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Kennedy KE, Kerlero de Rosbo N, Uccelli A, Cellerino M, Ivaldi F, Contini P, De Palma R, Harbo HF, Berge T, Bos SD, Høgestøl EA, Brune-Ingebretsen S, de Rodez Benavent SA, Paul F, Brandt AU, Bäcker-Koduah P, Behrens J, Kuchling J, Asseyer S, Scheel M, Chien C, Zimmermann H, Motamedi S, Kauer-Bonin J, Saez-Rodriguez J, Rinas M, Alexopoulos LG, Andorra M, Llufriu S, Saiz A, Blanco Y, Martinez-Heras E, Solana E, Pulido-Valdeolivas I, Martinez-Lapiscina EH, Garcia-Ojalvo J, Villoslada P. Multiscale networks in multiple sclerosis. PLoS Comput Biol 2024; 20:e1010980. [PMID: 38329927 PMCID: PMC10852301 DOI: 10.1371/journal.pcbi.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 12/12/2023] [Indexed: 02/10/2024] Open
Abstract
Complex diseases such as Multiple Sclerosis (MS) cover a wide range of biological scales, from genes and proteins to cells and tissues, up to the full organism. In fact, any phenotype for an organism is dictated by the interplay among these scales. We conducted a multilayer network analysis and deep phenotyping with multi-omics data (genomics, phosphoproteomics and cytomics), brain and retinal imaging, and clinical data, obtained from a multicenter prospective cohort of 328 patients and 90 healthy controls. Multilayer networks were constructed using mutual information for topological analysis, and Boolean simulations were constructed using Pearson correlation to identified paths within and among all layers. The path more commonly found from the Boolean simulations connects protein MK03, with total T cells, the thickness of the retinal nerve fiber layer (RNFL), and the walking speed. This path contains nodes involved in protein phosphorylation, glial cell differentiation, and regulation of stress-activated MAPK cascade, among others. Specific paths identified were subsequently analyzed by flow cytometry at the single-cell level. Combinations of several proteins (GSK3AB, HSBP1 or RS6) and immune cells (Th17, Th1 non-classic, CD8, CD8 Treg, CD56 neg, and B memory) were part of the paths explaining the clinical phenotype. The advantage of the path identified from the Boolean simulations is that it connects information about these known biological pathways with the layers at higher scales (retina damage and disability). Overall, the identified paths provide a means to connect the molecular aspects of MS with the overall phenotype.
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Affiliation(s)
- Keith E. Kennedy
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicole Kerlero de Rosbo
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
- TomaLab, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche (CNR), Rome, Italy
| | - Antonio Uccelli
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Maria Cellerino
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Federico Ivaldi
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Paola Contini
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Raffaele De Palma
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Hanne F. Harbo
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Steffan D. Bos
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Einar A. Høgestøl
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Synne Brune-Ingebretsen
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Sigrid A. de Rodez Benavent
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Friedemann Paul
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Alexander U. Brandt
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
- Department of Neurology, University of California, Irvine, California, United States of America
| | - Priscilla Bäcker-Koduah
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Janina Behrens
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Joseph Kuchling
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Susanna Asseyer
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Michael Scheel
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Claudia Chien
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Hanna Zimmermann
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Seyedamirhosein Motamedi
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Josef Kauer-Bonin
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Melanie Rinas
- Institute for Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Leonidas G. Alexopoulos
- ProtATonce Ltd, Athens, Greece
- School of Mechanical Engineering, National Technical University of Athens, Zografou, Greece
| | - Magi Andorra
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Sara Llufriu
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Albert Saiz
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Yolanda Blanco
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Eloy Martinez-Heras
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Elisabeth Solana
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Irene Pulido-Valdeolivas
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Elena H. Martinez-Lapiscina
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Pablo Villoslada
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Neurology, Hospital del Mar Research Institute, Barcelona, Spain
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McClatchy DB, Powell SB, Yates JR. In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571320. [PMID: 38168169 PMCID: PMC10759996 DOI: 10.1101/2023.12.12.571320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Genetic analyses of Schizophrenia (SCZ) patients have identified thousands of risk factors. In silico protein-protein interaction (PPI) network analysis has provided strong evidence that disrupted PPI networks underlie SCZ pathogenesis. In this study, we performed in vivo PPI analysis of several SCZ risk factors in the rodent brain. Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. These findings demonstrate that quantitating PPI in perturbed biological states can reveal alterations to network biology.
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Letarouilly JG, Vermersch P, Flipo RM. Therapeutic consequences in patients with both inflammatory rheumatic diseases and multiple sclerosis. Rheumatology (Oxford) 2023; 62:2352-2359. [PMID: 36440887 DOI: 10.1093/rheumatology/keac665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/19/2022] [Indexed: 07/20/2023] Open
Abstract
Dealing with patients with both multiple sclerosis (MS) and inflammatory rheumatic disorders (IRDs) is not uncommon for a rheumatologist, as there is a statistical association between SpA and MS. As several CNS demyelinating events have been reported in patients treated with TNF inhibitor (TNFi), the pre-existing demyelinating disease was considered a contraindication for TNFi. However, this contraindication is mainly based on a randomized controlled trial in MS and not on large epidemiological studies. According to the last epidemiological studies, TNFi might not be an inducer of MS. Moreover, there are no clear recommendations on the use of the other DMARDs in patients suffering from an IRD and MS. In this review, we summarize the link between MS and IRDs and the impact of DMARDs on MS, especially TNFi. We also look at the impact of disease-modifying drugs for adults with MS and IRDs.
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Affiliation(s)
| | - Patrick Vermersch
- Université de Lille, CHU Lille, INSERM UMR1172 LilNCog, FHU PRECISE, Service de Neurologie, Lille, France
| | - René-Marc Flipo
- Université de Lille, CHU Lille, FHU PRECISE, Service de Rhumatologie, Lille, France
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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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Valori M, Lehikoinen J, Jansson L, Clancy J, Lundgren SA, Mustjoki S, Tienari P. High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls. PLoS One 2022; 17:e0278245. [PMID: 36441748 PMCID: PMC9704626 DOI: 10.1371/journal.pone.0278245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Somatic mutations have a central role in cancer, but there are also a few rare autoimmune diseases in which somatic mutations play a major role. We have recently shown that nonsynonymous somatic mutations with low allele fractions are preferentially detectable in CD8+ cells and that the STAT3 gene is a promising target for screening. Here, we analyzed somatic mutations in the STAT3 SH2 domain in peripheral blood CD8+ cells in a set of 94 multiple sclerosis (MS) patients and 99 matched controls. PCR amplicons targeting the exons 20 and 21 of STAT3 were prepared and sequenced using the Illumina MiSeq instrument with 2x300bp reads. We designed a novel variant calling method, optimized for large number of samples, high sequencing depth (>25,000x) and small target genomic area. Overall, we discovered 64 STAT3 somatic mutations in the 193 donors, of which 63 were non-synonymous and 77% have been previously reported in cancer or lymphoproliferative disease. The overall median variant allele fraction was 0.065% (range 0.007-1.2%), without significant difference between MS and controls (p = 0.82). There were 26 (28%) MS patients vs. 24 (24%) controls with mutations (p = 0.62). Two or more mutations were found in 9 MS patients vs. 2 controls (p = 0.03, pcorr = 0.12). Carriership of mutations associated with older age and lower neutrophil counts. These results demonstrate that STAT3 SH2 domain is a hotspot for somatic mutations in CD8+ cells with a prevalence of 26% among the participants. There were no significant differences in the mutation prevalences between MS patients and controls. Further research is needed to elucidate the role of antigenic stimuli in the expansion of the mutant clones. Furthermore, the high discovered prevalence of STAT3 somatic mutations makes it feasible to analyze these mutations directly in tissue-infiltrating CD8+ cells in autoimmune diseases.
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Affiliation(s)
- Miko Valori
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Joonas Lehikoinen
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Neurocenter, Helsinki University Hospital, Helsinki, Finland
| | - Lilja Jansson
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Neurocenter, Helsinki University Hospital, Helsinki, Finland
| | - Jonna Clancy
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Sofie A. Lundgren
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Satu Mustjoki
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Pentti Tienari
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Neurocenter, Helsinki University Hospital, Helsinki, Finland
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Pathway Analysis of Genome Wide Association Studies (GWAS) Data Associated with Male Infertility. REPRODUCTIVE MEDICINE 2022. [DOI: 10.3390/reprodmed3030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Infertility is a common condition affecting approximately 10–20% of the reproductive age population. Idiopathic infertility cases are thought to have a genetic basis, but the underlying causes are largely unknown. However, the genetic basis underlying male infertility in humans is only partially understood. The Purpose of the study is to understand the current state of research on the genetics of male infertility and its association with significant biological mechanisms. Results: We performed an Identify Candidate Causal SNPs and Pathway (ICSN Pathway) analysis using a genome-wide association study (GWAS) dataset, and NCBI-PubMed search which included 632 SNPs in GWAS and 451 SNPs from the PubMed server, respectively. The ICSN Pathway analysis produced three hypothetical biological mechanisms associated with male infertility: (1) rs8084 and rs7192→HLA-DRA→inflammatory pathways and cell adhesion; rs7550231 and rs2234167→TNFRSF14→TNF Receptor Superfamily Member 14→T lymphocyte proliferation and activation; rs1105879 and rs2070959→UGT1A6→UDP glucuronosyltransferase family 1 member A6→Metabolism of Xenobiotics, androgen, estrogen, retinol, and carbohydrates. Conclusions: We believe that our results may be helpful to study the genetic mechanisms of male infertility. Pathway-based methods have been applied to male infertility GWAS datasets to investigate the biological mechanisms and reported some novel male infertility risk pathways. This pathway analysis using GWAS dataset suggests that the biological process related to inflammation and metabolism might contribute to male infertility susceptibility. Our analysis suggests that genetic contribution to male infertility operates through multiple genes affecting common inflammatory diseases interacting in functional pathways.
