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Sun Y, Huang ZL, Chen WX, Zhang YF, Lei HT, Huang QJ, Lun ZR, Qu LH, Zheng LL. GateView: A Multi-Omics Platform for Gene Feature Analysis of Virus Receptors within Human Normal Tissues and Tumors. Biomolecules 2024; 14:516. [PMID: 38785923 PMCID: PMC11118183 DOI: 10.3390/biom14050516] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Viruses are obligate intracellular parasites that rely on cell surface receptor molecules to complete the first step of invading host cells. The experimental method for virus receptor screening is time-consuming, and receptor molecules have been identified for less than half of known viruses. This study collected known human viruses and their receptor molecules. Through bioinformatics analysis, common characteristics of virus receptor molecules (including sequence, expression, mutation, etc.) were obtained to study why these membrane proteins are more likely to become virus receptors. An in-depth analysis of the cataloged virus receptors revealed several noteworthy findings. Compared to other membrane proteins, human virus receptors generally exhibited higher expression levels and lower sequence conservation. These receptors were found in multiple tissues, with certain tissues and cell types displaying significantly higher expression levels. While most receptor molecules showed noticeable age-related variations in expression across different tissues, only a limited number of them exhibited gender-related differences in specific tissues. Interestingly, in contrast to normal tissues, virus receptors showed significant dysregulation in various types of tumors, particularly those associated with dsRNA and retrovirus receptors. Finally, GateView, a multi-omics platform, was established to analyze the gene features of virus receptors in human normal tissues and tumors. Serving as a valuable resource, it enables the exploration of common patterns among virus receptors and the investigation of virus tropism across different tissues, population preferences, virus pathogenicity, and oncolytic virus mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | - Liang-Hu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Y.S.); (Z.-L.H.); (W.-X.C.); (Y.-F.Z.); (H.-T.L.); (Q.-J.H.); (Z.-R.L.)
| | - Ling-Ling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Y.S.); (Z.-L.H.); (W.-X.C.); (Y.-F.Z.); (H.-T.L.); (Q.-J.H.); (Z.-R.L.)
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2
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Srikrishna D. Pentagon Found Daily, Metagenomic Detection of Novel Bioaerosol Threats to Be Cost-Prohibitive: Can Virtualization and AI Make It Cost-Effective? Health Secur 2024; 22:108-129. [PMID: 38625036 DOI: 10.1089/hs.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
In 2022, the Pentagon Force Protection Agency found threat agnostic detection of novel bioaerosol threats to be "not feasible for daily operations" due to the cost of reagents used for metagenomics, cost of sequencing instruments, and cost of labor for subject matter experts to analyze bioinformatics. Similar operational difficulties might extend to many of the 280,000 buildings (totaling 2.3 billion square feet) at 5,000 secure US Department of Defense military sites, 250 Navy ships, as well as many civilian buildings. These economic barriers can still be addressed in a threat agnostic manner by dynamically pooling samples from dry filter units, called spike-triggered virtualization, whereby pooling and sequencing depth are automatically modulated based on novel biothreats in the sequencing output. By running at a high average pooling factor, the daily and annual cost per dry filter unit can be reduced by 10 to 100 times depending on the chosen trigger thresholds. Artificial intelligence can further enhance the sensitivity of spike-triggered virtualization. The risk of infection during the 12- to 24-hour window between a bioaerosol incident and its detection remains, but in some cases it can be reduced by 80% or more with high-speed indoor air cleaning exceeding 12 air changes per hour, which is similar to the rate of air cleaning in passenger airplanes in flight. That level of air changes per hour or higher is likely to be cost-prohibitive using central heating ventilation and air conditioning systems, but it can be achieved economically by using portable air filtration in rooms with typical ceiling heights (less than 10 feet) for a cost of approximately $0.50 to $1 per square foot for do-it-yourself units and $2 to $5 per square foot for high-efficiency particulate air filters.
