1
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Guo C, Wang X, Ren H. Databases and computational methods for the identification of piRNA-related molecules: A survey. Comput Struct Biotechnol J 2024; 23:813-833. [PMID: 38328006 PMCID: PMC10847878 DOI: 10.1016/j.csbj.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.
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Affiliation(s)
- Chang Guo
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Han Ren
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
- Laboratory of Language and Artificial Intelligence, Guangdong University of Foreign Studies, Guangzhou 510420, China
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2
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Shaker FH, Sanad EF, Elghazaly H, Hsia SM, Hamdy NM. piR-823 tale as emerging cancer-hallmark molecular marker in different cancer types: a step-toward ncRNA-precision. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03308-z. [PMID: 39102033 DOI: 10.1007/s00210-024-03308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
PIWI-interacting RNAs (piRNAs) have received a lot of attention for their functions in cancer research. This class of short non-coding RNAs (ncRNA) has roles in genomic stability, chromatin remodeling, messenger RNA (mRNA) integrity, and genome structure. We summarized the mechanisms underlying the biogenesis and regulatory molecular functions of piRNAs. Among all piRNAs studied in cancer, this review offers a comprehensive analysis of the emerging roles of piR-823 in various types of cancer, including colorectal, gastric, liver, breast, and renal cancers, as well as multiple myeloma. piR-823 has emerged as a crucial modulator of various cancer hallmarks through regulating multiple pathways. In the current review, we analyzed several databases and conducted an extensive literature search to explore the influence of piR-823 in carcinogenesis in addition to describing the potential application of piR-823 as prognostic and diagnostic markers as well as the therapeutic potential toward ncRNA precision.
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Affiliation(s)
- Fatma H Shaker
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Eman F Sanad
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Hesham Elghazaly
- Department of Clinical Oncology, Faculty of Medicine, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Shih-Min Hsia
- School of Food and Safety, Nutrition Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 110301, Taiwan
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei, 110301, Taiwan
| | - Nadia M Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt.
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3
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Zhang Y, Yang Y, Ren L, Ning L, Zou Q, Luo N, Zhang Y, Liu R. RDscan: Extracting RNA-disease relationship from the literature based on pre-training model. Methods 2024; 228:48-54. [PMID: 38789016 DOI: 10.1016/j.ymeth.2024.05.012] [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: 04/06/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
With the rapid advancements in molecular biology and genomics, a multitude of connections between RNA and diseases has been unveiled, making the efficient and accurate extraction of RNA-disease (RD) relationships from extensive biomedical literature crucial for advancing research in this field. This study introduces RDscan, a novel text mining method developed based on the pre-training and fine-tuning strategy, aimed at automatically extracting RD-related information from a vast corpus of literature using pre-trained biomedical large language models (LLM). Initially, we constructed a dedicated RD corpus by manually curating from literature, comprising 2,082 positive and 2,000 negative sentences, alongside an independent test dataset (comprising 500 positive and 500 negative sentences) for training and evaluating RDscan. Subsequently, by fine-tuning the Bioformer and BioBERT pre-trained models, RDscan demonstrated exceptional performance in text classification and named entity recognition (NER) tasks. In 5-fold cross-validation, RDscan significantly outperformed traditional machine learning methods (Support Vector Machine, Logistic Regression and Random Forest). In addition, we have developed an accessible webserver that assists users in extracting RD relationships from text. In summary, RDscan represents the first text mining tool specifically designed for RD relationship extraction, and is poised to emerge as an invaluable tool for researchers dedicated to exploring the intricate interactions between RNA and diseases. Webserver of RDscan is free available at https://cellknowledge.com.cn/RDscan/.
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Affiliation(s)
- Yang Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China; School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China.
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Nanchao Luo
- School of Computer Science and Technology, Aba Teachers College, WenChuan, Sichuan, 623002, China
| | - Yinghui Zhang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China.
| | - Ruijun Liu
- School of Software, Beihang University, Beijing 100191, China.
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4
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Sun W, Guo C, Wan J, Ren H. piRNA-disease association prediction based on multi-channel graph variational autoencoder. PeerJ Comput Sci 2024; 10:e2216. [PMID: 39145234 PMCID: PMC11323097 DOI: 10.7717/peerj-cs.2216] [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: 10/30/2023] [Accepted: 07/03/2024] [Indexed: 08/16/2024]
Abstract
Piwi-interacting RNA (piRNA) is a type of non-coding small RNA that is highly expressed in mammalian testis. PiRNA has been implicated in various human diseases, but the experimental validation of piRNA-disease associations is costly and time-consuming. In this article, a novel computational method for predicting piRNA-disease associations using a multi-channel graph variational autoencoder (MC-GVAE) is proposed. This method integrates four types of similarity networks for piRNAs and diseases, which are derived from piRNA sequences, disease semantics, piRNA Gaussian Interaction Profile (GIP) kernel, and disease GIP kernel, respectively. These networks are modeled by a graph VAE framework, which can learn low-dimensional and informative feature representations for piRNAs and diseases. Then, a multi-channel method is used to fuse the feature representations from different networks. Finally, a three-layer neural network classifier is applied to predict the potential associations between piRNAs and diseases. The method was evaluated on a benchmark dataset containing 5,002 experimentally validated associations with 4,350 piRNAs and 21 diseases, constructed from the piRDisease v1.0 database. It achieved state-of-the-art performance, with an average AUC value of 0.9310 and an AUPR value of 0.9247 under five-fold cross-validation. This demonstrates the method's effectiveness and superiority in piRNA-disease association prediction.
