1
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Magnusson R, Rundquist O, Kim MJ, Hellberg S, Na CH, Benson M, Gomez-Cabrero D, Kockum I, Tegnér JN, Piehl F, Jagodic M, Mellergård J, Altafini C, Ernerudh J, Jenmalm MC, Nestor CE, Kim MS, Gustafsson M. RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases. Front Mol Biosci 2022; 9:916128. [PMID: 36106020 PMCID: PMC9465313 DOI: 10.3389/fmolb.2022.916128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/25/2022] [Indexed: 12/18/2022] Open
Abstract
Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between mRNA expression and protein abundance. We hypothesised that these correlations could be improved by mathematical models based on measuring splice variants and time delay in protein translation. We characterised time-series of primary human naïve CD4+ T cells during early T helper type 1 differentiation with RNA-sequencing and mass-spectrometry proteomics. We performed computational time-series analysis in this system and in two other key human and murine immune cell types. Linear mathematical mixed time delayed splice variant models were used to predict protein abundances, and the models were validated using out-of-sample predictions. Lastly, we re-analysed RNA-seq datasets to evaluate biomarker discovery in five T-cell associated diseases, further validating the findings for multiple sclerosis (MS) and asthma. The new models significantly out-performing models not including the usage of multiple splice variants and time delays, as shown in cross-validation tests. Our mathematical models provided more differentially expressed proteins between patients and controls in all five diseases. Moreover, analysis of these proteins in asthma and MS supported their relevance. One marker, sCD27, was validated in MS using two independent cohorts for evaluating response to treatment and disease prognosis. In summary, our splice variant and time delay models substantially improved the prediction of protein abundance from mRNA expression in three different immune cell types. The models provided valuable biomarker candidates, which were further validated in MS and asthma.
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Affiliation(s)
- Rasmus Magnusson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Olof Rundquist
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Min Jung Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in, South Korea
| | - Sandra Hellberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
| | - David Gomez-Cabrero
- Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra, IdiSNA, Pamplona, Spain
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Jesper N. Tegnér
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johan Mellergård
- Department of Neurology, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudio Altafini
- Department of Automatic Control, Linköping University, Linköping, Sweden
| | - Jan Ernerudh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Linköping University, Linköping, Sweden
| | - Maria C. Jenmalm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Maria C. Jenmalm, ; Mika Gustafsson,
| | - Colm E. Nestor
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
- *Correspondence: Maria C. Jenmalm, ; Mika Gustafsson,
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2
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de Weerd HA, Åkesson J, Guala D, Gustafsson M, Lubovac-Pilav Z. MODalyseR-a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data. BIOINFORMATICS ADVANCES 2022; 2:vbac006. [PMID: 36699378 PMCID: PMC9710626 DOI: 10.1093/bioadv/vbac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023]
Abstract
Motivation Network-based disease modules have proven to be a powerful concept for extracting knowledge about disease mechanisms, predicting for example disease risk factors and side effects of treatments. Plenty of tools exist for the purpose of module inference, but less effort has been put on simultaneously utilizing knowledge about regulatory mechanisms for predicting disease module hub regulators. Results We developed MODalyseR, a novel software for identifying disease module regulators and reducing modules to the most disease-associated genes. This pipeline integrates and extends previously published software packages MODifieR and ComHub and hereby provides a user-friendly network medicine framework combining the concepts of disease modules and hub regulators for precise disease gene identification from transcriptomics data. To demonstrate the usability of the tool, we designed a case study for multiple sclerosis that revealed IKZF1 as a promising hub regulator, which was supported by independent ChIP-seq data. Availability and implementation MODalyseR is available as a Docker image at https://hub.docker.com/r/ddeweerd/modalyser with user guide and installation instructions found at https://gustafsson-lab.gitlab.io/MODalyseR/. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Hendrik A de Weerd
- School of Bioscience, Systems Biology Research Center, University of Skövde, Skövde 541 45, Sweden,Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - Julia Åkesson
- School of Bioscience, Systems Biology Research Center, University of Skövde, Skövde 541 45, Sweden,Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - Dimitri Guala
- Department of Biochemistry and Biophysics, Stockholm University, Solna 17121, Sweden,Merck AB, Solna 16970, Sweden
| | - Mika Gustafsson
- Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden,To whom correspondence should be addressed. or
| | - Zelmina Lubovac-Pilav
- School of Bioscience, Systems Biology Research Center, University of Skövde, Skövde 541 45, Sweden,To whom correspondence should be addressed. or
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3
