions remain largely unknown. Herein, we describe the epigenetic silencing of the uc.160+ T‐UCR in gliomas and mechanistically define a novel RNA–RNA regulatory network in which uc.160+ modulates the biogenesis of several members of the miR‐376 cluster. This includes the positive regulation of primary microRNA (pri‐miRNA) cleavage and an enhanced A‐to‐I editing on its mature sequence. As a consequence, the expression of uc.160+ affects the downstream, miR‐376‐regulated genes, including the transcriptional coregulators RING1 and YY1‐binding protein (RYBP) and forkhead box P2 (FOXP2). Finally, we elucidate the clinical impact of our findings, showing that hypermethylation of the uc.160+ CpG island is an independent prognostic factor associated with better overall survival in lower‐grade gliomas, highlighting the importance of T‐UCRs in cancer pathophysiology.
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Affiliation(s)
- Marta Soler
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Anaís Sánchez-Castillo
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands
| | - Carlos Mora-Martinez
- Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland
| | - Fernando Setién
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Conselho Nacional de Desenvolvimento Cientifico e Tecnológico (CNPq), Brasilia, Brazil
| | | | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Germans Trias i Pujol Health Science Research Institute, Barcelona, Spain
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21
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Kavakiotis I, Alexiou A, Tastsoglou S, Vlachos IS, Hatzigeorgiou AG. DIANA-miTED: a microRNA tissue expression database. Nucleic Acids Res 2021; 50:D1055-D1061. [PMID: 34469540 PMCID: PMC8728140 DOI: 10.1093/nar/gkab733] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
microRNAs (miRNAs) are short (∼23nt) single-stranded non-coding RNAs that act as potent post-transcriptional gene expression regulators. Information about miRNA expression and distribution across cell types and tissues is crucial to the understanding of their function and for their translational use as biomarkers or therapeutic targets. DIANA-miTED is the most comprehensive and systematic collection of miRNA expression values derived from the analysis of 15 183 raw human small RNA-Seq (sRNA-Seq) datasets from the Sequence Read Archive (SRA) and The Cancer Genome Atlas (TCGA). Metadata quality maximizes the utility of expression atlases, therefore we manually curated SRA and TCGA-derived information to deliver a comprehensive and standardized set, incorporating in total 199 tissues, 82 anatomical sublocations, 267 cell lines and 261 diseases. miTED offers rich instant visualizations of the expression and sample distributions of requested data across variables, as well as study-wide diagrams and graphs enabling efficient content exploration. Queries also generate links towards state-of-the-art miRNA functional resources, deeming miTED an ideal starting point for expression retrieval, exploration, comparison, and downstream analysis, without requiring bioinformatics support or expertise. DIANA-miTED is freely available at http://www.microrna.gr/mited.
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Affiliation(s)
- Ioannis Kavakiotis
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, Univ. of Thessaly, 35131 Lamia, Greece
| | - Athanasios Alexiou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, Univ. of Thessaly, 35131 Lamia, Greece.,Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Spyros Tastsoglou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, Univ. of Thessaly, 35131 Lamia, Greece.,Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Ioannis S Vlachos
- Cancer Research Institute
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, Univ. of Thessaly, 35131 Lamia, Greece.,Hellenic Pasteur Institute, 11521 Athens, Greece
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22
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De Paolis V, Lorefice E, Orecchini E, Carissimi C, Laudadio I, Fulci V. Epitranscriptomics: A New Layer of microRNA Regulation in Cancer. Cancers (Basel) 2021; 13:3372. [PMID: 34282776 PMCID: PMC8268402 DOI: 10.3390/cancers13133372] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.
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Affiliation(s)
| | | | | | - Claudia Carissimi
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
| | - Ilaria Laudadio
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
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23
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Oda S, Yokoi T. Recent progress in the use of microRNAs as biomarkers for drug-induced toxicities in contrast to traditional biomarkers: A comparative review. Drug Metab Pharmacokinet 2021; 37:100372. [PMID: 33461055 DOI: 10.1016/j.dmpk.2020.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 02/09/2023]
Abstract
microRNAs (miRNAs) are small non-coding RNAs with 18-25 nucleotides. They play key regulatory roles in versatile biological process including development and apoptosis, and in disease pathogenesis, for example carcinogenesis, by negatively regulating gene expression. miRNAs often exhibit characteristics suitable for biomarkers such as tissue-specific expression patterns, high stability in serum/plasma, and change in abundance in circulation immediately after toxic injury. Since the discovery of circulating miRNAs in extracellular biological fluids in 2008, there have been many reports on the use of miRNAs as biomarkers for various diseases including cancer and organ injury in humans and experimental animals. In this review article, we have summarized the utility and limitation of circulating miRNAs as safety/toxicology biomarkers for specific tissue injuries including liver, skeletal muscle, heart, retina, and pancreas, by comparing them with conventional protein biomarkers. We have also covered the discovery of miRNAs in serum/plasma and their stability, the knowledge of which is essential for understanding the kinetics of miRNA biomarkers. Since numerous studies have reported the use of these circulating miRNAs as safety biomarkers with high sensitivity and specificity, we believe that circulating miRNAs can promote pre-clinical drug development and improve the monitoring of tissue injuries in clinical pharmacotherapy.