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Large-scale genomic analyses reveal insights into pleiotropy across circulatory system diseases and nervous system disorders. Nat Commun 2022; 13:3428. [PMID: 35701404 PMCID: PMC9198016 DOI: 10.1038/s41467-022-30678-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
Clinical and epidemiological studies have shown that circulatory system diseases and nervous system disorders often co-occur in patients. However, genetic susceptibility factors shared between these disease categories remain largely unknown. Here, we characterized pleiotropy across 107 circulatory system and 40 nervous system traits using an ensemble of methods in the eMERGE Network and UK Biobank. Using a formal test of pleiotropy, five genomic loci demonstrated statistically significant evidence of pleiotropy. We observed region-specific patterns of direction of genetic effects for the two disease categories, suggesting potential antagonistic and synergistic pleiotropy. Our findings provide insights into the relationship between circulatory system diseases and nervous system disorders which can provide context for future prevention and treatment strategies.
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Mascia E, Clarelli F, Zauli A, Guaschino C, Sorosina M, Barizzone N, Basagni C, Santoro S, Ferrè L, Bonfiglio S, Biancolini D, Pozzato M, Guerini FR, Protti A, Liguori M, Moiola L, Vecchio D, Bresolin N, Comi G, Filippi M, Esposito F, D'Alfonso S, Martinelli-Boneschi F. Burden of rare coding variants in an Italian cohort of familial multiple sclerosis. J Neuroimmunol 2022; 362:577760. [PMID: 34922125 DOI: 10.1016/j.jneuroim.2021.577760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/18/2021] [Accepted: 10/31/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system. It is a complex and heterogeneous disease caused by a combination of genetic and environmental factors, and it can cluster in families. OBJECTIVE to evaluate at gene-level the aggregate contribution of predicted damaging low-frequency and rare variants to MS risk in multiplex families. METHODS We performed whole exome sequencing (WES) in 28 multiplex MS families with at least 3 MS cases (81 affected and 42 unaffected relatives) and 38 unrelated healthy controls. A gene-based burden test was then performed, focusing on two sets of candidate genes: i) literature-driven selection and ii) data-driven selection. RESULTS We identified 11 genes enriched with predicted damaging low-frequency and rare variants in MS compared to healthy individuals. Among them, UBR2 and DST were the two genes with the strongest enrichment (p = 5 × 10-4 and 3 × 10-4, respectively); interestingly enough the association signal in UBR2 is driven by rs62414610, which was present in 25% of analysed families. CONCLUSION Despite limitations, this is one of the first studies evaluating the aggregate contribution of predicted damaging low-frequency and rare variants in MS families using WES data. A replication effort in independent cohorts is warranted to validate our findings and to evaluate the role of identified genes in MS pathogenesis.
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Affiliation(s)
- E Mascia
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - F Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - A Zauli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - C Guaschino
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Department of Neurology, Sant'Antonio Abate Hospital, Gallarate, Italy
| | - M Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - N Barizzone
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), UPO, University of Eastern Piedmont, A. Avogadro, 28100 Novara, Italy
| | - C Basagni
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), UPO, University of Eastern Piedmont, A. Avogadro, 28100 Novara, Italy
| | - S Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - L Ferrè
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - S Bonfiglio
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - D Biancolini
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - M Pozzato
- Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy
| | - F R Guerini
- IRCCS Fondazione Don Carlo Gnocchi, ONLUS, Milan, Italy
| | - A Protti
- Ospedale Niguarda, Department of Neurology, Milan, Italy
| | - M Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy
| | - L Moiola
- Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - D Vecchio
- SCDU Neurology, AOU Maggiore della Carità, 28100 Novara, Italy
| | - N Bresolin
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - G Comi
- Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - M Filippi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy; Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Neurophysiology Unit, IRCCS San Raffaele Scientific Institute, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - F Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - S D'Alfonso
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), UPO, University of Eastern Piedmont, A. Avogadro, 28100 Novara, Italy
| | - F Martinelli-Boneschi
- Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy.
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9
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Manuel AM, Dai Y, Freeman LA, Jia P, Zhao Z. An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. Mol Cell Neurosci 2021; 115:103656. [PMID: 34284104 PMCID: PMC8802913 DOI: 10.1016/j.mcn.2021.103656] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/05/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder leading to chronic disability. Brain lesions in MS commonly arise in normal-appearing white matter (NAWM). Genome-wide association studies (GWAS) have identified genetic variants associated with MS. Transcriptome alterations have been observed in case-control studies of NAWM. We developed a Cross-Dataset Evaluation (CDE) function for our network-based tool, Edge-Weighted Dense Module Search of GWAS (EW_dmGWAS). We applied CDE to integrate publicly available MS GWAS summary statistics of 41,505 cases and controls with collectively 38 NAWM expression samples, using the human protein interactome as the reference network, to investigate biological underpinnings of MS etiology. We validated the resulting modules with colocalization of GWAS and expression quantitative trait loci (eQTL) signals, using GTEx Consortium expression data for MS-relevant tissues: 14 brain tissues and 4 immune-related tissues. Other network assessments included a drug target query and functional gene set enrichment analysis. CDE prioritized a MS NAWM network containing 55 unique genes. The gene list was enriched (p-value = 2.34 × 10-7) with GWAS-eQTL colocalized genes: CDK4, IFITM3, MAPK1, MAPK3, METTL12B and PIK3R2. The resultant network also included drug signatures of FDA-approved medications. Gene set enrichment analysis revealed the top functional term "intracellular transport of virus", among other viral pathways. We prioritize critical genes from the resultant network: CDK4, IFITM3, MAPK1, MAPK3, METTL12B and PIK3R2. Enriched drug signatures suggest potential drug targets and drug repositioning strategies for MS. Finally, we propose mechanisms of potential MS viral onset, based on prioritized gene set and functional enrichment analysis.
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Affiliation(s)
- Astrid M Manuel
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Leorah A Freeman
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
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10
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Park HH. Structural feature of TRAFs, their related human diseases and therapeutic intervention. Arch Pharm Res 2021; 44:475-486. [PMID: 33970438 DOI: 10.1007/s12272-021-01330-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Several studies have been conducted over the years to unravel the structural information on the receptors that bind to tumor necrosis factor receptor-associated factor (TRAF) and the driving forces for the TRAF/receptor complex. In addition, studies have also been performed to highlight the influence of TRAF malfunctioning and mutations on the development of human disease. However, a holistic study that systematically summarizes the available information and the existing clinical trends towards development of the TRAF-targeting drugs has not been conducted to date. Herein, I reviewed existing research that focused on the structural information of various receptors recognized by the different members of the TRAF family. I also reviewed studies on the different human diseases that occur due to TRAF malfunctioning or mutations as well as the clinical trials undertaken to treat TRAF-associated diseases.
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Affiliation(s)
- Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea. .,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
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11
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Cai R, Dong Y, Fang M, Fan Y, Cheng Z, Zhou Y, Gao J, Han F, Guo C, Ma X. Genome-Wide Association Identifies Risk Pathways for SAPHO Syndrome. Front Cell Dev Biol 2021; 9:643644. [PMID: 33816493 PMCID: PMC8012550 DOI: 10.3389/fcell.2021.643644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
SAPHO syndrome is a rare chronic inflammatory disease which is characterized by the comprehensive manifestations of bone, joint, and skin. However, little is known about the pathogenesis of SAPHO syndrome. A genome-wide association study (GWAS) of 49 patients and 121 control subjects have primarily focused on identification of common genetic variants associated with SAPHO, the data were analyzed by classical multiple logistic regression. Later, GWAS findings were further validated using whole exome sequencing (WES) in 16 patients and 15 controls to identify potentially functional pathways involved in SAPHO pathogenesis. In general, 40588 SNPs in genomic regions were associated with P < 0.05 after filter process, only 9 SNPs meet the expected cut-off P-value, however, none of them had association with SAPHO syndrome based on published literatures. And then, 15 pathways were found involved in SAPHO pathogenesis, of them, 6 pathways including osteoclast differentiation, bacterial invasion of epithelial cells, et al., had strong association with skin, osteoarticular manifestations of SAPHO or inflammatory reaction based published research. This study identified aberrant osteoclast differentiation and other pathways were involved in SAPHO syndrome. This finding may give insight into the understanding of pathogenic genes of SAPHO and provide the basis for SAPHO research and treatment.
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Affiliation(s)
- Ruikun Cai
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Yichao Dong
- National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Mingxia Fang
- National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Yuxuan Fan
- National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Zian Cheng
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Yue Zhou
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Jianen Gao
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Feifei Han
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Changlong Guo
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China
- National Human Genetic Resources Center, Beijing, China
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12
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Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
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Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
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Marrodan M, Farez MF, Balbuena Aguirre ME, Correale J. Obesity and the risk of Multiple Sclerosis. The role of Leptin. Ann Clin Transl Neurol 2020; 8:406-424. [PMID: 33369280 PMCID: PMC7886048 DOI: 10.1002/acn3.51291] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/03/2020] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To investigate the effects of leptin on different T-cell populations, in order to gain more insight into the link between leptin and obesity. METHODS Three hundred and nine RRMS patients and 322 controls participated in a cross-sectional survey, to confirm whether excess weight/obesity in adolescence or early adulthood increased the risk of MS. Serum leptin levels were determined by ELISA. MBP83-102 , and MOG63-87 peptide-specific T cells lines were expanded from peripheral blood mononuclear cells. Leptin receptor expression was measured by RT-PCR and flow cytometry. Bcl-2, p-STAT3, pERK1/2, and p27kip1 expression were assayed using ELISA, and apoptosis induction was determined by Annexin V detection. Cytokines were assessed by ELISPOT and ELISA, and regulatory T cells (Tregs) by flow cytometry. RESULTS Logistic regression analysis, showed excess weight at age 15, and obesity at 20 years of age increased MS risk (OR = 2.16, P = 0.01 and OR = 3.9, P = 0.01). Leptin levels correlated with BMI in both groups. The addition of Leptin increased autoreactive T-cell proliferation, reduced apoptosis induction, and promoted proinflammatory cytokine secretion. Obese patients produced more proinflammatory cytokines compared to overweight/normal/underweight subjects. Inverse correlation was found between leptin levels and circulating Treg cells (r = -0.97, P < 0.0001). Leptin inhibited Treg proliferation. Effects of leptin on CD4+ CD25- effector T cells were mediated by increased STAT3 and ERK1/2 phosphorylation, and down modulation of the cell cycle inhibitor P27kip1 . In contrast, leptin effects on Tregs resulted from decreased phosphorylation of ERK1/2 and upregulation of p27kip1 . INTERPRETATION Leptin promotes autoreactive T-cell proliferation and proinflammatory cytokine secretion, but inhibits Treg-cell proliferation.