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Affiliation(s)
- Wei Sun
- School of Information Science and Technology, Qiongtai Normal University, Haikou, China
| | - Chang Guo
- School of Modern Information Industry, Guangzhou College of Commerce, Guangzhou, China
| | - Jing Wan
- Center for Lexicographical Studies, Guangdong University of Foreign Studies, Guangzhou, China
| | - Han Ren
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou, China
- Laboratory of Language and Artificial Intelligence, Guangdong University of Foreign Studies, Guangzhou, China
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5
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Yuan H, Hu J, Ge QQ, Liu WJ, Ma F, Zhang CY. Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells. NANO LETTERS 2024; 24:8732-8740. [PMID: 38958407 DOI: 10.1021/acs.nanolett.4c02230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.
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Affiliation(s)
- Huimin Yuan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Qi-Qin Ge
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
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Chaudhary U, Banerjee S. Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration. ACS Pharmacol Transl Sci 2024; 7:1901-1915. [PMID: 39022352 PMCID: PMC11249652 DOI: 10.1021/acsptsci.3c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
Non-coding RNAs are pivotal regulators of gene and protein expression, exerting crucial influences on diverse biological processes. Their dysregulation is frequently implicated in the onset and progression of diseases, notably cancer. A profound comprehension of the intricate mechanisms governing ncRNAs is imperative for devising innovative therapeutic interventions against these debilitating conditions. Significantly, nearly 80% of our genome comprises ncRNAs, underscoring their centrality in cellular processes. The elucidation of ncRNA functions is pivotal for grasping the complexities of gene regulation and its implications for human health. Modern genome sequencing techniques yield vast datasets, stored in specialized databases. To harness this wealth of information and to understand the crosstalk of non-coding RNAs, knowledge of available databases is required, and many new sophisticated computational tools have emerged. These tools play a pivotal role in the identification, prediction, and annotation of ncRNAs, thereby facilitating their experimental validation. This Review succinctly outlines the current understanding of ncRNAs, emphasizing their involvement in disease development. It also highlights the databases and tools instrumental in classifying, annotating, and evaluating ncRNAs. By extracting meaningful biological insights from seemingly "junk" data, these tools empower scientists to unravel the intricate roles of ncRNAs in shaping human health.
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Affiliation(s)
- Uma Chaudhary
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
| | - Satarupa Banerjee
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
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7
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Jiang M, Hong X, Gao Y, Kho AT, Tantisira KG, Li J. piRNA associates with immune diseases. Cell Commun Signal 2024; 22:347. [PMID: 38943141 PMCID: PMC11214247 DOI: 10.1186/s12964-024-01724-5] [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: 04/01/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024] Open
Abstract
PIWI-interacting RNA (piRNA) is the most abundant small non-coding RNA in animal cells, typically 26-31 nucleotides in length and it binds with PIWI proteins, a subfamily of Argonaute proteins. Initially discovered in germ cells, piRNA is well known for its role in silencing transposons and maintaining genome integrity. However, piRNA is also present in somatic cells as well as in extracellular vesicles and exosomes. While piRNA has been extensively studied in various diseases, particular cancer, its function in immune diseases remains unclear. In this review, we summarize current research on piRNA in immune diseases. We first introduce the basic characteristics, biogenesis and functions of piRNA. Then, we review the association of piRNA with different types of immune diseases, including autoimmune diseases, immunodeficiency diseases, infectious diseases, and other immune-related diseases. piRNA is considered a promising biomarker for diseases, highlighting the need for further research into its potential mechanisms in disease pathogenesis.
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Affiliation(s)
- Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yunfei Gao
- Department of Otolaryngology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Guangdong, Shenzhen, China.
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8
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Chen Q, Zhang L, Liu Y, Qin Z, Zhao T. PUTransGCN: identification of piRNA-disease associations based on attention encoding graph convolutional network and positive unlabelled learning. Brief Bioinform 2024; 25:bbae144. [PMID: 38581419 PMCID: PMC10998538 DOI: 10.1093/bib/bbae144] [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: 01/25/2024] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a crucial role in various biological processes and are implicated in disease. Consequently, there is an escalating demand for computational tools to predict piRNA-disease interactions. Although there have been computational methods proposed for the detection of piRNA-disease associations, the problem of imbalanced and sparse dataset has brought great challenges to capture the complex relationships between piRNAs and diseases. In response to this necessity, we have developed a novel computational architecture, denoted as PUTransGCN, which uses heterogeneous graph convolutional networks to uncover potential piRNA-disease associations. Additionally, the attention mechanism was used to adjust the weight parameters of aggregation heterogeneous node features automatically. For tackling the imbalanced dataset problem, the combined positive unlabelled learning (PUL) method comprising PU bagging, two-step and spy technique was applied to select reliable negative associations. The features of piRNAs and diseases were derived from three distinct biological sources by PUTransGCN, including information on piRNA sequences, semantic terms related to diseases and the existing network of piRNA-disease associations. In the experiment, PUTransGCN performs in 5-fold cross-validation with an AUC of 0.93 and 0.95 on two datasets, respectively, which outperforms the other six state-of-the-art models. We compared three different PUL methods, and the results of the ablation experiment indicate that the combined PUL method yields the best results. The PUTransGCN could serve as a valuable piRNA-disease prediction tool for upcoming studies in the biomedical field. The code for PUTransGCN is available at https://github.com/chenqiuhao/PUTransGCN.
