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Wu F, Chen X, Ma Y, Wu Y, Li R, Huang Y, Zhang R, Zhou Y, Zhan J, Liu S, Xu W. Glycosylated, Lipid-Binding, CDR-Like Domains of SARS-CoV-2 ORF8 Indicate Unique Sites of Immune Regulation. Microbiol Spectr 2023; 11:e0123423. [PMID: 37318366 PMCID: PMC10434001 DOI: 10.1128/spectrum.01234-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/23/2023] [Indexed: 06/16/2023] Open
Abstract
The outbreak of the novel coronavirus SARS-CoV-2 has posed a significant threat to human health and the global economy since the end of 2019. Unfortunately, due to the virus's rapid evolution, preventingand controlling the epidemic remains challenging. The ORF8 protein is a unique accessory protein in SARS-CoV-2 that plays a crucial role in immune regulation, but its molecular details are still largely unknown. In this study, we successfully expressed SARS-CoV-2 ORF8 in mammalian cells and determined its structure using X-ray crystallography at a resolution of 2.3 Å. Our findings reveal several novel features of ORF8. We found that four pairs of disulfide bonds and glycosylation at residue N78 are essential for stabilizing ORF8's protein structure. Additionally, we identified a lipid-binding pocket and three functional loops that tend to form CDR-like domains that may interact with immune-related proteins to regulate the host immune system. On cellular experiments also demonstrated that glycosylation at N78 regulats of ORF8's ability to bind to monocytes cells. These novel features of ORF8 provide structural insights to into its immune-related function and may serve as new targets for developing ORF8-mediated immune regulation inhibitors. IMPORTANCE COVID-19, caused by the novel coronavirus SARS-CoV-2 virus, has triggered a global outbreak. The virus's continuous mutation increases its infectivity and may be directly related to the immune escape response of viral proteins. In this study, we used X-ray crystallography to determine the structure of SARS-CoV-2 ORF8 protein, a unique accessory protein expressed in mammalian cells, at a resolution of 2.3 Å. Our novel structure reveals important structure details that shed light on ORF8's involvement in immune regulation, including conservation disulfide bonds, a glycosylation site at N78, a lipid-binding pocket, and three functional loops that tend to form CDR-like domains that may interact with immune-related proteins to modulate the host immune system. We also conducted preliminary validation experiments on immune cells. These new insights into ORF8's structure and function provide potential targets for developing inhibitors to block the ORF8-mediated immune regulation between viral protein and host, ultimately contributing to the development of novel therapeutics for COVID-19.
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Affiliation(s)
- Fang Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Xin Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yanhong Ma
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yuzhe Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Rui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yuanwei Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Rong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China
| | - Yaoqi Zhou
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Jian Zhan
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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2
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Al Ali F, Marr AK, Tatari-Calderone Z, Alfaki M, Toufiq M, Roelands J, Syed Ahamed Kabeer B, Bedognetti D, Marr N, Garand M, Rinchai D, Chaussabel D. Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers. F1000Res 2023; 10:275. [PMID: 37448622 PMCID: PMC10336363 DOI: 10.12688/f1000research.36395.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 07/15/2023] Open
Abstract
Early-career researchers must acquire the skills necessary to effectively search and extract information from biomedical literature. This ability is for instance crucial for evaluating the novelty of experimental results, and assessing potential publishing opportunities. Given the rapidly growing volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. In this context, we present a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. The curriculum was implemented in a workshop in January 2021. Here we provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Workshop participants can learn several skills, including: 1) building and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) identifying key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) measuring the prevalence of these concepts in the gene literature; 4) extracting key information from relevant articles, and 5) developing a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.
