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Lian X, Zhang Y, Zhou Y, Sun X, Huang S, Dai H, Han L, Zhu F. SingPro: a knowledge base providing single-cell proteomic data. Nucleic Acids Res 2024; 52:D552-D561. [PMID: 37819028 PMCID: PMC10767818 DOI: 10.1093/nar/gkad830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/03/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
Single-cell proteomics (SCP) has emerged as a powerful tool for detecting cellular heterogeneity, offering unprecedented insights into biological mechanisms that are masked in bulk cell populations. With the rapid advancements in AI-based time trajectory analysis and cell subpopulation identification, there exists a pressing need for a database that not only provides SCP raw data but also explicitly describes experimental details and protein expression profiles. However, no such database has been available yet. In this study, a database, entitled 'SingPro', specializing in single-cell proteomics was thus developed. It was unique in (a) systematically providing the SCP raw data for both mass spectrometry-based and flow cytometry-based studies and (b) explicitly describing experimental detail for SCP study and expression profile of any studied protein. Anticipating a robust interest from the research community, this database is poised to become an invaluable repository for OMICs-based biomedical studies. Access to SingPro is unrestricted and does not mandate a login at: http://idrblab.org/singpro/.
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Affiliation(s)
- Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai 315211, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yintao Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shijie Huang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Haibin Dai
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Lianyi Han
- Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai 315211, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Zhang Y, Liu X, Li F, Yin J, Yang H, Li X, Liu X, Chai X, Niu T, Zeng S, Jia Q, Zhu F. INTEDE 2.0: the metabolic roadmap of drugs. Nucleic Acids Res 2024; 52:D1355-D1364. [PMID: 37930837 PMCID: PMC10767827 DOI: 10.1093/nar/gkad1013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023] Open
Abstract
The metabolic roadmap of drugs (MRD) is a comprehensive atlas for understanding the stepwise and sequential metabolism of certain drug in living organisms. It plays a vital role in lead optimization, personalized medication, and ADMET research. The MRD consists of three main components: (i) the sequential catalyses of drug and its metabolites by different drug-metabolizing enzymes (DMEs), (ii) a comprehensive collection of metabolic reactions along the entire MRD and (iii) a systematic description on efficacy & toxicity for all metabolites of a studied drug. However, there is no database available for describing the comprehensive metabolic roadmaps of drugs. Therefore, in this study, a major update of INTEDE was conducted, which provided the stepwise & sequential metabolic roadmaps for a total of 4701 drugs, and a total of 22 165 metabolic reactions containing 1088 DMEs and 18 882 drug metabolites. Additionally, the INTEDE 2.0 labeled the pharmacological properties (pharmacological activity or toxicity) of metabolites and provided their structural information. Furthermore, 3717 drug metabolism relationships were supplemented (from 7338 to 11 055). All in all, INTEDE 2.0 is highly expected to attract broad interests from related research community and serve as an essential supplement to existing pharmaceutical/biological/chemical databases. INTEDE 2.0 can now be accessible freely without any login requirement at: http://idrblab.org/intede/.
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Affiliation(s)
- Yang Zhang
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Xingang Liu
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- The Children's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Department of Clinical Pharmacy, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Hao Yang
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Xuedong Li
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Xinyu Liu
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Xu Chai
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Tianle Niu
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Su Zeng
- College of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Qingzhong Jia
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Feng Zhu
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
- College of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Wang Y, Pan Z, Mou M, Xia W, Zhang H, Zhang H, Liu J, Zheng L, Luo Y, Zheng H, Yu X, Lian X, Zeng Z, Li Z, Zhang B, Zheng M, Li H, Hou T, Zhu F. A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder. Nucleic Acids Res 2023; 51:e110. [PMID: 37889083 PMCID: PMC10682500 DOI: 10.1093/nar/gkad929] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/01/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.
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Affiliation(s)
- Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Jin Liu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanqi Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Mingyue Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglin Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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Wang Y, Chen Z, Pan Z, Huang S, Liu J, Xia W, Zhang H, Zheng M, Li H, Hou T, Zhu F. RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. Nucleic Acids Res 2023:7160191. [PMID: 37166951 DOI: 10.1093/nar/gkad404] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023] Open
Abstract
Ribonucleic acids (RNAs) involve in various physiological/pathological processes by interacting with proteins, compounds, and other RNAs. A variety of powerful computational methods have been developed to predict such valuable interactions. However, all these methods rely heavily on the 'digitalization' (also known as 'encoding') of RNA-associated interacting pairs into a computer-recognizable descriptor. In other words, it is urgently needed to have a powerful tool that can not only represent each interacting partner but also integrate both partners into a computer-recognizable interaction. Herein, RNAincoder (deep learning-based encoder for RNA-associated interactions) was therefore proposed to (a) provide a comprehensive collection of RNA encoding features, (b) realize the representation of any RNA-associated interaction based on a well-established deep learning-based embedding strategy and (c) enable large-scale scanning of all possible feature combinations to identify the one of optimal performance in RNA-associated interaction prediction. The effectiveness of RNAincoder was extensively validated by case studies on benchmark datasets. All in all, RNAincoder is distinguished for its capability in providing a more accurate representation of RNA-associated interactions, which makes it an indispensable complement to other available tools. RNAincoder can be accessed at https://idrblab.org/rnaincoder/.
