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Karimi N, Motovali-Bashi M, Ghaderi-Zefrehei M. Gene network reveals LASP1, TUBA1C, and S100A6 are likely playing regulatory roles in multiple sclerosis. Front Neurol 2023; 14:1090631. [PMID: 36970516 PMCID: PMC10035600 DOI: 10.3389/fneur.2023.1090631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionMultiple sclerosis (MS), a non-contagious and chronic disease of the central nervous system, is an unpredictable and indirectly inherited disease affecting different people in different ways. Using Omics platforms genomics, transcriptomics, proteomics, epigenomics, interactomics, and metabolomics database, it is now possible to construct sound systems biology models to extract full knowledge of the MS and recognize the pathway to uncover the personalized therapeutic tools.MethodsIn this study, we used several Bayesian Networks in order to find the transcriptional gene regulation networks that drive MS disease. We used a set of BN algorithms using the R add-on package bnlearn. The BN results underwent further downstream analysis and were validated using a wide range of Cytoscape algorithms, web based computational tools and qPCR amplification of blood samples from 56 MS patients and 44 healthy controls. The results were semantically integrated to improve understanding of the complex molecular architecture underlying MS, distinguishing distinct metabolic pathways and providing a valuable foundation for the discovery of involved genes and possibly new treatments.ResultsResults show that the LASP1, TUBA1C, and S100A6 genes were most likely playing a biological role in MS development. Results from qPCR showed a significant increase (P < 0.05) in LASP1 and S100A6 gene expression levels in MS patients compared to that in controls. However, a significant down regulation of TUBA1C gene was observed in the same comparison.ConclusionThis study provides potential diagnostic and therapeutic biomarkers for enhanced understanding of gene regulation underlying MS.
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Affiliation(s)
- Nafiseh Karimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- *Correspondence: Majid Motovali-Bashi
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2
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Howlett-Prieto Q, Oommen C, Carrithers MD, Wunsch DC, Hier DB. Subtypes of relapsing-remitting multiple sclerosis identified by network analysis. Front Digit Health 2023; 4:1063264. [PMID: 36714613 PMCID: PMC9874946 DOI: 10.3389/fdgth.2022.1063264] [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: 10/06/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
We used network analysis to identify subtypes of relapsing-remitting multiple sclerosis subjects based on their cumulative signs and symptoms. The electronic medical records of 113 subjects with relapsing-remitting multiple sclerosis were reviewed, signs and symptoms were mapped to classes in a neuro-ontology, and classes were collapsed into sixteen superclasses by subsumption. After normalization and vectorization of the data, bipartite (subject-feature) and unipartite (subject-subject) network graphs were created using NetworkX and visualized in Gephi. Degree and weighted degree were calculated for each node. Graphs were partitioned into communities using the modularity score. Feature maps visualized differences in features by community. Network analysis of the unipartite graph yielded a higher modularity score (0.49) than the bipartite graph (0.25). The bipartite network was partitioned into five communities which were named fatigue, behavioral, hypertonia/weakness, abnormal gait/sphincter, and sensory, based on feature characteristics. The unipartite network was partitioned into five communities which were named fatigue, pain, cognitive, sensory, and gait/weakness/hypertonia based on features. Although we did not identify pure subtypes (e.g., pure motor, pure sensory, etc.) in this cohort of multiple sclerosis subjects, we demonstrated that network analysis could partition these subjects into different subtype communities. Larger datasets and additional partitioning algorithms are needed to confirm these findings and elucidate their significance. This study contributes to the literature investigating subtypes of multiple sclerosis by combining feature reduction by subsumption with network analysis.
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Affiliation(s)
- Quentin Howlett-Prieto
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, IL, United States
| | - Chelsea Oommen
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, IL, United States
| | - Michael D. Carrithers
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, IL, United States
| | - Donald C. Wunsch
- Department of Electrical and Computer Engineering, Missouri University of Science and Technology, Rolla, MO, United States
| | - Daniel B. Hier
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, IL, United States,Department of Electrical and Computer Engineering, Missouri University of Science and Technology, Rolla, MO, United States,Correspondence: Daniel B. Hier
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3
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Hyland PL, Chekka LMS, Samarth DP, Rosenzweig BA, Decker E, Mohamed EG, Guo Y, Matta MK, Sun Q, Wheeler W, Sanabria C, Weaver JL, Schrieber SJ, Florian J, Wang YM, Strauss DG. Evaluating the Utility of Proteomics for the Identification of Circulating Pharmacodynamic Biomarkers of IFNβ-1a Biologics. Clin Pharmacol Ther 2023; 113:98-107. [PMID: 36308070 DOI: 10.1002/cpt.2778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Proteomics has the potential to identify pharmacodynamic (PD) biomarkers for similarity assessment of proposed biosimilars without relying on clinical efficacy end points. In this study, with 36 healthy participants randomized to therapeutic doses of interferon-beta 1a products (IFNβ-1a) or pegylated-IFNβ-1a (pegIFNβ-1a) approved to treat multiple sclerosis or placebo, we evaluated the utility of a proteomic assay that profiles > 7,000 plasma proteins. IFNβ-1a and pegIFNβ-1a resulted in 248 and 528 differentially expressed protein analytes, respectively, between treatment and placebo groups over the time course. Thirty-one proteins were prioritized based on a maximal fold change ≥ 2 from baseline, baseline adjusted area under the effect curve (AUEC) and overlap between the 2 products. Of these, the majority had a significant AUEC compared with placebo in response to either product; 8 proteins showed > 4-fold maximal change from baseline. We identified previously reported candidates, beta-2microglobulin and interferon-induced GTP-binding protein (Mx1) with ~ 50% coefficient of variation (CV) for AUEC, and many new candidates (including I-TAC, C1QC, and IP-10) with CVs ranging from 26%-129%. Upstream regulator analysis of differentially expressed proteins predicted activation of IFNβ1 signaling as well as other cytokine, enzyme, and transcription signaling networks by both products. Although independent replication is required to confirm present results, our study demonstrates the utility of proteomics for the identification of individual and composite candidate PD biomarkers that may be leveraged to support clinical pharmacology studies for biosimilar approvals, especially when biologics have complex mechanisms of action or do not have previously characterized PD biomarkers.