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Affiliation(s)
| | | | | | | | | | | | | | - Davide Bedognetti
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, 16126, Italy
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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3
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Toufiq M, Huang SSY, Boughorbel S, Alfaki M, Rinchai D, Saraiva LR, Chaussabel D, Garand M. SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis. THE JOURNAL OF IMMUNOLOGY 2021; 207:2195-2202. [PMID: 34663591 DOI: 10.4049/jimmunol.2100697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/30/2021] [Indexed: 11/19/2022]
Abstract
Sepsis develops after a dysregulated host inflammatory response to a systemic infection. Identification of sepsis biomarkers has been challenging because of the multifactorial causes of disease susceptibility and progression. Public transcriptomic data are a valuable resource for mechanistic discoveries and cross-studies concordance of heterogeneous diseases. Nonetheless, the approach requires structured methodologies and effective visualization tools for meaningful data interpretation. Currently, no such database exists for sepsis or systemic inflammatory diseases in human. Hence we curated SysInflam HuDB (http://sepsis.gxbsidra.org/dm3/geneBrowser/list), a unique collection of human blood transcriptomic datasets associated with systemic inflammatory responses to sepsis. The transcriptome collection and the associated clinical metadata are integrated onto a user-friendly and Web-based interface that allows the simultaneous exploration, visualization, and interpretation of multiple datasets stemming from different study designs. To date, the collection encompasses 62 datasets and 5719 individual profiles. Concordance of gene expression changes with the associated literature was assessed, and additional analyses are presented to showcase database utility. Combined with custom data visualization at the group and individual levels, SysInflam HuDB facilitates the identification of specific human blood gene signatures in response to infection (e.g., patients with sepsis versus healthy control subjects) and the delineation of major genetic drivers associated with inflammation onset and progression under various conditions.
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Affiliation(s)
| | - Susie Shih Yin Huang
- Sidra Medicine, Doha, Qatar.,Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO; and
| | | | | | | | - Luis R Saraiva
- Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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4
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Al Ali F, Marr AK, Tatari-Calderone Z, Alfaki M, Toufiq M, Roelands J, Syed Ahamed Kabeer B, Bedognetti D, Marr N, Garand M, Rinchai D, Chaussabel D. Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers. F1000Res 2021. [DOI: 10.12688/f1000research.36395.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.
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5
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Sawyer AJ, Garand M, Chaussabel D, Feng CG. Transcriptomic Profiling Identifies Neutrophil-Specific Upregulation of Cystatin F as a Marker of Acute Inflammation in Humans. Front Immunol 2021; 12:634119. [PMID: 33868254 PMCID: PMC8047108 DOI: 10.3389/fimmu.2021.634119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
Cystatin F encoded by CST7 is a cysteine peptidase inhibitor known to be expressed in natural killer (NK) and CD8+ T cells during steady-state conditions. However, little is known about its expression during inflammatory disease states in humans. We have developed an analytic approach capable of not only identifying previously poorly characterized disease-associated genes but also defining regulatory mechanisms controlling their expression. By exploring multiple cohorts of public transcriptome data comprising 43 individual datasets, we showed that CST7 is upregulated in the blood during a diverse set of infectious and non-infectious inflammatory conditions. Interestingly, this upregulation of CST7 was neutrophil-specific, as its expression was unchanged in NK and CD8+ T cells during sepsis. Further analysis demonstrated that known microbial products or cytokines commonly associated with inflammation failed to increase CST7 expression, suggesting that its expression in neutrophils is induced by an endogenous serum factor commonly present in human inflammatory conditions. Overall, through the identification of CST7 upregulation as a marker of acute inflammation in humans, our study demonstrates the value of publicly available transcriptome data in knowledge generation and potential biomarker discovery.
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Affiliation(s)
- Andrew J Sawyer
- Immunology and Host Defense Group, Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | | | | | - Carl G Feng
- Immunology and Host Defense Group, Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney, NSW, Australia
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6
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Hemorrhagic Shock Induces a Rapid Transcriptomic Shift of the Immune Balance in Leukocytes after Experimental Multiple Injury. Mediators Inflamm 2021; 2021:6654318. [PMID: 33574730 PMCID: PMC7857921 DOI: 10.1155/2021/6654318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Abstract
The immune response following trauma represents a major driving force of organ dysfunction and poor outcome. Therefore, we investigated the influence of an additional hemorrhagic shock (HS) on the early posttraumatic immune dysbalance in the whole population of blood leukocytes. A well-established murine polytrauma (PT) model with or without an additional pressure-controlled HS (mean arterial pressure of 30 mmHg (±5 mmHg) for 60 mins, afterwards fluid resuscitation with balanced electrolyte solution four times the volume of blood drawn) was used. C57BL/6 mice were randomized into a control, PT, and PT + HS group with three animals in each group. Four hours after trauma, corresponding to three hours after induction of hemorrhage, RNA was isolated from all peripheral blood leukocytes, and a microarray analysis was performed. Enrichment analysis was conducted on selected genes strongly modulated by the HS. After additional HS in PT mice, the gene expression of pathways related to the innate immunity, such as IL-6 production, neutrophil chemotaxis, cell adhesion, and toll-like receptor signaling was upregulated, whereas pathways of the adaptive immune system, such as B- and T-cell activation as well as the MHC class II protein complex, were downregulated. These results demonstrate that an additional HS plays an important role in the immune dysregulation early after PT by shifting the balance to increased innate and reduced adaptive immune responses.