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Affiliation(s)
- Shingo Oda
- Department of Drug Safety Sciences, Division of Clinical Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Tsuyoshi Yokoi
- Department of Drug Safety Sciences, Division of Clinical Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
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24
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The Physiological MicroRNA Landscape in Nipple Aspirate Fluid: Differences and Similarities with Breast Tissue, Breast Milk, Plasma and Serum. Int J Mol Sci 2020; 21:ijms21228466. [PMID: 33187146 PMCID: PMC7696615 DOI: 10.3390/ijms21228466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background: MicroRNAs (miRNAs) target 60% of human messenger RNAs and can be detected in tissues and biofluids without loss of stability during sample processing, making them highly appraised upcoming biomarkers for evaluation of disease. However, reporting of the abundantly expressed miRNAs in healthy samples is often surpassed. Here, we characterized for the first time the physiological miRNA landscape in a biofluid of the healthy breast: nipple aspirate fluid (NAF), and compared NAF miRNA expression patterns with publically available miRNA expression profiles of healthy breast tissue, breast milk, plasma and serum. Methods: MiRNA RT-qPCR profiling of NAF (n = 41) and serum (n = 23) samples from two healthy female cohorts was performed using the TaqMan OpenArray Human Advanced MicroRNA 754-Panel. MiRNA quantification data based on non-targeted or multi-targeted profiling techniques for breast tissue, breast milk, plasma and serum were retrieved from the literature by means of a systematic search. MiRNAs from each individual study were orderly ranked between 1 and 50, combined into an overall ranking per sample type and compared. Results: NAF expressed 11 unique miRNAs and shared 21/50 miRNAs with breast tissue. Seven miRNAs were shared between the five sample types. Overlap between sample types varied between 42% and 62%. Highly ranked NAF miRNAs have established roles in breast carcinogenesis. Conclusion: This is the first study to characterize and compare the unique physiological NAF-derived miRNA landscape with the physiological expression pattern in breast tissue, breast milk, plasma and serum. Breast-specific sources did not mutually overlap more than with systemic sources. Given their established role in carcinogenesis, NAF miRNA assessment could be a valuable tool in breast tumor diagnostics.
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25
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De Novo A-to-I RNA Editing Discovery in lncRNA. Cancers (Basel) 2020; 12:cancers12102959. [PMID: 33066171 PMCID: PMC7650826 DOI: 10.3390/cancers12102959] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Long non-coding RNAs are emerging as key regulators of gene expression at both transcriptional and translational levels, and their alterations (in expression or sequence) are linked to tumorigenesis and tumor progression. RNA editing has the unique ability to change the RNA sequence without altering the integrity or sequence of genomic DNA, with adenosine to inosine (A-to-I) RNA editing being the most common event in humans. With the ability to change the genetic information after transcription, RNA editing is an essential player in the transcriptome and proteome enrichment; however, when deregulated, it can contribute to cell transformation. In this article, we performed the first deep de novo editing survey in lncRNA, demonstrating that RNA editing is a pervasive phenomenon involving lncRNAs important in the brain and brain cancer. Our study will open a new field of research in which the interplay between lncRNA and RNA editing can add novel insights into cancer. Abstract Background: Adenosine to inosine (A-to-I) RNA editing is the most frequent editing event in humans. It converts adenosine to inosine in double-stranded RNA regions (in coding and non-coding RNAs) through the action of the adenosine deaminase acting on RNA (ADAR) enzymes. Long non-coding RNAs, particularly abundant in the brain, account for a large fraction of the human transcriptome, and their important regulatory role is becoming progressively evident in both normal and transformed cells. Results: Herein, we present a bioinformatic analysis to generate a comprehensive inosinome picture in long non-coding RNAs (lncRNAs), using an ad hoc index and searching for de novo editing events in the normal brain cortex as well as in glioblastoma, a highly aggressive human brain cancer. We discovered >10,000 new sites and 335 novel lncRNAs that undergo editing, never reported before. We found a generalized downregulation of editing at multiple lncRNA sites in glioblastoma samples when compared to the normal brain cortex. Conclusion: Overall, our study discloses a novel layer of complexity that controls lncRNAs in the brain and brain cancer.
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26
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Giroux P, Bhajun R, Segard S, Picquenot C, Charavay C, Desquilles L, Pinna G, Ginestier C, Denis J, Cherradi N, Guyon L. miRViz: a novel webserver application to visualize and interpret microRNA datasets. Nucleic Acids Res 2020; 48:W252-W261. [PMID: 32319523 PMCID: PMC7319447 DOI: 10.1093/nar/gkaa259] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in the regulation of major pathways in eukaryotic cells through their binding to and repression of multiple mRNAs. With high-throughput methodologies, various outcomes can be measured that produce long lists of miRNAs that are often difficult to interpret. A common question is: after differential expression or phenotypic screening of miRNA mimics, which miRNA should be chosen for further investigation? Here, we present miRViz (http://mirviz.prabi.fr/), a webserver application designed to visualize and interpret large miRNA datasets, with no need for programming skills. MiRViz has two main goals: (i) to help biologists to raise data-driven hypotheses and (ii) to share miRNA datasets in a straightforward way through publishable quality data representation, with emphasis on relevant groups of miRNAs. MiRViz can currently handle datasets from 11 eukaryotic species. We present real-case applications of miRViz, and provide both datasets and procedures to reproduce the corresponding figures. MiRViz offers rapid identification of miRNA families, as demonstrated here for the miRNA-320 family, which is significantly exported in exosomes of colon cancer cells. We also visually highlight a group of miRNAs associated with pluripotency that is particularly active in control of a breast cancer stem-cell population in culture.
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Affiliation(s)
- Pierre Giroux
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Ricky Bhajun
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Stéphane Segard
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Claire Picquenot
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Céline Charavay
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Lise Desquilles
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Guillaume Pinna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, University Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Christophe Ginestier
- Aix-Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer lab, F-13273 Marseille, France
| | - Josiane Denis
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Nadia Cherradi
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Laurent Guyon
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France.,Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
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27
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Ma L, Zhang Y, Hu F. miR‑28‑5p inhibits the migration of breast cancer by regulating WSB2. Int J Mol Med 2020; 46:1562-1570. [PMID: 32945370 PMCID: PMC7447326 DOI: 10.3892/ijmm.2020.4685] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) play an important role in the tumorigenesis and progression of breast cancer. However, the function of miR‑28‑5p in breast cancer migration has yet to be determined. In the present study, Human MicroRNA Expression Database (HMED) analysis revealed that the expression level of miR‑28‑5p was significantly lower in breast cancer tissue than in normal breast tissue. Kaplan-‑Meier plotter (KMPLOT) analysis revealed that the low expression level of miR‑28‑5p was associated with a poor survival in breast cancer. In addition, reverse transcription‑quantitative PCR (RT‑qPCR) revealed that the expression of miR‑28‑5p was significantly lower in breast cancer cell lines compared with that in human mammary epithelial cells (HMECs). Moreover, transfection with miR‑28‑5p mimics suppressed the migration of MCF‑7 cells, whereas an miR‑28‑5p inhibitor exerted the opposite effect. Gene chip assay identified 648 differentially expressed genes (DEGs) in cells overexpressing miR‑28‑5p. The DEGs are enriched in the 'focal adhesion' and 'pathway in cancer' pathways. The expression levels of Ras‑related protein Rap‑1b (RAP1B), WD repeat and SOCS box containing 2 (WSB2) and vascular endothelial growth factor A (VEGFA) were confirmed by RT‑qPCR. Furthermore, transfection with miR‑28‑5p mimics decreased WSB2 expression, whereas the miR‑28‑5p inhibitor increased the expression of WSB2, at both the transcriptional and translational levels. miR‑28‑5p targets the 3'UTR of WSB2, and the binding site is conserved in multiple species, with a consensus motif of 5'‑AGCUCCUU‑3'. Moreover, WSB2 overexpression promoted the migration of MCF‑7 cells which had been inhibited by miR‑28‑5p. UALCAN analysis revealed that WSB2 was significantly upregulated in primary breast tumor tissue, and a high expression level of WSB2 was associated with a poor survival in breast cancer. Furthermore, immunohistochemistry revealed that the expression of WSB2 was markedly higher in breast cancer tissue compared with that in adjacent normal breast tissue. Taken together, the findings of the present study demonstrate that miR‑28‑5p inhibits the migration of breast cancer cells by regulating WSB2 expression, and the miR‑28‑5p/WSB2 axis may be a novel therapeutic target in breast cancer.