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Badam TV, Hellberg S, Mehta RB, Lechner-Scott J, Lea RA, Tost J, Mariette X, Svensson-Arvelund J, Nestor CE, Benson M, Berg G, Jenmalm MC, Gustafsson M, Ernerudh J. CD4 + T-cell DNA methylation changes during pregnancy significantly correlate with disease-associated methylation changes in autoimmune diseases. Epigenetics 2021; 17:1040-1055. [PMID: 34605719 PMCID: PMC9487751 DOI: 10.1080/15592294.2021.1982510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Epigenetics may play a central, yet unexplored, role in the profound changes that the maternal immune system undergoes during pregnancy and could be involved in the pregnancy-induced modulation of several autoimmune diseases. We investigated changes in the methylome in isolated circulating CD4+ T-cells in non-pregnant and pregnant women, during the 1st and 2nd trimester, using the Illumina Infinium Human Methylation 450K array, and explored how these changes were related to autoimmune diseases that are known to be affected during pregnancy. Pregnancy was associated with several hundreds of methylation differences, particularly during the 2nd trimester. A network-based modular approach identified several genes, e.g., CD28, FYN, VAV1 and pathways related to T-cell signalling and activation, highlighting T-cell regulation as a central component of the observed methylation alterations. The identified pregnancy module was significantly enriched for disease-associated methylation changes related to multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus. A negative correlation between pregnancy-associated methylation changes and disease-associated changes was found for multiple sclerosis and rheumatoid arthritis, diseases that are known to improve during pregnancy whereas a positive correlation was found for systemic lupus erythematosus, a disease that instead worsens during pregnancy. Thus, the directionality of the observed changes is in line with the previously observed effect of pregnancy on disease activity. Our systems medicine approach supports the importance of the methylome in immune regulation of T-cells during pregnancy. Our findings highlight the relevance of using pregnancy as a model for understanding and identifying disease-related mechanisms involved in the modulation of autoimmune diseases.Abbreviations: BMIQ: beta-mixture quantile dilation; DMGs: differentially methylated genes; DMPs: differentially methylated probes; FE: fold enrichment; FDR: false discovery rate; GO: gene ontology; GWAS: genome-wide association studies; MDS: multidimensional scaling; MS: multiple sclerosis; PBMC: peripheral blood mononuclear cells; PBS: phosphate buffered saline; PPI; protein-protein interaction; RA: rheumatoid arthritis; SD: standard deviation; SLE: systemic lupus erythematosus; SNP: single nucleotide polymorphism; TH: CD4+ T helper cell; VIStA: diVIsive Shuffling Approach.
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Affiliation(s)
- Tejaswi V Badam
- Bioinformatics Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,School of Bioscience, Skövde University, Skövde, Sweden
| | - Sandra Hellberg
- Bioinformatics Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ratnesh B Mehta
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jeannette Lechner-Scott
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia.,Centre for Brain and Mental Health, Hunter Medical Research Institute, New Lambton Heights, Australia.,Department of Neurology, John Hunter Hospital, New Lambton Heights, Australia
| | - Rodney A Lea
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia.,Centre for Brain and Mental Health, Hunter Medical Research Institute, New Lambton Heights, Australia.,Institute of Health and Biomedical Innovations, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, Australia
| | - Jorg Tost
- Laboratory of Epigenetics and Environment, Centre National De Recherche En Génomique Humaine, CEA-Institut De Biologie Francois Jacob, Evry, France
| | - Xavier Mariette
- Université Paris-Saclay, AP-HP-Université Paris-Saclay, Hôpital Bicêtre, Institut National de la Santé et de la Recherche Médicale (Inserm) U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, France
| | - Judit Svensson-Arvelund
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Colm E Nestor
- The Centre for Individualized Medicine, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mikael Benson
- The Centre for Individualized Medicine, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Göran Berg
- Department of Obstetrics and Gynaecology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maria C Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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4
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Altered Expression of TSPAN32 during B Cell Activation and Systemic Lupus Erythematosus. Genes (Basel) 2021; 12:genes12060931. [PMID: 34207245 PMCID: PMC8234828 DOI: 10.3390/genes12060931] [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: 05/17/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 01/02/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic inflammatory disease with various clinical features. Autoreactive B cells play a role in disease pathogenesis, through the production of multiple autoantibodies, which form immune complexes and induce the inflammatory response and tissue damage associated with SLE. Recently, tetraspanins, and in particular, TSPAN32, have been recognized to play a central role in immunity, as they are involved in various biological processes, such as the antigen presentation and the activation of lymphocytes. Evidence suggests that tetraspanins could represent in the future a target for therapeutic purposes in patients suffering from autoimmune/immunoinflammatory disorders. In the present study, by performing in silico analyses of high-throughput data, we evaluated the expression levels of TSPAN32 in B cell activation and investigated its modulation in circulating B cells from SLE patients. Our data show that B cell activation is associated with a significant downregulation of TSPAN32. Additionally, significantly lower levels of TSPAN32 were observed in circulating plasmablasts from SLE patients as compared to healthy donor plasmablasts. In addition, type I interferons (IFNs)-related genes were enriched among the genes negatively correlated to TSPAN32, in SLE plasmablasts. Accordingly, IFN-α is able to induce a dose-dependent downregulation of TSPAN32 in B cells. Overall, the data here presented suggest the potential use of TSPAN32 as a diagnostic marker and therapeutic target for the evaluation and management of humoral immune responses in chronic diseases, such as SLE.
