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Koebbe LL, Hess T, Giel AS, Bigge J, Gehlen J, Schueller V, Geppert M, Dumoulin FL, Heller J, Schepke M, Plaßmann D, Vieth M, Venerito M, Schumacher J, Maj C. The genetic regulation of the gastric transcriptome is associated with metabolic and obesity-related traits and diseases. Physiol Genomics 2024; 56:384-396. [PMID: 38406838 DOI: 10.1152/physiolgenomics.00120.2023] [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: 10/13/2023] [Revised: 01/26/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
Tissue-specific gene expression and gene regulation lead to a better understanding of tissue-specific physiology and pathophysiology. We analyzed the transcriptome and genetic regulatory profiles of two distinct gastric sites, corpus and antrum, to identify tissue-specific gene expression and its regulation. Gastric corpus and antrum mucosa biopsies were collected during routine gastroscopies from up to 431 healthy individuals. We obtained genotype and transcriptome data and performed transcriptome profiling and expression quantitative trait locus (eQTL) studies. We further used data from genome-wide association studies (GWAS) of various diseases and traits to partition their heritability and to perform transcriptome-wide association studies (TWAS). The transcriptome data from corpus and antral mucosa highlights the heterogeneity of gene expression in the stomach. We identified enriched pathways revealing distinct and common physiological processes in gastric corpus and antrum. Furthermore, we found an enrichment of the single nucleotide polymorphism (SNP)-based heritability of metabolic, obesity-related, and cardiovascular traits and diseases by considering corpus- and antrum-specifically expressed genes. Particularly, we could prioritize gastric-specific candidate genes for multiple metabolic traits, like NQO1 which is involved in glucose metabolism, MUC1 which contributes to purine and protein metabolism or RAB27B being a regulator of weight and body composition. Our findings show that gastric corpus and antrum vary in their transcriptome and genetic regulatory profiles indicating physiological differences which are mostly related to digestion and epithelial protection. Moreover, our findings demonstrate that the genetic regulation of the gastric transcriptome is linked to biological mechanisms associated with metabolic, obesity-related, and cardiovascular traits and diseases. NEW & NOTEWORTHY We analyzed the transcriptomes and genetic regulatory profiles of gastric corpus and for the first time also of antrum mucosa in 431 healthy individuals. Through tissue-specific gene expression and eQTL analyses, we uncovered unique and common physiological processes across both primary gastric sites. Notably, our findings reveal that stomach-specific eQTLs are enriched in loci associated with metabolic traits and diseases, highlighting the pivotal role of gene expression regulation in gastric physiology and potential pathophysiology.
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Affiliation(s)
- Laura L Koebbe
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Timo Hess
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Ann-Sophie Giel
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Jessica Bigge
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Jan Gehlen
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | | | | | | | - Joerg Heller
- Marienhaus Hospital Ahrweiler, Ahrweiler, Germany
| | - Michael Schepke
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | | | - Michael Vieth
- Institute for Pathology, Klinikum Bayreuth, University of Erlangen-Nuremberg, Bayreuth, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | | | - Carlo Maj
- Center for Human Genetics, University of Marburg, Marburg, Germany
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2
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Mathey CM, Maj C, Eriksson N, Krebs K, Westmeier J, David FS, Koromina M, Scheer AB, Szabo N, Wedi B, Wieczorek D, Amann PM, Löffler H, Koch L, Schöffl C, Dickel H, Ganjuur N, Hornung T, Buhl T, Greve J, Wurpts G, Aygören-Pürsün E, Steffens M, Herms S, Heilmann-Heimbach S, Hoffmann P, Schmidt B, Mavarani L, Andresen T, Sørensen SB, Andersen V, Vogel U, Landén M, Bulik CM, Bygum A, Magnusson PKE, von Buchwald C, Hallberg P, Rye Ostrowski S, Sørensen E, Pedersen OB, Ullum H, Erikstrup C, Bundgaard H, Milani L, Rasmussen ER, Wadelius M, Ghouse J, Sachs B, Nöthen MM, Forstner AJ. Meta-analysis of ACE inhibitor-induced angioedema identifies novel risk locus. J Allergy Clin Immunol 2024; 153:1073-1082. [PMID: 38300190 DOI: 10.1016/j.jaci.2023.11.921] [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: 05/31/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND Angioedema is a rare but potentially life-threatening adverse drug reaction in patients receiving angiotensin-converting enzyme inhibitors (ACEis). Research suggests that susceptibility to ACEi-induced angioedema (ACEi-AE) involves both genetic and nongenetic risk factors. Genome- and exome-wide studies of ACEi-AE have identified the first genetic risk loci. However, understanding of the underlying pathophysiology remains limited. OBJECTIVE We sought to identify further genetic factors of ACEi-AE to eventually gain a deeper understanding of its pathophysiology. METHODS By combining data from 8 cohorts, a genome-wide association study meta-analysis was performed in more than 1000 European patients with ACEi-AE. Secondary bioinformatic analyses were conducted to fine-map associated loci, identify relevant genes and pathways, and assess the genetic overlap between ACEi-AE and other traits. Finally, an exploratory cross-ancestry analysis was performed to assess shared genetic factors in European and African-American patients with ACEi-AE. RESULTS Three genome-wide significant risk loci were identified. One of these, located on chromosome 20q11.22, has not been implicated previously in ACEi-AE. Integrative secondary analyses highlighted previously reported genes (BDKRB2 [bradykinin receptor B2] and F5 [coagulation factor 5]) as well as biologically plausible novel candidate genes (PROCR [protein C receptor] and EDEM2 [endoplasmic reticulum degradation enhancing alpha-mannosidase like protein 2]). Lead variants at the risk loci were found with similar effect sizes and directions in an African-American cohort. CONCLUSIONS The present results contributed to a deeper understanding of the pathophysiology of ACEi-AE by (1) providing further evidence for the involvement of bradykinin signaling and coagulation pathways and (2) suggesting, for the first time, the involvement of the fibrinolysis pathway in this adverse drug reaction. An exploratory cross-ancestry comparison implicated the relevance of the associated risk loci across diverse ancestries.