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Affiliation(s)
- Liang Ma
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, P.R. China
| | - Yunfeng Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, Hebei 063000, P.R. China
| | - Fen Hu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, P.R. China
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28
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van der Kwast RVCT, Parma L, van der Bent ML, van Ingen E, Baganha F, Peters HAB, Goossens EAC, Simons KH, Palmen M, de Vries MR, Quax PHA, Nossent AY. Adenosine-to-Inosine Editing of Vasoactive MicroRNAs Alters Their Targetome and Function in Ischemia. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:932-953. [PMID: 32814251 PMCID: PMC7452086 DOI: 10.1016/j.omtn.2020.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing in the seed sequence of microRNAs can shift the microRNAs’ targetomes and thus their function. Using public RNA-sequencing data, we identified 35 vasoactive microRNAs that are A-to-I edited. We quantified A-to-I editing of the primary (pri-)microRNAs in vascular fibroblasts and endothelial cells. Nine pri-microRNAs were indeed edited, and editing consistently increased under ischemia. We determined mature microRNA editing for the highest expressed microRNAs, i.e., miR-376a-3p, miR-376c-3p, miR-381-3p, and miR-411-5p. All four mature microRNAs were edited in their seed sequence. We show that both ADAR1 and ADAR2 (adenosine deaminase acting on RNA 1 and RNA 2) can edit pri-microRNAs in a microRNA-specific manner. MicroRNA editing also increased under ischemia in vivo in a murine hindlimb ischemia model and ex vivo in human veins. For each edited microRNA, we confirmed a shift in targetome. Expression of the edited microRNA targetomes, not the wild-type targetomes, was downregulated under ischemia in vivo. Furthermore, microRNA editing enhanced angiogenesis in vitro and ex vivo. In conclusion, we show that microRNA A-to-I editing is a widespread phenomenon, induced by ischemia. Each editing event results in a novel microRNA with a unique targetome, leading to increased angiogenesis.
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Affiliation(s)
- Reginald V C T van der Kwast
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Laura Parma
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - M Leontien van der Bent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Fabiana Baganha
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hendrika A B Peters
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Karin H Simons
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Meindert Palmen
- Department of Cardiothoracic Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria.
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29
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Human Brain Shows Recurrent Non-Canonical MicroRNA Editing Events Enriched for Seed Sequence with Possible Functional Consequence. Noncoding RNA 2020; 6:ncrna6020021. [PMID: 32498345 PMCID: PMC7345632 DOI: 10.3390/ncrna6020021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
RNA editing is a post-transcriptional modification, which can provide tissue-specific functions not encoded in DNA. Adenosine-to-inosine is the predominant editing event and, along with cytosine-to-uracil changes, constitutes canonical editing. The rest is non-canonical editing. In this study, we have analysed non-canonical editing of microRNAs in the human brain. We have performed massively parallel small RNA sequencing of frontal cortex (FC) and corpus callosum (CC) pairs from nine normal individuals (post-mortem). We found 113 and 90 unique non-canonical editing events in FC and CC samples, respectively. More than 70% of events were in the miRNA seed sequence—implicating an altered set of target mRNAs and possibly resulting in a functional consequence. Up to 15% of these events were recurring and found in at least three samples, also supporting the biological relevance of such variations. Two specific sequence variations, C-to-A and G-to-U, accounted for over 80% of non-canonical miRNA editing events—and revealed preferred sequence motifs. Our study is one of the first reporting non-canonical editing in miRNAs in the human brain. Our results implicate miRNA non-canonical editing as one of the contributing factors towards transcriptomic diversity in the human brain.
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30
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Demirel G, Guzel E, Creighton CJ, Ozturk YE, Kucuk C, Asliyuksek H, Yurdun T. MDMA Abuse in Relation to MicroRNA Variation in Human Brain Ventral Tegmental Area and Nucleus Accumbens. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2020; 18:1989-1999. [PMID: 32184864 PMCID: PMC7059052 DOI: 10.22037/ijpr.2019.15097.12874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
3,4-methylenedioxymethamphetamine (MDMA) is one of the most widespread illegal drugs, that have been used particularly by young people in the 15-34 age group. MicroRNAs (miRNAs) are endogenously synthesized, non-coding, and small RNAs that post-transcriptionally regulate their target genes' expression by inhibiting protein translation or degradation. miRNAs are increasingly implicated in drug-related gene expressions and functions. Notably, there are no reports of miRNA variation in the human brain in MDMA abuse. We here present a miRNA profiling study - the first such study, to the best of our knowledge - into the post-mortem human brains of a sample of people with MDMA abuse, along with non-drug dependent controls. The miRNA profiling of nucleus accumbens (NAc) and ventral tegmental areas (VTA) was performed by microarray analysis. Subsequently, two candidate miRNA putative biomarkers were selected according to significant regional differential expression (miR-1202 and miR-7975), using quantitative reverse-transcription PCR (qRT-PCR). We showed that the expression level of miR-7975 was significantly lower in the VTA regions of the 30 MDMA users, as compared with the 30 control samples. Another significantly deregulated miR-1202 was down-regulated in the NAc regions of 30 MDMA samples in comparison to the control samples. Alteration of these miRNAs can potentially serve as novel biomarkers for MDMA abuse, and warrant further research in independent and larger samples of patients.
