1
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Lyu C, Chen L, Liu X. Detecting tipping points of complex diseases by network information entropy. Brief Bioinform 2024; 25:bbae311. [PMID: 38960408 PMCID: PMC11221888 DOI: 10.1093/bib/bbae311] [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: 02/22/2024] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024] Open
Abstract
The progression of complex diseases often involves abrupt and non-linear changes characterized by sudden shifts that trigger critical transformations. Identifying these critical states or tipping points is crucial for understanding disease progression and developing effective interventions. To address this challenge, we have developed a model-free method named Network Information Entropy of Edges (NIEE). Leveraging dynamic network biomarkers, sample-specific networks, and information entropy theories, NIEE can detect critical states or tipping points in diverse data types, including bulk, single-sample expression data. By applying NIEE to real disease datasets, we successfully identified critical predisease stages and tipping points before disease onset. Our findings underscore NIEE's potential to enhance comprehension of complex disease development.
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Affiliation(s)
- Chengshang Lyu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Branch Alley, Xihu District, Hangzhou 310024, China
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Kowloon, Hong Kong 999077, China
| | - Lingxi Chen
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Kowloon, Hong Kong 999077, China
| | - Xiaoping Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Branch Alley, Xihu District, Hangzhou 310024, China
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2
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Masuda N, Aihara K, MacLaren NG. Anticipating regime shifts by mixing early warning signals from different nodes. Nat Commun 2024; 15:1086. [PMID: 38316802 PMCID: PMC10844243 DOI: 10.1038/s41467-024-45476-9] [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: 08/24/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024] Open
Abstract
Real systems showing regime shifts, such as ecosystems, are often composed of many dynamical elements interacting on a network. Various early warning signals have been proposed for anticipating regime shifts from observed data. However, it is unclear how one should combine early warning signals from different nodes for better performance. Based on theory of stochastic differential equations, we propose a method to optimize the node set from which to construct an early warning signal. The proposed method takes into account that uncertainty as well as the magnitude of the signal affects its predictive performance, that a large magnitude or small uncertainty of the signal in one situation does not imply the signal's high performance, and that combining early warning signals from different nodes is often but not always beneficial. The method performs well particularly when different nodes are subjected to different amounts of dynamical noise and stress.
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Affiliation(s)
- Naoki Masuda
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, 14260-2900, USA.
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, NY, 14260-5030, USA.
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Bunkyo City, Japan
| | - Neil G MacLaren
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, 14260-2900, USA
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3
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Lou C, Yang H, Hou Y, Huang H, Qiu J, Wang C, Sang Y, Liu H, Han L. Microfluidic Platforms for Real-Time In Situ Monitoring of Biomarkers for Cellular Processes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307051. [PMID: 37844125 DOI: 10.1002/adma.202307051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Indexed: 10/18/2023]
Abstract
Cellular processes are mechanisms carried out at the cellular level that are aimed at guaranteeing the stability of the organism they comprise. The investigation of cellular processes is key to understanding cell fate, understanding pathogenic mechanisms, and developing new therapeutic technologies. Microfluidic platforms are thought to be the most powerful tools among all methodologies for investigating cellular processes because they can integrate almost all types of the existing intracellular and extracellular biomarker-sensing methods and observation approaches for cell behavior, combined with precisely controlled cell culture, manipulation, stimulation, and analysis. Most importantly, microfluidic platforms can realize real-time in situ detection of secreted proteins, exosomes, and other biomarkers produced during cell physiological processes, thereby providing the possibility to draw the whole picture for a cellular process. Owing to their advantages of high throughput, low sample consumption, and precise cell control, microfluidic platforms with real-time in situ monitoring characteristics are widely being used in cell analysis, disease diagnosis, pharmaceutical research, and biological production. This review focuses on the basic concepts, recent progress, and application prospects of microfluidic platforms for real-time in situ monitoring of biomarkers in cellular processes.
