1
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Lasantha D, Vidanagamachchi S, Nallaperuma S. CRIECNN: Ensemble convolutional neural network and advanced feature extraction methods for the precise forecasting of circRNA-RBP binding sites. Comput Biol Med 2024; 174:108466. [PMID: 38615462 DOI: 10.1016/j.compbiomed.2024.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Circular RNAs (circRNAs) have surfaced as important non-coding RNA molecules in biology. Understanding interactions between circRNAs and RNA-binding proteins (RBPs) is crucial in circRNA research. Existing prediction models suffer from limited availability and accuracy, necessitating advanced approaches. In this study, we propose CRIECNN (Circular RNA-RBP Interaction predictor using an Ensemble Convolutional Neural Network), a novel ensemble deep learning model that enhances circRNA-RBP binding site prediction accuracy. CRIECNN employs advanced feature extraction methods and evaluates four distinct sequence datasets and encoding techniques (BERT, Doc2Vec, KNF, EIIP). The model consists of an ensemble convolutional neural network, a BiLSTM, and a self-attention mechanism for feature refinement. Our results demonstrate that CRIECNN outperforms state-of-the-art methods in accuracy and performance, effectively predicting circRNA-RBP interactions from both full-length sequences and fragments. This novel strategy makes an enormous advancement in the prediction of circRNA-RBP interactions, improving our understanding of circRNAs and their regulatory roles.
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Affiliation(s)
- Dilan Lasantha
- Department of Computer Science, University of Ruhuna, Sri Lanka.
| | | | - Sam Nallaperuma
- Department of Engineering, University of Cambridge, United Kingdom.
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2
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Liu L, Wei Y, Tan Z, Zhang Q, Sun J, Zhao Q. Predicting circRNA-RBP Binding Sites Using a Hybrid Deep Neural Network. Interdiscip Sci 2024:10.1007/s12539-024-00616-z. [PMID: 38381315 DOI: 10.1007/s12539-024-00616-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Circular RNAs (circRNAs) are non-coding RNAs generated by reverse splicing. They are involved in biological process and human diseases by interacting with specific RNA-binding proteins (RBPs). Due to traditional biological experiments being costly, computational methods have been proposed to predict the circRNA-RBP interaction. However, these methods have problems of single feature extraction. Therefore, we propose a novel model called circ-FHN, which utilizes only circRNA sequences to predict circRNA-RBP interactions. The circ-FHN approach involves feature coding and a hybrid deep learning model. Feature coding takes into account the physicochemical properties of circRNA sequences and employs four coding methods to extract sequence features. The hybrid deep structure comprises a convolutional neural network (CNN) and a bidirectional gated recurrent unit (BiGRU). The CNN learns high-level abstract features, while the BiGRU captures long-term dependencies in the sequence. To assess the effectiveness of circ-FHN, we compared it to other computational methods on 16 datasets and conducted ablation experiments. Additionally, we conducted motif analysis. The results demonstrate that circ-FHN exhibits exceptional performance and surpasses other methods. circ-FHN is freely available at https://github.com/zhaoqi106/circ-FHN .
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Affiliation(s)
- Liwei Liu
- College of Science, Dalian Jiaotong University, Dalian, 116028, China
- Key Laboratory of Computational Science and Application of Hainan Province, Hainan Normal University, Haikou, 571158, China
| | - Yixin Wei
- College of Science, Dalian Jiaotong University, Dalian, 116028, China
| | - Zhebin Tan
- College of Software, Dalian Jiaotong University, Dalian, 116028, China
| | - Qi Zhang
- College of Science, Dalian Jiaotong University, Dalian, 116028, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi, 276000, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China.
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3
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Gao D, Cui C, Jiao Y, Zhang H, Li M, Wang J, Sheng X. Circular RNA and its potential diagnostic and therapeutic values in breast cancer. Mol Biol Rep 2024; 51:258. [PMID: 38302635 DOI: 10.1007/s11033-023-09172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024]
Abstract
Breast cancer (BC) is one of the most common malignant tumors in women and still poses a significant threat to women worldwide. Recurrence of BC in situ, metastasis to distant organs, and resistance to chemotherapy are all attached to high mortality in patients with BC. Non-coding RNA (ncRNA) of the type known as "circRNA" links together from one end to another to create a covalently closed, single-stranded circular molecule. With characteristics including plurality, evolutionary conservation, stability, and particularity, they are extensively prevalent in various species and a range of human cells. CircRNAs are new and significant contributors to several kinds of disorders, including cardiovascular disease, multiple organ inflammatory responses and malignancies. Recent studies have shown that circRNAs play crucial roles in the occurrence of breast cancer by interacting with miRNAs to regulate gene expression at the transcriptional or post-transcriptional levels. CircRNAs offer the potential to be therapeutic targets for breast cancer treatment as well as prospective biomarkers for early diagnosis and prognosis of BC. Here, we are about to present an overview of the functions of circRNAs in the proliferation, invasion, migration, and resistance to medicines of breast cancer cells and serve as a promising resource for future investigations on the pathogenesis and therapeutic strategies.
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Affiliation(s)
- Di Gao
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
- Institute of Digestive Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Can Cui
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Yaoxuan Jiao
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Han Zhang
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Min Li
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Junjie Wang
- Department of Pathophysiology, Jiangsu University School of Medicine, Zhenjiang, 212013, Jiangsu, China
| | - Xiumei Sheng
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
- Institute of Digestive Diseases, Jiangsu University, Zhenjiang, Jiangsu, China.
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4
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Nguyen TH, Nguyen HN, Vu TN. CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs. BMC Bioinformatics 2024; 25:31. [PMID: 38233808 PMCID: PMC10795305 DOI: 10.1186/s12859-024-05646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
Analyzing the interactions of circular RNAs (circRNAs) is a crucial step in understanding their functional impacts. While there are numerous visualization tools available for investigating circRNA interaction networks, these tools are typically limited to known circRNAs from specific databases. Moreover, these existing tools usually require complex installation procedures which can be time-consuming and challenging for users. There is a lack of a user-friendly web application that facilitates interactive exploration and visualization of circRNA interaction networks. CircNetVis is an interactive online web application to enhance the analysis of human/mouse circRNA interactions. The tool allows three different input formats of circRNAs including circRNA IDs from CircBase, circRNA coordinates (chromosome, start position, end position), and circRNA sequences in the FASTA format. It integrates multiple interaction networks for visualization and investigation of the interplay between circRNA, microRNAs, mRNAs and RNA binding proteins. CircNetVis also enables users to interactively explore the interactions of unknown circRNAs which are not reported from previous databases. The tool can generate interactive plots and allows users to save results as output files for offline usage. CircNetVis is implemented as a web application using R-shiny and freely available for academic use at https://www.meb.ki.se/shiny/truvu/CircNetVis/ .
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Affiliation(s)
- Thi-Hau Nguyen
- University of Engineering and Technology, Vietnam National University in Hanoi, Hanoi, 84024, Vietnam
| | - Ha-Nam Nguyen
- University of Engineering and Technology, Vietnam National University in Hanoi, Hanoi, 84024, Vietnam
- Department of Information Technology, Electric Power University, Hanoi, 84024, Vietnam
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177, Stockholm, Sweden.
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5
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Cao C, Wang C, Yang S, Zou Q. CircSI-SSL: circRNA-binding site identification based on self-supervised learning. Bioinformatics 2024; 40:btae004. [PMID: 38180876 PMCID: PMC10789309 DOI: 10.1093/bioinformatics/btae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/13/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
MOTIVATION In recent years, circular RNAs (circRNAs), the particular form of RNA with a closed-loop structure, have attracted widespread attention due to their physiological significance (they can directly bind proteins), leading to the development of numerous protein site identification algorithms. Unfortunately, these studies are supervised and require the vast majority of labeled samples in training to produce superior performance. But the acquisition of sample labels requires a large number of biological experiments and is difficult to obtain. RESULTS To resolve this matter that a great deal of tags need to be trained in the circRNA-binding site prediction task, a self-supervised learning binding site identification algorithm named CircSI-SSL is proposed in this article. According to the survey, this is unprecedented in the research field. Specifically, CircSI-SSL initially combines multiple feature coding schemes and employs RNA_Transformer for cross-view sequence prediction (self-supervised task) to learn mutual information from the multi-view data, and then fine-tuning with only a few sample labels. Comprehensive experiments on six widely used circRNA datasets indicate that our CircSI-SSL algorithm achieves excellent performance in comparison to previous algorithms, even in the extreme case where the ratio of training data to test data is 1:9. In addition, the transplantation experiment of six linRNA datasets without network modification and hyperparameter adjustment shows that CircSI-SSL has good scalability. In summary, the prediction algorithm based on self-supervised learning proposed in this article is expected to replace previous supervised algorithms and has more extensive application value. AVAILABILITY AND IMPLEMENTATION The source code and data are available at https://github.com/cc646201081/CircSI-SSL.