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Affiliation(s)
- Qiuhao Chen
- Institute of Bioinformatics, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Liyuan Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Yaojia Liu
- School of Computer Science and Technology, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Zhonghao Qin
- State Key Laboratory of Robotics and System, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
| | - Tianyi Zhao
- School of Computer Science and Technology, Harbin Institute of Technology, 150000, Harbin, Heilongjiang, China
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Hou J, Wei H, Liu B. iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network. PLoS Comput Biol 2023; 19:e1011242. [PMID: 37339125 DOI: 10.1371/journal.pcbi.1011242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
Accurately identifying potential piRNA-disease associations is of great importance in uncovering the pathogenesis of diseases. Recently, several machine-learning-based methods have been proposed for piRNA-disease association detection. However, they are suffering from the high sparsity of piRNA-disease association network and the Boolean representation of piRNA-disease associations ignoring the confidence coefficients. In this study, we propose a supplementarily weighted strategy to solve these disadvantages. Combined with Graph Convolutional Networks (GCNs), a novel predictor called iPiDA-SWGCN is proposed for piRNA-disease association prediction. There are three main contributions of iPiDA-SWGCN: (i) Potential piRNA-disease associations are preliminarily supplemented in the sparse piRNA-disease network by integrating various basic predictors to enrich network structure information. (ii) The original Boolean piRNA-disease associations are assigned with different relevance confidence to learn node representations from neighbour nodes in varying degrees. (iii) The experimental results show that iPiDA-SWGCN achieves the best performance compared with the other state-of-the-art methods, and can predict new piRNA-disease associations.
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Affiliation(s)
- Jialu Hou
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Hang Wei
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
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10
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Meng X, Shang J, Ge D, Yang Y, Zhang T, Liu JX. ETGPDA: identification of piRNA-disease associations based on embedding transformation graph convolutional network. BMC Genomics 2023; 24:279. [PMID: 37226081 PMCID: PMC10210294 DOI: 10.1186/s12864-023-09380-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs) have been proven to be closely associated with human diseases. The identification of the potential associations between piRNA and disease is of great significance for complex diseases. Traditional "wet experiment" is time-consuming and high-priced, predicting the piRNA-disease associations by computational methods is of great significance. METHODS In this paper, a method based on the embedding transformation graph convolution network is proposed to predict the piRNA-disease associations, named ETGPDA. Specifically, a heterogeneous network is constructed based on the similarity information of piRNA and disease, as well as the known piRNA-disease associations, which is applied to extract low-dimensional embeddings of piRNA and disease based on graph convolutional network with an attention mechanism. Furthermore, the embedding transformation module is developed for the problem of embedding space inconsistency, which is lightweighter, stronger learning ability and higher accuracy. Finally, the piRNA-disease association score is calculated by the similarity of the piRNA and disease embedding. RESULTS Evaluated by fivefold cross-validation, the AUC of ETGPDA achieves 0.9603, which is better than the other five selected computational models. The case studies based on Head and neck squamous cell carcinoma and Alzheimer's disease further prove the superior performance of ETGPDA. CONCLUSIONS Hence, the ETGPDA is an effective method for predicting the hidden piRNA-disease associations.
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Affiliation(s)
- Xianghan Meng
- School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Junliang Shang
- School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Daohui Ge
- School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Yi Yang
- School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Tongdui Zhang
- Science and Technology Innovation Service Institution of Rizhao, Rizhao, 276826 China
| | - Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao, 276826 China
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11
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Zheng K, Zhang XL, Wang L, You ZH, Ji BY, Liang X, Li ZW. SPRDA: a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs. Brief Bioinform 2023; 24:6850564. [PMID: 36445194 DOI: 10.1093/bib/bbac498] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the current research is not strong enough to further clarify the functions of piRNA in cancer and its underlying mechanism. Therefore, how to provide large-scale and serious piRNA candidates for biological research has grown up to be a pressing issue. In this study, a novel computational model based on the structural perturbation method is proposed to predict potential disease-associated piRNAs, called SPRDA. Notably, SPRDA belongs to positive-unlabeled learning, which is unaffected by negative examples in contrast to previous approaches. In the 5-fold cross-validation, SPRDA shows high performance on the benchmark dataset piRDisease, with an AUC of 0.9529. Furthermore, the predictive performance of SPRDA for 10 diseases shows the robustness of the proposed method. Overall, the proposed approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.
