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Parodis I, Lindblom J, Toro-Domínguez D, Borghi MO, Enman Y, Repsilber D, Mohan C, Alarcon-Riquelme M, Barturen G. POS0187 DRUG REPURPOSING FOR TREATING LUPUS NEPHRITIS BASED ON TRANSCRIPTOME PROFILING AND AUTOIMMUNITY-RELATED SEROLOGICAL MARKERS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.5348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundLupus nephritis (LN) is one of the most severe organ manifestations of systemic lupus erythematosus (SLE) and constitutes an important cause of morbidity and death among patients with SLE [1]. The associated renal injury, and ultimately damage, is the result of an immune-mediated process which involves leukocytes, immune complexes, complement and cytokines [2].ObjectivesLupus nephritis (LN) is one of the most severe organ manifestations of systemic lupus erythematosus (SLE) and constitutes an important cause of morbidity and death among patients with SLE [1]. The associated renal injury, and ultimately damage, is the result of an immune-mediated process which involves leukocytes, immune complexes, complement and cytokines [2].MethodsWe analysed differentially expressed genes (DEGs), pathways and their druggability via the Drug Gene Interaction database (DGIdb) [3] in active LN (n=41) versus healthy controls (HC; n=497), and eQTLs in active or past LN (n=87), based on validated (identified in two independent SLE populations) DEGs in SLE (n=350) vs HC (n=497), in whole blood collected within the frame of the European PRECISESADS consortium [4]. Genome-wide RNA-sequencing and genotyping was previously performed by Illumina assays, and serum levels of 17 cytokines and 18 autoantibodies were analysed using a Luminex assay, ELISA, IDS-iSYS and SPAPLUS analyser [4].ResultsA total of 6 869 significant and validated DEGs were identified in active LN patients compared with HC. Of these, 1010 validated DEGs were tagged to 34 KEGG pathways including 24 DEGs with a |fold change (FC)| > 1.5, genes of 18 cis-eQTLs and 3 trans-eQTLs, and 1 gene from cytokines that differed significantly between active LN and HC. Moreover, 2446 validated DEGs were tagged to 216 Reactome pathways included 85 DEGs with a |FC| > 1.5, genes of 21 cis-eQTLs and 5 trans-eQTLs, and 1 gene from cytokines that differed significantly between active LN and HC. These genes could be targeted by 203 different drugs, with the proteasome inhibitor bortezomib interfering with cathepsin B (CTSB) regulation and cyclophosphamide interfering with the regulation of tumour necrosis factor receptor superfamily member 1A (TNFRSF1A) being of particular interest.ConclusionIntegrated multilevel omics analysis in LN revealed a set of enriched pathways of potential interest for future drug investigation. A prospect for proteasome inhibition was implicated.References[1]Croca SC, Rodrigues T, Isenberg DA. Assessment of a lupus nephritis cohort over a 30-year period. Rheumatology (Oxford). 2011 Aug; 50(8):1424-1430.[2]Anders HJ, Saxena R, Zhao MH, Parodis I, Salmon JE, Mohan C. Lupus nephritis. Nat Rev Dis Primers. 2020 Jan 23; 6(1):7.[3]Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, et al. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res. 2016 Jan 4; 44(D1):D1036-1044.[4]Barturen G, Babaei S, Català-Moll F, Martínez-Bueno M, Makowska Z, Martorell-Marugán J, et al. Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases. Arthritis Rheumatol. 2021 Jun; 73(6):1073-1085.[5]Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017 Jan 4; 45(D1):D353-d361.[6]Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8; 48(D1):D498-d503.AcknowledgementsThe PRECISESADS Clinical ConsortiumDisclosure of InterestsNone declared
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Lindblom J, Toro-Domínguez D, Borghi MO, Iacobaeus E, Enman Y, Repsilber D, Mohan C, Alarcon-Riquelme M, Barturen G, Parodis I. POS0188 TRANSCRIPTOME PROFILING AND AUTOIMMUNITY-RELATED SEROLOGICAL MARKERS IDENTIFY TP53 and C3aR AS DRUG TARGETS IN NEUROPSYCHIATRIC SYSTEMIC LUPUS ERYTHEMATOSUS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.5349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundInvolvement of the nervous system is a common but poorly understood manifestation of systemic lupus erythematosus (SLE), termed neuropsychiatric SLE (NPSLE). Although studies have reported varying prevalence estimates [1], NPSLE affects at least 20% of patients with SLE within the first years of the disease course [2]. The management of neuropsychiatric SLE (NPSLE) is poorly optimised and specific treatment is lacking.ObjectivesThe aim of this study was to investigate expression quantitative trait loci (eQTLs), the transcriptome, and autoimmunity-related cytokines and autoantibodies in patients with central nervous system (CNS) lupus to gain insights into underlying genetics and biologic mechanisms towards identification of novel drug targets.MethodsWe analysed differentially expressed genes (DEGs), pathways and their druggability via the Drug Gene