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Affiliation(s)
- Goksun Demirel
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Biruni University, Istanbul, Turkey.,Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Çukurova University, Adana, Turkey.,G D and E G. These authors contributed equally to this work
| | - Esra Guzel
- Department of Molecular Biology and Genetics, Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey.,G D and E G. These authors contributed equally to this work
| | - Chad J Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Cancer Center Division of Biostatistics, Houston, Texas
| | - Yeter Erol Ozturk
- Chemistry Department, Council of Forensic Medicine, Istanbul, Turkey
| | | | | | - Türkan Yurdun
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
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31
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Ali Syeda Z, Langden SSS, Munkhzul C, Lee M, Song SJ. Regulatory Mechanism of MicroRNA Expression in Cancer. Int J Mol Sci 2020; 21:E1723. [PMID: 32138313 PMCID: PMC7084905 DOI: 10.3390/ijms21051723] [Citation(s) in RCA: 515] [Impact Index Per Article: 128.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022] Open
Abstract
Altered gene expression is the primary molecular mechanism responsible for the pathological processes of human diseases, including cancer. MicroRNAs (miRNAs) are virtually involved at the post-transcriptional level and bind to 3' UTR of their target messenger RNA (mRNA) to suppress expression. Dysfunction of miRNAs disturbs expression of oncogenic or tumor-suppressive target genes, which is implicated in cancer pathogenesis. As such, a large number of miRNAs have been found to be downregulated or upregulated in human cancers and to function as oncomiRs or oncosuppressor miRs. Notably, the molecular mechanism underlying the dysregulation of miRNA expression in cancer has been recently uncovered. The genetic deletion or amplification and epigenetic methylation of miRNA genomic loci and the transcription factor-mediated regulation of primary miRNA often alter the landscape of miRNA expression in cancer. Dysregulation of the multiple processing steps in mature miRNA biogenesis can also cause alterations in miRNA expression in cancer. Detailed knowledge of the regulatory mechanism of miRNAs in cancer is essential for understanding its physiological role and the implications of cancer-associated dysfunction and dysregulation. In this review, we elucidate how miRNA expression is deregulated in cancer, paying particular attention to the cancer-associated transcriptional and post-transcriptional factors that execute miRNA programs.
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Affiliation(s)
- Zainab Ali Syeda
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea; (Z.A.S.); (S.S.S.L.); (C.M.)
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Siu Semar Saratu’ Langden
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea; (Z.A.S.); (S.S.S.L.); (C.M.)
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Choijamts Munkhzul
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea; (Z.A.S.); (S.S.S.L.); (C.M.)
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea; (Z.A.S.); (S.S.S.L.); (C.M.)
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Su Jung Song
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea; (Z.A.S.); (S.S.S.L.); (C.M.)
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
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32
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Chen J, Wang L, Wang F, Liu J, Bai Z. Genomic Identification of RNA Editing Through Integrating Omics Datasets and the Clinical Relevance in Hepatocellular Carcinoma. Front Oncol 2020; 10:37. [PMID: 32117713 PMCID: PMC7033493 DOI: 10.3389/fonc.2020.00037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
RNA editing is a widespread post-transcriptional mechanism to introduce single nucleotide changes to RNA in human cancers. Here, we characterized the global RNA editing profiles of 373 hepatocellular carcinoma (HCC) and 50 adjacent normal liver samples from The Cancer Genome Atlas (TCGA) and revealed that most editing events tend to occur in minor percentage of samples with moderate editing degrees (20–30%). Moreover, these RNA editing prefer to be A-to-I RNA editing in protein coding genes, especially in 3′UTR regions. Considering the association between DNA mutation and RNA editing, our analysis found that RNA editing maybe a complementary event for DNA mutation of HCC risk genes in HCC patients. We next identified 454 HCC-related editing sites, and many locate on the same genes with the same editing patterns. The functional consequences of editing revealed 2,086 functional editing sites and demonstrated that most editing in coding regions are non-synonymous variations. Furthermore, our results showed that editing in the 3′UTR regions tend to influence miRNA–target binding, and the editing degree seems to be negatively correlated with gene expression. Finally, we found that 46 HCC-related editing sites with consequence are able to distinguish the prognosis differences of HCC patients, suggesting their clinical relevance. Together, our results highlight RNA editing as a valuable molecular resource for investigating HCC mechanisms and clinical treatments.
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Affiliation(s)
- Juan Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Fangbin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China.,Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei, China
| | - Zhenyu Bai
- Department of Laboratory, General Hospital of Pingmei Shenma Medical Group, Pingdingshan, China
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33
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Jacinta-Fernandes A, Xavier JM, Magno R, Lage JG, Maia AT. Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk. NPJ Genom Med 2020; 5:4. [PMID: 32128252 PMCID: PMC7018948 DOI: 10.1038/s41525-019-0112-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Most breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms-TargetScan and miRanda-to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant ( P ≤ 5 × 10 - 8 ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3'-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.
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Affiliation(s)
- Ana Jacinta-Fernandes
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Joana M Xavier
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Ramiro Magno
- 2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Joel G Lage
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Ana-Teresa Maia
- 1Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, 8005-139 Portugal.,2Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal.,3Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, 8005-139 Portugal
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34
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The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
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35
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Xu X, Wang Y, Mojumdar K, Zhou Z, Jeong KJ, Mangala LS, Yu S, Tsang YH, Rodriguez-Aguayo C, Lu Y, Lopez-Berestein G, Sood AK, Mills GB, Liang H. A-to-I-edited miRNA-379-5p inhibits cancer cell proliferation through CD97-induced apoptosis. J Clin Invest 2019; 129:5343-5356. [PMID: 31682236 PMCID: PMC6877318 DOI: 10.1172/jci123396] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 05/29/2019] [Indexed: 12/26/2022] Open
Abstract
Both miRNAs and A-to-I RNA editing, a widespread nucleotide modification mechanism, have recently emerged as key players in cancer pathophysiology. However, the functional impact of RNA editing of miRNAs in cancer remains largely unexplored. Here, we focused on an ADAR2-catalyzed RNA editing site within the miR-379-5p seed region. This site was under-edited in tumors relative to normal tissues, with a high editing level being correlated with better patient survival times across cancer types. We demonstrated that in contrast to wild-type miRNA, edited miR-379-5p inhibited cell proliferation and promoted apoptosis in diverse tumor contexts in vitro, which was due to the ability of edited but not wild-type miR-379-5p to target CD97. Importantly, through nanoliposomal delivery, edited miR-379-5p mimics significantly inhibited tumor growth and extended survival of mice. Our study indicates a role of RNA editing in diversifying miRNA function during cancer progression and highlights the translational potential of edited miRNAs as a new class of cancer therapeutics.