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Affiliation(s)
- Chao Cao
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324003, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Shuhong Yang
- Faculty of Mathematics and Computer Science, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324003, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
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6
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Zhu W, Huang Y, Yu C. The emerging role of circRNAs on skeletal muscle development in economical animals. Anim Biotechnol 2023; 34:2778-2792. [PMID: 36052979 DOI: 10.1080/10495398.2022.2118130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
CircRNAs are a novel type of closed circular molecules formed through a covalent bond lacking a 5'cap and 3' end tail, which mainly arise from mRNA precursor. They are widely distributed in plants and animals and are characterized by stable structure, high conservativeness in cells or tissues, and showed the expression specificity at different stages of development in different tissues. CircRNAs have been gradually attracted wide attention with the development of RNA sequencing, which become a new research hotspot in the field of RNA. CircRNAs play an important role in gene expression regulation. Presently, the related circRNAs research in the regulation of animal muscle development is still at the initial stage. In this review, the formation, properties, biological functions of circRNAs were summarized. The recent research progresses of circRNAs in skeletal muscle growth and development from economic animals including livestock, poultry and fishes were introduced. Finally, we proposed a prospective for further studies of circRNAs in muscle development, and we hope our research could provide new ideas, some theoretical supports and helps for new molecular genetic markers exploitation and animal genetic breeding in future.
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Affiliation(s)
- Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Chuan Yu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
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7
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Shen Z, Liu W, Zhao S, Zhang Q, Wang S, Yuan L. Nucleotide-level prediction of CircRNA-protein binding based on fully convolutional neural network. Front Genet 2023; 14:1283404. [PMID: 37867600 PMCID: PMC10587422 DOI: 10.3389/fgene.2023.1283404] [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: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction: CircRNA-protein binding plays a critical role in complex biological activity and disease. Various deep learning-based algorithms have been proposed to identify CircRNA-protein binding sites. These methods predict whether the CircRNA sequence includes protein binding sites from the sequence level, and primarily concentrate on analysing the sequence specificity of CircRNA-protein binding. For model performance, these methods are unsatisfactory in accurately predicting motif sites that have special functions in gene expression. Methods: In this study, based on the deep learning models that implement pixel-level binary classification prediction in computer vision, we viewed the CircRNA-protein binding sites prediction as a nucleotide-level binary classification task, and use a fully convolutional neural networks to identify CircRNA-protein binding motif sites (CPBFCN). Results: CPBFCN provides a new path to predict CircRNA motifs. Based on the MEME tool, the existing CircRNA-related and protein-related database, we analysed the motif functions discovered by CPBFCN. We also investigated the correlation between CircRNA sponge and motif distribution. Furthermore, by comparing the motif distribution with different input sequence lengths, we found that some motifs in the flanking sequences of CircRNA-protein binding region may contribute to CircRNA-protein binding. Conclusion: This study contributes to identify circRNA-protein binding and provides help in understanding the role of circRNA-protein binding in gene expression regulation.
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Affiliation(s)
- Zhen Shen
- School of Computer and Software, Nanyang Institute of Technology, Nanyang, Henan, China
| | - Wei Liu
- School of Computer and Software, Nanyang Institute of Technology, Nanyang, Henan, China
| | - ShuJun Zhao
- School of Computer and Software, Nanyang Institute of Technology, Nanyang, Henan, China
| | - QinHu Zhang
- EIT Institute for Advanced Study, Ningbo, Zhejiang, China
| | - SiGuo Wang
- EIT Institute for Advanced Study, Ningbo, Zhejiang, China
| | - Lin Yuan
- Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, China
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8
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Cao C, Yang S, Li M, Li C. CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization. BMC Bioinformatics 2023; 24:220. [PMID: 37254080 DOI: 10.1186/s12859-023-05352-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) play a significant role in some diseases by acting as transcription templates. Therefore, analyzing the interaction mechanism between circRNA and RNA-binding proteins (RBPs) has far-reaching implications for the prevention and treatment of diseases. Existing models for circRNA-RBP identification usually adopt convolution neural network (CNN), recurrent neural network (RNN), or their variants as feature extractors. Most of them have drawbacks such as poor parallelism, insufficient stability, and inability to capture long-term dependencies. METHODS In this paper, we propose a new method completely using the self-attention mechanism to capture deep semantic features of RNA sequences. On this basis, we construct a CircSSNN model for the cirRNA-RBP identification. The proposed model constructs a feature scheme by fusing circRNA sequence representations with statistical distributions, static local contexts, and dynamic global contexts. With a stable and efficient network architecture, the distance between any two positions in a sequence is reduced to a constant, so CircSSNN can quickly capture the long-term dependencies and extract the deep semantic features. RESULTS Experiments on 37 circRNA datasets show that the proposed model has overall advantages in stability, parallelism, and prediction performance. Keeping the network structure and hyperparameters unchanged, we directly apply the CircSSNN to linRNA datasets. The favorable results show that CircSSNN can be transformed simply and efficiently without task-oriented tuning. CONCLUSIONS In conclusion, CircSSNN can serve as an appealing circRNA-RBP identification tool with good identification performance, excellent scalability, and wide application scope without the need for task-oriented fine-tuning of parameters, which is expected to reduce the professional threshold required for hyperparameter tuning in bioinformatics analysis.
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Affiliation(s)
- Chao Cao
- School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China
| | - Shuhong Yang
- Key Laboratory of Guangxi Universities on Intelligent Computing and Distributed Information Processing, Guangxi University of Science and Technology, Liuzhou, China.
| | - Mengli Li
- School of Technology, Guilin University, Guilin, China
| | - Chungui Li
- School of Computer Science and Technology, Guangxi University of Science and Technology, Liuzhou, China.
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9
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Wangzhou K, Lu Z, Lai Z, Fu W, Liu C, Tan Y, Hao C. Upregulated circ_0002141 facilitates oral squamous cell carcinoma progression via the miR-1231/EGFR axis. Oral Dis 2023; 29:902-912. [PMID: 34739167 DOI: 10.1111/odi.14070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/06/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The dysregulation of circular RNAs (circRNAs) is implicated in the progression of various cancers. This study was aimed at expounding the role and mechanism of hsa_circ_0002141 in the OSCC progression. MATERIALS AND METHODS Circ_0002141 expression was examined in 52 pairs of OSCC tissues and matched adjacent tissue samples by quantitative real-time polymerase chain reaction (qRT-PCR) assay. After circ_0002141 was overexpressed or knocked down in OSCC cell lines, cell counting kit-8 (CCK-8) assay, Transwell assay, flow cytometry, and Western blotting were conducted to detect the changes in the growth, migration, invasion and apoptosis of OSCC cells. Western blot assay, qRT-PCR and dual-luciferase reporter assay were performed to clarify the interplay among circ_0002141, miR-1231, and epidermal growth factor receptor (EGFR). RESULTS Circ_0002141 expression was significantly upregulated in OSCC tissues and cell lines. Circ_0002141 overexpression markedly promoted the proliferation, migration, and invasion of OSCC cells whereas reduced the apoptotic of OSCC cells. Also, circ_0002141 knockdown suppressed the malignant characteristics of OSCC cells. EGFR was validated as the target of miR-1231. Besides, circ_0002141 could sponge miR-1231 and upregulate EGFR expression in OSCC cells. CONCLUSION Circ_0002141/miR-1231/EGFR axis is involved in the progression of OSCC.
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Affiliation(s)
- Kaixin Wangzhou
- School of Management, Hainan Medical University, Haikou, Hainan, China
| | - Zishao Lu
- School of Stomatology, Hainan Medical University, Haikou, Hainan, China
| | - Zhiying Lai
- School of Stomatology, Hainan Medical University, Haikou, Hainan, China
| | - Wanren Fu
- School of Stomatology, Hainan Medical University, Haikou, Hainan, China
| | - Cheng Liu
- Department of Stomatology, Harbin Stomatological Hospital, Harbin, Heilongjiang, China
| | - Yi Tan
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Chunbo Hao
- Department of Stomatology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
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10
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Involvement of circRNAs in the Development of Heart Failure. Int J Mol Sci 2022; 23:ijms232214129. [PMID: 36430607 PMCID: PMC9697219 DOI: 10.3390/ijms232214129] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/05/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
In recent years, interest in non-coding RNAs as important physiological regulators has grown significantly. Their participation in the pathophysiology of cardiovascular diseases is extremely important. Circular RNA (circRNA) has been shown to be important in the development of heart failure. CircRNA is a closed circular structure of non-coding RNA fragments. They are formed in the nucleus, from where they are transported to the cytoplasm in a still unclear mechanism. They are mainly located in the cytoplasm or contained in exosomes. CircRNA expression varies according to the type of tissue. In the brain, almost 12% of genes produce circRNA, while in the heart it is only 9%. Recent studies indicate a key role of circRNA in cardiomyocyte hypertrophy, fibrosis, autophagy and apoptosis. CircRNAs act mainly by interacting with miRNAs through a "sponge effect" mechanism. The involvement of circRNA in the development of heart failure leads to the suggestion that they may be promising biomarkers and useful targets in the treatment of cardiovascular diseases. In this review, we will provide a brief introduction to circRNA and up-to-date understanding of their role in the mechanisms leading to the development of heart failure.