Interaction database (DGIdb) [3] in active CNS lupus (n=26) versus healthy controls (HC; n=497), and eQTLs in active or past CNS lupus (n=53), based on validated (identified in two independent SLE populations) DEGs in SLE (n=350) versus HC (n=497), in whole blood collected within the frame of the European PRECISESADS consortium [4]. CNS lupus was defined according to SLE Disease Activity Index 2000 (SLEDAI-2K) [5] CNS items or by CNS manifestations such as chorea, acute confusional state, transverse myelitis, aseptic meningitis, and optic neuritis in the absence of predisposing conditions unrelated to SLE. Genome-wide RNA-sequencing and genotyping was previously performed by Illumina assays, and serum levels of 17 cytokines were analysed using a Luminex assay and ELISA [4].ResultsAmong 5631 significant and validated DEGs in active CNS patients compared with HC, 1922 unique DEGs were tagged to 21 and 176 significant KEGG [6] and Reactome [7] pathways, respectively. Pathways included “Interferon signalling”, “TNF signalling” and “Toll-like Receptor Cascades”. The pathways included 29 of 59 DEGs with a |fold change (FC)| > 1.5, 6 genes from 14 significant cis-eQTLs and 10 genes from 22 trans-eQTLs, and 2 genes from 8 cytokines that differed significantly between active CNS lupus and HC. These genes could be targeted by 496 different drugs, with the Bruton tyrosine kinase (BTK) inhibitor ibrutinib and the anti-CD20 B cell depleting monoclonal rituximab with ability to interfere with tumour protein P53 (TP53) activity, and a complement C3a Receptor (C3aR) antagonist being of particular interest.ConclusionIntegrated multilevel omics analysis revealed a set of enriched pathways of potential interest for future drug investigation in CNS lupus, including BTK and C3aR inhibition, and B cell depletion.References[1]Unterman A, Nolte JE, Boaz M, Abady M, Shoenfeld Y, Zandman-Goddard G. Neuropsychiatric syndromes in systemic lupus erythematosus: a meta-analysis. Semin Arthritis Rheum. 2011 Aug; 41(1):1-11[2]Hanly JG, Urowitz MB, Su L, Bae SC, Gordon C, Wallace DJ, et al. Prospective analysis of neuropsychiatric events in an international disease inception cohort of patients with systemic lupus erythematosus. Ann Rheum Dis. 2010 Mar; 69(3):529-535[3]Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, et al. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res. 2016 Jan 4; 44(D1):D1036-1044[4]Barturen G, Babaei S, Català-Moll F, Martínez-Bueno M, Makowska Z, Martorell-Marugán J, et al. Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases. Arthritis Rheumatol. 2021 Jun; 73(6):1073-1085[5]Gladman DD, Ibanez D, Urowitz MB. Systemic lupus erythematosus disease activity index 2000. J Rheumatol. 2002 Feb; 29(2):288-291[6]Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017 Jan 4; 45(D1):D353-d361[7]Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8; 48(D1):D498-d503AcknowledgementsThe PRECISESADS clinical consortiumDisclosure of InterestsNone declared
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Franks PW, Melén E, Friedman M, Sundström J, Kockum I, Klareskog L, Almqvist C, Bergen SE, Czene K, Hägg S, Hall P, Johnell K, Malarstig A, Catrina A, Hagström H, Benson M, Gustav Smith J, Gomez MF, Orho-Melander M, Jacobsson B, Halfvarson J, Repsilber D, Oresic M, Jern C, Melin B, Ohlsson C, Fall T, Rönnblom L, Wadelius M, Nordmark G, Johansson Å, Rosenquist R, Sullivan PF. Technological readiness and implementation of genomic-driven precision medicine for complex diseases. J Intern Med 2021; 290:602-620. [PMID: 34213793 DOI: 10.1111/joim.13330] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 03/21/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022]
Abstract
The fields of human genetics and genomics have generated considerable knowledge about the mechanistic basis of many diseases. Genomic approaches to diagnosis, prognostication, prevention and treatment - genomic-driven precision medicine (GDPM) - may help optimize medical practice. Here, we provide a comprehensive review of GDPM of complex diseases across major medical specialties. We focus on technological readiness: how rapidly a test can be implemented into health care. Although these areas of medicine are diverse, key similarities exist across almost all areas. Many medical areas have, within their standards of care, at least one GDPM test for a genetic variant of strong effect that aids the identification/diagnosis of a more homogeneous subset within a larger disease group or identifies a subset with different therapeutic requirements. However, for almost all complex diseases, the majority of patients do not carry established single-gene mutations with large effects. Thus, research is underway that seeks to determine the polygenic basis of many complex diseases. Nevertheless, most complex diseases are caused by the interplay of genetic, behavioural and environmental risk factors, which will likely necessitate models for prediction and diagnosis that incorporate genetic and non-genetic data.
