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Ödling M, Andersson N, Ekström S, Roxhed N, Schwenk JM, Björkander S, Bergström A, Melén E, Kull I. COVID-19 vaccine uptake among young adults: Influence of asthma and sociodemographic factors. J Allergy Clin Immunol Glob 2024; 3:100231. [PMID: 38524785 PMCID: PMC10959661 DOI: 10.1016/j.jacig.2024.100231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 03/26/2024]
Abstract
Background Asthma was initially described as a risk factor for severe coronavirus disease 2019 (COVID-19), but the uptake of COVID-19 vaccine among young adults with asthma is not well studied. Objective The aims were to assess COVID-19 vaccine uptake among young adults in general and to explore potential determinants including sociodemographic factors and asthma. Methods Participants from the population-based birth cohort BAMSE (Barn/Child, Allergy, Milieu, Stockholm, Epidemiology) were included: 4,064 in the study population, 3,064 in a follow-up at age 24 years, and 2,049 in a COVID-19 follow-up (mean age, 26.5 years). Asthma and asthma-associated characteristics were assessed through questionnaires and clinical data. Data on all COVID-19 vaccines registered between January 1, 2021, and February 15, 2023, were extracted from the National Vaccination Register. Results In the study population (n = 4,064), 53.9% had ≥3 COVID-19 vaccine doses registered. In the 24-year follow-up population (n = 3,064), vaccine uptake differed in relation to education (P < .001). Among the participants with university/college education, 65.7% had an uptake of ≥3 doses of vaccine, compared to 54.1% among the participants with elementary school/high school education. Participants with asthma had decreased odds of receiving ≥3 doses (adjusted odds ratio = 0.62; 95% confidence interval, 0.41-0.92) and ≥2 compared to peers without asthma. Those with uncontrolled disease also had decreased odds of receiving ≥3 doses (adjusted odds ratio = 0.30; 95% confidence interval, 0.13-0.66) and ≥2 compared to participants with controlled asthma. Conclusions COVID-19 vaccine uptake among young adults is lower in individuals from households with lower socioeconomic status and among those with asthma, including uncontrolled asthma.
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Affiliation(s)
- Maria Ödling
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Niklas Andersson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sandra Ekström
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Niclas Roxhed
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden
- MedTechLabs, Bioclinicum, Karolinska University Hospital, Solna, Sweden
| | - Jochen M. Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute Technology, Solna, Sweden
| | - Sophia Björkander
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children and Youth Hospital, Stockholm, Sweden
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children and Youth Hospital, Stockholm, Sweden
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2
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Eriksen R, White MC, Dawed AY, Perez IG, Posma JM, Haid M, Sharma S, Prehn C, Thomas LE, Koivula RW, Bizzotto R, Mari A, Giordano GN, Pavo I, Schwenk JM, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Rutters F, Beulens J, Muilwijk M, Blom M, Elders P, Hansen TH, Fernandez-Tajes J, Jones A, Jennison C, Walker M, McCarthy MI, Pedersen O, Ruetten H, Forgie I, Holst JJ, Thomsen HS, Ridderstråle M, Bell JD, Adamski J, Franks PW, Hansen T, Holmes E, Frost G, Pearson ER. The association of cardiometabolic, diet and lifestyle parameters with plasma glucagon-like peptide-1: An IMI DIRECT study. J Clin Endocrinol Metab 2024:dgae119. [PMID: 38686701 DOI: 10.1210/clinem/dgae119] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/20/2023] [Accepted: 02/27/2024] [Indexed: 05/02/2024]
Abstract
CONTEXT The role of glucagon-like peptide-1(GLP-1) in Type 2 diabetes (T2D) and obesity is not fully understood. OBJECTIVE We investigate the association of cardiometabolic, diet and lifestyle parameters on fasting and postprandial GLP-1 in people at risk of, or living with, T2D. METHOD We analysed cross-sectional data from the two Innovative Medicines Initiative (IMI) Diabetes Research on Patient Stratification (DIRECT) cohorts, cohort 1(n=2127) individuals at risk of diabetes; cohort 2 (n=789) individuals with new-onset of T2D. RESULTS Our multiple regression analysis reveals that fasting total GLP-1 is associated with an insulin resistant phenotype and observe a strong independent relationship with male sex, increased adiposity and liver fat particularly in the prediabetes population. In contrast, we showed that incremental GLP-1 decreases with worsening glycaemia, higher adiposity, liver fat, male sex and reduced insulin sensitivity in the prediabetes cohort. Higher fasting total GLP-1 was associated with a low intake of wholegrain, fruit and vegetables inpeople with prediabetes, and with a high intake of red meat and alcohol in people with diabetes. CONCLUSION These studies provide novel insights into the association between fasting and incremental GLP-1, metabolic traits of diabetes and obesity, and dietary intake and raise intriguing questions regarding the relevance of fasting GLP-1 in the pathophysiology T2D.
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Affiliation(s)
- Rebeca Eriksen
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, UK
| | - Margaret C White
- Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Adem Y Dawed
- Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Isabel Garcia Perez
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, UK
| | - Joram M Posma
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, London, UK
- Health Data Research UK, London, UK
| | - Mark Haid
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany
| | - Sapna Sharma
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany
| | - Louise E Thomas
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK
| | - Robert W Koivula
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Radcliffe Department of Medicine, Oxford, UK
| | - Roberto Bizzotto
- Institute of Neuroscience - National Research Council, Padova, Italy
| | - Andrea Mari
- Institute of Neuroscience - National Research Council, Padova, Italy
| | - Giuseppe N Giordano
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Federico De Masi
- Department of Health Technology, Technical University of Denmark, Kgs Lyngby and The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Konstantinos D Tsirigos
- Department of Health Technology, Technical University of Denmark, Kgs Lyngby and The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Kgs Lyngby and The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ana Viñuela
- Biosciences Institute, Newcastle University. Newcastle upon Tyne. United Kingdom
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Timothy J McDonald
- Medical School, Exeter, UK NIHR Exeter Clinical Research Facility, University of Exeter
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Femke Rutters
- Department of Epidemiology and data Science, Amsterdam Public Health Institute, Amsterdam UMC, location VUMC, Amsterdam, The Netherlands
| | - Joline Beulens
- Department of Epidemiology and data Science, Amsterdam Public Health Institute, Amsterdam UMC, location VUMC, Amsterdam, The Netherlands
| | - Mirthe Muilwijk
- Department of Epidemiology and data Science, Amsterdam Public Health Institute, Amsterdam UMC, location VUMC, Amsterdam, The Netherlands
| | - Marieke Blom
- Department of Epidemiology and data Science, Amsterdam Public Health Institute, Amsterdam UMC, location VUMC, Amsterdam, The Netherlands
| | - Petra Elders
- Department of Epidemiology and data Science, Amsterdam Public Health Institute, Amsterdam UMC, location VUMC, Amsterdam, The Netherlands
| | - Tue H Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Angus Jones
- Medical School, Exeter, UK NIHR Exeter Clinical Research Facility, University of Exeter
| | - Chris Jennison
- Department of Mathematical Sciences, University of Bath, Bath, UK
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, UK
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Radcliffe Department of Medicine, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Hartmut Ruetten
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main, Germany
| | - Ian Forgie
- Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Jens J Holst
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik S Thomsen
- Faculty of Medical and Health Sciences, University of Copenhagen, Denmark
| | | | - Jimmy D Bell
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Elaine Holmes
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, UK
| | - Gary Frost
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, UK
| | - Ewan R Pearson
- Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
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Fredolini C, Dodig-Crnković T, Bendes A, Dahl L, Dale M, Albrecht V, Mattsson C, Thomas CE, Torinsson Naluai Å, Gisslen M, Beck O, Roxhed N, Schwenk JM. Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections. Commun Med (Lond) 2024; 4:55. [PMID: 38565620 PMCID: PMC10987641 DOI: 10.1038/s43856-024-00480-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Self-sampling of dried blood spots (DBS) offers new routes to gather valuable health-related information from the general population. Yet, the utility of using deep proteome profiling from home-sampled DBS to obtain clinically relevant insights about SARS-CoV-2 infections remains largely unexplored. METHODS Our study involved 228 individuals from the general Swedish population who used a volumetric DBS sampling device and completed questionnaires at home during spring 2020 and summer 2021. Using multi-analyte COVID-19 serology, we stratified the donors by their response phenotypes, divided them into three study sets, and analyzed 276 proteins by proximity extension assays (PEA). After normalizing the data to account for variances in layman-collected samples, we investigated the association of DBS proteomes with serology and self-reported information. RESULTS Our three studies display highly consistent variance of protein levels and share associations of proteins with sex (e.g., MMP3) and age (e.g., GDF-15). Studying seropositive (IgG+) and seronegative (IgG-) donors from the first pandemic wave reveals a network of proteins reflecting immunity, inflammation, coagulation, and stress response. A comparison of the early-infection phase (IgM+IgG-) with the post-infection phase (IgM-IgG+) indicates several proteins from the respiratory system. In DBS from the later pandemic wave, we find that levels of a virus receptor on B-cells differ between seropositive (IgG+) and seronegative (IgG-) donors. CONCLUSIONS Proteome analysis of volumetric self-sampled DBS facilitates precise analysis of clinically relevant proteins, including those secreted into the circulation or found on blood cells, augmenting previous COVID-19 reports with clinical blood collections. Our population surveys support the usefulness of DBS, underscoring the role of timing the sample collection to complement clinical and precision health monitoring initiatives.
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Affiliation(s)
- Claudia Fredolini
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
- Affinity Proteomics Unit, SciLifeLab Infrastructure, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Tea Dodig-Crnković
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Annika Bendes
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Leo Dahl
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Matilda Dale
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
- Affinity Proteomics Unit, SciLifeLab Infrastructure, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Vincent Albrecht
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Cecilia Mattsson
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
- Affinity Proteomics Unit, SciLifeLab Infrastructure, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Cecilia E Thomas
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Åsa Torinsson Naluai
- Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Magnus Gisslen
- Department of Infectious Diseases, The Sahlgrenska Academy at University of Gothenburg, 405 30, Gothenburg, Sweden
- Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
- Public Health Agency of Sweden, 171 65, Solna, Sweden
| | - Olof Beck
- Department of Clinical Neuroscience, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Niclas Roxhed
- MedTechLabs, BioClinicum, Karolinska University Hospital, 171 64, Solna, Sweden.
- Department of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology Stockholm, 100 44, Stockholm, Sweden.
| | - Jochen M Schwenk
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 171 65, Solna, Sweden.
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4
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Grassmann F, Mälarstig A, Dahl L, Bendes A, Dale M, Thomas CE, Gabrielsson M, Hedman ÅK, Eriksson M, Margolin S, Huang TH, Ulfstedt M, Forsberg S, Eriksson P, Johansson M, Hall P, Schwenk JM, Czene K. The impact of circulating protein levels identified by affinity proteomics on short-term, overall breast cancer risk. Br J Cancer 2024; 130:620-627. [PMID: 38135714 PMCID: PMC10876928 DOI: 10.1038/s41416-023-02541-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
OBJECTIVE Current breast cancer risk prediction scores and algorithms can potentially be further improved by including molecular markers. To this end, we studied the association of circulating plasma proteins using Proximity Extension Assay (PEA) with incident breast cancer risk. SUBJECTS In this study, we included 1577 women participating in the prospective KARMA mammographic screening cohort. RESULTS In a targeted panel of 164 proteins, we found 8 candidates nominally significantly associated with short-term breast cancer risk (P < 0.05). Similarly, in an exploratory panel consisting of 2204 proteins, 115 were found nominally significantly associated (P < 0.05). However, none of the identified protein levels remained significant after adjustment for multiple testing. This lack of statistically significant findings was not due to limited power, but attributable to the small effect sizes observed even for nominally significant proteins. Similarly, adding plasma protein levels to established risk factors did not improve breast cancer risk prediction accuracy. CONCLUSIONS Our results indicate that the levels of the studied plasma proteins captured by the PEA method are unlikely to offer additional benefits for risk prediction of short-term overall breast cancer risk but could provide interesting insights into the biological basis of breast cancer in the future.
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Affiliation(s)
- Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany.
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Annika Bendes
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Matilda Dale
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Cecilia Engel Thomas
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Marike Gabrielsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Åsa K Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Tzu-Hsuan Huang
- Cancer Immunology Discovery, Pfizer Inc., San Diego, CA, USA
| | | | | | - Per Eriksson
- Olink Proteomics, Uppsala Science Park, Uppsala, Sweden
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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5
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Cederroth CR, Hong MG, Freydin MB, Edvall NK, Trpchevska N, Jarach C, Schlee W, Schwenk JM, Lopez-Escamez JA, Gallus S, Canlon B, Bulla J, Williams FMK. Screening for Circulating Inflammatory Proteins Does Not Reveal Plasma Biomarkers of Constant Tinnitus. J Assoc Res Otolaryngol 2023; 24:593-606. [PMID: 38079022 PMCID: PMC10752855 DOI: 10.1007/s10162-023-00920-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/22/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Tinnitus would benefit from an objective biomarker. The goal of this study is to identify plasma biomarkers of constant and chronic tinnitus among selected circulating inflammatory proteins. METHODS A case-control retrospective study on 548 cases with constant tinnitus and 548 matched controls from the Swedish Tinnitus Outreach Project (STOP), whose plasma samples were examined using Olink's Inflammatory panel. Replication and meta-analysis were performed using the same method on samples from the TwinsUK cohort. Participants from LifeGene, whose blood was collected in Stockholm and Umeå, were recruited to STOP for a tinnitus subtyping study. An age and sex matching was performed at the individual level. TwinsUK participants (n = 928) were selected based on self-reported tinnitus status over 2 to 10 years. Primary outcomes include normalized levels for 96 circulating proteins, which were used as an index test. No reference standard was available in this study. RESULTS After adjustment for age, sex, BMI, smoking, hearing loss, and laboratory site, the top proteins identified were FGF-21, MCP4, GDNF, CXCL9, and MCP-1; however, these were no longer statistically significant after correction for multiple testing. Stratification by sex did not yield any significant associations. Similarly, associations with hearing loss or other tinnitus-related comorbidities such as stress, anxiety, depression, hyperacusis, temporomandibular joint disorders, and headache did not yield any significant associations. Analysis in the TwinsUK failed in replicating the top candidates. Meta-analysis of STOP and TwinsUK did not reveal any significant association. Using elastic net regularization, models exhibited poor predictive capacity tinnitus based on inflammatory markers [sensitivity = 0.52 (95% CI 0.47-0.57), specificity = 0.53 (0.48-0.58), positive predictive value = 0.52 (0.47-0.56), negative predictive values = 0.53 (0.49-0.58), and AUC = 0.53 (0.49-0.56)]. DISCUSSION Our results did not identify significant associations of the selected inflammatory proteins with constant tinnitus. Future studies examining longitudinal relations among those with more severe tinnitus and using more recent expanded proteomics platforms and sampling of cerebrospinal fluid could increase the likelihood of identifying relevant molecular biomarkers.
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Affiliation(s)
- Christopher R Cederroth
- Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden.
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Ropewalk House, Nottingham, UK.
- Department of Otolaryngology, Head and Neck Surgery, Translational Hearing Research, Tübingen Hearing Research Center, University of Tübingen, Tubingen, Germany.