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11
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A pseudo-Siamese framework for circRNA-RBP binding sites prediction integrating BiLSTM and soft attention mechanism. Methods 2022; 207:57-64. [PMID: 36113743 DOI: 10.1016/j.ymeth.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/24/2022] [Accepted: 09/09/2022] [Indexed: 11/20/2022] Open
Abstract
Circular RNAs (circRNAs) are widely expressed in tissues and play a key role in diseases through interacting with RNA binding proteins (RBPs). Since the high cost of traditional technology, computational methods are developed to identify the binding sites between circRNAs and RBPs. Unfortunately, these methods suffer from the insufficient learning of features and the single classification of output. To address these limitations, we propose a novel method named circ-pSBLA which constructs a pseudo-Siamese framework integrating Bi-directional long short-term memory (BiLSTM) network and soft attention mechanism for circRNA-RBP binding sites prediction. Softmax function and CatBoost are adopted to classify, respectively, and then a pseudo-Siamese framework is constructed. circ-pSBLA combines them to get final output. To validate the effectiveness of circ-pSBLA, we compare it with other state-of-the-art methods and carry out an ablation experiment on 17 sub-datasets. Moreover, we do motif analysis on 3 sub-datasets. The results show that circ-pSBLA achieves superior performance and outperforms other methods. All supporting source codes can be downloaded from https://github.com/gyj9811/circ-pSBLA.
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12
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Wang Z, Lei X. A web server for identifying circRNA-RBP variable-length binding sites based on stacked generalization ensemble deep learning network. Methods 2022; 205:179-190. [PMID: 35810958 DOI: 10.1016/j.ymeth.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022] Open
Abstract
Circular RNA (circRNA) can exert biological functions by interacting with RNA-binding protein (RBP), and some deep learning-based methods have been developed to predict RBP binding sites on circRNA. However, most of these methods identify circRNA-RBP binding sites are only based on single data resource and cannot provide exact binding sites, only providing the probability value of a sequence fragment. To solve these problems, we propose a binding sites localization algorithm that fuses binding sites from multiple databases, and further design a stacked generalization ensemble deep learning model named CirRBP to identify RBP binding sites on circRNA. The CirRBP is trained by combining the binding sites from multiple databases and makes predictions by weighted aggregating the predictions of each sub-model. The results show that the CirRBP outperforms any sub-model and existing online prediction model. For better access to our research results, we develop an open-source web application called CRWS (CircRNA-RBP Web Server). Its back-end learning model of the CRWS is a stacked generalization ensemble learning model CirRBP based on different deep learning frameworks. Given a full-length circRNA or fragment sequence and a target RBP, the CRWS can analyze and provide the exact potential binding sites of the target RBP on the given sequence through the binding sites localization algorithm, and visualize it. In addition, the CRWS can discover the most widely distributed motif in each RBP dataset. Up to now, CRWS is the first significant online tool that uses multi-source data to train models and predict exact binding sites. CRWS is now publicly and freely available without login requirement at: http://www.bioinformatics.team.
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Affiliation(s)
- Zhengfeng Wang
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China; College of Information Science and Engineering, Guilin University of Technology, Guilin 541004, China; Guangxi Key Laboratory of Embedded Technology and Intelligent System, Guilin University of Technology, Guilin 541004, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China.
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13
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Abstract
The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences.
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14
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Niu ZS, Wang WH. Circular RNAs in hepatocellular carcinoma: Recent advances. World J Gastrointest Oncol 2022; 14:1067-1085. [PMID: 35949213 PMCID: PMC9244981 DOI: 10.4251/wjgo.v14.i6.1067] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/22/2021] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) have covalently closed loop structures at both ends, exhibiting characteristics dissimilar to those of linear RNAs. Emerging evidence suggests that aberrantly expressed circRNAs play crucial roles in hepatocellular carcinoma (HCC) by affecting the proliferation, apoptosis and invasive capacity of HCC cells. Certain circRNAs may be used as biomarkers to diagnose and predict the prognosis of HCC. Therefore, circRNAs are expected to become novel biomarkers and therapeutic targets for HCC. Herein, we briefly review the characteristics and biological functions of circRNAs, focusing on their roles in HCC to provide new insights for the early diagnosis and targeted therapy of HCC.
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Affiliation(s)
- Zhao-Shan Niu
- Laboratory of Micromorphology, School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Wen-Hong Wang
- Department of Pathology, School of Basic Medicine, Qingdao University, Qingdao 266071, Shandong Province, China
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15
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Singh M, Dwibedy SLL, Biswal SR, Muthuswamy S, Kumar A, Kumar S. Circular RNA: A novel and potential regulator in pathophysiology of schizophrenia. Metab Brain Dis 2022; 37:1309-1316. [PMID: 35435609 DOI: 10.1007/s11011-022-00978-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022]
Abstract
Circular RNAs (CircRNAs) are a sub-class of non-coding RNA, which are covalently closed at the ends through a non-canonical process called, backsplicing from the precursor linear RNAs. These molecules are involved in several biological phenomena including regulation of gene expression, synaptic plasticity, and cognition. Several studies have shown that circRNA are present abundantly inside the mammalian brain and they are believed to be associated with the development of neurons and neuronal functions. It is also evident that alterations in intracellular and extracellular levels of circRNAs are linked with various neurological and neuropsychiatric disorders including schizophrenia (SZ). Detailed studies of circRNAs are required to decode the molecular mechanism behind the onset of SZ and the related biological activities during disease progression. This can help unravel their role in this neurobehavioral disorder and develop effective therapeutics against the disease. The present review mainly focuses on the expression and activities of the circRNAs in the post-mortem brain, peripheral blood, and exosomes. It also gives an insight into the role of circRNA interaction with RNA binding proteins (RBPs) and nucleotide modification and their therapeutic potential in the context of schizophrenia.
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Affiliation(s)
- Mandakini Singh
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India
| | | | - Smruti Rekha Biswal
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India
| | - Srinivasan Muthuswamy
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India
| | - Ajay Kumar
- Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India.
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16
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Wang X, Song Z, Meng Q, Xia S, Wang C, Huang X. Circular RNA circ_0006089 regulates the IGF1R expression by targeting miR-143-3p to promote gastric cancer proliferation, migration and invasion. Cell Cycle 2022:1-14. [PMID: 35545863 DOI: 10.1080/15384101.2022.2075197] [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: 06/03/2021] [Revised: 04/13/2022] [Accepted: 05/03/2022] [Indexed: 02/08/2023] Open
Abstract
Circular RNAs (circRNAs) figure prominently in regulating the progression of a variety of human malignancies. This study was performed to probe how circ_0006089 functioned in gastric cancer (GC). CircRNA expression profile GSE83521 was downloaded from Gene Expression Omnibus (GEO) database, and circRNAs and analyzed. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure circ_0006089, microRNA-143-3p (miR-143-3p) and insulin-like growth factor 1 receptor (IGF1R) mRNA expressions in GC tissues and cell lines. Kaplan-Meier curves were used to detect the relationship between circ_0006089 expression and overall survival time of GC patients. Cell counting kit-8 (CCK-8) and 5-bromo-2-deoxyuridine (BrdU) assays were employed to detect the proliferative ability of GC cells after circ_0006089 was overexpressed or knocked down. Wound healing assay and Transwell assay were executed to examine the migration and invasion ability of GC cells. Western blot was adopted to detect IGF1R protein expressions. Circ_0006089 expression was up-regulated in GC samples and cell lines. And high circ_0006089 expression was associated with shorter survival time in GC patients. Circ_0006089 overexpression in GC cells significantly accelerated GC cell proliferation, migration and invasion, whereas circ_0006089 knockdown resulted in the opposite effects. Additionally, miR-143-3p was validated as a downstream target of circ_0006089, and circ_0006089 could positively regulate IGF1R expression via repressing miR-143-3p. Circ_0006089 is highly expressed in GC, and it promotes the malignancy of GC cells via modulating miR-143-3p/IGF1R axis, suggesting that circ_0006089 may serve as a promising therapeutic target for GC.
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Affiliation(s)
- Xian Wang
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China
| | - Zhou Song
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qingyu Meng
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Shaoyou Xia
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chunxi Wang
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaohui Huang
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, Beijing, China
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17
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Wang W, Xu R, Zhao H, Xiong Y, He P. CircEXOC5 promotes ferroptosis by enhancing ACSL4 mRNA stability via binding to PTBP1 in sepsis-induced acute lung injury. Immunobiology 2022; 227:152219. [DOI: 10.1016/j.imbio.2022.152219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/29/2022] [Accepted: 04/09/2022] [Indexed: 12/16/2022]
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18
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Yang Y, Hou Z, Wang Y, Ma H, Sun P, Ma Z, Wong KC, Li X. HCRNet: high-throughput circRNA-binding event identification from CLIP-seq data using deep temporal convolutional network. Brief Bioinform 2022; 23:6533504. [PMID: 35189638 DOI: 10.1093/bib/bbac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 01/11/2023] Open
Abstract
Identifying genome-wide binding events between circular RNAs (circRNAs) and RNA-binding proteins (RBPs) can greatly facilitate our understanding of functional mechanisms within circRNAs. Thanks to the development of cross-linked immunoprecipitation sequencing technology, large amounts of genome-wide circRNA binding event data have accumulated, providing opportunities for designing high-performance computational models to discriminate RBP interaction sites and thus to interpret the biological significance of circRNAs. Unfortunately, there are still no computational models sufficiently flexible to accommodate circRNAs from different data scales and with various degrees of feature representation. Here, we present HCRNet, a novel end-to-end framework for identification of circRNA-RBP binding events. To capture the hierarchical relationships, the multi-source biological information is fused to represent circRNAs, including various natural language sequence features. Furthermore, a deep temporal convolutional network incorporating global expectation pooling was developed to exploit the latent nucleotide dependencies in an exhaustive manner. We benchmarked HCRNet on 37 circRNA datasets and 31 linear RNA datasets to demonstrate the effectiveness of our proposed method. To evaluate further the model's robustness, we performed HCRNet on a full-length dataset containing 740 circRNAs. Results indicate that HCRNet generally outperforms existing methods. In addition, motif analyses were conducted to exhibit the interpretability of HCRNet on circRNAs. All supporting source code and data can be downloaded from https://github.com/yangyn533/HCRNet and https://doi.org/10.6084/m9.figshare.16943722.v1. And the web server of HCRNet is publicly accessible at http://39.104.118.143:5001/.