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5
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de Weerd HA, Badam TVS, Martínez-Enguita D, Åkesson J, Muthas D, Gustafsson M, Lubovac-Pilav Z. MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks. Bioinformatics 2020; 36:3918-3919. [PMID: 32271876 DOI: 10.1093/bioinformatics/btaa235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/27/2020] [Accepted: 04/02/2020] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Complex diseases are due to the dense interactions of many disease-associated factors that dysregulate genes that in turn form the so-called disease modules, which have shown to be a powerful concept for understanding pathological mechanisms. There exist many disease module inference methods that rely on somewhat different assumptions, but there is still no gold standard or best-performing method. Hence, there is a need for combining these methods to generate robust disease modules. RESULTS We developed MODule IdentiFIER (MODifieR), an ensemble R package of nine disease module inference methods from transcriptomics networks. MODifieR uses standardized input and output allowing the possibility to combine individual modules generated from these methods into more robust disease-specific modules, contributing to a better understanding of complex diseases. AVAILABILITY AND IMPLEMENTATION MODifieR is available under the GNU GPL license and can be freely downloaded from https://gitlab.com/Gustafsson-lab/MODifieR and as a Docker image from https://hub.docker.com/r/ddeweerd/modifier. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hendrik A de Weerd
- School of Bioscience, Systems Biology Research Center, Skövde 541 45, Sweden.,Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - Tejaswi V S Badam
- School of Bioscience, Systems Biology Research Center, Skövde 541 45, Sweden.,Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - David Martínez-Enguita
- Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - Julia Åkesson
- School of Bioscience, Systems Biology Research Center, Skövde 541 45, Sweden.,Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - Daniel Muthas
- Translational Science and Experimental Medicine, Early Respiratory, Inflammation and Autoimmunity, BioPharmaceuticals R&D, AstraZeneca, Mölndal 43183, Sweden
| | - Mika Gustafsson
- Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
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6
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Lombardo SD, Bramanti A, Ciurleo R, Basile MS, Pennisi M, Bella R, Mangano K, Bramanti P, Nicoletti F, Fagone P. Profiling of inhibitory immune checkpoints in glioblastoma: Potential pathogenetic players. Oncol Lett 2020; 20:332. [PMID: 33123243 PMCID: PMC7583708 DOI: 10.3892/ol.2020.12195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/06/2020] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma (GBM) represents the most frequent glial tumor, with almost 3 new cases per 100,000 people per year. Despite treatment, the prognosis for GBM patients remains extremely poor, with a median survival of 14.6 months, and a 5-year survival less than 5%. It is generally believed that GBM creates a highly immunosuppressive microenvironment, sustained by the expression of immune-regulatory factors, including inhibitory immune checkpoints, on both infiltrating cells and tumor cells. However, the trials assessing the efficacy of current immune checkpoint inhibitors in GBM are still disappointing. In the present study, the expression levels of several inhibitory immune checkpoints in GBM (CD276, VTCN1, CD47, PVR, TNFRSF14, CD200, LGALS9, NECTIN2 and CD48) were characterized in order to evaluate their potential as prognostic and eventually, therapeutic targets. Among the investigated immune checkpoints, TNFRSF14 and NECTIN2 were identified as the most promising targets in GBM. In particular, a higher TNFRSF14 expression was associated with worse overall survival and disease-free survival, and with a lower Th1 response.
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Affiliation(s)
- Salvo Danilo Lombardo
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | | | - Rosella Ciurleo
- IRCCS Centro Neurolesi Bonino Pulejo, I-98124 Messina, Italy
| | | | - Manuela Pennisi
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Rita Bella
- Department of Medical Sciences, Surgery and Advanced Technologies, University of Catania, I-95123 Catania, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
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7
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Basile MS, Mazzon E, Mangano K, Pennisi M, Petralia MC, Lombardo SD, Nicoletti F, Fagone P, Cavalli E. Impaired Expression of Tetraspanin 32 (TSPAN32) in Memory T Cells of Patients with Multiple Sclerosis. Brain Sci 2020; 10:brainsci10010052. [PMID: 31963428 PMCID: PMC7016636 DOI: 10.3390/brainsci10010052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 02/08/2023] Open
Abstract
Tetraspanins are a conserved family of proteins involved in a number of biological processes. We have previously shown that Tetraspanin-32 (TSPAN32) is significantly downregulated upon activation of T helper cells via anti-CD3/CD28 stimulation. On the other hand, TSPAN32 is marginally modulated in activated Treg cells. A role for TSPAN32 in controlling the development of autoimmune responses is consistent with our observation that encephalitogenic T cells from myelin oligodendrocyte glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE) mice exhibit significantly lower levels of TSPAN32 as compared to naïve T cells. In the present study, by making use of ex vivo and in silico analysis, we aimed to better characterize the pathophysiological and diagnostic/prognostic role of TSPAN32 in T cell immunity and in multiple sclerosis (MS). We first show that TSPAN32 is significantly downregulated in memory T cells as compared to naïve T cells, and that it is further diminished upon ex vivo restimulation. Accordingly, following antigenic stimulation, myelin-specific memory T cells from MS patients showed significantly lower expression of TSPAN32 as compared to memory T cells from healthy donors (HD). The expression levels of TSPAN32 was significantly downregulated in peripheral blood mononuclear cells (PBMCs) from drug-naïve MS patients as compared to HD, irrespective of the disease state. Finally, when comparing patients undergoing early relapses in comparison to patients with longer stable disease, moderate but significantly lower levels of TSPAN32 expression were observed in PBMCs from the former group. Our data suggest a role for TSPAN32 in the immune responses underlying the pathophysiology of MS and represent a proof-of-concept for additional studies aiming at dissecting the eventual contribution of TSPAN32 in other autoimmune diseases and its possible use of TSPAN32 as a diagnostic factor and therapeutic target.
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Affiliation(s)
- Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (K.M.); (M.P.); (S.D.L.); (F.N.)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.M.); (M.C.P.); (E.C.)
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (K.M.); (M.P.); (S.D.L.); (F.N.)
| | - Manuela Pennisi
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (K.M.); (M.P.); (S.D.L.); (F.N.)
| | - Maria Cristina Petralia
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.M.); (M.C.P.); (E.C.)
| | - Salvo Danilo Lombardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (K.M.); (M.P.); (S.D.L.); (F.N.)