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3
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Valero-Rello A, Baeza-Delgado C, Andreu-Moreno I, Sanjuán R. Cellular receptors for mammalian viruses. PLoS Pathog 2024; 20:e1012021. [PMID: 38377111 PMCID: PMC10906839 DOI: 10.1371/journal.ppat.1012021] [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: 10/05/2023] [Revised: 03/01/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
The interaction of viral surface components with cellular receptors and other entry factors determines key features of viral infection such as host range, tropism and virulence. Despite intensive research, our understanding of these interactions remains limited. Here, we report a systematic analysis of published work on mammalian virus receptors and attachment factors. We build a dataset twice the size of those available to date and specify the role of each factor in virus entry. We identify cellular proteins that are preferentially used as virus receptors, which tend to be plasma membrane proteins with a high propensity to interact with other proteins. Using machine learning, we assign cell surface proteins a score that predicts their ability to function as virus receptors. Our results also reveal common patterns of receptor usage among viruses and suggest that enveloped viruses tend to use a broader repertoire of alternative receptors than non-enveloped viruses, a feature that might confer them with higher interspecies transmissibility.
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Affiliation(s)
- Ana Valero-Rello
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Carlos Baeza-Delgado
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Iván Andreu-Moreno
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
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4
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Amahong K, Zhang W, Liu Y, Li T, Huang S, Han L, Tao L, Zhu F. RVvictor: Virus RNA-directed molecular interactions for RNA virus infection. Comput Biol Med 2024; 169:107886. [PMID: 38157777 DOI: 10.1016/j.compbiomed.2023.107886] [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: 08/06/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
RNA viruses are major human pathogens that cause seasonal epidemics and occasional pandemic outbreaks. Due to the nature of their RNA genomes, it is anticipated that virus's RNA interacts with host protein (INTPRO), messenger RNA (INTmRNA), and non-coding RNA (INTncRNA) to perform their particular functions during their transcription and replication. In other words, thus, it is urgently needed to have such valuable data on virus RNA-directed molecular interactions (especially INTPROs), which are highly anticipated to attract broad research interests in the fields of RNA virus translation and replication. In this study, a new database was constructed to describe the virus RNA-directed interaction (INTPRO, INTmRNA, INTncRNA) for RNA virus (RVvictor). This database is unique in a) unambiguously characterizing the interactions between viruses RNAs and host proteins, b) providing, for the first time, the most systematic RNA-directed interaction data resources in providing clues to understand the molecular mechanisms of RNA viruses' translation, and replication, and c) in RVvictor, comprehensive enrichment analysis is conducted for each virus RNA based on its associated target genes/proteins, and the enrichment results were explicitly illustrated using various graphs. We found significant enrichment of a suite of pathways related to infection, translation, and replication, e.g., HIV infection, coronavirus disease, regulation of viral genome replication, and so on. Due to the devastating and persistent threat posed by the RNA virus, RVvictor constructed, for the first time, a possible network of cross-talk in RNA-directed interaction, which may ultimately explain the pathogenicity of RNA virus infection. The knowledge base might help develop new anti-viral therapeutic targets in the future. It's now free and publicly accessible at: https://idrblab.org/rvvictor/.
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Affiliation(s)
- Kuerbannisha Amahong
- 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
| | - Wei Zhang
- 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
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Teng Li
- 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; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Lianyi Han
- Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai, 315211, China.