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Affiliation(s)
- Paula L Hyland
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Lakshmi Manasa S Chekka
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Deepti P Samarth
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Barry A Rosenzweig
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Erica Decker
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Esraa G Mohamed
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yan Guo
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Murali K Matta
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Qin Sun
- Therapeutic Biologics Protein Team, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - William Wheeler
- Information Management Services, Inc., Rockville, Maryland, USA
| | | | - James L Weaver
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sarah J Schrieber
- Office of Therapeutic Biologics and Biosimilars, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jeffry Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yow-Ming Wang
- Therapeutic Biologics Protein Team, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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4
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Diakou I, Papakonstantinou E, Papageorgiou L, Pierouli K, Dragoumani K, Spandidos DA, Bacopoulou F, Chrousos GP, Goulielmos GΝ, Eliopoulos E, Vlachakis D. Multiple sclerosis and computational biology (Review). Biomed Rep 2022; 17:96. [PMID: 36382258 PMCID: PMC9634047 DOI: 10.3892/br.2022.1579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune neurodegenerative disease whose prevalence has increased worldwide. The resultant symptoms may be debilitating and can substantially reduce the of patients. Computational biology, which involves the use of computational tools to answer biomedical questions, may provide the basis for novel healthcare approaches in the context of MS. The rapid accumulation of health data, and the ever-increasing computational power and evolving technology have helped to modernize and refine MS research. From the discovery of novel biomarkers to the optimization of treatment and a number of quality-of-life enhancements for patients, computational biology methods and tools are shaping the field of MS diagnosis, management and treatment. The final goal in such a complex disease would be personalized medicine, i.e., providing healthcare services that are tailored to the individual patient, in accordance to the particular biology of their disease and the environmental factors to which they are subjected. The present review article summarizes the current knowledge on MS, modern computational biology and the impact of modern computational approaches of MS.
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Affiliation(s)
- Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
| | - Georges Ν. Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of The Academy of Athens, 11527 Athens, Greece
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5
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Al Hrout A, Cervantes-Gracia K, Chahwan R, Amin A. Modelling liver cancer microenvironment using a novel 3D culture system. Sci Rep 2022; 12:8003. [PMID: 35568708 PMCID: PMC9107483 DOI: 10.1038/s41598-022-11641-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/27/2022] [Indexed: 12/22/2022] Open
Abstract
The tumor microenvironment and its contribution to tumorigenesis has been a focal highlight in recent years. A two-way communication between the tumor and the surrounding microenvironment sustains and contributes to the growth and metastasis of tumors. Progression and metastasis of hepatocellular carcinoma (HCC) have been reported to be exceedingly influenced by diverse microenvironmental cues. In this study, we present a 3D-culture model of liver cancer to better mimic in vivo tumor settings. By creating novel 3D co-culture model that combines free-floating and scaffold-based 3D-culture techniques of liver cancer cells and fibroblasts, we aimed to establish a simple albeit reproducible ex vivo cancer microenvironment model that captures tumor-stroma interactions. The model presented herein exhibited unique gene expression and protein expression profiles when compared to 2D and 3D mono-cultures of liver cancer cells. Our results showed that in vivo like conditions cannot be mimicked by simply growing cancer cells as spheroids, but by co-culturing them with 3D fibroblast with which they were able to crosstalk. This was evident by the upregulation of several pathways involved in HCC, and the increase in secreted factors by co-cultured cancer cells, many of which are also involved in tumor-stroma interactions. Compared to the conventional 2D culture, the proposed model exhibits an increase in the expression of genes associated with development, progression, and poor prognosis of HCC. Our results correlated with an aggressive outcome that better mirrors in vivo HCC, and therefore, a more reliable platform for molecular understanding of HCC.
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Affiliation(s)
- Ala'a Al Hrout
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, United Arab Emirates
| | - Karla Cervantes-Gracia
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Amr Amin
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, United Arab Emirates.
- The University of Chicago, Chicago, IL, 60637, USA.
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6
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Yurduseven K, Babal YK, Celik E, Kerman BE, Kurnaz IA. Multiple Sclerosis Biomarker Candidates Revealed by Cell-Type-Specific Interactome Analysis. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:305-317. [PMID: 35483054 DOI: 10.1089/omi.2022.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multiple sclerosis (MS) is a demyelinating disorder that affects multiple regions of the central nervous system such as the brain, spinal cord, and optic nerves. Susceptibility to MS, as well as disease progression rates, displays marked patient-to-patient variability. To date, biomarkers that forecast differences in clinical phenotypes and outcomes have been limited. In this context, cell-type-specific interactome analyses offer important prospects and hope for novel diagnostics and therapeutics. We report here an original study using bioinformatic analysis of MS data sets that revealed interaction profiles as well as specific hub proteins in white matter (WM) and gray matter (GM) that appear critical for disease mechanisms. First, cell-type-specific interactome analyses suggested that while interactions within the WM were focused on oligodendrocytes, interactions within the GM were mostly neuron centric. Second, hub proteins such as APP, EGLN3, PTEN, and LRRK2 were identified to be differentially regulated in MS data sets. Lastly, a comparison of the brain and peripheral blood samples identified biomarker candidates such as NRGN, CRTC1, CDC42, and IFITM3 to be differentially expressed in different types of MS. These findings offer a unique cell-type-specific cell-to-cell interaction network in MS and identify potential biomarkers by comparative analysis of the brain and the blood transcriptomics. From a study design and methodology perspective, we suggest that the cell-type-specific interactome analysis is an important systems science frontier that might offer new insights on other neurodegenerative and brain disorders as well.