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Affiliation(s)
- Yuning Yang
- School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China
| | - Zilong Hou
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, China
| | - Yansong Wang
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, China
| | - Hongli Ma
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China
| | - Ka-Chun Wong
- School of Computer Science, City University of Hong Kong, Hong Kong SAR
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, China
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19
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Niu M, Zou Q, Lin C. CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach. PLoS Comput Biol 2022; 18:e1009798. [PMID: 35051187 PMCID: PMC8806072 DOI: 10.1371/journal.pcbi.1009798] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/01/2022] [Accepted: 01/02/2022] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced formed by the reverse splicing mechanism. Increasing evidence shows that circular RNAs can directly bind to RNA-binding proteins (RBP) and play an important role in a variety of biological activities. The interactions between circRNAs and RBPs are key to comprehending the mechanism of posttranscriptional regulation. Accurately identifying binding sites is very useful for analyzing interactions. In past research, some predictors on the basis of machine learning (ML) have been presented, but prediction accuracy still needs to be ameliorated. Therefore, we present a novel calculation model, CRBPDL, which uses an Adaboost integrated deep hierarchical network to identify the binding sites of circular RNA-RBP. CRBPDL combines five different feature encoding schemes to encode the original RNA sequence, uses deep multiscale residual networks (MSRN) and bidirectional gating recurrent units (BiGRUs) to effectively learn high-level feature representations, it is sufficient to extract local and global context information at the same time. Additionally, a self-attention mechanism is employed to train the robustness of the CRBPDL. Ultimately, the Adaboost algorithm is applied to integrate deep learning (DL) model to improve prediction performance and reliability of the model. To verify the usefulness of CRBPDL, we compared the efficiency with state-of-the-art methods on 37 circular RNA data sets and 31 linear RNA data sets. Moreover, results display that CRBPDL is capable of performing universal, reliable, and robust. The code and data sets are obtainable at https://github.com/nmt315320/CRBPDL.git. More and more evidences show that circular RNA can directly bind to proteins and participate in countless different biological processes. The calculation method can quickly and accurately predict the binding site of circular RNA and RBP. In order to identify the interaction of circRNA with 37 different types of circRNA binding proteins, we developed an integrated deep learning network based on hierarchical network, called CRBPDL. It can effectively learn high-level feature representations. The performance of the model was verified through comparative experiments of different feature extraction algorithms, different deep learning models and classifier models. Moreover, the CRBPDL model was applied to 31 linear RNAs, and the effectiveness of our method was proved by comparison with the results of current excellent algorithms. It is expected that the CRBPDL model can effectively predict the binding site of circular RNA-RBP and provide reliable candidates for further biological experiments.
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Affiliation(s)
- Mengting Niu
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
| | - Chen Lin
- School of Informatics, Xiamen University, Xiamen, China
- * E-mail:
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20
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Hsa_circ_0008259 modulates miR-21-5p and PDCD4 expression to restrain osteosarcoma progression. Aging (Albany NY) 2021; 13:25484-25495. [PMID: 34905503 PMCID: PMC8714152 DOI: 10.18632/aging.203769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Osteosarcoma (OS) is one of the most common primary bone tumors in children and adolescents. However, the molecular mechanism of OS tumorigenesis is still little known. Circular RNA (circRNA) is a key player in the progression of many cancers. This study is performed to decipher the role and mechanism of circ_0008259 in the progression of OS. METHODS A differentially expressed circRNA, circ_0008259, was screened out by analyzing the expression profile of circRNA in OS tissue. Circ_0008259, miR-21-5p and programmable cell death 4 (PDCD4) mRNA expression levels in OS tissues and cells were detected by qRT-PCR. Cell viability, metastatic potential and apoptosis were evaluated by cell counting kit-8 assay, Transwell and flow cytometry. The targeting relationship between circ_0008259 and miR-21-5p, and miR-21-5p and PDCD4 mRNA was analyzed and probed by bioinformatics analysis and dual-luciferase reporter assay, RNA-binding protein immunoprecipitation assay and RNA-pull down assay. The regulatory effects of circ_0008259 and miR-21-5p on PDCD4 protein expression in OS cells were detected by Western blot assay. RESULTS Circ_0008259 expression and PDCD4 expression were down-regulated and miR-21-5p expression was elevated in the OS tissues and cells. Functional experiments showed that circ_0008259 overexpression significantly inhibited the proliferation and metastatic potential of OS cells and promoted the apoptosis. Besides, PDCD4 was validated as the target gene of miR-21-5p, and circ_0008259 could competitively bind to miR-21-5p, thus up-regulating PDCD4 expression in OS cells. CONCLUSIONS Circ_0008259 suppresses OS progression via regulating miR-21-5p/PDCD4 axis.
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21
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Xing Z, Li S, Liu Z, Zhang C, Bai Z. CircSERPINA3 regulates SERPINA3-mediated apoptosis, autophagy and aerobic glycolysis of prostate cancer cells by competitively binding to MiR-653-5p and recruiting BUD13. J Transl Med 2021; 19:492. [PMID: 34861864 PMCID: PMC8642898 DOI: 10.1186/s12967-021-03063-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/01/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) belongs to an epithelial malignancy that occurs in the prostate gland and is the most common malignancy of the male genitourinary system. Referring to related literature, circSERPINA3 has been reported to be up-regulated in PCa. However, its biological function remains unclear. PURPOSE This study aimed to reveal the specific role and relevant molecular mechanism of circSERPINA3 in PCa. METHODS RT-qPCR was used to examine gene expression and functional analyses were conducted to verify the effect of circSERPINA3 on cell apoptosis, autophagy and aerobic glycolysis in PCa cells. Mechanism assays were applied to evaluate the relationship among circSERPINA3/miR-653-5p/SERPINA3/BUD13. RESULTS CircSERPINA3 was verified to be up-regulated in PCa cells and to inhibit cell apoptosis while promoting aerobic glycolysis and autophagy in PCa cells. CircSERPINA3 and SERPINA3 were also testified to bind to miR-653-5p through a line of mechanism experiments. Moreover, it was discovered that circSERPINA3 could stabilize SERPINA3 mRNA via recruiting BUD13. Additionally, SERPINA3 was verified to inhibit cell apoptosis, while promoting aerobic glycolysis and autophagy in PCa cells. CONCLUSIONS Our study suggested that circSERPINA3 regulated apoptosis, autophagy and aerobic glycolysis of PCa cells by competitively binding to miR-653-5p and recruiting BUD13.
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Affiliation(s)
- Zengshu Xing
- Department of Urology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, No. 43 Renmin Road, Meilan District, Haikou, 570208, Hainan, China.
| | - Sailian Li
- Department of Gastroenterology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, No.43 Renmin Road, Meilan District, Haikou, 570208, Hainan, China
| | - Zhenxiang Liu
- Department of Urology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, No. 43 Renmin Road, Meilan District, Haikou, 570208, Hainan, China
| | - Chong Zhang
- Department of Urology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, No. 43 Renmin Road, Meilan District, Haikou, 570208, Hainan, China
| | - Zhiming Bai
- Department of Urology, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, No. 43 Renmin Road, Meilan District, Haikou, 570208, Hainan, China
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22
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Zhang Y, Zeng S, Wang T. Circular RNA hsa_circ_0002360 promotes non-small cell lung cancer progression through upregulating matrix metalloproteinase 16 and sponging multiple micorRNAs. Bioengineered 2021; 12:12767-12777. [PMID: 34747300 PMCID: PMC8809917 DOI: 10.1080/21655979.2021.1999370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Dysregulated circular RNAs (circRNAs) are involved in the progression of non-small cell lung cancer (NSCLC). However, the role of has_circ_0002360 (circ_0002360) in NSCLC has rarely been reported. In this study, circ_0002360 expression in NSCLC tissues and cell lines was measured using microarray data and quantitative real-time PCR (qRT-PCR). After gain-of-function and loss-of-function, cell models were established; 5-bromo-2-deoxyuridine (BrdU) and transwell assays were conducted to detect NSCLC cell growth, migration, and invasion. What is more, bioinformatic analysis and dual-luciferase reporter assay were adopted to show how circ_0002360, microRNAs (miR-127-5p, miR-145-5p, miR-585-3p, and miR-758-3p), and matrix metalloproteinase 16 (MMP16) 3ʹUTR interact with each other. Western blotting was executed to probe the regulatory effects of circ_0002360 and these miRNAs on MMP16 protein expression in NSCLC cells. We found that circ_0002360 expression was raised in NSCLC tissues. High circ_0002360 expression predicted a short overall survival time for NSCLC patients. Circ_0002360 overexpression promoted NSCLC cell proliferative, migrative, and invasive abilities, and circ_0002360 depletion worked oppositely. MiR-127-5p, miR-145-5p, miR-585-3p, and miR-758-3p were the targets of circ_0002360, and circ_0002360 could regulate MMP16 expression by competitively binding with the above miRNAs. In summary, circ_0002360 serves as a competitive endogenous RNA to raise MMP16 expressions by competitively binding to miR-127-5p, miR-145-5p, miR-585-3p, and miR-758-3p, thereby promoting NSCLC progression.
