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Zhang Y, Wang Z, Wei H, Chen M. Exploring potential circRNA biomarkers for cancers based on double-line heterogeneous graph representation learning. BMC Med Inform Decis Mak 2024; 24:159. [PMID: 38844961 PMCID: PMC11157868 DOI: 10.1186/s12911-024-02564-6] [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: 02/10/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Compared with the time-consuming and labor-intensive for biological validation in vitro or in vivo, the computational models can provide high-quality and purposeful candidates in an instant. Existing computational models face limitations in effectively utilizing sparse local structural information for accurate predictions in circRNA-disease associations. This study addresses this challenge with a proposed method, CDA-DGRL (Prediction of CircRNA-Disease Association based on Double-line Graph Representation Learning), which employs a deep learning framework leveraging graph networks and a dual-line representation model integrating graph node features. METHOD CDA-DGRL comprises several key steps: initially, the integration of diverse biological information to compute integrated similarities among circRNAs and diseases, leading to the construction of a heterogeneous network specific to circRNA-disease associations. Subsequently, circRNA and disease node features are derived using sparse autoencoders. Thirdly, a graph convolutional neural network is employed to capture the local graph network structure by inputting the circRNA-disease heterogeneous network alongside node features. Fourthly, the utilization of node2vec facilitates depth-first sampling of the circRNA-disease heterogeneous network to grasp the global graph network structure, addressing issues associated with sparse raw data. Finally, the fusion of local and global graph network structures is inputted into an extra trees classifier to identify potential circRNA-disease associations. RESULTS The results, obtained through a rigorous five-fold cross-validation on the circR2Disease dataset, demonstrate the superiority of CDA-DGRL with an AUC value of 0.9866 and an AUPR value of 0.9897 compared to existing state-of-the-art models. Notably, the hyper-random tree classifier employed in this model outperforms other machine learning classifiers. CONCLUSION Thus, CDA-DGRL stands as a promising methodology for reliably identifying circRNA-disease associations, offering potential avenues to alleviate the necessity for extensive traditional biological experiments. The source code and data for this study are available at https://github.com/zywait/CDA-DGRL .
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Affiliation(s)
- Yi Zhang
- School of Computer 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
| | - ZhenMei Wang
- School of Big Data, Guangxi Vocational and Technical College, Nanning, 530003, China.
| | - Hanyan Wei
- Pharmacy School, Guilin Medical University, Guilin, 541004, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, 421010, China
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2
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Yang X, Sun J, Jin B, Lu Y, Cheng J, Jiang J, Zhao Q, Shuai J. Multi-task aquatic toxicity prediction model based on multi-level features fusion. J Adv Res 2024:S2090-1232(24)00226-1. [PMID: 38844122 DOI: 10.1016/j.jare.2024.06.002] [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: 02/18/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024] Open
Abstract
INTRODUCTION With the escalating menace of organic compounds in environmental pollution imperiling the survival of aquatic organisms, the investigation of organic compound toxicity across diverse aquatic species assumes paramount significance for environmental protection. Understanding how different species respond to these compounds helps assess the potential ecological impact of pollution on aquatic ecosystems as a whole. Compared with traditional experimental methods, deep learning methods have higher accuracy in predicting aquatic toxicity, faster data processing speed and better generalization ability. OBJECTIVES This article presents ATFPGT-multi, an advanced multi-task deep neural network prediction model for organic toxicity. METHODS The model integrates molecular fingerprints and molecule graphs to characterize molecules, enabling the simultaneous prediction of acute toxicity for the same organic compound across four distinct fish species. Furthermore, to validate the advantages of multi-task learning, we independently construct prediction models, named ATFPGT-single, for each fish species. We employ cross-validation in our experiments to assess the performance and generalization ability of ATFPGT-multi. RESULTS The experimental results indicate, first, that ATFPGT-multi outperforms ATFPGT-single on four fish datasets with AUC improvements of 9.8%, 4%, 4.8%, and 8.2%, respectively, demonstrating the superiority of multi-task learning over single-task learning. Furthermore, in comparison with previous algorithms, ATFPGT-multi outperforms comparative methods, emphasizing that our approach exhibits higher accuracy and reliability in predicting aquatic toxicity. Moreover, ATFPGT-multi utilizes attention scores to identify molecular fragments associated with fish toxicity in organic molecules, as demonstrated by two organic molecule examples in the main text, demonstrating the interpretability of ATFPGT-multi. CONCLUSION In summary, ATFPGT-multi provides important support and reference for the further development of aquatic toxicity assessment. All of codes and datasets are freely available online at https://github.com/zhaoqi106/ATFPGT-multi.
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Affiliation(s)
- Xin Yang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi 276000, China
| | - Bingyu Jin
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Yuer Lu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Jinyan Cheng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Jiaju Jiang
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China.
| | - Jianwei Shuai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China; Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou 325001, China.
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Wu J, Lu P, Zhang W. Predicting associations between CircRNA and diseases through structure-aware graph transformer and path-integral convolution. Anal Biochem 2024; 692:115554. [PMID: 38710353 DOI: 10.1016/j.ab.2024.115554] [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: 03/03/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]
Abstract
A series of biological experiments has demonstrated that circular RNAs play a crucial regulatory role in cellular processes and may be potentially associated with diseases. Uncovering these connections helps in understanding potential disease mechanisms and advancing the development of treatment strategies. However, in biology, traditional experiments face limitations in terms of efficiency and cost, especially when enumerating possible associations. To address these limitations, several computational methods have been proposed, but existing methods only measure from a nodal perspective and cannot capture structural similarities between edges. In this study, we introduce an advanced computational method called SATPIC2CD for analyzing potential associations between circular RNAs and diseases. Specifically, we first employ an Structure-Aware Graph Transformer (SAT), which extracts five predefined metapath representations before calculating attention. This adaptive network integrates structural information into the original self-attention by aggregating information within and between paths. Subsequently, we use Path Integral Convolutional Networks (PACN) to integrate feature information for all path weights between two nodes. Afterward, we complement the network node features with feature loss and feature smoothing using Gated Recurrent Units (GRU) and node centrality. Finally, a Multi-Layer Perceptron (MLP) is employed to obtain the ultimate prediction scores for each circular RNA-disease pair. SATPIC2CD performs remarkably well, with an accuracy of up to 0.9715 measured by the Area Under the Curve (AUC) in a 5-fold cross-validation, surpassing other comparative models. Case studies further emphasize the high precision of our method in identifying circular RNA-disease associations, laying a solid foundation for guiding future biological research efforts.
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Affiliation(s)
- Jinkai Wu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
| | - PengLi Lu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China.
| | - Wenqi Zhang
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
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Wu H, Li H, Zhang Q, Song J, Chen Y, Wang ZM, Jiang W. CircBCL2L13 attenuates cardiomyocyte oxidative stress and apoptosis in cardiac ischemia‒reperfusion injury via miR-1246/PEG3 signaling. J Biochem Mol Toxicol 2024; 38:e23711. [PMID: 38605443 DOI: 10.1002/jbt.23711] [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: 11/05/2023] [Revised: 02/16/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Abstract
Ischemia‒reperfusion (I/R) is a common complication in the clinical treatment of acute myocardial infarction (MI), in which cardiomyocytes play a pivotal role in the recovery of cardiac function after reperfusion injury. The expression of numerous circular ribonucleic acids (circRNAs) is disrupted in I/R-induced cardiac damage, but the potential role of circRNAs in I/R damage has not been fully elucidated. The purpose of the present study was to clarify the biological action and molecular mechanism of circRNA 002166 (also termed circCL2L13) in postmyocardial I/R. Oxygen-glucose deprivation/reoxygenation (OGD/R) in an in vivo model was performed to simulate I/R damage. real-time polymerase chain reaction analysis was also conducted to evaluate the relationships of the SOD1, SOD2, NRF2, HO1 and GPX4 indicators with oxidative stress injury. TUNEL immunofluorescence was used to evaluate the degree of cardiomyocyte apoptosis in the different treatment groups. The circBCL2L13 level was markedly upregulated in myocardial tissues from a mouse I/R model. Overexpression of circBCL2L13 markedly attenuated the expression of oxidative stress-related genes and apoptosis in OGD/R-induced cardiomyocytes. A mechanistic study revealed that circBCL2L13 functions as a ceRNA for miR-1246 and modulates paternally expressed gene 3 (PEG3). Eventually, circBCL2L13 was proven to regulate PEG3 by targeting miR-1246, thereby protecting against OGD/R-induced cardiomyocyte oxidative damage and apoptosis. In conclusion, our study confirmed that the circBCL2L13/miR-1246/PEG3 axis suppressed the progression of OGD/R injury in cardiomyocytes, which might lead to new therapeutic strategies for cardiac I/R injury.
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Affiliation(s)
- Hua Wu
- Department of Radiology, First People's Hospital of Jingdezhen, Jingdezhen, Jiangxi, China
| | - Hairui Li
- Cardiology Division, Department of Medicine, The University of Hong Kong Shen Zhen Hospital, Shenzhen, Guangdong, China
| | - Qian Zhang
- Cardiology Division, Department of Medicine, The University of Hong Kong Shen Zhen Hospital, Shenzhen, Guangdong, China
| | - Jia Song
- Department of Medicine (Section of Cardiovascular Research), Baylor College of Medicine, Houston, Texas, USA
| | - Yongbin Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ze-Mu Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weipeng Jiang
- Department of Cardiology, South China Hospital of Shenzhen University, Shenzhen, Guangdong, China
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Yang J, Lei X, Zhang F. Identification of circRNA-disease associations via multi-model fusion and ensemble learning. J Cell Mol Med 2024; 28:e18180. [PMID: 38506066 PMCID: PMC10951890 DOI: 10.1111/jcmm.18180] [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: 12/18/2023] [Revised: 01/21/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024] Open
Abstract
Circular RNA (circRNA) is a common non-coding RNA and plays an important role in the diagnosis and therapy of human diseases, circRNA-disease associations prediction based on computational methods can provide a new way for better clinical diagnosis. In this article, we proposed a novel method for circRNA-disease associations prediction based on ensemble learning, named ELCDA. First, the association heterogeneous network was constructed via collecting multiple information of circRNAs and diseases, and multiple similarity measures are adopted here, then, we use metapath, matrix factorization and GraphSAGE-based models to extract features of nodes from different views, the final comprehensive features of circRNAs and diseases via ensemble learning, finally, a soft voting ensemble strategy is used to integrate the predicted results of all classifier. The performance of ELCDA is evaluated by fivefold cross-validation and compare with other state-of-the-art methods, the experimental results show that ELCDA is outperformance than others. Furthermore, three common diseases are used as case studies, which also demonstrate that ELCDA is an effective method for predicting circRNA-disease associations.