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Affiliation(s)
- Kübra Yurduseven
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Yigit Koray Babal
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Esref Celik
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Bilal Ersen Kerman
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Işıl Aksan Kurnaz
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
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7
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Noble AJ, Purcell RV, Adams AT, Lam YK, Ring PM, Anderson JR, Osborne AJ. A Final Frontier in Environment-Genome Interactions? Integrated, Multi-Omic Approaches to Predictions of Non-Communicable Disease Risk. Front Genet 2022; 13:831866. [PMID: 35211161 PMCID: PMC8861380 DOI: 10.3389/fgene.2022.831866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/19/2022] [Indexed: 12/26/2022] Open
Abstract
Epidemiological and associative research from humans and animals identifies correlations between the environment and health impacts. The environment—health inter-relationship is effected through an individual’s underlying genetic variation and mediated by mechanisms that include the changes to gene regulation that are associated with the diversity of phenotypes we exhibit. However, the causal relationships have yet to be established, in part because the associations are reduced to individual interactions and the combinatorial effects are rarely studied. This problem is exacerbated by the fact that our genomes are highly dynamic; they integrate information across multiple levels (from linear sequence, to structural organisation, to temporal variation) each of which is open to and responds to environmental influence. To unravel the complexities of the genomic basis of human disease, and in particular non-communicable diseases that are also influenced by the environment (e.g., obesity, type II diabetes, cancer, multiple sclerosis, some neurodegenerative diseases, inflammatory bowel disease, rheumatoid arthritis) it is imperative that we fully integrate multiple layers of genomic data. Here we review current progress in integrated genomic data analysis, and discuss cases where data integration would lead to significant advances in our ability to predict how the environment may impact on our health. We also outline limitations which should form the basis of future research questions. In so doing, this review will lay the foundations for future research into the impact of the environment on our health.
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Affiliation(s)
- Alexandra J Noble
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel V Purcell
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Ying K Lam
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Paulina M Ring
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jessica R Anderson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy J Osborne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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8
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Cervantes-Gracia K, Chahwan R, Husi H. Integrative OMICS Data-Driven Procedure Using a Derivatized Meta-Analysis Approach. Front Genet 2022; 13:828786. [PMID: 35186042 PMCID: PMC8855827 DOI: 10.3389/fgene.2022.828786] [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: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
The wealth of high-throughput data has opened up new opportunities to analyze and describe biological processes at higher resolution, ultimately leading to a significant acceleration of scientific output using high-throughput data from the different omics layers and the generation of databases to store and report raw datasets. The great variability among the techniques and the heterogeneous methodologies used to produce this data have placed meta-analysis methods as one of the approaches of choice to correlate the resultant large-scale datasets from different research groups. Through multi-study meta-analyses, it is possible to generate results with greater statistical power compared to individual analyses. Gene signatures, biomarkers and pathways that provide new insights of a phenotype of interest have been identified by the analysis of large-scale datasets in several fields of science. However, despite all the efforts, a standardized regulation to report large-scale data and to identify the molecular targets and signaling networks is still lacking. Integrative analyses have also been introduced as complementation and augmentation for meta-analysis methodologies to generate novel hypotheses. Currently, there is no universal method established and the different methods available follow different purposes. Herein we describe a new unifying, scalable and straightforward methodology to meta-analyze different omics outputs, but also to integrate the significant outcomes into novel pathways describing biological processes of interest. The significance of using proper molecular identifiers is highlighted as well as the potential to further correlate molecules from different regulatory levels. To show the methodology’s potential, a set of transcriptomic datasets are meta-analyzed as an example.
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Affiliation(s)
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- *Correspondence: Richard Chahwan, ; Holger Husi,
| | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
- Division of Biomedical Sciences, Centre for Health Science, University of the Highlands and Islands, Inverness, United Kingdom
- *Correspondence: Richard Chahwan, ; Holger Husi,
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9
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The analysis of a subset of HLA region associations in type 1 diabetes and multiple sclerosis suggests the involvement mechanisms other than antigen presentation in the pathogenesis. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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10
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Onisiforou A, Spyrou GM. Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. Brief Bioinform 2021; 22:bbab141. [PMID: 34237135 PMCID: PMC8574625 DOI: 10.1093/bib/bbab141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
During the course of a viral infection, virus-host protein-protein interactions (PPIs) play a critical role in allowing viruses to replicate and survive within the host. These interspecies molecular interactions can lead to viral-mediated perturbations of the human interactome causing the generation of various complex diseases. Evidences suggest that viral-mediated perturbations are a possible pathogenic etiology in several neurodegenerative diseases (NDs). These diseases are characterized by chronic progressive degeneration of neurons, and current therapeutic approaches provide only mild symptomatic relief; therefore, there is unmet need for the discovery of novel therapeutic interventions. In this paper, we initially review databases and tools that can be utilized to investigate viral-mediated perturbations in complex NDs using network-based analysis by examining the interaction between the ND-related PPI disease networks and the virus-host PPI network. Afterwards, we present our theoretical-driven integrative network-based bioinformatics approach that accounts for pathogen-genes-disease-related PPIs with the aim to identify viral-mediated pathogenic mechanisms focusing in multiple sclerosis (MS) disease. We identified seven high centrality nodes that can act as disease communicator nodes and exert systemic effects in the MS-enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways network. In addition, we identified 12 KEGG pathways, 5 Reactome pathways and 52 Gene Ontology Immune System Processes by which 80 viral proteins from eight viral species might exert viral-mediated pathogenic mechanisms in MS. Finally, our analysis highlighted the Th17 differentiation pathway, a disease communicator node and part of the 12 underlined KEGG pathways, as a key viral-mediated pathogenic mechanism and a possible therapeutic target for MS disease.