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Affiliation(s)
- Xiaoyan Xu
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning Province, China
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhicheng Zhou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Systems Biology
| | | | - Lingegowda S. Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, and
- Center for RNA Interference and Non–Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Gabriel Lopez-Berestein
- Center for RNA Interference and Non–Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, and
- Center for RNA Interference and Non–Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas, USA
- Department of Systems Biology
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36
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miR-1185-1 and miR-548q Are Biomarkers of Response to Weight Loss and Regulate the Expression of GSK3B. Cells 2019; 8:cells8121548. [PMID: 31801236 PMCID: PMC6953011 DOI: 10.3390/cells8121548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022] Open
Abstract
The aim of the present investigation was to identify putative miRNAs involved in the response to weight loss. Reverse-transcribed RNA isolated from white blood cells (WBCs) of a subpopulation from the Reduction of the Metabolic Syndrome in Navarra-Spain (RESMENA-S) study (low-responders (LR) and high-responders (HR)) was hybridized in a gene expression microarray. Moreover, miRNAs were sequenced by miRNA-Seq. It was found that miR-548q and miR-1185-1 were overexpressed in HR, both in the microarray and in the miRNA-Seq. A bioinformatic prediction of putative target genes of the selected miRNAs found that GSK3B, a putative target for miR-548q and miR-1185-1, was downregulated in HR. Particular 3′-UTR binding regions of GSK3B were cloned downstream of the firefly luciferase gene. HEK-293T cells were co-transfected with either 0.25 μg of empty pmiR-GLO or pmiR-GLO-548q-3′-UTR/pmiR-GLO-1185-1-3′-UTR, and 7.5 pmol of miR-548q/miR-1185-1 mimics, demonstrating that miR-1185-1 bound to the 3′-UTR region of GSK3B. THP-1 cells were transfected with either 20/40 nM of miR-548q/miR-1185-1 mimics, evidencing that miR-1185-1inhibited the expression of the gene when transfected at doses of 20/40 nM, whereas miR-548q inhibited GSK3B expression at a dose of 40 nM. As a conclusion, miR-548q and miR-1185-1 levels in WBCs are biomarkers of response to weight-loss diets and could be involved in the regulation of the proinflammatory gene GSK3B.
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Khani-Habibabadi F, Askari S, Zahiri J, Javan M, Behmanesh M. Novel BDNF-regulatory microRNAs in neurodegenerative disorders pathogenesis: An in silico study. Comput Biol Chem 2019; 83:107153. [PMID: 31751881 DOI: 10.1016/j.compbiolchem.2019.107153] [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] [Received: 06/10/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 11/28/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) is a neurotrophic factor with various roles in the central nervous system neurogenesis, neuroprotection, and axonal guide. By attaching to Tropomyosin receptor kinase B (TrkB) receptor, this protein triggers downstream signaling pathways which lead to cellular growth, proliferation, survival, and neuroplasticity. Deregulation at mRNA level is involved in various central nervous system disorders including, Huntington, Alzheimer's, Multiple Sclerosis, and Amyotrophic Lateral Sclerosis diseases. Considering the importance of BDNF functions, deciphering the regulatory mechanisms controlling BDNF expression level could pave the way to develop more accurate and efficient treatments for neurological diseases. Among different regulatory systems, microRNAs (miRNAs) play prominent roles by targeting genes 3' untranslated regions. In this study, 127 validated and bioinformatic-predicted miRNAs with potentially regulatory roles in BDNF expression were analyzed. Various aspects of miRNAsö possible functions were assessed by bioinformatic online tools to find their potential regulatory functions in signaling pathways, neurological disorders, expression of transcription factors and miRNAs sponge. Analyzed data led to introduce 5 newly reported miRNAs that could regulate BDNF expression level. Finally, high throughput sequencing data from different brain regions and neurological disorders were analyzed to measure correlation of candidate miRNAs with BDNF level in experimental studies. In this study, a list of novel miRNAs with possible regulatory roles in BDNF expression level involving in different neurological disorders was introduced.
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Affiliation(s)
- Fatemeh Khani-Habibabadi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shahrzad Askari
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Javan
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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38
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Hernández-Romero IA, Guerra-Calderas L, Salgado-Albarrán M, Maldonado-Huerta T, Soto-Reyes E. The Regulatory Roles of Non-coding RNAs in Angiogenesis and Neovascularization From an Epigenetic Perspective. Front Oncol 2019; 9:1091. [PMID: 31709179 PMCID: PMC6821677 DOI: 10.3389/fonc.2019.01091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Angiogenesis is a crucial process for organ morphogenesis and growth during development, and it is especially relevant during the repair of wounded tissue in adults. It is coordinated by an equilibrium of pro- and anti-angiogenic factors; nevertheless, when affected, it promotes several diseases. Lately, a growing body of evidence is indicating that non-coding RNAs (ncRNAs), such as miRNAs, circRNAs, and lncRNAs, play critical roles in angiogenesis. These ncRNAs can act in cis or trans and alter gene transcription by several mechanisms including epigenetic processes. In the following pages, we will discuss the functions of ncRNAs in the regulation of angiogenesis and neovascularization, both in normal and disease contexts, from an epigenetic perspective. Additionally, we will describe the contribution of Next-Generation Sequencing (NGS) techniques to the discovery and understanding of the role of ncRNAs in angiogenesis.