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, 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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5
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Deng Y, Lu Y, Li M, Shen J, Qin S, Zhang W, Zhang Q, Shen Z, Li C, Jia T, Chen P, Peng L, Chen Y, Zhang W, Liu H, Zhang L, Rong L, Wang X, Chen D. SCAN: Spatiotemporal Cloud Atlas for Neural cells. Nucleic Acids Res 2024; 52:D998-D1009. [PMID: 37930842 PMCID: PMC10767991 DOI: 10.1093/nar/gkad895] [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: 08/14/2023] [Revised: 09/20/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
The nervous system is one of the most complicated and enigmatic systems within the animal kingdom. Recently, the emergence and development of spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq) technologies have provided an unprecedented ability to systematically decipher the cellular heterogeneity and spatial locations of the nervous system from multiple unbiased aspects. However, efficiently integrating, presenting and analyzing massive multiomic data remains a huge challenge. Here, we manually collected and comprehensively analyzed high-quality scRNA-seq and ST data from the nervous system, covering 10 679 684 cells. In addition, multi-omic datasets from more than 900 species were included for extensive data mining from an evolutionary perspective. Furthermore, over 100 neurological diseases (e.g. Alzheimer's disease, Parkinson's disease, Down syndrome) were systematically analyzed for high-throughput screening of putative biomarkers. Differential expression patterns across developmental time points, cell types and ST spots were discerned and subsequently subjected to extensive interpretation. To provide researchers with efficient data exploration, we created a new database with interactive interfaces and integrated functions called the Spatiotemporal Cloud Atlas for Neural cells (SCAN), freely accessible at http://47.98.139.124:8799 or http://scanatlas.net. SCAN will benefit the neuroscience research community to better exploit the spatiotemporal atlas of the neural system and promote the development of diagnostic strategies for various neurological disorders.
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Affiliation(s)
- Yushan Deng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yubao Lu
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Mengrou Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Jiayi Shen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Siying Qin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wei Zhang
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Qiang Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Zhaoyang Shen
- Life Sciences and Technology College, China Pharmaceutical University, Nanjing 211198, China
| | - Changxiao Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Tengfei Jia
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Peixin Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Lingmin Peng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yangfeng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wensheng Zhang
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Liangming Zhang
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai 200000, China
| | - Dongsheng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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6
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Deng Y, Chen P, Xiao J, Li M, Shen J, Qin S, Jia T, Li C, Chang A, Zhang W, Liu H, Xue R, Zhang N, Wang X, Huang L, Chen D. SCAR: Single-cell and Spatially-resolved Cancer Resources. Nucleic Acids Res 2024; 52:D1407-D1417. [PMID: 37739405 PMCID: PMC10767865 DOI: 10.1093/nar/gkad753] [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: 06/08/2023] [Revised: 08/16/2023] [Accepted: 09/05/2023] [Indexed: 09/24/2023] Open
Abstract
Advances in sequencing and imaging technologies offer a unique opportunity to unravel cell heterogeneity and develop new immunotherapy strategies for cancer research. There is an urgent need for a resource that effectively integrates a vast amount of transcriptomic profiling data to comprehensively explore cancer tissue heterogeneity and the tumor microenvironment. In this context, we developed the Single-cell and Spatially-resolved Cancer Resources (SCAR) database, a combined tumor spatial and single-cell transcriptomic platform, which is freely accessible at http://8.142.154.29/SCAR2023 or http://scaratlas.com. SCAR contains spatial transcriptomic data from 21 tumor tissues and single-cell transcriptomic data from 11 301 352 cells encompassing 395 cancer subtypes and covering a wide variety of tissues, organoids, and cell lines. This resource offers diverse functional modules to address key cancer research questions at multiple levels, including the screening of tumor cell types, metabolic features, cell communication and gene expression patterns within the tumor microenvironment. Moreover, SCAR enables the analysis of biomarker expression patterns and cell developmental trajectories. SCAR also provides a comprehensive analysis of multi-dimensional datasets based on 34 state-of-the-art omics techniques, serving as an essential tool for in-depth mining and understanding of cell heterogeneity and spatial location. The implications of this resource extend to both cancer biology research and cancer immunotherapy development.