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Affiliation(s)
- P W Franks
- From the, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Malmö, Sweden.,Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - E Melén
- Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - M Friedman
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - J Sundström
- Department of Cardiology, Akademiska Sjukhuset, Uppsala, Sweden.,George Institute for Global Health, Camperdown, NSW, Australia.,Medical Sciences, Uppsala University, Uppsala, Sweden
| | - I Kockum
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - L Klareskog
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Rheumatology, Karolinska Institutet, Stockholm, Sweden
| | - C Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - S E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - K Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - S Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - P Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - K Johnell
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - A Malarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Pfizer, Worldwide Research and Development, Stockholm, Sweden
| | - A Catrina
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - H Hagström
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Division of Hepatology, Department of Upper GI, Karolinska University Hospital, Stockholm, Sweden
| | - M Benson
- Department of Pediatrics, Linkopings Universitet, Linkoping, Sweden.,Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - J Gustav Smith
- Department of Cardiology and Wallenberg Center for Molecular Medicine, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden.,Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - M F Gomez
- From the, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - M Orho-Melander
- From the, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - B Jacobsson
- Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Genetics and Bioinformatics, Oslo, Norway.,Department of Obstetrics and Gynecology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - J Halfvarson
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Repsilber
- Functional Bioinformatics, Örebro University, Örebro, Sweden
| | - M Oresic
- School of Medical Sciences, Örebro University, Örebro, Sweden.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, FI, Finland
| | - C Jern
- Department of Clinical Genetics and Genomics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - B Melin
- Department of Radiation Sciences, Oncology, Umeå Universitet, Umeå, Sweden
| | - C Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, CBAR, University of Gothenburg, Gothenburg, Sweden.,Department of Drug Treatment, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - T Fall
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - L Rönnblom
- Department of Medical Sciences, Rheumatology & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - M Wadelius
- Department of Medical Sciences, Clinical Pharmacogenomics & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - G Nordmark
- Department of Medical Sciences, Rheumatology & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Å Johansson
- Institute for Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - R Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - P F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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4
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Kalla R, Adams AT, Bergemalm D, Vatn S, Kennedy NA, Ricanek P, Lindstrom J, Ocklind A, Hjelm F, Ventham NT, Ho GT, Petren C, Repsilber D, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjorn C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Serum proteomic profiling at diagnosis predicts clinical course, and need for intensification of treatment in inflammatory bowel disease. J Crohns Colitis 2021; 15:699-708. [PMID: 33201212 PMCID: PMC8095384 DOI: 10.1093/ecco-jcc/jjaa230] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Success in personalized medicine in complex disease is critically dependent on biomarker discovery. We profiled serum proteins using a novel proximity extension assay [PEA] to identify diagnostic and prognostic biomarkers in inflammatory bowel disease [IBD]. METHODS We conducted a prospective case-control study in an inception cohort of 552 patients [328 IBD, 224 non-IBD], profiling proteins recruited across six centres. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. Nested leave-one-out cross-validation was used to examine the performance of diagnostic and prognostic proteins. RESULTS A total of 66 serum proteins differentiated IBD from symptomatic non-IBD controls, including matrix metallopeptidase-12 [MMP-12; Holm-adjusted p = 4.1 × 10-23] and oncostatin-M [OSM; p = 3.7 × 10-16]. Nine of these proteins are associated with cis-germline variation [59 independent single nucleotide polymorphisms]. Fifteen proteins, all members of tumour necrosis factor-independent pathways including interleukin-1 (IL-1) and OSM, predicted escalation, over a median follow-up of 518 [interquartile range 224-756] days. Nested cross-validation of the entire data set allowed characterization of five-protein models [96% comprising five core proteins ITGAV, EpCAM, IL18, SLAMF7 and IL8], which define a high-risk subgroup in IBD [hazard ratio 3.90, confidence interval: 2.43-6.26], or allowed distinct two- and three-protein models for ulcerative colitis and Crohn's disease respectively. CONCLUSION We have characterized a simple oligo-protein panel that has the potential to identify IBD from symptomatic controls and to predict future disease course. Further prospective work is required to validate our findings.
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Affiliation(s)
- R Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - A T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - D Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - S Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - N A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, UK
| | - P Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | | | - F Hjelm
- Olink Proteomics, Uppsala, Sweden
| | - N T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - G T Ho
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - C Petren
- Olink Proteomics, Uppsala, Sweden
| | - D Repsilber
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - M Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - M D’Amato
- BioCruces Health Research Institute and Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- School of Biological Sciences, Monash University, Victoria, Australia
| | - F Gomollón
- HCU ‘Lozano Blesa’, IIS Aragón, Zaragoza, Spain
| | - C Olbjorn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - M H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - J Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Holster S, Repsilber D, Geng D, Hyötyläinen T, Salonen A, Lindqvist CM, Rajan SK, de Vos WM, Brummer RJ, König J. Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. Benef Microbes 2020; 12:17-30. [PMID: 33350360 DOI: 10.3920/bm2020.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of a patient with the aim to restore a disturbed gut microbiota. In this study, it was investigated whether FMT has an effect on faecal microbial composition, its functional capacity, faecal metabolite profiles and their interactions in 16 irritable bowel syndrome (IBS) patients. Faecal samples from eight different time points before and until six months after allogenic FMT (faecal material from a healthy donor) as well as autologous FMT (own faecal material) were analysed by 16S RNA gene amplicon sequencing and gas chromatography coupled to mass spectrometry (GS-MS). The results showed that the allogenic FMT resulted in alterations in the microbial composition that were detectable up to six months, whereas after autologous FMT this was not the case. Similar results were found for the functional profiles, which were predicted from the phylogenetic sequencing data. While both allogenic FMT as well as autologous FMT did not have an effect on the faecal metabolites measured in this study, correlations between the microbial composition and the metabolites showed that the microbe-metabolite interactions seemed to be disrupted after allogenic FMT compared to autologous FMT. This shows that FMT can lead to altered interactions between the gut microbiota and its metabolites in IBS patients. Further research should investigate if and how this affects efficacy of FMT treatments.