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Affiliation(s)
- Yunting Zhang
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Shaolin Zeng
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Tao Wang
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
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Wang Z, Lei X. Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture. Brief Bioinform 2021; 22:6355419. [PMID: 34415289 DOI: 10.1093/bib/bbab342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/14/2021] [Accepted: 08/02/2021] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is considered to be an important pathway for circRNA function, such as acting as an oncogenic RBP sponge to inhibit cancer. In this study, we design a deep learning framework, CRPBsites, to predict the binding sites of RBPs on circRNAs. In this model, the sequences of variable-length binding sites are transformed into embedding vectors by word2vec model. Bidirectional LSTM is used to encode the embedding vectors of binding sites, and then they are fed into another LSTM decoder for decoding and classification tasks. To train and test the model, we construct four datasets that contain sequences of variable-length binding sites on circRNAs, and each set corresponds to an RBP, which is overexpressed in bladder cancer tissues. Experimental results on four datasets and comparison with other existing models show that CRPBsites has superior performance. Afterwards, we found that there were highly similar binding motifs in the four binding site datasets. Finally, we applied well-trained CRPBsites to identify the binding sites of IGF2BP1 on circCDYL, and the results proved the effectiveness of this method. In conclusion, CRPBsites is an effective prediction model for circRNA-RBP interaction site identification. We hope that CRPBsites can provide valuable guidance for experimental studies on the influence of circRNA on post-transcriptional regulation.
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Affiliation(s)
- Zhengfeng Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, China.,College of Information Science and Engineering, Guilin University of Technology, Guilin, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
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Tayara H, Chong KT. Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2526-2534. [PMID: 32191896 DOI: 10.1109/tcbb.2020.2981335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA-binding proteins (RBPs) have a significant role in various regulatory tasks. However, the mechanism by which RBPs identify the subsequence target RNAs is still not clear. In recent years, several machine and deep learning-based computational models have been proposed for understanding the binding preferences of RBPs. These methods required integrating multiple features with raw RNA sequences such as secondary structure and their performances can be further improved. In this paper, we propose an efficient and simple convolution neural network, RBPCNN, that relies on the combination of the raw RNA sequence and evolutionary information. We show that conservation scores (evolutionary information) for the RNA sequences can significantly improve the overall performance of the proposed predictor. In addition, the automatic extraction of the binding sequence motifs can enhance our understanding of the binding specificities of RBPs. The experimental results show that RBPCNN outperforms significantly the current state-of-the-art methods. More specifically, the average area under the receiver operator curve was improved by 2.67 percent and the mean average precision was improved by 8.03 percent. The datasets and results can be downloaded from https://home.jbnu.ac.kr/NSCL/RBPCNN.htm.
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25
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Yuan DD, Jia CD, Yan MY, Wang J. Circular RNA hsa_circ_0000730 restrains cell proliferation, migration, and invasion in cervical cancer through miR-942-5p/PTEN axis. Kaohsiung J Med Sci 2021; 37:964-972. [PMID: 34562344 DOI: 10.1002/kjm2.12443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) play prominent roles in regulating the progression of cancers. This study is aimed to decipher the role of hsa_circ_0000730 in cervical cancer (CC).The differentially expressed circRNAs of CC were screened out from the Gene Expression Omnibus database. qRT-PCR was used to detect circ_0000730 expression in CC tissues and cell lines, and the Kaplan-Meier curve was adopted to figure out the relationship between circ_000730 expression and the overall survival time of CC patients. BrdU assay and Tanswell assay were utilized to examine the proliferation, migration, and invasion of CC cells. Western blot was adopted to detect PTEN protein expression. Bioinformatics analysis and dual-luciferase reporter assay were used to examine the target relationship between miR-942-5p and circ_0000730 or PTEN, respectively.Circ_0000730 was among the differentially expressed circRNAs in CC. Circ_0000730 was significantly down-regulated in the cancer tissues of 50 CC patients and CC cell lines. Additionally, underexpression of circ_0000730 was associated with the shorter survival time of CC patients. Gain- and loss-of-function assays highlighted that circ_0000730 significantly inhibited the proliferation, migration, and invasion of CC cells. Mechanistically, miR-942-5p was identified as a downstream target of circ_0000730, and circ_0000730 could positively regulate PTEN expression via repressing miR-942-5p in CC cells.Circ_0000730 inhibits the proliferation, migration, and invasion of CC cells via regulating miR-942-5p/PTEN axis. Circ_0000730 probably acts as a tumor suppressor in CC, and it may be a candidate target for the treatment of CC.
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Affiliation(s)
- Dan-Dan Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, PR China
| | - Cun-De Jia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, PR China
| | - Ming-Yu Yan
- Department of Respiratory, The Third Affiliated Hospital of Inner Mongolia Medical College, Baotou, PR China
| | - Jian Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, PR China
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Wang G, Zhao H, Duan X, Ren Z. CircRNA pappalysin 1 facilitates prostate cancer development through miR-515-5p/FKBP1A axis. Andrologia 2021; 53:e14227. [PMID: 34469009 DOI: 10.1111/and.14227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/19/2022] Open
Abstract
The role of circular RNA (circRNA) pappalysin 1 (circ-PAPPA; hsa_circ_0088233) in prostate cancer (PCa) cells was explored in the current study. Circ-PAPPA abundance was markedly enhanced in PCa. Circ-PAPPA interference restrained cell viability, proliferation, motility and glycolysis while elevated the apoptosis rate of PCa cells. Circ-PAPPA negatively regulated microRNA-515-5p (miR-515-5p) abundance. MiR-515-5p silencing largely diminished circ-PAPPA knockdown-mediated effects in PCa cells. MiR-515-5p directly bound to FKBP prolyl isomerase 1A (FKBP1A). MiR-515-5p overexpression-mediated impacts were partly counteracted by FKBP1A overexpression. Circ-PAPPA silencing reduced FKBP1A protein level partly by elevating miR-515-5p expression. Circ-PAPPA knockdown significantly restrained the tumour growth in vivo. Circ-PAPPA elevated the malignant phenotypes of PCa cells by sequestering miR-515-5p to induce the expression of FKBP1A.
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Affiliation(s)
- Guangwen Wang
- Department of Urology, The People Hospital of Guangrao County, Guangrao, China
| | - Haiyang Zhao
- Department of Urology, The People Hospital of Guangrao County, Guangrao, China
| | - Xiaohong Duan
- Department of Respiratory Medicine, The People Hospital of Guangrao County, Guangrao, China
| | - Zhiqiang Ren
- Department of Urology, The People Hospital of Guangrao County, Guangrao, China
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27
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Cheng B, Tian J, Chen Y. Identification of RNA binding protein interacting with circular RNA and hub candidate network for hepatocellular carcinoma. Aging (Albany NY) 2021; 13:16124-16143. [PMID: 34133325 PMCID: PMC8266373 DOI: 10.18632/aging.203139] [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: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022]
Abstract
The interaction between RNA binding protein (RBP) and circular RNA (circRNA) is important for the regulation of tumor progression. This study aimed to identify the RBP-circRNA network in hepatocellular carcinoma (HCC). 22 differentially expressed (DE) circRNAs in HCC were screened out from Gene Expression Omnibus (GEO) database and their binding RBPs were predicted by Circular RNA Interactome. Among them, 17 DERBPs, which were commonly dysregulated in HCC from The Clinical Proteomic Tumor Analysis Consortium (CPTAC), The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) projects, were utilized to construct the RBP-circRNA network. Through survival analysis, we found TARDBP was the only prognostic RBP for HCC in CPTAC, TCGA and ICGC projects. High expression of TARDBP was correlated with high grade, advanced stage and low macrophage infiltration of HCC. Additionally, gene set enrichment analysis showed that dysregulated TARDBP might be involved in some pathways related to the HCC pathogenesis. Therefore, a hub RBP-circRNA network was generated based on TARDBP. RNA immunoprecipitation and RNA pull-down confirmed that hsa_circ_0004913 binds to TARDBP. These findings indicated certain RBP-circRNA regulatory network potentially involved in the pathogenesis of HCC, which provides novel insights into the mechanism study and biomarker identification for HCC.