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Affiliation(s)
- Yushan Deng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Peixin Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Jiedan Xiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Mengrou Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Jiayi Shen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Siying Qin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Tengfei Jia
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Changxiao Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Ashley Chang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Ruidong Xue
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University Health Science Center & Translational Cancer Research Center, Peking University First Hospital, Beijing 100191, China
| | - Ning Zhang
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University Health Science Center & Translational Cancer Research Center, Peking University First Hospital, Beijing 100191, China
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai 200000, China
| | - Li Huang
- The Future Laboratory, Tsinghua University, Beijing 100084, China
| | - Dongsheng Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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7
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Qiu X, Wang HY, Yang ZY, Sun LM, Liu SN, Fan CQ, Zhu F. Uncovering the prominent role of satellite cells in paravertebral muscle development and aging by single-nucleus RNA sequencing. Genes Dis 2023; 10:2597-2613. [PMID: 37554180 PMCID: PMC10404979 DOI: 10.1016/j.gendis.2023.01.005] [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: 06/18/2022] [Revised: 11/06/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023] Open
Abstract
To uncover the role of satellite cells (SCs) in paravertebral muscle development and aging, we constructed a single-nucleus transcriptomic atlas of mouse paravertebral muscle across seven timepoints spanning the embryo (day 16.5) to old (month 24) stages. Eight cell types, including SCs, fast muscle cells, and slow muscle cells, were identified. An energy metabolism-related gene set, TCA CYCLE IN SENESCENCE, was enriched in SCs. Forty-two skeletal muscle disease-related genes were highly expressed in SCs and exhibited similar expression patterns. Among them, Pdha1 was the core gene in the TCA CYCLE IN SENESCENCE; Pgam2, Sod1, and Suclg1 are transcription factors closely associated with skeletal muscle energy metabolism. Transcription factor enrichment analysis of the 42 genes revealed that Myod1 and Mef2a were also highly expressed in SCs, which regulated Pdha1 expression and were associated with skeletal muscle development. These findings hint that energy metabolism may be pivotal in SCs development and aging. Three ligand-receptor pairs of extracellular matrix (ECM)-receptor interactions, Lamc1-Dag1, Lama2-Dag1, and Hspg2-Dag1, may play a vital role in SCs interactions with slow/fast muscle cells and SCs self-renewal. Finally, we built the first database of a skeletal muscle single-cell transcriptome, the Musculoskeletal Cell Atlas (http://www.mskca.tech), which lists 630,040 skeletal muscle cells and provides interactive visualization, a useful resource for revealing skeletal muscle cellular heterogeneity during development and aging. Our study could provide new targets and ideas for developing drugs to inhibit skeletal muscle aging and treat skeletal muscle diseases.
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Affiliation(s)
- Xin Qiu
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
- Department of Orthopedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Hao-Yu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100000, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, Shandong 266000, China
| | - Zhen-Yu Yang
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
| | - Li-Ming Sun
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Forth Military Medical University, Xi'an, Shaanxi 710000, China
| | - Shu-Nan Liu
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
| | - Chui-Qin Fan
- China Medical University, Shenyang, Liaoning 110000, China
| | - Feng Zhu
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
- Department of Orthopedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
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8
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Wang X, Ding P, Sun C, Wang D, Zhu J, Wu W, Wei Y, Xiang R, Ding X, Luo L, Li M, Zhang W, Jin X, Sun J, Liu H, Chen D. Comparative analysis of single cell lung atlas of bat, cat, tiger, and pangolin. Cell Biol Toxicol 2023; 39:2431-2435. [PMID: 36169743 PMCID: PMC9516514 DOI: 10.1007/s10565-022-09771-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
Abstract
Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as severe acute respiratory syndrome coronavirus (SARS-CoV). Bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the coronavirus disease 2019 (COVID-19) pandemic, multiple animal species were diseased by coronavirus infection, especially in the respiratory system. Herein, a comparative analysis with single nucleus transcriptomic data of the lungs across four species, including horseshoe bat, cat, tiger, and pangolin, were conducted. The distribution of entry factors for twenty-eight respiratory viruses was characterized for the four species. Our findings might increase our understanding of the immune background of horseshoe bats.