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7
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Aljohmani A, Yildiz D. A Disintegrin and Metalloproteinase-Control Elements in Infectious Diseases. Front Cardiovasc Med 2020; 7:608281. [PMID: 33392273 PMCID: PMC7772189 DOI: 10.3389/fcvm.2020.608281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Despite recent advances in treatment strategies, infectious diseases are still under the leading causes of death worldwide. Although the activation of the inflammatory cascade is one prerequisite of defense, persistent and exuberant immune response, however, may lead to chronicity of inflammation predisposing to a temporal or permanent tissue damage not only of the site of infection but also among different body organs. The initial response to invading pathogens is mediated by the recognition through various pattern-recognition receptors along with cellular engulfment resulting in a coordinated release of soluble effector molecules and cytokines aiming to terminate the external stimuli. Members of the ‘a disintegrin and metalloproteinase’ (ADAM) family have the capability to proteolytically cleave transmembrane molecules close to the plasma membrane, a process called ectodomain shedding. In fact, in infectious diseases dysregulation of numerous ADAM substrates such as junction molecules (e.g., E-cadherin, VE-cadherin, JAM-A), adhesion molecules (e.g., ICAM-1, VCAM-1, L-selectin), and chemokines and cytokines (e.g., CXCL16, TNF-α) has been observed. The alpha-cleavage by ADAM proteases represents a rate limiting step for downstream regulated intramembrane proteolysis (RIPing) of several substrates, which influence cellular differentiation, cell signaling pathways and immune modulation. Both the substrates mentioned above and RIPing crucially contribute to a systematic damage in cardiovascular, endocrine, and/or gastrointestinal systems. This review will summarize the current knowledge of ADAM function and the subsequent RIPing in infectious diseases (e.g., pathogen recognition and clearance) and discuss the potential long-term effect on pathophysiological changes such as cardiovascular diseases.
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Affiliation(s)
- Ahmad Aljohmani
- Institute of Experimental and Clinical Pharmacology and Toxicology, PZMS, ZHMB, Saarland University, Homburg, Germany
| | - Daniela Yildiz
- Institute of Experimental and Clinical Pharmacology and Toxicology, PZMS, ZHMB, Saarland University, Homburg, Germany
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8
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Chou CW, Huang YK, Kuo TT, Liu JP, Sher YP. An Overview of ADAM9: Structure, Activation, and Regulation in Human Diseases. Int J Mol Sci 2020; 21:ijms21207790. [PMID: 33096780 PMCID: PMC7590139 DOI: 10.3390/ijms21207790] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
ADAM9 (A disintegrin and a metalloprotease 9) is a membrane-anchored protein that participates in a variety of physiological functions, primarily through the disintegrin domain for adhesion and the metalloprotease domain for ectodomain shedding of a wide variety of cell surface proteins. ADAM9 influences the developmental process, inflammation, and degenerative diseases. Recently, increasing evidence has shown that ADAM9 plays an important role in tumor biology. Overexpression of ADAM9 has been found in several cancer types and is correlated with tumor aggressiveness and poor prognosis. In addition, through either proteolytic or non-proteolytic pathways, ADAM9 promotes tumor progression, therapeutic resistance, and metastasis of cancers. Therefore, comprehensively understanding the mechanism of ADAM9 is crucial for the development of therapeutic anti-cancer strategies. In this review, we summarize the current understanding of ADAM9 in biological function, pathophysiological diseases, and various cancers. Recent advances in therapeutic strategies using ADAM9-related pathways are presented as well.