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Affiliation(s)
- Chengming Lou
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Hongru Yang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Ying Hou
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Haina Huang
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Jichuan Qiu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Chunhua Wang
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Yuanhua Sang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Hong Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266000, P. R. China
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4
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Zhang L, Du F, Jin Q, Sun L, Wang B, Tan Z, Meng X, Huang B, Zhan Y, Su W, Song R, Wu C, Chen L, Chen X, Ding X. Identification and Characterization of CD8 + CD27 + CXCR3 - T Cell Dysregulation and Progression-Associated Biomarkers in Systemic Lupus Erythematosus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300123. [PMID: 37875396 PMCID: PMC10724430 DOI: 10.1002/advs.202300123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/04/2023] [Indexed: 10/26/2023]
Abstract
Systemic Lupus Erythematosus (SLE) etiopathogenesis highlights the contributions of overproduction of CD4+ T cells and loss of immune tolerance. However, the involvement of CD8+ T cells in SLE pathology and disease progression remains unclear. Here, the comprehensive immune cell dysregulation in total 263 clinical peripheral blood samples composed of active SLE (aSLE), remission SLE (rSLE) and healthy controls (HCs) is investigated via mass cytometry, flow cytometry and single-cell RNA sequencing. This is observed that CD8+ CD27+ CXCR3- T cells are increased in rSLE compare to aSLE. Meanwhile, the effector function of CD8+ CD27+ CXCR3- T cells are overactive in aSLE compare to HCs and rSLE, and are positively associated with clinical SLE activity. In addition, the response of peripheral blood mononuclear cells (PBMCs) is monitored to interleukin-2 stimulation in aSLE and rSLE to construct dynamic network biomarker (DNB) model. It is demonstrated that DNB score-related parameters can faithfully predict the remission of aSLE and the flares of rSLE. The abundance and functional dysregulation of CD8+ CD27+ CXCR3- T cells can be potential biomarkers for SLE prognosis and concomitant diagnosis. The DNB score with accurate prediction to SLE disease progression can provide clinical treatment suggestions especially for drug dosage determination.
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Affiliation(s)
- Lulu Zhang
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200001China
| | - Fang Du
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200001China
| | - Qiqi Jin
- Key Laboratory of Systems BiologyCenter for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Li Sun
- Department of Rheumatology and ImmunologyThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Boqian Wang
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200001China
| | - Ziyang Tan
- Science for Life LaboratoryDepartment of Women's and Children's HealthKarolinska InstitutetSolna17121Sweden
| | - Xinyu Meng
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200001China
| | - Baozhen Huang
- Department of Chemical PathologyLi Ka Shing Institute of Health SciencesFaculty of MedicineThe Chinese University of Hong KongHong Kong999077China
| | - Yifan Zhan
- Drug DiscoveryShanghai Huaota Biopharmaceutical Co. Ltd.Shanghai200131China
| | - Wenqiong Su
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200001China
| | - Rui Song
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
- Nantong First People's HospitalAffiliated Hospital 2 of Nantong UniversityNantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
| | - Chunmei Wu
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
| | - Luonan Chen
- Key Laboratory of Systems BiologyCenter for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesChinese Academy of SciencesHangzhou310024China
| | - Xiaoxiang Chen
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
| | - Xianting Ding
- Department of RheumatologyShanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and School of Biomedical EngineeringShanghai200030China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200001China
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Sukko N, Kalapanulak S, Saithong T. Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation. Sci Rep 2023; 13:19973. [PMID: 37968317 PMCID: PMC10651926 DOI: 10.1038/s41598-023-47095-8] [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: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.