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Affiliation(s)
- Anna Onisiforou
- Department of Bioinformatics, Cyprus Institute of Neurology & Genetics, and the Cyprus School of Molecular Medicine, Cyprus
| | - George M Spyrou
- Department of Bioinformatics, Cyprus Institute of Neurology & Genetics, and professor at the Cyprus School of Molecular Medicine, Cyprus
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11
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Yue JL, Zheng SF. Analysis of association between MALAT1 haplotype and the severity of normal-tension glaucoma (NTG). J Cell Mol Med 2021; 25:9918-9926. [PMID: 34599867 PMCID: PMC8572781 DOI: 10.1111/jcmm.15906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/20/2020] [Accepted: 09/02/2020] [Indexed: 12/29/2022] Open
Abstract
MALAT1, which is disorderly expressed in the growth, invasion, migration and cancer cell apoptosis, was shown to be associated with normal-tension glaucoma (NTG), a type of optic neuropathy. The haplotype in MALAT1 affects its expression and is correlated with human diseases like normal-tension glaucoma (NTG). However, the underlying detailed mechanism remains unclear. In this study, we aimed to analyse the association between MALAT1 haplotype and the severity of NTG in a molecular level. Quantitative real-time PCR, ELISA and luciferase assays were performed to establish the underlying signalling pathways. RNFL thickness, RA and C/D ratio were calculated for NTG patients. Accordingly, GGGT haplotype was demonstrated to be associated with a decreased risk of NTG. The MALAT1 level in serum of NTG patients carrying GGGT haplotype was significantly decreased compared with NTG patients carrying other haplotypes, along with elevated miR-1 expression and diminished IL-6 expression. NTG patients carrying GGGT haplotype had thicker RNFL and RA, but a smaller C/D ratio. Sequence analysis found potential target sites of miR-1 on MALAT1 and IL-6, and luciferase assay confirmed the inhibitory effect of miR-1 on MALAT1 and IL-6 expression. Meanwhile, MALAT1 also down-regulated miR-1 expression and consequently up-regulated IL-6 expression. This study presented evidence for a regulatory network containing MALAT1, miR-1 and IL-6, and further demonstrated the effect of MALAT1 haplotype on the risk and severity of NTG.
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Affiliation(s)
- Jin-Liang Yue
- Ophthalmology Department, Zhoukou Central Hospital, Zhoukou, China
| | - Shu-Feng Zheng
- Ophthalmology Department, Eye Hospital, Traditional Chinese Medicine Hospital of Yulin, Yulin, China
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12
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Derakhshani A, Safarpour H, Abdoli Shadbad M, Hemmat N, Leone P, Asadzadeh Z, Pashazadeh M, Baradaran B, Racanelli V. The Role of Hemoglobin Subunit Delta in the Immunopathy of Multiple Sclerosis: Mitochondria Matters. Front Immunol 2021; 12:709173. [PMID: 34504491 PMCID: PMC8421544 DOI: 10.3389/fimmu.2021.709173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/06/2021] [Indexed: 01/11/2023] Open
Abstract
Background Although the exact pathophysiology of MS has not been identified, mitochondrial stress can be one of the culprits in MS development. Herein, we have applied microarray analysis, single-cell sequencing analysis, and ex vivo study to elucidate the role of mitochondrial stress in PBMCs of MS patients. Methods For this purpose, we analyzed the GSE21942 and GSE138266 datasets to identify the DEGs and hub genes in the PBMCS of MS patients and describe the expression of shared genes in the different immune cells. The GO pathway analysis of DEGs and turquoise module genes were conducted to shed light on their biological significance. To validate the obtained results, the gene expression of HBD, as the most remarkable DEG in the PBMCS of affected patients, was measured in the PBMCS of healthy donors, treatment-naïve MS patients, and MS patients treated with GA, fingolimod, DMF, and IFNβ-1α. Results Based on WGCNA and DEGs analysis, HBD, HBM, SLC4A1, LILRA5, SLC25A37, SELENBP1, ALYREF, SNRNP40, and HINT3 are the identified common genes in the PMBCS. Using single-cell sequencing analysis on PBMCS, we have characterized various cell populations in MS and illustrated the common gene expression on the different immune cells. Furthermore, GO pathway analysis of DEGs, and turquoise module genes have indicated that these genes are involved in immune responses, myeloid cell activation, leukocyte activation, oxygen carrier activity, and replication fork processing bicarbonate transport pathways. Our ex vivo investigation has shown that HBD expression in the treatment-naïve RRMS patients is significantly increased compared to healthy donors. Of interest, immunomodulatory therapies with fingolimod, DMF, and IFNβ-1α have significantly decreased HBD expression. Conclusion HBD is one of the remarkably up-regulated genes in the PBMCS of MS patients. HBD is substantially up-regulated in treatment-naïve MS patients, and immunomodulatory therapies with fingolimod, DMF, and IFNβ-1α can remarkably down-regulate HBD expression. Based on the currently available evidence, the cytoprotective nature of HBD against oxidative stress can be the underlying reason for HBD up-regulation in MS. Nevertheless, further investigations are needed to shed light on the molecular mechanisms of HBD in the oxidative stress of MS patients.