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Affiliation(s)
| | | | | | | | - Ernesto Soto-Reyes
- Natural Sciences Department, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
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39
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Huang W, Hu H, Zhang Q, Wu X, Wei F, Yang F, Gan L, Wang N, Yang X, Guo AY. Regulatory networks in mechanotransduction reveal key genes in promoting cancer cell stemness and proliferation. Oncogene 2019; 38:6818-6834. [PMID: 31406247 PMCID: PMC6988105 DOI: 10.1038/s41388-019-0925-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/21/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022]
Abstract
Tumor-repopulating cells (TRCs) are cancer stem cell (CSC)-like cells with highly tumorigenic and self-renewing abilities, which were selected from tumor cells in soft three-dimensional (3D) fibrin gels with unidentified mechanisms. Here we evaluated the transcriptome alteration during TRCs generation in 3D culture and revealed that a variety of molecules related with integrin/membrane and stemness were continuously altered by mechanical environment. Some key regulators such as MYC/STAT3/hsa-miR-199a-5p, were changed in the TRCs generation. They regulated membrane genes and the downstream mechanotransduction pathways such as Hippo/WNT/TGF-β/PI3K-AKT pathways, thus further affecting the expression of downstream cancer-related genes. By integrating networks for membrane proteins, the WNT pathway and cancer-related genes, we identified key molecules in the selection of TRCs, such as ATF4, SLC3A2, CCT3, and hsa-miR-199a-5p. Silencing ATF4 or CCT3 inhibited the selection and growth of TRCs whereas reduction of SLC3A2 or hsa-miR-199a-5p promoted TRCs growth. Further studies showed that CCT3 promoted cell proliferation and stemness in vitro, while its suppression inhibited TRCs-induced tumor formation. We also contemplated CCT3 as a stemness-related gene. Our findings provide insights in the mechanism of TRCs selection through transcriptome analysis.
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Affiliation(s)
- Wei Huang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Hui Hu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Qiong Zhang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Xian Wu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Fuxiang Wei
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Fang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Lu Gan
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Ning Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
- Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China.
| | - An-Yuan Guo
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China.
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40
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Ghanbari M, Munshi ST, Ma B, Lendemeijer B, Bansal S, Adams HH, Wang W, Goth K, Slump DE, den Hout MC, IJcken WF, Bellusci S, Pan Q, Erkeland SJ, Vrij FM, Kushner SA, Ikram MA. A functional variant in the miR‐142 promoter modulating its expression and conferring risk of Alzheimer disease. Hum Mutat 2019; 40:2131-2145. [DOI: 10.1002/humu.23872] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
- Department of Genetics, School of Medicine Mashhad University of Medical Sciences Mashhad Iran
| | - Shashini T. Munshi
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Buyun Ma
- Department of Gastroenterology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Bas Lendemeijer
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Sakshi Bansal
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Hieab H. Adams
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Wenshi Wang
- Department of Gastroenterology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Kerstin Goth
- Department of Lung Matrix Remodeling, Excellence Cluster Cardio‐Pulmonary System (ECCPS) University Justus Liebig Giessen Giessen Germany
| | - Denise E. Slump
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Mirjam C.G.N. den Hout
- Center for Biomics, Department of Cell Biology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Wilfred F.J. IJcken
- Center for Biomics, Department of Cell Biology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Saverio Bellusci
- Department of Lung Matrix Remodeling, Excellence Cluster Cardio‐Pulmonary System (ECCPS) University Justus Liebig Giessen Giessen Germany
| | - Qiuwei Pan
- Department of Gastroenterology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Stefan J. Erkeland
- Department of Immunology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Femke M.S. Vrij
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Steven A. Kushner
- Department of Psychiatry, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
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Cesarini V, Silvestris DA, Tassinari V, Tomaselli S, Alon S, Eisenberg E, Locatelli F, Gallo A. ADAR2/miR-589-3p axis controls glioblastoma cell migration/invasion. Nucleic Acids Res 2019; 46:2045-2059. [PMID: 29267965 PMCID: PMC5829642 DOI: 10.1093/nar/gkx1257] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/05/2017] [Indexed: 12/26/2022] Open
Abstract
Recent studies have reported the emerging role of microRNAs (miRNAs) in human cancers. We systematically characterized miRNA expression and editing in the human brain, which displays the highest number of A-to-I RNA editing sites among human tissues, and in de novo glioblastoma brain cancer. We identified 299 miRNAs altered in their expression and 24 miRNAs differently edited in human brain compared to glioblastoma tissues. We focused on the editing site within the miR-589–3p seed. MiR-589–3p is a unique miRNA almost fully edited (∼100%) in normal brain and with a consistent editing decrease in glioblastoma. The edited version of miR-589–3p inhibits glioblastoma cell proliferation, migration and invasion, while the unedited version boosts cell proliferation and motility/invasion, thus being a potential cancer-promoting factor. We demonstrated that the editing of this miRNA is mediated by ADAR2, and retargets miR-589–3p from the tumor-suppressor PCDH9 to ADAM12, which codes for the metalloproteinase 12 promoting glioblastoma invasion. Overall, our study dissects the role of a unique brain-specific editing site within miR-589–3p, with important anticancer features, and highlights the importance of RNA editing as an essential player not only for diversifying the genomic message but also for correcting not-tolerable/critical genomic coding sites.
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Affiliation(s)
- Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico A Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Sara Tomaselli
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Shahar Alon
- Media Laboratory and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Franco Locatelli
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy.,Department of Pediatric Science, University of Pavia, 27100 Pavia, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
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42
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Pinto Y, Buchumenski I, Levanon EY, Eisenberg E. Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets. Nucleic Acids Res 2019; 46:71-82. [PMID: 29165639 PMCID: PMC5758889 DOI: 10.1093/nar/gkx1176] [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: 09/20/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
A-to-I RNA editing is an important post-transcriptional modification, known to be altered in tumors. It targets dozens of sites within miRNAs, some of which impact miRNA biogenesis and function, as well as many miRNA recognition sites. However, the full extent of the effect of editing on regulation by miRNAs and its behavior in human cancers is still unknown. Here we systematically characterized miRNA editing in 10 593 human samples across 32 cancer types and normal controls. We find that the majority of previously reported sites show little to no evidence for editing in this dataset, compile a list of 58 reliable miRNA editing sites, and study them across normal and cancer samples. Edited miRNA versions tend to suppress expression of known oncogenes, and, consistently, we observe a clear global tendency for hypo-editing in tumors, in strike contrast to the behavior for mRNA editing, allowing an accurate classification of normal/tumor samples based on their miRNA editing profile. In many cancers this profile correlates with patients' survival. Finally, thousands of miRNA binding sites are differentially edited in cancer. Our study thus establishes the important effect of RNA editing on miRNA-regulation in the tumor cell, with prospects for diagnostic and prognostic applications.