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Affiliation(s)
- Jing Yang
- School of Computer ScienceShaanxi Normal UniversityXi'anShaanxiChina
| | - Xiujuan Lei
- School of Computer ScienceShaanxi Normal UniversityXi'anShaanxiChina
| | - Fa Zhang
- School of Medical TechnologyBeijing Institute of TechnologyBeijingChina
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Liu X, Chu X, Li L, Man S, Wang L, Bian Y, Zhou H. Differential expression of circular RNAs in human umbilical cord mesenchymal stem cells treated with icariin. Medicine (Baltimore) 2024; 103:e37549. [PMID: 38517991 PMCID: PMC10956971 DOI: 10.1097/md.0000000000037549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/19/2024] [Indexed: 03/24/2024] Open
Abstract
Human umbilical cord mesenchymal stem cells (hUMSCs) belong to a multipotent stem cell population. Transplantation of icariin (ICA)-treated hUMSCs have better tissue repairing function in chronic liver injury. This study was to investigate whether the tissue-repairing effects and migration of hUMSCs after ICA treatment were regulated by circular RNAs (circRNAs). ICA was used to treat hUMSCs in vitro for 1 week and the expression profiles of circRNAs were generated using RNA sequencing. Differentially expressed circRNAs in hUMSCs after ICA intervention were screened. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were carried out to predict the potential function of dysregulated circRNAs. There were 52 differentially expressed circRNAs (32 circRNAs up-regulated and 20 circRNAs down-regulated) with fold change ≥2.0 before and after ICA treatment. ADP-ribosylation factors were associated with the dysregulated circRNAs among Gene Ontology analysis. Kyoto Encyclopedia of Genes and Genomes analysis showed that only endocytosis pathway was associated with up-regulated circRNAs, whereas 4 pathways including homologous recombination, RNA transport, axon guidance, and proteoglycans in cancer were related to down-regulated circRNAs. Fifty-two differentially expressed circRNAs and 238 predicted microRNAs were included in circRNAs-microRNAs network. The mechanism of ICA inducing hUMSCs migration may be through regulating circRNAs expression which affects ADP-ribosylation factors protein signal pathways.
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Affiliation(s)
- Xiaokun Liu
- Department of Pharmacy, Tianjin Second People’s Hospital, Tianjin, China
| | - Xiaoqian Chu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lingling Li
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shanshan Man
- Department of Pharmacy, Tianjin Second People’s Hospital, Tianjin, China
| | - Li Wang
- Department of Pharmacy, Tianjin Second People’s Hospital, Tianjin, China
| | - Yuhong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huifang Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Chen Z, Zhang L, Li J, Fu M. MLFLHMDA: predicting human microbe-disease association based on multi-view latent feature learning. Front Microbiol 2024; 15:1353278. [PMID: 38371933 PMCID: PMC10869561 DOI: 10.3389/fmicb.2024.1353278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Introduction A growing body of research indicates that microorganisms play a crucial role in human health. Imbalances in microbial communities are closely linked to human diseases, and identifying potential relationships between microbes and diseases can help elucidate the pathogenesis of diseases. However, traditional methods based on biological or clinical experiments are costly, so the use of computational models to predict potential microbe-disease associations is of great importance. Methods In this paper, we present a novel computational model called MLFLHMDA, which is based on a Multi-View Latent Feature Learning approach to predict Human potential Microbe-Disease Associations. Specifically, we compute Gaussian interaction profile kernel similarity between diseases and microbes based on the known microbe-disease associations from the Human Microbe-Disease Association Database and perform a preprocessing step on the resulting microbe-disease association matrix, namely, weighting K nearest known neighbors (WKNKN) to reduce the sparsity of the microbe-disease association matrix. To obtain unobserved associations in the microbe and disease views, we extract different latent features based on the geometrical structure of microbes and diseases, and project multi-modal latent features into a common subspace. Next, we introduce graph regularization to preserve the local manifold structure of Gaussian interaction profile kernel similarity and add L p , q -norms to the projection matrix to ensure the interpretability and sparsity of the model. Results The AUC values for global leave-one-out cross-validation and 5-fold cross validation implemented by MLFLHMDA are 0.9165 and 0.8942+/-0.0041, respectively, which perform better than other existing methods. In addition, case studies of different diseases have demonstrated the superiority of the predictive power of MLFLHMDA. The source code of our model and the data are available on https://github.com/LiangzheZhang/MLFLHMDA_master.
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Zhao RJ, Zhang WY, Fan XX. Circular RNAs: Potential biomarkers and therapeutic targets for autoimmune diseases. Heliyon 2024; 10:e23694. [PMID: 38205329 PMCID: PMC10776946 DOI: 10.1016/j.heliyon.2023.e23694] [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: 07/25/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
The outcomes and prognosis of autoimmune diseases depend on early diagnosis and effective treatments. However, symptoms of early autoimmune diseases are often remarkably similar to many inflammatory diseases, leading to difficulty in precise diagnosis. Circular RNAs (circRNAs) belong to a novel class of endogenous RNAs, functioning as microRNA (miRNA) sponges or participating in protein coding. It has been shown in many studies that patients with autoimmune diseases have aberrant circRNA expression in liquid biopsy samples (such as plasma, saliva, and urine). Thus, circRNAs are potential biomarkers for the diagnosis and prognosis of autoimmune diseases. Moreover, overexpression and depletion of target circRNAs can be utilized as possible therapeutic approaches for treating autoimmune diseases. In this review, we summarized recent progress in the roles of circRNAs in the pathogenesis of autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, and type 1 diabetes. We also discussed their potential as biomarkers and therapeutic targets.
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Affiliation(s)
| | | | - Xing-Xing Fan
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau(SAR), China
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Wang M, Chen L, Li J, You Y, Qian Z, Liu J, Jiang Y, Zhou T, Gu Y, Zhang Y. An omics review and perspective of researches on intrahepatic cholestasis of pregnancy. Front Endocrinol (Lausanne) 2024; 14:1267195. [PMID: 38260124 PMCID: PMC10801044 DOI: 10.3389/fendo.2023.1267195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Intrahepatic cholestasis of pregnancy (ICP) is one of the common pregnancy complications that may threaten the health of both pregnant women and their fetuses. Hence, it is of vital importance to identify key moleculars and the associated functional pathways of ICP, which will help us to better understand the pathological mechanisms as well as to develop precise clinical biomarkers. The emerging and developing of multiple omics approaches enable comprehensive studies of the genome, transcriptome, proteome and metabolome of clinical samples. The present review collected and summarized the omics based studies of ICP, aiming to provide an overview of the current progress, limitations and future directions. Briefly, these studies covered a broad range of research contents by the comparing of different experimental groups including ICP patients, ICP subtypes, ICP fetuses, ICP models and other complications. Correspondingly, the studied samples contain various types of clinical samples, in vitro cultured tissues, cell lines and the samples from animal models. According to the main research objectives, we further categorized these studies into two groups: pathogenesis and diagnosis analyses. The pathogenesis studies identified tens of functional pathways that may represent the key regulatory events for the occurrence, progression, treatment and fetal effects of ICP. On the other hand, the diagnosis studies tested more than 40 potential models for the early-prediction, diagnosis, grading, prognosis or differential diagnosis of ICP. Apart from these achievements, we also evaluated the limitations of current studies, and emphasized that many aspects of clinical characteristics, sample processing, and analytical method can greatly affect the reliability and repeatability of omics results. Finally, we also pointed out several new directions for the omics based analyses of ICP and other perinatal associated conditions in the future.
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Affiliation(s)
- Min Wang
- Center for Reproductive Medicine, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Lingyan Chen
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Jingyang Li
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Yilan You
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Zhiwen Qian
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Jiayu Liu
- Wuxi Maternity and Child Health Care Hospital, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Ying Jiang
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Tao Zhou
- Wuxi Maternity and Child Health Care Hospital, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Ying Gu
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
- Wuxi Maternity and Child Health Care Hospital, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yan Zhang
- Department of Gynaecology and Obstetrics, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
- Wuxi Maternity and Child Health Care Hospital, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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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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Wang J, Zhang L, Sun J, Yang X, Wu W, Chen W, Zhao Q. Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints. Methods 2024; 221:18-26. [PMID: 38040204 DOI: 10.1016/j.ymeth.2023.11.014] [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: 10/21/2023] [Revised: 11/14/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023] Open
Abstract
Drug-induced liver injury (DILI) is a significant issue in drug development and clinical treatment due to its potential to cause liver dysfunction or damage, which, in severe cases, can lead to liver failure or even fatality. DILI has numerous pathogenic factors, many of which remain incompletely understood. Consequently, it is imperative to devise methodologies and tools for anticipatory assessment of DILI risk in the initial phases of drug development. In this study, we present DMFPGA, a novel deep learning predictive model designed to predict DILI. To provide a comprehensive description of molecular properties, we employ a multi-head graph attention mechanism to extract features from the molecular graphs, representing characteristics at the level of compound nodes. Additionally, we combine multiple fingerprints of molecules to capture features at the molecular level of compounds. The fusion of molecular fingerprints and graph features can more fully express the properties of compounds. Subsequently, we employ a fully connected neural network to classify compounds as either DILI-positive or DILI-negative. To rigorously evaluate DMFPGA's performance, we conduct a 5-fold cross-validation experiment. The obtained results demonstrate the superiority of our method over four existing state-of-the-art computational approaches, exhibiting an average AUC of 0.935 and an average ACC of 0.934. We believe that DMFPGA is helpful for early-stage DILI prediction and assessment in drug development.
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Affiliation(s)
- Jifeng Wang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi 276000, China
| | - Xin Yang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Wei Wu
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China.
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Zhao Y, Yin J, Zhang L, Zhang Y, Chen X. Drug-drug interaction prediction: databases, web servers and computational models. Brief Bioinform 2023; 25:bbad445. [PMID: 38113076 PMCID: PMC10782925 DOI: 10.1093/bib/bbad445] [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: 07/21/2023] [Revised: 10/26/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
In clinical treatment, two or more drugs (i.e. drug combination) are simultaneously or successively used for therapy with the purpose of primarily enhancing the therapeutic efficacy or reducing drug side effects. However, inappropriate drug combination may not only fail to improve efficacy, but even lead to adverse reactions. Therefore, according to the basic principle of improving the efficacy and/or reducing adverse reactions, we should study drug-drug interactions (DDIs) comprehensively and thoroughly so as to reasonably use drug combination. In this review, we first introduced the basic conception and classification of DDIs. Further, some important publicly available databases and web servers about experimentally verified or predicted DDIs were briefly described. As an effective auxiliary tool, computational models for predicting DDIs can not only save the cost of biological experiments, but also provide relevant guidance for combination therapy to some extent. Therefore, we summarized three types of prediction models (including traditional machine learning-based models, deep learning-based models and score function-based models) proposed during recent years and discussed the advantages as well as limitations of them. Besides, we pointed out the problems that need to be solved in the future research of DDIs prediction and provided corresponding suggestions.
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Affiliation(s)
- Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Yong Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Xing Chen
- School of Science, Jiangnan University, Wuxi 214122, China
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13
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Hu H, Zhao H, Zhong T, Dong X, Wang L, Han P, Li Z. Adaptive deep propagation graph neural network for predicting miRNA-disease associations. Brief Funct Genomics 2023; 22:453-462. [PMID: 37078739 DOI: 10.1093/bfgp/elad010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/13/2023] [Accepted: 03/09/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND A large number of experiments show that the abnormal expression of miRNA is closely related to the occurrence, diagnosis and treatment of diseases. Identifying associations between miRNAs and diseases is important for clinical applications of complex human diseases. However, traditional biological experimental methods and calculation-based methods have many limitations, which lead to the development of more efficient and accurate deep learning methods for predicting miRNA-disease associations. RESULTS In this paper, we propose a novel model on the basis of adaptive deep propagation graph neural network to predict miRNA-disease associations (ADPMDA). We first construct the miRNA-disease heterogeneous graph based on known miRNA-disease pairs, miRNA integrated similarity information, miRNA sequence information and disease similarity information. Then, we project the features of miRNAs and diseases into a low-dimensional space. After that, attention mechanism is utilized to aggregate the local features of central nodes. In particular, an adaptive deep propagation graph neural network is employed to learn the embedding of nodes, which can adaptively adjust the local and global information of nodes. Finally, the multi-layer perceptron is leveraged to score miRNA-disease pairs. CONCLUSION Experiments on human microRNA disease database v3.0 dataset show that ADPMDA achieves the mean AUC value of 94.75% under 5-fold cross-validation. We further conduct case studies on the esophageal neoplasm, lung neoplasms and lymphoma to confirm the effectiveness of our proposed model, and 49, 49, 47 of the top 50 predicted miRNAs associated with these diseases are confirmed, respectively. These results demonstrate the effectiveness and superiority of our model in predicting miRNA-disease associations.