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Affiliation(s)
- S Holster
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Repsilber
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Geng
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - T Hyötyläinen
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - A Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - C M Lindqvist
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - S K Rajan
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - W M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - R J Brummer
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J König
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
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Jacobsen M, Repsilber D, Gutschmidt A, Neher A, Feldmann K, Mollenkopf HJ, Kaufmann SHE, Ziegler A. Deconfounding Microarray Analysis. Methods Inf Med 2018. [DOI: 10.1055/s-0038-1634118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Summary
Objectives:
Microarray analysis requires standardized specimens and evaluation procedures to achieve acceptable results. A major limitation of this method is caused by heterogeneity in the cellular composition of tissue specimens, which frequently confounds data analysis. We introduce a linear model to deconfound gene expression data from tissue heterogeneity for genes exclusively expressed by a single cell type.
Methods:
Gene expression data are deconfounded from tissue heterogeneity effects by analyzing them using an appropriate linear regression model. In our illustrating data set tissue heterogeneity is being measured using flow cytometry. Gene expression data are determined in parallel by real time quantitative polymerase chain reaction (qPCR) and microarray analyses. Verification of deconfounding is enabled using protein quantification for the respective marker genes.
Results:
For our illustrating dataset, quantification of cell type proportions for peripheral blood mononuclear cells (PBMC) from tuberculosis patients and controls revealed differences in B cell and monocyte proportions between both study groups, and thus heterogeneity for the tissue under investigation. Gene expression analyses reflected these differences in celltype distribution. Fitting an appropriate linear model allowed us to deconfound measured transcriptome levels from tissue heterogeneity effects. In the case of monocytes, additional differential expression on the single cell level could be proposed. Protein quantification verified these deconfounded results.
Conclusions:
Deconfounding of transcriptome analyses for cellular heterogeneity greatly improves interpretability, and hence the validity of transcriptome profiling results.
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Abstract
Summary
Objectives:
With the collection of articles presented in this special issue, we aim at educating interested statisticians and biometricians on the one hand as well as biologists and medical researchers on the other with respect to basic necessities in planning, conducting and analyzing microarray gene expression experiments. The reader should get comprehensive directions to understand both the overall structure of this approach as well as the decisive details, which enable – or thwart – a meaningful data analysis.
Methods:
For a one-day workshop with tutorial character we brought together experts in design, conduct and analysis of microarray gene expression experiments who prepared a series of comprehensive lessons. These contributions were then reworked into a series of introductory articles and bundled in form and content as a Special Topic.
Results:
It was possible to present a tutorial overview of the field. The interested reader was able to learn the basic necessities and was referred to further references for details on the possible alternatives. A recipe style all-embracing plan, covering all eventualities and possibilities was not only beyond the scope of an introductory tutorial-like presentation, but was also not yet agreed upon by the scientific society.
Conclusions:
It proved feasible to find a framework for integrating the interdisciplinary approaches to the challenging field of gene expression analysis with microarrays, hopefully contributing to a rapid and comprehensive introduction for novices.
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8
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Abstract
Summary
Objectives:
The choice of biomedical samples for microarray gene expression studies is decisive for both validity and interpretability of results. We present a consistent, comprehensive framework to deal with the typical selection problems in microarray studies.
Methods:
Microarray studies are designed either as case-control studies or as comparisons of parallel groups from cohort studies, since high levels of random variation in the experimental approach thwart absolute measurements of gene expression levels. Validity and results of gene expression studies heavily rely on the appropriate choice of these study groups. Therefore, the so-called principles of comparability, which are well known from both clinical and epidemiological studies, need to be applied to microarray experiments.
Results:
The principles of comparability are the study-base principle, the principle of deconfounding and the principle of comparable accuracy in measurements. We explain each of these principles, show how they apply to microarray experiments, and illustrate them with examples. The examples are chosen as to represent typical stumbling blocks of microarray experimental design, and to exemplify the benefits of implementing the principles of comparability in the setting of micro-array experiments.
Conclusions:
Microarray studies are closely related to classical study designs and therefore have to obey the same principles of comparability as these. Their validity should not be compromised by selection, confounding or information bias. The so-called study-base principle, calling for comparability and thorough definition of the compared cell populations, is the key principle for the choice of biomedical samples and controls in microarray studies.
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Rangel I, Sundin J, Fuentes S, Repsilber D, de Vos WM, Brummer RJ. The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects. Aliment Pharmacol Ther 2015; 42:1211-21. [PMID: 26376728 DOI: 10.1111/apt.13399] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/02/2015] [Accepted: 08/19/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND The faecal-associated microbiota is commonly seen as a surrogate of the mucosal-associated microbiota. However, previous studies indicate that they are different. Furthermore, analyses of the mucosal microbiota are commonly done after standard bowel cleansing, affecting the microbial composition. AIM To compare the mucosal-associated microbiota, obtained from unprepared colon, with faecal-associated microbiota in healthy subjects and irritable bowel syndrome (IBS) patients. METHODS Faecal and mucosal biopsies were obtained from 33 IBS patients and 16 healthy controls. Of IBS patients, 49% belonged to the diarrhoea-predominant subgroup and 80% suffered from IBS symptoms during at least 5 years. Biopsies were collected from unprepared sigmoid colon and faecal samples a day before colonoscopy. Microbiota analyses were performed with a phylogenetic microarray and redundancy discriminant analysis. RESULTS The composition of the mucosal- and the faecal-associated microbiota in unprepared sigmoid colon differs significantly (P = 0.002). Clinical characteristics of IBS did not correlate with this difference. Bacteroidetes dominate the mucosal-associated microbiota. Firmicutes, Actinobacteria and Proteobacteria dominate the faecal-associated microbiota. Healthy subjects had a significantly higher (P < 0.005) abundance (1.9%) of the bacterial group uncultured Clostridiales I in the mucosal-associated microbiota than IBS patients (0.3%). Bacterial diversity was higher in faecal- compared with mucosal-associated microbiota in IBS patients (P < 0.005). No differences were found in healthy subjects. CONCLUSIONS Differences in the mucosal-associated microbiota between healthy individuals and IBS patients are minimal (one bacterial group) compared to differences in the faecal microbiota of both groups (53 bacterial groups). Microbial aberrations characterising IBS are more pronounced in the faeces than in the mucosa.