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14
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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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15
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Anagnostouli M, Markoglou N, Chrousos G. Psycho-neuro-endocrino-immunologic issues in multiple sclerosis: a critical review of clinical and therapeutic implications. Hormones (Athens) 2020; 19:485-496. [PMID: 32488815 DOI: 10.1007/s42000-020-00197-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Multiple sclerosis (MS) is a multifactorial, chronic, immune-mediated, and neurodegenerative disease, having a well-known hypothalamic-pituitary-adrenal (HPA) axis dysfunction. Several hormones have a great impact in the immune dysregulation, psychology, and cognitive status of patients with MS, as also in the fertility and response to treatment. In this comprehensive review, as an introduction, we mention basic data concerning MS: epidemiology, genetics, immunogenetics, epigenetics, pathophysiology, and neuroimmunology. Hormonal components of the disease cascade, mainly glucocorticoids (stress-related hormone), estrogens, prolactin and dehydroepiandrosterone (sex-related hormones), melatonin, and vitamin D, are discussed, aiming at focusing on core data regarding the impact of these hormones in MS pathophysiology, severity of the disease, correlation with comorbid mental disorders, and fertility. A great focus is given in the pre- and post-pregnancy period of MS patients, in the context of the disease-modifying treatments (DMTs) and HPA status, having in mind that there are only very limited knowledge and few papers on this specific life period of these women, having MS. All this data are presented in the main text and also in the workable tables, for the first time, suggesting targeted topics that need to be addressed in the near future.
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Affiliation(s)
- Maria Anagnostouli
- Demyelinating Diseases Clinic, 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Aeginition Hospital, Vasilissis Sofias 72-74, 115 28, Athens, Greece.
- Immunogenetics Laboratory, 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Aeginition Hospital, Vasilissis Sofias 72-74, 115 28, Athens, Greece.
| | - Nikolaos Markoglou
- Immunogenetics Laboratory, 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Aeginition Hospital, Vasilissis Sofias 72-74, 115 28, Athens, Greece
| | - George Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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16
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Li J, Chen F, Zhang Q, Meng X, Yao X, Risacher SL, Yan J, Saykin AJ, Liang H, Shen L. Genome-wide Network-assisted Association and Enrichment Study of Amyloid Imaging Phenotype in Alzheimer's Disease. Curr Alzheimer Res 2020; 16:1163-1174. [PMID: 31755389 DOI: 10.2174/1567205016666191121142558] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The etiology of Alzheimer's disease remains poorly understood at the mechanistic level, and genome-wide network-based genetics have the potential to provide new insights into the disease mechanisms. OBJECTIVE The study aimed to explore the collective effects of multiple genetic association signals on an AV-45 PET measure, which is a well-known Alzheimer's disease biomarker, by employing a network assisted strategy. METHODS First, we took advantage of a dense module search algorithm to identify modules enriched by genetic association signals in a protein-protein interaction network. Next, we performed statistical evaluation to the modules identified by dense module search, including a normalization process to adjust the topological bias in the network, a replication test to ensure the modules were not found randomly , and a permutation test to evaluate unbiased associations between the modules and amyloid imaging phenotype. Finally, topological analysis, module similarity tests and functional enrichment analysis were performed for the identified modules. RESULTS We identified 24 consensus modules enriched by robust genetic signals in a genome-wide association analysis. The results not only validated several previously reported AD genes (APOE, APP, TOMM40, DDAH1, PARK2, ATP5C1, PVRL2, ELAVL1, ACTN1 and NRF1), but also nominated a few novel genes (ABL1, ABLIM2) that have not been studied in Alzheimer's disease but have shown associations with other neurodegenerative diseases. CONCLUSION The identified genes, consensus modules and enriched pathways may provide important clues to future research on the neurobiology of Alzheimer's disease and suggest potential therapeutic targets.
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Affiliation(s)
- Jin Li
- College of Automation, Harbin Engineering University, Harbin, China
| | - Feng Chen
- College of Automation, Harbin Engineering University, Harbin, China
| | - Qiushi Zhang
- College of Information Engineering, Northeast Dianli University, Jilin, China
| | - Xianglian Meng
- College of Automation, Harbin Engineering University, Harbin, China
| | - Xiaohui Yao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, PA, United States
| | - Jingwen Yan
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, PA, United States
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, PA, United States
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, China
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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Abstract
Over the last several years, next-generation sequencing and its recent push toward single-cell resolution have transformed the landscape of immunology research by revealing novel complexities about all components of the immune system. With the vast amounts of diverse data currently being generated, and with the methods of analyzing and combining diverse data improving as well, integrative systems approaches are becoming more powerful. Previous integrative approaches have combined multiple data types and revealed ways that the immune system, both as a whole and as individual parts, is affected by genetics, the microbiome, and other factors. In this review, we explore the data types that are available for studying immunology with an integrative systems approach, as well as the current strategies and challenges for conducting such analyses.
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Affiliation(s)
- Silvia Pineda
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, 28029 Madrid, Spain
| | - Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
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18
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Tian Z, Song Y, Yao Y, Guo J, Gong Z, Wang Z. Genetic Etiology Shared by Multiple Sclerosis and Ischemic Stroke. Front Genet 2020; 11:646. [PMID: 32719717 PMCID: PMC7348066 DOI: 10.3389/fgene.2020.00646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
Although dramatic progress has been achieved in the understanding and treatment of multiple sclerosis (MS) and ischemic stroke (IS), more precise and instructive support is required for further research. Recent large-scale genome-wide association studies (GWASs) have already revealed risk variants for IS and MS, but the common genetic etiology between MS and IS remains an unresolved issue. This research was designed to overlapping genes between MS and IS and unmask their transcriptional features. We designed a three-section analysis process. Firstly, we computed gene-based analyses of MS GWAS and IS GWAS data sets by VGEAS2. Secondly, overlapping genes of significance were identified in a meta-analysis using the Fisher’s procedure. Finally, we performed gene expression analyses to confirm transcriptional changes. We identified 24 shared genes with Bonferroni correction (Pcombined < 2.31E-04), and five (FOXP1, CAMK2G, CLEC2D, LBH, and SLC2A4RG) had significant expression differences in MS and IS gene expression omnibus data sets. These meaningful shared genes between IS and MS shed light on the underlying genetic etiologies shared by the diseases. Our results provide a basis for in-depth genomic studies of associations between MS and IS.
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Affiliation(s)
- Zhu Tian
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Yang Song
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Yang Yao
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Jie Guo
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Zhongying Gong
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Zhiyun Wang
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
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Graves JS, Barcellos LF, Krupp L, Belman A, Shao X, Quach H, Hart J, Chitnis T, Weinstock-Guttman B, Aaen G, Benson L, Gorman M, Greenberg B, Lotze T, Soe M, Ness J, Rodriguez M, Rose J, Schreiner T, Tillema JM, Waldman A, Casper TC, Waubant E. Vitamin D genes influence MS relapses in children. Mult Scler 2020; 26:894-901. [PMID: 31081484 PMCID: PMC6851448 DOI: 10.1177/1352458519845842] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE The aim of this study was to determine whether a vitamin D genetic risk score (vitDGRS) is associated with 25-hydroxyvitamin D (25(OH)D) level and multiple sclerosis (MS) relapses in children. METHODS DNA samples were typed for single nucleotide polymorphisms (SNPs) from four genes previously identified to be associated with 25(OH)D levels. SNPs with strong associations with 25(OH)D after multiple comparison correction were used to create a genetic risk score (vitDGRS). Cox regression models tested associations of vitDGRS with relapse hazard. RESULTS Two independent SNPs within or near GC and NADSYN1/DHCR7 genes were strongly associated with 25(OH)D levels in the discovery cohort (n = 182) after Bonferroni correction. The vitDGRS of these SNPs explained 4.5% of the variance of 25(OH)D level after adjustment for genetic ancestry. Having the highest versus lowest vitDGRS was associated with 11 ng/mL lower 25(OH)D level (95% confidence interval (CI) = -17.5, -4.5, p = 0.001) in the discovery cohort. Adjusting for ancestry, sex, disease-modifying therapy (DMT), and HLA-DRB1*15 carrier status, the highest versus lowest vitDGRS was associated with 2.6-fold (95% CI = 1.37, 5.03, p = 0.004) and 2.0-fold (95% CI = 0.75, 5.20, p = 0.16) higher relapse hazard in the discovery and replication cohorts, respectively. CONCLUSION The vitDGRS identifies children at greater risk of relapse. These findings support a causal role for vitamin D in MS course.