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Affiliation(s)
- Hua Hu
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277122, China
| | - Huan Zhao
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221008, China
| | - Tangbo Zhong
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221008, China
| | - Xishang Dong
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277122, China
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277122, China
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning 541006, China
| | - Pengyong Han
- Central Lab, Changzhi Medical College, Changzhi 046012, China
| | - Zhengwei Li
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277122, China
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning 541006, China
- KUNPAND Communications (Kunshan) Co., Ltd., Suzhou 215300, China
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14
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Lu Q, Li J, Zhao Y, Zhang J, Shi M, Yu S, Liang Y, Fan H, Meng X. Identification of potentially functional circRNAs and prediction of the circRNA-miRNA-hub gene network in mice with primary blast lung injury. BMC Pulm Med 2023; 23:410. [PMID: 37891516 PMCID: PMC10612283 DOI: 10.1186/s12890-023-02717-9] [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: 04/18/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
OBJECTIVES Primary blast lung injury (PBLI) is the main cause of death in blast injury patients, and is often ignored due to the absence of a specific diagnosis. Circular RNAs (circRNAs) are becoming recognized as new regulators of various diseases, but the role of circRNAs in PBLI remain largely unknown. This study aimed to investigate PBLI-related circRNAs and their probable roles as new regulators in PBLI in order to provide new ideas for PBLI diagnosis and treatment. METHODS The differentially expressed (DE) circRNA and mRNA profiles were screened by transcriptome high-throughput sequencing and validated by quantitative real-time PCR (qRT-PCR). The GO and KEGG pathway enrichment was used to investigate the potential function of DE mRNAs. The interactions between proteins were analyzed using the STRING database and hub genes were identified using the MCODE plugin. Then, Cytoscape software was used to illustrate the circRNA-miRNA-hub gene network. RESULTS A total of 117 circRNAs and 681 mRNAs were aberrantly expressed in PBLI, including 64 up-regulated and 53 down-regulated circRNAs, and 315 up-regulated and 366 down-regulated mRNAs. GO and KEGG analysis revealed that the DE mRNAs might be involved in the TNF signaling pathway and Fanconi anemia pathway. Hub genes, including Cenpf, Ndc80, Cdk1, Aurkb, Ttk, Aspm, Ccnb1, Kif11, Bub1 and Top2a, were obtained using the MCODE plugin. The network consist of 6 circRNAs (chr18:21008725-21020999 + , chr4:44893533-44895989 + , chr4:56899026-56910247-, chr5:123709382-123719528-, chr9:108528589-108544977 + and chr15:93452117-93465245 +), 7 miRNAs (mmu-miR-3058-5p, mmu-miR-3063-5p, mmu-miR-668-5p, mmu-miR-7038-3p, mmu-miR-761, mmu-miR-7673-5p and mmu-miR-9-5p) and 6 mRNAs (Aspm, Aurkb, Bub1, Cdk1, Cenpf and Top2a). CONCLUSIONS This study examined a circRNA-miRNA-hub gene regulatory network associated with PBLI and explored the potential functions of circRNAs in the network for the first time. Six circRNAs in the circRNA-miRNA-hub gene regulatory network, including chr18:21008725-21020999 + , chr4:44893533-44895989 + , chr4:56899026-56910247-, chr5:123709382-123719528-, chr9:108528589-108544977 + and chr15:93452117-93465245 + may play an essential role in PBLI.
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Affiliation(s)
- Qianying Lu
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Junfeng Li
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yanmei Zhao
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jianfeng Zhang
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Mingyu Shi
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Sifan Yu
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yangfan Liang
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Haojun Fan
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute, Tianjin University, Wenzhou, 325000, China
| | - Xiangyan Meng
- Institute of Disaster and Emergency Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
- Tianjin Key Laboratory of Disaster Medicine Technology, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
- Wenzhou Safety (Emergency) Institute, Tianjin University, Wenzhou, 325000, China.
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15
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Chen Z, Zhang L, Sun J, Meng R, Yin S, Zhao Q. DCAMCP: A deep learning model based on capsule network and attention mechanism for molecular carcinogenicity prediction. J Cell Mol Med 2023; 27:3117-3126. [PMID: 37525507 PMCID: PMC10568665 DOI: 10.1111/jcmm.17889] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
The carcinogenicity of drugs can have a serious impact on human health, so carcinogenicity testing of new compounds is very necessary before being put on the market. Currently, many methods have been used to predict the carcinogenicity of compounds. However, most methods have limited predictive power and there is still much room for improvement. In this study, we construct a deep learning model based on capsule network and attention mechanism named DCAMCP to discriminate between carcinogenic and non-carcinogenic compounds. We train the DCAMCP on a dataset containing 1564 different compounds through their molecular fingerprints and molecular graph features. The trained model is validated by fivefold cross-validation and external validation. DCAMCP achieves an average accuracy (ACC) of 0.718 ± 0.009, sensitivity (SE) of 0.721 ± 0.006, specificity (SP) of 0.715 ± 0.014 and area under the receiver-operating characteristic curve (AUC) of 0.793 ± 0.012. Meanwhile, comparable results can be achieved on an external validation dataset containing 100 compounds, with an ACC of 0.750, SE of 0.778, SP of 0.727 and AUC of 0.811, which demonstrate the reliability of DCAMCP. The results indicate that our model has made progress in cancer risk assessment and could be used as an efficient tool in drug design.
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Affiliation(s)
- Zhe Chen
- School of Mathematics and StatisticsLiaoning UniversityShenyangChina
| | - Li Zhang
- School of Life ScienceLiaoning UniversityShenyangChina
| | - Jianqiang Sun
- School of Information Science and EngineeringLinyi UniversityLinyiChina
| | - Rui Meng
- School of Computer Science and Software EngineeringUniversity of Science and Technology LiaoningAnshanChina
| | - Shuaidong Yin
- School of Computer Science and Software EngineeringUniversity of Science and Technology LiaoningAnshanChina
| | - Qi Zhao
- School of Computer Science and Software EngineeringUniversity of Science and Technology LiaoningAnshanChina
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16
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Meng R, Yin S, Sun J, Hu H, Zhao Q. scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention. Comput Biol Med 2023; 165:107414. [PMID: 37660567 DOI: 10.1016/j.compbiomed.2023.107414] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating cellular heterogeneity and structure. However, analyzing scRNA-seq data remains challenging, especially in the context of COVID-19 research. Single-cell clustering is a key step in analyzing scRNA-seq data, and deep learning methods have shown great potential in this area. In this work, we propose a novel scRNA-seq analysis framework called scAAGA. Specifically, we utilize an asymmetric autoencoder with a gene attention module to learn important gene features adaptively from scRNA-seq data, with the aim of improving the clustering effect. We apply scAAGA to COVID-19 peripheral blood mononuclear cell (PBMC) scRNA-seq data and compare its performance with state-of-the-art methods. Our results consistently demonstrate that scAAGA outperforms existing methods in terms of adjusted rand index (ARI), normalized mutual information (NMI), and adjusted mutual information (AMI) scores, achieving improvements ranging from 2.8% to 27.8% in NMI scores. Additionally, we discuss a data augmentation technology to expand the datasets and improve the accuracy of scAAGA. Overall, scAAGA presents a robust tool for scRNA-seq data analysis, enhancing the accuracy and reliability of clustering results in COVID-19 research.
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Affiliation(s)
- Rui Meng
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Shuaidong Yin
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi, 276000, China
| | - Huan Hu
- Institute of Applied Genomics, Fuzhou University, Fuzhou, 350108, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China.
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17
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Wu J, Ning Z, Ding Y, Wang Y, Peng Q, Fu L. KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations. Brief Bioinform 2023; 24:bbad292. [PMID: 37587836 DOI: 10.1093/bib/bbad292] [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: 03/31/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023] Open
Abstract
Recent studies have demonstrated the significant role that circRNA plays in the progression of human diseases. Identifying circRNA-disease associations (CDA) in an efficient manner can offer crucial insights into disease diagnosis. While traditional biological experiments can be time-consuming and labor-intensive, computational methods have emerged as a viable alternative in recent years. However, these methods are often limited by data sparsity and their inability to explore high-order information. In this paper, we introduce a novel method named Knowledge Graph Encoder from Transformer for predicting CDA (KGETCDA). Specifically, KGETCDA first integrates more than 10 databases to construct a large heterogeneous non-coding RNA dataset, which contains multiple relationships between circRNA, miRNA, lncRNA and disease. Then, a biological knowledge graph is created based on this dataset and Transformer-based knowledge representation learning and attentive propagation layers are applied to obtain high-quality embeddings with accurately captured high-order interaction information. Finally, multilayer perceptron is utilized to predict the matching scores of CDA based on their embeddings. Our empirical results demonstrate that KGETCDA significantly outperforms other state-of-the-art models. To enhance user experience, we have developed an interactive web-based platform named HNRBase that allows users to visualize, download data and make predictions using KGETCDA with ease. The code and datasets are publicly available at https://github.com/jinyangwu/KGETCDA.
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Affiliation(s)
- Jinyang Wu
- School of Automation Science and Engineering, Xi'an Jiaotong University, 710049, Shaanxi, China
| | - Zhiwei Ning
- School of Automation Science and Engineering, Xi'an Jiaotong University, 710049, Shaanxi, China
| | - Yidong Ding
- School of Automation Science and Engineering, Xi'an Jiaotong University, 710049, Shaanxi, China
| | - Ying Wang
- School of Automation Science and Engineering, Xi'an Jiaotong University, 710049, Shaanxi, China
| | - Qinke Peng
- School of Automation Science and Engineering, Xi'an Jiaotong University, 710049, Shaanxi, China
| | - Laiyi Fu
- School of Automation Science and Engineering, Xi'an Jiaotong University, 710049, Shaanxi, China
- Research Institute of Xi'an Jiaotong University, 311200, Zhejiang, China
- Sichuan Digital Economy Industry Development Research Institute, 610036, Sichuan, China
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18
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Gao H, Sun J, Wang Y, Lu Y, Liu L, Zhao Q, Shuai J. Predicting metabolite-disease associations based on auto-encoder and non-negative matrix factorization. Brief Bioinform 2023; 24:bbad259. [PMID: 37466194 DOI: 10.1093/bib/bbad259] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/18/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
Metabolism refers to a series of orderly chemical reactions used to maintain life activities in organisms. In healthy individuals, metabolism remains within a normal range. However, specific diseases can lead to abnormalities in the levels of certain metabolites, causing them to either increase or decrease. Detecting these deviations in metabolite levels can aid in diagnosing a disease. Traditional biological experiments often rely on a lot of manpower to do repeated experiments, which is time consuming and labor intensive. To address this issue, we develop a deep learning model based on the auto-encoder and non-negative matrix factorization named as MDA-AENMF to predict the potential associations between metabolites and diseases. We integrate a variety of similarity networks and then acquire the characteristics of both metabolites and diseases through three specific modules. First, we get the disease characteristics from the five-layer auto-encoder module. Later, in the non-negative matrix factorization module, we extract both the metabolite and disease characteristics. Furthermore, the graph attention auto-encoder module helps us obtain metabolite characteristics. After obtaining the features from three modules, these characteristics are merged into a single, comprehensive feature vector for each metabolite-disease pair. Finally, we send the corresponding feature vector and label to the multi-layer perceptron for training. The experiment demonstrates our area under the receiver operating characteristic curve of 0.975 and area under the precision-recall curve of 0.973 in 5-fold cross-validation, which are superior to those of existing state-of-the-art predictive methods. Through case studies, most of the new associations obtained by MDA-AENMF have been verified, further highlighting the reliability of MDA-AENMF in predicting the potential relationships between metabolites and diseases.