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Stockholm, Sweden
| | - Maxim B Freydin
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Niklas K Edvall
- Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Natalia Trpchevska
- Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Carlotta Jarach
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Winfried Schlee
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Stockholm, Sweden
| | - Jose-Antonio Lopez-Escamez
- Faculty of Medicine & Health, School of Medical Sciences, Meniere's Disease Neuroscience Research Program, The Kolling Institute, University of Sydney, Sydney, NSW, Australia
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, PTS, Junta de Andalucía, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, GranadaGranada, Spain
| | - Silvano Gallus
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Barbara Canlon
- Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Jan Bulla
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
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6
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Iglesias MJ, Sanchez-Rivera L, Ibrahim-Kosta M, Naudin C, Munsch G, Goumidi L, Farm M, Smith PM, Thibord F, Kral-Pointner JB, Hong MG, Suchon P, Germain M, Schrottmaier W, Dusart P, Boland A, Kotol D, Edfors F, Koprulu M, Pietzner M, Langenberg C, Damrauer SM, Johnson AD, Klarin DM, Smith NL, Smadja DM, Holmström M, Magnusson M, Silveira A, Uhlén M, Renné T, Martinez-Perez A, Emmerich J, Deleuze JF, Antovic J, Soria Fernandez JM, Assinger A, Schwenk JM, Souto Andres JC, Morange PE, Butler LM, Trégouët DA, Odeberg J. Author Correction: Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism. Nat Commun 2023; 14:7752. [PMID: 38012230 PMCID: PMC10682365 DOI: 10.1038/s41467-023-43764-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- Maria Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Division of Internal Medicine, University Hospital of North Norway (UNN), PB100, 9038, Tromsø, Norway
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Laura Sanchez-Rivera
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Manal Ibrahim-Kosta
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Clément Naudin
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Gaëlle Munsch
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France
| | - Louisa Goumidi
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Maria Farm
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Philip M Smith
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Theme of Emergency and Reparative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
- The Framingham Heart Study, Boston University, Framingham, MA, USA
| | - Julia Barbara Kral-Pointner
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Mun-Gwan Hong
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Pierre Suchon
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Marine Germain
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France
- Laboratory of Excellence GENMED (Medical Genomics), Bordeaux, France
| | - Waltraud Schrottmaier
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Philip Dusart
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
- Laboratory of Excellence GENMED (Medical Genomics), Evry, France
| | - David Kotol
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Scott M Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Surgery and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
- The Framingham Heart Study, Boston University, Framingham, MA, USA
| | - Derek M Klarin
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - David M Smadja
- Hematology Department and Biosurgical Research Lab (Carpentier Foundation), European Georges Pompidou Hospital, Assistance Publique Hôpitaux de Paris, 20 rue Leblanc, Paris, 75015, France
- Innovative Therapies in Haemostasis, INSERM, Université de Paris, 4 avenue de l'Observatoire, Paris, 75270, France
| | - Margareta Holmström
- Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Maria Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Angela Silveira
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, D-20246, Hamburg, Germany
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, D-55131, Mainz, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, D02 YN77, Ireland
| | - Angel Martinez-Perez
- Genomics of Complex Diseases Group, Research Institute Hospital de la Santa Creu i Sant Pau. IIB Sant Pau, Barcelona, Spain
| | - Joseph Emmerich
- Department of vascular medicine, Paris Saint-Joseph Hospital Group, INSERM 1153-CRESS, University of Paris Cité, 185 rue Raymond Losserand, Paris, 75674, France
| | - Jean-Francois Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
- Laboratory of Excellence GENMED (Medical Genomics), Evry, France
- Centre D'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Jovan Antovic
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Jose Manuel Soria Fernandez
- Genomics of Complex Diseases Group, Research Institute Hospital de la Santa Creu i Sant Pau. IIB Sant Pau, Barcelona, Spain
| | - Alice Assinger
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Joan Carles Souto Andres
- Unitat d'Hemostàsia i Trombosi, Hospital de la Santa Creu i Sant Pau and IIB-Sant Pau, Barcelona, Spain
| | - Pierre-Emmanuel Morange
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Lynn Marie Butler
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - David-Alexandre Trégouët
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France.
- Laboratory of Excellence GENMED (Medical Genomics), Bordeaux, France.
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden.
- Division of Internal Medicine, University Hospital of North Norway (UNN), PB100, 9038, Tromsø, Norway.
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway.
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.
- Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
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7
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Mälarstig A, Grassmann F, Dahl L, Dimitriou M, McLeod D, Gabrielson M, Smith-Byrne K, Thomas CE, Huang TH, Forsberg SKG, Eriksson P, Ulfstedt M, Johansson M, Sokolov AV, Schiöth HB, Hall P, Schwenk JM, Czene K, Hedman ÅK. Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation. Nat Commun 2023; 14:7680. [PMID: 37996402 PMCID: PMC10667261 DOI: 10.1038/s41467-023-43485-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Biomarkers for early detection of breast cancer may complement population screening approaches to enable earlier and more precise treatment. The blood proteome is an important source for biomarker discovery but so far, few proteins have been identified with breast cancer risk. Here, we measure 2929 unique proteins in plasma from 598 women selected from the Karolinska Mammography Project to explore the association between protein levels, clinical characteristics, and gene variants, and to identify proteins with a causal role in breast cancer. We present 812 cis-acting protein quantitative trait loci for 737 proteins which are used as instruments in Mendelian randomisation analyses of breast cancer risk. Of those, we present five proteins (CD160, DNPH1, LAYN, LRRC37A2 and TLR1) that show a potential causal role in breast cancer risk with confirmatory results in independent cohorts. Our study suggests that these proteins should be further explored as biomarkers and potential drug targets in breast cancer.
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Affiliation(s)
- Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden.
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Marios Dimitriou
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden
| | - Dianna McLeod
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Cecilia E Thomas
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Tzu-Hsuan Huang
- Cancer Immunology Discovery, Pfizer Inc., San Diego, California, USA
| | | | | | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aleksandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Åsa K Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden
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8
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Kotliar IB, Bendes A, Dahl L, Chen Y, Saarinen M, Ceraudo E, Dodig-Crnković T, Uhlén M, Svenningsson P, Schwenk JM, Sakmar TP. Expanding the GPCR-RAMP interactome. bioRxiv 2023:2023.11.22.568247. [PMID: 38045268 PMCID: PMC10690247 DOI: 10.1101/2023.11.22.568247] [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] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Receptor activity-modifying proteins (RAMPs) can form complexes with G protein-coupled receptors (GPCRs) and regulate their cellular trafficking and pharmacology. RAMP interactions have been identified for about 50 GPCRs, but only a few GPCR-RAMP complexes have been studied in detail. To elucidate a complete interactome between GPCRs and the three RAMPs, we developed a customized library of 215 Dual Epitope-Tagged (DuET) GPCRs representing all GPCR subfamilies. Using a multiplexed suspension bead array (SBA) assay, we identified 122 GPCRs that showed strong evidence for interaction with at least one RAMP. We screened for native interactions in three cell lines and found 23 GPCRs that formed complexes with RAMPs. Mapping the GPCR-RAMP interactome expands the current system-wide functional characterization of RAMP-interacting GPCRs to inform the design of selective GPCR-targeted therapeutics. One-Sentence Summary Novel complexes between G protein-coupled receptors and interacting proteins point to a system-wide regulation of GPCR function.
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9
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FitzGerald O, Behrens F, Barton A, Bertheussen H, Boutouyrie-Dumont B, Coates L, Davies O, de Wit M, Fagni F, Goodyear CS, Gurke R, Hahnefeld L, Huppertz C, Ioannidis V, Ibberson M, Katz A, Klippstein M, Koehm M, Korish S, Mackay S, Martin DA, O’Sullivan D, Patel K, Rueping S, Schett G, Scholich K, Schwenk JM, Siebert S, Simon D, Vivekanantham A, Pennington SR. Application of clinical and molecular profiling data to improve patient outcomes in psoriatic arthritis. Ther Adv Musculoskelet Dis 2023; 15:1759720X231192315. [PMID: 37694182 PMCID: PMC10492462 DOI: 10.1177/1759720x231192315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Achieving a good outcome for a person with Psoriatic Arthritis (PsA) is made difficult by late diagnosis, heterogenous clinical disease expression and in many cases, failure to adequately suppress inflammatory disease features. Single-centre studies have certainly contributed to our understanding of disease pathogenesis, but to adequately address the major areas of unmet need, multi-partner, collaborative research programmes are now required. HIPPOCRATES is a 5-year, Innovative Medicines Initiative (IMI) programme which includes 17 European academic centres experienced in PsA research, 5 pharmaceutical industry partners, 3 small-/medium-sized industry partners and 2 patient-representative organizations. In this review, the ambitious programme of work to be undertaken by HIPPOCRATES is outlined and common approaches and challenges are identified. It is expected that, when completed, the results will ultimately allow for changes in the approaches to diagnosing, managing and treating PsA allowing for better short-term and long-term outcomes.
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Affiliation(s)
- Oliver FitzGerald
- School of Medicine, UCD Conway Institute for Biomolecular Research, University College Dublin, Ireland
| | - Frank Behrens
- Translational Rheumatology, Immunology – Inflammation Medicine, University Hospital Goethe-University, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | - Anne Barton
- Centre for Musculoskeletal Research, the University of Manchester, Manchester, UK
| | | | | | - Laura Coates
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Maarten de Wit
- GRAPPA Patient Research Partner, Zaltbommel, the Netherlands
| | - Filippo Fagni
- Department of Internal Medicine 3 – Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Carl S. Goodyear
- School of Infection & Immunity, College of Medical, Veterinar & Life Sciences, University of Glasgow, Glasgow, UK
| | - Robert Gurke
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | - Lisa Hahnefeld
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | | | - Vassilios Ioannidis
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Maximilian Klippstein
- Translational Rheumatology, Immunology – Inflammation Medicine, University Hospital Goethe-University, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | - Michaela Koehm
- Translational Rheumatology, Immunology – Inflammation Medicine, University Hospital Goethe-University, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | | | - Sina Mackay
- Fraunhofer Institute for Intelligent Analysis and Information Systems IAIS, Sankt Augustin and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | - David A. Martin
- Pfizer Immunology & Inflammation Research Unit, Cambridge, MA, USA
| | | | - Khadijah Patel
- Centre for Musculoskeletal Research, the University of Manchester, Manchester, UK
| | - Stefan Rueping
- Fraunhofer Institute for Intelligent Analysis and Information Systems IAIS, Sankt Augustin and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | - Georg Schett
- Department of Internal Medicine 3 – Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Klaus Scholich
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP and Fraunhofer Cluster of Excellence Immune Mediated Diseases, Frankfurt, Germany
| | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Stefan Siebert
- School of Infection & Immunity, College of Medical, Veterinar & Life Sciences, University of Glasgow, Glasgow, UK
| | - David Simon
- Department of Internal Medicine 3 – Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Arani Vivekanantham
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Stephen R. Pennington
- School of Medicine, UCD Conway Institute for Biomolecular Research, University College Dublin, Ireland
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10
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Brown AA, Fernandez-Tajes JJ, Hong MG, Brorsson CA, Koivula RW, Davtian D, Dupuis T, Sartori A, Michalettou TD, Forgie IM, Adam J, Allin KH, Caiazzo R, Cederberg H, De Masi F, Elders PJM, Giordano GN, Haid M, Hansen T, Hansen TH, Hattersley AT, Heggie AJ, Howald C, Jones AG, Kokkola T, Laakso M, Mahajan A, Mari A, McDonald TJ, McEvoy D, Mourby M, Musholt PB, Nilsson B, Pattou F, Penet D, Raverdy V, Ridderstråle M, Romano L, Rutters F, Sharma S, Teare H, 't Hart L, Tsirigos KD, Vangipurapu J, Vestergaard H, Brunak S, Franks PW, Frost G, Grallert H, Jablonka B, McCarthy MI, Pavo I, Pedersen O, Ruetten H, Walker M, Adamski J, Schwenk JM, Pearson ER, Dermitzakis ET, Viñuela A. Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits. Nat Commun 2023; 14:5062. [PMID: 37604891 PMCID: PMC10442420 DOI: 10.1038/s41467-023-40569-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
We evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant associates with multiple molecular phenotypes over multiple genomic regions. The highest proportion of share genetic regulation is detected between gene expression and proteins (66.6%), with a further median shared genetic associations across 49 different tissues of 78.3% and 62.4% between plasma proteins and gene expression. We represent the genetic and molecular associations in networks including 2828 known GWAS variants, showing that GWAS variants are more often connected to gene expression in trans than other molecular phenotypes in the network. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants using different molecular phenotypes in an accessible tissue.
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Affiliation(s)
- Andrew A Brown
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, United Kingdom
| | - Juan J Fernandez-Tajes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Mun-Gwan Hong
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Solna, SE-171 21, Sweden
| | - Caroline A Brorsson
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Robert W Koivula
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LJ, United Kingdom
| | - David Davtian
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, United Kingdom
| | - Théo Dupuis
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, United Kingdom
| | - Ambra Sartori
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland
- Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Theodora-Dafni Michalettou
- Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, NE1 4EP, United Kingdom
| | - Ian M Forgie
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, United Kingdom
| | - Jonathan Adam
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Kristine H Allin
- The Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Robert Caiazzo
- University of Lille, Inserm, Lille Pasteur Institute, Lille, France
| | - Henna Cederberg
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Federico De Masi
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Petra J M Elders
- Department of General Practice, Amsterdam UMC- location Vumc, Amsterdam Public Health research institute, Amsterdam, The Netherlands
| | - Giuseppe N Giordano
- Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Malmö, Sweden
| | - Mark Haid
- Metabolomics and Proteomics Core, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Torben Hansen
- The Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Tue H Hansen
- The Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, University of Exeter College of Medicine & Health, Exeter, EX25DW, United Kingdom
| | - Alison J Heggie
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Cédric Howald
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland
- Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Angus G Jones
- Department of Clinical and Biomedical Sciences, University of Exeter College of Medicine & Health, Exeter, EX25DW, United Kingdom
| | - Tarja Kokkola
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Andrea Mari
- Institute of Neuroscience, National Research Council, Padova, 35127, Italy
| | - Timothy J McDonald
- Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Donna McEvoy
- Diabetes Research Network, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Miranda Mourby
- Nuffield Department of Population Health, Centre for Health, Law and Emerging Technologies (HeLEX), University of Oxford, Oxford, OX2 7DD, United Kingdom
| | - Petra B Musholt
- Global Development, Sanofi-Aventis Deutschland GmbH, Hoechst Industrial Park, Frankfurt am Main, 65926, Germany
| | - Birgitte Nilsson
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Francois Pattou
- University of Lille, Inserm, Lille Pasteur Institute, Lille, France
| | - Deborah Penet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland
- Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Violeta Raverdy
- University of Lille, Inserm, Lille Pasteur Institute, Lille, France
| | | | - Luciana Romano
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland
- Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Femke Rutters
- Epidemiology and Data Science, VUMC, Amsterdam, The Netherlands
| | - Sapna Sharma
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, 85764, Germany
- Food Chemistry and Molecular and Sensory Science, Technical University of Munich, München, Germany
| | - Harriet Teare
- Centre for Health Law and Emerging Technologies, Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7DQ, United Kingdom
| | - Leen 't Hart
- Epidemiology and Data Science, VUMC, Amsterdam, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Biomedical Data Sciences, Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jagadish Vangipurapu
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henrik Vestergaard
- The Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Steno Diabetes Center Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Paul W Franks
- Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Malmö, Sweden
| | - Gary Frost
- Nutrition and Dietetics Research Group, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Bernd Jablonka
- Sanofi Partnering, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, 65926, Germany
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- GENENTECH, 1 DNA Way, San Francisco, CA, 94080, USA
| | - Imre Pavo
- Eli Lilly Regional Operations Ges.m.b.H, Vienna, 1030, Austria
| | - Oluf Pedersen
- Center for Clinical Metabolic Research, Herlev and Gentofte University Hospital, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Hartmut Ruetten
- Sanofi Partnering, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, 65926, Germany
| | - Mark Walker
- Translational and Clinical Research Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Jerzy Adamski
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Institute of Experimental Genetics, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, 85764, Germany
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Solna, SE-171 21, Sweden
| | - Ewan R Pearson
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, United Kingdom
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211, Switzerland.
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland.
- Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland.
| | - Ana Viñuela
- Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, NE1 4EP, United Kingdom.
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11
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Zenlander R, Fredolini C, Schwenk JM, Rydén I, Påhlsson P, Löwbeer C, Eggertsen G, Stål P. A wide scan of plasma proteins demonstrates thioredoxin reductase 1 as a potential new diagnostic biomarker for hepatocellular carcinoma. Scand J Gastroenterol 2023; 58:998-1008. [PMID: 37017178 DOI: 10.1080/00365521.2023.2194008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Patients with liver cirrhosis are recommended ultrasonography screening for early detection of hepatocellular carcinoma to increase the chances of curative treatment. However, ultrasonography alone lacks in sensitivity. Adding plasma biomarkers may increase the detection rate. We performed a broad exploratory analysis to find new plasma proteins with potential applicability for HCC screening in patients with cirrhosis. METHODS In a protein discovery cohort of 172 patients with cirrhosis or HCC, we screened for 481 proteins with suspension bead array or proximity extension assay. From these, 24 proteins were selected for further analysis in a protein verification cohort (n = 160), using ELISA, Luminex or an electrochemiluminescence platform. A cut-off model and a stepwise logistic regression model were used to find combinations of proteins with the best discriminatory performance between HCC and cirrhosis. RESULTS Stepwise logistic regression revealed alpha-fetoprotein (AFP), decarboxy-prothrombin (DCP), thioredoxin reductase 1 (TXNRD1), and fibroblast growth factor 21 (FGF21) as the proteins with the best discriminatory performance between HCC and cirrhosis. Adding TXNRD1 to DCP and AFP increased the AUC from 0.844 to 0.878, and combining AFP, DCP and TXNRD1 with age and sex resulted in an AUC of 0.920. FGF21, however, did not further increase the performance when including age and sex. CONCLUSION In the present study, TXNRD1 improves the sensitivity and specificity of AFP and DCP as HCC screening tools in patients with cirrhosis. We suggest that TXNRD1 should be validated in prospective settings as a new complementary HCC biomarker together with AFP and DCP.