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Affiliation(s)
- Kai Zheng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China.,College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China
| | - Xin-Lu Zhang
- Civil Product General Research Institute, The 36th Research Institute of China Electronics Technology Group Corporation, Jiaxing, 314000, China
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Bo-Ya Ji
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410006, China
| | - Xiao Liang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Zheng-Wei Li
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
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12
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Zhang P, Sun W, Wei D, Li G, Xu J, You Z, Zhao B, Li L. PDA-PRGCN: identification of Piwi-interacting RNA-disease associations through subgraph projection and residual scaling-based feature augmentation. BMC Bioinformatics 2023; 24:18. [PMID: 36650439 PMCID: PMC9843905 DOI: 10.1186/s12859-022-05073-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/10/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Emerging evidences show that Piwi-interacting RNAs (piRNAs) play a pivotal role in numerous complex human diseases. Identifying potential piRNA-disease associations (PDAs) is crucial for understanding disease pathogenesis at molecular level. Compared to the biological wet experiments, the computational methods provide a cost-effective strategy. However, few computational methods have been developed so far. RESULTS Here, we proposed an end-to-end model, referred to as PDA-PRGCN (PDA prediction using subgraph Projection and Residual scaling-based feature augmentation through Graph Convolutional Network). Specifically, starting with the known piRNA-disease associations represented as a graph, we applied subgraph projection to construct piRNA-piRNA and disease-disease subgraphs for the first time, followed by a residual scaling-based feature augmentation algorithm for node initial representation. Then, we adopted graph convolutional network (GCN) to learn and identify potential PDAs as a link prediction task on the constructed heterogeneous graph. Comprehensive experiments, including the performance comparison of individual components in PDA-PRGCN, indicated the significant improvement of integrating subgraph projection, node feature augmentation and dual-loss mechanism into GCN for PDA prediction. Compared with state-of-the-art approaches, PDA-PRGCN gave more accurate and robust predictions. Finally, the case studies further corroborated that PDA-PRGCN can reliably detect PDAs. CONCLUSION PDA-PRGCN provides a powerful method for PDA prediction, which can also serve as a screening tool for studies of complex diseases.
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Affiliation(s)
- Ping Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weicheng Sun
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengguo Wei
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Guodong Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Xu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuhong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Bowei Zhao
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People's Republic of China.
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13
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Zheng K, Zhang XL, Wang L, You ZH, Zhan ZH, Li HY. Line graph attention networks for predicting disease-associated Piwi-interacting RNAs. Brief Bioinform 2022; 23:6748487. [PMID: 36198846 DOI: 10.1093/bib/bbac393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and somatic tissues, and correlate with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes gradually, new bioinformatics methods for large-scale identification and prioritization of potential associations are therefore of interest. However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining. Line graphs can extend many heterogeneous networks to replace dichotomous networks. In this study, we present a new graph neural network framework, line graph attention networks (LGAT). And we apply it to predict PiRNA disease association (GAPDA). In the experiment, GAPDA performs excellently in 5-fold cross-validation with an AUC of 0.9038. Not only that, it still has superior performance compared with methods based on collaborative filtering and attribute features. The experimental results show that GAPDA ensures the prospect of the graph neural network on such problems and can be an excellent supplement for future biomedical research.
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Affiliation(s)
- Kai Zheng
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | | | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhao-Hui Zhan
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Hao-Yuan Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
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14
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Chen J, Lin J, Hu Y, Ye M, Yao L, Wu L, Zhang W, Wang M, Deng T, Guo F, Huang Y, Zhu B, Wang D. RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. Nucleic Acids Res 2022; 51:D1397-D1404. [PMID: 36134718 PMCID: PMC9825423 DOI: 10.1093/nar/gkac814] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 02/06/2023] Open
Abstract
Numerous studies have shown that RNA plays an important role in the occurrence and development of diseases, and RNA-disease associations are not limited to noncoding RNAs in mammals but also exist for protein-coding RNAs. Furthermore, RNA-associated diseases are found across species including plants and nonmammals. To better analyze diseases at the RNA level and facilitate researchers in exploring the pathogenic mechanism of diseases, we decided to update and change MNDR v3.0 to RNADisease v4.0, a repository for RNA-disease association (http://www.rnadisease.org/ or http://www.rna-society.org/mndr/). Compared to the previous version, new features include: (i) expanded data sources and categories of species, RNA types, and diseases; (ii) the addition of a comprehensive analysis of RNAs from thousands of high-throughput sequencing data of cancer samples and normal samples; (iii) the addition of an RNA-disease enrichment tool and (iv) the addition of four RNA-disease prediction tools. In summary, RNADisease v4.0 provides a comprehensive and concise data resource of RNA-disease associations which contains a total of 3 428 058 RNA-disease entries covering 18 RNA types, 117 species and 4090 diseases to meet the needs of biological research and lay the foundation for future therapeutic applications of diseases.