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Affiliation(s)
- Hongyan Gao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianqiang Sun
- School of Automation and Electrical Engineering, Linyi University, Linyi, 276000, China
| | - Yukun Wang
- School of Electronic and Information Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Yuer Lu
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, 325001, China
| | - Liyu Liu
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, 325001, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, 325001, China
| | - Jianwei Shuai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, 325001, China
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19
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Wu Q, Deng Z, Zhang W, Pan X, Choi KS, Zuo Y, Shen HB, Yu DJ. MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. Bioinformatics 2023; 39:btad499. [PMID: 37561093 PMCID: PMC10457666 DOI: 10.1093/bioinformatics/btad499] [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: 05/17/2023] [Revised: 06/17/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023] Open
Abstract
MOTIVATION CircRNAs play a critical regulatory role in physiological processes, and the abnormal expression of circRNAs can mediate the processes of diseases. Therefore, exploring circRNAs-disease associations is gradually becoming an important area of research. Due to the high cost of validating circRNA-disease associations using traditional wet-lab experiments, novel computational methods based on machine learning are gaining more and more attention in this field. However, current computational methods suffer to insufficient consideration of latent features in circRNA-disease interactions. RESULTS In this study, a multilayer attention neural graph-based collaborative filtering (MLNGCF) is proposed. MLNGCF first enhances multiple biological information with autoencoder as the initial features of circRNAs and diseases. Then, by constructing a central network of different diseases and circRNAs, a multilayer cooperative attention-based message propagation is performed on the central network to obtain the high-order features of circRNAs and diseases. A neural network-based collaborative filtering is constructed to predict the unknown circRNA-disease associations and update the model parameters. Experiments on the benchmark datasets demonstrate that MLNGCF outperforms state-of-the-art methods, and the prediction results are supported by the literature in the case studies. AVAILABILITY AND IMPLEMENTATION The source codes and benchmark datasets of MLNGCF are available at https://github.com/ABard0/MLNGCF.
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Affiliation(s)
- Qunzhuo Wu
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Zhaohong Deng
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Wei Zhang
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
| | - Kup-Sze Choi
- The Centre for Smart Health, The Hong Kong Polytechnic University, Hong Kong
| | - Yun Zuo
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
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20
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Bao X, Sun J, Yi M, Qiu J, Chen X, Shuai SC, Zhao Q. MPFFPSDC: A multi-pooling feature fusion model for predicting synergistic drug combinations. Methods 2023:S1046-2023(23)00098-1. [PMID: 37321525 DOI: 10.1016/j.ymeth.2023.06.006] [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: 05/16/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023] Open
Abstract
Drug combination therapies are common practice in the treatment of cancer, but not all combinations result in synergy. As traditional screening approaches are restricted in their ability to uncover synergistic drug combinations, computer-aided medicine is becoming a increasingly prevalent in this field. In this work, a predictive model of potential interactions between drugs named MPFFPSDC is presented, which can maintain the symmetry of drug inputs and eliminate inconsistencies in predictive results caused by different drug inputting sequences or positions. The experimental results show that MPFFPSDC outperforms comparative models in major performance indicators and exhibits better generalization for independent data. Furthermore, the case study demonstrates that our model can capture molecular substructures that contribute to the synergistic effect of two drugs. These results indicate that MPFFPSDC not only offers strong predictive performance, but also has good model interpretability that may provide new insights for the study of drug interaction mechanisms and the development of new drugs.
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Affiliation(s)
- Xin Bao
- School of Automation and Electrical Engineering, Linyi University, Linyi 276000, China
| | - Jianqiang Sun
- School of Automation and Electrical Engineering, Linyi University, Linyi 276000, China.
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430000, China
| | - Jianlong Qiu
- School of Automation and Electrical Engineering, Linyi University, Linyi 276000, China
| | - Xiangyong Chen
- School of Automation and Electrical Engineering, Linyi University, Linyi 276000, China
| | - Stella C Shuai
- Biological Science, Northwestern University, Evanston, IL 60208, USA
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China.
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21
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Ying A, Zhao Y, Hu X. Identification of biomarkers related to prostatic hyperplasia based on bioinformatics and machine learning. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:12024-12038. [PMID: 37501430 DOI: 10.3934/mbe.2023534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In older adults, benign prostatic hyperplasia (BPH) is the most common cause of lower urinary tract symptoms (LUTS). This study aimed to explore the genes with diagnostic value in patients with BPH, reveal the relationship between the expression of diagnosis-related genes and the immune microenvironment, and provide a reference for molecular diagnosis and immunotherapy of BPH. The combined gene expression data of GSE6099, GSE7307 and GSE119195 in the GEO database were used. The differential expression of autophagy-related genes between BPH patients and healthy controls was obtained by differential analysis. Then the genes related to BPH diagnosis were screened by a machine learning algorithm and verified. Finally, five important genes (IGF1, PSIP1, SLC1A3, SLC2A1 and T1A1) were obtained by random forest (RF) algorithm, and their relationships with the immune microenvironment were discussed. Five genes play an essential role in the occurrence and development of BPH and may become new diagnostic markers of BPH. Among them, immune cells have significant correlation with some genes. The signal transduction of IL-4 mediated by M2 macrophages is closely related to the progress of BPH. There are abundant active mast cells in BPH. The adoption and metastasis of regulatory T cells may be an important method to treat BPH.
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Affiliation(s)
- Aiying Ying
- Department of Urology, Yongkang first people's Hospital, Yongkang, China
| | - Yueguang Zhao
- Department of Urology, Yongkang first people's Hospital, Yongkang, China
| | - Xiang Hu
- Department of Urology, Yongkang first people's Hospital, Yongkang, China
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22
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Cao J, Pan C, Zhang J, Chen Q, Li T, He D, Cheng X. Analysis and verification of the circRNA regulatory network RNO_CIRCpedia_ 4214/RNO-miR-667-5p/Msr1 axis as a potential ceRNA promoting macrophage M2-like polarization in spinal cord injury. BMC Genomics 2023; 24:181. [PMID: 37020267 PMCID: PMC10077679 DOI: 10.1186/s12864-023-09273-w] [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: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND CircRNAs are involved in the pathogenesis of several central nervous system diseases. However, their functions and mechanisms in spinal cord injury (SCI) are still unclear. Therefore, the purpose of this study was to evaluate circRNA and mRNA expression profiles in the pathological setting of SCI and to predict the potential function of circRNA through bioinformatics. METHODS A microarray-based approach was used for the simultaneous measurement of circRNAs and mRNAs, together with qPCR, fluorescence in situ hybridization, western immunoblotting, and dual-luciferase reporter assays to investigate the associated regulatory mechanisms in a rat SCI model. RESULTS SCI was found to be associated with the differential expression of 414 and 5337 circRNAs and mRNAs, respectively. Pathway enrichment analyses were used to predict the primary function of these circRNAs and mRNAs. GSEA analysis showed that differentially expressed mRNAs were primarily associated with inflammatory immune response activity. Further screening of these inflammation-associated genes was used to construct and analyze a competing endogenous RNA network. RNO_CIRCpedia_4214 was knocked down in vitro, resulting in reduced expression of Msr1, while the expression of RNO-miR-667-5p and Arg1 was increased. Dual-luciferase assays demonstrated that RNO_CIRCpedia_4214 bound to RNO-miR-667-5p. The RNO_CIRCpedia_4214/RNO-miR-667-5p/Msr1 axis may be a potential ceRNA that promotes macrophage M2-like polarization in SCI. CONCLUSION Overall, these results highlighted the critical role that circRNAs may play in the pathophysiology of SCI and the discovery of a potential ceRNA mechanism based on novel circRNAs that regulates macrophage polarization, providing new targets for the treatment of SCI.
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Affiliation(s)
- Jian Cao
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Chongzhi Pan
- Institute of Orthopedics of Jiangxi Province, Nanchang, Jiangxi, 330006, China
| | - Jian Zhang
- Institute of Minimally Invasive Orthopedics, Nanchang University, Jiangxi, 330006, China
| | - Qi Chen
- Jiangxi Key Laboratory of Intervertebral Disc Disease, Nanchang University, Jiangxi, 330006, China
| | - Tao Li
- Institute of Orthopedics of Jiangxi Province, Nanchang, Jiangxi, 330006, China
| | - Dingwen He
- Institute of Minimally Invasive Orthopedics, Nanchang University, Jiangxi, 330006, China
| | - Xigao Cheng
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China.
- Institute of Orthopedics of Jiangxi Province, Nanchang, Jiangxi, 330006, China.
- Institute of Minimally Invasive Orthopedics, Nanchang University, Jiangxi, 330006, China.
- Jiangxi Key Laboratory of Intervertebral Disc Disease, Nanchang University, Jiangxi, 330006, China.
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, East Laker District, Nanchang, Jiangxi, China.
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Zhang GZ, Gao YL. BRWMC: Predicting lncRNA-disease associations based on bi-random walk and matrix completion on disease and lncRNA networks. Comput Biol Chem 2023; 103:107833. [PMID: 36812824 DOI: 10.1016/j.compbiolchem.2023.107833] [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: 08/21/2022] [Revised: 12/29/2022] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Many experiments have proved that long non-coding RNAs (lncRNAs) in humans have been implicated in disease development. The prediction of lncRNA-disease association is essential in promoting disease treatment and drug development. It is time-consuming and laborious to explore the relationship between lncRNA and diseases in the laboratory. The computation-based approach has clear advantages and has become a promising research direction. This paper proposes a new lncRNA disease association prediction algorithm BRWMC. Firstly, BRWMC constructed several lncRNA (disease) similarity networks based on different measurement angles and fused them into an integrated similarity network by similarity network fusion (SNF). In addition, the random walk method is used to preprocess the known lncRNA-disease association matrix and calculate the estimated scores of potential lncRNA-disease associations. Finally, the matrix completion method accurately predicts the potential lncRNA-disease associations. Under the framework of leave-one-out cross-validation and 5-fold cross-validation, the AUC values obtained by BRWMC are 0.9610 and 0.9739, respectively. In addition, case studies of three common diseases show that BRWMC is a reliable method for prediction.
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Affiliation(s)
- Guo-Zheng Zhang
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Ying-Lian Gao
- Qufu Normal University Library, Qufu Normal University, Rizhao, China.