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Affiliation(s)
- Afshin Derakhshani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Laboratory of Experimental Pharmacology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Mahdi Abdoli Shadbad
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nima Hemmat
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Patrizia Leone
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Bari, Italy
| | - Zahra Asadzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehrdad Pashazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran,*Correspondence: Vito Racanelli, ; Behzad Baradaran,
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Bari, Italy,*Correspondence: Vito Racanelli, ; Behzad Baradaran,
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13
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Chase Huizar C, Raphael I, Forsthuber TG. Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. Cell Immunol 2020; 358:104219. [PMID: 33039896 PMCID: PMC7927152 DOI: 10.1016/j.cellimm.2020.104219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder characterized by autoimmune-mediated inflammatory lesions in CNS leading to myelin damage and axonal loss. MS is a heterogenous disease with variable and unpredictable disease course. Due to its complex nature, MS is difficult to diagnose and responses to specific treatments may vary between individuals. Therefore, there is an indisputable need for biomarkers for early diagnosis, prediction of disease exacerbations, monitoring the progression of disease, and for measuring responses to therapy. Genomic and proteomic studies have sought to understand the molecular basis of MS and find biomarker candidates. Advances in next-generation sequencing and mass-spectrometry techniques have yielded an unprecedented amount of genomic and proteomic data; yet, translation of the results into the clinic has been underwhelming. This has prompted the development of novel data science techniques for exploring these large datasets to identify biologically relevant relationships and ultimately point towards useful biomarkers. Herein we discuss optimization of omics study designs, advances in the generation of omics data, and systems biology approaches aimed at improving biomarker discovery and translation to the clinic for MS.
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Affiliation(s)
- Carol Chase Huizar
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Itay Raphael
- Department of Neurological Surgery, University of Pittsburgh, UPMC Children's Hospital, Pittsburgh, PA, USA.
| | - Thomas G Forsthuber
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA.
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14
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Sol N, Leurs CE, Veld SGI', Strijbis EM, Vancura A, Schweiger MW, Teunissen CE, Mateen FJ, Tannous BA, Best MG, Würdinger T, Killestein J. Blood platelet RNA enables the detection of multiple sclerosis. Mult Scler J Exp Transl Clin 2020; 6:2055217320946784. [PMID: 32843989 PMCID: PMC7418262 DOI: 10.1177/2055217320946784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/05/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background In multiple sclerosis (MS), clinical assessment, MRI and cerebrospinal fluid are important in the diagnostic process. However, no blood biomarker has been confirmed as a useful tool in the diagnostic work-up. Objectives Blood platelets contain a rich spliced mRNA repertoire that can alter during megakaryocyte development but also during platelet formation and platelet circulation. In this proof of concept study, we evaluate the diagnostic potential of spliced blood platelet RNA for the detection of MS. Methods We isolated and sequenced platelet RNA of blood samples obtained from 57 MS patients and 66 age- and gender-matched healthy controls (HCs). 60% was used to develop a particle swarm-optimized (PSO) support vector machine classification algorithm. The remaining 40% served as an independent validation series. Results In total, 1249 RNAs with differential spliced junction expression levels were identified between platelets of MS patients as compared to HCs, including EPSTI1, IFI6, and RPS6KA3, in line with reported inflammatory signatures in the blood of MS patients. The RNAs were subsequently used as input for a MS classifier, capable of detecting MS with 80% accuracy in the independent validation series. Conclusions Spliced platelet RNA may enable the blood-based diagnosis of MS, warranting large-scale validation.
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Affiliation(s)
- Nik Sol
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Cyra E Leurs
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sjors Gjg In 't Veld
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Eva M Strijbis
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Adrienne Vancura
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Markus W Schweiger
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Neuroscience Campus Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Farrah J Mateen
- Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Bakhos A Tannous
- Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Myron G Best
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Pathology, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Thomas Würdinger
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Joep Killestein
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
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15
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Kharati M, Foroutanparsa S, Rabiee M, Salarian R, Rabiee N, Rabiee G. Early Diagnosis of Multiple Sclerosis Based on Optical and Electrochemical Biosensors: Comprehensive Perspective. CURR ANAL CHEM 2020. [DOI: 10.2174/1573411014666180829111004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background:
Multiple Sclerosis (MS) involves an immune-mediated response in which
body’s immune system destructs the protective sheath (myelin). Part of the known MS biomarkers are
discovered in cerebrospinal fluid like oligoclonal lgG (OCGB), and also in blood like myelin Oligodendrocyte
Glycoprotein (MOG). The conventional MS diagnostic methods often fail to detect the
disease in early stages such as Clinically Isolated Syndrome (CIS), which considered as a concerning
issue since CIS highlighted as a prognostic factor of MS development in most cases.
Methods:
MS diagnostic techniques include Magnetic Resonance Imaging (MRI) of the brain and spinal
cord, lumbar puncture (or spinal tap) that evaluate cerebrospinal fluid, evoked potential testing revealing
abnormalities in the brain and spinal cord. These conventional diagnostic methods have some
negative points such as extensive processing time as well as restriction in the quantity of samples that
can be analyzed concurrently. Scientists have focused on developing the detection methods especially
early detection which belongs to ultra-sensitive, non-invasive and needed for the Point of Care (POC)
diagnosis because the situation was complicated by false positive or negative results.
Results:
As a result, biosensors are utilized and investigated since they could be ultra-sensitive to specific
compounds, cost effective devices, body-friendly and easy to implement. In addition, it has been
proved that the biosensors on physiological fluids (blood, serum, urine, saliva, milk etc.) have quick
response in a non-invasive rout. In general form, a biosensor system for diagnosis and early detection
process usually involves; biomarker (target molecule), bio receptor (recognition element) and compatible
bio transducer.
Conclusion:
Studies underlined that early treatment of patients with high possibility of MS can be advantageous
by postponing further abnormalities on MRI and subsequent attacks.
:
This Review highlights variable disease diagnosis approaches such as Surface Plasmon Resonance
(SPR), electrochemical biosensors, Microarrays and microbeads based Microarrays, which are considered
as promising methods for detection and early detection of MS.