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Affiliation(s)
- I Rangel
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - J Sundin
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - S Fuentes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - D Repsilber
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - W M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.,Departments of Bacteriology & Immunology and Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - R J Brummer
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
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10
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Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D. Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci 2013; 96:1521-34. [PMID: 23438684 DOI: 10.3168/jds.2012-5743] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022]
Abstract
In the field of dairy cattle research, it is of great interest to improve the detection and prevention of diseases (e.g., mastitis and ketosis) and monitor specific traits related to the state of health and management. During the standard milk performance test, traditional milk traits are monitored, and quality and quantity are screened. In addition to the standard test, it is also now possible to analyze milk metabolites in a high-throughput manner and to consider them in connection with milk traits to identify functionally important metabolites that can also serve as biomarker candidates. We present a study in which 190 milk metabolites and 14 milk traits of 1,305 Holstein cows on 18 commercial farms were investigated to characterize interrelations of milk metabolites between each other, to milk traits from the milk standard performance test, and to influencing factors such as farm and sire effect (half-sib structure). The effect of influencing factors (e.g., farm) varied among metabolites and traditional milk traits. The investigations of associations between metabolites and milk traits revealed groups of metabolites that show, for example, positive correlations to protein and casein, and negative correlations to lactose and pH. On the other hand, groups of metabolites jointly associated with the investigated milk traits can be identified and functionally discussed. To enable a multivariate investigation, 2 machine learning methods were applied to detect important metabolites that are highly correlated with the investigated traditional milk traits. For somatic cell score, uracil, lactic acid, and 9 other important metabolites were detected. Lactic acid has already been proposed as a biomarker candidate for mastitis in the recent literature. In conclusion, we found sets of metabolites eligible to predict milk traits, enabling the analysis of milk traits from a metabolic perspective and discussion of the possible functional background for some of the detected associations.
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Affiliation(s)
- N Melzer
- Research Unit Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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11
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Wittenburg D, Melzer N, Willmitzer L, Lisec J, Kesting U, Reinsch N, Repsilber D. Milk metabolites and their genetic variability. J Dairy Sci 2013; 96:2557-2569. [PMID: 23403187 DOI: 10.3168/jds.2012-5635] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 12/13/2012] [Indexed: 11/19/2022]
Abstract
The composition of milk is crucial to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g., fat, protein, lactose) traditionally recorded during milk performance test via infrared spectroscopy, novel techniques, such as gas chromatography-mass spectrometry, allow for a further analysis of milk into its metabolic components. Gas chromatography-mass spectrometry is suitable for measuring several hundred metabolites with high throughput, and thus it is applicable to study sources of genetic and nongenetic variation of milk metabolites in dairy cows. Heritability and mode of inheritance of metabolite measurements were studied in a linear mixed model approach including expected (pedigree) and realized (genomic) relationship between animals. The genetic variability of 190 milk metabolite intensities was analyzed from 1,295 cows held on 18 farms in Mecklenburg-Western Pomerania, Germany. Besides extensive pedigree information, genotypic data comprising 37,180 single nucleotide polymorphism markers were available. Goodness of fit and significance of genetic variance components based on likelihood ratio tests were investigated with a full model, including marker- and pedigree-based genetic effects. Broad-sense heritability varied from zero to 0.699, with a median of 0.125. Significant additive genetic variance was observed for highly heritable metabolites, but dominance variance was not significantly present. As some metabolites are particularly favorable for human nutrition, for instance, future research should address the identification of locus-specific genetic effects and investigate metabolites as the molecular basis of traditional milk performance test traits.