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Affiliation(s)
| | | | | | | | | | - Le Wu
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wenhai Zhang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meiyi Wang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tingting Deng
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feng Guo
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Correspondence may also be addressed to Bofeng Zhu. Tel: +86 20 61648787; Fax: +86 20 61648787;
| | - Dong Wang
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279;
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15
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Corsello T, Kudlicki AS, Liu T, Casola A. Respiratory syncytial virus infection changes the piwi-interacting RNA content of airway epithelial cells. Front Mol Biosci 2022; 9:931354. [PMID: 36158569 PMCID: PMC9493205 DOI: 10.3389/fmolb.2022.931354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are small non-coding RNAs (sncRNAs) of about 26–32 nucleotides in length and represent the largest class of sncRNA molecules expressed in animal cells. piRNAs have been shown to play a crucial role to safeguard the genome, maintaining genome complexity and integrity, as they suppress the insertional mutations caused by transposable elements. However, there is growing evidence for the role of piRNAs in controlling gene expression in somatic cells as well. Little is known about changes in piRNA expression and possible function occurring in response to viral infections. In this study, we investigated the piRNA expression profile, using a human piRNA microarray, in human small airway epithelial (SAE) cells infected with respiratory syncytial virus (RSV), a leading cause of acute respiratory tract infections in children. We found a time-dependent increase in piRNAs differentially expressed in RSV-infected SAE cells. We validated the top piRNAs upregulated and downregulated at 24 h post-infection by RT-qPCR and identified potential targets. We then used Gene Ontology (GO) tool to predict the biological processes of the predicted targets of the most represented piRNAs in infected cells over the time course of RSV infection. We found that the most significant groups of targets of regulated piRNAs are related to cytoskeletal or Golgi organization and nucleic acid/nucleotide binding at 15 and 24 h p.i. To identify common patterns of time-dependent responses to infection, we clustered the significantly regulated expression profiles. Each of the clusters of temporal profiles have a distinct set of potential targets of the piRNAs in the cluster Understanding changes in piRNA expression in RSV-infected airway epithelial cells will increase our knowledge of the piRNA role in viral infection and might identify novel therapeutic targets for viral lung-mediated diseases.
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Affiliation(s)
- Tiziana Corsello
- Department of Pediatrics, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
| | - Andrzej S Kudlicki
- Institute for Translational Sciences, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
| | - Tianshuang Liu
- Department of Pediatrics, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
| | - Antonella Casola
- Department of Pediatrics, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- *Correspondence: Antonella Casola,
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16
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Zheng K, Liang Y, Liu YY, Yasir M, Wang P. A decision support system based on multi-sources information to predict piRNA–disease associations using stacked autoencoder. Soft comput 2022. [DOI: 10.1007/s00500-022-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Zhang W, Hou J, Liu B. iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank. PLoS Comput Biol 2022; 18:e1010404. [PMID: 35969645 PMCID: PMC9410559 DOI: 10.1371/journal.pcbi.1010404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/25/2022] [Accepted: 07/18/2022] [Indexed: 12/01/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are regarded as drug targets and biomarkers for the diagnosis and therapy of diseases. However, biological experiments cost substantial time and resources, and the existing computational methods only focus on identifying missing associations between known piRNAs and diseases. With the fast development of biological experiments, more and more piRNAs are detected. Therefore, the identification of piRNA-disease associations of newly detected piRNAs has significant theoretical value and practical significance on pathogenesis of diseases. In this study, the iPiDA-LTR predictor is proposed to identify associations between piRNAs and diseases based on Learning to Rank. The iPiDA-LTR predictor not only identifies the missing associations between known piRNAs and diseases, but also detects diseases associated with newly detected piRNAs. Experimental results demonstrate that iPiDA-LTR effectively predicts piRNA-disease associations outperforming the other related methods.
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Affiliation(s)
- Wenxiang Zhang
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Jialu Hou
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
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18
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Zhang T, Chen L, Li R, Liu N, Huang X, Wong G. PIWI-interacting RNAs in human diseases: databases and computational models. Brief Bioinform 2022; 23:6603448. [PMID: 35667080 DOI: 10.1093/bib/bbac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
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Affiliation(s)
- Tianjiao Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Liang Chen
- Department of Computer Science, School of Engineering, Shantou University, Shantou, China
| | - Rongzhen Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Ning Liu
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Xiaobing Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
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19
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Ali SD, Tayara H, Chong KT. Identification of piRNA disease associations using deep learning. Comput Struct Biotechnol J 2022; 20:1208-1217. [PMID: 35317234 PMCID: PMC8908038 DOI: 10.1016/j.csbj.2022.02.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/09/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a pivotal role in maintaining genome integrity by repression of transposable elements, gene stability, and association with various disease progressions. Cost-efficient computational methods for the identification of piRNA disease associations promote the efficacy of disease-specific drug development. In this regard, we developed a simple, robust, and efficient deep learning method for identifying the piRNA disease associations known as piRDA. The proposed architecture extracts the most significant and abstract information from raw sequences represented in a simplicated piRNA disease pair without any involvement of features engineering. Two-step positive unlabeled learning and bootstrapping technique are utilized to abstain from the false-negative and biased predictions dealing with positive unlabeled data. The performance of proposed method piRDA is evaluated using k-fold cross-validation. The piRDA is significantly improved in all the performance evaluation measures for the identification of piRNA disease associations in comparison to state-of-the-art method. Moreover, it is thus projected conclusively that the proposed computational method could play a significant role as a supportive and practical tool for primitive disease mechanisms and pharmaceutical research such as in academia and drug design. Eventually, the proposed model can be accessed using publicly available and user-friendly web tool athttp://nsclbio.jbnu.ac.kr/tools/piRDA/.