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Affiliation(s)
- Cheng-Wei Chou
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; (C.-W.C.); (Y.-K.H.); (J.-P.L.)
- Department of Medicine, Division of Hematology/Medical Oncology, Taichung Veterans General Hospital, Taichung 407, Taiwan
| | - Yu-Kai Huang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; (C.-W.C.); (Y.-K.H.); (J.-P.L.)
| | - Ting-Ting Kuo
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan;
| | - Jing-Pei Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; (C.-W.C.); (Y.-K.H.); (J.-P.L.)
| | - Yuh-Pyng Sher
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; (C.-W.C.); (Y.-K.H.); (J.-P.L.)
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan;
- Chinese Medicine Research Center, China Medical University, Taichung 404, Taiwan
- Correspondence: ; Tel.: +886-4-2205-2121
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9
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Transketolase and vitamin B1 influence on ROS-dependent neutrophil extracellular traps (NETs) formation. PLoS One 2019; 14:e0221016. [PMID: 31415630 PMCID: PMC6695114 DOI: 10.1371/journal.pone.0221016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are a recently identified, web-like, extracellular structure composed of decondensed nuclear DNA and associated antimicrobial granules. NETs are extruded into the extracellular environment via the reactive oxygen species (ROS)-dependent cell death pathway participating in inflammation and autoimmune diseases. Transketolase (TKT) is a thiamine pyrophosphate (vitamin B1)-dependent enzyme that links the pentose phosphate pathway with the glycolytic pathway by feeding excess sugar phosphates into the main carbohydrate metabolic pathways to generate biosynthetic reducing capacity in the form of NADPH as a substrate for ROS generation. In this work, TKT was selected as a lead candidate from 24 NET-associated proteins obtained by literature screening and knowledge gap assessment. Consequently, we determined whether TKT influenced NET formation in vitro. We firstly established that the release of ROS-dependent NETs was significantly decreased after purified human PMNs were pretreated with oxythiamine, a TKT inhibitor, and in a concentration dependent manner. As a cofactor for TKT reaction, we evaluated the release of NET formation either in vitamin B1 treatment or in combined use of oxythiamine and vitamin B1, and found that those treatments also exerted a significant suppressive effect on the amount of NET-DNA and ROS production. The regulation of TKT by oxythiamine and/or vitamin B1 may therefore be associated with response to the modulation of NET formation by preventing generation of excessive NETs in inflammatory diseases.
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10
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Huang SSY, Al Ali F, Boughorbel S, Toufiq M, Chaussabel D, Garand M. A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases. Database (Oxford) 2019; 2019:baz066. [PMID: 31290545 PMCID: PMC6616200 DOI: 10.1093/database/baz066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/14/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]
Abstract
Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). Thirty-three datasets from the Gene Expression Omnibus, encompassing 1860 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization and annotation of metadata. The thematic compositions, disease categories, sample number and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (http://ige.gxbsidra.org/dm3/geneBrowser/list). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.
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Affiliation(s)
| | - Fatima Al Ali
- Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar
| | | | | | | | - Mathieu Garand
- Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar
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11
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Chaussabel D, Rinchai D. Using 'collective omics data' for biomedical research training. Immunology 2018; 155:18-23. [PMID: 29705995 DOI: 10.1111/imm.12944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022] Open
Abstract
Systems-scale molecular profiling data accumulating in public repositories may constitute a useful resource for immunologists. It is for instance likely that information relevant to their chosen line of research be found among the more than 90,000 data series available in the NCBI Gene Expression Omnibus. Such 'collective omics data' may also be employed as source material for training purposes. This is the case when training curricula aim at the development of bioinformatics skills necessary for the analysis, interpretation or visualization of data generated on global scales. But 'collective omics data' may also be reused for training purposes to foster the development of the skills and 'mental habits' underpinning traditional reductionist science approaches. This review describes a small-scale initiative involving investigators, for the most part immunologists, having engaged in a range of training activities relying on 'collective omics data'.