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Affiliation(s)
- Robin Zenlander
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Ingvar Rydén
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Peter Påhlsson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Christian Löwbeer
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Chemistry, SYNLAB Sverige, Täby, Sweden
| | - Gösta Eggertsen
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Per Stål
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Hepatology, Department of Upper GI diseases, Karolinska University Hospital, Stockholm, Sweden
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12
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Allesøe RL, Lundgaard AT, Hernández Medina R, Aguayo-Orozco A, Johansen J, Nissen JN, Brorsson C, Mazzoni G, Niu L, Biel JH, Leal Rodríguez C, Brasas V, Webel H, Benros ME, Pedersen AG, Chmura PJ, Jacobsen UP, Mari A, Koivula R, Mahajan A, Vinuela A, Tajes JF, Sharma S, Haid M, Hong MG, Musholt PB, De Masi F, Vogt J, Pedersen HK, Gudmundsdottir V, Jones A, Kennedy G, Bell J, Thomas EL, Frost G, Thomsen H, Hansen E, Hansen TH, Vestergaard H, Muilwijk M, Blom MT, 't Hart LM, Pattou F, Raverdy V, Brage S, Kokkola T, Heggie A, McEvoy D, Mourby M, Kaye J, Hattersley A, McDonald T, Ridderstråle M, Walker M, Forgie I, Giordano GN, Pavo I, Ruetten H, Pedersen O, Hansen T, Dermitzakis E, Franks PW, Schwenk JM, Adamski J, McCarthy MI, Pearson E, Banasik K, Rasmussen S, Brunak S. Author Correction: Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models. Nat Biotechnol 2023; 41:1026. [PMID: 37130959 PMCID: PMC10344774 DOI: 10.1038/s41587-023-01805-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Rosa Lundbye Allesøe
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Agnete Troen Lundgaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ricardo Hernández Medina
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Aguayo-Orozco
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jakob Nybo Nissen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Brorsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gianluca Mazzoni
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jorge Hernansanz Biel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cristina Leal Rodríguez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valentas Brasas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Eriksen Benros
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Gorm Pedersen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Piotr Jaroslaw Chmura
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrik Plesner Jacobsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea Mari
- C.N.R. Institute of Neuroscience, Padova, Italy
| | - Robert Koivula
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ana Vinuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | - Sapna Sharma
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Freising, Germany
| | - Mark Haid
- Metabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Petra B Musholt
- Research and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany
| | - Federico De Masi
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Josef Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle Krogh Pedersen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valborg Gudmundsdottir
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Angus Jones
- University of Exeter Medical School, Exeter, UK
| | - Gwen Kennedy
- The Immunoassay Biomarker Core Laboratory, School of Medicine, University of Dundee, Dundee, UK
| | - Jimmy Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK
| | - E Louise Thomas
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK
| | - Gary Frost
- Section for Nutrition Research, Faculty of Medicine, Imperial College London, London, UK
| | - Henrik Thomsen
- Department of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark
| | - Elizaveta Hansen
- Department of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mirthe Muilwijk
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Marieke T Blom
- Department of General Practice, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Leen M 't Hart
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Biomedical Data Science, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Francois Pattou
- Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France
| | - Violeta Raverdy
- Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France
| | - Soren Brage
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Alison Heggie
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Donna McEvoy
- Diabetes Research Network, Royal Victoria Infirmary, Newcastle, UK
| | - Miranda Mourby
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK
| | - Jane Kaye
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK
| | | | | | - Martin Ridderstråle
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Mark Walker
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Ian Forgie
- Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Giuseppe N Giordano
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, CRC, Lund University, SUS, Malmö, Sweden
| | - Imre Pavo
- Eli Lilly Regional Operations, Vienna, Austria
| | - Hartmut Ruetten
- Research and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emmanouil Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Paul W Franks
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Ewan Pearson
- Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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13
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Iglesias MJ, Sanchez-Rivera L, Ibrahim-Kosta M, Naudin C, Munsch G, Goumidi L, Farm M, Smith PM, Thibord F, Kral-Pointner JB, Hong MG, Suchon P, Germain M, Schrottmaier W, Dusart P, Boland A, Kotol D, Edfors F, Koprulu M, Pietzner M, Langenberg C, Damrauer SM, Johnson AD, Klarin DM, Smith NL, Smadja DM, Holmström M, Magnusson M, Silveira A, Uhlén M, Renné T, Martinez-Perez A, Emmerich J, Deleuze JF, Antovic J, Soria Fernandez JM, Assinger A, Schwenk JM, Souto Andres JC, Morange PE, Butler LM, Trégouët DA, Odeberg J. Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism. Nat Commun 2023; 14:3280. [PMID: 37286573 PMCID: PMC10247781 DOI: 10.1038/s41467-023-38383-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 04/28/2023] [Indexed: 06/09/2023] Open
Abstract
Venous thromboembolism (VTE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. Here we show, using proteomics profiling to screen plasma from patients with suspected acute VTE, and several case-control studies for VTE, how Complement Factor H Related 5 protein (CFHR5), a regulator of the alternative pathway of complement activation, is a VTE-associated plasma biomarker. In plasma, higher CFHR5 levels are associated with increased thrombin generation potential and recombinant CFHR5 enhanced platelet activation in vitro. GWAS analysis of ~52,000 participants identifies six loci associated with CFHR5 plasma levels, but Mendelian randomization do not demonstrate causality between CFHR5 and VTE. Our results indicate an important role for the regulation of the alternative pathway of complement activation in VTE and that CFHR5 represents a potential diagnostic and/or risk predictive plasma biomarker.
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Affiliation(s)
- Maria Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Division of Internal Medicine, University Hospital of North Norway (UNN), PB100, 9038, Tromsø, Norway
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Laura Sanchez-Rivera
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Manal Ibrahim-Kosta
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Clément Naudin
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Gaëlle Munsch
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France
| | - Louisa Goumidi
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Maria Farm
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Philip M Smith
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Theme of Emergency and Reparative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
- The Framingham Heart Study, Boston University, Framingham, MA, USA
| | - Julia Barbara Kral-Pointner
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Mun-Gwan Hong
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Pierre Suchon
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Marine Germain
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France
- Laboratory of Excellence GENMED (Medical Genomics), Bordeaux, France
| | - Waltraud Schrottmaier
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Philip Dusart
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
- Laboratory of Excellence GENMED (Medical Genomics), Evry, France
| | - David Kotol
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Scott M Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Surgery and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
- The Framingham Heart Study, Boston University, Framingham, MA, USA
| | - Derek M Klarin
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - David M Smadja
- Hematology Department and Biosurgical Research Lab (Carpentier Foundation), European Georges Pompidou Hospital, Assistance Publique Hôpitaux de Paris, 20 rue Leblanc, Paris, 75015, France
- Innovative Therapies in Haemostasis, INSERM, Université de Paris, 4 avenue de l'Observatoire, Paris, 75270, France
| | - Margareta Holmström
- Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Maria Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Angela Silveira
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, D-20246, Hamburg, Germany
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, D-, 55131, Mainz, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, D02 YN77, Ireland
| | - Angel Martinez-Perez
- Genomics of Complex Diseases Group, Research Institute Hospital de la Santa Creu i Sant Pau. IIB Sant Pau, Barcelona, Spain
| | - Joseph Emmerich
- Department of vascular medicine, Paris Saint-Joseph Hospital Group, INSERM 1153-CRESS, University of Paris Cité, 185 rue Raymond Losserand, Paris, 75674, France
| | - Jean-Francois Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
- Laboratory of Excellence GENMED (Medical Genomics), Evry, France
- Centre D'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Jovan Antovic
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Jose Manuel Soria Fernandez
- Genomics of Complex Diseases Group, Research Institute Hospital de la Santa Creu i Sant Pau. IIB Sant Pau, Barcelona, Spain
| | - Alice Assinger
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
| | - Joan Carles Souto Andres
- Unitat d'Hemostàsia i Trombosi. Hospital de la Santa Creu i Sant Pau and IIB-Sant Pau, Barcelona, Spain
| | - Pierre-Emmanuel Morange
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique-Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France
| | - Lynn Marie Butler
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - David-Alexandre Trégouët
- University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France.
- Laboratory of Excellence GENMED (Medical Genomics), Bordeaux, France.
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, SE-171 21, Stockholm, Sweden.
- Division of Internal Medicine, University Hospital of North Norway (UNN), PB100, 9038, Tromsø, Norway.
- Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway.
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.
- Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
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14
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Sendic S, Mansouri L, Hong MG, Schwenk JM, Eriksson MJ, Hylander B, Lundahl J, Jacobson SH. Soluble CD14 and Osteoprotegerin Associate with Ankle-Brachial Index as a Measure of Arterial Stiffness in Patients with Mild-to-Moderate Chronic Kidney Disease in a Five-Year Prospective Study. Cardiorenal Med 2023; 13:189-201. [PMID: 37231818 DOI: 10.1159/000530985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023] Open
Abstract
INTRODUCTION Vascular lesions and arterial stiffness appear at early stages of chronic kidney disease (CKD) and follow an accelerated course with disease progression, contributing to high cardiovascular mortality. There are limited prospective data on mechanisms contributing to progression of arterial stiffness in mild-to-moderate CKD (stages 2-3). METHODS We applied an affinity proteomics approach to identify candidates of circulating biomarkers with potential impact on vascular lesions in CKD and selected soluble cluster of differentiation 14 (sCD14), angiogenin (ANG), and osteoprotegerin (OPG) for further analysis. We studied their association with ankle-brachial index (ABI) and carotid intima-media thickness, as measures of arteriosclerosis and atherosclerosis, respectively, in 48 patients with CKD stages 2-3, who were prospectively followed and intensively treated for 5 years, and 44 healthy controls. RESULTS Concentrations of sCD14 (p < 0.001), ANG (p < 0.001), and OPG (p < 0.05) were higher in patients with CKD 2-3 at baseline, and sCD14 (p < 0.001) and ANG (p < 0.001) remained elevated in CKD patients at follow-up. There were positive correlations between ABI and sCD14 levels (r = 0.36, p = 0.01) and between ABI and OPG (r = 0.31, p = 0.03) at 5 years. The changes in sCD14 during follow-up correlated to changes in ABI from baseline to 5 years (r = 0.41, p = 0.004). CONCLUSION Elevated levels of circulating sCD14 and OPG in patients with CKD 2-3 were significantly associated with ABI, a measure of arterial stiffness. An increase in sCD14 over time in CKD 2-3 patients was associated with a corresponding increase in ABI. Further studies are needed to examine if early intensive multifactorial medication to align with international treatment targets may influence cardiovascular outcomes.
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Affiliation(s)
- Senka Sendic
- Division of Nephrology, Department of Clinical Sciences, Karolinska Institutet, Danderyd University Hospital, Stockholm, Sweden
| | - Ladan Mansouri
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maria J Eriksson
- Department of Clinical Physiology, Karolinska University Hospital, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Britta Hylander
- Division of Nephrology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Joachim Lundahl
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Stefan H Jacobson
- Division of Nephrology, Department of Clinical Sciences, Karolinska Institutet, Danderyd University Hospital, Stockholm, Sweden
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15
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Andreassi MG, Haddy N, Harms-Ringdahl M, Campolo J, Borghini A, Chevalier F, Schwenk JM, Fresneau B, Bolle S, Fuentes M, Haghdoost S. A Longitudinal Study of Individual Radiation Responses in Pediatric Patients Treated with Proton and Photon Radiotherapy, and Interventional Cardiology: Rationale and Research Protocol of the HARMONIC Project. Int J Mol Sci 2023; 24:ijms24098416. [PMID: 37176123 PMCID: PMC10178896 DOI: 10.3390/ijms24098416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The Health Effects of Cardiac Fluoroscopy and Modern Radiotherapy (photon and proton) in Pediatrics (HARMONIC) is a five-year project funded by the European Commission that aimed to improve the understanding of the long-term ionizing radiation (IR) risks for pediatric patients. In this paper, we provide a detailed overview of the rationale, design, and methods for the biological aspect of the project with objectives to provide a mechanistic understanding of the molecular pathways involved in the IR response and to identify potential predictive biomarkers of individual response involved in long-term health risks. Biological samples will be collected at three time points: before the first exposure, at the end of the exposure, and one year after the exposure. The average whole-body dose, the dose to the target organ, and the dose to some important out-of-field organs will be estimated. State-of-the-art analytical methods will be used to assess the levels of a set of known biomarkers and also explore high-resolution approaches of proteomics and miRNA transcriptomes to provide an integrated assessment. By using bioinformatics and systems biology, biological pathways and novel pathways involved in the response to IR exposure will be deciphered.
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Affiliation(s)
| | - Nadia Haddy
- Radiation Epidemiology Team, Center for Research in Epidemiology and Population Health, INSERM U1018, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Mats Harms-Ringdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Jonica Campolo
- CNR National Research Council Institute of Clinical Physiology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy
| | - Andrea Borghini
- CNR National Research Council Institute of Clinical Physiology, 56125 Pisa, Italy
| | - François Chevalier
- UMR6252 CIMAP, CEA-CNRS-ENSICAEN-University of Caen Normandy, 14000 Caen, France
- Advanced Resource Center for HADrontherapy in Europe (ARCHADE), 14000 Caen, France
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Brice Fresneau
- Department of Children and Adolescents Oncology, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
- Cancer and Radiation Team, Center for Research in Epidemiology and Population Health, INSERM U1018, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Stephanie Bolle
- Department of Radiation Therapy, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Manuel Fuentes
- Deparment of Medicine and General Service of Cytometry, Proteomics Unit, Cancer Research Centre-IBMCC, CSIC-USAL, IBSAL, Campus Miguel de Unamuno s/n, University of Salamanca-CSIC, 37007 Salamanca, Spain
| | - Siamak Haghdoost
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- UMR6252 CIMAP, CEA-CNRS-ENSICAEN-University of Caen Normandy, 14000 Caen, France
- Advanced Resource Center for HADrontherapy in Europe (ARCHADE), 14000 Caen, France
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16
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Dahl L, Kotliar IB, Bendes A, Dodig-Crnković T, Fromm S, Elofsson A, Uhlén M, Sakmar TP, Schwenk JM. Multiplexed selectivity screening of anti-GPCR antibodies. Sci Adv 2023; 9:eadf9297. [PMID: 37134173 PMCID: PMC10156119 DOI: 10.1126/sciadv.adf9297] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/31/2023] [Indexed: 05/05/2023]
Abstract
G protein-coupled receptors (GPCRs) control critical cellular signaling pathways. Therapeutic agents including anti-GPCR antibodies (Abs) are being developed to modulate GPCR function. However, validating the selectivity of anti-GPCR Abs is challenging because of sequence similarities among individual receptors within GPCR subfamilies. To address this challenge, we developed a multiplexed immunoassay to test >400 anti-GPCR Abs from the Human Protein Atlas targeting a customized library of 215 expressed and solubilized GPCRs representing all GPCR subfamilies. We found that ~61% of Abs tested were selective for their intended target, ~11% bound off-target, and ~28% did not bind to any GPCR. Antigens of on-target Abs were, on average, significantly longer, more disordered, and less likely to be buried in the interior of the GPCR protein than the other Abs. These results provide important insights into the immunogenicity of GPCR epitopes and form a basis for designing therapeutic Abs and for detecting pathological auto-Abs against GPCRs.
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Affiliation(s)
- Leo Dahl
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Ilana B. Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, USA
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Samuel Fromm
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Arne Elofsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Solna, Sweden
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
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17
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Kotliar IB, Ceraudo E, Kemelmakher-Liben K, Oren DA, Lorenzen E, Dodig-Crnković T, Horioka-Duplix M, Huber T, Schwenk JM, Sakmar TP. Itch receptor MRGPRX4 interacts with the receptor activity-modifying proteins. J Biol Chem 2023; 299:104664. [PMID: 37003505 PMCID: PMC10165273 DOI: 10.1016/j.jbc.2023.104664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Cholestatic itch is a severe and debilitating symptom in liver diseases with limited treatment options. The class A G protein-coupled receptor (GPCR) Mas-related GPCR subtype X4 (MRGPRX4) has been identified as a receptor for bile acids, which are potential cholestatic pruritogens. An increasing number of GPCRs have been shown to interact with receptor activity-modifying proteins (RAMPs), which can modulate different aspects of GPCR biology. Using a combination of multiplexed immunoassay and proximity ligation assay, we show that MRGPRX4 interacts with RAMPs. The interaction of MRGPRX4 with RAMP2, but not RAMP1 or 3, causes attenuation of basal and agonist-dependent signaling, which correlates with a decrease of MRGPRX4 cell surface expression as measured using a quantitative NanoBRET pulse-chase assay. Finally, we use AlphaFold Multimer to predict the structure of the MRGPRX4-RAMP2 complex. The discovery that RAMP2 regulates MRGPRX4 may have direct implications for future drug development for cholestatic itch.
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Affiliation(s)
- Ilana B Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA; Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA
| | - Kevin Kemelmakher-Liben
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA
| | - Deena A Oren
- Structural Biology Resource Center, The Rockefeller University, New York, New York, USA
| | - Emily Lorenzen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA
| | - Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Mizuho Horioka-Duplix
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York, USA; Department of Neurobiology, Care Sciences and Society, Section for Neurogeriatrics, Karolinska Institutet, Solna, Sweden.