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Affiliation(s)
- Nattavat Sukko
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
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Akagi K, Koizumi K, Kadowaki M, Kitajima I, Saito S. New Possibilities for Evaluating the Development of Age-Related Pathologies Using the Dynamical Network Biomarkers Theory. Cells 2023; 12:2297. [PMID: 37759519 PMCID: PMC10528308 DOI: 10.3390/cells12182297] [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: 08/20/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is the slowest process in a living organism. During this process, mortality rate increases exponentially due to the accumulation of damage at the cellular level. Cellular senescence is a well-established hallmark of aging, as well as a promising target for preventing aging and age-related diseases. However, mapping the senescent cells in tissues is extremely challenging, as their low abundance, lack of specific markers, and variability arise from heterogeneity. Hence, methodologies for identifying or predicting the development of senescent cells are necessary for achieving healthy aging. A new wave of bioinformatic methodologies based on mathematics/physics theories have been proposed to be applied to aging biology, which is altering the way we approach our understand of aging. Here, we discuss the dynamical network biomarkers (DNB) theory, which allows for the prediction of state transition in complex systems such as living organisms, as well as usage of Raman spectroscopy that offers a non-invasive and label-free imaging, and provide a perspective on potential applications for the study of aging.
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Affiliation(s)
- Kazutaka Akagi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Isao Kitajima
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
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7
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Oshima Y, Haruki T, Koizumi K, Yonezawa S, Taketani A, Kadowaki M, Saito S. Practices, Potential, and Perspectives for Detecting Predisease Using Raman Spectroscopy. Int J Mol Sci 2023; 24:12170. [PMID: 37569541 PMCID: PMC10418989 DOI: 10.3390/ijms241512170] [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: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Raman spectroscopy shows great potential for practical clinical applications. By analyzing the structure and composition of molecules through real-time, non-destructive measurements of the scattered light from living cells and tissues, it offers valuable insights. The Raman spectral data directly link to the molecular composition of the cells and tissues and provides a "molecular fingerprint" for various disease states. This review focuses on the practical and clinical applications of Raman spectroscopy, especially in the early detection of human diseases. Identifying predisease, which marks the transition from a healthy to a disease state, is crucial for effective interventions to prevent disease onset. Raman spectroscopy can reveal biological processes occurring during the transition states and may eventually detect the molecular dynamics in predisease conditions.
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Affiliation(s)
- Yusuke Oshima
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Takayuki Haruki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Sustainable Design, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-8555, Japan
| | - Shota Yonezawa
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Akinori Taketani
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
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Proverbio D, Skupin A, Gonçalves J. Systematic analysis and optimization of early warning signals for critical transitions using distribution data. iScience 2023; 26:107156. [PMID: 37456849 PMCID: PMC10338236 DOI: 10.1016/j.isci.2023.107156] [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: 11/04/2022] [Revised: 04/21/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Abrupt shifts between alternative regimes occur in complex systems, from cell regulation to brain functions to ecosystems. Several model-free early warning signals (EWS) have been proposed to detect impending transitions, but failure or poor performance in some systems have called for better investigation of their generic applicability. Notably, there are still ongoing debates whether such signals can be successfully extracted from data in particular from biological experiments. In this work, we systematically investigate properties and performance of dynamical EWS in different deteriorating conditions, and we propose an optimized combination to trigger warnings as early as possible, eventually verified on experimental data from microbiological populations. Our results explain discrepancies observed in the literature between warning signs extracted from simulated models and from real data, provide guidance for EWS selection based on desired systems and suggest an optimized composite indicator to alert for impending critical transitions using distribution data.
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Affiliation(s)
- Daniele Proverbio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue Du Swing, 4367 Belvaux, Luxembourg
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QL, UK
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue Du Swing, 4367 Belvaux, Luxembourg
- National Center for Microscopy and Imaging Research, University of California San Diego, Gilman Drive, La Jolla, CA 9500, USA
- Department of Physics and Material Science, University of Luxembourg, 162a Avenue de La Faiencerie, 1511 Luxembourg, Luxembourg
| | - Jorge Gonçalves
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue Du Swing, 4367 Belvaux, Luxembourg
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Selvarajoo K, Giuliani A. Systems Biology and Omics Approaches for Complex Human Diseases. Biomolecules 2023; 13:1080. [PMID: 37509116 PMCID: PMC10377378 DOI: 10.3390/biom13071080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
For many years, there has been general interest in developing virtual cells or digital twin models [...].