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Affiliation(s)
- Jennifer S Graves
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Lisa F Barcellos
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Lauren Krupp
- Pediatric Multiple Sclerosis Center, New York University Langone Medical Center, New York, NY, USA
| | | | - Xiaorong Shao
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Hong Quach
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Janace Hart
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Tanuja Chitnis
- Partners Pediatric Multiple Sclerosis Center, Massachusetts General Hospital for Children, Boston, MA, USA
| | | | - Gregory Aaen
- Pediatric Multiple Sclerosis Center, Loma Linda University Children's Hospital, San Bernardino, CA, USA
| | - Leslie Benson
- Pediatric Multiple Sclerosis and Related Disorders Program, Boston Children's Hospital, Boston, MA, USA
| | - Mark Gorman
- Pediatric Multiple Sclerosis and Related Disorders Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Timothy Lotze
- The Blue Bird Circle Clinic for Multiple Sclerosis, Texas Children's Hospital, Houston, TX, USA
| | - Mar Soe
- Pediatric MS & Demyelinating Disease Center, Washington University, St. Louis, MI, USA
| | - Jayne Ness
- Center for Pediatric-Onset Demyelinating Disease, Children's of Alabama, Birmingham, AL, USA
| | - Moses Rodriguez
- Pediatric Multiple Sclerosis Center, Mayo Clinic, Rochester, MA, USA
| | - John Rose
- Department of Neurology, The University of Utah, Salt Lake City, UT, USA
| | - Teri Schreiner
- Rocky Mountain MS Center, University of Colorado, Denver, Denver, CO, USA
| | | | - Amy Waldman
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - T Charles Casper
- Department of Pediatrics, The University of Utah, Salt Lake City, UT, USA
| | - Emmanuelle Waubant
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
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Fyn Tyrosine Kinase as Harmonizing Factor in Neuronal Functions and Dysfunctions. Int J Mol Sci 2020; 21:ijms21124444. [PMID: 32580508 PMCID: PMC7352836 DOI: 10.3390/ijms21124444] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/25/2022] Open
Abstract
Fyn is a non-receptor or cytoplasmatic tyrosine kinase (TK) belonging to the Src family kinases (SFKs) involved in multiple transduction pathways in the central nervous system (CNS) including synaptic transmission, myelination, axon guidance, and oligodendrocyte formation. Almost one hundred years after the original description of Fyn, this protein continues to attract extreme interest because of its multiplicity of actions in the molecular signaling pathways underlying neurodevelopmental as well as neuropathologic events. This review highlights and summarizes the most relevant recent findings pertinent to the role that Fyn exerts in the brain, emphasizing aspects related to neurodevelopment and synaptic plasticity. Fyn is a common factor in healthy and diseased brains that targets different proteins and shapes different transduction signals according to the neurological conditions. We will primarily focus on Fyn-mediated signaling pathways involved in neuronal differentiation and plasticity that have been subjected to considerable attention lately, opening the fascinating scenario to target Fyn TK for the development of potential therapeutic interventions for the treatment of CNS injuries and certain neurodegenerative disorders like Alzheimer’s disease.
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Chiricosta L, Gugliandolo A, Bramanti P, Mazzon E. Could the Heat Shock Proteins 70 Family Members Exacerbate the Immune Response in Multiple Sclerosis? An in Silico Study. Genes (Basel) 2020; 11:genes11060615. [PMID: 32503176 PMCID: PMC7348765 DOI: 10.3390/genes11060615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 01/08/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune demyelinating disease of the central nervous system. It represents one of the main causes of neurological disability in young people. In MS, the autoimmune response is directed against myelin antigens but other possible bio-molecular markers are investigated. The aim of this work was, through an in silico study, the evaluation of the transcriptional modifications between healthy subjects and MS patients in six brain areas (corpus callosum, hippocampus, internal capsule, optic chiasm, frontal and parietal cortex) in order to identify genes representative of the disease. Our results show the upregulation of the Heat Shock Proteins (HSPs) HSPA1A, HSPA1B, HSPA7, HSPA6, HSPH1 and HSPA4L of the HSP70 family, among which HSPA1A and HSPA1B are upregulated in all the brain areas. HSP70s are molecular chaperones indispensable for protein folding, recently associated with immune system maintenance. The little overexpression of the HSPs protects the cells from stress but extreme upregulation can contribute to the MS pathogenesis. We also investigated the genes involved in the immune system that result in overall upregulation in the corpus callosum, hippocampus, internal capsule, optic chiasm and are absent in the cortex. Interestingly, the genes of the immune system and the HSP70s have comparable levels of expression.
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22
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Li T, Li X, Zamani A, Wang W, Lee CN, Li M, Luo G, Eiler E, Sun H, Ghosh S, Jin J, Murali R, Ruan Q, Shi W, Chen YH. c-Rel Is a Myeloid Checkpoint for Cancer Immunotherapy. ACTA ACUST UNITED AC 2020; 1:507-517. [PMID: 33458695 DOI: 10.1038/s43018-020-0061-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immunotherapy that targets lymphoid cell checkpoints holds great promise for curing cancer. However, a majority of cancer patients do not respond to this form of therapy. In addition to lymphoid cells, myeloid cells play essential roles in controlling immunity to cancer. Whether myeloid checkpoints exist that can be targeted to treat cancer is not well established. Here we show that c-Rel, a member of the nuclear factor (NF)-B family, specified the generation of myeloid-derived suppressor cells (MDSCs) by selectively turning on pro-tumoral genes while switching off anti-tumoral genes through a c-Rel enhanceosome. c-Rel deficiency in myeloid cells markedly inhibited cancer growth in mice, and pharmaceutical inhibition of c-Rel had the same effect. Combination therapy that blocked both c-Rel and the lymphoid checkpoint protein PD1 was more effective in treating cancer than blocking either alone. Thus, c-Rel is a myeloid checkpoint that can be targeted for treating cancer.
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Affiliation(s)
- Ting Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Contributed equally to this work
| | - Xinyuan Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Contributed equally to this work
| | - Ali Zamani
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chin-Nien Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George Luo
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Eiler
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Honghong Sun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sankar Ghosh
- Department of Microbiology and Immunology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Qingguo Ruan
- Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Weiyun Shi
- Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Youhai H Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Sirko A, Dzyak L, Chekha E, Malysheva T, Romanukha D. Coexistence of multiple sclerosis and brain tumours: Case report and review. INTERDISCIPLINARY NEUROSURGERY 2020. [DOI: 10.1016/j.inat.2019.100585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Nabirotchkin S, Peluffo AE, Rinaudo P, Yu J, Hajj R, Cohen D. Next-generation drug repurposing using human genetics and network biology. Curr Opin Pharmacol 2020; 51:78-92. [PMID: 31982325 DOI: 10.1016/j.coph.2019.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022]
Abstract
Drug repurposing has attracted increased attention, especially in the context of drug discovery rates that remain too low despite a recent wave of approvals for biological therapeutics (e.g. gene therapy). These new biological entities-based treatments have high costs that are difficult to justify for small markets that include rare diseases. Drug repurposing, involving the identification of single or combinations of existing drugs based on human genetics data and network biology approaches represents a next-generation approach that has the potential to increase the speed of drug discovery at a lower cost. This Pharmacological Perspective reviews progress and perspectives in combining human genetics, especially genome-wide association studies, with network biology to drive drug repurposing for rare and common diseases with monogenic or polygenic etiologies. Also, highlighted here are important features of this next generation approach to drug repurposing, which can be combined with machine learning methods to meet the challenges of personalized medicine.
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Affiliation(s)
- Serguei Nabirotchkin
- Network Biology & Drug Discovery Department, Pharnext, 11 rue René Jacques, 92130 Issy-les-Moulineaux, France
| | - Alex E Peluffo
- Data Science Department, Pharnext, 11 rue René Jacques, 92130 Issy-les-Moulineaux, France.
| | - Philippe Rinaudo
- Data Science Department, Pharnext, 11 rue René Jacques, 92130 Issy-les-Moulineaux, France
| | - Jinchao Yu
- Data Science Department, Pharnext, 11 rue René Jacques, 92130 Issy-les-Moulineaux, France
| | - Rodolphe Hajj
- Preclinical Research and Pharmacology Department, Pharnext, 11 rue René Jacques, 92130 Issy-les-Moulineaux, France
| | - Daniel Cohen
- Chief Executive Officer, Pharnext, 11 rue René Jacques, 92130 Issy-les-Moulineaux, France
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25
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Reworking GWAS Data to Understand the Role of Nongenetic Factors in MS Etiopathogenesis. Genes (Basel) 2020; 11:genes11010097. [PMID: 31947683 PMCID: PMC7017269 DOI: 10.3390/genes11010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/03/2020] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified more than 200 multiple sclerosis (MS)-associated loci across the human genome over the last decade, suggesting complexity in the disease etiology. This complexity poses at least two challenges: the definition of an etiological model including the impact of nongenetic factors, and the clinical translation of genomic data that may be drivers for new druggable targets. We reviewed studies dealing with single genes of interest, to understand how MS-associated single nucleotide polymorphism (SNP) variants affect the expression and the function of those genes. We then surveyed studies on the bioinformatic reworking of genome-wide association studies (GWAS) data, with aggregate analyses of many GWAS loci, each contributing with a small effect to the overall disease predisposition. These investigations uncovered new information, especially when combined with nongenetic factors having possible roles in the disease etiology. In this context, the interactome approach, defined as “modules of genes whose products are known to physically interact with environmental or human factors with plausible relevance for MS pathogenesis”, will be reported in detail. For a future perspective, a polygenic risk score, defined as a cumulative risk derived from aggregating the contributions of many DNA variants associated with a complex trait, may be integrated with data on environmental factors affecting the disease risk or protection.
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26
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He P, Mo XB, Lei SF, Deng FY. Epigenetically regulated co-expression network of genes significant for rheumatoid arthritis. Epigenomics 2019; 11:1601-1612. [PMID: 31693422 DOI: 10.2217/epi-2019-0028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To identify epigenetically regulated network of genes in peripheral blood mononuclear cells significant for rheumatoid arthritis (RA). Methods: Differentially expressed genes (DEGs) and their associated differentially expressed miRNAs and differentially methylated positions (DMPs) were identified. Causal inference test (CIT) identified the causal regulation chains. The analyses, for example, weighted gene co-expression network (WGCNA), protein-protein interaction and functional enrichment, evaluated interaction patterns among the DEGs and the associated epigenetic factors. Results: A total of 181 DEGs were identified. The DEGs were significantly regulated by DMPs and/or differentially expressed miRNAs. Causal inference test analyses identified 18 causal chains of DMP-DEG-RA and 16 intermediate DEGs enriched in 'protein kinase inhibitor activity'. BTN2A1 was co-expressed with other 9 intermediate genes and 11 known RA-associated genes and played a pivotal role in the co-expression network. Conclusion: Epigenetically regulated network of genes in peripheral blood mononuclear cells (PBMC) contributed to RA. The causal DMPs and key intermediate genes may serve as potential biomarkers for RA.