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18
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Allesøe RL, Lundgaard AT, Hernández Medina R, Aguayo-Orozco A, Johansen J, Nissen JN, Brorsson C, Mazzoni G, Niu L, Biel JH, Brasas V, Webel H, Benros ME, Pedersen AG, Chmura PJ, Jacobsen UP, Mari A, Koivula R, Mahajan A, Vinuela A, Tajes JF, Sharma S, Haid M, Hong MG, Musholt PB, De Masi F, Vogt J, Pedersen HK, Gudmundsdottir V, Jones A, Kennedy G, Bell J, Thomas EL, Frost G, Thomsen H, Hansen E, Hansen TH, Vestergaard H, Muilwijk M, Blom MT, 't Hart LM, Pattou F, Raverdy V, Brage S, Kokkola T, Heggie A, McEvoy D, Mourby M, Kaye J, Hattersley A, McDonald T, Ridderstråle M, Walker M, Forgie I, Giordano GN, Pavo I, Ruetten H, Pedersen O, Hansen T, Dermitzakis E, Franks PW, Schwenk JM, Adamski J, McCarthy MI, Pearson E, Banasik K, Rasmussen S, Brunak S, Thomas CE, Haussler R, Beulens J, Rutters F, Nijpels G, van Oort S, Groeneveld L, Elders P, Giorgino T, Rodriquez M, Nice R, Perry M, Bianzano S, Graefe-Mody U, Hennige A, Grempler R, Baum P, Stærfeldt HH, Shah N, Teare H, Ehrhardt B, Tillner J, Dings C, Lehr T, Scherer N, Sihinevich I, Cabrelli L, Loftus H, Bizzotto R, Tura A, Dekkers K, van Leeuwen N, Groop L, Slieker R, Ramisch A, Jennison C, McVittie I, Frau F, Steckel-Hamann B, Adragni K, Thomas M, Pasdar NA, Fitipaldi H, Kurbasic A, Mutie P, Pomares-Millan H, Bonnefond A, Canouil M, Caiazzo R, Verkindt H, Holl R, Kuulasmaa T, Deshmukh H, Cederberg H, Laakso M, Vangipurapu J, Dale M, Thorand B, Nicolay C, Fritsche A, Hill A, Hudson M, Thorne C, Allin K, Arumugam M, Jonsson A, Engelbrechtsen L, Forman A, Dutta A, Sondertoft N, Fan Y, Gough S, Robertson N, McRobert N, Wesolowska-Andersen A, Brown A, Davtian D, Dawed A, Donnelly L, Palmer C, White M, Ferrer J, Whitcher B, Artati A, Prehn C, Adam J, Grallert H, Gupta R, Sackett PW, Nilsson B, Tsirigos K, Eriksen R, Jablonka B, Uhlen M, Gassenhuber J, Baltauss T, de Preville N, Klintenberg M, Abdalla M. Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models. Nat Biotechnol 2023; 41:399-408. [PMID: 36593394 PMCID: PMC10017515 DOI: 10.1038/s41587-022-01520-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 01/03/2023]
Abstract
The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug-omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug-drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.
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Affiliation(s)
- Rosa Lundbye Allesøe
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.,Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Agnete Troen Lundgaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ricardo Hernández Medina
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Aguayo-Orozco
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jakob Nybo Nissen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Brorsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gianluca Mazzoni
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jorge Hernansanz Biel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valentas Brasas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Eriksen Benros
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Gorm Pedersen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Piotr Jaroslaw Chmura
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrik Plesner Jacobsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea Mari
- C.N.R. Institute of Neuroscience, Padova, Italy
| | - Robert Koivula
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ana Vinuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | - Sapna Sharma
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany.,Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Freising, Germany
| | - Mark Haid
- Metabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Petra B Musholt
- Research and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany
| | - Federico De Masi
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Josef Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle Krogh Pedersen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valborg Gudmundsdottir
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Angus Jones
- University of Exeter Medical School, Exeter, UK
| | - Gwen Kennedy
- The Immunoassay Biomarker Core Laboratory, School of Medicine, University of Dundee, Dundee, UK
| | - Jimmy Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK
| | - E Louise Thomas
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK
| | - Gary Frost
- Section for Nutrition Research, Faculty of Medicine, Imperial College London, London, UK
| | - Henrik Thomsen
- Department of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark
| | - Elizaveta Hansen
- Department of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mirthe Muilwijk
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Marieke T Blom
- Department of General Practice, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Leen M 't Hart
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.,Department of Biomedical Data Science, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Francois Pattou
- Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France
| | - Violeta Raverdy
- Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France
| | - Soren Brage
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Alison Heggie
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Donna McEvoy
- Diabetes Research Network, Royal Victoria Infirmary, Newcastle, UK
| | - Miranda Mourby
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK
| | - Jane Kaye
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK
| | | | | | - Martin Ridderstråle
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Mark Walker
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Ian Forgie
- Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Giuseppe N Giordano
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, CRC, Lund University, SUS, Malmö, Sweden
| | - Imre Pavo
- Eli Lilly Regional Operations, Vienna, Austria
| | - Hartmut Ruetten
- Research and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emmanouil Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Paul W Franks
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden.,Harvard T.H. Chan School of Public Health, Boston, MA, USA.,OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.,Genentech, South San Francisco, CA, USA
| | - Ewan Pearson
- Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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19
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Ribet F, Bendes A, Fredolini C, Dobielewski M, Böttcher M, Beck O, Schwenk JM, Stemme G, Roxhed N. Microneedle Patch for Painless Intradermal Collection of Interstitial Fluid Enabling Multianalyte Measurement of Small Molecules, SARS-CoV-2 Antibodies, and Protein Profiling. Adv Healthc Mater 2023; 12:e2202564. [PMID: 36748807 DOI: 10.1002/adhm.202202564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/19/2023] [Indexed: 02/08/2023]
Abstract
Blood sampling is a common practice to monitor health, but it entails a series of drawbacks for patients including pain and discomfort. Thus, there is a demand for more convenient ways to obtain samples. Modern analytical techniques enable monitoring of multiple bioanalytes in smaller samples, opening possibilities for new matrices, and microsampling technologies to be adopted. Interstitial fluid (ISF) is an attractive alternative matrix that shows good correlation with plasma concentration dynamics for several analytes and can be sampled in a minimally invasive and painless manner from the skin at the point-of-care. However, there is currently a lack of sampling devices compatible with clinical translation. Here, to tackle state-of-the-art limitations, a cost-effective and compact single-microneedle-based device designed to painlessly collect precisely 1.1 µL of dermal ISF within minutes is presented. The fluid is volume-metered, dried, and stably stored into analytical-grade paper within the microfluidic device. The obtained sample can be mailed to a laboratory, quantitatively analyzed, and provide molecular insights comparable to blood testing. In a human study, the possibility to monitor various classes of molecular analytes is demonstrated in ISF microsamples, including caffeine, hundreds of proteins, and SARS-CoV-2 antibodies, some being detected in ISF for the first time.
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Affiliation(s)
- Federico Ribet
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, 10044, Sweden
| | - Annika Bendes
- Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), SciLifeLab, Solna, 17165, Sweden
| | - Claudia Fredolini
- Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), SciLifeLab, Solna, 17165, Sweden
| | - Mikolaj Dobielewski
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, 10044, Sweden
| | - Michael Böttcher
- MVZ Medizinische Labor Dessau Kassel GmbH, D-06847, Dessau-Rosslau, Germany
| | - Olof Beck
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, 17177, Sweden
| | - Jochen M Schwenk
- Division of Affinity Proteomics, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), SciLifeLab, Solna, 17165, Sweden
| | - Göran Stemme
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, 10044, Sweden
| | - Niclas Roxhed
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, 10044, Sweden
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20
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Kotliar IB, Lorenzen E, Schwenk JM, Hay DL, Sakmar TP. Elucidating the Interactome of G Protein-Coupled Receptors and Receptor Activity-Modifying Proteins. Pharmacol Rev 2023; 75:1-34. [PMID: 36757898 PMCID: PMC9832379 DOI: 10.1124/pharmrev.120.000180] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/27/2022] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are known to interact with several other classes of integral membrane proteins that modulate their biology and pharmacology. However, the extent of these interactions and the mechanisms of their effects are not well understood. For example, one class of GPCR-interacting proteins, receptor activity-modifying proteins (RAMPs), comprise three related and ubiquitously expressed single-transmembrane span proteins. The RAMP family was discovered more than two decades ago, and since then GPCR-RAMP interactions and their functional consequences on receptor trafficking and ligand selectivity have been documented for several secretin (class B) GPCRs, most notably the calcitonin receptor-like receptor. Recent bioinformatics and multiplexed experimental studies suggest that GPCR-RAMP interactions might be much more widespread than previously anticipated. Recently, cryo-electron microscopy has provided high-resolution structures of GPCR-RAMP-ligand complexes, and drugs have been developed that target GPCR-RAMP complexes. In this review, we provide a summary of recent advances in techniques that allow the discovery of GPCR-RAMP interactions and their functional consequences and highlight prospects for future advances. We also provide an up-to-date list of reported GPCR-RAMP interactions based on a review of the current literature. SIGNIFICANCE STATEMENT: Receptor activity-modifying proteins (RAMPs) have emerged as modulators of many aspects of G protein-coupled receptor (GPCR)biology and pharmacology. The application of new methodologies to study membrane protein-protein interactions suggests that RAMPs interact with many more GPCRs than had been previously known. These findings, especially when combined with structural studies of membrane protein complexes, have significant implications for advancing GPCR-targeted drug discovery and the understanding of GPCR pharmacology, biology, and regulation.
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Affiliation(s)
- Ilana B Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Emily Lorenzen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Jochen M Schwenk
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Debbie L Hay
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
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21
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Hauser J, Dale M, Beck O, Schwenk JM, Stemme G, Fredolini C, Roxhed N. Microfluidic Device for Patient-Centric Multiplexed Assays with Readout in Centralized Laboratories. Anal Chem 2022; 95:1350-1358. [PMID: 36548393 PMCID: PMC9850402 DOI: 10.1021/acs.analchem.2c04318] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Patient-centric sampling strategies, where the patient performs self-sampling and ships the sample to a centralized laboratory for readout, are on the verge of widespread adaptation. However, the key to a successful patient-centric workflow is user-friendliness, with few noncritical user interactions, and simple, ideally biohazard-free shipment. Here, we present a capillary-driven microfluidic device designed to perform the critical biomarker capturing step of a multiplexed immunoassay at the time of sample collection. On-chip sample drying enables biohazard-free shipment and allows us to make use of advanced analytics of specialized laboratories that offer the needed analytical sensitivity, reliability, and affordability. Using C-Reactive Protein, MCP1, S100B, IGFBP1, and IL6 as model blood biomarkers, we demonstrate the multiplexing capability and applicability of the device to a patient-centric workflow. The presented quantification of a biomarker panel opens up new possibilities for e-doctor and e-health applications.
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Affiliation(s)
- Janosch Hauser
- KTH
Royal Institute of Technology, Micro and Nanosystems, 10044 Stockholm, Sweden
| | - Matilda Dale
- KTH
Royal Institute of Technology, Affinity Proteomics, Science for Life
Laboratory, 17165 Solna, Sweden
| | - Olof Beck
- Karolinska
Institutet, Clinical Neuroscience, 17177 Stockholm, Sweden
| | - Jochen M. Schwenk
- KTH
Royal Institute of Technology, Affinity Proteomics, Science for Life
Laboratory, 17165 Solna, Sweden
| | - Göran Stemme
- KTH
Royal Institute of Technology, Micro and Nanosystems, 10044 Stockholm, Sweden
| | - Claudia Fredolini
- KTH
Royal Institute of Technology, Affinity Proteomics, Science for Life
Laboratory, 17165 Solna, Sweden,
| | - Niclas Roxhed
- KTH
Royal Institute of Technology, Micro and Nanosystems, 10044 Stockholm, Sweden,MedTechLabs,
BioClinicum, Karolinska University Hospital, 17164 Solna, Sweden,
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22
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Yu X, Schwenk JM, Xu P, LaBaer J. Advances in plasma proteomics: Moving from technology to precision medicine. Proteomics Clin Appl 2022; 16:e2200083. [PMID: 36377435 DOI: 10.1002/prca.202200083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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23
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Yang Z, Macdonald-Dunlop E, Chen J, Zhai R, Li T, Richmond A, Klarić L, Pirastu N, Ning Z, Zheng C, Wang Y, Huang T, He Y, Guo H, Ying K, Gustafsson S, Prins B, Ramisch A, Dermitzakis ET, Png G, Eriksson N, Haessler J, Hu X, Zanetti D, Boutin T, Hwang SJ, Wheeler E, Pietzner M, Raffield LM, Kalnapenkis A, Peters JE, Viñuela A, Gilly A, Elmståhl S, Dedoussis G, Petrie JR, Polašek O, Folkersen L, Chen Y, Yao C, Võsa U, Pairo-Castineira E, Clohisey S, Bretherick AD, Rawlik K, Esko T, Enroth S, Johansson Å, Gyllensten U, Langenberg C, Levy D, Hayward C, Assimes TL, Kooperberg C, Manichaikul AW, Siegbahn A, Wallentin L, Lind L, Zeggini E, Schwenk JM, Butterworth AS, Michaëlsson K, Pawitan Y, Joshi PK, Baillie JK, Mälarstig A, Reiner AP, Wilson JF, Shen X. Genetic Landscape of the ACE2 Coronavirus Receptor. Circulation 2022; 145:1398-1411. [PMID: 35387486 PMCID: PMC9047645 DOI: 10.1161/circulationaha.121.057888] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood. METHODS We have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data. RESULTS We identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells. CONCLUSIONS Human plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.
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Affiliation(s)
- Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
| | - Jiantao Chen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Ting Li
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Lucija Klarić
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- Human Technopole Viale Rita Levi-Montalcini, Milan, Italy (N.P.)
| | - Zheng Ning
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
| | - Yipeng Wang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
| | - Tingting Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Yazhou He
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu (Y.H.)
| | - Huiming Guo
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital Guangdong Academy of Medical Sciences, Guangzhou, China (H.G.)
| | - Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA (K.Y.)
- T.H. Chan School of Public Health, Harvard University, Boston, MA (K.Y.)
| | - Stefan Gustafsson
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Bram Prins
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
| | - Anna Ramisch
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Technical University of Munich (TUM), School of Medicine, Germany (G.P.)
| | | | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville (X.H., A.W.M.)
| | - Daniela Zanetti
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (D.Z., T.L.A.)
- Stanford Cardiovascular Institute, Stanford University, CA (D.Z., T.L.A.)
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Shih-Jen Hwang
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin, Germany (M.P., C.L.)
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill (L.M.R.)
| | - Anette Kalnapenkis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
- Institute of Molecular and Cell Biology, University of Tartu, Estonia (A.K.)
| | - James E. Peters
- Department of Immunology and Inflammation, Imperial College London, UK (J.E.P.)
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK (A.V.)
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (A.G., E.Z.)
| | - Sölve Elmståhl
- Faculty of Medicine, Lund University, Sweden (S. Elmståhl)
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Greece (G.D.)
| | - John R. Petrie
- Institute of Cardiovascular & Medical Sciences, University of Glasgow, UK (J. Petrie)
| | - Ozren Polašek
- University of Split School of Medicine, Croatia (O.P.)
- Algebra University College, Ilica, Zagreb, Croatia (O.P.)
| | | | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Chen Yao
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
| | - Erola Pairo-Castineira
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | - Andrew D. Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | | | | | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin, Germany (M.P., C.L.)
| | - Daniel Levy
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Themistocles L. Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (D.Z., T.L.A.)
- Stanford Cardiovascular Institute, Stanford University, CA (D.Z., T.L.A.)
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville (X.H., A.W.M.)
| | - Agneta Siegbahn
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Lars Wallentin
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (A.G., E.Z.)
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Germany (E.Z.)
| | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden (J.M.S.)
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
- British Heart Foundation Centre of Research Excellence, University of Cambridge, UK (A.S.B.)
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, UK (A.S.B.)
| | - Karl Michaëlsson
- Department of Surgical Sciences, Uppsala University, Sweden (K.M.)
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
- Intensive Care Unit, Royal Infirmary of Edinburgh, UK (J.K.B.)
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden (A.M.)
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China (X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
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24
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Thomas CE, Dahl L, Byström S, Chen Y, Uhlén M, Mälarstig A, Czene K, Hall P, Schwenk JM, Gabrielson M. Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer. Transl Oncol 2022; 17:101339. [PMID: 35033985 PMCID: PMC8760550 DOI: 10.1016/j.tranon.2022.101339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 11/15/2022] Open
Abstract
Accessible risk predictors are crucial for improving the early detection and prognosis of breast cancer. Blood samples are widely available and contain proteins that provide important information about human health and disease, however, little is still known about the contribution of circulating proteins to breast cancer risk prediction. We profiled EDTA plasma samples collected before diagnosis from the Swedish KARMA breast cancer cohort to evaluate circulating proteins as molecular predictors. A data-driven analysis strategy was applied to the molecular phenotypes built on 700 circulating proteins to identify and annotate clusters of women. The unsupervised analysis of 183 future breast cancer cases and 366 age-matched controls revealed five stable clusters with distinct proteomic plasma profiles. Among these women, those in the most stable cluster (N = 19; mean Jaccard index: 0.70 ± 0.29) were significantly more likely to have used menopausal hormonal therapy (MHT), get a breast cancer diagnosis, and were older compared to the remaining clusters. The circulating proteins associated with this cluster (FDR < 0.001) represented physiological processes related to cell junctions (F11R, CLDN15, ITGAL), DNA repair (RBBP8), cell replication (TJP3), and included proteins found in female reproductive tissue (PTCH1, ZP4). Using a data-driven approach on plasma proteomics data revealed the potential long-lasting molecular effects of menopausal hormonal therapy (MHT) on the circulating proteome, even after women had ended their treatment. This provides valuable insights concerning proteomics efforts to identify molecular markers for breast cancer risk prediction.
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Affiliation(s)
- Cecilia E Thomas
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Sanna Byström
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden.
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden.