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Affiliation(s)
- Carina M Mathey
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany; Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Niclas Eriksson
- Uppsala Clinical Research Center, Uppsala, Sweden; Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Julia Westmeier
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Friederike S David
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | | | - Annika B Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Nora Szabo
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Bettina Wedi
- Department of Dermatology and Allergy, Comprehensive Allergy Center, Hannover Medical School, Hannover, Germany
| | - Dorothea Wieczorek
- Department of Dermatology and Allergy, Comprehensive Allergy Center, Hannover Medical School, Hannover, Germany
| | - Philipp M Amann
- Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University, Krems, Austria
| | - Harald Löffler
- Department of Dermatology, SLK Hospital Heilbronn, Heilbronn, Germany
| | - Lukas Koch
- Department of Dermatology and Venereology, Medical University Graz, Graz, Austria
| | - Clemens Schöffl
- Department of Dermatology and Venereology, Medical University Graz, Graz, Austria
| | - Heinrich Dickel
- Department of Dermatology, Venereology and Allergology, St Josef Hospital, University Medical Center, Ruhr University Bochum, Bochum, Germany
| | - Nomun Ganjuur
- Department of Dermatology, Venereology and Allergology, St Josef Hospital, University Medical Center, Ruhr University Bochum, Bochum, Germany; Institute of Health Care Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Hornung
- Department of Dermatology and Allergy, University Hospital of Bonn, Bonn, Germany
| | - Timo Buhl
- Department of Dermatology, Venereology and Allergology, University Medical Center Göttingen, Göttingen, Germany
| | - Jens Greve
- Department of Otorhinolaryngology-Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Gerda Wurpts
- Department of Dermatology and Allergy, Aachen Comprehensive Allergy Center, University Hospital RWTH Aachen, Aachen, Germany
| | - Emel Aygören-Pürsün
- Department for Children and Adolescents, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Börge Schmidt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Laven Mavarani
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Trine Andresen
- Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Signe Bek Sørensen
- Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Vibeke Andersen
- Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark; Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark; OPEN, University of Southern Denmark, Odense, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Mikael Landén
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Cynthia M Bulik
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anette Bygum
- Department of Clinical Institute, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christian von Buchwald
- Department of Otorhinolaryngology-Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Pär Hallberg
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen Hospital Biobank Unit, Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen Hospital Biobank Unit, Rigshospitalet, Copenhagen, Denmark
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Christian Erikstrup
- Departments of Clinical Immunology, Aarhus University, Aarhus, Denmark; Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Eva Rye Rasmussen
- Department of Otorhinolaryngology-Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Departments of Private Practice Ølsemaglevej, Køge, Denmark
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Ghouse
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark; Laboratory for Molecular Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bernhardt Sachs
- Department of Dermatology and Allergy, Aachen Comprehensive Allergy Center, University Hospital RWTH Aachen, Aachen, Germany; Research Division, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany; Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany.
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Went M, Sud A, Mills C, Hyde A, Culliford R, Law P, Vijayakrishnan J, Gockel I, Maj C, Schumacher J, Palles C, Kaiser M, Houlston R. Phenome-wide Mendelian randomisation analysis of 378,142 cases reveals risk factors for eight common cancers. Nat Commun 2024; 15:2637. [PMID: 38527997 PMCID: PMC10963765 DOI: 10.1038/s41467-024-46927-z] [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: 03/07/2023] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
For many cancers there are only a few well-established risk factors. Here, we use summary data from genome-wide association studies (GWAS) in a Mendelian randomisation (MR) phenome-wide association study (PheWAS) to identify potentially causal relationships for over 3,000 traits. Our outcome datasets comprise 378,142 cases across breast, prostate, colorectal, lung, endometrial, oesophageal, renal, and ovarian cancers, as well as 485,715 controls. We complement this analysis by systematically mining the literature space for supporting evidence. In addition to providing supporting evidence for well-established risk factors (smoking, alcohol, obesity, lack of physical activity), we also find sex steroid hormones, plasma lipids, and telomere length as determinants of cancer risk. A number of the molecular factors we identify may prove to be potential biomarkers. Our analysis, which highlights aetiological similarities and differences in common cancers, should aid public health prevention strategies to reduce cancer burden. We provide a R/Shiny app to visualise findings.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Abi Hyde
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | | | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Carlo Maj
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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Stiehler S, Sembill S, Schleicher O, Marx M, Rauh M, Krumbholz M, Karow A, Suttorp M, Woelfle J, Maj C, Metzler M. Imatinib treatment and longitudinal growth in pediatric patients with chronic myeloid leukemia: Influence of demographic, pharmacological, and genetic factors in the German CML-PAED cohort. Haematologica 2024. [PMID: 38497150 DOI: 10.3324/haematol.2023.284668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Indexed: 03/19/2024] Open
Abstract
In children and adolescents, impaired growth due to tyrosine kinase inhibitor therapy remains an insufficiently studied adverse effect. This study examines demographic, pharmacological, and genetic factors associated with impaired longitudinal growth in a uniform pediatric cohort treated with imatinib. We analyzed 94 pediatric patients with chronic myeloid leukemia (CML) diagnosed in the chronic phase and treated with imatinib for >12 months who participated in the Germany-wide CML-PAEDII study between February 2006 and February 2021. During imatinib treatment, significant height reduction occurred, with medians of -0.35 standard deviation score (SDS) at 12 months and -0.76 SDS at 24 months. Cumulative height SDS change (Δheight SDS) showed a more pronounced effect in prepubertal patients during the first year but were similar between prepubertal and pubertal subgroups by the second year (-0.55 vs. -0.50). From months 12 to 18 on imatinib, only 18% patients achieved individually longitudinal growth adequate to the growth standard (Δheight SDS≥0). When patients were divided into two subgroups based on median Δheight SDS (classifier Δheight SDS > or ≤-0.37) after one year on imatinib therapy, cohort 1 (Δheight SDS extending -0.37) showed younger age at diagnosis, a higher proportion of prepubertal children, but also better treatment response and higher imatinib serum levels. Exploring the association of growth parameters with pharmacokinetically relevant single nucleotide polymorphisms, known for affecting imatinib response, showed no correlation. This retrospective study provides new insights into imatinib-related growth impairment. We emphasize the importance of optimizing treatment strategies for pediatric patients to realize their maximum growth potential.
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Affiliation(s)
- Sophie Stiehler
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg
| | - Stephanie Sembill
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen.
| | - Oliver Schleicher
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany; Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg
| | - Michaela Marx
- Pediatric Endocrinology, Department of Pediatrics and Adolescent Medicine, University Children's Hospital, Friedrich-Alexander-Universität, Erlangen-Nürnberg
| | - Manfred Rauh
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg
| | - Manuela Krumbholz
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen
| | - Axel Karow
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen
| | - Meinolf Suttorp
- Pediatric Hemato-Oncology, Medical Faculty, Technical University Dresden, Dresden
| | - Joachim Woelfle
- Pediatric Endocrinology, Department of Pediatrics and Adolescent Medicine, University Children's Hospital, Friedrich-Alexander-Universität, Erlangen-Nürnberg
| | - Carlo Maj
- Centre for Human Genetics, University of Marburg, Marburg
| | - Markus Metzler
- Pediatric Oncology and Hematology, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen
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5
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Maj C, Eberts A, Schumacher J, Dasmeh P. Single-cell analysis reveals the spatial-temporal expression of genes associated with esophageal malformations. Sci Rep 2024; 14:3752. [PMID: 38355689 PMCID: PMC10866870 DOI: 10.1038/s41598-024-53098-w] [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: 11/24/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding the molecular mechanisms of congenital diseases is challenging due to their occurrence within specific developmental stages. Esophageal malformations are examples of such conditions, characterized by abnormalities in the development of esophagus during embryogenesis. These developmental malformations encompass a range of anomalies, including esophageal atresia, and tracheoesophageal fistula. Here, we investigated the preferential expression of 29 genes that are implicated in such malformations and their immediate interactome (a total of 67 genes). We conducted our analyses across several single-cell atlases of embryonic development, encompassing approximately 150,000 cells from the mouse foregut, 180,000 cells from human embryos, and 500,000 cells from 24 human organs. Our study, spanning diverse mesodermal and endodermal cell populations and early developmental stages, shows that the genes associated with esophageal malformations show their highest cell-type specific expression in lateral plate mesoderm cells and at the developmental stage of E8.75-E9.0 days. In human embryos, these genes show a significant cell-type specific expression among subpopulations of epithelial cells, fibroblasts and progenitor cells including basal cells. Notably, members of the forkhead-box family of transcription factors, namely FOXF1, FOXC1, and FOXD1, as well as the SRY-box transcription factor, SOX2, demonstrate the most significant preferential expression in both mouse and human embryos. Overall, our findings provide insights into the temporal and cellular contexts contributing to esophageal malformations.