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Affiliation(s)
- Pei He
- Center for Genetic Epidemiology & Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China.,Jiangsu Key Laboratory of Preventive & Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xing-Bo Mo
- Center for Genetic Epidemiology & Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China.,Jiangsu Key Laboratory of Preventive & Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology & Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China.,Jiangsu Key Laboratory of Preventive & Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology & Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China.,Jiangsu Key Laboratory of Preventive & Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, Jiangsu 215123, PR China
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27
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Milo R, Korczyn AD, Manouchehri N, Stüve O. The temporal and causal relationship between inflammation and neurodegeneration in multiple sclerosis. Mult Scler 2019; 26:876-886. [PMID: 31682184 DOI: 10.1177/1352458519886943] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
It is currently incompletely understood whether inflammation and neurodegeneration are causally related in multiple sclerosis (MS). The sequence of a potential causal relationship is also unknown. Inflammation is present in rather all clinical stages of MS. Its role in the pathogenesis of MS is supported by histopathological analyses, genetic data, and numerous animal models of MS. All approved disease-modifying therapies that reduce clinical relapses and diminish the accumulation of lesions on neuroimaging are anti-inflammatory. Axonal loss and accelerated brain volume loss can also be detected from clinical disease onset throughout all stages. The expression of neurofilament light chain in cerebrospinal fluid and serum, a scaffolding protein in axons and dendrites, is a biomarker of neuronal injury associated with clinical relapses and reflects neuronal loss during episodes of acute inflammation. The recent association of human endogenous retrovirus (HERV) and its envelope proteins with MS illustrates a pathogenic pathway that causally links central nervous system (CNS)-intrinsic proinflammatory effects and inhibition of myelin repair and neuroregeneration. A review of current data on the causal relationship between inflammation and neurodegeneration in MS identified numerous plausible pathomechanisms that link the two events. Observations from most experimental models appear to favor a pathogenesis in which inflammation precedes neurodegeneration.
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Affiliation(s)
- Ron Milo
- Department of Neurology, Barzilai Medical Center, Ashkelon, Israel/Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Amos D Korczyn
- Department of Neurology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Navid Manouchehri
- Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Olaf Stüve
- Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center, Dallas, TX, USA/Neurology Section, Medical Service, VA North Texas Health Care System, Dallas, TX, USA/Department of Neurology, Klinikum rechts der Isar, Technische Universität München, München, Germany
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28
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Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis. J Clin Med 2019; 8:jcm8091284. [PMID: 31443559 PMCID: PMC6780767 DOI: 10.3390/jcm8091284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
Using next-generation sequencing to decipher methylome and transcriptome and underlying molecular mechanisms contributing to rheumatoid arthritis (RA) for improving future therapies, we performed methyl-seq and RNA-seq on peripheral blood mononuclear cells (PBMCs) from RA subjects and normal donors. Principal component analysis and hierarchical clustering revealed distinct methylation signatures in RA with methylation aberrations noted across chromosomes. Methylation alterations varied with CpG features and genic characteristics. Typically, CpG islands and CpG shores were hypermethylated and displayed the greatest methylation variance. Promoters were hypermethylated and enhancers/gene bodies were hypomethylated, with methylation variance associated with expression variance. RA genetically associated genes preferentially displayed differential methylation and differential expression or interacted with differentially methylated and differentially expressed genes. These differentially methylated and differentially expressed genes were enriched with several signaling pathways and disease categories. 10 genes (CD86, RAB20, XAF1, FOLR3, LTBR, KCNH8, DOK7, PDGFA, PITPNM2, CELSR1) with concomitantly differential methylation in enhancers/promoters/gene bodies and differential expression in B cells were validated. This integrated analysis of methylome and transcriptome identified novel epigenetic signatures associated with RA and highlighted the interaction between genetics and epigenetics in RA. These findings help our understanding of the pathogenesis of RA and advance epigenetic studies in regards to the disease.
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29
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Bonham LW, Steele NZR, Karch CM, Broce I, Geier EG, Wen NL, Momeni P, Hardy J, Miller ZA, Gorno-Tempini ML, Hess CP, Lewis P, Miller BL, Seeley WW, Manzoni C, Desikan RS, Baranzini SE, Ferrari R, Yokoyama JS. Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia. Sci Rep 2019; 9:10854. [PMID: 31350420 PMCID: PMC6659677 DOI: 10.1038/s41598-019-46415-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/28/2019] [Indexed: 12/28/2022] Open
Abstract
The semantic variant of primary progressive aphasia (svPPA) is a clinical syndrome characterized by neurodegeneration and progressive loss of semantic knowledge. Unlike many other forms of frontotemporal lobar degeneration (FTLD), svPPA has a highly consistent underlying pathology composed of TDP-43 (a regulator of RNA and DNA transcription metabolism). Previous genetic studies of svPPA are limited by small sample sizes and a paucity of common risk variants. Despite this, svPPA's relatively homogenous clinicopathologic phenotype makes it an ideal investigative model to examine genetic processes that may drive neurodegenerative disease. In this study, we used GWAS metadata, tissue samples from pathologically confirmed frontotemporal lobar degeneration, and in silico techniques to identify and characterize protein interaction networks associated with svPPA risk. We identified 64 svPPA risk genes that interact at the protein level. The protein pathways represented in this svPPA gene network are critical regulators of RNA metabolism and cell death, such as SMAD proteins and NOTCH1. Many of the genes in this network are involved in TDP-43 metabolism. Contrary to the conventional notion that svPPA is a clinical syndrome with few genetic risk factors, our analyses show that svPPA risk is complex and polygenic in nature. Risk for svPPA is likely driven by multiple common variants in genes interacting with TDP-43, along with cell death,x` working in combination to promote neurodegeneration.
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Affiliation(s)
- Luke W Bonham
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.,Neuroradiology Section, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Natasha Z R Steele
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Iris Broce
- Neuroradiology Section, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Ethan G Geier
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Natalie L Wen
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Parastoo Momeni
- Texas Tech University Health Science Center, Laboratory of Neurogenetics, Lubbock, TX, USA
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Zachary A Miller
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Maria Luisa Gorno-Tempini
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher P Hess
- Neuroradiology Section, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick Lewis
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,School of Pharmacy, University of Reading, Whiteknights, Reading, UK
| | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - William W Seeley
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Claudia Manzoni
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,School of Pharmacy, University of Reading, Whiteknights, Reading, UK
| | - Rahul S Desikan
- Neuroradiology Section, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Sergio E Baranzini
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Raffaele Ferrari
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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Madireddy L, Patsopoulos NA, Cotsapas C, Bos SD, Beecham A, McCauley J, Kim K, Jia X, Santaniello A, Caillier SJ, Andlauer TFM, Barcellos LF, Berge T, Bernardinelli L, Martinelli-Boneschi F, Booth DR, Briggs F, Celius EG, Comabella M, Comi G, Cree BAC, D’Alfonso S, Dedham K, Duquette P, Dardiotis E, Esposito F, Fontaine B, Gasperi C, Goris A, Dubois B, Gourraud PA, Hadjigeorgiou G, Haines J, Hawkins C, Hemmer B, Hintzen R, Horakova D, Isobe N, Kalra S, Kira JI, Khalil M, Kockum I, Lill CM, Lincoln M, Luessi F, Martin R, Oturai A, Palotie A, Pericak-Vance MA, Henry R, Saarela J, Ivinson A, Olsson T, Taylor BV, Stewart GJ, Harbo HF, Compston A, Hauser SL, Hafler DA, Zipp F, De Jager P, Sawcer S, Oksenberg JR, Baranzini SE. A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis. Nat Commun 2019; 10:2236. [PMID: 31110181 PMCID: PMC6527683 DOI: 10.1038/s41467-019-09773-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/26/2019] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which particular gene(s) are relevant continues to be a challenge. Here, we conduct a cell-specific pathway analysis of the latest GWAS in multiple sclerosis (MS), which had analyzed a total of 47,351 cases and 68,284 healthy controls and found more than 200 non-MHC genome-wide associations. Our analysis identifies pan immune cell as well as cell-specific susceptibility genes in T cells, B cells and monocytes. Finally, genotype-level data from 2,370 patients and 412 controls is used to compute intra-individual and cell-specific susceptibility pathways that offer a biological interpretation of the individual genetic risk to MS. This approach could be adopted in any other complex trait for which genome-wide data is available.
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MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis. Proc Natl Acad Sci U S A 2019; 116:9671-9676. [PMID: 31004050 DOI: 10.1073/pnas.1818347116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dysregulation of signaling pathways in multiple sclerosis (MS) can be analyzed by phosphoproteomics in peripheral blood mononuclear cells (PBMCs). We performed in vitro kinetic assays on PBMCs in 195 MS patients and 60 matched controls and quantified the phosphorylation of 17 kinases using xMAP assays. Phosphoprotein levels were tested for association with genetic susceptibility by typing 112 single-nucleotide polymorphisms (SNPs) associated with MS susceptibility. We found increased phosphorylation of MP2K1 in MS patients relative to the controls. Moreover, we identified one SNP located in the PHDGH gene and another on IRF8 gene that were associated with MP2K1 phosphorylation levels, providing a first clue on how this MS risk gene may act. The analyses in patients treated with disease-modifying drugs identified the phosphorylation of each receptor's downstream kinases. Finally, using flow cytometry, we detected in MS patients increased STAT1, STAT3, TF65, and HSPB1 phosphorylation in CD19+ cells. These findings indicate the activation of cell survival and proliferation (MAPK), and proinflammatory (STAT) pathways in the immune cells of MS patients, primarily in B cells. The changes in the activation of these kinases suggest that these pathways may represent therapeutic targets for modulation by kinase inhibitors.
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33
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Statistical methods for genome-wide association studies. Semin Cancer Biol 2019; 55:53-60. [DOI: 10.1016/j.semcancer.2018.04.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022]
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34
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Li H, Chen L, Ma X, Cui P, Lang W, Hao J. Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke. Front Genet 2019; 9:598. [PMID: 30809253 PMCID: PMC6379658 DOI: 10.3389/fgene.2018.00598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/15/2018] [Indexed: 01/22/2023] Open
Abstract
Patients with multiple sclerosis (MS) appear to have an increased risk of ischemic stroke (IS). Although MS and IS have very different phenotypes, gene-based and pathway-based analyses of large-scale genome-wide association studies (GWAS) have increasingly enhanced our understanding of these two diseases. Whether there are common molecular mechanisms connecting MS and IS is still unclear. Here, we describe the outcome of gene-based test and pathway-based analysis of GWAS datasets that explored potential gene expression links between MS and IS. After identifying significant gene sets individually of MS and IS, we performed pathway-based analysis in four biological pathway databases (KEGG, PANTHER, REACTOME, and WikiPathways) and GO categories. We discovered that there were 9 shared pathways between MS and IS in KEGG, 2 in PANTHER, 14 in REACTOME, 1 in WikiPathways, and 194 in GO annotations (p < 0.05). These results provide an improved understanding about possible shared mechanisms and treatments strategies for MS and IS. They also provide some basis for further studies of how these two diseases are linked at the molecular level.