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Affiliation(s)
- D Wittenburg
- Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
| | - N Melzer
- Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - L Willmitzer
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - J Lisec
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - U Kesting
- Landeskontrollverband für Leistungs- und Qualitätsprüfung Mecklenburg-Vorpommern e.V. (LKV), 18273 Güstrow, Germany
| | - N Reinsch
- Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - D Repsilber
- Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
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12
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Krappmann K, Wurmser C, Repsilber D, Fries R, Weikard R, Kesting U, Kühn C. Short communication: evaluation of bovine milk residues from routine milk testing programs as DNA source for genotyping. J Dairy Sci 2012; 95:5436-5441. [PMID: 22916950 DOI: 10.3168/jds.2011-5259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/22/2012] [Indexed: 11/19/2022]
Abstract
Genome-wide association studies and genomic evaluation using a dense set of genetic markers both require a large number of genotyped individuals. Collection of the respective samples contributes substantially to the cost of the approach. In dairy cattle research, the use of residues from routine milk recording would be a cost-saving alternative to obtain samples for an appropriate number of individuals with specific phenotypes in a very short time. To assess the suitability of milk recording residues, we concurrently investigated milk residues obtained after standardized milk recording procedures and blood samples from 115 cows originating from 3 farms with different milking systems by genotyping 15 microsatellite markers. We found that 4% of the milk samples were possibly assigned to the wrong animal (i.e., conflicts) and that at least 27% of the milk residues were contaminated, as indicated by an extra allele not present in the blood sample. These additional alleles primarily originated from a sample with a higher somatic cell score that went through the milk sample analyzer in the milk laboratory before the target sample. Furthermore, additional allele carryover was observed across more than one sample, when the difference in somatic cell count between samples exceeded 100,000 cells/mL. Finally, in several samples, the extra allele could not be traced back to previous samples passing through the milk sample analyzer. One source of those contaminations might be sample collection on-farm due to milk traces from the previously milked cow in the hose. No correlation was found between the farm management and conflicts or contaminations. We conclude that residues from routine milk recording are not suitable for genomic evaluation or genome-wide association studies because of the high prevalence of contamination generated at several steps during the collection and processing of milk residual samples.
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Affiliation(s)
- K Krappmann
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - C Wurmser
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany
| | - D Repsilber
- Research Unit Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - R Fries
- Chair of Animal Breeding, Technische Universität München, 85354 Freising, Germany
| | - R Weikard
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - U Kesting
- Landeskontrollverband für Leistungs- und Qualitätsprüfung Mecklenburg, 18273, Güstrow, Germany
| | - C Kühn
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
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13
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Maertzdorf J, Repsilber D, Parida SK, Stanley K, Roberts T, Black G, Walzl G, Kaufmann SHE. Human gene expression profiles of susceptibility and resistance in tuberculosis. Genes Immun 2010; 12:15-22. [PMID: 20861863 DOI: 10.1038/gene.2010.51] [Citation(s) in RCA: 239] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB) still poses a profound burden on global health, owing to significant morbidity and mortality worldwide. Although a fully functional immune system is essential for the control of Mycobacterium tuberculosis infection, the underlying mechanisms and reasons for failure in part of the infected population remain enigmatic. Here, whole-blood microarray gene expression analyses were performed in TB patients and in latently as well as uninfected healthy controls to define biomarkers predictive of susceptibility and resistance. Fc gamma receptor 1B (FCGRIB)was identified as the most differentially expressed gene, and, in combination with four other markers, produced a high degree of accuracy in discriminating TB patients and latently infected donors. We determined differentially expressed genes unique for active disease and identified profiles that correlated with susceptibility and resistance to TB. Elevated expression of innate immune-related genes in active TB and higher expression of particular gene clusters involved in apoptosis and natural killer cell activity in latently infected donors are likely to be the major distinctive factors determining failure or success in controlling M. tuberculosis infection. The gene expression profiles defined in this study provide valuable clues for better understanding of progression from latent infection to active disease and pave the way for defining predictive correlates of protection in TB.
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Affiliation(s)
- J Maertzdorf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany.
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14
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Jacobsen M, Repsilber D, Kleinsteuber K, Gutschmidt A, Schommer-Leitner S, Black G, Walzl G, Kaufmann SHE. Suppressor of cytokine signaling-3 is affected in T-cells from tuberculosisTB patients. Clin Microbiol Infect 2010; 17:1323-31. [PMID: 20673263 DOI: 10.1111/j.1469-0691.2010.03326.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
T-cells and T-cell-derived cytokines are crucial mediators of protection against Mycobacterium tuberculosis infection, but these factors are insufficient as biomarkers for disease susceptibility. In order to define T-cell molecules involved in tuberculosis (TB), we compared gene expression profiles of T-cells from patients with active TB, healthy donors with latent M. tuberculosis infection (LTBIs) and non-infected healthy donors (NIDs) by microarray analysis. Pathway-focused analyses identified a prevalent subset of candidate genes involved in the Janus kinase (JAK)-signal transducer and activator of transcription signalling pathway, including those encoding suppressor of cytokine signalling (SOCS) molecules, in the subset of protection-associated genes. Differential expression was verified by quantitative PCR analysis for the cytokine-inducible SH2-containing protein (CISH), SOCS3, JAK3, interleukin-2 receptor α-chain (IL2RA), and the proto-oncogene serine/threonine protein kinase (PIM1). Classification analyses revealed that this set of molecules was able to discriminate efficiently between T-cells from TB patients and those from LTBIs, and, notably, to achieve optimal discrimination between LTBIs and NIDs. Further characterization by quantitative PCR revealed highly variable candidate gene expression in CD4(+) and CD8(+) T-cells from TB patients and only minor differences between CD4(+) and CD8(+) T-cell subpopulations. These results point to a role of cytokine receptor signalling regulation in T-cells in susceptibility to TB.
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Affiliation(s)
- M Jacobsen
- Department of Immunology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.