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Affiliation(s)
- Syed Danish Ali
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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20
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Hanusek K, Poletajew S, Kryst P, Piekiełko-Witkowska A, Bogusławska J. piRNAs and PIWI Proteins as Diagnostic and Prognostic Markers of Genitourinary Cancers. Biomolecules 2022; 12:biom12020186. [PMID: 35204687 PMCID: PMC8869487 DOI: 10.3390/biom12020186] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
piRNAs (PIWI-interacting RNAs) are small non-coding RNAs capable of regulation of transposon and gene expression. piRNAs utilise multiple mechanisms to affect gene expression, which makes them potentially more powerful regulators than microRNAs. The mechanisms by which piRNAs regulate transposon and gene expression include DNA methylation, histone modifications, and mRNA degradation. Genitourinary cancers (GC) are a large group of neoplasms that differ by their incidence, clinical course, biology, and prognosis for patients. Regardless of the GC type, metastatic disease remains a key therapeutic challenge, largely affecting patients’ survival rates. Recent studies indicate that piRNAs could serve as potentially useful biomarkers allowing for early cancer detection and therapeutic interventions at the stage of non-advanced tumour, improving patient’s outcomes. Furthermore, studies in prostate cancer show that piRNAs contribute to cancer progression by affecting key oncogenic pathways such as PI3K/AKT. Here, we discuss recent findings on biogenesis, mechanisms of action and the role of piRNAs and the associated PIWI proteins in GC. We also present tools that may be useful for studies on the functioning of piRNAs in cancers.
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Affiliation(s)
- Karolina Hanusek
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
| | - Sławomir Poletajew
- Centre of Postgraduate Medical Education, II Department of Urology, 01-813 Warsaw, Poland; (S.P.); (P.K.)
| | - Piotr Kryst
- Centre of Postgraduate Medical Education, II Department of Urology, 01-813 Warsaw, Poland; (S.P.); (P.K.)
| | - Agnieszka Piekiełko-Witkowska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
- Correspondence: (A.P.-W.); (J.B.)
| | - Joanna Bogusławska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
- Correspondence: (A.P.-W.); (J.B.)
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21
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Ghosh B, Sarkar A, Mondal S, Bhattacharya N, Khatua S, Ghosh Z. piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species. RNA Biol 2021; 19:12-25. [PMID: 34965192 PMCID: PMC8786328 DOI: 10.1080/15476286.2021.2010960] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2.
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Affiliation(s)
- Byapti Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Arijita Sarkar
- Division of Bioinformatics, Bose Institute, Kolkata, India.,Present Affiliation: Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Namrata Bhattacharya
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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22
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Huang S, Yoshitake K, Asakawa S. A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans. Int J Mol Sci 2021; 22:ijms222011166. [PMID: 34681826 PMCID: PMC8538981 DOI: 10.3390/ijms222011166] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.
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Affiliation(s)
- Songqian Huang
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
| | | | - Shuichi Asakawa
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
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23
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Wang K, Wang T, Gao XQ, Chen XZ, Wang F, Zhou LY. Emerging functions of piwi-interacting RNAs in diseases. J Cell Mol Med 2021; 25:4893-4901. [PMID: 33942984 PMCID: PMC8178273 DOI: 10.1111/jcmm.16466] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
PIWI‐interacting RNAs (piRNAs) are recently discovered small non‐coding RNAs consisting of 24‐35 nucleotides, usually including a characteristic 5‐terminal uridine and an adenosine at position 10. PIWI proteins can specifically bind to the unique structure of the 3′ end of piRNAs. In the past, it was thought that piRNAs existed only in the reproductive system, but recently, it was reported that piRNAs are also expressed in several other human tissues with tissue specificity. Growing evidence shows that piRNAs and PIWI proteins are abnormally expressed in various diseases, including cancers, neurodegenerative diseases and ageing, and may be potential biomarkers and therapeutic targets. This review aims to discuss the current research status regarding piRNA biogenetic processes, functions, mechanisms and emerging roles in various diseases.
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Affiliation(s)
- Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Tao Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Xiang-Qian Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Xin-Zhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu-Yu Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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24
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Computational Methods and Online Resources for Identification of piRNA-Related Molecules. Interdiscip Sci 2021; 13:176-191. [PMID: 33886096 DOI: 10.1007/s12539-021-00428-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
piRNAs are a class of small non-coding RNA molecules, which interact with the PIWI family and have many important and diverse biological functions. The present review is aimed to provide guidelines and contribute to piRNA research. We focused on the four types of identification models on piRNA-related molecules, including piRNA, piRNA cluster, piRNA target, and disease-related piRNA. We evaluated the types of tools for the identification of piRNAs based on five aspects: datasets, features, classifiers, performance, and usability. We found the precision of 2lpiRNApred was the highest in datasets of model organisms, piRNN had a better performance of datasets of non-model organisms, and 2L-piRNA had the fastest recognition speed of all tools. In addition, we presented an overview of piRNA databases. The databases were divided into six categories: basic annotation, comprehensive annotation, isoform, cluster, target, and disease. We found that piRNA data of non-model organisms, piRNA target data, and piRNA-disease-associated data should be strengthened. Our review might assist researchers in selecting appropriate tools or datasets for their studies, reveal potential problems and shed light on future bioinformatics studies.
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25
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López-Jiménez E, Andrés-León E. The Implications of ncRNAs in the Development of Human Diseases. Noncoding RNA 2021; 7:17. [PMID: 33668203 PMCID: PMC8006041 DOI: 10.3390/ncrna7010017] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
The mammalian genome comprehends a small minority of genes that encode for proteins (barely 2% of the total genome in humans) and an immense majority of genes that are transcribed into RNA but not encoded for proteins (ncRNAs). These non-coding genes are intimately related to the expression regulation of protein-coding genes. The ncRNAs subtypes differ in their size, so there are long non-coding genes (lncRNAs) and other smaller ones, like microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs). Due to their important role in the maintenance of cellular functioning, any deregulation of the expression profiles of these ncRNAs can dissemble in the development of different types of diseases. Among them, we can highlight some of high incidence in the population, such as cancer, neurodegenerative, or cardiovascular disorders. In addition, thanks to the enormous advances in the field of medical genomics, these same ncRNAs are starting to be used as possible drugs, approved by the FDA, as an effective treatment for diseases.