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (K.M.); (M.P.); (S.D.L.); (F.N.)
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (K.M.); (M.P.); (S.D.L.); (F.N.)
- Correspondence:
| | - Eugenio Cavalli
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.M.); (M.C.P.); (E.C.)
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8
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Lombardo SD, Mazzon E, Basile MS, Campo G, Corsico F, Presti M, Bramanti P, Mangano K, Petralia MC, Nicoletti F, Fagone P. Modulation of Tetraspanin 32 (TSPAN32) Expression in T Cell-Mediated Immune Responses and in Multiple Sclerosis. Int J Mol Sci 2019; 20:ijms20184323. [PMID: 31487788 PMCID: PMC6770290 DOI: 10.3390/ijms20184323] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/30/2019] [Indexed: 01/25/2023] Open
Abstract
Tetraspanins are a conserved family of proteins involved in a number of biological processes including, cell–cell interactions, fertility, cancer metastasis and immune responses. It has previously been shown that TSPAN32 knockout mice have normal hemopoiesis and B-cell responses, but hyperproliferative T cells. Here, we show that TSPAN32 is expressed at higher levels in the lymphoid lineage as compared to myeloid cells. In vitro activation of T helper cells via anti-CD3/CD28 is associated with a significant downregulation of TSPAN32. Interestingly, engagement of CD3 is sufficient to modulate TSPAN32 expression, and its effect is potentiated by costimulation with anti-CD28, but not anti-CTLA4, -ICOS nor -PD1. Accordingly, we measured the transcriptomic levels of TSPAN32 in polarized T cells under Th1 and Th2 conditions and TSPAN32 resulted significantly reduced as compared with unstimulated cells. On the other hand, in Treg cells, TSPAN32 underwent minor changes upon activation. The in vitro data were finally translated into the context of multiple sclerosis (MS). Encephalitogenic T cells from Myelin Oligodendrocyte Glycoprotein (MOG)-Induced Experimental Autoimmune Encephalomyelitis (EAE) mice showed significantly lower levels of TSPAN32 and increased levels of CD9, CD53, CD82 and CD151. Similarly, in vitro-activated circulating CD4 T cells from MS patients showed lower levels of TSPAN32 as compared with cells from healthy donors. Overall, these data suggest an immunoregulatory role for TSPAN32 in T helper immune response and may represent a target of future immunoregulatory therapies for T cell-mediated autoimmune diseases.
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Affiliation(s)
- Salvo Danilo Lombardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Giorgia Campo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Federica Corsico
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Mario Presti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Placido Bramanti
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
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9
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Petralia MC, Mazzon E, Fagone P, Falzone L, Bramanti P, Nicoletti F, Basile MS. Retrospective follow-up analysis of the transcriptomic patterns of cytokines, cytokine receptors and chemokines at preconception and during pregnancy, in women with post-partum depression. Exp Ther Med 2019; 18:2055-2062. [PMID: 31410161 PMCID: PMC6676209 DOI: 10.3892/etm.2019.7774] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/08/2019] [Indexed: 12/29/2022] Open
Abstract
Post-partum depression (PPD) occurs in approximately 20% of women usually early following child delivery. PPD represents an important unmet medical need as it is frequently underdiagnosed and, as the neurobiology of the disease is limitedly known, no pathogenic-tailored approach is available and only symptomatic medications are used. In the present study, we carried out a DNA microarray analysis to evaluate the fluctuation of cytokines, cytokine receptors and chemokines during the preconception period, the 1st and 3th trimester of pregnancy and the early post-partum period. The data demonstrated that, as compared to always-depressed patients and euthymic controls, women who developed PPD exhibited significant fluctuations in the levels of different cytokines and cytokine receptors, primarily related to tumor necrosis factor (TNF) and interleukin (IL)18. These data emphasize the role of the immune system in PPD. However, additional studies aimed at evaluating if and how these functional modifications of the immune system during pregnancy are related to the development of PPD warranted to confirm our findings.
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Affiliation(s)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi 'Bonino-Pulejo', I-98124 Messina, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
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10
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Characterization of the Pathophysiological Role of CD47 in Uveal Melanoma. Molecules 2019; 24:molecules24132450. [PMID: 31277366 PMCID: PMC6651482 DOI: 10.3390/molecules24132450] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 02/08/2023] Open
Abstract
Uveal melanoma (UM) represents the most frequent primary intraocular tumor, however, limited therapeutic options are still available. We have previously shown that cluster of differentiation 47 (CD47) is significantly upregulated in UM cells following inflammatory stimuli and that it represents a predictor of disease progression. Here, we aimed to better characterize the pathophysiological role of CD47 in UM. We show that CD47 is not modulated at different cancer stages, although patients with the lowest expression of CD47 show significant better progression-free survival, after correcting for the presence of BAP1, GNAQ, and GNA11 mutations. By stratifying patients based on the expression of CD47 in the tumor, we observed that patients with high levels of CD47 have a significant increase in immune score as compared to patients with low levels of CD47. In particular, deconvolution analysis of infiltrating immune cell populations revealed that a significantly higher number of CD4+ and CD8+ T cells can be found in patients with high CD47 levels, with the most enriched populations being the Th2, Treg, and CD8+ Tcm cells. We also show that a large number of transcripts are significantly modulated between the groups of patients with high and low levels of CD47, with a significant enrichment of interferon IFN-alpha regulated genes. The results from this study may propel the development of anti-CD47 therapies for UM patients.