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Affiliation(s)
- Carlo Maj
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany.
| | - Antonia Eberts
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany
| | - Johannes Schumacher
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany.
| | - Pouria Dasmeh
- Center for Human Genetics, Marburg University and Marburg University Hospital, Marburg, Germany.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA.
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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Kumar S, Borisov O, Maj C, Ralser DJ, Humbatova A, Hanneken S, Schmieder A, Groß J, Maintz L, Heineke A, Knuever J, Fagerberg C, Parmentier L, Anemüller W, Oji V, Tantcheva-Poór I, Fölster-Holst R, Wenzel J, Krawitz PM, Frank J, Betz RC. Founder Variants in KRT5 and POGLUT1 Are Implicated in Dowling-Degos Disease. J Invest Dermatol 2024; 144:181-184. [PMID: 37468035 DOI: 10.1016/j.jid.2023.04.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Damian J Ralser
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Aytaj Humbatova
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | | | - Astrid Schmieder
- Department of Dermatology, Venereology and Allergology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Janina Groß
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Laura Maintz
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany; Christine Kuehne - Center for Allergy Research and Education Davos (CK-CARE), Davos, Switzerland
| | - Andre Heineke
- Dermatologist practice, Dr. Karches/Dr. Thielert, Hannover, Germany
| | - Jana Knuever
- Department of Dermatology, University of Cologne, Cologne, Germany
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Waltraud Anemüller
- Department of Dermatology, Allergology and Venereology, University of Luebeck, Luebeck, Germany
| | - Vinzenz Oji
- Department of Dermatology, University of Muenster, Muenster, Germany
| | | | - Regina Fölster-Holst
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Joerg Wenzel
- Department of Dermatology, Venereology and Allergology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Jorge Frank
- Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Goettingen, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany.
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Dueñas N, Klinkhammer H, Bonifaci N, Spier I, Mayr A, Hassanin E, Diez-Villanueva A, Moreno V, Pineda M, Maj C, Capellà G, Aretz S, Brunet J. Ability of a polygenic risk score to refine colorectal cancer risk in Lynch syndrome. J Med Genet 2023; 60:1044-1051. [PMID: 37321833 DOI: 10.1136/jmg-2023-109344] [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: 04/21/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Polygenic risk scores (PRSs) have been used to stratify colorectal cancer (CRC) risk in the general population, whereas its role in Lynch syndrome (LS), the most common type of hereditary CRC, is still conflicting. We aimed to assess the ability of PRS to refine CRC risk prediction in European-descendant individuals with LS. METHODS 1465 individuals with LS (557 MLH1, 517 MSH2/EPCAM, 299 MSH6 and 92 PMS2) and 5656 CRC-free population-based controls from two independent cohorts were included. A 91-SNP PRS was applied. A Cox proportional hazard regression model with 'family' as a random effect and a logistic regression analysis, followed by a meta-analysis combining both cohorts were conducted. RESULTS Overall, we did not observe a statistically significant association between PRS and CRC risk in the entire cohort. Nevertheless, PRS was significantly associated with a slightly increased risk of CRC or advanced adenoma (AA), in those with CRC diagnosed <50 years and in individuals with multiple CRCs or AAs diagnosed <60 years. CONCLUSION The PRS may slightly influence CRC risk in individuals with LS in particular in more extreme phenotypes such as early-onset disease. However, the study design and recruitment strategy strongly influence the results of PRS studies. A separate analysis by genes and its combination with other genetic and non-genetic risk factors will help refine its role as a risk modifier in LS.
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Affiliation(s)
- Nuria Dueñas
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, Netherlands
| | - Hannah Klinkhammer
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Nuria Bonifaci
- Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Isabel Spier
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, Netherlands
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- National Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Emadeldin Hassanin
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Diez-Villanueva
- Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology - ICO, L'Hospitalet de Llobregat, Spain
- Colorectal Cancer Group (ONCOBELL), Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Instituto Salud Carlos III, Madrid, Spain
| | - Victor Moreno
- Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology - ICO, L'Hospitalet de Llobregat, Spain
- Colorectal Cancer Group (ONCOBELL), Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Instituto Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, Netherlands
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Gabriel Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, Netherlands
| | - Stefan Aretz
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, Netherlands
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- National Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS), Nijmegen, Netherlands
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Girona, Spain
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Henne SK, Aldisi R, Sivalingam S, Hochfeld LM, Borisov O, Krawitz PM, Maj C, Nöthen MM, Heilmann-Heimbach S. Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss. Nat Commun 2023; 14:5492. [PMID: 37737258 PMCID: PMC10517150 DOI: 10.1038/s41467-023-41186-w] [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: 09/21/2022] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Male-pattern hair loss (MPHL) is common and highly heritable. While genome-wide association studies (GWAS) have generated insights into the contribution of common variants to MPHL etiology, the relevance of rare variants remains unclear. To determine the contribution of rare variants to MPHL etiology, we perform gene-based and single-variant analyses in exome-sequencing data from 72,469 male UK Biobank participants. While our population-level risk prediction suggests that rare variants make only a minor contribution to general MPHL risk, our rare variant collapsing tests identified a total of five significant gene associations. These findings provide additional evidence for previously implicated genes (EDA2R, WNT10A) and highlight novel risk genes at and beyond GWAS loci (HEPH, CEPT1, EIF3F). Furthermore, MPHL-associated genes are enriched for genes considered causal for monogenic trichoses. Together, our findings broaden the MPHL-associated allelic spectrum and provide insights into MPHL pathobiology and a shared basis with monogenic hair loss disorders.
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Affiliation(s)
- Sabrina Katrin Henne
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Rana Aldisi
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Department of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Lara Maleen Hochfeld
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter Michael Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Markus Maria Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
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9
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Aldisi R, Hassanin E, Sivalingam S, Buness A, Klinkhammer H, Mayr A, Fröhlich H, Krawitz P, Maj C. Gene-based burden scores identify rare variant associations for 28 blood biomarkers. BMC Genom Data 2023; 24:50. [PMID: 37667186 PMCID: PMC10476296 DOI: 10.1186/s12863-023-01155-0] [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: 11/14/2022] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND A relevant part of the genetic architecture of complex traits is still unknown; despite the discovery of many disease-associated common variants. Polygenic risk score (PRS) models are based on the evaluation of the additive effects attributable to common variants and have been successfully implemented to assess the genetic susceptibility for many phenotypes. In contrast, burden tests are often used to identify an enrichment of rare deleterious variants in specific genes. Both kinds of genetic contributions are typically analyzed independently. Many studies suggest that complex phenotypes are influenced by both low effect common variants and high effect rare deleterious variants. The aim of this paper is to integrate the effect of both common and rare functional variants for a more comprehensive genetic risk modeling. METHODS We developed a framework combining gene-based scores based on the enrichment of rare functionally relevant variants with genome-wide PRS based on common variants for association analysis and prediction models. We applied our framework on UK Biobank dataset with genotyping and exome data and considered 28 blood biomarkers levels as target phenotypes. For each biomarker, an association analysis was performed on full cohort using gene-based scores (GBS). The cohort was then split into 3 subsets for PRS construction and feature selection, predictive model training, and independent evaluation, respectively. Prediction models were generated including either PRS, GBS or both (combined). RESULTS Association analyses of the cohort were able to detect significant genes that were previously known to be associated with different biomarkers. Interestingly, the analyses also revealed heterogeneous effect sizes and directionality highlighting the complexity of the blood biomarkers regulation. However, the combined models for many biomarkers show little or no improvement in prediction accuracy compared to the PRS models. CONCLUSION This study shows that rare variants play an important role in the genetic architecture of complex multifactorial traits such as blood biomarkers. However, while rare deleterious variants play a strong role at an individual level, our results indicate that classical common variant based PRS might be more informative to predict the genetic susceptibility at the population level.