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24
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Su Q, Hua F, Xiao W, Liu B, Wang D, Qin X. Investigation of Hippo pathway-related prognostic lncRNAs and molecular subtypes in liver hepatocellular carcinoma. Sci Rep 2023; 13:4521. [PMID: 36941336 PMCID: PMC10027880 DOI: 10.1038/s41598-023-31754-x] [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: 11/17/2022] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
This study aimed to investigate Hippo pathway-related prognostic long noncoding RNAs (lncRNAs) and their prognostic value in liver hepatocellular carcinoma (LIHC). Expression and clinical data regarding LIHC were acquired from The Cancer Genome Atlas and European Bioinformatics Institute array databases. Hippo pathway-related lncRNAs and their prognostic value were revealed, followed by molecular subtype investigations. Differences in survival, clinical characteristics, immune cell infiltration, and checkpoint expression between the subtypes were explored. LASSO regression was used to determine the most valuable prognostic lncRNAs, followed by the establishment of a prognostic model. Survival and differential expression analyses were conducted between two groups (high- and low-risk). A total of 313 Hippo pathway-related lncRNAs were identified from LIHC, of which 88 were associated with prognosis, and two molecular subtypes were identified based on their expression patterns. These two subtypes showed significant differences in overall survival, pathological stage and grade, vascular invasion, infiltration abundance of seven immune cells, and expression of several checkpoints, such as CTLA-4 and PD-1/L1 (P < 0.05). LASSO regression identified the six most valuable independent prognostic lncRNAs for establishing a prognosis risk model. Risk scores calculated by the risk model assigned patients into two risk groups with an AUC of 0.913 and 0.731, respectively, indicating that the high-risk group had poor survival. The risk score had an independent prognostic value with an HR of 2.198. In total, 3007 genes were dysregulated between the two risk groups, and the expression of most genes was elevated in the high-risk group, involving the cell cycle and pathways in cancers. Hippo pathway-related lncRNAs could stratify patients for personalized treatment and predict the prognosis of patients with LIHC.
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Affiliation(s)
- Qiongfei Su
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China
| | - Fengyang Hua
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China
| | - Wanying Xiao
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China
| | - Baoqiu Liu
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China
| | - Dongxia Wang
- Department of Radiation Oncology, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, China.
| | - Xintian Qin
- Department of Oncology, The First Affiliated Hospital of Guangdong, Pharmaceutical University, Guangzhou, China.
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25
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Hu F, Peng Y, Fan X, Zhang X, Jin Z. Circular RNAs: implications of signaling pathways and bioinformatics in human cancer. Cancer Biol Med 2023; 20:j.issn.2095-3941.2022.0466. [PMID: 36861443 PMCID: PMC9978890 DOI: 10.20892/j.issn.2095-3941.2022.0466] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Circular RNAs (circRNAs) form a class of endogenous single-stranded RNA transcripts that are widely expressed in eukaryotic cells. These RNAs mediate post-transcriptional control of gene expression and have multiple functions in biological processes, such as transcriptional regulation and splicing. They serve predominantly as microRNA sponges, RNA-binding proteins, and templates for translation. More importantly, circRNAs are involved in cancer progression, and may serve as promising biomarkers for tumor diagnosis and therapy. Although traditional experimental methods are usually time-consuming and laborious, substantial progress has been made in exploring potential circRNA-disease associations by using computational models, summarized signaling pathway data, and other databases. Here, we review the biological characteristics and functions of circRNAs, including their roles in cancer. Specifically, we focus on the signaling pathways associated with carcinogenesis, and the status of circRNA-associated bioinformatics databases. Finally, we explore the potential roles of circRNAs as prognostic biomarkers in cancer.
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Affiliation(s)
- Fan Hu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Yin Peng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Xinmin Fan
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Xiaojing Zhang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
- Correspondence to: Zhe Jin and Xiaojing Zhang, E-mail: and
| | - Zhe Jin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
- Correspondence to: Zhe Jin and Xiaojing Zhang, E-mail: and
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26
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Zhu Y, Zhang F, Zhang S, Yi M. Predicting latent lncRNA and cancer metastatic event associations via variational graph auto-encoder. Methods 2023; 211:1-9. [PMID: 36709790 DOI: 10.1016/j.ymeth.2023.01.006] [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: 10/20/2022] [Revised: 12/05/2022] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Long non-coding RNA (lncRNA) are shown to be closely associated with cancer metastatic events (CME, e.g., cancer cell invasion, intravasation, extravasation, proliferation) that collaboratively accelerate malignant cancer spread and cause high mortality rate in patients. Clinical trials may accurately uncover the relationships between lncRNAs and CMEs; however, it is time-consuming and expensive. With the accumulation of data, there is an urgent need to find efficient ways to identify these relationships. Herein, a graph embedding representation-based predictor (VGEA-LCME) for exploring latent lncRNA-CME associations is introduced. In VGEA-LCME, a heterogeneous combined network is constructed by integrating similarity and linkage matrix that can maintain internal and external characteristics of networks, and a variational graph auto-encoder serves as a feature generator to represent arbitrary lncRNA and CME pair. The final robustness predicted result is obtained by ensemble classifier strategy via cross-validation. Experimental comparisons and literature verification show better remarkable performance of VGEA-LCME, although the similarities between CMEs are challenging to calculate. In addition, VGEA-LCME can further identify organ-specific CMEs. To the best of our knowledge, this is the first computational attempt to discover the potential relationships between lncRNAs and CMEs. It may provide support and new insight for guiding experimental research of metastatic cancers. The source code and data are available at https://github.com/zhuyuan-cug/VGAE-LCME.
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Affiliation(s)
- Yuan Zhu
- School of Automation, China University of Geosciences, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China; Hubei Key Laboratory of Advanced Control and Intelligent Automation for Complex Systems, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China; Engineering Research Center of Intelligent Technology for Geo-Exploration, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China
| | - Feng Zhang
- School of Mathematics and Physics, China University of Geosciences, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China
| | - Shihua Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, 974 Heping Avenue, Qingshan District, 430081, Wuhan, Hubei, China.
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China.
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27
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Wang H, Han J, Li H, Duan L, Liu Z, Cheng H. CDA-SKAG: Predicting circRNA-disease associations using similarity kernel fusion and an attention-enhancing graph autoencoder. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:7957-7980. [PMID: 37161181 DOI: 10.3934/mbe.2023345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Circular RNAs (circRNAs) constitute a category of circular non-coding RNA molecules whose abnormal expression is closely associated with the development of diseases. As biological data become abundant, a lot of computational prediction models have been used for circRNA-disease association prediction. However, existing prediction models ignore the non-linear information of circRNAs and diseases when fusing multi-source similarities. In addition, these models fail to take full advantage of the vital feature information of high-similarity neighbor nodes when extracting features of circRNAs or diseases. In this paper, we propose a deep learning model, CDA-SKAG, which introduces a similarity kernel fusion algorithm to integrate multi-source similarity matrices to capture the non-linear information of circRNAs or diseases, and construct a circRNA information space and a disease information space. The model embeds an attention-enhancing layer in the graph autoencoder to enhance the associations between nodes with higher similarity. A cost-sensitive neural network is introduced to address the problem of positive and negative sample imbalance, consequently improving our model's generalization capability. The experimental results show that the prediction performance of our model CDA-SKAG outperformed existing circRNA-disease association prediction models. The results of the case studies on lung and cervical cancer suggest that CDA-SKAG can be utilized as an effective tool to assist in predicting circRNA-disease associations.
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Affiliation(s)
- Huiqing Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
| | - Jiale Han
- College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
| | - Haolin Li
- College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
| | - Liguo Duan
- College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
| | - Zhihao Liu
- College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
| | - Hao Cheng
- College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
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28
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Gong J, Du C, Sun N, Xiao X, Wu H. CircADSS contributes to hepatocellular carcinoma development by regulating miR-431-5p/TOP2A. Clin Exp Pharmacol Physiol 2023; 50:415-424. [PMID: 36786410 DOI: 10.1111/1440-1681.13761] [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: 08/05/2022] [Revised: 01/09/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
CircRNAs participated in regulating hepatocellular carcinoma (HCC), and the regulation function of circRNA adenylosuccinate synthase (circADSS) on HCC development is not clear. RT-qPCR and western blot were performed to detect RNA expression. Cell proliferation was analysed by CCK-8 and EdU assay. Cell cycle distribution was analysed by flow cytometry assay. Cell migration and invasion were measured by transwell assay. Mechanism assays were employed to examine the interaction between miR-431-5p and circADSS, or TOP2A. Xenograft mouse model was constructed for in vivo assay. CircADSS and TOP2A expression were boosted, while miR-431-5p was limited in tumour tissues and cells. CircADSS silencing decreased HCC cell proliferation, cell cycle progression, migration, invasion, as well as EMT. MiR-431-5p inhibitors or ectopic TOP2A expression could restore the effect of circADSS knockdown on HCC progression. There was target relationship between miR-431-5p and circADSS, or TOP2A. Knockdown of circADSS suppressed tumour growth in vivo. CircADSS could regulate HCC cell malignancy by miR-431-5p/TOP2A axis.
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Affiliation(s)
- Jianzhuang Gong
- Department of Digestive Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Chenxu Du
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Nai Sun
- Department of Anesthesiology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xingguo Xiao
- Department of Digestive Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Huili Wu
- Department of Digestive Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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29
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Myocardial Infarction-Induced INSL6 Decrease Contributes to Breast Cancer Progression. DISEASE MARKERS 2023; 2023:8702914. [PMID: 36798786 PMCID: PMC9928516 DOI: 10.1155/2023/8702914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 11/25/2022] [Indexed: 02/10/2023]
Abstract
Myocardial infarction (MI) induces early-stage breast cancer progression and increases breast cancer patients' mortality and morbidity. Insulin-like peptide 6 (INSL6) overexpression can impede cardiotoxin-induced injury through myofiber regeneration, playing a significant role in MI progression. To investigate the diverse significance of INSL6 in a variety of malignant tumors, we explored INSL6 through MI GEO dataset and multiple omics data integrative analysis, such as gene expression level, enriched pathway analysis, protein-protein interaction (PPI) analysis, and immune subtypes as well as diagnostic value and prognostic value in pancancer. INSL6 expression was downregulated in the MI group, and overall survival analysis demonstrated that INSL6 could be the prognostic biomarkers in the overall survival of breast cancer (BRCA). INSL6 expression differs significantly not only in most cancers but also in different molecular and immune subtypes of cancers. INSL6 might be a potential diagnostic and prognostic biomarker of cancers due to the high accuracy in diagnostic and prognostic value. Furthermore, we focused on BRCA and further investigated INSL6 from the perspective of the correlations with clinical characteristics, prognosis in different clinical subgroups, coexpression genes, and differentially expressed genes (DEGs) and PPI analysis. Overall survival and disease-specific survival analysis of subgroups in BRCA demonstrated that lower INSL6 expression had a worse prognosis. Therefore, INSL6 aberrant expression is associated with the progression and immune cell infiltration of the tumor, especially in KIRP and BRCA. Therefore, INSL6 may serve as a potential prognostic biomarker and the crosstalk between MI and tumor progression.
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30
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Zhu Y, He J, Li Z, Yang W. Cuproptosis-related lncRNA signature for prognostic prediction in patients with acute myeloid leukemia. BMC Bioinformatics 2023; 24:37. [PMID: 36737692 PMCID: PMC9896718 DOI: 10.1186/s12859-023-05148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been reported to have a crucial impact on the pathogenesis of acute myeloid leukemia (AML). Cuproptosis, a copper-triggered modality of mitochondrial cell death, might serve as a promising therapeutic target for cancer treatment and clinical outcome prediction. Nevertheless, the role of cuproptosis-related lncRNAs in AML is not fully understood. METHODS The RNA sequencing data and demographic characteristics of AML patients were downloaded from The Cancer Genome Atlas database. Pearson correlation analysis, the least absolute shrinkage and selection operator algorithm, and univariable and multivariable Cox regression analyses were applied to identify the cuproptosis-related lncRNA signature and determine its feasibility for AML prognosis prediction. The performance of the proposed signature was evaluated via Kaplan-Meier survival analysis, receiver operating characteristic curves, and principal component analysis. Functional analysis was implemented to uncover the potential prognostic mechanisms. Additionally, quantitative real-time PCR (qRT-PCR) was employed to validate the expression of the prognostic lncRNAs in AML samples. RESULTS A signature consisting of seven cuproptosis-related lncRNAs (namely NFE4, LINC00989, LINC02062, AC006460.2, AL353796.1, PSMB8-AS1, and AC000120.1) was proposed. Multivariable cox regression analysis revealed that the proposed signature was an independent prognostic factor for AML. Notably, the nomogram based on this signature showed excellent accuracy in predicting the 1-, 3-, and 5-year survival (area under curve = 0.846, 0.801, and 0.895, respectively). Functional analysis results suggested the existence of a significant association between the prognostic signature and immune-related pathways. The expression pattern of the lncRNAs was validated in AML samples. CONCLUSION Collectively, we constructed a prediction model based on seven cuproptosis-related lncRNAs for AML prognosis. The obtained risk score may reveal the immunotherapy response in patients with this disease.