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Affiliation(s)
- Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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43
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Identifying microRNAs and Their Editing Sites in Macaca mulatta. Cells 2019; 8:cells8070682. [PMID: 31284505 PMCID: PMC6678584 DOI: 10.3390/cells8070682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are critical in post-transcriptional regulation. Macaca mulatta is an important nonhuman primate that is often used in basic and translational researches. However, the annotation of miRNAs in Macaca mulatta is far from complete, and there are no reports of miRNA editing events in Macaca mulatta, although editing may affect the biogenesis or functions of the miRNAs. To improve miRNA annotation and to reveal editing events of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from eight tissues and performed comprehensive analysis of these profiles. We identified 479 conserved pre-miRNAs that have not been reported in Macaca mulatta and 17 species specific miRNAs. Furthermore, we identified 3386 editing sites with significant editing levels from 471 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from 17 different types of organs or tissues. In addition to 16 conserved A-to-I editing sites, we identified five conserved C-to-U editing sites in miRNAs of Macaca mulatta and Homo sapiens. We also identified 11 SNPs in the miRNAs of Macaca mulatta. The analysis of the potential targets of 69 miRNAs with editing or mutation events in their seed regions suggest that these editing or mutation events severely changed their targets and their potential functions. These results significantly increase our understanding of miRNAs and their mutation/editing events in Macaca mulatta.
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44
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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45
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Tseng AM, Mahnke AH, Wells AB, Salem NA, Allan AM, Roberts VH, Newman N, Walter NA, Kroenke CD, Grant KA, Akison LK, Moritz KM, Chambers CD, Miranda RC. Maternal circulating miRNAs that predict infant FASD outcomes influence placental maturation. Life Sci Alliance 2019; 2:2/2/e201800252. [PMID: 30833415 PMCID: PMC6399548 DOI: 10.26508/lsa.201800252] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023] Open
Abstract
Maternal gestational circulating microRNAs, predictive of adverse infant outcomes, including growth deficits, following prenatal alcohol exposure, contribute to placental pathology by impairing the EMT pathway in trophoblasts. Prenatal alcohol exposure (PAE), like other pregnancy complications, can result in placental insufficiency and fetal growth restriction, although the linking causal mechanisms are unclear. We previously identified 11 gestationally elevated maternal circulating miRNAs (HEamiRNAs) that predicted infant growth deficits following PAE. Here, we investigated whether these HEamiRNAs contribute to the pathology of PAE, by inhibiting trophoblast epithelial–mesenchymal transition (EMT), a pathway critical for placental development. We now report for the first time that PAE inhibits expression of placental pro-EMT pathway members in both rodents and primates, and that HEamiRNAs collectively, but not individually, mediate placental EMT inhibition. HEamiRNAs collectively, but not individually, also inhibited cell proliferation and the EMT pathway in cultured trophoblasts, while inducing cell stress, and following trophoblast syncytialization, aberrant endocrine maturation. Moreover, a single intravascular administration of the pooled murine-expressed HEamiRNAs, to pregnant mice, decreased placental and fetal growth and inhibited the expression of pro-EMT transcripts in the placenta. Our data suggest that HEamiRNAs collectively interfere with placental development, contributing to the pathology of PAE, and perhaps also, to other causes of fetal growth restriction.
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Affiliation(s)
- Alexander M Tseng
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Amanda H Mahnke
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Alan B Wells
- Clinical and Translational Research Institute, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Nihal A Salem
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Andrea M Allan
- Department of Neurosciences, University of New Mexico, Albuquerque, NM, USA
| | - Victoria Hj Roberts
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Natali Newman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Nicole Ar Walter
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Christopher D Kroenke
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Lisa K Akison
- Child Health Research Centre and School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Karen M Moritz
- Child Health Research Centre and School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Christina D Chambers
- Clinical and Translational Research Institute, University of California San Diego, San Diego, CA, USA .,Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rajesh C Miranda
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, Bryan, TX, USA
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46
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Wang XW, Hu LF, Hao J, Liao LQ, Chiu YT, Shi M, Wang Y. A microRNA-inducible CRISPR-Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool. Nat Cell Biol 2019; 21:522-530. [PMID: 30804503 DOI: 10.1038/s41556-019-0292-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) are small noncoding RNAs that play important regulatory roles in plants, animals and viruses. Measuring miRNA activity in vivo remains a big challenge. Here, using an miRNA-mediated single guide RNA (sgRNA)-releasing strategy and dCas9-VPR to drive a transgene red fluorescent protein, we create an miRNA sensor that can faithfully measure miRNA activity at cellular levels and use it to monitor differentiation status of stem cells. Furthermore, by designing sgRNAs to target endogenous loci, we adapted this system to control the expression of endogenous genes or mutate specific DNA bases upon induction by cell-type-specific miRNAs. Finally, by miRNA sensor library screening, we discover a previously undefined layer of heterogeneity associated with miR-21a activity in mouse embryonic stem cells. Together, these results highlight the utility of an miRNA-induced CRISPR-Cas9 system as miRNA sensors and cell-type-specific genome regulation tools.
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Affiliation(s)
- Xi-Wen Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Lu-Feng Hu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jing Hao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Le-Qi Liao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ya-Tzu Chiu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ming Shi
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.
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47
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Tassinari V, Cesarini V, Silvestris DA, Gallo A. The adaptive potential of RNA editing-mediated miRNA-retargeting in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:291-300. [PMID: 30605729 DOI: 10.1016/j.bbagrm.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
A-to-I RNA editing is a post-transcriptional mechanism that converts the genomically coded Adenosine (A) into Inosine (I) at the RNA level. This type of RNA editing is the most frequent in humans and is mediated by the ADAR enzymes. RNA editing can alter the genetic code of mRNAs, but also affect the functions of noncoding RNAs such as miRNAs. Recent studies have identified thousands of microRNA editing events in different cancer types. However, the important role played by miRNA-editing in cancer has been reported for just a few microRNAs. Herein, we recapitulate the current studies on cancer-related microRNA editing and discuss their importance in tumor growth and progression. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico Alessandro Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy.