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Affiliation(s)
- Binglin Cheng
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Jingdong Tian
- School of Biomedical Engineering, Xinhua College of Sun Yat-Sen University, Guangzhou, Guangdong Province 510520, China
| | - Yuhan Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, China
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Tang L, Li P, Jang M, Zhu W. Circular RNAs and Cardiovascular Regeneration. Front Cardiovasc Med 2021; 8:672600. [PMID: 33928139 PMCID: PMC8076501 DOI: 10.3389/fcvm.2021.672600] [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: 02/26/2021] [Accepted: 03/22/2021] [Indexed: 01/22/2023] Open
Abstract
circular RNAs (circRNAs) are a type of non-coding RNAs that are widely present in eukaryotic cells. They have the characteristics of stable structure, high abundance, and cell or tissue specific expression. circRNAs are single-stranded RNAs that are covalently back spliced to form closed circular loops. They may participate in gene expression and regulation through a variety of action modes. circRNAs can encode proteins or function by acting as miRNA sponges for protein translation. Since 2016, a growing number of research studies have shown that circRNAs play important role in the pathogenesis of cardiovascular disease. With the construction of circRNA database, the differential expression of circRNAs in the heart tissue samples from different species and the gradual elucidation of its mode of action in disease may become an ideal diagnosis biomarker and an effective therapeutic target. What can be expected surely has a broader application prospect. In this review, we summarize recent publications on circRNA biogenesis, expression profiles, functions, and the most recent studies of circRNAs in the field of cardiovascular diseases with special emphasis on cardiac regeneration.
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Affiliation(s)
- Ling Tang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Pengsheng Li
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Michelle Jang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Wuqiang Zhu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
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Jiang S, Fu R, Shi J, Wu H, Mai J, Hua X, Chen H, Liu J, Lu M, Li N. CircRNA-Mediated Regulation of Angiogenesis: A New Chapter in Cancer Biology. Front Oncol 2021; 11:553706. [PMID: 33777729 PMCID: PMC7988083 DOI: 10.3389/fonc.2021.553706] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
Angiogenesis is necessary for carcinoma progression and is regulated by a variety of pro- and anti-angiogenesis factors. CircRNAs are RNA molecules that do not have a 5'-cap or a 3'-polyA tail and are involved in a variety of biological functions. While circRNA-mediated regulation of tumor angiogenesis has received much attention, the detailed biological regulatory mechanism remains unclear. In this review, we investigated circRNAs in tumor angiogenesis from multiple perspectives, including its upstream and downstream factors. We believe that circRNAs have natural advantages and great potential for the diagnosis and treatment of tumors, which deserves further exploration.
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Affiliation(s)
- Shaotao Jiang
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Rongdang Fu
- Department of Hepatic Surgery, The First People's Hospital of Foshan, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, China
| | - Jiewei Shi
- Department of General Surgery, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Huijie Wu
- Department of Obstetrics, The First People's Hospital of Foshan, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, China
| | - Jialuo Mai
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xuefeng Hua
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Huan Chen
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jie Liu
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Minqiang Lu
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ning Li
- Department of HBP SURGERY II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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Tang L, Jiang B, Zhu H, Gao T, Zhou Y, Gong F, He R, Xie L, Li Y. The Biogenesis and Functions of circRNAs and Their Roles in Breast Cancer. Front Oncol 2021; 11:605988. [PMID: 33718157 PMCID: PMC7947672 DOI: 10.3389/fonc.2021.605988] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Recent statistics show that breast cancer is among the most frequent cancers in clinical practice. It is also the second-leading cause of cancer-related deaths among women worldwide. CircRNAs are a new class of endogenous regulatory RNA molecules whose 5’ end and 3’ end are connected together to form a covalently closed single-stranded loop by back-splicing. CircRNAs present the advantages of disease-specific expression and excellent expression stability, and they can modulate gene expression at posttranscriptional and transcriptional levels. CircRNAs are abnormally expressed in multiple cancers, such as breast cancer, and drive the initiation and progression of cancer. In this review, we describe current knowledge about the functions of circRNAs and generalize their roles in various aspects of breast cancer, including cell proliferation, cell cycle, apoptosis, invasion and metastasis, autophagy, angiogenesis, drug resistance, and tumor immunity, and their prognostic and diagnostic value. This may add to a better understanding of the functions and roles of circRNAs in breast cancer, which may become new diagnostic and predictive biomarkers of breast cancer.
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Affiliation(s)
- Liting Tang
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Baohong Jiang
- Department of Pharmacy, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Hongbo Zhu
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Ting Gao
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Yu Zhou
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Fuqiang Gong
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Rongfang He
- Department of Pathology The First Affiliated Hospital, University of South China, Hengyang, China
| | - Liming Xie
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Yuehua Li
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, Hengyang, China.,Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang, China
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31
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CircNet: an encoder–decoder-based convolution neural network (CNN) for circular RNA identification. Neural Comput Appl 2021. [DOI: 10.1007/s00521-020-05673-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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Lei X, Mudiyanselage TB, Zhang Y, Bian C, Lan W, Yu N, Pan Y. A comprehensive survey on computational methods of non-coding RNA and disease association prediction. Brief Bioinform 2020; 22:6042241. [PMID: 33341893 DOI: 10.1093/bib/bbaa350] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023] Open
Abstract
The studies on relationships between non-coding RNAs and diseases are widely carried out in recent years. A large number of experimental methods and technologies of producing biological data have also been developed. However, due to their high labor cost and production time, nowadays, calculation-based methods, especially machine learning and deep learning methods, have received a lot of attention and been used commonly to solve these problems. From a computational point of view, this survey mainly introduces three common non-coding RNAs, i.e. miRNAs, lncRNAs and circRNAs, and the related computational methods for predicting their association with diseases. First, the mainstream databases of above three non-coding RNAs are introduced in detail. Then, we present several methods for RNA similarity and disease similarity calculations. Later, we investigate ncRNA-disease prediction methods in details and classify these methods into five types: network propagating, recommend system, matrix completion, machine learning and deep learning. Furthermore, we provide a summary of the applications of these five types of computational methods in predicting the associations between diseases and miRNAs, lncRNAs and circRNAs, respectively. Finally, the advantages and limitations of various methods are identified, and future researches and challenges are also discussed.
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Affiliation(s)
- Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | | | - Yuchen Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Chen Bian
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Wei Lan
- School of Computer, Electronics and Information at Guangxi University, Nanning, China
| | - Ning Yu
- Department of Computing Sciences at the College at Brockport, State University of New York, Rochester, NY, USA
| | - Yi Pan
- Computer Science Department at Georgia State University, Atlanta, GA, USA
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Corson TW. Cancer Research in the "Chemical Biology" Section of the Journal Molecules. Molecules 2020; 25:molecules25225275. [PMID: 33198208 PMCID: PMC7697467 DOI: 10.3390/molecules25225275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- Timothy W Corson
- Departments of Ophthalmology, Biochemistry and Molecular Biology, and Pharmacology and Toxicology, and the Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Zhang Y, Shi Z, Li Z, Wang X, Zheng P, Li H. Circ_0057553/miR-515-5p Regulates Prostate Cancer Cell Proliferation, Apoptosis, Migration, Invasion and Aerobic Glycolysis by Targeting YES1. Onco Targets Ther 2020; 13:11289-11299. [PMID: 33177837 PMCID: PMC7649234 DOI: 10.2147/ott.s272294] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 02/03/2023] Open
Abstract
Background Prostate cancer (PCa) is one of the most common malignant cancer in males worldwide. Circular RNAs (CircRNAs) are novel type of non-coding RNAs. Recently, circRNAs have been reported participating in various cancers, including prostate cancer. However, the function and mechanism of circ_0057553 remain to be elucidated. Methods and Materials The RNA expression levels of circ_0057553, miR-515-5p, YES proto-oncogene 1 (YES1) and glycolytic genes mRNA were detected by qRT-PCR in PCa tissues or cells. Western blotting was performed to analyze YES1 protein level. Cell viability, migration and invasion and cell apoptosis were assessed by cell counting kit-8 (CCK-8) assay, transwell assay and flow cytometry. In addition, the effects of cell glycolysis were evaluated by measuring lactate production, glucose consumption and adenosine triphosphate (ATP) level. Moreover, dual-luciferase reporter assay was used to detect the target sites of circ_0057553 and miR-515-5p, miR-515-5p and YES1. RNA immunoprecipitation (RIP) was conducted to evaluate the target relationship between circ_0057553 and miR-515-5p. Xenograft mouse model was conducted to measure tumor formation in vivo. Results Circ_0057553 was significantly up-regulated in PCa tissues and cells. Knockdown of circ_0057553 inhibited cell viability, migration, invasion and glycolysis and facilitated apoptosis in PCa cells. Furthermore, circ_0057553 bound to miR-515-5p and miR-515-5p directly targeted YES1. Interestingly, miR-515-5p inhibitor partially rescued the function of circ_0057553 knockdown, while YES1 restored the effects of miR-515-5p overexpression. Circ_0057553 down-regulation remarkably decreased tumor volume and weight in vivo. Conclusion Circ_0057553 affected PCa cell viability, migration, invasion, apoptosis and glycolysis through miR-515-5p/YES1 axis.