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Affiliation(s)
- Rana Aldisi
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany.
| | - Emadeldin Hassanin
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Sugirthan Sivalingam
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Core Unit for Bioinformatics Analysis, University Hospital Bonn, Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Core Unit for Bioinformatics Analysis, University Hospital Bonn, Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT (b-it), University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute of Genomic Statistic and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
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10
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Hess T, Maj C, Gehlen J, Borisov O, Haas SL, Gockel I, Vieth M, Piessen G, Alakus H, Vashist Y, Pereira C, Knapp M, Schüller V, Quaas A, Grabsch HI, Trautmann J, Malecka-Wojciesko E, Mokrowiecka A, Speller J, Mayr A, Schröder J, Hillmer AM, Heider D, Lordick F, Pérez-Aísa Á, Campo R, Espinel J, Geijo F, Thomson C, Bujanda L, Sopeña F, Lanas Á, Pellisé M, Pauligk C, Goetze TO, Zelck C, Reingruber J, Hassanin E, Elbe P, Alsabeah S, Lindblad M, Nilsson M, Kreuser N, Thieme R, Tavano F, Pastorino R, Arzani D, Persiani R, Jung JO, Nienhüser H, Ott K, Schumann RR, Kumpf O, Burock S, Arndt V, Jakubowska A, Ławniczak M, Moreno V, Martín V, Kogevinas M, Pollán M, Dąbrowska J, Salas A, Cussenot O, Boland-Auge A, Daian D, Deleuze JF, Salvi E, Teder-Laving M, Tomasello G, Ratti M, Senti C, De Re V, Steffan A, Hölscher AH, Messerle K, Bruns CJ, Sīviņš A, Bogdanova I, Skieceviciene J, Arstikyte J, Moehler M, Lang H, Grimminger PP, Kruschewski M, Vassos N, Schildberg C, Lingohr P, Ridwelski K, Lippert H, Fricker N, Krawitz P, Hoffmann P, Nöthen MM, Veits L, Izbicki JR, Mostowska A, Martinón-Torres F, Cusi D, Adolfsson R, Cancel-Tassin G, Höblinger A, Rodermann E, Ludwig M, Keller G, Metspalu A, Brenner H, Heller J, Neef M, Schepke M, Dumoulin FL, Hamann L, Cannizzaro R, Ghidini M, Plaßmann D, Geppert M, Malfertheiner P, Glehen O, Skoczylas T, Majewski M, Lubiński J, Palmieri O, Boccia S, Latiano A, Aragones N, Schmidt T, Dinis-Ribeiro M, Medeiros R, Al-Batran SE, Leja M, Kupcinskas J, García-González MA, Venerito M, Schumacher J. Corrigendum to "Dissecting the genetic heterogeneity of gastric cancer". EBioMedicine 2023; 94:104709. [PMID: 37480624 PMCID: PMC10393529 DOI: 10.1016/j.ebiom.2023.104709] [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] [Indexed: 07/24/2023] Open
Affiliation(s)
- Timo Hess
- Institute of Human Genetics, University of Marburg, Marburg, Germany; Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute of Human Genetics, University of Marburg, Marburg, Germany; Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Stephan L Haas
- Department of Upper GI Diseases, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Karolinska Institutet, Stockholm, Sweden
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuernberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Guillaume Piessen
- Department of Digestive and Oncological Surgery, Claude Huriez Hospital, CHU Lille, Lille, France
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany; Centre for Surgical Oncology, Medias Klinikum Burghausen, Burghausen, Germany
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), 4200-072 Porto, Portugal; Porto Comprehensive Cancer Center & RISE @ CI-IPO, University of Porto, 4200-450, Porto, Portugal
| | - Michael Knapp
- Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), Medical Faculty, University of Bonn, Bonn, Germany
| | - Vitalia Schüller
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Alexander Quaas
- Institute of Pathology, University Hospital Cologne, Medical Faculty, University of Cologne, Germany
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jessica Trautmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Anna Mokrowiecka
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Jan Speller
- Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), Medical Faculty, University of Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), Medical Faculty, University of Bonn, Bonn, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Axel M Hillmer
- Institute of Pathology, University Hospital Cologne, Medical Faculty, University of Cologne, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Florian Lordick
- University Cancer Center Leipzig, Leipzig University Medical Center, Leipzig, Germany
| | | | - Rafael Campo
- Department of Gastroenterology, Hospital Parc Tauli, Sabadell, Spain
| | - Jesús Espinel
- Department of Gastroenterology, Complejo Hospitalario, León, Spain
| | - Fernando Geijo
- Department of Gastroenterology, Hospital Clínico Universitario, Salamanca, Spain
| | - Concha Thomson
- Department of Gastroenterology, Hospital Obispo Polanco, Teruel, Spain
| | - Luis Bujanda
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Federico Sopeña
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | - Ángel Lanas
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - María Pellisé
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Claudia Pauligk
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Thorsten Oliver Goetze
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Carolin Zelck
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Julian Reingruber
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Emadeldin Hassanin
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Peter Elbe
- Department of Upper GI Diseases, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Karolinska Institutet, Stockholm, Sweden
| | - Sandra Alsabeah
- Department of Upper GI Diseases, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Karolinska Institutet, Stockholm, Sweden
| | - Mats Lindblad
- Department of Upper GI Diseases, Karolinska University Hospital and Division of Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nilsson
- Department of Upper GI Diseases, Karolinska University Hospital and Division of Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Kreuser
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Francesca Tavano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Roberta Pastorino
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Dario Arzani
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Roberto Persiani
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Roma, Italy; Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Jin-On Jung
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany; Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Henrik Nienhüser
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Katja Ott
- Department of Surgery, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Ralf R Schumann
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oliver Kumpf
- Department of Anaesthesiology and operative Intensive care Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Poland
| | - Małgorzta Ławniczak
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Poland
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Hospital Duran I Reynals, Barcelona, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Vicente Martín
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; The Research Group in Gene - Environment and Health Interactions (GIIGAS)/Institute of Biomedicine (IBIOMED), Universidad de Leon, Leon, Spain; Department of Biomedical Sciences, Faculty of Health Sciences, Area of Preventive Medicine and Public Health, Universidad de Leon, Leon, Spain
| | - Manolis Kogevinas
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Campus Del Mar, Barcelona, Spain; IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Spain
| | - Marina Pollán
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; Cancer and Environmental Epidemiology Unit, Department of Epidemiology of Chronic Diseases, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poland
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Olivier Cussenot
- CeRePP, Paris, France; GRC n°5 Predictive Onco-Urology, Tenon Hospital, Sorbonne University, Paris, France
| | - Anne Boland-Auge
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Delphine Daian
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Jean-Francois Deleuze