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12
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Roelands J, Decock J, Boughorbel S, Rinchai D, Maccalli C, Ceccarelli M, Black M, Print C, Chou J, Presnell S, Quinn C, Jithesh P, Syed N, Al Bader SBJ, Bedri S, Wang E, Marincola FM, Chaussabel D, Kuppen P, Miller LD, Bedognetti D, Hendrickx W. A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification. F1000Res 2017. [PMID: 29527288 PMCID: PMC5820610 DOI: 10.12688/f1000research.10960.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). In this note, we describe a curated compendium of 13 public datasets on human breast cancer, representing a total of 2142 transcriptome profiles. We classified the samples according to different immune based classification systems and integrated this information into the datasets. Annotated and harmonized datasets were uploaded to GXB. Study samples were categorized in different groups based on their immunologic tumor response profiles, intrinsic molecular subtypes and multiple clinical parameters. Ranked gene lists were generated based on relevant group comparisons. In this data note, we demonstrate the utility of GXB to evaluate the expression of a gene of interest, find differential gene expression between groups and investigate potential associations between variables with a specific focus on immunologic classification in breast cancer. This interactive resource is publicly available online at:
http://breastcancer.gxbsidra.org/dm3/geneBrowser/list.
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Affiliation(s)
- Jessica Roelands
- Tumor Biology, Immunology and Therapy section, Sidra Medical and Research Center, Doha, Qatar
| | - Julie Decock
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Sabri Boughorbel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Darawan Rinchai
- Tumor Biology, Immunology and Therapy section, Sidra Medical and Research Center, Doha, Qatar
| | - Cristina Maccalli
- Tumor Biology, Immunology and Therapy section, Sidra Medical and Research Center, Doha, Qatar
| | | | - Michael Black
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Cris Print
- Department of Molecular Medicine and Pathology and Maurice Wilkins Institute, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Jeff Chou
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Puthen Jithesh
- Translational Bioinformatics, Division of Biomedical Informatics Research, Sidra Medical and Research Center, Doha, Qatar
| | - Najeeb Syed
- Technical Bioinformatics team, Biomedical Informatics Division, Sidra Medical and Research Center, Doha, Qatar
| | - Salha B J Al Bader
- National Center for Cancer Care and Research (NCCCR), Hamad General Hospital, Doha, Qatar
| | | | - Ena Wang
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Francesco M Marincola
- Office of the Chief Research Officer (CRO), Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Peter Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Davide Bedognetti
- Tumor Biology, Immunology and Therapy section, Sidra Medical and Research Center, Doha, Qatar
| | - Wouter Hendrickx
- Tumor Biology, Immunology and Therapy section, Sidra Medical and Research Center, Doha, Qatar
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13
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Rinchai D, Kewcharoenwong C, Kessler B, Lertmemongkolchai G, Chaussabel D. Increased abundance of ADAM9 transcripts in the blood is associated with tissue damage. F1000Res 2015; 4:89. [PMID: 27990250 PMCID: PMC5130078 DOI: 10.12688/f1000research.6241.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 12/22/2022] Open
Abstract
Background: Members of the ADAM (a disintegrin and metalloprotease domain) family have emerged as critical regulators of cell-cell signaling during development and homeostasis. ADAM9 is consistently overexpressed in various human cancers, and has been shown to play an important role in tumorigenesis. However, little is known about the involvement of ADAM9 during immune-mediated processes. Results: Mining of an extensive compendium of transcriptomic datasets identified important gaps in knowledge regarding the possible role of ADAM9 in immunological homeostasis and inflammation: 1) The abundance of ADAM9 transcripts in the blood was increased in patients with acute infection but, 2) changed very little after
in vitro exposure to a wide range of pathogen-associated molecular patterns (PAMPs). 3) Furthermore it was found to increase significantly in subjects as a result of tissue injury or tissue remodeling, in absence of infectious processes. Conclusions: Our findings indicate that ADAM9 may constitute a valuable biomarker for the assessment of tissue damage, especially in clinical situations where other inflammatory markers are confounded by infectious processes.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Chidchamai Kewcharoenwong
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Bianca Kessler
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Ganjana Lertmemongkolchai
- Cellular and Molecular Immunology Unit, The Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40000, Thailand
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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