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11
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Fagone P, Mazzon E, Mammana S, Di Marco R, Spinasanta F, Basile MS, Petralia MC, Bramanti P, Nicoletti F, Mangano K. Identification of CD4+ T cell biomarkers for predicting the response of patients with relapsing‑remitting multiple sclerosis to natalizumab treatment. Mol Med Rep 2019; 20:678-684. [PMID: 31180553 PMCID: PMC6580020 DOI: 10.3892/mmr.2019.10283] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/26/2019] [Indexed: 01/30/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system of autoimmune etiopathogenesis, and is characterized by various neurological symptoms. Glatiramer acetate and interferon-β are administered as first-line treatments for this disease. In non-responsive patients, several second-line therapies are available, including natalizumab; however, a percentage of MS patients does not respond, or respond partially. Therefore, it is of the utmost importance to develop a diagnostic test for the prediction of drug response in patients suffering from complex diseases, such as MS, where several therapeutic options are already available. By a machine learning approach, the UnCorrelated Shrunken Centroid algorithm was applied to identify a subset of genes of CD4+ T cells that may predict the pharmacological response of relapsing-remitting MS patients to natalizumab, before the initiation of therapy. The results from the present study may provide a basis for the design of personalized therapeutic strategies for patients with MS.
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Affiliation(s)
- Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi 'Bonino‑Pulejo', I‑98124 Messina, Italy
| | - Santa Mammana
- IRCCS Centro Neurolesi 'Bonino‑Pulejo', I‑98124 Messina, Italy
| | - Roberto Di Marco
- Department of Medicine and Health Sciences, University of Molise, I‑86100 Campobasso, Italy
| | - Flaminia Spinasanta
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | | | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
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12
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Conrad T, Kniemeyer O, Henkel SG, Krüger T, Mattern DJ, Valiante V, Guthke R, Jacobsen ID, Brakhage AA, Vlaic S, Linde J. Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC SYSTEMS BIOLOGY 2018; 12:88. [PMID: 30342519 PMCID: PMC6195963 DOI: 10.1186/s12918-018-0620-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/08/2018] [Indexed: 12/20/2022]
Abstract
Background Omics data provide deep insights into overall biological processes of organisms. However, integration of data from different molecular levels such as transcriptomics and proteomics, still remains challenging. Analyzing lists of differentially abundant molecules from diverse molecular levels often results in a small overlap mainly due to different regulatory mechanisms, temporal scales, and/or inherent properties of measurement methods. Module-detecting algorithms identifying sets of closely related proteins from protein-protein interaction networks (PPINs) are promising approaches for a better data integration. Results Here, we made use of transcriptome, proteome and secretome data from the human pathogenic fungus Aspergillus fumigatus challenged with the antifungal drug caspofungin. Caspofungin targets the fungal cell wall which leads to a compensatory stress response. We analyzed the omics data using two different approaches: First, we applied a simple, classical approach by comparing lists of differentially expressed genes (DEGs), differentially synthesized proteins (DSyPs) and differentially secreted proteins (DSePs); second, we used a recently published module-detecting approach, ModuleDiscoverer, to identify regulatory modules from PPINs in conjunction with the experimental data. Our results demonstrate that regulatory modules show a notably higher overlap between the different molecular levels and time points than the classical approach. The additional structural information provided by regulatory modules allows for topological analyses. As a result, we detected a significant association of omics data with distinct biological processes such as regulation of kinase activity, transport mechanisms or amino acid metabolism. We also found a previously unreported increased production of the secondary metabolite fumagillin by A. fumigatus upon exposure to caspofungin. Furthermore, a topology-based analysis of potential key factors contributing to drug-caused side effects identified the highly conserved protein polyubiquitin as a central regulator. Interestingly, polyubiquitin UbiD neither belonged to the groups of DEGs, DSyPs nor DSePs but most likely strongly influenced their levels. Conclusion Module-detecting approaches support the effective integration of multilevel omics data and provide a deep insight into complex biological relationships connecting these levels. They facilitate the identification of potential key players in the organism’s stress response which cannot be detected by commonly used approaches comparing lists of differentially abundant molecules. Electronic supplementary material The online version of this article (10.1186/s12918-018-0620-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- T Conrad
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
| | - O Kniemeyer
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | | | - T Krüger
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - D J Mattern
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Present address: PerkinElmer Inc., Rodgau, Germany
| | - V Valiante
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - R Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - I D Jacobsen
- Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - A A Brakhage
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - S Vlaic
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - J Linde
- Research Group PiDOMICs, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health - Friedrich Loeffler Institute, Jena, Germany
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13
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Vlaic S, Conrad T, Tokarski-Schnelle C, Gustafsson M, Dahmen U, Guthke R, Schuster S. ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. Sci Rep 2018; 8:433. [PMID: 29323246 PMCID: PMC5764996 DOI: 10.1038/s41598-017-18370-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023] Open
Abstract
The identification of disease-associated modules based on protein-protein interaction networks (PPINs) and gene expression data has provided new insights into the mechanistic nature of diverse diseases. However, their identification is hampered by the detection of protein communities within large-scale, whole-genome PPINs. A presented successful strategy detects a PPIN's community structure based on the maximal clique enumeration problem (MCE), which is a non-deterministic polynomial time-hard problem. This renders the approach computationally challenging for large PPINs implying the need for new strategies. We present ModuleDiscoverer, a novel approach for the identification of regulatory modules from PPINs and gene expression data. Following the MCE-based approach, ModuleDiscoverer uses a randomization heuristic-based approximation of the community structure. Given a PPIN of Rattus norvegicus and public gene expression data, we identify the regulatory module underlying a rodent model of non-alcoholic steatohepatitis (NASH), a severe form of non-alcoholic fatty liver disease (NAFLD). The module is validated using single-nucleotide polymorphism (SNP) data from independent genome-wide association studies and gene enrichment tests. Based on gene enrichment tests, we find that ModuleDiscoverer performs comparably to three existing module-detecting algorithms. However, only our NASH-module is significantly enriched with genes linked to NAFLD-associated SNPs. ModuleDiscoverer is available at http://www.hki-jena.de/index.php/0/2/490 (Others/ModuleDiscoverer).