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Affiliation(s)
- He Li
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Lin Chen
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Xiaofeng Ma
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Pan Cui
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Wenjing Lang
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Junwei Hao
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
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35
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Mancini M, Caignard G, Charbonneau B, Dumaine A, Wu N, Leiva-Torres GA, Gerondakis S, Pearson A, Qureshi ST, Sladek R, Vidal SM. Rel-Dependent Immune and Central Nervous System Mechanisms Control Viral Replication and Inflammation during Mouse Herpes Simplex Encephalitis. THE JOURNAL OF IMMUNOLOGY 2019; 202:1479-1493. [DOI: 10.4049/jimmunol.1800063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023]
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36
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Rhead B, Brorson IS, Berge T, Adams C, Quach H, Moen SM, Berg-Hansen P, Celius EG, Sangurdekar DP, Bronson PG, Lea RA, Burnard S, Maltby VE, Scott RJ, Lechner-Scott J, Harbo HF, Bos SD, Barcellos LF. Increased DNA methylation of SLFN12 in CD4+ and CD8+ T cells from multiple sclerosis patients. PLoS One 2018; 13:e0206511. [PMID: 30379917 PMCID: PMC6209300 DOI: 10.1371/journal.pone.0206511] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is an epigenetic mark that is influenced by environmental factors and is associated with changes to gene expression and phenotypes. It may link environmental exposures to disease etiology or indicate important gene pathways involved in disease pathogenesis. We identified genomic regions that are differentially methylated in T cells of patients with relapsing remitting multiple sclerosis (MS) compared to healthy controls. DNA methylation was assessed at 450,000 genomic sites in CD4+ and CD8+ T cells purified from peripheral blood of 94 women with MS and 94 healthy women, and differentially methylated regions were identified using bumphunter. Differential DNA methylation was observed near four loci: MOG/ZFP57, HLA-DRB1, NINJ2/LOC100049716, and SLFN12. Increased methylation of the first exon of the SLFN12 gene was observed in both T cell subtypes and remained present after restricting analyses to samples from patients who had never been on treatment or had been off treatment for more than 2.5 years. Genes near the regions of differential methylation in T cells were assessed for differential expression in whole blood samples from a separate population of 1,329 women with MS and 97 healthy women. Gene expression of HLA-DRB1, NINJ2, and SLFN12 was observed to be decreased in whole blood in MS patients compared to controls. We conclude that T cells from MS patients display regions of differential DNA methylation compared to controls, and corresponding gene expression differences are observed in whole blood. Two of the genes that showed both methylation and expression differences, NINJ2 and SLFN12, have not previously been implicated in MS. SLFN12 is a particularly compelling target of further research, as this gene is known to be down-regulated during T cell activation and up-regulated by type I interferons (IFNs), which are used to treat MS.
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Affiliation(s)
- Brooke Rhead
- Computational Biology Graduate Group, University of California, Berkeley, Berkeley, CA, United States of America
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States of America
| | - Ina S. Brorson
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
| | - Cameron Adams
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States of America
| | - Stine Marit Moen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- MS-Centre Hakadal, Hakadal, Norway
| | - Pål Berg-Hansen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Elisabeth Gulowsen Celius
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Dipen P. Sangurdekar
- Translational & Integrative Analytics, Biogen, Inc., Cambridge, MA, United States of America
| | - Paola G. Bronson
- Statistical Genetics & Genetic Epidemiology, Biogen, Inc., Cambridge, MA, United States of America
| | - Rodney A. Lea
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
| | - Sean Burnard
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Vicki E. Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - Rodney J. Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Molecular Genetics, Pathology North, John Hunter Hospital, Newcastle, Australia
| | - Jeannette Lechner-Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
- Department of Neurology, John Hunter Hospital, Newcastle, Australia
| | - Hanne F. Harbo
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Steffan D. Bos
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Lisa F. Barcellos
- Computational Biology Graduate Group, University of California, Berkeley, Berkeley, CA, United States of America
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States of America
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Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. An integrative tissue-network approach to identify and test human disease genes. Nat Biotechnol 2018; 36:nbt.4246. [PMID: 30346941 PMCID: PMC7021177 DOI: 10.1038/nbt.4246] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Effective discovery of causal disease genes must overcome the statistical challenges of quantitative genetics studies and the practical limitations of human biology experiments. Here we developed diseaseQUEST, an integrative approach that combines data from human genome-wide disease studies with in silico network models of tissue- and cell-type-specific function in model organisms to prioritize candidates within functionally conserved processes and pathways. We used diseaseQUEST to predict candidate genes for 25 different diseases and traits, including cancer, longevity, and neurodegenerative diseases. Focusing on Parkinson's disease (PD), a diseaseQUEST-directed Caenhorhabditis elegans behavioral screen identified several candidate genes, which we experimentally verified and found to be associated with age-dependent motility defects mirroring PD clinical symptoms. Furthermore, knockdown of the top candidate gene, bcat-1, encoding a branched chain amino acid transferase, caused spasm-like 'curling' and neurodegeneration in C. elegans, paralleling decreased BCAT1 expression in PD patient brains. diseaseQUEST is modular and generalizable to other model organisms and human diseases of interest.
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Affiliation(s)
- Victoria Yao
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Rachel Kaletsky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - William Keyes
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Danielle E Mor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Aaron K Wong
- Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Salman Sohrabi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Flatiron Institute, Simons Foundation, New York, New York, USA
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38
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Hao T, Wang Q, Zhao L, Wu D, Wang E, Sun J. Analyzing of Molecular Networks for Human Diseases and Drug Discovery. Curr Top Med Chem 2018; 18:1007-1014. [PMID: 30101711 PMCID: PMC6174636 DOI: 10.2174/1568026618666180813143408] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 01/11/2023]
Abstract
Molecular networks represent the interactions and relations of genes/proteins, and also encode molecular mechanisms of biological processes, development and diseases. Among the molecular networks, protein-protein Interaction Networks (PINs) have become effective platforms for uncovering the molecular mechanisms of diseases and drug discovery. PINs have been constructed for various organisms and utilized to solve many biological problems. In human, most proteins present their complex functions by interactions with other proteins, and the sum of these interactions represents the human protein interactome. Especially in the research on human disease and drugs, as an emerging tool, the PIN provides a platform to systematically explore the molecular complexities of specific diseases and the references for drug design. In this review, we summarized the commonly used approaches to aid disease research and drug discovery with PINs, including the network topological analysis, identification of novel pathways, drug targets and sub-network biomarkers for diseases. With the development of bioinformatic techniques and biological networks, PINs will play an increasingly important role in human disease research and drug discovery.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Qian Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Lingxuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Dan Wu
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Edwin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,University of Calgary Cumming School of Medicine, Calgary, Alberta T2N 4Z6, Canada
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,Tianjin Bohai Fisheries Research Institute, Tianjin 300221, China
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Bonham LW, Steele NZR, Karch CM, Manzoni C, Geier EG, Wen N, Ofori-Kuragu A, Momeni P, Hardy J, Miller ZA, Hess CP, Lewis P, Miller BL, Seeley WW, Baranzini SE, Desikan RS, Ferrari R, Yokoyama JS. Protein network analysis reveals selectively vulnerable regions and biological processes in FTD. Neurol Genet 2018; 4:e266. [PMID: 30283816 PMCID: PMC6167176 DOI: 10.1212/nxg.0000000000000266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/31/2018] [Indexed: 11/15/2022]
Abstract
OBJECTIVE The neuroanatomical profile of behavioral variant frontotemporal dementia (bvFTD) suggests a common biological etiology of disease despite disparate pathologic causes; we investigated the genetic underpinnings of this selective regional vulnerability to identify new risk factors for bvFTD. METHODS We used recently developed analytical techniques designed to address the limitations of genome-wide association studies to generate a protein interaction network of 63 bvFTD risk genes. We characterized this network using gene expression data from healthy and diseased human brain tissue, evaluating regional network expression patterns across the lifespan as well as the cell types and biological processes most affected in bvFTD. RESULTS We found that bvFTD network genes show enriched expression across the human lifespan in vulnerable neuronal populations, are implicated in cell signaling, cell cycle, immune function, and development, and are differentially expressed in pathologically confirmed frontotemporal lobar degeneration cases. Five of the genes highlighted by our differential expression analyses, BAIAP2, ERBB3, POU2F2, SMARCA2, and CDC37, appear to be novel bvFTD risk loci. CONCLUSIONS Our findings suggest that the cumulative burden of common genetic variation in an interacting protein network expressed in specific brain regions across the lifespan may influence susceptibility to bvFTD.