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Affiliation(s)
- Yidong Zhu
- grid.412538.90000 0004 0527 0050Department of Traditional Chinese Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China
| | - Jun He
- grid.412538.90000 0004 0527 0050Department of Traditional Chinese Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China ,grid.412538.90000 0004 0527 0050Department of Hematology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China
| | - Zihua Li
- grid.412538.90000 0004 0527 0050Department of Traditional Chinese Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China ,grid.412538.90000 0004 0527 0050Department of Orthopedics, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, 200072 China
| | - Wenzhong Yang
- Department of Hematology, Shanghai Punan Hosptial of Pudong New District, Shanghai, 200125, China.
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31
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Wang T, Sun J, Zhao Q. Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism. Comput Biol Med 2023; 153:106464. [PMID: 36584603 DOI: 10.1016/j.compbiomed.2022.106464] [Citation(s) in RCA: 98] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Human ether-a-go-go-related gene (hERG) channel blockade by small molecules is a big concern during drug development in the pharmaceutical industry. Failure or inhibition of hERG channel activity caused by drug molecules can lead to prolonging QT interval, which will result in serious cardiotoxicity. Thus, evaluating the hERG blocking activity of all these small molecular compounds is technically challenging, and the relevant procedures are expensive and time-consuming. In this study, we develop a novel deep learning predictive model named DMFGAM for predicting hERG blockers. In order to characterize the molecule more comprehensively, we first consider the fusion of multiple molecular fingerprint features to characterize its final molecular fingerprint features. Then, we use the multi-head attention mechanism to extract the molecular graph features. Both molecular fingerprint features and molecular graph features are fused as the final features of the compounds to make the feature expression of compounds more comprehensive. Finally, the molecules are classified into hERG blockers or hERG non-blockers through the fully connected neural network. We conduct 5-fold cross-validation experiment to evaluate the performance of DMFGAM, and verify the robustness of DMFGAM on external validation datasets. We believe DMFGAM can serve as a powerful tool to predict hERG channel blockers in the early stages of drug discovery and development.
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Affiliation(s)
- Tianyi Wang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianqiang Sun
- School of Automation and Electrical 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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32
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Zhao J, Sun J, Shuai SC, Zhao Q, Shuai J. Predicting potential interactions between lncRNAs and proteins via combined graph auto-encoder methods. Brief Bioinform 2023; 24:6896030. [PMID: 36515153 DOI: 10.1093/bib/bbac527] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/23/2022] [Accepted: 11/06/2022] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNA (lncRNA) is a kind of noncoding RNA with a length of more than 200 nucleotide units. Numerous research studies have proven that although lncRNAs cannot be directly translated into proteins, lncRNAs still play an important role in human growth processes by interacting with proteins. Since traditional biological experiments often require a lot of time and material costs to explore potential lncRNA-protein interactions (LPI), several computational models have been proposed for this task. In this study, we introduce a novel deep learning method known as combined graph auto-encoders (LPICGAE) to predict potential human LPIs. First, we apply a variational graph auto-encoder to learn the low dimensional representations from the high-dimensional features of lncRNAs and proteins. Then the graph auto-encoder is used to reconstruct the adjacency matrix for inferring potential interactions between lncRNAs and proteins. Finally, we minimize the loss of the two processes alternately to gain the final predicted interaction matrix. The result in 5-fold cross-validation experiments illustrates that our method achieves an average area under receiver operating characteristic curve of 0.974 and an average accuracy of 0.985, which is better than those of existing six state-of-the-art computational methods. We believe that LPICGAE can help researchers to gain more potential relationships between lncRNAs and proteins effectively.
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Affiliation(s)
- Jingxuan Zhao
- University of Science and Technology Liaoning, 66459, Anshan, China
| | | | - Stella C Shuai
- Northwestern University, 3270, Evanston, IllinoisUnited States
| | - Qi Zhao
- University of Science and Technology Liaoning, 66459, Anshan, China
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Xiamen, China
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33
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Lan W, Dong Y, Zhang H, Li C, Chen Q, Liu J, Wang J, Chen YPP. Benchmarking of computational methods for predicting circRNA-disease associations. Brief Bioinform 2023; 24:6972300. [PMID: 36611256 DOI: 10.1093/bib/bbac613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/29/2022] [Accepted: 12/11/2022] [Indexed: 01/09/2023] Open
Abstract
Accumulating evidences demonstrate that circular RNA (circRNA) plays an important role in human diseases. Identification of circRNA-disease associations can help for the diagnosis of human diseases, while the traditional method based on biological experiments is time-consuming. In order to address the limitation, a series of computational methods have been proposed in recent years. However, few works have summarized these methods or compared the performance of them. In this paper, we divided the existing methods into three categories: information propagation, traditional machine learning and deep learning. Then, the baseline methods in each category are introduced in detail. Further, 5 different datasets are collected, and 14 representative methods of each category are selected and compared in the 5-fold, 10-fold cross-validation and the de novo experiment. In order to further evaluate the effectiveness of these methods, six common cancers are selected to compare the number of correctly identified circRNA-disease associations in the top-10, top-20, top-50, top-100 and top-200. In addition, according to the results, the observation about the robustness and the character of these methods are concluded. Finally, the future directions and challenges are discussed.
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Affiliation(s)
- Wei Lan
- School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Yi Dong
- School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Hongyu Zhang
- School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Chunling Li
- School of Computer, Electronic and Information and Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Qingfeng Chen
- School of Computer, Electronic and Information and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi 530004, China
| | - Jin Liu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, Victoria 3086, Australia
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Xie GB, Chen RB, Lin ZY, Gu GS, Yu JR, Liu ZG, Cui J, Lin LQ, Chen LC. Predicting lncRNA-disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation. Brief Bioinform 2023; 24:6966536. [PMID: 36592062 DOI: 10.1093/bib/bbac595] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 01/03/2023] Open
Abstract
Recent studies have revealed that long noncoding RNAs (lncRNAs) are closely linked to several human diseases, providing new opportunities for their use in detection and therapy. Many graph propagation and similarity fusion approaches can be used for predicting potential lncRNA-disease associations. However, existing similarity fusion approaches suffer from noise and self-similarity loss in the fusion process. To address these problems, a new prediction approach, termed SSMF-BLNP, based on organically combining selective similarity matrix fusion (SSMF) and bidirectional linear neighborhood label propagation (BLNP), is proposed in this paper to predict lncRNA-disease associations. In SSMF, self-similarity networks of lncRNAs and diseases are obtained by selective preprocessing and nonlinear iterative fusion. The fusion process assigns weights to each initial similarity network and introduces a unit matrix that can reduce noise and compensate for the loss of self-similarity. In BLNP, the initial lncRNA-disease associations are employed in both lncRNA and disease directions as label information for linear neighborhood label propagation. The propagation was then performed on the self-similarity network obtained from SSMF to derive the scoring matrix for predicting the relationships between lncRNAs and diseases. Experimental results showed that SSMF-BLNP performed better than seven other state of-the-art approaches. Furthermore, a case study demonstrated up to 100% and 80% accuracy in 10 lncRNAs associated with hepatocellular carcinoma and 10 lncRNAs associated with renal cell carcinoma, respectively. The source code and datasets used in this paper are available at: https://github.com/RuiBingo/SSMF-BLNP.
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Affiliation(s)
- Guo-Bo Xie
- School of Computer, Guangdong University of Technology, Guangzhou, 510000, China
| | - Rui-Bin Chen
- School of Computer, Guangdong University of Technology, Guangzhou, 510000, China
| | - Zhi-Yi Lin
- School of Computer, Guangdong University of Technology, Guangzhou, 510000, China
| | - Guo-Sheng Gu
- School of Computer, Guangdong University of Technology, Guangzhou, 510000, China
| | - Jun-Rui Yu
- School of Computer, Guangdong University of Technology, Guangzhou, 510000, China
| | - Zhen-Guo Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Ji Cui
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Lie-Qing Lin
- Center of Campus Network & Modern Educational Technology, Guangdong University of Technology, Guangzhou, 510000, China
| | - Lang-Cheng Chen
- Center of Campus Network & Modern Educational Technology, Guangdong University of Technology, Guangzhou, 510000, China
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35
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Wei C, Xiang X, Zhou X, Ren S, Zhou Q, Dong W, Lin H, Wang S, Zhang Y, Lin H, He Q, Lu Y, Jiang X, Shuai J, Jin X, Xie C. Development and validation of an interpretable radiomic nomogram for severe radiation proctitis prediction in postoperative cervical cancer patients. Front Microbiol 2023; 13:1090770. [PMID: 36713206 PMCID: PMC9877536 DOI: 10.3389/fmicb.2022.1090770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023] Open
Abstract
Background Radiation proctitis is a common complication after radiotherapy for cervical cancer. Unlike simple radiation damage to other organs, radiation proctitis is a complex disease closely related to the microbiota. However, analysis of the gut microbiota is time-consuming and expensive. This study aims to mine rectal information using radiomics and incorporate it into a nomogram model for cheap and fast prediction of severe radiation proctitis prediction in postoperative cervical cancer patients. Methods The severity of the patient's radiation proctitis was graded according to the RTOG/EORTC criteria. The toxicity grade of radiation proctitis over or equal to grade 2 was set as the model's target. A total of 178 patients with cervical cancer were divided into a training set (n = 124) and a validation set (n = 54). Multivariate logistic regression was used to build the radiomic and non-raidomic models. Results The radiomics model [AUC=0.6855(0.5174-0.8535)] showed better performance and more net benefit in the validation set than the non-radiomic model [AUC=0.6641(0.4904-0.8378)]. In particular, we applied SHapley Additive exPlanation (SHAP) method for the first time to a radiomics-based logistic regression model to further interpret the radiomic features from case-based and feature-based perspectives. The integrated radiomic model enables the first accurate quantitative assessment of the probability of radiation proctitis in postoperative cervical cancer patients, addressing the limitations of the current qualitative assessment of the plan through dose-volume parameters only. Conclusion We successfully developed and validated an integrated radiomic model containing rectal information. SHAP analysis of the model suggests that radiomic features have a supporting role in the quantitative assessment of the probability of radiation proctitis in postoperative cervical cancer patients.