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Affiliation(s)
- Maryam Kharati
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Sanam Foroutanparsa
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Mohammad Rabiee
- Biomaterials Group, Faculty of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Reza Salarian
- Biomedical Engineering Department, Maziar University, Noor, Royan, Iran
| | - Navid Rabiee
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - Ghazal Rabiee
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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16
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Oon S, Monaghan K, Ng M, Hoi A, Morand E, Vairo G, Maraskovsky E, Nash AD, Wicks IP, Wilson NJ. A potential association between IL-3 and type I and III interferons in systemic lupus erythematosus. Clin Transl Immunology 2019; 8:e01097. [PMID: 31890206 PMCID: PMC6928763 DOI: 10.1002/cti2.1097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 10/30/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Objectives Plasmacytoid dendritic cells (pDCs), through the production of type 1 interferons (IFNs) and other cytokines, are major contributors to systemic lupus erythematosus (SLE) pathogenesis. IL-3 promotes pDC survival, but its role in SLE is not well characterised. This study investigated serum IL-3 and IFN levels, and a whole blood 'IL-3 gene signature', in human SLE. Methods Serum cytokine levels were measured by ELISA in n = 42 SLE patients, and n = 44 healthy donors. IL-3-regulated genes were determined by RNASeq of healthy donor whole blood cells (WBCs) stimulated in vitro with IL-3 for 6 or 24 h. Whole blood cell RNASeq analysis was undertaken in a separate cohort of n = 31 SLE patients, and n = 28 healthy donors. Results Serum IL-3 levels correlated with IFNα (r = 0.612, 95% CI 0.455-0.733, P < 0.001) and type III IFN (r = 0.585, 95% CI 0.406-0.720, P < 0.0001). IL-3 stimulation of WBC in vitro altered 794 genes (-1 ≥ logFC ≥ 1, FDR < 0.05), of which 35 overlapped with genes differentially expressed between SLE and healthy donors. These 35 genes were expressed in 27/31 SLE donors, revealing the presence of an 'IL-3 gene signature'. There was strong correlation between the IL-3 signature and an IFN signature, as determined by hierarchical clustering of the 500 most variable genes in SLE donors (r = 0.939, 95% CI 0.898-0.964, P < 0.0001). Conclusion A dual IL-3/IFN gene signature is a feature of SLE. An association between IL-3 and IFN raises the possibility that dual blockade of IL-3 and IFN may be especially useful for SLE patients with this dual cytokine gene signature.
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Affiliation(s)
- Shereen Oon
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,The Royal Melbourne Hospital Parkville VIC Australia.,The University of Melbourne Parkville VIC Australia
| | | | | | | | | | | | - Eugene Maraskovsky
- The University of Melbourne Parkville VIC Australia.,CSL Limited Parkville VIC Australia
| | - Andrew D Nash
- The University of Melbourne Parkville VIC Australia.,CSL Limited Parkville VIC Australia
| | - Ian P Wicks
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,The Royal Melbourne Hospital Parkville VIC Australia.,The University of Melbourne Parkville VIC Australia
| | - Nicholas J Wilson
- The University of Melbourne Parkville VIC Australia.,CSL Limited Parkville VIC Australia
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17
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Marín M, Esteban FJ, Ramírez-Rodrigo H, Ros E, Sáez-Lara MJ. An integrative methodology based on protein-protein interaction networks for identification and functional annotation of disease-relevant genes applied to channelopathies. BMC Bioinformatics 2019; 20:565. [PMID: 31718537 PMCID: PMC6849233 DOI: 10.1186/s12859-019-3162-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background Biologically data-driven networks have become powerful analytical tools that handle massive, heterogeneous datasets generated from biomedical fields. Protein-protein interaction networks can identify the most relevant structures directly tied to biological functions. Functional enrichments can then be performed based on these structural aspects of gene relationships for the study of channelopathies. Channelopathies refer to a complex group of disorders resulting from dysfunctional ion channels with distinct polygenic manifestations. This study presents a semi-automatic workflow using protein-protein interaction networks that can identify the most relevant genes and their biological processes and pathways in channelopathies to better understand their etiopathogenesis. In addition, the clinical manifestations that are strongly associated with these genes are also identified as the most characteristic in this complex group of diseases. Results In particular, a set of nine representative disease-related genes was detected, these being the most significant genes in relation to their roles in channelopathies. In this way we attested the implication of some voltage-gated sodium (SCN1A, SCN2A, SCN4A, SCN4B, SCN5A, SCN9A) and potassium (KCNQ2, KCNH2) channels in cardiovascular diseases, epilepsies, febrile seizures, headache disorders, neuromuscular, neurodegenerative diseases or neurobehavioral manifestations. We also revealed the role of Ankyrin-G (ANK3) in the neurodegenerative and neurobehavioral disorders as well as the implication of these genes in other systems, such as the immunological or endocrine systems. Conclusions This research provides a systems biology approach to extract information from interaction networks of gene expression. We show how large-scale computational integration of heterogeneous datasets, PPI network analyses, functional databases and published literature may support the detection and assessment of possible potential therapeutic targets in the disease. Applying our workflow makes it feasible to spot the most relevant genes and unknown relationships in channelopathies and shows its potential as a first-step approach to identify both genes and functional interactions in clinical-knowledge scenarios of target diseases. Methods An initial gene pool is previously defined by searching general databases under a specific semantic framework. From the resulting interaction network, a subset of genes are identified as the most relevant through the workflow that includes centrality measures and other filtering and enrichment databases.
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Affiliation(s)
- Milagros Marín
- Department of Computer Architecture and Technology - CITIC, University of Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, University of Jaén, Jaén, Spain.
| | | | - Eduardo Ros
- Department of Computer Architecture and Technology - CITIC, University of Granada, Granada, Spain
| | - María José Sáez-Lara
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain.