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15
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Hartmann A, Nuernberg G, Repsilber D, Janczyk P, Walz C, Ponsuksili S, Souffrant WB, Schwerin M. Effects of threshold choice on the results of gene expression profiling, using microarray analysis, in a model feeding experiment with rats. Arch Anim Breed 2009. [DOI: 10.5194/aab-52-65-2009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Global gene expression studies using microarray technology are widely employed to identify biological processes which are influenced by a treatment e.g. a specific diet. Affected processes are characterized by a significant enrichment of differentially expressed genes (functional annotation analysis). However, different choices of statistical thresholds to select candidates for differential expression will alter the resulting candidates list. This study was conducted to investigate the effect of applying a False Discovery Rate (FDR) correction and different fold change thresholds in statistical analysis of microarray data on diet-affected biological processes based on a significantly increased proportion of differentially expressed genes. In a model feeding experiment with rats fed genetically modified food additives, animals received a supplement of either lyophilized inactivated recombinant VP60 baculovirus (rBV-VP60) or lyophilized inactivated wild type baculovirus (wtBV). Comparative expression profiling was done in spleen, liver and small intestine mucosa. We demonstrated the extent to which threshold choice can affect the biological processes identified as significantly regulated and thus the conclusion drawn from the microarray data. In our study, the combined application of a moderate fold change threshold (FC≥1.5) and a stringent FDR threshold (q≤0.05) exhibited high reliability of biological processes identified as differentially regulated. The application of a stringent FDR threshold of q≤0.05 seems to be an essential prerequisite to reduce considerably the number of false positives. Microarray results of selected differentially expressed molecules were validated successfully by using real-time RT-PCR.
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16
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Jacobsen M, Repsilber D, Gutschmidt A, Neher A, Feldmann K, Mollenkopf HJ, Kaufmann SHE, Ziegler A. Deconfounding microarray analysis - independent measurements of cell type proportions used in a regression model to resolve tissue heterogeneity bias. Methods Inf Med 2006; 45:557-63. [PMID: 17019511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
OBJECTIVES Microarray analysis requires standardized specimens and evaluation procedures to achieve acceptable results. A major limitation of this method is caused by heterogeneity in the cellular composition of tissue specimens, which frequently confounds data analysis. We introduce a linear model to deconfound gene expression data from tissue heterogeneity for genes exclusively expressed by a single cell type. METHODS Gene expression data are deconfounded from tissue heterogeneity effects by analyzing them using an appropriate linear regression model. In our illustrating data set tissue heterogeneity is being measured using flow cytometry. Gene expression data are determined in parallel by real time quantitative polymerase chain reaction (qPCR) and microarray analyses. Verification of deconfounding is enabled using protein quantification for the respective marker genes. RESULTS For our illustrating dataset, quantification of cell type proportions for peripheral blood mononuclear cells (PBMC) from tuberculosis patients and controls revealed differences in B cell and monocyte proportions between both study groups, and thus heterogeneity for the tissue under investigation. Gene expression analyses reflected these differences in celltype distribution. Fitting an appropriate linear model allowed us to deconfound measured transcriptome levels from tissue heterogeneity effects. In the case of monocytes, additional differential expression on the single cell level could be proposed. Protein quantification verified these deconfounded results. CONCLUSIONS Deconfounding of transcriptome analyses for cellular heterogeneity greatly improves interpretability, and hence the validity of transcriptome profiling results.
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Affiliation(s)
- M Jacobsen
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
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17
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Schumacher J, König IR, Plume E, Propping P, Warnke A, Manthey M, Duell M, Kleensang A, Repsilber D, Preis M, Remschmidt H, Ziegler A, Nöthen MM, Schulte-Körne G. Linkage analyses of chromosomal region 18p11-q12 in dyslexia. J Neural Transm (Vienna) 2005; 113:417-23. [PMID: 16075186 DOI: 10.1007/s00702-005-0336-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2005] [Accepted: 05/14/2005] [Indexed: 11/28/2022]
Abstract
Dyslexia is characterized as a significant impairment in reading and spelling ability that cannot be explained by low intelligence, low school attendance or deficits in sensory acuity. It is known to be a hereditary disorder that affects about 5% of school aged children, making it the most common of childhood learning disorders. Several susceptibility loci have been reported on chromosomes 1, 2, 3, 6, 15, and 18. The locus on chromosome 18 has been described as having the strongest influence on single word reading, phoneme awareness, and orthographic coding in the largest genome wide linkage study published to date (Fisher et al., 2002). Here we present data from 82 German families in order to investigate linkage of various dyslexia-related traits to the previously described region on chromosome 18p11-q12. Using two- and multipoint analyses, we did not find support for linkage of spelling, single word reading, phoneme awareness, orthographic coding and rapid naming to any of the 14 genotyped STR markers. Possible explanations for our non-replication include differences in study design, limited power of our study and overestimation of the effect of the chromosome 18 locus in the original study.
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Repsilber D, Mansmann U, Brunner E, Ziegler A. Tutorial on microarray gene expression experiments. An introduction. Methods Inf Med 2005; 44:392-9. [PMID: 16113762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OBJECTIVES With the collection of articles presented in this special issue, we aim at educating interested statisticians and biometricians on the one hand as well as biologists and medical researchers on the other with respect to basic necessities in planning, conducting and analyzing microarray gene expression experiments. The reader should get comprehensive directions to understand both the overall structure of this approach as well as the decisive details, which enable--or thwart--a meaningful data analysis. METHODS For a one-day workshop with tutorial character we brought together experts in design, conduct and analysis of microarray gene expression experiments who prepared a series of comprehensive lessons. These contributions were then reworked into a series of introductory articles and bundled in form and content as a Special Topic. RESULTS It was possible to present a tutorial overview of the field. The interested reader was able to learn the basic necessities and was referred to further references for details on the possible alternatives. A recipe style all-embracing plan, covering all eventualities and possibilities was not only beyond the scope of an introductory tutorial-like presentation, but was also not yet agreed upon by the scientific society. CONCLUSIONS It proved feasible to find a framework for integrating the interdisciplinary approaches to the challenging field of gene expression analysis with microarrays, hopefully contributing to a rapid and comprehensive introduction for novices.