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Affiliation(s)
- Chaoyi Wei
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Xinli Xiang
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiaobo Zhou
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Siyan Ren
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qingyu Zhou
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Wenjun Dong
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Haizhen Lin
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Saijun Wang
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yuyue Zhang
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hai Lin
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Qingzu He
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Yuer Lu
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Xiaoming Jiang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Jianwei Shuai
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Xiance Jin
- Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China,School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China,*Correspondence: Xiance Jin, ✉
| | - Congying Xie
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China,Congying Xie, ✉
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Identification of diagnostic biomarkers for idiopathic pulmonary hypertension with metabolic syndrome by bioinformatics and machine learning. Sci Rep 2023; 13:615. [PMID: 36635413 PMCID: PMC9837120 DOI: 10.1038/s41598-023-27435-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Idiopathic pulmonary hypertension (IPAH) is a condition that affects various tissues and organs and the metabolic and inflammatory systems. The most prevalent metabolic condition is metabolic syndrome (MS), which involves insulin resistance, dyslipidemia, and obesity. There may be a connection between IPAH and MS, based on a plethora of studies, although the underlying pathogenesis remains unclear. Through various bioinformatics analyses and machine learning algorithms, we identified 11 immune- and metabolism-related potential diagnostic genes (EVI5L, RNASE2, PARP10, TMEM131, TNFRSF1B, BSDC1, ACOT2, SAC3D1, SLA2, P4HB, and PHF1) for the diagnosis of IPAH and MS, and we herein supply a nomogram for the diagnosis of IPAH in MS patients. Additionally, we discovered IPAH's aberrant immune cells and discuss them here.
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Lin L, Chen R, Zhu Y, Xie W, Jing H, Chen L, Zou M. SCCPMD: Probability matrix decomposition method subject to corrected similarity constraints for inferring long non-coding RNA-disease associations. Front Microbiol 2023; 13:1093615. [PMID: 36713213 PMCID: PMC9874942 DOI: 10.3389/fmicb.2022.1093615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023] Open
Abstract
Accumulating evidence has demonstrated various associations of long non-coding RNAs (lncRNAs) with human diseases, such as abnormal expression due to microbial influences that cause disease. Gaining a deeper understanding of lncRNA-disease associations is essential for disease diagnosis, treatment, and prevention. In recent years, many matrix decomposition methods have also been used to predict potential lncRNA-disease associations. However, these methods do not consider the use of microbe-disease association information to enrich disease similarity, and also do not make more use of similarity information in the decomposition process. To address these issues, we here propose a correction-based similarity-constrained probability matrix decomposition method (SCCPMD) to predict lncRNA-disease associations. The microbe-disease associations are first used to enrich the disease semantic similarity matrix, and then the logistic function is used to correct the lncRNA and disease similarity matrix, and then these two corrected similarity matrices are added to the probability matrix decomposition as constraints to finally predict the potential lncRNA-disease associations. The experimental results show that SCCPMD outperforms the five advanced comparison algorithms. In addition, SCCPMD demonstrated excellent prediction performance in a case study for breast cancer, lung cancer, and renal cell carcinoma, with prediction accuracy reaching 80, 100, and 100%, respectively. Therefore, SCCPMD shows excellent predictive performance in identifying unknown lncRNA-disease associations.
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Affiliation(s)
- Lieqing Lin
- Center of Campus Network & Modern Educational Technology, Guangdong University of Technology, Guangzhou, China
| | - Ruibin Chen
- School of Computer, Guangdong University of Technology, Guangzhou, China
| | - Yinting Zhu
- School of Computer, Guangdong University of Technology, Guangzhou, China
| | - Weijie Xie
- School of Computer, Guangdong University of Technology, Guangzhou, China
| | - Huaiguo Jing
- Sports Department, Guangdong University of Technology, Guangzhou, China,*Correspondence: Huaiguo Jing,
| | - Langcheng Chen
- Center of Campus Network & Modern Educational Technology, Guangdong University of Technology, Guangzhou, China,Langcheng Chen,
| | - Minqing Zou
- Department of Experiment Teaching, Guangdong University of Technology, Guangzhou, China
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Yang R, Ma L, Wan J, Li Z, Yang Z, Zhao Z, Ming L. Ferroptosis-associated circular RNAs: Opportunities and challenges in the diagnosis and treatment of cancer. Front Cell Dev Biol 2023; 11:1160381. [PMID: 37152286 PMCID: PMC10157116 DOI: 10.3389/fcell.2023.1160381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Ferroptosis is an emerging form of non-apoptotic regulated cell death which is different from cell death mechanisms such as autophagy, apoptosis and necrosis. It is characterized by iron-dependent lipid peroxide accumulation. Circular RNA (circRNA) is a newly studied evolutionarily conserved type of non-coding RNA with a covalent closed-loop structure. It exhibits universality, conservatism, stability and particularity. At present, the functions that have been studied and found include microRNA sponge, protein scaffold, transcription regulation, translation and production of peptides, etc. CircRNA can be used as a biomarker of tumors and is a hotspot in RNA biology research. Studies have shown that ferroptosis can participate in tumor regulation through the circRNA molecular pathway and then affect cancer progression, which may become a direction of cancer diagnosis and treatment in the future. This paper reviews the molecular biological mechanism of ferroptosis and the role of circular RNA in tumors and summarizes the circRNA related to ferroptosis in tumors, which may inspire research prospects for the precise prevention and treatment of cancer in the future.
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Affiliation(s)
- Ruotong Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Liwei Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhuofang Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhengwu Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhuochen Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Clinical Laboratory of Henan Province, Zhengzhou, China
- *Correspondence: Liang Ming,
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lncRNA-disease association prediction based on the weight matrix and projection score. PLoS One 2023; 18:e0278817. [PMID: 36595551 PMCID: PMC9810171 DOI: 10.1371/journal.pone.0278817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 11/25/2022] [Indexed: 01/04/2023] Open
Abstract
With the development of medical science, long noncoding RNA (lncRNA), originally considered as a noise gene, has been found to participate in a variety of biological activities. Several recent studies have shown the involvement of lncRNA in various human diseases, such as gastric cancer, prostate cancer, lung cancer, and so forth. However, obtaining lncRNA-disease relationship only through biological experiments not only costs manpower and material resources but also gains little. Therefore, developing effective computational models for predicting lncRNA-disease association relationship is extremely important. This study aimed to propose an lncRNA-disease association prediction model based on the weight matrix and projection score (LDAP-WMPS). The model used the relatively perfect lncRNA-miRNA relationship data and miRNA-disease relationship data to predict the lncRNA-disease relationship. The integrated lncRNA similarity matrix and the integrated disease similarity matrix were established by fusing various methods to calculate the similarity between lncRNA and disease. This study improved the existing weight algorithm, applied it to the lncRNA-miRNA-disease triple network, and thus proposed a new lncRNA-disease weight matrix calculation method. Combined with the improved projection algorithm, the lncRNA-miRNA relationship and miRNA-disease relationship were used to predict the lncRNA-disease relationship. The simulation results showed that under the Leave-One-Out-Cross-Validation framework, the area under the receiver operating characteristic curve of LDAP-WMPS could reach 0.8822, which was better than the latest result. Taking adenocarcinoma and colorectal cancer as examples, the LDAP-WMPS model was found to effectively infer the lncRNA-disease relationship. The simulation results showed good prediction performance of the LDAP-WMPS model, which was an important supplement to the research of lncRNA-disease association prediction without lncRNA-disease relationship data.
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40
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Liao Q, Ye Y, Li Z, Chen H, Zhuo L. Prediction of miRNA-disease associations in microbes based on graph convolutional networks and autoencoders. Front Microbiol 2023; 14:1170559. [PMID: 37187536 PMCID: PMC10175670 DOI: 10.3389/fmicb.2023.1170559] [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: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 05/17/2023] Open
Abstract
MicroRNAs (miRNAs) are short RNA molecular fragments that regulate gene expression by targeting and inhibiting the expression of specific RNAs. Due to the fact that microRNAs affect many diseases in microbial ecology, it is necessary to predict microRNAs' association with diseases at the microbial level. To this end, we propose a novel model, termed as GCNA-MDA, where dual-autoencoder and graph convolutional network (GCN) are integrated to predict miRNA-disease association. The proposed method leverages autoencoders to extract robust representations of miRNAs and diseases and meantime exploits GCN to capture the topological information of miRNA-disease networks. To alleviate the impact of insufficient information for the original data, the association similarity and feature similarity data are combined to calculate a more complete initial basic vector of nodes. The experimental results on the benchmark datasets demonstrate that compared with the existing representative methods, the proposed method has achieved the superior performance and its precision reaches up to 0.8982. These results demonstrate that the proposed method can serve as a tool for exploring miRNA-disease associations in microbial environments.
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Affiliation(s)
- Qingquan Liao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Yuxiang Ye
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, China
| | - Zihang Li
- School of Computing and Data Science, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Hao Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
- *Correspondence: Hao Chen
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, China
- Linlin Zhuo
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Liu J, Dai Y, Lu Y, Liu X, Deng J, Lu W, Liu Q. Identification and validation of a new pyroptosis-associated lncRNA signature to predict survival outcomes, immunological responses and drug sensitivity in patients with gastric cancer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:1856-1881. [PMID: 36899512 DOI: 10.3934/mbe.2023085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gastric cancer (GC) ranks fifth in prevalence among carcinomas worldwide. Both pyroptosis and long noncoding RNAs (lncRNAs) play crucial roles in the occurrence and development of gastric cancer. Therefore, we aimed to construct a pyroptosis-associated lncRNA model to predict the outcomes of patients with gastric cancer. METHODS Pyroptosis-associated lncRNAs were identified through co-expression analysis. Univariate and multivariate Cox regression analyses were performed using the least absolute shrinkage and selection operator (LASSO). Prognostic values were tested through principal component analysis, a predictive nomogram, functional analysis and Kaplan‒Meier analysis. Finally, immunotherapy and drug susceptibility predictions and hub lncRNA validation were performed. RESULTS Using the risk model, GC individuals were classified into two groups: low-risk and high-risk groups. The prognostic signature could distinguish the different risk groups based on principal component analysis. The area under the curve and the conformance index suggested that this risk model was capable of correctly predicting GC patient outcomes. The predicted incidences of the one-, three-, and five-year overall survivals exhibited perfect conformance. Distinct changes in immunological markers were noted between the two risk groups. Finally, greater levels of appropriate chemotherapies were required in the high-risk group. AC005332.1, AC009812.4 and AP000695.1 levels were significantly increased in gastric tumor tissue compared with normal tissue. CONCLUSIONS We created a predictive model based on 10 pyroptosis-associated lncRNAs that could accurately predict the outcomes of GC patients and provide a promising treatment option in the future.
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Affiliation(s)
- Jinsong Liu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou 213017, China
| | - Yuyang Dai
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou 213017, China
- Department of Radiology, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, China
| | - Yueyao Lu
- Department of Oncology, The Changzhou Clinical School of Nanjing Medical University, Changzhou 213017, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou 213017, China
| | - Xiuling Liu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou 213017, China
| | - Jianzhong Deng
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou 213017, China
| | - Wenbin Lu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou 213017, China
- Department of Oncology, The Changzhou Clinical School of Nanjing Medical University, Changzhou 213017, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou 213017, China
| | - Qian Liu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou 213017, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou 213017, China
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Wang J, Zhang N, Yuan S, Shang J, Dai L, Li F, Liu J. Non-negative low-rank representation based on dictionary learning for single-cell RNA-sequencing data analysis. BMC Genomics 2022; 23:851. [PMID: 36564711 PMCID: PMC9789616 DOI: 10.1186/s12864-022-09027-0] [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: 09/14/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
In the analysis of single-cell RNA-sequencing (scRNA-seq) data, how to effectively and accurately identify cell clusters from a large number of cell mixtures is still a challenge. Low-rank representation (LRR) method has achieved excellent results in subspace clustering. But in previous studies, most LRR-based methods usually choose the original data matrix as the dictionary. In addition, the methods based on LRR usually use spectral clustering algorithm to complete cell clustering. Therefore, there is a matching problem between the spectral clustering method and the affinity matrix, which is difficult to ensure the optimal effect of clustering. Considering the above two points, we propose the DLNLRR method to better identify the cell type. First, DLNLRR can update the dictionary during the optimization process instead of using the predefined fixed dictionary, so it can realize dictionary learning and LRR learning at the same time. Second, DLNLRR can realize subspace clustering without relying on spectral clustering algorithm, that is, we can perform clustering directly based on the low-rank matrix. Finally, we carry out a large number of experiments on real single-cell datasets and experimental results show that DLNLRR is superior to other scRNA-seq data analysis algorithms in cell type identification.