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Affiliation(s)
- Xiran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Peiwen Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengcheng Sun
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wendi Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Yanan Wei
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | | | - Xiangning Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Wensheng Zhang
- School of Basic Medical Sciences, Binzhou Medical University, No. 346, Guanhai Road, Laishan District, Yantai City, Shandong, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dongsheng Chen
- BGI-Shenzhen, Shenzhen, 518083, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Liao Y, Wang J, Zou J, Liu Y, Liu Z, Huang Z. Multi-omics analysis reveals genomic, clinical and immunological features of SARS-CoV-2 virus target genes in pan-cancer. Front Immunol 2023; 14:1112704. [PMID: 36875081 PMCID: PMC9982007 DOI: 10.3389/fimmu.2023.1112704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
The SARS-CoV-2 virus, also known as the severe acute respiratory syndrome coronavirus 2, has raised great threats to humans. The connection between the SARS-CoV-2 virus and cancer is currently unclear. In this study, we thus evaluated the multi-omics data from the Cancer Genome Atlas (TCGA) database utilizing genomic and transcriptomic techniques to fully identify the SARS-CoV-2 target genes (STGs) in tumor samples from 33 types of cancers. The expression of STGs was substantially linked with the immune infiltration and may be used to predict survival in cancer patients. STGs were also substantially associated with immunological infiltration, immune cells, and associated immune pathways. At the molecular level, the genomic changes of STGs were frequently related with carcinogenesis and patient survival. In addition, pathway analysis revealed that STGs were involved in the control of signaling pathways associated with cancer. The prognostic features and nomogram of clinical factors of STGs in cancers have been developed. Lastly, by mining the cancer drug sensitivity genomics database, a list of potential STG-targeting medicines was compiled. Collectively, this work demonstrated comprehensively the genomic alterations and clinical characteristics of STGs, which may offer new clues to explore the mechanisms on a molecular level between SARS-CoV-2 virus and cancers as well as provide new clinical guidance for cancer patients who are threatened by the COVID-19 epidemic.
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Affiliation(s)
- Yong Liao
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Department of Pharmacy, Maoming People's Hospital, Maoming, China
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Jiaojiao Wang
- Center of Scientific Research, Department of Cardiology, Maoming People's Hospital, Maoming, China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jiami Zou
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Yong Liu
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zhiping Liu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Zunnan Huang
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
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10
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Chen D, Luo Y, Cheng G. Single cell and immunity: Better understanding immune cell heterogeneities with single cell sequencing. Clin Transl Med 2023; 13:e1159. [PMID: 36579366 PMCID: PMC9797918 DOI: 10.1002/ctm2.1159] [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: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/30/2022] Open
Abstract
Single-cell sequencing has scientific impacts on better understanding the immunity. There is a rapid development in single cell-based databases and analytic tools to provide the potential of clinical and translational discovery. The understanding of single-cell based immunity needs a strong program and solid evidence of preclinical and clinical validation and evaluation. The current special topic issue on single cell and immunity aimed to provide a strong communication for the progress of single cell-based studies on immune cell functional diversity in development and disease. The topic has a clear scope on the application of single cell sequencing to better understand immune cell heterogeneities, functions, cell-cell interactions, responses and regulatory roles in systems immunology and diseases.
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Affiliation(s)
- Dongsheng Chen
- Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
- Suzhou Institute of Systems MedicineSuzhouChina
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI‐Qingdao, BGI‐ShenzhenQingdaoChina
- Department of BiomedicineAarhus UniversityAarhusDenmark
| | - Genhong Cheng
- Department of MicrobiologyImmunology & Molecular GeneticsUniversity of California Los Angeles (UCLA), Los Angeles, California, USA
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11
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Chen Y, Zhang X, Peng X, Jin Y, Ding P, Xiao J, Li C, Wang F, Chang A, Yue Q, Pu M, Chen P, Shen J, Li M, Jia T, Wang H, Huang L, Guo G, Zhang W, Liu H, Wang X, Chen D. SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases. Nucleic Acids Res 2022; 51:D1150-D1159. [PMID: 36305818 PMCID: PMC9825432 DOI: 10.1093/nar/gkac930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 01/30/2023] Open
Abstract
It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.