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48
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Computational approaches for detection and quantification of A-to-I RNA-editing. Methods 2018; 156:25-31. [PMID: 30465820 DOI: 10.1016/j.ymeth.2018.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 02/07/2023] Open
Abstract
Adenosine deaminases that act on RNA (ADARs) catalyze adenosine-to-inosine (A-to-I) RNA editing in double-stranded RNA. Such editing is important for protection against false activation of the immune system, but also confers plasticity on the transcriptome by generating several versions of a transcript from a single genomic locus. Recently, great efforts were made in developing computational methods for detecting editing events directly from RNA-sequencing (RNA-seq) data. These efforts have led to an improved understanding of the makeup of the editome in various genomes. Here we review recent advances in editing detection based on the data available to the researcher, with emphasis on the principles underlying the various methods and the limitations they were designed to overcome. We also discuss the available various methods for analyzing and quantifying editing levels. This review collects and organizes the available approaches for analyzing RNA editing and discuss the current status of the different A-to-I detection methods with possible directions for extending these approaches.
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49
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Fan K, Ritter C, Nghiem P, Blom A, Verhaegen ME, Dlugosz A, Ødum N, Woetmann A, Tothill RW, Hicks RJ, Sand M, Schrama D, Schadendorf D, Ugurel S, Becker JC. Circulating Cell-Free miR-375 as Surrogate Marker of Tumor Burden in Merkel Cell Carcinoma. Clin Cancer Res 2018; 24:5873-5882. [PMID: 30061360 DOI: 10.1158/1078-0432.ccr-18-1184] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/15/2018] [Accepted: 07/24/2018] [Indexed: 01/10/2023]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is an aggressive skin cancer with neuroendocrine differentiation. There is an unmet need for MCC-specific blood-based surrogate biomarkers of tumor burden; circulating cell-free miRNA may serve this purpose. EXPERIMENTAL DESIGN Expression of miR-375 was quantified in 24 MCC and 23 non-MCC cell lines, 67 MCC and 58 non-MCC tumor tissues, sera of 2 preclinical MCC models, and sera of 109 patients with MCC and 30 healthy controls by nCounter human-v2-miRNA expression or miR-375-specific real-time PCR assays. The patients' sera consisted of two retrospective (discovery and training) and two prospective (validation) cohorts. RESULTS miR-375 expression was high in MCC cell lines and tissues compared with non-MCCs. It was readily detected in MCC-conditioned medium and sera of preclinical models bearing MCC xenografts. miR-375 levels were higher in sera from tumor-bearing patients with MCC than in tumor-free patients or healthy controls (P < 0.0005). Moreover, miR-375 serum levels correlated with tumor stage in tumor-bearing (P = 0.037) but not in tumor-free (P = 0.372) patients with MCC. miR-375 serum level showed high diagnostic accuracy to discriminate tumor-bearing and tumor-free patients with MCC as demonstrated by ROC curve analysis in the retrospective cohorts (AUC = 0.954 and 0.800) as well as in the prospective cohorts (AUC = 0.929 and 0.959). miR-375 serum level reflected dynamic changes in tumor burden of patients with MCC during therapeutic interventions. CONCLUSIONS Circulating cell-free miR-375 proved as a surrogate marker for tumor burden in MCC without restriction to polyomavirus positivity; it thus appears to be useful for therapy monitoring and the follow-up of patients with MCC.
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Affiliation(s)
- Kaiji Fan
- Department of Dermatology, Medical University of Graz, Graz, Austria.,Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cathrin Ritter
- Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Nghiem
- Department of Dermatology/Medicine, University of Washington, Seattle, Washington
| | - Astrid Blom
- Department of Dermatology/Medicine, University of Washington, Seattle, Washington
| | | | - Andrzej Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Niels Ødum
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Richard W Tothill
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia.,Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Rodney J Hicks
- Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Michael Sand
- Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - David Schrama
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Schadendorf
- German Cancer Consortium (DKTK), Essen, Germany.,Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Jürgen C Becker
- Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany. .,German Cancer Consortium (DKTK), Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, University Hospital Essen, Essen, Germany
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50
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Lu Y, Baras AS, Halushka MK. miRge 2.0 for comprehensive analysis of microRNA sequencing data. BMC Bioinformatics 2018; 19:275. [PMID: 30153801 PMCID: PMC6112139 DOI: 10.1186/s12859-018-2287-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/18/2018] [Indexed: 12/21/2022] Open
Abstract
Background miRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive, robust, user-friendly and standardized bioinformatics tools to analyze these large datasets. We present miRge 2.0, in which multiple enhancements were made towards these goals. Results miRge 2.0 has become more comprehensive with increased functionality including a novel miRNA detection method, A-to-I editing analysis, integrated standardized GFF3 isomiR reporting, and improved alignment to miRNAs. The novel miRNA detection method uniquely uses both miRNA hairpin sequence structure and composition of isomiRs resulting in higher specificity for potential miRNA identification. Using known miRNA data, our support vector machine (SVM) model predicted miRNAs with an average Matthews correlation coefficient (MCC) of 0.939 over 32 human cell datasets and outperformed miRDeep2 and miRAnalyzer regarding phylogenetic conservation. The A-to-I editing detection strongly correlated with a reference dataset with adjusted R2 = 0.96. miRge 2.0 is the most up-to-date aligner with custom libraries to both miRBase v22 and MirGeneDB v2.0 for 6 species: human, mouse, rat, fruit fly, nematode and zebrafish; and has a tool to create custom libraries. For user-friendliness, miRge 2.0 is incorporated into bcbio-nextgen and implementable through Bioconda. Conclusions miRge 2.0 is a redesigned, leading miRNA RNA-seq aligner with several improvements and novel utilities. miRge 2.0 is freely available at: https://github.com/mhalushka/miRge. Electronic supplementary material The online version of this article (10.1186/s12859-018-2287-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yin Lu
- Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA
| | - Alexander S Baras
- Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA.
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