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Affiliation(s)
- Juan Wang
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
| | - Nana Zhang
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
| | - Shasha Yuan
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
| | - Junliang Shang
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
| | - Lingyun Dai
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
| | - Feng Li
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
| | - Jinxing Liu
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, China
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Du XX, Liu Y, Wang B, Zhang JF. lncRNA-disease association prediction method based on the nearest neighbor matrix completion model. Sci Rep 2022; 12:21653. [PMID: 36522410 PMCID: PMC9755128 DOI: 10.1038/s41598-022-25730-0] [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: 08/20/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
State-of-the-art medical studies proved that long noncoding ribonucleic acids (lncRNAs) are closely related to various diseases. However, their large-scale detection in biological experiments is problematic and expensive. To aid screening and improve the efficiency of biological experiments, this study introduced a prediction model based on the nearest neighbor concept for lncRNA-disease association prediction. We used a new similarity algorithm in the model that fused potential associations. The experimental validation of the proposed algorithm proved its superiority over the available Cosine, Pearson, and Jaccard similarity algorithms. Satisfactory results in the comparative leave-one-out cross-validation test (with AUC = 0.96) confirmed its excellent predictive performance. Finally, the proposed model's reliability was confirmed by performing predictions using a new dataset, yielding AUC = 0.92.
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Affiliation(s)
- Xiao-xin Du
- grid.412616.60000 0001 0002 2355College of Computer and Control, Qiqihar University, Qiqihar, 161006 China
| | - Yan Liu
- grid.412616.60000 0001 0002 2355College of Computer and Control, Qiqihar University, Qiqihar, 161006 China
| | - Bo Wang
- grid.412616.60000 0001 0002 2355College of Computer and Control, Qiqihar University, Qiqihar, 161006 China
| | - Jian-fei Zhang
- grid.412616.60000 0001 0002 2355College of Computer and Control, Qiqihar University, Qiqihar, 161006 China
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Xiong L, He X, Wang L, Dai P, Zhao J, Zhou X, Tang H. Hypoxia-associated prognostic markers and competing endogenous RNA coexpression networks in lung adenocarcinoma. Sci Rep 2022; 12:21340. [PMID: 36494419 PMCID: PMC9734750 DOI: 10.1038/s41598-022-25745-7] [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: 07/31/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common form of non-small cell lung cancer (NSCLC). Hypoxia has been found in 50-60% of locally advanced solid tumors and is associated with poor prognosis in various tumors, including NSCLC. This study focused on hypoxia-associated molecular hallmarks in LUAD. Fifteen hypoxia-related genes were selected to define the hypoxia status of LUAD by ConsensusClusterPlus based on data from The Cancer Genome Atlas (TCGA). Then, we investigated the immune status under different hypoxia statuses. Subsequently, we constructed prognostic models based on hypoxia-related differentially expressed genes (DEGs), identified hypoxia-related microRNAs, lncRNAs and mRNAs, and built a network based on the competing endogenous RNA (ceRNA) theory. Two clusters (Cluster 1 and Cluster 2) were identified with different hypoxia statuses. Cluster 1 was defined as the hypoxia subgroup, in which all 15 hypoxia-associated genes were upregulated. The infiltration of CD4+ T cells and Tfh cells was lower, while the infiltration of regulatory T (Treg) cells, the expression of PD-1/PD-L1 and TMB scores were higher in Cluster 1, indicating an immunosuppressive status. Based on the DEGs, a risk signature containing 7 genes was established. Furthermore, three differentially expressed microRNAs (hsa-miR-9, hsa-miR-31, hsa-miR-196b) associated with prognosis under different hypoxia clusters and their related mRNAs and lncRNAs were identified, and a ceRNA network was built. This study showed that hypoxia was associated with poor prognosis in LUAD and explored the potential mechanism from the perspective of the gene signature and ceRNA theory.
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Affiliation(s)
- Lecai Xiong
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xueyu He
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Le Wang
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Peng Dai
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Jinping Zhao
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xuefeng Zhou
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Hexiao Tang
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
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Li P, Tiwari P, Xu J, Qian Y, Ai C, Ding Y, Guo F. Sparse regularized joint projection model for identifying associations of non-coding RNAs and human diseases. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Zhang ML, Zhao BW, Su XR, He YZ, Yang Y, Hu L. RLFDDA: a meta-path based graph representation learning model for drug-disease association prediction. BMC Bioinformatics 2022; 23:516. [PMID: 36456957 PMCID: PMC9713188 DOI: 10.1186/s12859-022-05069-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Drug repositioning is a very important task that provides critical information for exploring the potential efficacy of drugs. Yet developing computational models that can effectively predict drug-disease associations (DDAs) is still a challenging task. Previous studies suggest that the accuracy of DDA prediction can be improved by integrating different types of biological features. But how to conduct an effective integration remains a challenging problem for accurately discovering new indications for approved drugs. METHODS In this paper, we propose a novel meta-path based graph representation learning model, namely RLFDDA, to predict potential DDAs on heterogeneous biological networks. RLFDDA first calculates drug-drug similarities and disease-disease similarities as the intrinsic biological features of drugs and diseases. A heterogeneous network is then constructed by integrating DDAs, disease-protein associations and drug-protein associations. With such a network, RLFDDA adopts a meta-path random walk model to learn the latent representations of drugs and diseases, which are concatenated to construct joint representations of drug-disease associations. As the last step, we employ the random forest classifier to predict potential DDAs with their joint representations. RESULTS To demonstrate the effectiveness of RLFDDA, we have conducted a series of experiments on two benchmark datasets by following a ten-fold cross-validation scheme. The results show that RLFDDA yields the best performance in terms of AUC and F1-score when compared with several state-of-the-art DDAs prediction models. We have also conducted a case study on two common diseases, i.e., paclitaxel and lung tumors, and found that 7 out of top-10 diseases and 8 out of top-10 drugs have already been validated for paclitaxel and lung tumors respectively with literature evidence. Hence, the promising performance of RLFDDA may provide a new perspective for novel DDAs discovery over heterogeneous networks.
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Affiliation(s)
- Meng-Long Zhang
- grid.9227.e0000000119573309The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Bo-Wei Zhao
- grid.9227.e0000000119573309The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Xiao-Rui Su
- grid.9227.e0000000119573309The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Yi-Zhou He
- grid.162110.50000 0000 9291 3229School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Yue Yang
- grid.162110.50000 0000 9291 3229School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Lun Hu
- grid.9227.e0000000119573309The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
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DRGCNCDA: Predicting circRNA-disease interactions based on knowledge graph and disentangled relational graph convolutional network. Methods 2022; 208:35-41. [DOI: 10.1016/j.ymeth.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/15/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
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Fu Y, Yang R, Zhang L. Association prediction of CircRNAs and diseases using multi-homogeneous graphs and variational graph auto-encoder. Comput Biol Med 2022; 151:106289. [PMID: 36401973 DOI: 10.1016/j.compbiomed.2022.106289] [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: 08/18/2022] [Revised: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022]
Abstract
As a non-coding RNA molecule with closed-loop structure, circular RNA (circRNA) is tissue-specific and cell-specific in expression pattern. It regulates disease development by modulating the expression of disease-related genes. Therefore, exploring the circRNA-disease relationship can reveal the molecular mechanism of disease pathogenesis. Biological experiments for detecting circRNA-disease associations are time-consuming and laborious. Constrained by the sparsity of known circRNA-disease associations, existing algorithms cannot obtain relatively complete structural information to represent features accurately. To this end, this paper proposes a new predictor, VGAERF, combining Variational Graph Auto-Encoder (VGAE) and Random Forest (RF). Firstly, circRNA homogeneous graph structure and disease homogeneous graph structure are constructed by Gaussian interaction profile (GIP) kernel similarity, semantic similarity, and known circRNA-disease associations. VGAEs with the same structure are employed to extract the higher-order features by the encoding and decoding of input graph structures. To further increase the completeness of the network structure information, the deep features acquired from the two VGAEs are summed, and then train the RF with sparse data processing capability to perform the prediction task. On the independent test set, the Area Under ROC Curve (AUC), accuracy, and Area Under PR Curve (AUPR) of the proposed method reach up to 0.9803, 0.9345, and 0.9894, respectively. On the same dataset, the AUC, accuracy, and AUPR of VGAERF are 2.09%, 5.93%, and 1.86% higher than the best-performing method (AEDNN). It is anticipated that VGAERF will provide significant information to decipher the molecular mechanisms of circRNA-disease associations, and promote the diagnosis of circRNA-related diseases.
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Affiliation(s)
- Yao Fu
- The School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, China.
| | - Runtao Yang
- The School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, China.
| | - Lina Zhang
- The School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, China.
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Peng L, Yang J, Wang M, Zhou L. Editorial: Machine learning-based methods for RNA data analysis—Volume II. Front Genet 2022; 13:1010089. [DOI: 10.3389/fgene.2022.1010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
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Wang W, Zhang L, Sun J, Zhao Q, Shuai J. Predicting the potential human lncRNA-miRNA interactions based on graph convolution network with conditional random field. Brief Bioinform 2022; 23:6775599. [PMID: 36305458 DOI: 10.1093/bib/bbac463] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/10/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) and microRNA (miRNA) are two typical types of non-coding RNAs (ncRNAs), their interaction plays an important regulatory role in many biological processes. Exploring the interactions between unknown lncRNA and miRNA can help us better understand the functional expression between lncRNA and miRNA. At present, the interactions between lncRNA and miRNA are mainly obtained through biological experiments, but such experiments are often time-consuming and labor-intensive, it is necessary to design a computational method that can predict the interactions between lncRNA and miRNA. In this paper, we propose a method based on graph convolutional neural (GCN) network and conditional random field (CRF) for predicting human lncRNA-miRNA interactions, named GCNCRF. First, we construct a heterogeneous network using the known interactions of lncRNA and miRNA in the LncRNASNP2 database, the lncRNA/miRNA integration similarity network, and the lncRNA/miRNA feature matrix. Second, the initial embedding of nodes is obtained using a GCN network. A CRF set in the GCN hidden layer can update the obtained preliminary embeddings so that similar nodes have similar embeddings. At the same time, an attention mechanism is added to the CRF layer to reassign weights to nodes to better grasp the feature information of important nodes and ignore some nodes with less influence. Finally, the final embedding is decoded and scored through the decoding layer. Through a 5-fold cross-validation experiment, GCNCRF has an area under the receiver operating characteristic curve value of 0.947 on the main dataset, which has higher prediction accuracy than the other six state-of-the-art methods.
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Affiliation(s)
- Wenya Wang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Jianqiang Sun
- School of Automation and Electrical Engineering, Linyi University, Linyi, 276000, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianwei Shuai
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), and Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China.,Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, 361005, China.,National Institute for Data Science in Health and Medicine, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, 361005, China
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