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25
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Wesolowska-Andersen A, Brorsson CA, Bizzotto R, Mari A, Tura A, Koivula R, Mahajan A, Vinuela A, Tajes JF, Sharma S, Haid M, Prehn C, Artati A, Hong MG, Musholt PB, Kurbasic A, De Masi F, Tsirigos K, Pedersen HK, Gudmundsdottir V, Thomas CE, Banasik K, Jennison C, Jones A, Kennedy G, Bell J, Thomas L, Frost G, Thomsen H, Allin K, Hansen TH, Vestergaard H, Hansen T, Rutters F, Elders P, t’Hart L, Bonnefond A, Canouil M, Brage S, Kokkola T, Heggie A, McEvoy D, Hattersley A, McDonald T, Teare H, Ridderstrale M, Walker M, Forgie I, Giordano GN, Froguel P, Pavo I, Ruetten H, Pedersen O, Dermitzakis E, Franks PW, Schwenk JM, Adamski J, Pearson E, McCarthy MI, Brunak S. Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study. Cell Rep Med 2022; 3:100477. [PMID: 35106505 PMCID: PMC8784706 DOI: 10.1016/j.xcrm.2021.100477] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022]
Abstract
The presentation and underlying pathophysiology of type 2 diabetes (T2D) is complex and heterogeneous. Recent studies attempted to stratify T2D into distinct subgroups using data-driven approaches, but their clinical utility may be limited if categorical representations of complex phenotypes are suboptimal. We apply a soft-clustering (archetype) method to characterize newly diagnosed T2D based on 32 clinical variables. We assign quantitative clustering scores for individuals and investigate the associations with glycemic deterioration, genetic risk scores, circulating omics biomarkers, and phenotypic stability over 36 months. Four archetype profiles represent dysfunction patterns across combinations of T2D etiological processes and correlate with multiple circulating biomarkers. One archetype associated with obesity, insulin resistance, dyslipidemia, and impaired β cell glucose sensitivity corresponds with the fastest disease progression and highest demand for anti-diabetic treatment. We demonstrate that clinical heterogeneity in T2D can be mapped to heterogeneity in individual etiological processes, providing a potential route to personalized treatments.
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Affiliation(s)
| | - Caroline A. Brorsson
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrea Mari
- C.N.R. Institute of Neuroscience, Padova, Italy
| | - Andrea Tura
- C.N.R. Institute of Neuroscience, Padova, Italy
| | - Robert Koivula
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ana Vinuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - Sapna Sharma
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Mark Haid
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Anna Artati
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Petra B. Musholt
- R&D Global Development, Translational Medicine & Clinical Pharmacology (TMCP), Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Azra Kurbasic
- University of Lund, Clinical Sciences, Malmö, Sweden
| | - Federico De Masi
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kostas Tsirigos
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helle Krogh Pedersen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valborg Gudmundsdottir
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cecilia Engel Thomas
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Angus Jones
- University of Exeter Medical School, Exeter, UK
| | - Gwen Kennedy
- The Immunoassay Biomarker Core Laboratory, Shool of Medicine, University of Dundee, Dundee, UK
| | - Jimmy Bell
- Research Centre for Optimal Health, Deparment of Life Sciences, University of Westminster, London, UK
| | - Louise Thomas
- Research Centre for Optimal Health, Deparment of Life Sciences, University of Westminster, London, UK
| | - Gary Frost
- Section for Nutrition Research, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK
| | - Henrik Thomsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Allin
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Femke Rutters
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC-location VUmc, Amsterdam, the Netherlands
| | - Petra Elders
- Department of General Practice, Amsterdam UMC-location VUmc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Leen t’Hart
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC-location VUmc, Amsterdam, the Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Amelie Bonnefond
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille, France
| | - Mickaël Canouil
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille, France
| | - Soren Brage
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Alison Heggie
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Donna McEvoy
- Diabetes Research Network, Royal Victoria Infirmary, Newcastle, UK
| | | | | | - Harriet Teare
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK
| | | | - Mark Walker
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | - Giuseppe N. Giordano
- R&D Global Development, Translational Medicine & Clinical Pharmacology (TMCP), Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Philippe Froguel
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille, France
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Hartmut Ruetten
- R&D Global Development, Translational Medicine & Clinical Pharmacology (TMCP), Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emmanouil Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | | | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - IMI DIRECT Consortium
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- C.N.R. Institute of Neuroscience, Padova, Italy
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
- R&D Global Development, Translational Medicine & Clinical Pharmacology (TMCP), Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
- University of Lund, Clinical Sciences, Malmö, Sweden
- Department of Mathematical Sciences, University of Bath, Bath, UK
- University of Exeter Medical School, Exeter, UK
- The Immunoassay Biomarker Core Laboratory, Shool of Medicine, University of Dundee, Dundee, UK
- Research Centre for Optimal Health, Deparment of Life Sciences, University of Westminster, London, UK
- Section for Nutrition Research, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC-location VUmc, Amsterdam, the Netherlands
- Department of General Practice, Amsterdam UMC-location VUmc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille, France
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
- Diabetes Research Network, Royal Victoria Infirmary, Newcastle, UK
- Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- University of Dundee, Dundee, UK
- Eli Lilly Regional Operations GmbH, Vienna, Austria
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
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26
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Bauer W, Weber M, Diehl-Wiesenecker E, Galtung N, Prpic M, Somasundaram R, Tauber R, Schwenk JM, Micke P, Kappert K. Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection. Viruses 2021; 13:v13122456. [PMID: 34960725 PMCID: PMC8706135 DOI: 10.3390/v13122456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 01/01/2023] Open
Abstract
Background: We evaluated how plasma proteomic signatures in patients with suspected COVID-19 can unravel the pathophysiology, and determine kinetics and clinical outcome of the infection. Methods: Plasma samples from patients presenting to the emergency department (ED) with symptoms of COVID-19 were stratified into: (1) patients with suspected COVID-19 that was not confirmed (n = 44); (2) non-hospitalized patients with confirmed COVID-19 (n = 44); (3) hospitalized patients with confirmed COVID-19 (n = 53) with variable outcome; and (4) patients presenting to the ED with minor diseases unrelated to SARS-CoV-2 infection (n = 20). Besides standard of care diagnostics, 177 circulating proteins related to inflammation and cardiovascular disease were analyzed using proximity extension assay (PEA, Olink) technology. Results: Comparative proteome analysis revealed 14 distinct proteins as highly associated with SARS-CoV-2 infection and 12 proteins with subsequent hospitalization (p < 0.001). ADM, IL-6, MCP-3, TRAIL-R2, and PD-L1 were each predictive for death (AUROC curve 0.80–0.87). The consistent increase of these markers, from hospital admission to intensive care and fatality, supported the concept that these proteins are of major clinical relevance. Conclusions: We identified distinct plasma proteins linked to the presence and course of COVID-19. These plasma proteomic findings may translate to a protein fingerprint, helping to assist clinical management decisions.
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Affiliation(s)
- Wolfgang Bauer
- Department of Emergency Medicine, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (W.B.); (E.D.-W.); (N.G.); (R.S.)
| | - Marcus Weber
- Zuse Institute Berlin (ZIB), Takustraße 7, 14195 Berlin, Germany;
| | - Eva Diehl-Wiesenecker
- Department of Emergency Medicine, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (W.B.); (E.D.-W.); (N.G.); (R.S.)
| | - Noa Galtung
- Department of Emergency Medicine, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (W.B.); (E.D.-W.); (N.G.); (R.S.)
| | - Monika Prpic
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; (M.P.); (R.T.)
| | - Rajan Somasundaram
- Department of Emergency Medicine, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; (W.B.); (E.D.-W.); (N.G.); (R.S.)
| | - Rudolf Tauber
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; (M.P.); (R.T.)
- Labor Berlin—Charité Vivantes GmbH, 13353 Berlin, Germany
| | - Jochen M. Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, Tomtebodavägen 23, 17165 Solna, Sweden;
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Dag Hammarskjölds Väg 20, 75185 Uppsala, Sweden;
| | - Kai Kappert
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; (M.P.); (R.T.)
- Labor Berlin—Charité Vivantes GmbH, 13353 Berlin, Germany
- Correspondence: ; Tel.: +49-30-450-569-001; Fax: +49-30-450-569-900
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27
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Wu C, Borné Y, Gao R, López Rodriguez M, Roell WC, Wilson JM, Regmi A, Luan C, Aly DM, Peter A, Machann J, Staiger H, Fritsche A, Birkenfeld AL, Tao R, Wagner R, Canouil M, Hong MG, Schwenk JM, Ahlqvist E, Kaikkonen MU, Nilsson P, Shore AC, Khan F, Natali A, Melander O, Orho-Melander M, Nilsson J, Häring HU, Renström E, Wollheim CB, Engström G, Weng J, Pearson ER, Franks PW, White MF, Duffin KL, Vaag AA, Laakso M, Stefan N, Groop L, De Marinis Y. Elevated circulating follistatin associates with an increased risk of type 2 diabetes. Nat Commun 2021; 12:6486. [PMID: 34759311 PMCID: PMC8580990 DOI: 10.1038/s41467-021-26536-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/05/2021] [Indexed: 12/23/2022] Open
Abstract
The hepatokine follistatin is elevated in patients with type 2 diabetes (T2D) and promotes hyperglycemia in mice. Here we explore the relationship of plasma follistatin levels with incident T2D and mechanisms involved. Adjusted hazard ratio (HR) per standard deviation (SD) increase in follistatin levels for T2D is 1.24 (CI: 1.04–1.47, p < 0.05) during 19-year follow-up (n = 4060, Sweden); and 1.31 (CI: 1.09–1.58, p < 0.01) during 4-year follow-up (n = 883, Finland). High circulating follistatin associates with adipose tissue insulin resistance and non-alcoholic fatty liver disease (n = 210, Germany). In human adipocytes, follistatin dose-dependently increases free fatty acid release. In genome-wide association study (GWAS), variation in the glucokinase regulatory protein gene (GCKR) associates with plasma follistatin levels (n = 4239, Sweden; n = 885, UK, Italy and Sweden) and GCKR regulates follistatin secretion in hepatocytes in vitro. Our findings suggest that GCKR regulates follistatin secretion and that elevated circulating follistatin associates with an increased risk of T2D by inducing adipose tissue insulin resistance. Follistatin promotes in type 2 diabetes (T2D) pathogenesis in model animals and is elevated in patients with T2D. Here the authors report that plasma follistatin associates with increased risk of incident T2D in two longitudinal cohorts, and show that follistatin regulates insulin-induced suppression lipolysis in cultured human adipocytes.
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Affiliation(s)
- Chuanyan Wu
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,School of Control Science and Engineering, Shandong University, Jinan, Shandong, China.,School of Intelligent Engineering, Shandong Management University, Jinan, Shandong, China
| | - Yan Borné
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, Shandong, China
| | - Maykel López Rodriguez
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.,A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - William C Roell
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Jonathan M Wilson
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Ajit Regmi
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Cheng Luan
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | - Andreas Peter
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Jürgen Machann
- Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany.,Section of Experimental Radiology, Department of Radiology, University of Tübingen, Tübingen, Germany
| | - Harald Staiger
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Andreas Fritsche
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Andreas L Birkenfeld
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Rongya Tao
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Wagner
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Mickaël Canouil
- Inserm U1283 / CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille; University of Lille, Lille University Hospital, Lille, France
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Emma Ahlqvist
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Peter Nilsson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Angela C Shore
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter Hospital and University of Exeter Medical School, Exeter, Devon, UK
| | - Faisel Khan
- Division of Systems Medicine, University of Dundee, Ninewells Hospital & Medical School, Dundee, UK
| | - Andrea Natali
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | - Jan Nilsson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Hans-Ulrich Häring
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Erik Renström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Claes B Wollheim
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,Department of Cell Physiology and Metabolism, University Medical Centre, Geneva, Switzerland
| | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jianping Weng
- Department of Endocrinology and Metabolism, Division of Life Sciences of Medicine, University of Science and Technology of China, Hefei, China
| | - Ewan R Pearson
- Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Paul W Franks
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Morris F White
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kevin L Duffin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | | | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.,Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Norbert Stefan
- Department of Internal Medicine IV, Division of Endocrinology, Diabetology and Nephrology; and Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.,Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Leif Groop
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Yang De Marinis
- Department of Clinical Sciences, Lund University, Malmö, Sweden. .,School of Control Science and Engineering, Shandong University, Jinan, Shandong, China. .,Department of Endocrinology and Metabolism, Division of Life Sciences of Medicine, University of Science and Technology of China, Hefei, China.
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28
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Iglesias MJ, Kruse LD, Sanchez-Rivera L, Enge L, Dusart P, Hong MG, Uhlén M, Renné T, Schwenk JM, Bergstrom G, Odeberg J, Butler LM. Identification of Endothelial Proteins in Plasma Associated With Cardiovascular Risk Factors. Arterioscler Thromb Vasc Biol 2021; 41:2990-3004. [PMID: 34706560 PMCID: PMC8608011 DOI: 10.1161/atvbaha.121.316779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Supplemental Digital Content is available in the text. Objective: Endothelial cell (EC) dysfunction is a well-established response to cardiovascular disease risk factors, such as smoking and obesity. Risk factor exposure can modify EC signaling and behavior, leading to arterial and venous disease development. Here, we aimed to identify biomarker panels for the assessment of EC dysfunction, which could be useful for risk stratification or to monitor treatment response. Approach and Results: We used affinity proteomics to identify EC proteins circulating in plasma that were associated with cardiovascular disease risk factor exposure. Two hundred sixteen proteins, which we previously predicted to be EC-enriched across vascular beds, were measured in plasma samples (N=1005) from the population-based SCAPIS (Swedish Cardiopulmonary Bioimage Study) pilot. Thirty-eight of these proteins were associated with body mass index, total cholesterol, low-density lipoprotein, smoking, hypertension, or diabetes. Sex-specific analysis revealed that associations predominantly observed in female- or male-only samples were most frequently with the risk factors body mass index, or total cholesterol and smoking, respectively. We show a relationship between individual cardiovascular disease risk, calculated with the Framingham risk score, and the corresponding biomarker profiles. Conclusions: EC proteins in plasma could reflect vascular health status.
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Affiliation(s)
- Maria J Iglesias
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.).,Division of Internal Medicine, University Hospital of North Norway, Tromsø (M.J.I., J.O.)
| | - Larissa D Kruse
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Laura Sanchez-Rivera
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Linnea Enge
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Philip Dusart
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Mun-Gwan Hong
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, Germany (T.R.).,Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland (T.R.).,Centre for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany (T.R.)
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.)
| | - Göran Bergstrom
- Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Sweden (G.B.)
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.).,Division of Internal Medicine, University Hospital of North Norway, Tromsø (M.J.I., J.O.).,Department of Clinical Medicine, The Arctic University of Norway, Tromsø (J.O., L.M.B.).,Coagulation Unit, Department of Hematology (J.O.), Karolinska University Hospital, Stockholm, Sweden
| | - Lynn M Butler
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden (M.J.I., L.D.K., L.S.-R., L.E., P.D., M.G.H., M.U., J.M.S., J.O., L.M.B.).,Department of Clinical Medicine, The Arctic University of Norway, Tromsø (J.O., L.M.B.).,Clinical Chemistry, Karolinska University Laboratory (L.M.B.), Karolinska University Hospital, Stockholm, Sweden.,Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden (L.M.B.)
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29
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Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. J Proteome Res 2021; 20:5241-5263. [PMID: 34672606 PMCID: PMC9469506 DOI: 10.1021/acs.jproteome.1c00657] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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: 02/08/2023]
Abstract
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Maria Pernemalm
- Department of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 171 65 Stockholm, Sweden
| | | | - Natasha Letunica
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, B207 SCSB Building, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Philipp E Geyer
- OmicEra Diagnostics GmbH, Behringstr. 6, 82152 Planegg, Germany
| | - Vera Ignjatovic
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
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30
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Zeybel M, Altay O, Arif M, Li X, Yang H, Fredolini C, Akyildiz M, Saglam B, Gonenli MG, Ural D, Kim W, Schwenk JM, Zhang C, Shoaie S, Nielsen J, Uhlén M, Borén J, Mardinoglu A. Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients. Mol Syst Biol 2021; 17:e10459. [PMID: 34694070 PMCID: PMC8724764 DOI: 10.15252/msb.202110459] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/16/2021] [Accepted: 09/29/2021] [Indexed: 12/29/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.