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Affiliation(s)
- Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore (NUS), Singapore 117456, Singapore
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore 639798, Singapore
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
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10
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Han Y, Akhtar J, Liu G, Li C, Wang G. Early warning and diagnosis of liver cancer based on dynamic network biomarker and deep learning. Comput Struct Biotechnol J 2023; 21:3478-3489. [PMID: 38213892 PMCID: PMC10782000 DOI: 10.1016/j.csbj.2023.07.002] [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: 04/12/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 01/13/2024] Open
Abstract
Background Early detection of complex diseases like hepatocellular carcinoma remains challenging due to their network-driven pathology. Dynamic network biomarkers (DNB) based on monitoring changes in molecular correlations may enable earlier predictions. However, DNB analysis often overlooks disease heterogeneity. Methods We integrated DNB analysis with graph convolutional neural networks (GCN) to identify critical transitions during hepatocellular carcinoma development in a mouse model. A DNB-GCN model was constructed using transcriptomic data and gene expression levels as node features. Results DNB analysis identified a critical transition point at 7 weeks of age despite histological examinations being unable to detect cancerous changes at that time point. The DNB-GCN model achieved 100% accuracy in classifying healthy and cancerous mice, and was able to accurately predict the health status of newly introduced mice. Conclusion The integration of DNB analysis and GCN demonstrates potential for the early detection of complex diseases by capturing network structures and molecular features that conventional biomarker discovery methods overlook. The approach warrants further development and validation.
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Affiliation(s)
- Yukun Han
- Institute of Modern Biology, Nanjing University, Nanjing 210023, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Javed Akhtar
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guozhen Liu
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chenzhong Li
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guanyu Wang
- Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen 518055, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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11
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Jiang F, Yang L, Jiao X. Dynamic network biomarker to determine the critical point of breast cancer stage progression. Breast Cancer 2023; 30:453-465. [PMID: 36807044 DOI: 10.1007/s12282-023-01438-5] [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: 08/28/2022] [Accepted: 02/11/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND The discovery of early warning signs and biomarkers in patients with early breast cancer is crucial for the prevention and treatment of breast cancer. Dynamic Network Biomarker (DNB) is an approach based on nonlinear dynamics theory, which we exploited to identify a set of DNB members and their key genes as early warning signals during breast cancer staging progression. METHODS First, based on the gene expression profile of breast cancer in the TCGA database, the DNB algorithm was used to calculate the composite index (CI) of each gene cluster in the process of breast cancer anatomical staging. Then we calculated gene modules associated with the clinical phenotype stage based on weighted gene co-expression network analysis (WGCNA), combined with DNB membership to identify key genes in the network. RESULTS We identified a set of gene clusters with the highest CI in Stage II as DNBs, whose roles in related pathways indicate the emergence of a tipping point and impact on breast cancer development. In addition, analysis of the key gene GPRIN1 showed that high expression of GPRIN1 predicts poor prognosis, and related immune analysis showed that GPRIN1 is involved in the development of breast cancer through immune aspects. CONCLUSION The discovery of DNBs and the key gene GPRIN1 can provide potential biomarkers and therapeutic targets for breast cancer.
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Affiliation(s)
- Fa Jiang
- College of Biomedical Engineering, Taiyuan University of Technology, Jinzhong, 030600, China
| | - Lifeng Yang
- College of Information and Computer, Taiyuan University of Technology, Jinzhong, 030600, China
| | - Xiong Jiao
- College of Biomedical Engineering, Taiyuan University of Technology, Jinzhong, 030600, China.