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Affiliation(s)
- D Repsilber
- Institute für Medizinische Biometrie und Statistik, Universität za Lübeck, Lübeck, Germany.
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Repsilber D, Ziegler A. Two-color microarray experiments. Technology and sources of variance. Methods Inf Med 2005; 44:400-4. [PMID: 16113763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OBJECTIVES Microarray gene expression experiments have a complex technical background. Knowledge about certain technical details is inevitable to judge alternatives for both experimental design and analysis. Here, we introduce the necessary details for the so-called two-color microarray experiments and review major sources of technical variance. METHODS We follow the sequence of experimental steps during a typical two-color microarray gene expression experiment, stressing decisive points in the choice of technique, experimental handling and biophysical basics. We point out where technical variation is to be expected. RESULTS Tissue storage, RNA extraction techniques, as well as the microarray hybridization represent major components of technical variance to be considered. Depending on the possibilities for access to the biomedical material under investigation, choice of amplification and labeling techniques can also be decisive to avoid additional technical variance. The two-color microarray experimental approach seeks to avoid a group of probe-level technical biases making use of the advantages of an incomplete block-design. CONCLUSIONS It is worth to know the major sources of technical variance during the typical experimental sequence, both for choice of experimental design and techniques of molecular biology, as well as for the understanding of quality control and normalization approaches. Here, early investments pay at the level of reduced technical variance, allowing for enhanced detection levels for the effects under investigation.
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Affiliation(s)
- D Repsilber
- Institut für Medizinische Biometrie und Statistik Universitätsklinikum Schleswig-Holstein, Campus Lübeck Ratzeburger Allee 160, Haus 4 23538 Lübeck, Germany.
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Repsilber D, Fink L, Jacobsen M, Bläsing O, Ziegler A. Sample selection for microarray gene expression studies. Methods Inf Med 2005; 44:461-7. [PMID: 16113774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OBJECTIVES The choice of biomedical samples for microarray gene expression studies is decisive for both validity and interpretability of results. We present a consistent, comprehensive framework to deal with the typical selection problems in microarray studies. METHODS Microarray studies are designed either as case-control studies or as comparisons of parallel groups from cohort studies, since high levels of random variation in the experimental approach thwart absolute measurements of gene expression levels. Validity and results of gene expression studies heavily rely on the appropriate choice of these study groups. Therefore, the so-called principles of comparability, which are well known from both clinical and epidemiological studies, need to be applied to microarray experiments. RESULTS The principles of comparability are the study-base principle, the principle of deconfounding and the principle of comparable accuracy in measurements. We explain each of these principles, show how they apply to microarray experiments, and illustrate them with examples. The examples are chosen as to represent typical stumbling blocks of microarray experimental design, and to exemplify the benefits of implementing the principles of comparability in the setting of microarray experiments. CONCLUSIONS Microarray studies are closely related to classical study designs and therefore have to obey the same principles of comparability as these. Their validity should not be compromised by selection, confounding or information bias. The so-called study-base principle, calling for comparability and thorough definition of the compared cell populations, is the key principle for the choice of biomedical samples and controls in microarray studies.
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Affiliation(s)
- D Repsilber
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Lübeck, Germany
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21
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Repsilber D, Wiese S, Rachen M, Schröder AW, Riesner D, Steger G. Formation of metastable RNA structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis. RNA 1999; 5:574-84. [PMID: 10199573 PMCID: PMC1369783 DOI: 10.1017/s1355838299982018] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A model of functional elements critical for replication and infectivity of the potato spindle tuber viroid (PSTVd) was proposed earlier: a thermodynamically metastable structure containing a specific hairpin (HP II) in the (-)-strand replication intermediate is essential for template activity during (+)-strand synthesis. We present here a detailed kinetic analysis on how PSTVd (-)-strands fold during synthesis by sequential folding into a variety of metastable structures that rearrange only slowly into the structure distribution of the thermodynamic equilibrium. Synthesis of PSTVd (-)-strands was performed by T7-RNA-polymerase; the rate of synthesis was varied by altering the concentration of nucleoside triphosphates to mimic the in vivo synthesis rate of DNA-dependent RNA polymerase II. With dependence on rate and duration of the synthesis, the structure distributions were analyzed by temperature-gradient gel electrophoresis (TGGE). Metastable structures are generated preferentially at low transcription rates--similar to in vivo rates--or at short transcription times at higher rates. Higher transcription rates or longer transcription times lead to metastable structures in low or undetectable amounts. Instead different structures do gradually appear having a more rod-like shape and higher thermodynamic stability, and the thermodynamically optimal rod-like structure dominates finally. It is concluded that viroids are able to use metastable as well as stable structures for their biological functions.
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Affiliation(s)
- D Repsilber
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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