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Affiliation(s)
- Luke W Bonham
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Natasha Z R Steele
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Celeste M Karch
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Claudia Manzoni
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Ethan G Geier
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Natalie Wen
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Aaron Ofori-Kuragu
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Parastoo Momeni
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - John Hardy
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Zachary A Miller
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Christopher P Hess
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Patrick Lewis
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Bruce L Miller
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - William W Seeley
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Sergio E Baranzini
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Rahul S Desikan
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Raffaele Ferrari
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
| | - Jennifer S Yokoyama
- Department of Neurology (L.W.B., N.Z.R.S., E.G.G., Z.A.M., B.L.M., W.W.S., J.S.Y.), Memory and Aging Center, University of California, San Francisco; Department of Psychiatry (C.M.K., N.W., A.O.-K.), Washington University, St. Louis, MO; School of Pharmacy (C.M., P.L.), University of Reading, Reading, UK; Laboratory of Neurogenetics (P.M.), Texas Tech University Health Science Center, Lubbock; Department of Molecular Neuroscience (C.M., J.H., P.L., R.F.), UCL Institute of Neurology, London, UK; Department of Radiology and Biomedical Imaging, Neuroradiology Section (C.P.H., R.S.D.), University of California, San Francisco; and Department of Neurology (S.E.B.), University of California, San Francisco
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40
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Chang X, Lima LDA, Liu Y, Li J, Li Q, Sleiman PMA, Hakonarson H. Common and Rare Genetic Risk Factors Converge in Protein Interaction Networks Underlying Schizophrenia. Front Genet 2018; 9:434. [PMID: 30323833 PMCID: PMC6172705 DOI: 10.3389/fgene.2018.00434] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022] Open
Abstract
Hundreds of genomic loci have been identified with the recent advances of schizophrenia in genome-wide association studies (GWAS) and sequencing studies. However, the functional interactions among those genes remain largely unknown. We developed a network-based approach to integrate multiple genetic risk factors, which lead to the discovery of new susceptibility genes and causal sub-networks, or pathways in schizophrenia. We identified significantly and consistently over-represented pathways in the largest schizophrenia GWA studies, which are highly relevant to synaptic plasticity, neural development and signaling transduction, such as long-term potentiation, neurotrophin signaling pathway, and the ERBB signaling pathway. We also demonstrated that genes targeted by common SNPs are more likely to interact with genes harboring de novo mutations (DNMs) in the protein-protein interaction (PPI) network, suggesting a mutual interplay of both common and rare variants in schizophrenia. We further developed an edge-based search algorithm to identify the top-ranked gene modules associated with schizophrenia risk. Our results suggest that the N-methyl-D-aspartate receptor (NMDAR) interactome may play a leading role in the pathology of schizophrenia, as it is highly targeted by multiple types of genetic risk factors.
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Affiliation(s)
- Xiao Chang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Leandro de Araujo Lima
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yichuan Liu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jin Li
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Qingqin Li
- Janssen Research & Development, LLC, Titusville, NJ, United States
| | - Patrick M A Sleiman
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
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41
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Enabling Precision Medicine through Integrative Network Models. J Mol Biol 2018; 430:2913-2923. [DOI: 10.1016/j.jmb.2018.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/15/2018] [Accepted: 07/03/2018] [Indexed: 11/17/2022]
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42
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Bacanu SA, Kendler KS. Method to estimate the approximate samples size that yield a certain number of significant GWAS signals in polygenic traits. Genet Epidemiol 2018; 42:488-496. [PMID: 29761553 DOI: 10.1002/gepi.22125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 11/11/2022]
Abstract
To argue for increased sample collection for disorders without significant findings, researchers resorted to plotting, for multiple traits, the number of significant findings as a function of the sample size. However, for polygenic traits, the prevalence of the disorder confounds the relationship between the number of significant findings and the sample size. To adjust the number of significant findings for prevalence, we develop a method that uses the expected noncentrality of the contrast between liabilities of cases and controls. We empirically find that, when compared to the sample size, this measure is a better predictor of number of significant findings. Even more, we show that the sample size effect on the number of signals is explained by the noncentrality measure. Finally, we provide an R script to estimate the required sample size (noncentrality) needed to yield a prespecified number of significant findings, along with the converse.
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Affiliation(s)
- Silviu-Alin Bacanu
- Psychiatric Department, Virginia Commonwealth University, Richmond, VA, USA
| | - Kenneth S Kendler
- Psychiatric Department, Virginia Commonwealth University, Richmond, VA, USA
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43
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Narayan RN, Forsthuber T, Stüve O. Emerging drugs for primary progressive multiple sclerosis. Expert Opin Emerg Drugs 2018; 23:97-110. [DOI: 10.1080/14728214.2018.1463370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ram Narendra Narayan
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Olaf Stüve
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Neurology Section, VA North Texas Health Care System, Dallas VA Medical Center, Dallas, TX, USA
- Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
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44
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Graetz C, Groppa S, Zipp F, Siller N. Preservation of neuronal function as measured by clinical and MRI endpoints in relapsing-remitting multiple sclerosis: how effective are current treatment strategies? Expert Rev Neurother 2018; 18:203-219. [PMID: 29411688 DOI: 10.1080/14737175.2018.1438190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Approved medications for relapsing-remitting multiple sclerosis have shown to be effective in terms of their anti-inflammatory potential. However, it is also crucial to evaluate what long-term effects a patient can expect from current MS drugs in terms of preventing neurodegeneration. Here we aim to provide an overview of the current treatment strategies in MS with a specific focus on potential neuroprotective effects. Areas covered: Randomized, double-blind and placebo or referral-drug controlled phase 2a/b and phase 3 trials were examined; non-blinded phase 4 studies (extension studies) were included to provide long-term data, if not otherwise available. Endpoints considered were expanded disability status scale, various neuropsychological tests, percent brain volume change and T1-hypointense lesions as well as multiple sclerosis functional composite, confirmed disease progression, and no evidence of disease activity. Expert commentary: Overall, neuroprotective functions of classical MS therapeutics are not sufficiently investigated, but available data show limited effects. Thus, further research and development in neuroprotection are warranted. When counselling patients, potential long-term beneficial effects should be presented more conservatively.
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Affiliation(s)
- Christiane Graetz
- a Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2) , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Sergiu Groppa
- a Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2) , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Frauke Zipp
- a Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2) , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Nelly Siller
- a Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2) , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
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45
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Pazhouhandeh M, Sahraian MA, Siadat SD, Fateh A, Vaziri F, Tabrizi F, Ajorloo F, Arshadi AK, Fatemi E, Piri Gavgani S, Mahboudi F, Rahimi Jamnani F. A systems medicine approach reveals disordered immune system and lipid metabolism in multiple sclerosis patients. Clin Exp Immunol 2018; 192:18-32. [PMID: 29194580 DOI: 10.1111/cei.13087] [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: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023] Open
Abstract
Identification of autoimmune processes and introduction of new autoantigens involved in the pathogenesis of multiple sclerosis (MS) can be helpful in the design of new drugs to prevent unresponsiveness and side effects in patients. To find significant changes, we evaluated the autoantibody repertoires in newly diagnosed relapsing-remitting MS patients (NDP) and those receiving disease-modifying therapy (RP). Through a random peptide phage library, a panel of NDP- and RP-specific peptides was identified, producing two protein data sets visualized using Gephi, based on protein--protein interactions in the STRING database. The top modules of NDP and RP networks were assessed using Enrichr. Based on the findings, a set of proteins, including ATP binding cassette subfamily C member 1 (ABCC1), neurogenic locus notch homologue protein 1 (NOTCH1), hepatocyte growth factor receptor (MET), RAF proto-oncogene serine/threonine-protein kinase (RAF1) and proto-oncogene vav (VAV1) was found in NDP and was involved in over-represented terms correlated with cell-mediated immunity and cancer. In contrast, transcription factor RelB (RELB), histone acetyltransferase p300 (EP300), acetyl-CoA carboxylase 2 (ACACB), adiponectin (ADIPOQ) and phosphoenolpyruvate carboxykinase 2 mitochondrial (PCK2) had major contributions to viral infections and lipid metabolism as significant events in RP. According to these findings, further research is required to demonstrate the pathogenic roles of such proteins and autoantibodies targeting them in MS and to develop therapeutic agents which can ameliorate disease severity.
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Affiliation(s)
- M Pazhouhandeh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - M-A Sahraian
- MS Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - S D Siadat
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - A Fateh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Vaziri
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Tabrizi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Ajorloo
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Faculty of Science, Islamic Azad University, East Tehran Branch, Tehran, Iran
| | - A K Arshadi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - E Fatemi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S Piri Gavgani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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46
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Luo D, Fu J. Identifying characteristic miRNAs-genes and risk pathways of multiple sclerosis based on bioinformatics analysis. Oncotarget 2018; 9:5287-5300. [PMID: 29435179 PMCID: PMC5797050 DOI: 10.18632/oncotarget.23866] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 12/18/2017] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis is a chronic autoimmune disorder of the central nervous system. In MS, the genetic susceptibility is high and currently there is no effective treatment. MicroRNA, a small non-coding RNA, plays a vital role in immune responses. Aberrant or dysfunctional miRNAs may cause several diseases, including MS, thus miRNAs and miRNA related genes may be therapeutic weapons against MS. Here, we identified 21 miRNAs in peripheral blood mono-nuclear cells from over 600 persons, including healthy controls. By using informatics databases, 1637 susceptibility genes were evaluated and Cytoscape was used to integrate and visualize the relation between the miRNA identified and susceptibility genes. By using the cluster Profile package, a total of 10 risk pathways were discovered. Top pathways included: hsa05200 (pathway in cancer), hsa04010 (MAPK signaling pathway), and hsa04060 (cytokine-cytokine receptor interaction). By using the STRING database, a protein-protein interaction network was conducted to identify highly susceptibility genes. Moreover, the GSE21942 dataset was used to indicate the gene expression profiles and to correct prediction results, thereby identifying the most pivotal genes. The MiRSystem database provided information on both pivotal miRNAs and genes. In conclusion, miR-199a and miR-142-3p may be crucial for MS by targeting pivotal susceptibility genes, in particular KRAS and IL7R.
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Affiliation(s)
- Deling Luo
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Nangang District, Harbin 150086, China
| | - Jin Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Nangang District, Harbin 150086, China
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47
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Lalani AI, Zhu S, Gokhale S, Jin J, Xie P. TRAF molecules in inflammation and inflammatory diseases. ACTA ACUST UNITED AC 2017. [PMID: 29527458 DOI: 10.1007/s40495-017-0117-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Purpose of Review This review presents an overview of the current knowledge of TRAF molecules in inflammation with an emphasis on available human evidence and direct in vivo evidence of mouse models that demonstrate the contribution of TRAF molecules in the pathogenesis of inflammatory diseases. Recent Findings The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of cytoplasmic proteins was initially identified as signaling adaptors that bind directly to the intracellular domains of receptors of the TNF-R superfamily. It is now appreciated that TRAF molecules are widely employed in signaling by a variety of adaptive and innate immune receptors as well as cytokine receptors. TRAF-dependent signaling pathways typically lead to the activation of nuclear factor-κBs (NF-κBs), mitogen-activated protein kinases (MAPKs), or interferon-regulatory factors (IRFs). Most of these signaling pathways have been linked to inflammation, and therefore TRAF molecules were expected to regulate inflammation and inflammatory responses since their discovery in 1990s. However, direct in vivo evidence of TRAFs in inflammation and especially in inflammatory diseases had been lacking for many years, partly due to the difficulty imposed by early lethality of TRAF2-/-, TRAF3-/-, and TRAF6-/- mice. With the creation of conditional knockout and lineage-specific transgenic mice of different TRAF molecules, our understanding about TRAFs in inflammation and inflammatory responses has rapidly advanced during the past decade. Summary Increasing evidence indicates that TRAF molecules are versatile and indispensable regulators of inflammation and inflammatory responses and that aberrant expression or function of TRAFs contributes to the pathogenesis of inflammatory diseases.