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Affiliation(s)
- Mujdat Zeybel
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust & University of NottinghamNottinghamUK
- Nottingham Digestive Diseases Centre, School of MedicineUniversity of NottinghamNottinghamUK
- Department of Gastroenterology and Hepatology, School of MedicineKoç UniversityIstanbulTurkey
| | - Ozlem Altay
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Muhammad Arif
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Xiangyu Li
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Hong Yang
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Claudia Fredolini
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Murat Akyildiz
- Department of Gastroenterology and Hepatology, School of MedicineKoç UniversityIstanbulTurkey
| | - Burcin Saglam
- Department of Gastroenterology and Hepatology, School of MedicineKoç UniversityIstanbulTurkey
| | - Mehmet Gokhan Gonenli
- Department of Gastroenterology and Hepatology, School of MedicineKoç UniversityIstanbulTurkey
| | - Dilek Ural
- Department of Cardiology, School of MedicineKoç UniversityIstanbulTurkey
| | - Woonghee Kim
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Jochen M Schwenk
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Cheng Zhang
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
- School of Pharmaceutical SciencesZhengzhou UniversityZhengzhouChina
| | - Saeed Shoaie
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
- Centre for Host‐Microbiome Interactions, Faculty of DentistryOral & Craniofacial Sciences, King’s College LondonLondonUK
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Mathias Uhlén
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
| | - Jan Borén
- Department of Molecular and Clinical MedicineUniversity of Gothenburg and Sahlgrenska University HospitalGothenburgSweden
| | - Adil Mardinoglu
- Science for Life LaboratoryKTH ‐ Royal Institute of TechnologyStockholmSweden
- Centre for Host‐Microbiome Interactions, Faculty of DentistryOral & Craniofacial Sciences, King’s College LondonLondonUK
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31
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Tura A, Grespan E, Göbl CS, Koivula RW, Franks PW, Pearson ER, Walker M, Forgie IM, Giordano GN, Pavo I, Ruetten H, Dermitzakis ET, McCarthy MI, Pedersen O, Schwenk JM, Adamski J, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Vangipurapu J, Cederberg H, Laakso M, Rutters F, Elders PJM, Koopman ADM, Beulens JW, Ridderstråle M, Hansen TH, Allin KH, Hansen T, Vestergaard H, Mari A. Profiles of Glucose Metabolism in Different Prediabetes Phenotypes, Classified by Fasting Glycemia, 2-Hour OGTT, Glycated Hemoglobin, and 1-Hour OGTT: An IMI DIRECT Study. Diabetes 2021; 70:2092-2106. [PMID: 34233929 DOI: 10.2337/db21-0227] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022]
Abstract
Differences in glucose metabolism among categories of prediabetes have not been systematically investigated. In this longitudinal study, participants (N = 2,111) underwent a 2-h 75-g oral glucose tolerance test (OGTT) at baseline and 48 months. HbA1c was also measured. We classified participants as having isolated prediabetes defect (impaired fasting glucose [IFG], impaired glucose tolerance [IGT], or HbA1c indicative of prediabetes [IA1c]), two defects (IFG+IGT, IFG+IA1c, or IGT+IA1c), or all defects (IFG+IGT+IA1c). β-Cell function (BCF) and insulin sensitivity were assessed from OGTT. At baseline, in pooling of participants with isolated defects, they showed impairment in both BCF and insulin sensitivity compared with healthy control subjects. Pooled groups with two or three defects showed progressive further deterioration. Among groups with isolated defect, those with IGT showed lower insulin sensitivity, insulin secretion at reference glucose (ISRr), and insulin secretion potentiation (P < 0.002). Conversely, those with IA1c showed higher insulin sensitivity and ISRr (P < 0.0001). Among groups with two defects, we similarly found differences in both BCF and insulin sensitivity. At 48 months, we found higher type 2 diabetes incidence for progressively increasing number of prediabetes defects (odds ratio >2, P < 0.008). In conclusion, the prediabetes groups showed differences in type/degree of glucometabolic impairment. Compared with the pooled group with isolated defects, those with double or triple defect showed progressive differences in diabetes incidence.
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Affiliation(s)
- Andrea Tura
- CNR Institute of Neuroscience, Padova, Italy
| | | | - Christian S Göbl
- Division of Obstetrics and Feto-Maternal Medicine, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Robert W Koivula
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Genetic and Molecular Epidemiology, Department of Clinical Science, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Paul W Franks
- Genetic and Molecular Epidemiology, Department of Clinical Science, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Ewan R Pearson
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, U.K
| | - Mark Walker
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, U.K
| | - Ian M Forgie
- Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, U.K
| | - Giuseppe N Giordano
- Genetic and Molecular Epidemiology, Department of Clinical Science, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Imre Pavo
- Eli Lilly Regional Operations Ges.m.b.H., Vienna, Austria
| | - Hartmut Ruetten
- CardioMetabolism & Respiratory Medicine, Boehringer Ingelheim International GmbH, Ingelheim/Rhein, Germany
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Mark I McCarthy
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Oluf Pedersen
- Section of Metabolic Genetics, Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Federico De Masi
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Konstantinos D Tsirigos
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, U.K
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Timothy J McDonald
- Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Tarja Kokkola
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jagadish Vangipurapu
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henna Cederberg
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Femke Rutters
- Department of Epidemiology and Data Science, Amsterdam Medical Centre, location VUMC, Amsterdam, the Netherlands
| | - Petra J M Elders
- Department of Epidemiology and Data Science, Amsterdam Medical Centre, location VUMC, Amsterdam, the Netherlands
| | - Anitra D M Koopman
- Department of Epidemiology and Data Science, Amsterdam Medical Centre, location VUMC, Amsterdam, the Netherlands
| | - Joline W Beulens
- Department of Epidemiology and Data Science, Amsterdam Medical Centre, location VUMC, Amsterdam, the Netherlands
| | - Martin Ridderstråle
- Department of Clinical Sciences, Diabetes & Endocrinology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Tue H Hansen
- Section of Metabolic Genetics, Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Kristine H Allin
- Section of Metabolic Genetics, Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Section of Metabolic Genetics, Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- Section of Metabolic Genetics, Novo Nordisk Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
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32
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Roxhed N, Bendes A, Dale M, Mattsson C, Hanke L, Dodig-Crnković T, Christian M, Meineke B, Elsässer S, Andréll J, Havervall S, Thålin C, Eklund C, Dillner J, Beck O, Thomas CE, McInerney G, Hong MG, Murrell B, Fredolini C, Schwenk JM. Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2. Nat Commun 2021; 12:3695. [PMID: 34140485 PMCID: PMC8211676 DOI: 10.1038/s41467-021-23893-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
Serological testing is essential to curb the consequences of the COVID-19 pandemic. However, most assays are still limited to single analytes and samples collected within healthcare. Thus, we establish a multianalyte and multiplexed approach to reliably profile IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots (DBS). We analyse DBS collected during spring of 2020 from 878 random and undiagnosed individuals from the population in Stockholm, Sweden, and use classification approaches to estimate an accumulated seroprevalence of 12.5% (95% CI: 10.3%-14.7%). This includes 5.4% of the samples being IgG+IgM+ against several SARS-CoV-2 proteins, as well as 2.1% being IgG-IgM+ and 5.0% being IgG+IgM- for the virus' S protein. Subjects classified as IgG+ for several SARS-CoV-2 proteins report influenza-like symptoms more frequently than those being IgG+ for only the S protein (OR = 6.1; p < 0.001). Among all seropositive cases, 30% are asymptomatic. Our strategy enables an accurate individual-level and multiplexed assessment of antibodies in home-sampled blood, assisting our understanding about the undiagnosed seroprevalence and diversity of the immune response against the coronavirus.
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Affiliation(s)
- Niclas Roxhed
- Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.
- MedTechLabs, BioClinicum, Karolinska University Hospital, Solna, Sweden.
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Matilda Dale
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Cecilia Mattsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Murray Christian
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Birthe Meineke
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Simon Elsässer
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Juni Andréll
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Sebastian Havervall
- Division of Internal Medicine, Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Danderyd, Sweden
| | - Charlotte Thålin
- Division of Internal Medicine, Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Danderyd, Sweden
| | - Carina Eklund
- Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Dillner
- Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Olof Beck
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia E Thomas
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Mun-Gwan Hong
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.
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33
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Stockfelt M, Hong MG, Hesselmar B, Adlerberth I, Wold AE, Schwenk JM, Lundell AC, Rudin A. Circulating proteins associated with allergy development in infants-an exploratory analysis. Clin Proteomics 2021; 18:11. [PMID: 33722194 PMCID: PMC7958444 DOI: 10.1186/s12014-021-09318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/07/2021] [Indexed: 12/15/2022] Open
Abstract
Background Protein profiles that can predict allergy development in children are lacking and the ideal sampling age is unknown. By applying an exploratory proteomics approach in the prospective FARMFLORA birth cohort, we sought to identify previously unknown circulating proteins in early life that associate to protection or risk for development of allergy up to 8 years of age. Methods We analyzed plasma prepared from umbilical cord blood (n = 38) and blood collected at 1 month (n = 42), 4 months (n = 39), 18 months (n = 42), 36 months (n = 42) and 8 years (n = 44) of age. We profiled 230 proteins with a multiplexed assay and evaluated the global structure of the data with principal component analysis (PCA). Protein profiles informative to allergic disease at 18 months, 36 months and/or 8 years were evaluated using Lasso logistic regression and random forest. Results Two clusters emerged in the PCA analysis that separated samples obtained at birth and at 1 month of age from samples obtained later. Differences between the clusters were mostly driven by abundant plasma proteins. For the prediction of allergy, both Lasso logistic regression and random forest were most informative with samples collected at 1 month of age. A Lasso model with 27 proteins together with farm environment differentiated children who remained healthy from those developing allergy. This protein panel was primarily composed of antigen-presenting MHC class I molecules, interleukins and chemokines. Conclusion Sampled at one month of age, circulating proteins that reflect processes of the immune system may predict the development of allergic disease later in childhood. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09318-w.
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Affiliation(s)
- Marit Stockfelt
- Institute of Medicine, Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, Box 480, 405 30, Göteborg, Sweden.
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bill Hesselmar
- Institute of Clinical Sciences, Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Agnes E Wold
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna-Carin Lundell
- Institute of Medicine, Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, Box 480, 405 30, Göteborg, Sweden
| | - Anna Rudin
- Institute of Medicine, Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, Box 480, 405 30, Göteborg, Sweden
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34
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Bizzotto R, Jennison C, Jones AG, Kurbasic A, Tura A, Kennedy G, Bell JD, Thomas EL, Frost G, Eriksen R, Koivula RW, Brage S, Kaye J, Hattersley AT, Heggie A, McEvoy D, 't Hart LM, Beulens JW, Elders P, Musholt PB, Ridderstråle M, Hansen TH, Allin KH, Hansen T, Vestergaard H, Lundgaard AT, Thomsen HS, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Forgie IM, Giordano GN, Pavo I, Ruetten H, Dermitzakis E, McCarthy MI, Pedersen O, Schwenk JM, Adamski J, Franks PW, Walker M, Pearson ER, Mari A. Processes Underlying Glycemic Deterioration in Type 2 Diabetes: An IMI DIRECT Study. Diabetes Care 2021; 44:511-518. [PMID: 33323478 DOI: 10.2337/dc20-1567] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/31/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We investigated the processes underlying glycemic deterioration in type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS A total of 732 recently diagnosed patients with T2D from the Innovative Medicines Initiative Diabetes Research on Patient Stratification (IMI DIRECT) study were extensively phenotyped over 3 years, including measures of insulin sensitivity (OGIS), β-cell glucose sensitivity (GS), and insulin clearance (CLIm) from mixed meal tests, liver enzymes, lipid profiles, and baseline regional fat from MRI. The associations between the longitudinal metabolic patterns and HbA1c deterioration, adjusted for changes in BMI and in diabetes medications, were assessed via stepwise multivariable linear and logistic regression. RESULTS Faster HbA1c progression was independently associated with faster deterioration of OGIS and GS and increasing CLIm; visceral or liver fat, HDL-cholesterol, and triglycerides had further independent, though weaker, roles (R 2 = 0.38). A subgroup of patients with a markedly higher progression rate (fast progressors) was clearly distinguishable considering these variables only (discrimination capacity from area under the receiver operating characteristic = 0.94). The proportion of fast progressors was reduced from 56% to 8-10% in subgroups in which only one trait among OGIS, GS, and CLIm was relatively stable (odds ratios 0.07-0.09). T2D polygenic risk score and baseline pancreatic fat, glucagon-like peptide 1, glucagon, diet, and physical activity did not show an independent role. CONCLUSIONS Deteriorating insulin sensitivity and β-cell function, increasing insulin clearance, high visceral or liver fat, and worsening of the lipid profile are the crucial factors mediating glycemic deterioration of patients with T2D in the initial phase of the disease. Stabilization of a single trait among insulin sensitivity, β-cell function, and insulin clearance may be relevant to prevent progression.
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Affiliation(s)
| | | | - Angus G Jones
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K.,Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Azra Kurbasic
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Clinical Research Centre, Lund University, Skåne University Hospital, Malmö, Malmö, Sweden
| | - Andrea Tura
- CNR Institute of Neuroscience, Padova, Italy
| | - Gwen Kennedy
- Immunoassay Biomarker Core Laboratory, School of Medicine, Ninewells Hospital, Dundee, U.K
| | - Jimmy D Bell
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, U.K
| | - E Louise Thomas
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, U.K
| | - Gary Frost
- Section for Nutrition Research, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, U.K
| | - Rebeca Eriksen
- Section for Nutrition Research, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, U.K
| | - Robert W Koivula
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Clinical Research Centre, Lund University, Skåne University Hospital, Malmö, Malmö, Sweden.,Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K
| | - Soren Brage
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Jane Kaye
- Faculty of Law, Centre for Health, Law and Emerging Technologies, University of Oxford, Oxford, U.K.,Melbourne Law School, Centre for Health, Law and Emerging Technologies, University of Melbourne, Carlton, Victoria, Australia
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K.,Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Alison Heggie
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - Donna McEvoy
- Diabetes Research Network, Royal Victoria Infirmary, Newcastle upon Tyne, U.K
| | - Leen M 't Hart
- Department of Epidemiology and Data Science, Amsterdam UMC-Location VUmc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Biomedical Data Sciences, Molecular Epidemiology Section, Leiden University Medical Center, Leiden, the Netherlands
| | - Joline W Beulens
- Department of Epidemiology and Data Science, Amsterdam UMC-Location VUmc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Petra Elders
- Department of General Practice, Amsterdam UMC-Location VUmc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Petra B Musholt
- R&D Global Development, Translational Medicine & Clinical Pharmacology, Sanofi Deutschland GmbH, Frankfurt, Germany
| | - Martin Ridderstråle
- Clinical Pharmacology and Translational Medicine, Novo Nordisk A/S, Søborg, Denmark
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine H Allin
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Bornholms Hospital, Rønne, Denmark
| | - Agnete T Lundgaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Henrik S Thomsen
- Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Federico De Masi
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Konstantinos D Tsirigos
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle, U.K
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Timothy J McDonald
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K.,Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ian M Forgie
- Population Health and Genomics, School of Medicine, University of Dundee, Dundee, U.K
| | - Giuseppe N Giordano
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Clinical Research Centre, Lund University, Skåne University Hospital, Malmö, Malmö, Sweden
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Hartmut Ruetten
- R&D Global Development, Translational Medicine & Clinical Pharmacology, Sanofi Deutschland GmbH, Frankfurt, Germany
| | - Emmanouil Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Mark I McCarthy
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, U.K.,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, U.K
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jerzy Adamski
- Research Unit of Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany.,Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Clinical Research Centre, Lund University, Skåne University Hospital, Malmö, Malmö, Sweden
| | - Mark Walker
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle, U.K
| | - Ewan R Pearson
- Population Health and Genomics, School of Medicine, University of Dundee, Dundee, U.K
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35
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Koivula RW, Atabaki-Pasdar N, Giordano GN, White T, Adamski J, Bell JD, Beulens J, Brage S, Brunak S, De Masi F, Dermitzakis ET, Forgie IM, Frost G, Hansen T, Hansen TH, Hattersley A, Kokkola T, Kurbasic A, Laakso M, Mari A, McDonald TJ, Pedersen O, Rutters F, Schwenk JM, Teare HJA, Thomas EL, Vinuela A, Mahajan A, McCarthy MI, Ruetten H, Walker M, Pearson E, Pavo I, Franks PW. Correction to: The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes: an IMI DIRECT study. Diabetologia 2021; 64:260-261. [PMID: 33184701 PMCID: PMC7852866 DOI: 10.1007/s00125-020-05311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Unfortunately, 'Present address' was omitted from one of the addresses provided for Mark I. McCarthy (#26).
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Affiliation(s)
- Robert W Koivula
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Naeimeh Atabaki-Pasdar
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
| | - Giuseppe N Giordano
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
| | - Tom White
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Jimmy D Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminister, London, UK
| | - Joline Beulens
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, the Netherlands
| | - Søren Brage
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Søren Brunak
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Federico De Masi
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ian M Forgie
- Population Health & Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, UK
| | - Gary Frost
- Nutrition and Dietetics Research Group, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Imperial College London, Hammersmith Campus, London, UK
| | - Torben Hansen
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Tue H Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hattersley
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Azra Kurbasic
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Andrea Mari
- Institute of Neurosciences, National Research Council, Padova, Italy
| | - Timothy J McDonald
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Femke Rutters
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, the Netherlands
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Harriet J A Teare
- HeLEX, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Headington, Oxford, UK
| | - E Louise Thomas
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminister, London, UK
| | - Ana Vinuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
| | - Hartmut Ruetten
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main, Germany
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, UK
| | - Ewan Pearson
- Population Health & Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, UK
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Paul W Franks
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Department of Public Health & Clinical Medicine, Section for Medicine, Umeå University Hospital, Umeå, Sweden
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36
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Bendes A, Dale M, Mattsson C, Dodig-Crnković T, Iglesias MJ, Schwenk JM, Fredolini C. Bead-Based Assays for Validating Proteomic Profiles in Body Fluids. Methods Mol Biol 2021; 2344:65-78. [PMID: 34115352 DOI: 10.1007/978-1-0716-1562-1_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/09/2023]
Abstract
Protein biomarkers in biological fluids represent an important resource for improving the clinical management of diseases. Current proteomics technologies are capable of performing high-throughput and multiplex profiling in different types of fluids, often leading to the shortlisting of tens of candidate biomarkers per study. However, before reaching any clinical setting, these discoveries require thorough validation and an assay that would be suitable for routine analyses. In the path from biomarker discovery to validation, the performance of the assay implemented for the intended protein quantification is extremely critical toward achieving reliable and reproducible results. Development of robust sandwich immunoassays for individual candidates is challenging and labor and resource intensive, and multiplies when evaluating a panel of interesting candidates at the same time. Here we describe a versatile pipeline that facilitates the systematic and parallel development of multiple sandwich immunoassays using a bead-based technology.