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Affiliation(s)
- Sebastian Vlaic
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Systems Biology and Bioinformatics, Jena, 07745, Germany.
- Friedrich-Schiller-University, Department of Bioinformatics, Jena, 07743, Germany.
| | - Theresia Conrad
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Systems Biology and Bioinformatics, Jena, 07745, Germany
| | - Christian Tokarski-Schnelle
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Systems Biology and Bioinformatics, Jena, 07745, Germany
- University Hospital Jena, Friedrich-Schiller-University, General, Visceral and Vascular Surgery, Jena, 07749, Germany
| | - Mika Gustafsson
- Linköping University, Bioinformatics, Department of Physics, Chemistry and Biology, Linköping, 581 83, Sweden
| | - Uta Dahmen
- University Hospital Jena, Friedrich-Schiller-University, General, Visceral and Vascular Surgery, Jena, 07749, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Systems Biology and Bioinformatics, Jena, 07745, Germany
| | - Stefan Schuster
- Friedrich-Schiller-University, Department of Bioinformatics, Jena, 07743, Germany
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14
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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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15
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Pouladi N, Achour I, Li H, Berghout J, Kenost C, Gonzalez-Garay ML, Lussier YA. Biomechanisms of Comorbidity: Reviewing Integrative Analyses of Multi-omics Datasets and Electronic Health Records. Yearb Med Inform 2016; 25:194-206. [PMID: 27830251 PMCID: PMC5171562 DOI: 10.15265/iy-2016-040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Disease comorbidity is a pervasive phenomenon impacting patients' health outcomes, disease management, and clinical decisions. This review presents past, current and future research directions leveraging both phenotypic and molecular information to uncover disease similarity underpinning the biology and etiology of disease comorbidity. METHODS We retrieved ~130 publications and retained 59, ranging from 2006 to 2015, that comprise a minimum number of five diseases and at least one type of biomolecule. We surveyed their methods, disease similarity metrics, and calculation of comorbidities in the electronic health records, if present. RESULTS Among the surveyed studies, 44% generated or validated disease similarity metrics in context of comorbidity, with 60% being published in the last two years. As inputs, 87% of studies utilized intragenic loci and proteins while 13% employed RNA (mRNA, LncRNA or miRNA). Network modeling was predominantly used (35%) followed by statistics (28%) to impute similarity between these biomolecules and diseases. Studies with large numbers of biomolecules and diseases used network models or naïve overlap of disease-molecule associations, while machine learning, statistics, and information retrieval were utilized in smaller and moderate sized studies. Multiscale computations comprising shared function, network topology, and phenotypes were performed exclusively on proteins. CONCLUSION This review highlighted the growing methods for identifying the molecular mechanisms underpinning comorbidities that leverage multiscale molecular information and patterns from electronic health records. The survey unveiled that intergenic polymorphisms have been overlooked for similarity imputation compared to their intragenic counterparts, offering new opportunities to bridge the mechanistic and similarity gaps of comorbidity.
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Affiliation(s)
| | | | | | | | | | | | - Y A Lussier
- Dr. Yves A. Lussier, The University of Arizona, Bio5 Building, 1657 East Helen Street, Tucson, AZ 85721, USA, Fax: +1 520 626 4824, E-Mail:
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16
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Gustafsson M, Gawel DR, Alfredsson L, Baranzini S, Björkander J, Blomgran R, Hellberg S, Eklund D, Ernerudh J, Kockum I, Konstantinell A, Lahesmaa R, Lentini A, Liljenström HRI, Mattson L, Matussek A, Mellergård J, Mendez M, Olsson T, Pujana MA, Rasool O, Serra-Musach J, Stenmarker M, Tripathi S, Viitala M, Wang H, Zhang H, Nestor CE, Benson M. A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases. Sci Transl Med 2016; 7:313ra178. [PMID: 26560356 DOI: 10.1126/scitranslmed.aad2722] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development.