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Affiliation(s)
- Yang Zhang
- Department of Urology Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, People's Republic of China
| | - Zhenguo Shi
- Department of Urology Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, People's Republic of China
| | - Zhijun Li
- Department of Urology Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, People's Republic of China
| | - Xiaohui Wang
- Department of Urology Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, People's Republic of China
| | - Pengyi Zheng
- Department of Urology Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, People's Republic of China
| | - Huibing Li
- Department of Urology Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, People's Republic of China
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Yang Y, Hou Z, Ma Z, Li X, Wong KC. iCircRBP-DHN: identification of circRNA-RBP interaction sites using deep hierarchical network. Brief Bioinform 2020; 22:5943796. [PMID: 33126261 DOI: 10.1093/bib/bbaa274] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/07/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are widely expressed in eukaryotes. The genome-wide interactions between circRNAs and RNA-binding proteins (RBPs) can be probed from cross-linking immunoprecipitation with sequencing data. Therefore, computational methods have been developed for identifying RBP binding sites on circRNAs. Unfortunately, those computational methods often suffer from the low discriminative power of feature representations, numerical instability and poor scalability. To address those limitations, we propose a novel computational method called iCircRBP-DHN using deep hierarchical network for discriminating circRNA-RBP binding sites. The network architecture can be regarded as a deep multi-scale residual network followed by bidirectional gated recurrent units (BiGRUs) with the self-attention mechanism, which can simultaneously extract local and global contextual information. Meanwhile, we propose novel encoding schemes by integrating CircRNA2Vec and the K-tuple nucleotide frequency pattern to represent different degrees of nucleotide dependencies. To validate the effectiveness of our proposed iCircRBP-DHN, we compared its performance with other computational methods on 37 circRNAs datasets and 31 linear RNAs datasets, respectively. The experimental results reveal that iCircRBP-DHN can achieve superior performance over those state-of-the-art algorithms. Moreover, we perform motif analysis on circRNAs bound by those different RBPs, demonstrating that our proposed CircRNA2Vec encoding scheme can be promising. The iCircRBP-DHN method is made available at https://github.com/houzl3416/iCircRBP-DHN.
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Affiliation(s)
- Yuning Yang
- School of Information Science and Technology, Northeast Normal University
| | - Zilong Hou
- School of Artificial Intelligence, Jilin University
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University
| | - Ka-Chun Wong
- School of Artificial Intelligence, Jilin University
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Li H, He L, Tuo Y, Huang Y, Qian B. Circular RNA hsa_circ_0000282 contributes to osteosarcoma cell proliferation by regulating miR-192/XIAP axis. BMC Cancer 2020; 20:1026. [PMID: 33097010 PMCID: PMC7583201 DOI: 10.1186/s12885-020-07515-8] [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: 07/20/2020] [Accepted: 10/09/2020] [Indexed: 01/20/2023] Open
Abstract
Background Circular RNAs (circRNAs) have emerged as a novel category of non-coding RNA, which exhibit a pivotal effect on regulating gene expression and biological functions, yet how circRNAs function in osteosarcoma (OSA) still demands further investigation. This study aimed at probing into the function of hsa_circ_0000282 in OSA. Methods The expressions of circ_0000282 and miR-192 in OSA tissues and cell lines were examined by quantitative real-time polymerase chain reaction (qRT-PCR), and the correlation between the expression level of circ_0000282 and clinicopathological features of OSA patients was analyzed. The expressions of X-linked inhibitor of apoptosis protein (XIAP), B-cell lymphoma-2 (Bcl-2) and Bcl-2 associated X protein (Bax) in OSA cells were assayed by Western blot. The proliferation and apoptosis of OSA cells were examined by CCK-8, BrdU and flow cytometry, respectively. Bioinformatics analysis, dual-luciferase reporter gene assay and RIP experiments were employed to predict and validate the targeting relationships between circ_0000282 and miR-192, and between miR-192 and XIAP, respectively. Results Circ_0000282 was highly expressed in OSA tissues and cell lines, which represented positive correlation with Enneking stage of OSA patients and negative correlation with tumor differentiation degree. In vitro experiments confirmed that overexpression of circ_0000282 markedly facilitated OSA cell proliferation and repressed cancer cell apoptosis in comparison to control group. Besides, knockdown of circ_0000282 repressed OSA cell proliferation and promoted apoptosis. Additionally, the binding relationships between circ_0000282 and miR-192, and between miR-192 and XIAP were validated. Circ_0000282 indirectly up-regulated XIAP expression by adsorbing miR-192, thereby playing a role in promoting cancer in OSA. Conclusion Circ_0000282 was a novel oncogenic circRNA in OSA. Circ_0000282/miR-192/XIAP axis regulated OSA cell proliferation apoptosis with competitive endogenous RNA mechanism.
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Affiliation(s)
- Houkun Li
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, No. 76 Nanguo Road, Xi'an, 710054, Shaanxi, China.
| | - Limin He
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, No. 76 Nanguo Road, Xi'an, 710054, Shaanxi, China
| | - Yuan Tuo
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, No. 76 Nanguo Road, Xi'an, 710054, Shaanxi, China
| | - Yansheng Huang
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, No. 76 Nanguo Road, Xi'an, 710054, Shaanxi, China
| | - Bing Qian
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, No. 76 Nanguo Road, Xi'an, 710054, Shaanxi, China
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Non-coding RNAs in Brain Tumors, the Contribution of lncRNAs, circRNAs, and snoRNAs to Cancer Development-Their Diagnostic and Therapeutic Potential. Int J Mol Sci 2020; 21:ijms21197001. [PMID: 32977537 PMCID: PMC7582339 DOI: 10.3390/ijms21197001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 12/17/2022] Open
Abstract
Brain tumors are one of the most frightening ailments that afflict human beings worldwide. They are among the most lethal of all adult and pediatric solid tumors. The unique cell-intrinsic and microenvironmental properties of neural tissues are some of the most critical obstacles that researchers face in the diagnosis and treatment of brain tumors. Intensifying the search for potential new molecular markers in order to develop new effective treatments for patients might resolve this issue. Recently, the world of non-coding RNAs (ncRNAs) has become a field of intensive research since the discovery of their essential impact on carcinogenesis. Some of the most promising diagnostic and therapeutic regulatory RNAs are long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small nucleolar RNAs (snoRNAs). Many recent reports indicate the important role of these molecules in brain tumor development, as well as their implications in metastasis. In the following review, we summarize the current state of knowledge about regulatory RNAs, namely lncRNA, circRNAs, and snoRNAs, and their impact on the development of brain tumors in children and adults with particular emphasis on malignant primary brain tumors-gliomas and medulloblastomas (MB). We also provide an overview of how these different ncRNAs may act as biomarkers in these tumors and we present their potential clinical implications.
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Fan C, Lei X, Pan Y. Prioritizing CircRNA-Disease Associations With Convolutional Neural Network Based on Multiple Similarity Feature Fusion. Front Genet 2020; 11:540751. [PMID: 33193615 PMCID: PMC7525185 DOI: 10.3389/fgene.2020.540751] [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: 03/25/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022] Open
Abstract
Accumulating evidence shows that circular RNAs (circRNAs) have significant roles in human health and in the occurrence and development of diseases. Biological researchers have identified disease-related circRNAs that could be considered as potential biomarkers for clinical diagnosis, prognosis, and treatment. However, identification of circRNA–disease associations using traditional biological experiments is still expensive and time-consuming. In this study, we propose a novel method named MSFCNN for the task of circRNA–disease association prediction, involving two-layer convolutional neural networks on a feature matrix that fuses multiple similarity kernels and interaction features among circRNAs, miRNAs, and diseases. First, four circRNA similarity kernels and seven disease similarity kernels are constructed based on the biological or topological properties of circRNAs and diseases. Subsequently, the similarity kernel fusion method is used to integrate the similarity kernels into one circRNA similarity kernel and one disease similarity kernel, respectively. Then, a feature matrix for each circRNA–disease pair is constructed by integrating the fused circRNA similarity kernel and fused disease similarity kernel with interactions and features among circRNAs, miRNAs, and diseases. The features of circRNA–miRNA and disease–miRNA interactions are selected using principal component analysis. Finally, taking the constructed feature matrix as an input, we used two-layer convolutional neural networks to predict circRNA–disease association labels and mine potential novel associations. Five-fold cross validation shows that our proposed model outperforms conventional machine learning methods, including support vector machine, random forest, and multilayer perception approaches. Furthermore, case studies of predicted circRNAs for specific diseases and the top predicted circRNA–disease associations are analyzed. The results show that the MSFCNN model could be an effective tool for mining potential circRNA–disease associations.