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Affiliation(s)
- Annika Bendes
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Matilda Dale
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Mattsson
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsö, Tromsö, Norway
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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37
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Abstract
Systematic exploration of the dynamic human plasma proteome enables the discovery of novel protein biomarkers. Using state-of-the-art technologies holds the promise to facilitate a better diagnosis and risk prediction of diseases. Cardiovascular disease (CVD) pathophysiology is characterized for unbalancing of processes such as vascular inflammation, endothelial dysfunction, or lipid profiles among others. Such processes have a direct impact on the dynamic and complex composition of blood and hence the plasma proteome. Therefore, the study of the plasma proteome comprises an excellent exploratory source of biomarker research particularly for CVD. We describe the protocol for performing the discovery of protein biomarker candidates using the suspension bead array technology. The process does not require depletion steps to remove abundant proteins and consumes only a few microliters of sample from the body fluid of interest. The approach is scalable to measure many analytes as well as large numbers of samples. Moreover, we describe a bead-assisted antibody-labeling process that helps to develop quantitative assays for validation purposes and facilitate the translation of the identified candidates into clinical studies.
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Affiliation(s)
- Maria Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden. .,Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsø, Tromsø, Norway.
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.,Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsø, Tromsø, Norway.,Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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38
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Obura M, Beulens JWJ, Slieker R, Koopman ADM, Hoekstra T, Nijpels G, Elders P, Koivula RW, Kurbasic A, Laakso M, Hansen TH, Ridderstråle M, Hansen T, Pavo I, Forgie I, Jablonka B, Ruetten H, Mari A, McCarthy MI, Walker M, Heggie A, McDonald TJ, Perry MH, De Masi F, Brunak S, Mahajan A, Giordano GN, Kokkola T, Dermitzakis E, Viñuela A, Pedersen O, Schwenk JM, Adamski J, Teare HJA, Pearson ER, Franks PW, ‘t Hart LM, Rutters F. Post-load glucose subgroups and associated metabolic traits in individuals with type 2 diabetes: An IMI-DIRECT study. PLoS One 2020; 15:e0242360. [PMID: 33253307 PMCID: PMC7703960 DOI: 10.1371/journal.pone.0242360] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/31/2020] [Indexed: 11/19/2022] Open
Abstract
Aim Subclasses of different glycaemic disturbances could explain the variation in characteristics of individuals with type 2 diabetes (T2D). We aimed to examine the association between subgroups based on their glucose curves during a five-point mixed-meal tolerance test (MMT) and metabolic traits at baseline and glycaemic deterioration in individuals with T2D. Methods The study included 787 individuals with newly diagnosed T2D from the Diabetes Research on Patient Stratification (IMI-DIRECT) Study. Latent class trajectory analysis (LCTA) was used to identify distinct glucose curve subgroups during a five-point MMT. Using general linear models, these subgroups were associated with metabolic traits at baseline and after 18 months of follow up, adjusted for potential confounders. Results At baseline, we identified three glucose curve subgroups, labelled in order of increasing glucose peak levels as subgroup 1–3. Individuals in subgroup 2 and 3 were more likely to have higher levels of HbA1c, triglycerides and BMI at baseline, compared to those in subgroup 1. At 18 months (n = 651), the beta coefficients (95% CI) for change in HbA1c (mmol/mol) increased across subgroups with 0.37 (-0.18–1.92) for subgroup 2 and 1.88 (-0.08–3.85) for subgroup 3, relative to subgroup 1. The same trend was observed for change in levels of triglycerides and fasting glucose. Conclusions Different glycaemic profiles with different metabolic traits and different degrees of subsequent glycaemic deterioration can be identified using data from a frequently sampled mixed-meal tolerance test in individuals with T2D. Subgroups with the highest peaks had greater metabolic risk.
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Affiliation(s)
- Morgan Obura
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
| | - Joline W. J. Beulens
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
| | - Roderick Slieker
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anitra D. M. Koopman
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
| | - Trynke Hoekstra
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Giel Nijpels
- Department of General Practice and Elderly Care Medicine, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
| | - Petra Elders
- Department of General Practice and Elderly Care Medicine, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
| | - Robert W. Koivula
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Oxford, United Kingdom
| | - Azra Kurbasic
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Tue H. Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology and Endocrinology, Slagelse Hospital, Slagelse, Denmark
| | - Martin Ridderstråle
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Ian Forgie
- Division of Cardiovascular & Diabetes Medicine, Medical Research Institute, University of Dundee, Dundee, United Kingdom
| | - Bernd Jablonka
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main, Germany
| | - Hartmut Ruetten
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main, Germany
| | - Andrea Mari
- Institute of Biomedical Engineering, National Research Council, Padova, Italy
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alison Heggie
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Timothy J. McDonald
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School and Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Mandy H. Perry
- Department of Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Federico De Masi
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Giuseppe N. Giordano
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Emmanouil Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH—Royal Institute of Technology, Solna, Sweden
| | - Jurek Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Harriet J. A. Teare
- HeLEX, Nuffield Department of Population Health, University of Oxford, Headington, Oxford, United Kingdom
| | - Ewan R. Pearson
- Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Oxford, United Kingdom
- Department of Nutrition, Harvard School of Public Health, Boston, MA, United States of America
| | - Leen M. ‘t Hart
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Biomedical Data Sciences, Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Femke Rutters
- Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VU University Medical Center, Amsterdam, The Netherlands
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39
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Sivertsson Å, Lindström E, Oksvold P, Katona B, Hikmet F, Vuu J, Gustavsson J, Sjöstedt E, von Feilitzen K, Kampf C, Schwenk JM, Uhlén M, Lindskog C. Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins. J Proteome Res 2020; 19:4766-4781. [PMID: 33170010 PMCID: PMC7723238 DOI: 10.1021/acs.jproteome.0c00486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The localization of proteins at a
tissue- or cell-type-specific
level is tightly linked to the protein function. To better understand
each
protein’s role in cellular systems, spatial information constitutes
an important complement to quantitative data. The standard methods
for determining the spatial distribution of proteins in single cells
of complex tissue samples make use of antibodies. For a stringent
analysis of the human proteome, we used orthogonal methods and independent
antibodies to validate 5981 antibodies that show the expression of
3775 human proteins across all major human tissues. This enhanced
validation uncovered 56 proteins corresponding to the group of “missing
proteins” and 171 proteins of unknown function. The presented
strategy will facilitate further discussions around criteria for evidence
of protein existence based on immunohistochemistry and serves as a
useful guide to identify candidate proteins for integrative studies
with quantitative proteomics methods.
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Affiliation(s)
- Åsa Sivertsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Emil Lindström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Borbala Katona
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jimmy Vuu
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jonas Gustavsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.,Atlas Antibodies AB, 16869 Bromma, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
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40
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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41
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Tebani A, Gummesson A, Zhong W, Koistinen IS, Lakshmikanth T, Olsson LM, Boulund F, Neiman M, Stenlund H, Hellström C, Karlsson MJ, Arif M, Dodig-Crnković T, Mardinoglu A, Lee S, Zhang C, Chen Y, Olin A, Mikes J, Danielsson H, von Feilitzen K, Jansson PA, Angerås O, Huss M, Kjellqvist S, Odeberg J, Edfors F, Tremaroli V, Forsström B, Schwenk JM, Nilsson P, Moritz T, Bäckhed F, Engstrand L, Brodin P, Bergström G, Uhlen M, Fagerberg L. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun 2020; 11:4487. [PMID: 32900998 PMCID: PMC7479148 DOI: 10.1038/s41467-020-18148-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022] Open
Abstract
An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine. An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, the authors sample a longitudinal wellness cohort and analyse blood molecular profiles as well as gut microbiota composition.
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Affiliation(s)
- Abdellah Tebani
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Wen Zhong
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ina Schuppe Koistinen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Lisa M Olsson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Boulund
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maja Neiman
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Cecilia Hellström
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Max J Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjae Lee
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Axel Olin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Danielsson
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Per-Anders Jansson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Internal Medicine, Gothenburg, Sweden
| | - Oskar Angerås
- Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Cardiology, Gothenburg, Sweden
| | - Mikael Huss
- Codon Consulting, 118 26, Stockholm, Sweden.,Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Sanela Kjellqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Björn Forsström
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thomas Moritz
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 907 36, Umeå, Sweden
| | - Fredrik Bäckhed
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Engstrand
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Göran Bergström
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Center for Biosustainability, Danish Technical University, Copenhagen, Denmark
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
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Eriksen R, Perez IG, Posma JM, Haid M, Sharma S, Prehn C, Thomas LE, Koivula RW, Bizzotto R, Prehn C, Mari A, Giordano GN, Pavo I, Schwenk JM, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Rutter F, Teare H, Hansen TH, Fernandez J, Jones A, Jennison C, Walker M, McCarthy MI, Pedersen O, Ruetten H, Forgie I, Bell JD, Pearson ER, Franks PW, Adamski J, Holmes E, Frost G. Dietary metabolite profiling brings new insight into the relationship between nutrition and metabolic risk: An IMI DIRECT study. EBioMedicine 2020; 58:102932. [PMID: 32763829 PMCID: PMC7406914 DOI: 10.1016/j.ebiom.2020.102932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 07/15/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Dietary advice remains the cornerstone of prevention and management of type 2 diabetes (T2D). However, understanding the efficacy of dietary interventions is confounded by the challenges inherent in assessing free living diet. Here we profiled dietary metabolites to investigate glycaemic deterioration and cardiometabolic risk in people at risk of or living with T2D. METHODS We analysed data from plasma collected at baseline and 18-month follow-up in individuals from the Innovative Medicines Initiative (IMI) Diabetes Research on Patient Stratification (DIRECT) cohort 1 n = 403 individuals with normal or impaired glucose regulation (prediabetic) and cohort 2 n = 458 individuals with new onset of T2D. A dietary metabolite profile model (Tpred) was constructed using multivariable regression of 113 plasma metabolites obtained from targeted metabolomics assays. The continuous Tpred score was used to explore the relationships between diet, glycaemic deterioration and cardio-metabolic risk via multiple linear regression models. FINDINGS A higher Tpred score was associated with healthier diets high in wholegrain (β=3.36 g, 95% CI 0.31, 6.40 and β=2.82 g, 95% CI 0.06, 5.57) and lower energy intake (β=-75.53 kcal, 95% CI -144.71, -2.35 and β=-122.51 kcal, 95% CI -186.56, -38.46), and saturated fat (β=-0.92 g, 95% CI -1.56, -0.28 and β=-0.98 g, 95% CI -1.53, -0.42 g), respectively for cohort 1 and 2. In both cohorts a higher Tpred score was also associated with lower total body adiposity and favourable lipid profiles HDL-cholesterol (β=0.07 mmol/L, 95% CI 0.03, 0.1), (β=0.08 mmol/L, 95% CI 0.04, 0.1), and triglycerides (β=-0.1 mmol/L, 95% CI -0.2, -0.03), (β=-0.2 mmol/L, 95% CI -0.3, -0.09), respectively for cohort 1 and 2. In cohort 2, the Tpred score was negatively associated with liver fat (β=-0.74%, 95% CI -0.67, -0.81), and lower fasting concentrations of HbA1c (β=-0.9 mmol/mol, 95% CI -1.5, -0.1), glucose (β=-0.2 mmol/L, 95% CI -0.4, -0.05) and insulin (β=-11.0 pmol/mol, 95% CI -19.5, -2.6). Longitudinal analysis showed at 18-month follow up a higher Tpred score was also associated lower total body adiposity in both cohorts and lower fasting glucose (β=-0.2 mmol/L, 95% CI -0.3, -0.01) and insulin (β=-9.2 pmol/mol, 95% CI -17.9, -0.4) concentrations in cohort 2. INTERPRETATION Plasma dietary metabolite profiling provides objective measures of diet intake, showing a relationship to glycaemic deterioration and cardiometabolic health. FUNDING This work was supported by the Innovative Medicines Initiative Joint Undertaking under grant agreement no. 115,317 (DIRECT), resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies.
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Affiliation(s)
- Rebeca Eriksen
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, United Kingdom.
| | - Isabel Garcia Perez
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, United Kingdom
| | - Joram M Posma
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom; Health Data Research UK, London, United Kingdom
| | - Mark Haid
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany
| | - Sapna Sharma
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany
| | - Louise E Thomas
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
| | - Robert W Koivula
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Radcliffe Department of Medicine, Oxford, United Kingdom
| | - Roberto Bizzotto
- Institute of Neuroscience - National Research Council, Padova, Italy
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany
| | - Andrea Mari
- Institute of Neuroscience - National Research Council, Padova, Italy
| | - Giuseppe N Giordano
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Federico De Masi
- Department of Health Technology, Technical University of Denmark, Kgs Lyngby and The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Konstantinos D Tsirigos
- Department of Health Technology, Technical University of Denmark, Kgs Lyngby and The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Kgs Lyngby and The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Timothy J McDonald
- Medical School, Exeter, UK NIHR Exeter Clinical Research Facility, University of Exeter
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Femke Rutter
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam UMC, locationVUMC, Amsterdam, Netherlands
| | - Harriet Teare
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tue H Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Juan Fernandez
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Angus Jones
- Medical School, Exeter, UK NIHR Exeter Clinical Research Facility, University of Exeter
| | - Chris Jennison
- Department of Mathematical Sciences, University of Bath, Bath, United Kingdom
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Radcliffe Department of Medicine, Oxford, United Kingdom; Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Hartmut Ruetten
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main, Germany
| | - Ian Forgie
- Population Health & Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Jimmy D Bell
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
| | - Ewan R Pearson
- Population Health & Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology And Metabolism, Helmholtz Zentrum Muenchen, German Research Center for Environemental Health (GmbH), Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Elaine Holmes
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, United Kingdom
| | - Gary Frost
- Section for Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, United Kingdom; NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom.
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Hong MG, Dodig-Crnković T, Chen X, Drobin K, Lee W, Wang Y, Edfors F, Kotol D, Thomas CE, Sjöberg R, Odeberg J, Hamsten A, Silveira A, Hall P, Nilsson P, Pawitan Y, Uhlén M, Pedersen NL, Hägg S, Magnusson PK, Schwenk JM. Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality. Life Sci Alliance 2020; 3:3/10/e202000817. [PMID: 32737166 PMCID: PMC7409555 DOI: 10.26508/lsa.202000817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Despite recognizing aging as a common risk factor of many human diseases, little is known about its molecular traits. To identify age-associated proteins circulating in human blood, we screened 156 individuals aged 50-92 using exploratory and multiplexed affinity proteomics assays. Profiling eight additional study sets (N = 3,987), performing antibody validation, and conducting a meta-analysis revealed a consistent age association (P = 6.61 × 10-6) for circulating histidine-rich glycoprotein (HRG). Sequence variants of HRG influenced how the protein was recognized in the immunoassays. Indeed, only the HRG profiles affected by rs9898 were associated with age and predicted the risk of mortality (HR = 1.25 per SD; 95% CI = 1.12-1.39; P = 6.45 × 10-5) during a follow-up period of 8.5 yr after blood sampling (IQR = 7.7-9.3 yr). Our affinity proteomics analysis found associations between the particular molecular traits of circulating HRG with age and all-cause mortality. The distinct profiles of this multipurpose protein could serve as an accessible and informative indicator of the physiological processes related to biological aging.
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Affiliation(s)
- Mun-Gwan Hong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Tea Dodig-Crnković
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kimi Drobin
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Woojoo Lee
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - David Kotol
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Cecilia Engel Thomas
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Ronald Sjöberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Jacob Odeberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden.,Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Solna, Sweden
| | - Anders Hamsten
- Department of Medicine Solna, Cardiovascular Medicine Unit, Karolinska Institutet, Solna, Sweden
| | - Angela Silveira
- Department of Medicine Solna, Cardiovascular Medicine Unit, Karolinska Institutet, Solna, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Peter Nilsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlén
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik Ke Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jochen M Schwenk
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden
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44
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Dodig-Crnković T, Hong MG, Thomas CE, Häussler RS, Bendes A, Dale M, Edfors F, Forsström B, Magnusson PKE, Schuppe-Koistinen I, Odeberg J, Fagerberg L, Gummesson A, Bergström G, Uhlén M, Schwenk JM. Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling. EBioMedicine 2020; 57:102854. [PMID: 32629387 PMCID: PMC7334812 DOI: 10.1016/j.ebiom.2020.102854] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate. METHODS To provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals' short-term health trajectories. FINDINGS We found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed that 49% of the protein profiles were stable over one year. We also identified eight networks of proteins in which 11-242 proteins covaried over time. For each participant, there were unique protein profiles of which some could be explained by associations to genetic variants. INTERPRETATION This observational and non-interventional study identifyed noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. To enable more personal hence precise assessments of health states, longitudinal profiling of circulating proteomes can provide a valuable component for precision medicine approaches. FUNDING This work was supported by the Erling Persson Foundation, the Swedish Heart and Lung Foundation, the Knut and Alice Wallenberg Foundation, Science for Life Laboratory, and the Swedish Research Council.