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Affiliation(s)
- Almin I Lalani
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Sining Zhu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Juan Jin
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Department of Pharmacology, Anhui Medical University, Meishan Road 81st, Shushan District, Hefei, Anhui province, China
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Member, Rutgers Cancer Institute of New Jersey
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48
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Hellberg S, Eklund D, Gawel DR, Köpsén M, Zhang H, Nestor CE, Kockum I, Olsson T, Skogh T, Kastbom A, Sjöwall C, Vrethem M, Håkansson I, Benson M, Jenmalm MC, Gustafsson M, Ernerudh J. Dynamic Response Genes in CD4+ T Cells Reveal a Network of Interactive Proteins that Classifies Disease Activity in Multiple Sclerosis. Cell Rep 2017; 16:2928-2939. [PMID: 27626663 DOI: 10.1016/j.celrep.2016.08.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 12/11/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the CNS and has a varying disease course as well as variable response to treatment. Biomarkers may therefore aid personalized treatment. We tested whether in vitro activation of MS patient-derived CD4+ T cells could reveal potential biomarkers. The dynamic gene expression response to activation was dysregulated in patient-derived CD4+ T cells. By integrating our findings with genome-wide association studies, we constructed a highly connected MS gene module, disclosing cell activation and chemotaxis as central components. Changes in several module genes were associated with differences in protein levels, which were measurable in cerebrospinal fluid and were used to classify patients from control individuals. In addition, these measurements could predict disease activity after 2 years and distinguish low and high responders to treatment in two additional, independent cohorts. While further validation is needed in larger cohorts prior to clinical implementation, we have uncovered a set of potentially promising biomarkers.
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Affiliation(s)
- Sandra Hellberg
- Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Daniel Eklund
- Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden.
| | - Danuta R Gawel
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Mattias Köpsén
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden; Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Huan Zhang
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Colm E Nestor
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 171 77 Linköping, Sweden
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, 171 77 Linköping, Sweden
| | - Thomas Skogh
- Department of Rheumatology and Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Alf Kastbom
- Department of Rheumatology and Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Christopher Sjöwall
- Department of Rheumatology and Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Magnus Vrethem
- Department of Neurology and Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Irene Håkansson
- Department of Neurology and Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Mikael Benson
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Maria C Jenmalm
- Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden.
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine and Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
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49
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Kotelnikova E, Kiani NA, Abad E, Martinez-Lapiscina EH, Andorra M, Zubizarreta I, Pulido-Valdeolivas I, Pertsovskaya I, Alexopoulos LG, Olsson T, Martin R, Paul F, Tegnér J, Garcia-Ojalvo J, Villoslada P. Dynamics and heterogeneity of brain damage in multiple sclerosis. PLoS Comput Biol 2017; 13:e1005757. [PMID: 29073203 PMCID: PMC5657613 DOI: 10.1371/journal.pcbi.1005757] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/31/2017] [Indexed: 11/24/2022] Open
Abstract
Multiple Sclerosis (MS) is an autoimmune disease driving inflammatory and degenerative processes that damage the central nervous system (CNS). However, it is not well understood how these events interact and evolve to evoke such a highly dynamic and heterogeneous disease. We established a hypothesis whereby the variability in the course of MS is driven by the very same pathogenic mechanisms responsible for the disease, the autoimmune attack on the CNS that leads to chronic inflammation, neuroaxonal degeneration and remyelination. We propose that each of these processes acts more or less severely and at different times in each of the clinical subgroups. To test this hypothesis, we developed a mathematical model that was constrained by experimental data (the expanded disability status scale [EDSS] time series) obtained from a retrospective longitudinal cohort of 66 MS patients with a long-term follow-up (up to 20 years). Moreover, we validated this model in a second prospective cohort of 120 MS patients with a three-year follow-up, for which EDSS data and brain volume time series were available. The clinical heterogeneity in the datasets was reduced by grouping the EDSS time series using an unsupervised clustering analysis. We found that by adjusting certain parameters, albeit within their biological range, the mathematical model reproduced the different disease courses, supporting the dynamic CNS damage hypothesis to explain MS heterogeneity. Our analysis suggests that the irreversible axon degeneration produced in the early stages of progressive MS is mainly due to the higher rate of myelinated axon degeneration, coupled to the lower capacity for remyelination. However, and in agreement with recent pathological studies, degeneration of chronically demyelinated axons is not a key feature that distinguishes this phenotype. Moreover, the model reveals that lower rates of axon degeneration and more rapid remyelination make relapsing MS more resilient than the progressive subtype. Therefore, our results support the hypothesis of a common pathogenesis for the different MS subtypes, even in the presence of genetic and environmental heterogeneity. Hence, MS can be considered as a single disease in which specific dynamics can provoke a variety of clinical outcomes in different patient groups. These results have important implications for the design of therapeutic interventions for MS at different stages of the disease. Multiple Sclerosis (MS) is an autoimmune disease in which inflammatory and degenerative processes damage the brain. We tested the hypothesis that the variability in disease progression and the clinical heterogeneity observed in MS is driven by a single mechanism, namely the autoimmune attack on the CNS that provokes this chronic inflammation and degeneration. As such, it is the difference in the intensity of these processes at distinct times that is responsible for establishing each of the disease subtypes defined to date. Mathematical models of brain damage and disease course were generated that were fitted to clinical data. We found that the phenotypes of the different MS subtypes were reproduced by the model, supporting the concept of a common pathogenesis and thus, that of a single disease in which specific dynamics can produce a variety of clinical outcomes in different groups of patients. These results are likely to be helpful when designing new therapies for this disease.
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Affiliation(s)
- Ekaterina Kotelnikova
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Narsis A. Kiani
- Unit of Computational Medicine, Department of Medicine & Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Elena Abad
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena H. Martinez-Lapiscina
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Magi Andorra
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Irati Zubizarreta
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Irene Pulido-Valdeolivas
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Inna Pertsovskaya
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | | | - Tomas Olsson
- Unit of Neuroimmunology, Karolinska Institute, Stockholm, Sweden
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital, University Zurich, Zurich, Switzerland
| | - Friedemann Paul
- NeuroCure Clinical Research Center, and the Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine Berlin, Berlin, Germany
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine & Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
- Biological and Environmental Sciences and Engineering Division & Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | | | - Pablo Villoslada
- Center for Neuroimmunology, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- University of California, San Francisco, United States of America
- * E-mail:
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50
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Palluzzi F, Ferrari R, Graziano F, Novelli V, Rossi G, Galimberti D, Rainero I, Benussi L, Nacmias B, Bruni AC, Cusi D, Salvi E, Borroni B, Grassi M. A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PLoS One 2017; 12:e0185797. [PMID: 29020091 PMCID: PMC5636111 DOI: 10.1371/journal.pone.0185797] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 09/19/2017] [Indexed: 01/04/2023] Open
Abstract
Frontotemporal Dementia (FTD) is the form of neurodegenerative dementia with the highest prevalence after Alzheimer’s disease, equally distributed in men and women. It includes several variants, generally characterized by behavioural instability and language impairments. Although few mendelian genes (MAPT, GRN, and C9orf72) have been associated to the FTD phenotype, in most cases there is only evidence of multiple risk loci with relatively small effect size. To date, there are no comprehensive studies describing FTD at molecular level, highlighting possible genetic interactions and signalling pathways at the origin FTD-associated neurodegeneration. In this study, we designed a broad FTD genetic interaction map of the Italian population, through a novel network-based approach modelled on the concepts of disease-relevance and interaction perturbation, combining Steiner tree search and Structural Equation Model (SEM) analysis. Our results show a strong connection between Calcium/cAMP metabolism, oxidative stress-induced Serine/Threonine kinases activation, and postsynaptic membrane potentiation, suggesting a possible combination of neuronal damage and loss of neuroprotection, leading to cell death. In our model, Calcium/cAMP homeostasis and energetic metabolism impairments are primary causes of loss of neuroprotection and neural cell damage, respectively. Secondly, the altered postsynaptic membrane potentiation, due to the activation of stress-induced Serine/Threonine kinases, leads to neurodegeneration. Our study investigates the molecular underpinnings of these processes, evidencing key genes and gene interactions that may account for a significant fraction of unexplained FTD aetiology. We emphasized the key molecular actors in these processes, proposing them as novel FTD biomarkers that could be crucial for further epidemiological and molecular studies.
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Affiliation(s)
- Fernando Palluzzi
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
- * E-mail:
| | - Raffaele Ferrari
- Department of Molecular Neuroscience, Institute of Neurology, University College London (UCL), London, United Kingdom
| | - Francesca Graziano
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
| | - Valeria Novelli
- Department of Genetics, Fondazione Policlinico A. Gemelli, Roma, Italy
| | - Giacomina Rossi
- Division of Neurology V and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Daniela Galimberti
- Department of Neurological Sciences, Dino Ferrari Institute, University of Milan, Milano, Italy
| | - Innocenzo Rainero
- Department of Neuroscience, Neurology I, University of Torino and Città della Salute e della Scienza di Torino, Torino, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Firenze, Italy
| | - Amalia C. Bruni
- Neurogenetic Regional Centre ASPCZ Lamezia Terme, Lamezia Terme (CZ), Italy
| | - Daniele Cusi
- Department of Health Sciences, University of Milan at San Paolo Hospital, Milano, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Milano, Italy
| | - Erika Salvi
- Institute of Biomedical Technologies, Italian National Research Council, Milano, Italy
| | - Barbara Borroni
- Department of Medical Sciences, Neurology Clinic, University of Brescia, Brescia, Italy
| | - Mario Grassi
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
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