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Affiliation(s)
| | | | | | | | | | - Jiedan Xiao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China,Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Changxiao Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China,Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Fei Wang
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Ashley Chang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China,Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Qizhen Yue
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Mingyi Pu
- Department of Medicine, Sun Yat-sen University, Shenzhen 518106, China
| | - Peixin Chen
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China
| | - Jiayi Shen
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Mengrou Li
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Tengfei Jia
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- The Future Laboratory, Tsinghua University, Beijing 100084, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou 215123, China,Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou 215123, China
| | | | - Dongsheng Chen
- To whom correspondence should be addressed. Tel: +86 512 62873780; Fax: +86 512 62873779;
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12
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Chen D, Ou Z, Zhu J, Wang H, Ding P, Luo L, Ding X, Sun C, Lan T, Sahu SK, Wu W, Yuan Y, Wu W, Qiu J, Zhu Y, Yue Q, Jia Y, Wei Y, Qin Q, Li R, Zhao W, Lv Z, Pu M, Lv B, Yang S, Chang A, Wei X, Chen F, Yang T, Wei Z, Yang F, Zhang P, Guo G, Li Y, Hua Y, Liu H. Screening of cell-virus, cell-cell, gene-gene crosstalk among animal kingdom at single cell resolution. Clin Transl Med 2022; 12:e886. [PMID: 35917402 PMCID: PMC9345398 DOI: 10.1002/ctm2.886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The exact animal origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains obscure and understanding its host range is vital for preventing interspecies transmission. METHODS Herein, we applied single-cell sequencing to multiple tissues of 20 species (30 data sets) and integrated them with public resources (45 data sets covering 26 species) to expand the virus receptor distribution investigation. While the binding affinity between virus and receptor is essential for viral infectivity, understanding the receptor distribution could predict the permissive organs and tissues when infection occurs. RESULTS Based on the transcriptomic data, the expression profiles of receptor or associated entry factors for viruses capable of causing respiratory, blood, and brain diseases were described in detail. Conserved cellular connectomes and regulomes were also identified, revealing fundamental cell-cell and gene-gene cross-talks from reptiles to humans. CONCLUSIONS Overall, our study provides a resource of the single-cell atlas of the animal kingdom which could help to identify the potential host range and tissue tropism of viruses and reveal the host-virus co-evolution.
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Affiliation(s)
- Dongsheng Chen
- BGI‐ShenzhenShenzhenChina,Suzhou Institute of Systems MedicineSuzhouJiangsuChina
| | - Zhihua Ou
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen IdentificationBGI‐ShenzhenShenzhenChina
| | - Jiacheng Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Haoyu Wang
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Peiwen Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Lihua Luo
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xiangning Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Chengcheng Sun
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Weiying Wu
- The MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouChina
| | - Yuting Yuan
- Department of Physiology, School of Basic Medical SciencesBinzhou Medical UniversityYantaiChina
| | - Wendi Wu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Jiaying Qiu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yixin Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Qizhen Yue
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Yi Jia
- BGI‐ShenzhenShenzhenChina
| | - Yanan Wei
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Qiuyu Qin
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Runchu Li
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wandong Zhao
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Zhiyuan Lv
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Mingyi Pu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | | | - Shangchen Yang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | | | | | | | - Tao Yang
- China National GeneBankShenzhenChina
| | | | - Fan Yang
- China National GeneBankShenzhenChina
| | - Peijing Zhang
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | - Guoji Guo
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | | | - Yan Hua
- Guangdong Provincial Key Laboratory of SilvicultureProtection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Huan Liu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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13
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Rigden DJ, Fernández XM. The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Res 2022; 50:D1-D10. [PMID: 34986604 PMCID: PMC8728296 DOI: 10.1093/nar/gkab1195] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.
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Affiliation(s)
- Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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