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12
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Application of the Dynamical Network Biomarker Theory to Raman Spectra. Biomolecules 2022; 12:biom12121730. [PMID: 36551158 PMCID: PMC9776035 DOI: 10.3390/biom12121730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The dynamical network biomarker (DNB) theory detects the early warning signals of state transitions utilizing fluctuations in and correlations between variables in complex systems. Although the DNB theory has been applied to gene expression in several diseases, destructive testing by microarrays is a critical issue. Therefore, other biological information obtained by non-destructive testing is desirable; one such piece of information is Raman spectra measured by Raman spectroscopy. Raman spectroscopy is a powerful tool in life sciences and many other fields that enable the label-free non-invasive imaging of live cells and tissues along with detailed molecular fingerprints. Naïve and activated T cells have recently been successfully distinguished from each other using Raman spectroscopy without labeling. In the present study, we applied the DNB theory to Raman spectra of T cell activation as a model case. The dataset consisted of Raman spectra of the T cell activation process observed at 0 (naïve T cells), 2, 6, 12, 24 and 48 h (fully activated T cells). In the DNB analysis, the F-test and hierarchical clustering were used to detect the transition state and identify DNB Raman shifts. We successfully detected the transition state at 6 h and related DNB Raman shifts during the T cell activation process. The present results suggest novel applications of the DNB theory to Raman spectra ranging from fundamental research on cellular mechanisms to clinical examinations.
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Gao S, Chen Y, Wu Z, Kajigaya S, Wang X, Young NS. Time-Varying Gene Expression Network Analysis Reveals Conserved Transition States in Hematopoietic Differentiation between Human and Mouse. Genes (Basel) 2022; 13:genes13101890. [PMID: 36292775 PMCID: PMC9601530 DOI: 10.3390/genes13101890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: analyses of gene networks can elucidate hematopoietic differentiation from single-cell gene expression data, but most algorithms generate only a single, static network. Because gene interactions change over time, it is biologically meaningful to examine time-varying structures and to capture dynamic, even transient states, and cell-cell relationships. (2) Methods: a transcriptomic atlas of hematopoietic stem and progenitor cells was used for network analysis. After pseudo-time ordering with Monocle 2, LOGGLE was used to infer time-varying networks and to explore changes of differentiation gene networks over time. A range of network analysis tools were used to examine properties and genes in the inferred networks. (3) Results: shared characteristics of attributes during the evolution of differentiation gene networks showed a “U” shape of network density over time for all three branches for human and mouse. Differentiation appeared as a continuous process, originating from stem cells, through a brief transition state marked by fewer gene interactions, before stabilizing in a progenitor state. Human and mouse shared hub genes in evolutionary networks. (4) Conclusions: the conservation of network dynamics in the hematopoietic systems of mouse and human was reflected by shared hub genes and network topological changes during differentiation.
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Affiliation(s)
- Shouguo Gao
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Correspondence:
| | - Ye Chen
- Department of Mathematics and Statistics, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Zhijie Wu
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sachiko Kajigaya
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xujing Wang
- Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20817, USA
| | - Neal S. Young
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Iriki A, Tramacere A. “Natural Laboratory Complex” for novel primate neuroscience. Front Integr Neurosci 2022; 16:927605. [PMID: 36274659 PMCID: PMC9581230 DOI: 10.3389/fnint.2022.927605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
We propose novel strategies for primate experimentation that are ethically valuable and pragmatically useful for cognitive neuroscience and neuropsychiatric research. Specifically, we propose Natural Laboratory Complex or Natural Labs, which are a combination of indoor-outdoor structures for studying free moving and socially housed primates in natural or naturalistic environment. We contend that Natural Labs are pivotal to improve primate welfare, and at the same time to implement longitudinal and socio-ecological studies of primate brain and behavior. Currently emerging advanced technologies and social systems (including recent COVID-19 induced “remote” infrastructures) can speed-up cognitive neuroscience approaches in freely behaving animals. Experimental approaches in natural(istic) settings are not in competition with conventional approaches of laboratory investigations, and could establish several benefits at the ethical, experimental, and economic levels.