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Affiliation(s)
- Mika Gustafsson
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden. Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden.
| | - Danuta R Gawel
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Solna, Sweden
| | - Sergio Baranzini
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Janne Björkander
- Futurum-Academy for Health and Care, County Council of Jönköping, SE-551 85 Jönköping, Sweden
| | - Robert Blomgran
- Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Sandra Hellberg
- Department of Clinical and Experimental Medicine, Division of Clinical Immunology, Unit of Autoimmunity and Immune Regulation, Linköping University, SE-581 83 Linköping, Sweden
| | - Daniel Eklund
- Department of Clinical Immunology and Transfusion Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Jan Ernerudh
- Department of Clinical and Experimental Medicine, Division of Clinical Immunology, Unit of Autoimmunity and Immune Regulation, Linköping University, SE-581 83 Linköping, Sweden. Department of Clinical Immunology and Transfusion Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Ingrid Kockum
- Department of Clinical Neurosciences, Karolinska Institutet and Centrum for Molecular Medicine, SE-171 77 Stockholm, Sweden
| | - Aelita Konstantinell
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden. Department of Medical Biology, The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Riita Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Antonio Lentini
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden
| | - H Robert I Liljenström
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden
| | - Lina Mattson
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden
| | - Andreas Matussek
- Futurum-Academy for Health and Care, County Council of Jönköping, SE-551 85 Jönköping, Sweden
| | - Johan Mellergård
- Department of Neurology and Department of Clinical and Experimental Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Melissa Mendez
- Laboratorio de Investigación en Enfermedades Infecciosas, LID, Universidad Peruana Cayetano Heredia, Lima PE-15102, Peru
| | - Tomas Olsson
- Department of Clinical Neurosciences, Karolinska Institutet and Centrum for Molecular Medicine, SE-171 77 Stockholm, Sweden
| | - Miguel A Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Cancer and Systems Biology Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet del Llobregat, ES-08908 Barcelona, Spain
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Jordi Serra-Musach
- Program Against Cancer Therapeutic Resistance (ProCURE), Cancer and Systems Biology Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet del Llobregat, ES-08908 Barcelona, Spain
| | - Margaretha Stenmarker
- Futurum-Academy for Health and Care, County Council of Jönköping, SE-551 85 Jönköping, Sweden
| | - Subhash Tripathi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Miro Viitala
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Hui Wang
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden. Department of Immunology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huan Zhang
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden
| | - Colm E Nestor
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden
| | - Mikael Benson
- The Centre for Individualised Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linköping University, SE-581 83 Linköping, Sweden.
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17
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Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 2016; 22:600-6. [PMID: 27113568 DOI: 10.1016/j.cmi.2016.04.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 02/06/2023]
Abstract
In systems biology, researchers aim to understand complex biological systems as a whole, which is often achieved by mathematical modelling and the analyses of high-throughput data. In this review, we give an overview of medical applications of systems biology approaches with special focus on host-pathogen interactions. After introducing general ideas of systems biology, we focus on (1) the detection of putative biomarkers for improved diagnosis and support of therapeutic decisions, (2) network modelling for the identification of regulatory interactions between cellular molecules to reveal putative drug targets and (3) module discovery for the detection of phenotype-specific modules in molecular interaction networks. Biomarker detection applies supervised machine learning methods utilizing high-throughput data (e.g. single nucleotide polymorphism (SNP) detection, RNA-seq, proteomics) and clinical data. We demonstrate structural analysis of molecular networks, especially by identification of disease modules as a novel strategy, and discuss possible applications to host-pathogen interactions. Pioneering work was done to predict molecular host-pathogen interactions networks based on dual RNA-seq data. However, currently this network modelling is restricted to a small number of genes. With increasing number and quality of databases and data repositories, the prediction of large-scale networks will also be feasible that can used for multidimensional diagnosis and decision support for prevention and therapy of diseases. Finally, we outline further perspective issues such as support of personalized medicine with high-throughput data and generation of multiscale host-pathogen interaction models.
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18
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Liu H, Liu J, Toups M, Soos T, Arendt C. Gene signature-based mapping of immunological systems and diseases. BMC Bioinformatics 2016; 17:171. [PMID: 27089880 PMCID: PMC4836068 DOI: 10.1186/s12859-016-1012-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
Background The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular level, the adaptations of the immune system in host defense and its dysregulation in pathological conditions. A critical aspect of intersecting and investigating complex datasets is determining how to best integrate genomic data from diverse platforms and heterogeneous sample populations to capture immunological signatures in health and disease. Result We focus on gene signatures, representing highly enriched genes of immune cell subsets from both diseased and healthy tissues. From these, we construct a series of biomaps that illustrate the molecular linkages between cell subsets from different lineages, the connectivity between different immunological diseases, and the enrichment of cell subset signatures in diseased tissues. Finally, we overlay the downstream genes of drug targets with disease gene signatures to display the potential therapeutic applications for these approaches. Conclusion An in silico approach has been developed to characterize immune cell subsets and diseases based on the gene signatures that most differentiate them from other biological states. This modular ‘biomap’ reveals the linkages between different diseases and immune subtypes, and provides evidence for the presence of specific immunocyte subsets in mixed tissues. The over-represented genes in disease signatures of interest can be further investigated for their functions in both host defense and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1012-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hong Liu
- Bio-Innovation, Sanofi Global Biotherapeutics, 38 Sidney Street, Cambridge, MA, 02139, USA.