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Affiliation(s)
- Elena López-Jiménez
- Centre for Haematology, Immunology and Inflammation Department, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Eduardo Andrés-León
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, 18016 Granada, Spain
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Ramat A, Simonelig M. Functions of PIWI Proteins in Gene Regulation: New Arrows Added to the piRNA Quiver. Trends Genet 2021; 37:188-200. [DOI: 10.1016/j.tig.2020.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022]
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Ning L, Cui T, Zheng B, Wang N, Luo J, Yang B, Du M, Cheng J, Dou Y, Wang D. MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. Nucleic Acids Res 2021; 49:D160-D164. [PMID: 32833025 PMCID: PMC7779040 DOI: 10.1093/nar/gkaa707] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Many studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA-disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA-disease resources has become essential. Here, we have updated the mammal ncRNA-disease repository (MNDR, http://www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA-disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA-disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA-disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.
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Affiliation(s)
- Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Boyang Zheng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Nuo Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Beilei Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Mengze Du
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, B24 Yinquan South Road, Qingyuan 511518, Guangdong Province, People's Republic of China
| | - Jun Cheng
- Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital)
| | - Yiying Dou
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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Abstract
Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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Wei H, Ding Y, Liu B. iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples. Comput Biol Chem 2020; 88:107361. [PMID: 32916452 DOI: 10.1016/j.compbiolchem.2020.107361] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/31/2020] [Accepted: 08/15/2020] [Indexed: 12/31/2022]
Abstract
As a large group of small non-coding RNAs (ncRNAs), Piwi-interacting RNAs (piRNAs) have been detected to be associated with various diseases. Identifying disease associated piRNAs can provide promising candidate molecular targets to promote the drug design. Although, a few computational ensemble methods have been developed for identifying piRNA-disease associations, the low-quality negative associations even with positive associations used during the training process prevent the predictive performance improvement. In this study, we proposed a new computational predictor named iPiDA-sHN to predict potential piRNA-disease associations. iPiDA-sHN presented the piRNA-disease pairs by incorporating piRNA sequence information, the known piRNA-disease association network, and the disease semantic graph. High-level features of piRNA-disease associations were extracted by the Convolutional Neural Network (CNN). Two-step positive-unlabeled learning strategy based on Support Vector Machine (SVM) was employed to select the high quality negative samples from the unknown piRNA-disease pairs. Finally, the SVM predictor trained with the known piRNA-disease associations and the high quality negative associations was used to predict new piRNA-disease associations. The experimental results showed that iPiDA-sHN achieved superior predictive ability compared with other state-of-the-art predictors.
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Affiliation(s)
- Hang Wei
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.
| | - Yuxin Ding
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.
| | - Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China; School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China.
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30
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Lin Y, Zheng J, Lin D. PIWI-interacting RNAs in human cancer. Semin Cancer Biol 2020; 75:15-28. [PMID: 32877760 DOI: 10.1016/j.semcancer.2020.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/16/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022]
Abstract
P-element-induced wimpy testis (PIWI) interacting RNAs (piRNAs) are a class of small regulatory RNAs mechanistically similar to but much less studied than microRNAs and small interfering RNAs. Today the best understood function of piRNAs is transposon control in animal germ cells, which has earned them the name 'guardians of the germline'. Several molecular/cellular characteristics of piRNAs, including high sequence diversity, lack of secondary structures, and target-oriented generation seem to serve this purpose. Recently, aberrant expressions of piRNAs and PIWI proteins have been implicated in a variety of malignant tumors and associated with cancer hallmarks such as cell proliferation, inhibited apoptosis, invasion, metastasis and increased stemness. Researchers have also demonstrated multiple mechanisms of piRNA-mediated target deregulation associated with cancer initiation, progression or dissemination. We review current research findings on the biogenesis, normal functions and cancer associations of piRNAs, highlighting their potentials as cancer diagnostic/prognostic biomarkers and therapeutic tools. Whenever applicable, we draw connections with other research fields to encourage intercommunity conversations. We also offer recommendations and cautions regarding the general process of cancer-related piRNA studies and the methods/tools used at each step. Finally, we call attention to some issues that, if left unsolved, might impede the future development of this field.