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Affiliation(s)
- Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- *Correspondence: Atsushi Iriki,
| | - Antonella Tramacere
- Department of Philosophy and Communication Studies, University of Bologna, Bologna, Italy
- Department of Cultural and Linguistic Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
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15
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Proverbio D, Montanari AN, Skupin A, Gonçalves J. Buffering variability in cell regulation motifs close to criticality. Phys Rev E 2022; 106:L032402. [PMID: 36266798 DOI: 10.1103/physreve.106.l032402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Bistable biological regulatory systems need to cope with stochastic noise to fine tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative interactions buffer system variability, hampering noise-induced regime shifts. Our analysis also shows that, in the considered cooperativity range, impending regime shifts can be generically detected by statistical early warning signals from distributional data. Our generic framework, based on minimal models, can be used to extract robustness and variability properties of more complex models and empirical data close to criticality.
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Affiliation(s)
- Daniele Proverbio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, EX4 4QL, Exeter, United Kingdom
| | - Arthur N Montanari
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- Department of Physics and Material Science, University of Luxembourg, 162a Avenue de la Faiencerie, 1511 Luxembourg, Luxembourg
- Department of Neuroscience, University of California San Diego, 9500 Gilman Drive, La Jolla, California, United States
| | - Jorge Gonçalves
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- Department of Plant Sciences, University of Cambridge, CB2 3EA, Cambridge, United Kingdom
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16
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Egashira R, Sato T, Miyake A, Takeuchi M, Nakano M, Saito H, Moriguchi M, Tonari S, Hagihara K. The Japan Frailty Scale is a promising screening test for frailty and pre-frailty in Japanese elderly people. Gene X 2022; 844:146775. [PMID: 36007804 DOI: 10.1016/j.gene.2022.146775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/23/2022] Open
Abstract
Frailty is one of the most important problems in a super-aged society. It is necessary to identify frailty quickly and easily at the bedside. We developed a simple patient-reported frailty screening scale, the Japan Frailty Scale (JFS), based on the aging concept of Kampo medicine. Eight candidate questions were prepared by Kampo medicine experts, and a simple prediction model was created in the development cohort (n=434) and externally validated in an independent validation cohort (n=276). The physical indicators and questionnaires associated with frailty were also comprehensively evaluated. The reference standard for frailty or pre-frailty was determined based on the Kihon checklist. In the development cohort, four questions, nocturia (0-2), lumbago (0-2), cold sensitivity (0-2), exhaustion (0-4), and age (0-1) were selected by multivariable logistic regression analysis. The total JFS score is 0-11. Receiver-operating characteristic curve analysis of the JFS for identifying frailty status showed moderately good discrimination (area under the curve (AUC) =0.78, 95% confidence interval (CI): 0.73-0.82). At the JFS cutoff value of 3/4 for frailty or pre-frailty, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 86.9%, 53.3%, 62.8%, and 81.7%, respectively. External validation of the JFS showed moderately good discrimination (AUC=0.76, 95% CI: 0.70-0.81). The sensitivity, specificity, PPV, and NPV were 79.9%, 61.4%, 69.3%, and 73.7%, respectively. These results indicate that the JFS is a promising patient-reported clinical scale for early identification of pre-frail/frail patients at the bedside in primary care.
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Affiliation(s)
- Ryuichiro Egashira
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomoharu Sato
- Department of Biostatistics and Data Science, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Akimitsu Miyake
- Department of Medical Innovation, Osaka University Hospital, Suita, Osaka 565-0871, Japan; Tohoku University School of Medicine, Sendai 980-8575, Japan
| | - Mariko Takeuchi
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Mai Nakano
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hitomi Saito
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Misaki Moriguchi
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Satoko Tonari
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Keisuke Hagihara
- Department of Advanced Hybrid Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan.