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18
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Gnanakkumaar P, Murugesan R, Ahmed SSSJ. Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis. Sci Rep 2019; 9:12732. [PMID: 31484947 PMCID: PMC6726613 DOI: 10.1038/s41598-019-49124-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023] Open
Abstract
Multiple sclerosis (MS) is a complex, demyelinating disease with the involvement of autoimmunity and neurodegeneration. Increasing efforts have been made towards identifying the diagnostic markers to differentiate the classes of MS from other similar neurological conditions. Using a systems biology approach, we constructed four types of gene regulatory networks (GRNs) involved in peripheral blood mononuclear cells (PBMCs). The regulatory strength of each GRN across primary progressive MS (PPMS), relapsing-remitting MS (RRMS), secondary progressive MS (SPMS), and control were evaluated by an integrity algorithm. Among the constructed GRNs (referred as TF_gene_miRNA), POU3F2_CDK6_hsa-miR-590-3p, MEIS1_CASC3_hsa-miR-1261, STAT3_OGG1_hsa-miR-298, and TCF4_FMR1_hsa-miR-301b were top-ranked and differentially regulated in all classes of MS compared to control. These GRNs showed potential involvement in regulating various molecular pathways such as interleukin, integrin, glypican, sphingosine phosphate, androgen, and Wnt signaling pathways. For validation, the qPCR analysis of the GRN components (TFs, gene, and miRNAs) in PBMCs of healthy controls (n = 30), RRMS (n = 14), PPMS (n = 13) and SPMS (n = 12) were carried out. Real-time expression analysis of GRNs showed a similar regulatory pattern as derived from our systems biology approach. Also, our study provided several novel GRNs that regulate unique and common molecular mechanisms between MS conditions. Hence, these regulatory components of GRNs will help to understand the disease mechanism across MS classes and further insight may though light towards diagnosis.
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Affiliation(s)
- Perumal Gnanakkumaar
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Kelambakkam, 603103, India
| | - Ram Murugesan
- Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, 603103, India
| | - Shiek S S J Ahmed
- Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, 603103, India.
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19
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Severa M, Rizzo F, Srinivasan S, Di Dario M, Giacomini E, Buscarinu MC, Cruciani M, Etna MP, Sandini S, Mechelli R, Farina A, Trivedi P, Hertzog PJ, Salvetti M, Farina C, Coccia EM. A cell type-specific transcriptomic approach to map B cell and monocyte type I interferon-linked pathogenic signatures in Multiple Sclerosis. J Autoimmun 2019; 101:1-16. [PMID: 31047767 DOI: 10.1016/j.jaut.2019.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Alteration in endogenous Interferon (IFN) system may profoundly impact immune cell function in autoimmune diseases. Here, we provide evidence that dysregulation in IFN-regulated genes and pathways are involved in B cell- and monocyte-driven pathogenic contribution to Multiple Sclerosis (MS) development and maintenance. In particular, by using an Interferome-based cell type-specific approach, we characterized an increased susceptibility to an IFN-linked caspase-3 dependent apoptotic cell death in both B cells and monocytes of MS patients that may arise from their chronic activation and persistent stimulation by activated T cells. Ongoing caspase-3 activation functionally impacts on MS monocyte properties influencing the STAT-3/IL-16 axis, thus, driving increased expression and massive release of the bio-active IL-16 triggering and perpetuating CD4+ T cell migration. Importantly, our analysis also identified a previously unknown multi-component defect in type I IFN-mediated signaling and response to virus pathways specific of MS B cells, impacting on induction of anti-viral responses and Epstein-barr virus infection control in patients. Taking advantage of cell type-specific transcriptomics and in-depth functional validation, this study revealed pathogenic contribution of endogenous IFN signaling and IFN-regulated cell processes to MS pathogenesis with implications on fate and functions of B cells and monocytes that may hold therapeutic potential.
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Affiliation(s)
- Martina Severa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Fabiana Rizzo
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Sundararajan Srinivasan
- Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Marco Di Dario
- Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Elena Giacomini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Chiara Buscarinu
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University, Rome, Italy
| | - Melania Cruciani
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marilena P Etna
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Silvia Sandini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Rosella Mechelli
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University, Rome, Italy; Department of Human Science and Promotion of Quality of Life, San Raffaele Roma Open University and IRCCS San Raffaele-Pisana, Rome, Italy
| | - Antonella Farina
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Pankaj Trivedi
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Paul J Hertzog
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Marco Salvetti
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University, Rome, Italy; Istituto Neurologico Mediterraneo (INM) Neuromed, Pozzilli, Isernia, Italy
| | - Cinthia Farina
- Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Eliana M Coccia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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20
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Gregson A, Thompson K, Tsirka SE, Selwood DL. Emerging small-molecule treatments for multiple sclerosis: focus on B cells. F1000Res 2019; 8. [PMID: 30863536 PMCID: PMC6402079 DOI: 10.12688/f1000research.16495.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/20/2019] [Indexed: 12/27/2022] Open
Abstract
Multiple sclerosis (MS) is a major cause of disability in young adults. Following an unknown trigger (or triggers), the immune system attacks the myelin sheath surrounding axons, leading to progressive nerve cell death. Antibodies and small-molecule drugs directed against B cells have demonstrated good efficacy in slowing progression of the disease. This review focusses on small-molecule drugs that can affect B-cell biology and may have utility in disease management. The risk genes for MS are examined from the drug target perspective. Existing small-molecule therapies for MS with B-cell actions together with new drugs in development are described. The potential for experimental molecules with B-cell effects is also considered. Small molecules can have diverse actions on B cells and be cytotoxic, anti-inflammatory and anti-viral. The current B cell-directed therapies often kill B-cell subsets, which can be effective but lead to side effects and toxicity. A deeper understanding of B-cell biology and the effect on MS disease should lead to new drugs with better selectivity, efficacy, and an improved safety profile. Small-molecule drugs, once the patent term has expired, provide a uniquely sustainable form of healthcare.