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Affiliation(s)
- Chunyan Fan
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yi Pan
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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Chen Z, Zhou J, Wang M, Liu J, Zhang L, Loor JJ, Liang Y, Wu H, Yang Z. Circ09863 Regulates Unsaturated Fatty Acid Metabolism by Adsorbing miR-27a-3p in Bovine Mammary Epithelial Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8589-8601. [PMID: 32689797 DOI: 10.1021/acs.jafc.0c03917] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fatty acid composition plays a key role in regulating flavor and quality of milk. Therefore, in order to improve milk quality, it is particularly important to investigate regulatory mechanisms of milk fatty acid metabolism. Circular RNAs (circRNAs) regulate expression genes associated with several biological processes including fatty acid metabolism. In this study, high-throughput sequencing was used to detect differentially expressed genes in bovine mammary tissue at early lactation and peak lactation. Circ09863 profiles were influenced by the lactation stage. Functional studies in bovine mammary epithelial cells (BMECs) revealed that circ09863 promotes triglyceride (TAG) synthesis together with increased content of unsaturated fatty acids (C16:1 and C18:1). These results suggested that circ09863 is partly responsible for modulating fatty acid metabolism. Additionally, software prediction identified a miR-27a-3p binding site in the circ09863 sequence. Overexpression of miR-27a-3p in BMECs led to decreased TAG synthesis. However, overexpression of circ09863 (pcDNA-circ09863) in BMECs significantly reduced expression of miR-27a-3p and enhanced gene expression of fatty acid synthase (FASN), a target of miR-27a-3p. Overall, data suggest that circ09863 relieves the inhibitory effect of miR-27a-3p on FASN expression by binding miR-27a-3p and subsequently regulating TAG synthesis and fatty acid composition. Together, these mechanisms provide new research avenues and theoretical bases to improve milk quality.
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Affiliation(s)
- Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Jingpeng Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Mengjie Wang
- College of Agriculture and Animal Husbandry, Qinghai University, No.251 Ningda Road, Xining, Qinghai 810016, P. R. China
| | - Jiahua Liu
- College of Agriculture and Animal Husbandry, Qinghai University, No.251 Ningda Road, Xining, Qinghai 810016, P. R. China
| | - Longfei Zhang
- College of Agriculture and Animal Husbandry, Qinghai University, No.251 Ningda Road, Xining, Qinghai 810016, P. R. China
| | - Juan J Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Yusheng Liang
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Hua Wu
- College of Agriculture and Animal Husbandry, Qinghai University, No.251 Ningda Road, Xining, Qinghai 810016, P. R. China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
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Zhang G, Deng Y, Liu Q, Ye B, Dai Z, Chen Y, Dai X. Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning. Front Genet 2020; 11:655. [PMID: 32849764 PMCID: PMC7396586 DOI: 10.3389/fgene.2020.00655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
Circular RNA (circRNA) is a closed long non-coding RNA (lncRNA) formed by covalently closed loops through back-splicing. Emerging evidence indicates that circRNA can influence cellular physiology through various molecular mechanisms. Thus, accurate circRNA identification and prediction of its regulatory information are critical for understanding its biogenesis. Although several computational tools based on machine learning have been proposed for circRNA identification, the prediction accuracy remains to be improved. Here, first we present circLGB, a machine learning-based framework to discriminate circRNA from other lncRNAs. circLGB integrates commonly used sequence-derived features and three new features containing adenosine to inosine (A-to-I) deamination, A-to-I density and the internal ribosome entry site. circLGB categorizes circRNAs by utilizing a LightGBM classifier with feature selection. Second, we introduce circMRT, an ensemble machine learning framework to systematically predict the regulatory information for circRNA, including their interactions with microRNA, the RNA binding protein, and transcriptional regulation. Feature sets including sequence-based features, graph features, genome context, and regulatory information features were modeled in circMRT. Experiments on public and our constructed datasets show that the proposed algorithms outperform the available state-of-the-art methods. circLGB is available at http://www.circlgb.com. Source codes are available at https://github.com/Peppags/circLGB-circMRT.
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Affiliation(s)
- Guishan Zhang
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Yiyun Deng
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Qingyu Liu
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Bingxu Ye
- Key Laboratory of Digital Signal and Image Processing of Guangdong Provincial, College of Engineering, Shantou University, Shantou, China
| | - Zhiming Dai
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-sen University, Guangzhou, China
| | - Yaowen Chen
- Key Laboratory of Digital Signal and Image Processing of Guangdong Provincial, College of Engineering, Shantou University, Shantou, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Li Z, Cheng Y, Wu F, Wu L, Cao H, Wang Q, Tang W. The emerging landscape of circular RNAs in immunity: breakthroughs and challenges. Biomark Res 2020; 8:25. [PMID: 32665846 PMCID: PMC7348111 DOI: 10.1186/s40364-020-00204-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently linked RNAs that exhibit individual strand with a closed-loop framework compared with a conserving, steady and abundant linear counterpart. In recent years, as high-throughput sequencing advancement has been developing, functional circRNAs have been increasingly recognized, and more extensive analyses expounded their effect on different diseases. However, the study on the function of circRNAs in the immune system remains insufficient. This study discusses the basic principles of circRNAs regulation and the systems involved in physiology-related and pathology-related processes. The effect of circRNAs on immune regulation is elucidated. The ongoing development of circRNAs and basic immunology has multiplied their potential in treating diseases. Such perspective will summarize the status and effect of circRNAs on various immune cells in cancer, autoimmune diseases and infections. Moreover, this study will primarily expound the system of circRNAs in T lymphocytes, macrophages and other immune cells, which creates a novel perspective and lay a theoretical basis for treating diseases.
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Affiliation(s)
- Zhouxiao Li
- Department of Hand Surgery, Plastic Surgery and Aesthetic Surgery, Ludwig-Maximilians University, Munich, Germany
| | - Ye Cheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Liangliang Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Qian Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu China
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Wang Z, Lei X. Matrix factorization with neural network for predicting circRNA-RBP interactions. BMC Bioinformatics 2020; 21:229. [PMID: 32503474 PMCID: PMC7275382 DOI: 10.1186/s12859-020-3514-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/23/2020] [Indexed: 12/29/2022] Open
Abstract
Background Circular RNA (circRNA) has been extensively identified in cells and tissues, and plays crucial roles in human diseases and biological processes. circRNA could act as dynamic scaffolding molecules that modulate protein-protein interactions. The interactions between circRNA and RNA Binding Proteins (RBPs) are also deemed to an essential element underlying the functions of circRNA. Considering cost-heavy and labor-intensive aspects of these biological experimental technologies, instead, the high-throughput experimental data has enabled the large-scale prediction and analysis of circRNA-RBP interactions. Results A computational framework is constructed by employing Positive Unlabeled learning (P-U learning) to predict unknown circRNA-RBP interaction pairs with kernel model MFNN (Matrix Factorization with Neural Networks). The neural network is employed to extract the latent factors of circRNA and RBP in the interaction matrix, the P-U learning strategy is applied to alleviate the imbalanced characteristics of data samples and predict unknown interaction pairs. For this purpose, the known circRNA-RBP interaction data samples are collected from the circRNAs in cancer cell lines database (CircRic), and the circRNA-RBP interaction matrix is constructed as the input of the model. The experimental results show that kernel MFNN outperforms the other deep kernel models. Interestingly, it is found that the deeper of hidden layers in neural network framework does not mean the better in our model. Finally, the unlabeled interactions are scored using P-U learning with MFNN kernel, and the predicted interaction pairs are matched to the known interactions database. The results indicate that our method is an effective model to analyze the circRNA-RBP interactions. Conclusion For a poorly studied circRNA-RBP interactions, we design a prediction framework only based on interaction matrix by employing matrix factorization and neural network. We demonstrate that MFNN achieves higher prediction accuracy, and it is an effective method.
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Affiliation(s)
- Zhengfeng Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China.,College of Information Science and Engineering, Guilin University of Technology, Guilin, 541004, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China.
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Drula R, Braicu C, Harangus A, Nabavi SM, Trif M, Slaby O, Ionescu C, Irimie A, Berindan-Neagoe I. Critical function of circular RNAs in lung cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1592. [PMID: 32180372 DOI: 10.1002/wrna.1592] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Lung cancer is one of the main causes of cancer-related death in the world, especially due to its frequency and ineffective therapeutically approaches in the late stages of the disease. Despite the recent advent of promising new targeted therapies, lung cancer diagnostic strategies still have difficulty in identifying the disease at an early stage. Therefore, the characterizations of more sensible and specific cancer biomarkers have become an important goal for clinicians. Circular RNAs (circRNAs), a type of RNA with covalently closed continuous loop structures that display high structural resistance and tissue specificity pointed toward a potential biomarker role. Current investigations have identified that circRNAs have a prominent function in the regulation of oncogenic pathways, by regulating gene expression both at transcriptional and post-transcriptional level. The aim of this review is to provide novel information regarding the implications of circRNAs in lung cancer, with an emphasis on the role in disease development and progression. Initially, we explored the potential utility of circRNAs as biomarkers, focusing on function, mechanisms, and correlation with disease progression in lung cancer. Further, we will describe the interaction between circRNAs and other non-coding species of RNA (particularly microRNA) and their biological significance in lung cancer. Describing the nature of these interactions and their therapeutic potential will provide additional insight regarding the altered molecular landscape of lung cancer and consolidate the potential clinical value of these circular transcripts. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Rares Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Antonia Harangus
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,"Leon Daniello" Pneumology Clinic, Cluj-Napoca, Romania
| | - Seyed M Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Calin Ionescu
- 5th Surgical Department, Municipal Hospital, Cluj-Napoca, Romania.,Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandru Irimie
- Department of Surgery, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania.,Department of Surgical Oncology and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania.,Department of Functional Genomics and Experimental Pathology, The Oncology Institute Prof. Dr. Ion Chiricuta, Cluj-Napoca, Romania
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