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Affiliation(s)
- Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China; Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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31
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Mentis AFA, Dardiotis E, Romas NA, Papavassiliou AG. PIWI family proteins as prognostic markers in cancer: a systematic review and meta-analysis. Cell Mol Life Sci 2020; 77:2289-2314. [PMID: 31814070 PMCID: PMC11104808 DOI: 10.1007/s00018-019-03403-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND P-element-induced-wimpy-testis-(PIWI)-like proteins are implicated in germ cells' regulation and detected in numerous cancer types. In this meta-analysis, we aimed to associate, for the first time, the prognosis in cancer patients with intratumoral expression of PIWI family proteins. METHODS PubMed, Embase, and Web of Knowledge databases were searched, and studies investigating the association between intratumoral mRNA or protein expression of different PIWI family proteins and survival, metastasis, or recurrence of various cancer types were reviewed. Study qualities were assessed using the REMARK criteria. Studies' heterogeneity was evaluated using I2 index and Cochran Q test. Publication bias was assessed by funnel plots and Egger's regression. Pooled hazard ratios (HR) with 95% confidence intervals (95% CIs) were calculated for different PIWI family proteins separately. Specifically, log of calculated HR was pooled using random-effects model. RESULTS Twenty-six studies (4299 participants) were included. The pooled HR of mortality in high versus low expression of PIWIL1, PIWIL2, and PIWIL4 was 1.87 (95% CI: 1.31-2.66, p < 0.05), 1.09 (95% CI: 0.58-2.07, p = 0.79), and 0.44 (95% CI: 0.25-0.76, p < 0.05), respectively. The pooled HR of recurrence in high versus low expression of PIWIL1 and PIWIL2 was 1.72 (95% CI: 1.20-2.49, p < 0.05) and 1.98 (95% CI: 0.65-5.98, p = 0.23), respectively. CONCLUSIONS Highly variable results were observed for different cancer types. Higher PIWIL1 and lower piwil4 and PIWIL4 expression levels could potentially indicate worse prognosis in cancer. These proteins' expressions could be used for personalized prognosis and treatment in the future.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Public Health Laboratories, Hellenic Pasteur Institute, Athens, Greece
- Department of Microbiology, University Hospital of Thessaly, Larissa, Greece
| | | | - Nicholas A Romas
- Department of Urology, Columbia University Medical Center, Vagelos College of Physicians and Surgeons, New York, USA
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street - Bldg. 16, 11527, Athens, Greece.
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Wei H, Xu Y, Liu B. iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning. Brief Bioinform 2020; 22:5829704. [PMID: 32393982 DOI: 10.1093/bib/bbaa058] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/15/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Accumulated researches have revealed that Piwi-interacting RNAs (piRNAs) are regulating the development of germ and stem cells, and they are closely associated with the progression of many diseases. As the number of the detected piRNAs is increasing rapidly, it is important to computationally identify new piRNA-disease associations with low cost and provide candidate piRNA targets for disease treatment. However, it is a challenging problem to learn effective association patterns from the positive piRNA-disease associations and the large amount of unknown piRNA-disease pairs. In this study, we proposed a computational predictor called iPiDi-PUL to identify the piRNA-disease associations. iPiDi-PUL extracted the features of piRNA-disease associations from three biological data sources, including piRNA sequence information, disease semantic terms and the available piRNA-disease association network. Principal component analysis (PCA) was then performed on these features to extract the key features. The training datasets were constructed based on known positive associations and the negative associations selected from the unknown pairs. Various random forest classifiers trained with these different training sets were merged to give the predictive results via an ensemble learning approach. Finally, the web server of iPiDi-PUL was established at http://bliulab.net/iPiDi-PUL to help the researchers to explore the associated diseases for newly discovered piRNAs.
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Sundar IK, Li D, Rahman I. Small RNA-sequence analysis of plasma-derived extracellular vesicle miRNAs in smokers and patients with chronic obstructive pulmonary disease as circulating biomarkers. J Extracell Vesicles 2019; 8:1684816. [PMID: 31762962 PMCID: PMC6848892 DOI: 10.1080/20013078.2019.1684816] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 09/24/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) play a vital role in normal lung physiology to maintain homeostasis in the airways via intercellular communication. EVs include exosomes and microvesicles, and are characterized by their phospholipid bilayers. EVs have been recognized as novel circulating biomarkers of disease, which are released by different cell types. In this study, we used different EV isolation and purification methods to characterize the plasma-derived EV miRNAs from non-smokers, smokers and patients with COPD. A small RNA sequencing (RNA-seq) approach was adapted to identify novel circulating EV miRNAs. We found that plasma-derived EVs from non-smokers, smokers and patients with COPD vary in their size, concentration, distribution and phenotypic characteristics as confirmed by nanoparticle tracking analysis, transmission electron microscopy, and immunoblot analysis of EV surface markers. RNA-seq analysis confirmed the most abundant types of small RNAs, such as miRNAs, tRNAs, piRNAs snRNAs, snoRNAs and other biotypes in plasma-derived EVs. We mainly focused on miRNAs as novel biomarkers in smokers and patients with COPD for further analysis. Differential expression by DESeq2 identified distinct miRNA profiles (up-regulated: miR-22-3p, miR-99a-5p, miR-151a-5p, miR-320b, miR-320d; and down-regulated: miR-335-5p, miR-628-3p, miR-887-5p and miR-937-3p) in COPD versus smokers or non-smokers in a pairwise comparison. Gene set enrichment analysis (GSEA) of differentially expressed miRNAs revealed the top pathways, gene ontology and diseases associated with smokers and patients with COPD. We selectively validated miRNAs in EVs isolated from BEAS-2B cells treated with cigarette smoke extract by quantitative PCR analysis. For the first time, we report that plasma-derived EV miRNAs are novel circulating pulmonary disease biomarkers. Thus, molecular profiling of EV miRNAs has great translational potential for the development of biomarkers that may be used in the diagnosis, prognosis, and therapeutics of COPD.
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Affiliation(s)
- Isaac Kirubakaran Sundar
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
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