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Affiliation(s)
- Aaron Gregson
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Kaitlyn Thompson
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Stella E Tsirka
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - David L Selwood
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
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21
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Eftekharian MM, Noroozi R, Komaki A, Mazdeh M, Ghafouri-Fard S, Taheri M. MALAT1 Genomic Variants and Risk of Multiple Sclerosis. Immunol Invest 2019; 48:549-554. [PMID: 30822187 DOI: 10.1080/08820139.2019.1576728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long noncoding RNA (lncRNA) with a possible role in the regulation of immune responses. A previous study has demonstrated down-regulation of this lncRNA in multiple sclerosis (MS) patients. In the current study, we genotyped two MALAT1 single nucleotide polymorphisms (SNPs) in 428 Iranian MS patients and 505 healthy subjects. The G allele of the rs619586 was significantly under-represented in MS patients compared with controls (OR (95% CI) = 0.65 (0.46-0.92), adjusted P value = 0.03). This SNP was associated with lower MS risk in dominant model (OR (95% CI) = 0.63 (0.43-0.91), adjusted P value = 0.03). The rs3200401 was not associated with MS risk in any inheritance model. Moreover, the A T haplotype (rs619586 and rs3200401, respectively) within MALAT1 was associated with MS risk. The current study provides additional evidences for contribution of MALAT1 in the pathogenesis of MS.
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Affiliation(s)
| | - Rezvan Noroozi
- b Phytochemistry Research Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran.,c Department of Medical Genetics , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Alireza Komaki
- a Neurophysiology Research Center , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Mehrdokht Mazdeh
- a Neurophysiology Research Center , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Soudeh Ghafouri-Fard
- c Department of Medical Genetics , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mohammad Taheri
- d Urogenital Stem Cell Research Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
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Lorenzon R, Mariotti-Ferrandiz E, Aheng C, Ribet C, Toumi F, Pitoiset F, Chaara W, Derian N, Johanet C, Drakos I, Harris S, Amselem S, Berenbaum F, Benveniste O, Bodaghi B, Cacoub P, Grateau G, Amouyal C, Hartemann A, Saadoun D, Sellam J, Seksik P, Sokol H, Salem JE, Vicaut E, Six A, Rosenzwajg M, Bernard C, Klatzmann D. Clinical and multi-omics cross-phenotyping of patients with autoimmune and autoinflammatory diseases: the observational TRANSIMMUNOM protocol. BMJ Open 2018; 8:e021037. [PMID: 30166293 PMCID: PMC6119447 DOI: 10.1136/bmjopen-2017-021037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 07/02/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Autoimmune and autoinflammatory diseases (AIDs) represent a socioeconomic burden as the second cause of chronic illness in Western countries. In this context, the TRANSIMMUNOM clinical protocol is designed to revisit the nosology of AIDs by combining basic, clinical and information sciences. Based on classical and systems biology analyses, it aims to uncover important phenotypes that cut across diagnostic groups so as to discover biomarkers and identify novel therapeutic targets. METHODS AND ANALYSIS TRANSIMMUNOM is an observational clinical protocol that aims to cross-phenotype a set of 19 AIDs, six related control diseases and healthy volunteers . We assembled a multidisciplinary cohort management team tasked with (1) selecting informative biological (routine and omics type) and clinical parameters to be captured, (2) standardising the sample collection and shipment circuit, (3) selecting omics technologies and benchmarking omics data providers, (4) designing and implementing a multidisease electronic case report form and an omics database and (5) implementing supervised and unsupervised data analyses. ETHICS AND DISSEMINATION The study was approved by the institutional review board of Pitié-Salpêtrière Hospital (ethics committee Ile-De-France 48-15) and done in accordance with the Declaration of Helsinki and good clinical practice. Written informed consent is obtained from all participants before enrolment in the study. TRANSIMMUNOM's project website provides information about the protocol (https://www.transimmunom.fr/en/) including experimental set-up and tool developments. Results will be disseminated during annual scientific committees appraising the project progresses and at national and international scientific conferences. DISCUSSION Systems biology approaches are increasingly implemented in human pathophysiology research. The TRANSIMMUNOM study applies such approach to the pathophysiology of AIDs. We believe that this translational systems immunology approach has the potential to provide breakthrough discoveries for better understanding and treatment of AIDs. TRIAL REGISTRATION NUMBER NCT02466217; Pre-results.
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Affiliation(s)
- Roberta Lorenzon
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Caroline Aheng
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Claire Ribet
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Ferial Toumi
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
| | - Fabien Pitoiset
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Wahiba Chaara
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Derian
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Catherine Johanet
- Immunology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UFR 967, Sorbonne Université, Paris, France
| | - Iannis Drakos
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
| | - Sophie Harris
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
| | - Serge Amselem
- Laboratoire de génétique, UMR S933, Sorbonne Université, INSERM, Paris, France
| | - Francis Berenbaum
- Rheumatology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR S938, Sorbonne Université, INSERM, Paris, France
| | - Olivier Benveniste
- Internal Medicine and Clinical Immunology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR 974, Sorbonne Université, Paris, France
| | - Bahram Bodaghi
- Département Hospitalo-Universitaire Vision and Handicaps ‘ViewMaintain’, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Patrice Cacoub
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Internal Medicine and Clinical Immunology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Gilles Grateau
- Internal Medicine Department, Tenon Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR S933, Sorbonne Université, INSERM, Paris, France
| | - Chloe Amouyal
- Diabetology Department, Institute of Cardiometabolism and Nutrition (ICAN), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Agnes Hartemann
- Diabetology Department, Institute of Cardiometabolism and Nutrition (ICAN), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - David Saadoun
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Internal Medicine and Clinical Immunology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jeremie Sellam
- Rheumatology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR S938, Sorbonne Université, INSERM, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- GRC-UPMC 03, Sorbonne Université, Paris, France
| | - Harry Sokol
- Gastroenterology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- GRC-UPMC 03, Sorbonne Université, Paris, France
| | - Joe-Elie Salem
- CIC-1421, Pharmacology Department, INSERM, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eric Vicaut
- Unité de recherche clinique, UMR 942, Saint-Louis Lariboisière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Adrien Six
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Michelle Rosenzwajg
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Claude Bernard
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - David Klatzmann
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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