- University Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Erika Salvi
- Neuroalgology Unit Fondazione IRCCS, Instituto Neurologico 'Carlo Besta' Milan, Milan, Italy
| | - Maris Teder-Laving
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Gianluca Tomasello
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Chiara Senti
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Department of Medical Oncology, Institut Jules Bordet - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Valli De Re
- Unit of Immunopathologia e Biomarcatori Oncologici/Bio-proteomics facility, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Agostino Steffan
- Unit of Immunopathologia e Biomarcatori Oncologici, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Arnulf H Hölscher
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | - Katharina Messerle
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | | | - Armands Sīviņš
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia
| | - Inga Bogdanova
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia
| | - Jurgita Skieceviciene
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Justina Arstikyte
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Markus Moehler
- Department of Medicine I, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Peter P Grimminger
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Martin Kruschewski
- Department of General and Visceral Surgery, Klinikum Frankfurt (Oder), Germany
| | - Nikolaos Vassos
- Division of Surgical Oncology and Thoracic Surgery, Department of Surgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Claus Schildberg
- Department of General Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
| | - Philipp Lingohr
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany
| | - Karsten Ridwelski
- Department of General and Visceral Surgery, Klinikum Magdeburg GmbH, Magdeburg, Germany
| | - Hans Lippert
- Institute of Quality Assurance in Operative Medicine, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Lothar Veits
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuernberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poland
| | - Federico Martinón-Torres
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain; Genetics, Vaccines, Infectious Diseases and Pediatrics research group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniele Cusi
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy; Bio4Dreams-Business, Nursery for Life Sciences, Milan, Italy
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Geraldine Cancel-Tassin
- CeRePP, Paris, France; GRC n°5 Predictive Onco-Urology, Tenon Hospital, Sorbonne University, Paris, France
| | - Aksana Höblinger
- Department of Internal Medicine I, Community Hospital Mittelrhein, Koblenz, Germany
| | - Ernst Rodermann
- Association of Medical Practices in Hematology and Internal Oncology, Troisdorf, Germany
| | - Monika Ludwig
- Association for Oncological Studies (Gefos), Dortmund, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joerg Heller
- Department of Gastroenterology, Marienhaus Hospital Ahrweiler, Ahrweiler, Germany
| | - Markus Neef
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | - Michael Schepke
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | | | - Lutz Hamann
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato Cannizzaro
- Unit of Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Michele Ghidini
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany; Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Olivier Glehen
- Department of Surgical Oncology, Centre Hospitalier Lyon-sud, Lyon, France
| | - Tomasz Skoczylas
- 2nd Department of General Surgery, Medical University of Lublin, Lublin, Poland
| | - Marek Majewski
- 2nd Department of General Surgery, Medical University of Lublin, Lublin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Poland
| | - Orazio Palmieri
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefania Boccia
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Anna Latiano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Nuria Aragones
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; Epidemiology Section, Public Health Division, Department of Health of Madrid, Madrid, Spain
| | - Thomas Schmidt
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany; Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Mário Dinis-Ribeiro
- Porto Comprehensive Cancer Center & RISE @ CI-IPO, University of Porto, 4200-450, Porto, Portugal; Gastroenterology Department, Portuguese Institute of Oncology of Porto, 4200-072 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), 4200-072 Porto, Portugal; Research Department of the Portuguese League Against Cancer-North (LPCC-NRNorte), 4200-177 Porto, Portugal
| | - Salah-Eddin Al-Batran
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia; Digestive Diseases Centre GASTRO, Riga, Latvia
| | - Juozas Kupcinskas
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - María A García-González
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
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Hassanin E, Maj C, Klinkhammer H, Krawitz P, May P, Bobbili DR. Assessing the performance of European-derived cardiometabolic polygenic risk scores in South-Asians and their interplay with family history. BMC Med Genomics 2023; 16:164. [PMID: 37438803 PMCID: PMC10339617 DOI: 10.1186/s12920-023-01598-5] [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: 03/29/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND & AIMS We aimed to assess the performance of European-derived polygenic risk scores (PRSs) for common metabolic diseases such as coronary artery disease (CAD), obesity, and type 2 diabetes (T2D) in the South Asian (SAS) individuals in the UK Biobank. Additionally, we studied the interaction between PRS and family history (FH) in the same population. METHODS To calculate the PRS, we used a previously published model derived from the EUR population and applied it to the individuals of SAS ancestry from the UKB study. Each PRS was adjusted according to an individual's genotype location in the principal components (PC) space to derive an ancestry adjusted PRS (aPRS). We calculated the percentiles based on aPRS and stratified individuals into three aPRS categories: low, intermediate, and high. Considering the intermediate-aPRS percentile as a reference, we compared the low and high aPRS categories and generated the odds ratio (OR) estimates. Further, we measured the combined role of aPRS and first-degree family history (FH) in the SAS population. RESULTS The risk of developing severe obesity for SAS individuals was almost twofold higher for individuals with high aPRS than for those with intermediate aPRS, with an OR of 1.95 (95% CI = 1.71-2.23, P < 0.01). At the same time, the risk of severe obesity was lower in the low-aPRS group (OR = 0.60, CI = 0.53-0.67, P < 0.01). Results in the same direction were found in the EUR data, where the low-PRS group had an OR of 0.53 (95% CI = 0.51-0.56, P < 0.01) and the high-PRS group had an OR of 2.06 (95% CI = 2.00-2.12, P < 0.01). We observed similar results for CAD and T2D. Further, we show that SAS individuals with a familial history of CAD and T2D with high-aPRS are associated with a higher risk of these diseases, implying a greater genetic predisposition. CONCLUSION Our findings suggest that CAD, obesity, and T2D GWAS summary statistics generated predominantly from the EUR population can be potentially used to derive aPRS in SAS individuals for risk stratification. With future GWAS recruiting more SAS participants and tailoring the PRSs towards SAS ancestry, the predictive power of PRS is likely to improve further.
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Affiliation(s)
- Emadeldin Hassanin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux, L-4367, Luxembourg
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Carlo Maj
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Medical Faculty, Institute for Medical Biometry, Informatics and Epidemiology, University Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux, L-4367, Luxembourg
| | - Dheeraj Reddy Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux, L-4367, Luxembourg.
- Wellytics Technologies Pvt Ltd, Hyderabad, India.