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Affiliation(s)
- Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Mun-Gwan Hong
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Cecilia Engel Thomas
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Ragna S Häussler
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Annika Bendes
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Matilda Dale
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Björn Forsström
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm 171 77, Sweden
| | - Ina Schuppe-Koistinen
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden; Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm 171 77, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden; Department of Clinical Medicine, K.G. Jebsen Thrombosis Research and Expertise Center (TREC), UiT the Arctic University of Norway, Tromsø 9010, Norway; Coagulation unit, Department of Hematology, Karolinska University Hospital, Stockholm 171 76, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg 413 45, Sweden; Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg 413 45, Sweden; Region Västra Götaland, Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Tomtebodavägen 23, Stockholm 171 65, Sweden.
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45
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Zhong W, Gummesson A, Tebani A, Karlsson MJ, Hong MG, Schwenk JM, Edfors F, Bergström G, Fagerberg L, Uhlén M. Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort. Genome Med 2020; 12:53. [PMID: 32576278 PMCID: PMC7310558 DOI: 10.1186/s13073-020-00755-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors to determine the specific protein levels in individuals and to gain a deeper insight of the importance of genetic architecture related to the individual variability of plasma levels of proteins during adult life. METHODS We have combined whole-genome sequencing, multiplex plasma protein profiling, and extensive clinical phenotyping in a longitudinal 2-year wellness study of 101 healthy individuals with repeated sampling. Analyses of genetic and non-genetic associations related to the variability of blood levels of proteins in these individuals were performed. RESULTS The analyses showed that each individual has a unique protein profile, and we report on the intra-individual as well as inter-individual variation for 794 plasma proteins. A genome-wide association study (GWAS) using 7.3 million genetic variants identified by whole-genome sequencing revealed 144 independent variants across 107 proteins that showed strong association (P < 6 × 10-11) between genetics and the inter-individual variability on protein levels. Many proteins not reported before were identified (67 out of 107) with individual plasma level affected by genetics. Our longitudinal analysis further demonstrates that these levels are stable during the 2-year study period. The variability of protein profiles as a consequence of environmental factors was also analyzed with focus on the effects of weight loss and infections. CONCLUSIONS We show that the adult blood levels of many proteins are determined at birth by genetics, which is important for efforts aimed to understand the relationship between plasma proteome profiles and human biology and disease.
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Affiliation(s)
- Wen Zhong
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Abdellah Tebani
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Max J Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mun-Gwan Hong
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
- Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Koivula RW, Atabaki-Pasdar N, Giordano GN, White T, Adamski J, Bell JD, Beulens J, Brage S, Brunak S, De Masi F, Dermitzakis ET, Forgie IM, Frost G, Hansen T, Hansen TH, Hattersley A, Kokkola T, Kurbasic A, Laakso M, Mari A, McDonald TJ, Pedersen O, Rutters F, Schwenk JM, Teare HJA, Thomas EL, Vinuela A, Mahajan A, McCarthy MI, Ruetten H, Walker M, Pearson E, Pavo I, Franks PW. The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes: an IMI DIRECT study. Diabetologia 2020; 63:744-756. [PMID: 32002573 PMCID: PMC7054368 DOI: 10.1007/s00125-019-05083-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/29/2019] [Indexed: 11/17/2022]
Abstract
AIMS/HYPOTHESIS It is well established that physical activity, abdominal ectopic fat and glycaemic regulation are related but the underlying structure of these relationships is unclear. The previously proposed twin-cycle hypothesis (TC) provides a mechanistic basis for impairment in glycaemic control through the interactions of substrate availability, substrate metabolism and abdominal ectopic fat accumulation. Here, we hypothesise that the effect of physical activity in glucose regulation is mediated by the twin-cycle. We aimed to examine this notion in the Innovative Medicines Initiative Diabetes Research on Patient Stratification (IMI DIRECT) Consortium cohorts comprised of participants with normal or impaired glucose regulation (cohort 1: N ≤ 920) or with recently diagnosed type 2 diabetes (cohort 2: N ≤ 435). METHODS We defined a structural equation model that describes the TC and fitted this within the IMI DIRECT dataset. A second model, twin-cycle plus physical activity (TC-PA), to assess the extent to which the effects of physical activity in glycaemic regulation are mediated by components in the twin-cycle, was also fitted. Beta cell function, insulin sensitivity and glycaemic control were modelled from frequently sampled 75 g OGTTs (fsOGTTs) and mixed-meal tolerance tests (MMTTs) in participants without and with diabetes, respectively. Abdominal fat distribution was assessed using MRI, and physical activity through wrist-worn triaxial accelerometry. Results are presented as standardised beta coefficients, SE and p values, respectively. RESULTS The TC and TC-PA models showed better fit than null models (TC: χ2 = 242, p = 0.004 and χ2 = 63, p = 0.001 in cohort 1 and 2, respectively; TC-PA: χ2 = 180, p = 0.041 and χ2 = 60, p = 0.008 in cohort 1 and 2, respectively). The association of physical activity with glycaemic control was primarily mediated by variables in the liver fat cycle. CONCLUSIONS/INTERPRETATION These analyses partially support the mechanisms proposed in the twin-cycle model and highlight mechanistic pathways through which insulin sensitivity and liver fat mediate the association between physical activity and glycaemic control.
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Affiliation(s)
- Robert W Koivula
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Naeimeh Atabaki-Pasdar
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
| | - Giuseppe N Giordano
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
| | - Tom White
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Jimmy D Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminister, London, UK
| | - Joline Beulens
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, location VU University Medical Center, Amsterdam, the Netherlands
| | - Søren Brage
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Søren Brunak
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Federico De Masi
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ian M Forgie
- Population Health & Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, UK
| | - Gary Frost
- Nutrition and Dietetics Research Group, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Imperial College London, Hammersmith Campus, London, UK
| | - Torben Hansen
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Tue H Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hattersley
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Tarja Kokkola
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Azra Kurbasic
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Andrea Mari
- Institute of Neurosciences, National Research Council, Padova, Italy
| | - Timothy J McDonald
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Femke Rutters
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, location VU University Medical Center, Amsterdam, the Netherlands
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Harriet J A Teare
- HeLEX, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Headington, Oxford, UK
| | - E Louise Thomas
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminister, London, UK
| | - Ana Vinuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
| | - Hartmut Ruetten
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main, Germany
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, UK
| | - Ewan Pearson
- Population Health & Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, UK
| | - Imre Pavo
- Eli Lilly Regional Operations GmbH, Vienna, Austria
| | - Paul W Franks
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Building 91, Level 12, Jan Waldenströms gata 35, SE-205 02, Malmö, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Department of Public Health & Clinical Medicine, Section for Medicine, Umeå University Hospital, Umeå, Sweden
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47
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Drobin K, Marczyk M, Halle M, Danielsson D, Papiez A, Sangsuwan T, Bendes A, Hong MG, Qundos U, Harms-Ringdahl M, Wersäll P, Polanska J, Schwenk JM, Haghdoost S. Molecular Profiling for Predictors of Radiosensitivity in Patients with Breast or Head-and-Neck Cancer. Cancers (Basel) 2020; 12:cancers12030753. [PMID: 32235817 PMCID: PMC7140105 DOI: 10.3390/cancers12030753] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 02/07/2023] Open
Abstract
Nearly half of all cancers are treated with radiotherapy alone or in combination with other treatments, where damage to normal tissues is a limiting factor for the treatment. Radiotherapy-induced adverse health effects, mostly of importance for cancer patients with long-term survival, may appear during or long time after finishing radiotherapy and depend on the patient’s radiosensitivity. Currently, there is no assay available that can reliably predict the individual’s response to radiotherapy. We profiled two study sets from breast (n = 29) and head-and-neck cancer patients (n = 74) that included radiosensitive patients and matched radioresistant controls.. We studied 55 single nucleotide polymorphisms (SNPs) in 33 genes by DNA genotyping and 130 circulating proteins by affinity-based plasma proteomics. In both study sets, we discovered several plasma proteins with the predictive power to find radiosensitive patients (adjusted p < 0.05) and validated the two most predictive proteins (THPO and STIM1) by sandwich immunoassays. By integrating genotypic and proteomic data into an analysis model, it was found that the proteins CHIT1, PDGFB, PNKD, RP2, SERPINC1, SLC4A, STIM1, and THPO, as well as the VEGFA gene variant rs69947, predicted radiosensitivity of our breast cancer (AUC = 0.76) and head-and-neck cancer (AUC = 0.89) patients. In conclusion, circulating proteins and a SNP variant of VEGFA suggest that processes such as vascular growth capacity, immune response, DNA repair and oxidative stress/hypoxia may be involved in an individual’s risk of experiencing radiation-induced toxicity.
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Affiliation(s)
- Kimi Drobin
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Tomtebodavägen 23, 171 65 Stockholm, Sweden; (K.D.); (A.B.); (M.-G.H.); (U.Q.); (J.M.S.)
| | - Michal Marczyk
- Yale Cancer Center, Department of Internal Medicine, Yale University School of Medicine, 06511 New Haven, CT, USA;
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland; (A.P.); (J.P.)
| | - Martin Halle
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176, Stockholm, Sweden;
- Reconstructive Plastic Surgery, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Daniel Danielsson
- Department of Clinical Science, Intervention and Technology, Division of ENT Diseases, Karolinska Institutet, 14186 Stockholm, Sweden;
- Department of Oral and Maxillofacial Surgery, Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Anna Papiez
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland; (A.P.); (J.P.)
| | - Traimate Sangsuwan
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute Stockholm University, 10691 Stockholm, Sweden; (T.S.); (M.H.-R.)
| | - Annika Bendes
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Tomtebodavägen 23, 171 65 Stockholm, Sweden; (K.D.); (A.B.); (M.-G.H.); (U.Q.); (J.M.S.)
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Tomtebodavägen 23, 171 65 Stockholm, Sweden; (K.D.); (A.B.); (M.-G.H.); (U.Q.); (J.M.S.)
| | - Ulrika Qundos
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Tomtebodavägen 23, 171 65 Stockholm, Sweden; (K.D.); (A.B.); (M.-G.H.); (U.Q.); (J.M.S.)
| | - Mats Harms-Ringdahl
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute Stockholm University, 10691 Stockholm, Sweden; (T.S.); (M.H.-R.)
| | - Peter Wersäll
- Department of Radiotherapy, Karolinska University Hospital, 17176 Stockholm, Sweden;
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland; (A.P.); (J.P.)
| | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Tomtebodavägen 23, 171 65 Stockholm, Sweden; (K.D.); (A.B.); (M.-G.H.); (U.Q.); (J.M.S.)
| | - Siamak Haghdoost
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute Stockholm University, 10691 Stockholm, Sweden; (T.S.); (M.H.-R.)
- University of Caen Normandy, Department of medicine, Cimap-Laria, Advanced Resource Center for HADrontherapy in Europe (ARCHADE), 14076 Caen, France
- Correspondence:
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48
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Dezfouli M, Bergström S, Skattum L, Abolhassani H, Neiman M, Torabi-Rahvar M, Franco Jarava C, Martin-Nalda A, Ferrer Balaguer JM, Slade CA, Roos A, Fernandez Pereira LM, López-Trascasa M, Gonzalez-Granado LI, Allende-Martinez LM, Mizuno Y, Yoshida Y, Friman V, Lundgren Å, Aghamohammadi A, Rezaei N, Hernández-Gonzalez M, von Döbeln U, Truedsson L, Hara T, Nonoyama S, Schwenk JM, Nilsson P, Hammarström L. Newborn Screening for Presymptomatic Diagnosis of Complement and Phagocyte Deficiencies. Front Immunol 2020; 11:455. [PMID: 32256498 PMCID: PMC7090021 DOI: 10.3389/fimmu.2020.00455] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022] Open
Abstract
The clinical outcomes of primary immunodeficiencies (PIDs) are greatly improved by accurate diagnosis early in life. However, it is not common to consider PIDs before the manifestation of severe clinical symptoms. Including PIDs in the nation-wide newborn screening programs will potentially improve survival and provide better disease management and preventive care in PID patients. This calls for the detection of disease biomarkers in blood and the use of dried blood spot samples, which is a part of routine newborn screening programs worldwide. Here, we developed a newborn screening method based on multiplex protein profiling for parallel diagnosis of 22 innate immunodeficiencies affecting the complement system and respiratory burst function in phagocytosis. The proposed method uses a small fraction of eluted blood from dried blood spots and is applicable for population-scale performance. The diagnosis method is validated through a retrospective screening of immunodeficient patient samples. This diagnostic approach can pave the way for an earlier, more comprehensive and accurate diagnosis of complement and phagocytic disorders, which ultimately lead to a healthy and active life for the PID patients.
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Affiliation(s)
- Mahya Dezfouli
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Lillemor Skattum
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Region Skåne, Lund, Sweden
| | - Hassan Abolhassani
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maja Neiman
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Monireh Torabi-Rahvar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Clara Franco Jarava
- Immunology Department, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrea Martin-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juana M Ferrer Balaguer
- Immunology, Hospital Universitari Son Espases/Institut d'Investigació Sanitària Illes Balears, Palma, Spain
| | - Charlotte A Slade
- Royal Melbourne Hospital, Melbourne, VIC, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Anja Roos
- Department of Microbiology and Immunology, Sint Antonius Hospital, Nieuwegein, Netherlands
| | | | - Margarita López-Trascasa
- Departamento de Medicina, Hospital La Paz Institute for Health Research (IdiPAZ), Universidad Autónoma de Madrid and Complement Research Group, Madrid, Spain
| | - Luis I Gonzalez-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, University Hospital 12 de Octubre, Research Institute Hospital 12 Octubre (I+12), Madrid, Spain
| | - Luis M Allende-Martinez
- Immunology Department, University Hospital 12 de Octubre, Research Institute Hospital 12 Octubre (I+12), Madrid, Spain
| | - Yumi Mizuno
- Fukuoka Children's Hospital, Kyushu University, Fukuoka, Japan
| | - Yusuke Yoshida
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Vanda Friman
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Åsa Lundgren
- Departments of Infectious Diseases, Central Hospital, Kristianstad, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Manuel Hernández-Gonzalez
- Immunology Department, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ulrika von Döbeln
- Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Lennart Truedsson
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Toshiro Hara
- Fukuoka Children's Hospital, Kyushu University, Fukuoka, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Jochen M Schwenk
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
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49
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res 2019; 18:4098-4107. [PMID: 31430157 PMCID: PMC6898754 DOI: 10.1021/acs.jproteome.9b00434] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Room 425, Building #114, 50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, South Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Siqi Liu
- BGI Group-Shenzhen, Yantian District, Shenzhen 518083, China
| | - Stephen Pennington
- School of Medicine, University College Dublin, Conway Institute Belfield, Dublin 4, Ireland
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive and 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road, North Ryde, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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50
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Uhlén M, Karlsson MJ, Hober A, Svensson AS, Scheffel J, Kotol D, Zhong W, Tebani A, Strandberg L, Edfors F, Sjöstedt E, Mulder J, Mardinoglu A, Berling A, Ekblad S, Dannemeyer M, Kanje S, Rockberg J, Lundqvist M, Malm M, Volk AL, Nilsson P, Månberg A, Dodig-Crnkovic T, Pin E, Zwahlen M, Oksvold P, von Feilitzen K, Häussler RS, Hong MG, Lindskog C, Ponten F, Katona B, Vuu J, Lindström E, Nielsen J, Robinson J, Ayoglu B, Mahdessian D, Sullivan D, Thul P, Danielsson F, Stadler C, Lundberg E, Bergström G, Gummesson A, Voldborg BG, Tegel H, Hober S, Forsström B, Schwenk JM, Fagerberg L, Sivertsson Å. The human secretome. Sci Signal 2019; 12:12/609/eaaz0274. [PMID: 31772123 DOI: 10.1126/scisignal.aaz0274] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.
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Affiliation(s)
- Mathias Uhlén
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. .,Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Max J Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anne-Sophie Svensson
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Julia Scheffel
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - David Kotol
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Abdellah Tebani
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linnéa Strandberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Berling
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Siri Ekblad
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Melanie Dannemeyer
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sara Kanje
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Johan Rockberg
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Magnus Lundqvist
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Magdalena Malm
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna-Luisa Volk
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Månberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnkovic
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Elisa Pin
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Ragna S Häussler
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mun-Gwan Hong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Fredrik Ponten
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Borbala Katona
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Jimmy Vuu
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Emil Lindström
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jonathan Robinson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Burcu Ayoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Diana Mahdessian
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Devin Sullivan
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Thul
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Frida Danielsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Charlotte Stadler
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bjørn G Voldborg
- Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Hanna Tegel
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forsström
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
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