| | - Jessica Liu
- Bio-Innovation, Sanofi Global Biotherapeutics, 38 Sidney Street, Cambridge, MA, 02139, USA
| | - Michelle Toups
- Bioinformatics Program, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Timothy Soos
- Bio-Innovation, Sanofi Global Biotherapeutics, 38 Sidney Street, Cambridge, MA, 02139, USA
| | - Christopher Arendt
- Bio-Innovation, Sanofi Global Biotherapeutics, 38 Sidney Street, Cambridge, MA, 02139, USA
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Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT, Salit M, Ashley EA. Medical implications of technical accuracy in genome sequencing. Genome Med 2016; 8:24. [PMID: 26932475 PMCID: PMC4774017 DOI: 10.1186/s13073-016-0269-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Background As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome. Methods We examine the relationship between human genome complexity and genes/variants reported to be associated with human disease. Specifically, we map regions of medical relevance to benchmark regions of high or low confidence. We use benchmark data to assess the sensitivity and positive predictive value of two representative sequencing pipelines for specific classes of variation. Results We observe that the accuracy of a variant call depends on the genomic region, variant type, and read depth, and varies by analytical pipeline. We find that most false negative WGS calls result from filtering while most false negative WES variants relate to poor coverage. We find that only 74.6 % of the exonic bases in ClinVar and OMIM genes and 82.1 % of the exonic bases in ACMG-reportable genes are found in high-confidence regions. Only 990 genes in the genome are found entirely within high-confidence regions while 593 of 3,300 ClinVar/OMIM genes have less than 50 % of their total exonic base pairs in high-confidence regions. We find greater than 77 % of the pathogenic or likely pathogenic SNVs currently in ClinVar fall within high-confidence regions. We identify sites that are prone to sequencing errors, including thousands present in publicly available variant databases. Finally, we examine the clinical impact of mandatory reporting of secondary findings, highlighting a false positive variant found in BRCA2. Conclusions Together, these data illustrate the importance of appropriate use and continued improvement of technical benchmarks to ensure accurate and judicious interpretation of next-generation DNA sequencing results in the clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0269-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel L Goldfeder
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - James R Priest
- Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA. .,Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
| | - Justin M Zook
- Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Megan E Grove
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - Daryl Waggott
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - Matthew T Wheeler
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - Marc Salit
- Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Euan A Ashley
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA. .,Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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Zhang X, Gao L, Liu ZP, Chen L. Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. BMC Bioinformatics 2015; 16:92. [PMID: 25888350 PMCID: PMC4374500 DOI: 10.1186/s12859-015-0519-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 02/24/2015] [Indexed: 02/07/2023] Open
Abstract
Background Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this issue. Results We propose a strategy based on discriminative area of module activities to identify gene biomarkers which interconnect as a subnetwork or module by integrating gene expression data and protein-protein interactions. Then, we implement the procedure in T2DM as a case study and identify a module biomarker with 32 genes from mRNA expression data in skeletal muscle for T2DM. This module biomarker is enriched with known causal genes and related functions of T2DM. Further analysis shows that the module biomarker is of superior performance in classification, and has consistently high accuracies across tissues and experiments. Conclusion The proposed approach can efficiently identify robust and functionally meaningful module biomarkers in T2DM, and could be employed in biomarker discovery of other complex diseases characterized by expression profiles. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0519-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xindong Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, 710000, China. .,Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, 710000, China. .,Institute of Industrial Science, University of Tokyo, Tokyo, 153-8505, Japan.
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Shandong, 250061, China.
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,Institute of Industrial Science, University of Tokyo, Tokyo, 153-8505, Japan. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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21
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Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M. Modules, networks and systems medicine for understanding disease and aiding diagnosis. Genome Med 2014; 6:82. [PMID: 25473422 PMCID: PMC4254417 DOI: 10.1186/s13073-014-0082-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many common diseases, such as asthma, diabetes or obesity, involve
altered interactions between thousands of genes. High-throughput techniques (omics)
allow identification of such genes and their products, but functional understanding
is a formidable challenge. Network-based analyses of omics data have identified
modules of disease-associated genes that have been used to obtain both a systems
level and a molecular understanding of disease mechanisms. For example, in allergy a
module was used to find a novel candidate gene that was validated by functional and
clinical studies. Such analyses play important roles in systems medicine. This is an
emerging discipline that aims to gain a translational understanding of the complex
mechanisms underlying common diseases. In this review, we will explain and provide
examples of how network-based analyses of omics data, in combination with functional
and clinical studies, are aiding our understanding of disease, as well as helping to
prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve
significant problems and limitations, which will be discussed. We also highlight the
steps needed for clinical implementation.
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Affiliation(s)
- Mika Gustafsson
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
| | - Colm E Nestor
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
| | - Huan Zhang
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
| | - Albert-László Barabási
- Department of Physics, Biology and Computer Science, Center for Complex Network Research, Northeastern University, Boston, MA 02115 USA
| | - Sergio Baranzini
- Department of Neurology, University of California, San Francisco, CA 94143 USA
| | - Sören Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark ; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kian Fan Chung
- Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, SW3 6LY UK
| | - Howard J Federoff
- Department of Neurology and Neuroscience, Georgetown University Medical Center, Washington, DC 20057 USA
| | | | - Richard R Meehan
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Paola Picotti
- Institute of Biochemistry, University of Zürich, 8093 Zürich, Switzerland
| | - Miguel Àngel Pujana
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, 08908 Spain
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Kenneth Gc Smith
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY UK ; Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, CB2 0QQ UK
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Pablo Villoslada
- Center of Neuroimmunology and Department of Neurology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic of Barcelona, 08028 Barcelona, Spain
| | - Mikael Benson
- Centre for Individualized Medicine, Department of Pediatrics, Faculty of Medicine, 58185 Linköping, Sweden
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22
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Zhang H, Gustafsson M, Nestor C, Chung KF, Benson M. Targeted omics and systems medicine: personalising care. THE LANCET RESPIRATORY MEDICINE 2014; 2:785-7. [DOI: 10.1016/s2213-2600(14)70188-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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