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12
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Klau JH, Maj C, Klinkhammer H, Krawitz PM, Mayr A, Hillmer AM, Schumacher J, Heider D. AI-based multi-PRS models outperform classical single-PRS models. Front Genet 2023; 14:1217860. [PMID: 37441549 PMCID: PMC10335560 DOI: 10.3389/fgene.2023.1217860] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Polygenic risk scores (PRS) calculate the risk for a specific disease based on the weighted sum of associated alleles from different genetic loci in the germline estimated by regression models. Recent advances in genetics made it possible to create polygenic predictors of complex human traits, including risks for many important complex diseases, such as cancer, diabetes, or cardiovascular diseases, typically influenced by many genetic variants, each of which has a negligible effect on overall risk. In the current study, we analyzed whether adding additional PRS from other diseases to the prediction models and replacing the regressions with machine learning models can improve overall predictive performance. Results showed that multi-PRS models outperform single-PRS models significantly on different diseases. Moreover, replacing regression models with machine learning models, i.e., deep learning, can also improve overall accuracy.
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Affiliation(s)
- Jan Henric Klau
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Carlo Maj
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Peter M. Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Axel M. Hillmer
- Institute of Pathology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | | | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
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13
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Hess T, Maj C, Gehlen J, Borisov O, Haas SL, Gockel I, Vieth M, Piessen G, Alakus H, Vashist Y, Pereira C, Knapp M, Schüller V, Quaas A, Grabsch HI, Trautmann J, Malecka-Wojciesko E, Mokrowiecka A, Speller J, Mayr A, Schröder J, Hillmer AM, Heider D, Lordick F, Pérez-Aísa Á, Campo R, Espinel J, Geijo F, Thomson C, Bujanda L, Sopeña F, Lanas Á, Pellisé M, Pauligk C, Goetze TO, Zelck C, Reingruber J, Hassanin E, Elbe P, Alsabeah S, Lindblad M, Nilsson M, Kreuser N, Thieme R, Tavano F, Pastorino R, Arzani D, Persiani R, Jung JO, Nienhüser H, Ott K, Schumann RR, Kumpf O, Burock S, Arndt V, Jakubowska A, Ławniczak M, Moreno V, Martín V, Kogevinas M, Pollán M, Dąbrowska J, Salas A, Cussenot O, Boland-Auge A, Daian D, Deleuze JF, Salvi E, Teder-Laving M, Tomasello G, Ratti M, Senti C, De Re V, Steffan A, Hölscher AH, Messerle K, Bruns CJ, Sīviņš A, Bogdanova I, Skieceviciene J, Arstikyte J, Moehler M, Lang H, Grimminger PP, Kruschewski M, Vassos N, Schildberg C, Lingohr P, Ridwelski K, Lippert H, Fricker N, Krawitz P, Hoffmann P, Nöthen MM, Veits L, Izbicki JR, Mostowska A, Martinón-Torres F, Cusi D, Adolfsson R, Cancel-Tassin G, Höblinger A, Rodermann E, Ludwig M, Keller G, Metspalu A, Brenner H, Heller J, Neef M, Schepke M, Dumoulin FL, Hamann L, Cannizzaro R, Ghidini M, Plaßmann D, Geppert M, Malfertheiner P, Gehlen O, Skoczylas T, Majewski M, Lubiński J, Palmieri O, Boccia S, Latiano A, Aragones N, Schmidt T, Dinis-Ribeiro M, Medeiros R, Al-Batran SE, Leja M, Kupcinskas J, García-González MA, Venerito M, Schumacher J. Dissecting the genetic heterogeneity of gastric cancer. EBioMedicine 2023; 92:104616. [PMID: 37209533 DOI: 10.1016/j.ebiom.2023.104616] [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: 12/21/2022] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture. METHODS We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO. FINDINGS Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level. INTERPRETATION Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO. FUNDING German Research Foundation (DFG).
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Affiliation(s)
- Timo Hess
- Institute of Human Genetics, University of Marburg, Marburg, Germany; Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute of Human Genetics, University of Marburg, Marburg, Germany; Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Oleg Borisov
- Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Stephan L Haas
- Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Stockholm, Sweden
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuernberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Guillaume Piessen
- Department of Digestive and Oncological Surgery, Claude Huriez Hospital, CHU Lille, Lille, France
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany; Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Porto 4200-072, Portugal; Porto Comprehensive Cancer Center & RISE @ CI-IPO, University of Porto, Porto 4200-450, Portugal
| | - Michael Knapp
- Medical Faculty, Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), University of Bonn, Bonn, Germany
| | - Vitalia Schüller
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Alexander Quaas
- Medical Faculty, Institute of Pathology, University Hospital Cologne, University of Cologne, Germany
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jessica Trautmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Anna Mokrowiecka
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Jan Speller
- Medical Faculty, Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), University of Bonn, Bonn, Germany
| | - Andreas Mayr
- Medical Faculty, Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), University of Bonn, Bonn, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Axel M Hillmer
- Medical Faculty, Institute of Pathology, University Hospital Cologne, University of Cologne, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Florian Lordick
- University Cancer Center Leipzig, Leipzig University Medical Center, Leipzig, Germany
| | | | - Rafael Campo
- Department of Gastroenterology, Hospital Parc Tauli, Sabadell, Spain
| | - Jesús Espinel
- Department of Gastroenterology, Complejo Hospitalario, León, Spain
| | - Fernando Geijo
- Department of Gastroenterology, Hospital Clínico Universitario, Salamanca, Spain
| | - Concha Thomson
- Department of Gastroenterology, Hospital Obispo Polanco, Teruel, Spain
| | - Luis Bujanda
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Federico Sopeña
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | - Ángel Lanas
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - María Pellisé
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Claudia Pauligk
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Thorsten Oliver Goetze
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Carolin Zelck
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Julian Reingruber
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Emadeldin Hassanin
- Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter Elbe
- Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Stockholm, Sweden
| | - Sandra Alsabeah
- Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Stockholm, Sweden
| | - Mats Lindblad
- Division of Surgery, Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nilsson
- Division of Surgery, Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Kreuser
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Francesca Tavano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Roberta Pastorino
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Dario Arzani
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Roberto Persiani
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Roma, Italy; Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Jin-On Jung
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany; Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Henrik Nienhüser
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Katja Ott
- Department of Surgery, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Ralf R Schumann
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oliver Kumpf
- Department of Anaesthesiology and Operative Intensive Care Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Poland
| | - Małgorzta Ławniczak
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Poland
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Hospital Duran I Reynals, Barcelona, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; Faculty of Medicine, Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - Vicente Martín
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; The Research Group in Gene - Environment and Health Interactions (GIIGAS)/Institute of Biomedicine (IBIOMED), Universidad de Leon, Leon, Spain; Faculty of Health Sciences, Department of Biomedical Sciences, Area of Preventive Medicine and Public Health, Universidad de Leon, Leon, Spain
| | - Manolis Kogevinas
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Campus Del Mar, Barcelona, Spain; IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Spain