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17
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Yamamoto M. KAMPOmics: A framework for multidisciplinary and comprehensive research on Japanese traditional medicine. Gene X 2022; 831:146555. [PMID: 35569769 DOI: 10.1016/j.gene.2022.146555] [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: 11/24/2021] [Revised: 03/18/2022] [Accepted: 05/06/2022] [Indexed: 11/04/2022] Open
Abstract
Traditional Japanese medicines, known as "Kampo medicines", are pharmaceutical-grade multi-herbal treatments that are integrated within the modern medical system in Japan. Although basic and clinical research including placebo-controlled double-blind trials is attempting to clarify their effectiveness and mechanisms of action, such studies are seriously limited due to the multi-targeted, multi-component "long-tail" properties of Kampo medicines, which are fundamentally different from modern western therapeutics. However, recent progress in high-throughput analytical technology, coupled with an exponential increase in biomedical information on various levels from molecular biology to clinical "big" data, is enabling us to commence a multidisciplinary and comprehensive investigation of Kampo medicines based on multi-omics, bio-informatics, and systems biology. In addition to deriving an inclusive understanding of the benefits and mechanisms of Kampo medicines, "KAMPOmics" may lead to the development of new principles to control and treat diseases in a systems-oriented manner. Furthermore, elucidation of "sho" and "mibyo" - classical concepts of Kampo, which loosely approximate to the notions of "precise medicine" and "pre-symptomatic aberration", respectively - may contribute to the development of patient-oriented medicine, an area attracting enormous growth and interest in contemporary medicine.
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Affiliation(s)
- Masahiro Yamamoto
- Tsumura Research Laboratories, Tsumura & Co., Yoshiwara 3586, Ami, Inashiki, Ibaraki 300-1192, Japan.
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18
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Bao Z, Zheng Y, Li X, Huo Y, Zhao G, Zhang F, Li X, Xu P, Liu W, Han H. A simple pre-disease state prediction method based on variations of gene vector features. Comput Biol Med 2022; 148:105890. [DOI: 10.1016/j.compbiomed.2022.105890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/27/2022] [Accepted: 07/16/2022] [Indexed: 11/24/2022]
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19
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Song C, Qiao Z, Chen L, Ge J, Zhang R, Yuan S, Bian X, Wang C, Liu Q, Jia L, Fu R, Dou K. Identification of Key Genes as Early Warning Signals of Acute Myocardial Infarction Based on Weighted Gene Correlation Network Analysis and Dynamic Network Biomarker Algorithm. Front Immunol 2022; 13:879657. [PMID: 35795669 PMCID: PMC9251518 DOI: 10.3389/fimmu.2022.879657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose The specific mechanisms and biomarkersunderlying the progression of stable coronary artery disease (CAD) to acute myocardial infarction (AMI) remain unclear. The current study aims to explore novel gene biomarkers associated with CAD progression by analyzing the transcriptomic sequencing data of peripheral blood monocytes in different stages of CAD. Material and Methods A total of 24 age- and sex- matched patients at different CAD stages who received coronary angiography were enrolled, which included 8 patients with normal coronary angiography, 8 patients with angiographic intermediate lesion, and 8 patients with AMI. The RNA from peripheral blood monocytes was extracted and transcriptome sequenced to analyze the gene expression and the differentially expressed genes (DEG). A Gene Oncology (GO) enrichment analysis was performed to analyze the biological function of genes. Weighted gene correlation network analysis (WGCNA) was performed to classify genes into several gene modules with similar expression profiles, and correlation analysis was carried out to explore the association of each gene module with a clinical trait. The dynamic network biomarker (DNB) algorithm was used to calculate the key genes that promote disease progression. Finally, the overlapping genes between different analytic methods were explored. Results WGCNA analysis identified a total of nine gene modules, of which two modules have the highest positive association with CAD stages. GO enrichment analysis indicated that the biological function of genes in these two gene modules was closely related to inflammatory response, which included T-cell activation, cell response to inflammatory stimuli, lymphocyte activation, cytokine production, and the apoptotic signaling pathway. DNB analysis identified a total of 103 genes that may play key roles in the progression of atherosclerosis plaque. The overlapping genes between DEG/WGCAN and DNB analysis identified the following 13 genes that may play key roles in the progression of atherosclerosis disease: SGPP2, DAZAP2, INSIG1, CD82, OLR1, ARL6IP1, LIMS1, CCL5, CDK7, HBP1, PLAU, SELENOS, and DNAJB6. Conclusions The current study identified a total of 13 genes that may play key roles in the progression of atherosclerotic plaque and provides new insights for early warning biomarkers and underlying mechanisms underlying the progression of CAD.