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Affiliation(s)
- Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhen Chen
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shijie Huang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jin Liu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglin Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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Zhang H, Lu M, Lin G, Zheng L, Zhang W, Xu Z, Zhu F. SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data. Brief Bioinform 2023; 24:7081128. [PMID: 36941114 DOI: 10.1093/bib/bbad104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Doublets formed during single-cell RNA sequencing (scRNA-seq) severely affect downstream studies, such as differentially expressed gene analysis and cell trajectory inference, and limit the cellular throughput of scRNA-seq. Several doublet detection algorithms are currently available, but their generalization performance could be further improved due to the lack of effective feature-embedding strategies with suitable model architectures. Therefore, SoCube, a novel deep learning algorithm, was developed to precisely detect doublets in various types of scRNA-seq data. SoCube (i) proposed a novel 3D composite feature-embedding strategy that embedded latent gene information and (ii) constructed a multikernel, multichannel CNN-ensembled architecture in conjunction with the feature-embedding strategy. With its excellent performance on benchmark evaluation and several downstream tasks, it is expected to be a powerful algorithm to detect and remove doublets in scRNA-seq data. SoCube is freely provided as an end-to-end tool on the Python official package site PyPi (https://pypi.org/project/socube/) and open-source on GitHub (https://github.com/idrblab/socube/).
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Affiliation(s)
- Hongning Zhang
- Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Gaole Lin
- Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Lingyan Zheng
- Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wei Zhang
- Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhijian Xu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feng Zhu
- Polytechnic Institute, The Second Affiliated Hospital, College of Pharmaceutical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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Wu X, Kong X, Vatansever D, Liu Z, Zhang K, Sahakian BJ, Robbins TW, Feng J, Thompson P, Zhang J. Dynamic changes in brain lateralization correlate with human cognitive performance. PLoS Biol 2022; 20:e3001560. [PMID: 35298460 PMCID: PMC8929635 DOI: 10.1371/journal.pbio.3001560] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Hemispheric lateralization constitutes a core architectural principle of human brain organization underlying cognition, often argued to represent a stable, trait-like feature. However, emerging evidence underlines the inherently dynamic nature of brain networks, in which time-resolved alterations in functional lateralization remain uncharted. Integrating dynamic network approaches with the concept of hemispheric laterality, we map the spatiotemporal architecture of whole-brain lateralization in a large sample of high-quality resting-state fMRI data (N = 991, Human Connectome Project). We reveal distinct laterality dynamics across lower-order sensorimotor systems and higher-order associative networks. Specifically, we expose 2 aspects of the laterality dynamics: laterality fluctuations (LF), defined as the standard deviation of laterality time series, and laterality reversal (LR), referring to the number of zero crossings in laterality time series. These 2 measures are associated with moderate and extreme changes in laterality over time, respectively. While LF depict positive association with language function and cognitive flexibility, LR shows a negative association with the same cognitive abilities. These opposing interactions indicate a dynamic balance between intra and interhemispheric communication, i.e., segregation and integration of information across hemispheres. Furthermore, in their time-resolved laterality index, the default mode and language networks correlate negatively with visual/sensorimotor and attention networks, which are linked to better cognitive abilities. Finally, the laterality dynamics are associated with functional connectivity changes of higher-order brain networks and correlate with regional metabolism and structural connectivity. Our results provide insights into the adaptive nature of the lateralized brain and new perspectives for future studies of human cognition, genetics, and brain disorders. Hemispheric lateralization constitutes a core architectural principle of human brain organization, often argued to represent a stable, trait-like feature, but how does this fit with our increasing appreciation of the inherently dynamic nature of brain networks? This neuroimaging study reveals the dynamic nature of functional brain lateralization at resting-state and its relationship with language function and cognitive flexibility.
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Affiliation(s)
- Xinran Wu
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Xiangzhen Kong
- Department of Psychology and Behavioral Sciences, Zhejiang University, Zhejiang, China
| | - Deniz Vatansever
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Zhaowen Liu
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kai Zhang
- School of Computer Science and Technology, East China Normal University, Shanghai, China
| | - Barbara J. Sahakian
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Department of the Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Psychology, University of Cambridge, Cambridge, United Kingdom
| | - Trevor W. Robbins
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Department of the Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Psychiatry, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, United Kingdom
- Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
- Shanghai Center for Mathematical Sciences, Shanghai, China
| | - Paul Thompson
- Imaging Genetics Center, Mark & Mary Stevens Institute for Neuroimaging & Informatics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jie Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- * E-mail:
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Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Brief Bioinform 2022; 23:bbab397. [PMID: 34585235 PMCID: PMC8500159 DOI: 10.1093/bib/bbab397] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/11/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Some studies reported that genomic RNA of SARS-CoV-2 can absorb a few host miRNAs that regulate immune-related genes and then deprive their function. In this perspective, we conjecture that the absorption of the SARS-CoV-2 genome to host miRNAs is not a coincidence, which may be an indispensable approach leading to viral survival and development in host. In our study, we collected five datasets of miRNAs that were predicted to interact with the genome of SARS-CoV-2. The targets of these miRNAs in the five groups were consistently enriched immune-related pathways and virus-infectious diseases. Interestingly, the five datasets shared no one miRNA but their targets shared 168 genes. The signaling pathway enrichment of 168 shared targets implied an unbalanced immune response that the most of interleukin signaling pathways and none of the interferon signaling pathways were significantly different. Protein-protein interaction (PPI) network using the shared targets showed that PPI pairs, including IL6-IL6R, were related to the process of SARS-CoV-2 infection and pathogenesis. In addition, we found that SARS-CoV-2 absorption to host miRNA could benefit two popular mutant strains for more infectivity and pathogenicity. Conclusively, our results suggest that genomic RNA absorption to host miRNAs may be a vital approach by which SARS-CoV-2 disturbs the host immune system and infects host cells.
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Affiliation(s)
- Song Zhang
- College of Pharmaceutical Sciences in Zhejiang University, and the First Affiliated Hospital of Zhejiang University School of Medicine, China
| | | | - Chenyang Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Yunqing Qiu
- First Affiliated Hospital in Zhejiang University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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