| | - Marina Pollán
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; Cancer and Environmental Epidemiology Unit, Department of Epidemiology of Chronic Diseases, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poland
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Olivier Cussenot
- CeRePP, Paris, France; GRC n°5 Predictive Onco-Urology, Tenon Hospital, Sorbonne University, Paris, France
| | - Anne Boland-Auge
- Centre National de Recherche en Génomique Humaine, CEA, University Paris-Saclay, Evry, France
| | - Delphine Daian
- Centre National de Recherche en Génomique Humaine, CEA, University Paris-Saclay, Evry, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, CEA, University Paris-Saclay, Evry, France
| | - Erika Salvi
- Neuroalgology Unit Fondazione IRCCS, Instituto Neurologico 'Carlo Besta' Milan, Milan, Italy
| | - Maris Teder-Laving
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Gianluca Tomasello
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Chiara Senti
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Department of Medical Oncology, Institut Jules Bordet - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Valli De Re
- Unit of Immunopathologia e Biomarcatori Oncologici/Bio-proteomics Facility, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Agostino Steffan
- Unit of Immunopathologia e Biomarcatori Oncologici, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Arnulf H Hölscher
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | - Katharina Messerle
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | | | - Armands Sīviņš
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia
| | - Inga Bogdanova
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia
| | - Jurgita Skieceviciene
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Justina Arstikyte
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Markus Moehler
- Department of Medicine I, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Peter P Grimminger
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Martin Kruschewski
- Department of General and Visceral Surgery, Klinikum Frankfurt (Oder), Germany
| | - Nikolaos Vassos
- Division of Surgical Oncology and Thoracic Surgery, Department of Surgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Claus Schildberg
- Department of General Surgery, Brandenburg Medical School Theodor Fontane, University Hospital Brandenburg, Brandenburg, Germany
| | - Philipp Lingohr
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany
| | - Karsten Ridwelski
- Department of General and Visceral Surgery, Klinikum Magdeburg GmbH, Magdeburg, Germany
| | - Hans Lippert
- Institute of Quality Assurance in Operative Medicine, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Lothar Veits
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuernberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poland
| | - Federico Martinón-Torres
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Department of Pediatrics, Translational Pediatrics and Infectious Diseases Section, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain; Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniele Cusi
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy; Bio4Dreams-Business, Nursery for Life Sciences, Milan, Italy
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Geraldine Cancel-Tassin
- CeRePP, Paris, France; GRC n°5 Predictive Onco-Urology, Tenon Hospital, Sorbonne University, Paris, France
| | - Aksana Höblinger
- Department of Internal Medicine I, Community Hospital Mittelrhein, Koblenz, Germany
| | - Ernst Rodermann
- Association of Medical Practices in Hematology and Internal Oncology, Troisdorf, Germany
| | - Monika Ludwig
- Association for Oncological Studies (Gefos), Dortmund, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joerg Heller
- Department of Gastroenterology, Marienhaus Hospital Ahrweiler, Ahrweiler, Germany
| | - Markus Neef
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | - Michael Schepke
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | | | - Lutz Hamann
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato Cannizzaro
- Unit of Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Michele Ghidini
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany; Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Olivier Gehlen
- Department of Surgical Oncology, Centre Hospitalier Lyon-sud, Lyon, France
| | - Tomasz Skoczylas
- 2nd Department of General Surgery, Medical University of Lublin, Lublin, Poland
| | - Marek Majewski
- 2nd Department of General Surgery, Medical University of Lublin, Lublin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Poland
| | - Orazio Palmieri
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefania Boccia
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Anna Latiano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Nuria Aragones
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; Epidemiology Section, Public Health Division, Department of Health of Madrid, Madrid, Spain
| | - Thomas Schmidt
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany; Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Mário Dinis-Ribeiro
- Porto Comprehensive Cancer Center & RISE @ CI-IPO, University of Porto, Porto 4200-450, Portugal; Gastroenterology Department, Portuguese Institute of Oncology of Porto, Porto 4200-072, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Porto 4200-072, Portugal; Research Department of the Portuguese League Against Cancer-North (LPCC-NRNorte), Porto 4200-177, Portugal
| | - Salah-Eddin Al-Batran
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia; Digestive Diseases Centre GASTRO, Riga, Latvia
| | - Juozas Kupcinskas
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - María A García-González
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
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Grover S, Opoku VS, Debrah LB, Maj C, Osei-Mensah J, Mensah DA, Hoerauf A, Debrah AY, Schumacher J, Pfarr K. First genome-wide association study for lymphatic filariasis in a West African population points to an HLA-mediated disease pathophysiology. Int J Infect Dis 2023; 133:1-4. [PMID: 37146673 DOI: 10.1016/j.ijid.2023.04.408] [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: 02/22/2023] [Revised: 04/10/2023] [Accepted: 04/22/2023] [Indexed: 05/07/2023] Open
Abstract
OBJECTIVES Lymphatic filariasis (LF) represents a parasitic disease caused by filarial nematodes. While some infected individuals present an asymptomatic course, others suffer severe chronic lymphatic pathology, including lymphoedema (LE), hydrocele, and elephantiasis. Several studies have shown that host genetic factors influence LF susceptibility and chronic pathology. The present study aimed to conduct the first genome-wide association study (GWAS) to systematically determine LF susceptibility. METHODS We analyzed genome-wide single-nucleotide polymorphism (SNP) data from 1,459 LF cases and 1,492 asymptomatic controls of West African (Ghanaian) descent. RESULTS We identified two independent genome-wide significant associated genetic variants near the genes HLA-DQB2 (rs7742085) and HLA-DQA1 (rs4959107) contributing to LF and/or LE susceptibility (P < 5.0 × 10-8, odds ratios (ORs) > 1.30). We also observed suggestive evidence of LF associations (P < 1.0 × 10-6) at two non-HLA loci, near the genes ZFHX4-AS1 (rs79562145) and CHP2 (rs12933387). In contrast, we could not replicate any previously reported LF associations drawn from candidate gene association studies. On the polygenic level, we show that our GWAS data explain 24-42% of LF heritability, depending on an assumed population prevalence of 0.5-5.0%. CONCLUSION Our findings point to an involvement of HLA-mediated immune mechanisms in LF pathophysiology.
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Affiliation(s)
- Sandeep Grover
- Center for Human Genetics, Philipps University of Marburg, Marburg, Germany
| | - Vera S Opoku
- Kumasi Center for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Linda B Debrah
- Kumasi Center for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana; Department of Clinical Microbiology, School of Medicine and Dentistry, KNUST, Kumasi, Ghana
| | - Carlo Maj
- Center for Human Genetics, Philipps University of Marburg, Marburg, Germany
| | - Jubin Osei-Mensah
- Kumasi Center for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana; School of Veterinary Medicine, KNUST, Kumasi, Ghana
| | - Derrick A Mensah
- Kumasi Center for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Alexander Y Debrah
- Kumasi Center for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana; Department of Medical Diagnostics, School of Medicine and Dentistry, KNUST, Kumasi, Ghana
| | - Johannes Schumacher
- Center for Human Genetics, Philipps University of Marburg, Marburg, Germany.