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Affiliation(s)
- Chenxi Song
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Zheng Qiao
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jing Ge
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Zhang
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Sheng Yuan
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Xiaohui Bian
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Chunyue Wang
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Qianqian Liu
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Lei Jia
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
| | - Rui Fu
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
- *Correspondence: Rui Fu, ; Kefei Dou,
| | - Kefei Dou
- Cardiometabolic Medicine Center, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
- *Correspondence: Rui Fu, ; Kefei Dou,
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20
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Yan J, Hu Z, Li ZW, Sun S, Guo WF. Network Control Models With Personalized Genomics Data for Understanding Tumor Heterogeneity in Cancer. Front Oncol 2022; 12:891676. [PMID: 35712516 PMCID: PMC9195174 DOI: 10.3389/fonc.2022.891676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
Due to rapid development of high-throughput sequencing and biotechnology, it has brought new opportunities and challenges in developing efficient computational methods for exploring personalized genomics data of cancer patients. Because of the high-dimension and small sample size characteristics of these personalized genomics data, it is difficult for excavating effective information by using traditional statistical methods. In the past few years, network control methods have been proposed to solve networked system with high-dimension and small sample size. Researchers have made progress in the design and optimization of network control principles. However, there are few studies comprehensively surveying network control methods to analyze the biomolecular network data of individual patients. To address this problem, here we comprehensively surveyed complex network control methods on personalized omics data for understanding tumor heterogeneity in precision medicine of individual patients with cancer.
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Affiliation(s)
- Jipeng Yan
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Zhuo Hu
- School of Electrical Engineering, Zhengzhou University, Zhengzhou, China
| | - Zong-Wei Li
- School of Electrical Engineering, Zhengzhou University, Zhengzhou, China
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
- *Correspondence: Wei-Feng Guo, ; Shiren Sun,
| | - Wei-Feng Guo
- School of Electrical Engineering, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Wei-Feng Guo, ; Shiren Sun,
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21
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Brandão LAC, de Moura RR, Marzano AV, Moltrasio C, Tricarico PM, Crovella S. Variant Enrichment Analysis to Explore Pathways Functionality in Complex Autoinflammatory Skin Disorders through Whole Exome Sequencing Analysis. Int J Mol Sci 2022; 23:2278. [PMID: 35216413 PMCID: PMC8877088 DOI: 10.3390/ijms23042278] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
The challenge of unravelling the molecular basis of multifactorial disorders nowadays cannot rely just on association studies searching for potential causative variants shared by groups of patients and not present in healthy individuals; indeed, association studies have as a main limitation the lack of information on the interactions between the disease-causing variants. Thus, new genomic analysis tools focusing on disrupted pathways rather than associated gene variants are required to better understand the complexity of a disease. Therefore, we developed the Variant Enrichment Analysis (VEA) workflow, a tool applicable for whole exome sequencing data, able to find differences between the numbers of genetic variants in a given pathway in comparison with a reference dataset. In this study, we applied VEA to discover novel pathways altered in patients with complex autoinflammatory skin disorders, namely PASH (n = 9), 3 of whom are overlapping with SAPHO) and PAPASH (n = 3). With this approach we have been able to identify pathways related to neutrophil and endothelial cells homeostasis/activations, as disrupted in our patients. We hypothesized that unregulated neutrophil transendothelial migration could elicit increased neutrophil infiltration and tissue damage. Based on our findings, VEA, in our experimental dataset, allowed us to predict novel pathways impaired in subjects with autoinflammatory skin disorders.
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Affiliation(s)
- Lucas André Cavalcanti Brandão
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Ronald Rodrigues de Moura
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Angelo Valerio Marzano
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.V.M.); (C.M.)
- Department of Physiopathology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy
| | - Chiara Moltrasio
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.V.M.); (C.M.)
- Department of Medical Surgical and Health Sciences, University of Trieste, 34137 Trieste, Italy
| | - Paola Maura Tricarico
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, University of Qatar, Doha 2713, Qatar;
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