| | - Kenneth Pfarr
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
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15
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Went M, Sud A, Mills C, Hyde A, Culliford R, Law P, Vijayakrishnan J, Gockel I, Maj C, Schumacher J, Palles C, Kaiser M, Houlston R. Risk factors for eight common cancers revealed from a phenome-wide Mendelian randomisation analysis of 378,142 cases and 485,715 controls. medRxiv 2023:2023.02.15.23285952. [PMID: 37066289 PMCID: PMC10104236 DOI: 10.1101/2023.02.15.23285952] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
For many cancers there are few well-established risk factors. Summary data from genome-wide association studies (GWAS) can be used in a Mendelian randomisation (MR) phenome-wide association study (PheWAS) to identify causal relationships. We performed a MR-PheWAS of breast, prostate, colorectal, lung, endometrial, oesophageal, renal, and ovarian cancers, comprising 378,142 cases and 485,715 controls. To derive a more comprehensive insight into disease aetiology we systematically mined the literature space for supporting evidence. We evaluated causal relationships for over 3,000 potential risk factors. In addition to identifying well-established risk factors (smoking, alcohol, obesity, lack of physical activity), we provide evidence for specific factors, including dietary intake, sex steroid hormones, plasma lipids and telomere length as determinants of cancer risk. We also implicate molecular factors including plasma levels of IL-18, LAG-3, IGF-1, CT-1, and PRDX1 as risk factors. Our analyses highlight the importance of risk factors that are common to many cancer types but also reveal aetiological differences. A number of the molecular factors we identify have the potential to be biomarkers. Our findings should aid public health prevention strategies to reduce cancer burden. We provide a R/Shiny app (https://mrcancer.shinyapps.io/mrcan/) to visualise findings.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Haemato-oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, Sutton, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Abi Hyde
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | | | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Carlo Maj
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Haemato-oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, Sutton, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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16
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Schröder J, Chegwidden L, Maj C, Gehlen J, Speller J, Böhmer AC, Borisov O, Hess T, Kreuser N, Venerito M, Alakus H, May A, Gerges C, Schmidt T, Thieme R, Heider D, Hillmer AM, Reingruber J, Lyros O, Dietrich A, Hoffmeister A, Mehdorn M, Lordick F, Stocker G, Hohaus M, Reim D, Kandler J, Müller M, Ebigbo A, Fuchs C, Bruns CJ, Hölscher AH, Lang H, Grimminger PP, Dakkak D, Vashist Y, May S, Görg S, Franke A, Ellinghaus D, Galavotti S, Veits L, Weismüller J, Dommermuth J, Benner U, Rösch T, Messmann H, Schumacher B, Neuhaus H, Schmidt C, Wissinowski TT, Nöthen MM, Dong J, Ong JS, Buas MF, Thrift AP, Vaughan TL, Tomlinson I, Whiteman DC, Fitzgerald RC, Jankowski J, Vieth M, Mayr A, Gharahkhani P, MacGregor S, Gockel I, Palles C, Schumacher J. GWAS meta-analysis of 16 790 patients with Barrett's oesophagus and oesophageal adenocarcinoma identifies 16 novel genetic risk loci and provides insights into disease aetiology beyond the single marker level. Gut 2023; 72:612-623. [PMID: 35882562 DOI: 10.1136/gutjnl-2021-326698] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 07/07/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Oesophageal cancer (EC) is the sixth leading cause of cancer-related deaths. Oesophageal adenocarcinoma (EA), with Barrett's oesophagus (BE) as a precursor lesion, is the most prevalent EC subtype in the Western world. This study aims to contribute to better understand the genetic causes of BE/EA by leveraging genome wide association studies (GWAS), genetic correlation analyses and polygenic risk modelling. DESIGN We combined data from previous GWAS with new cohorts, increasing the sample size to 16 790 BE/EA cases and 32 476 controls. We also carried out a transcriptome wide association study (TWAS) using expression data from disease-relevant tissues to identify BE/EA candidate genes. To investigate the relationship with reported BE/EA risk factors, a linkage disequilibrium score regression (LDSR) analysis was performed. BE/EA risk models were developed combining clinical/lifestyle risk factors with polygenic risk scores (PRS) derived from the GWAS meta-analysis. RESULTS The GWAS meta-analysis identified 27 BE and/or EA risk loci, 11 of which were novel. The TWAS identified promising BE/EA candidate genes at seven GWAS loci and at five additional risk loci. The LDSR analysis led to the identification of novel genetic correlations and pointed to differences in BE and EA aetiology. Gastro-oesophageal reflux disease appeared to contribute stronger to the metaplastic BE transformation than to EA development. Finally, combining PRS with BE/EA risk factors improved the performance of the risk models. CONCLUSION Our findings provide further insights into BE/EA aetiology and its relationship to risk factors. The results lay the foundation for future follow-up studies to identify underlying disease mechanisms and improving risk prediction.
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Affiliation(s)
- Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Laura Chegwidden
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Carlo Maj
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Jan Gehlen
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Jan Speller
- Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), Medical Faculty, University of Bonn, Bonn, Germany
| | - Anne C Böhmer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Timo Hess
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Nicole Kreuser
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Cologne, Germany
| | - Andrea May
- Department of Gastroenterology, Oncology and Pneumology, Asklepios Paulinen Clinic Wiesbaden, Wiesbaden, Germany
| | - Christian Gerges
- Department of Internal Medicine II, Evangelisches Krankenhaus Dusseldorf, Dusseldorf, Germany
| | - Thomas Schmidt
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Cologne, Germany
| | - Rene Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Axel M Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University Hospital Cologne, Cologne, Germany
| | - Julian Reingruber
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Orestis Lyros
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Arne Dietrich
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | | | - Matthias Mehdorn
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Florian Lordick
- University Cancer Center Leipzig (UCCL), Leipzig University Medical Center, Leipzig, Germany
| | - Gertraud Stocker
- University Cancer Center Leipzig (UCCL), Leipzig University Medical Center, Leipzig, Germany
| | - Michael Hohaus
- Department for General and Visceral Surgery, Städt. Klinikum Dresden Friedrichstadt, Dresden, Germany
| | - Daniel Reim
- Department of Surgery, Technical University of Munich, School of Medicine, Klinikum Rechts der Isar, München, Germany
| | - Jennis Kandler
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty of Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Michaela Müller
- Department of Gastroenterology, Endocrinology, Metabolism and Infectiology, University Hospital Marburg and Philipps University, Marburg, Germany
| | - Alanna Ebigbo
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany
| | - Claudia Fuchs
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Cologne, Germany
| | - Christiane J Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital of Cologne, Cologne, Germany
| | - Arnulf H Hölscher
- Department for General, Visceral and Trauma Surgery, Elisabeth-Krankenhaus-Essen GmbH, Essen, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Peter P Grimminger
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Dani Dakkak
- Department of Internal Medicine and Gastroenterology, Elisabeth Hospital Essen, Essen, Germany
| | | | - Sandra May
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Siegfried Görg
- Institute of Transfusion Medicine, University Hospital of Schleswig-Holstein, Lübeck/Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sara Galavotti
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Lothar Veits
- Institute of Pathology, Friedrich-Alexander-Universiät Erlangen-Nürnberg, Klinikum Bayreuth, Bayreuth, Germany
| | | | | | - Udo Benner
- Gastroenterologische Gemeinschaftspraxis, Koblenz, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Helmut Messmann
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany
| | - Brigitte Schumacher
- Department of Internal Medicine and Gastroenterology, Elisabeth Hospital Essen, Essen, Germany
| | - Horst Neuhaus
- Department of Internal Medicine II, Evangelisches Krankenhaus Dusseldorf, Dusseldorf, Germany
| | - Carsten Schmidt
- Medical Clinic II (Gastroenterology, Hepatology, Endocrinology, Diabetology and Infektiology), Klinikum Fulda, University Medicine Marburg-Campus Fulda, Fulda, Germany
- Medical Faculty, Friedrich Schiller University Jena, Jena, Germany
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jing Dong
- Division of Hematology and Oncology, Department of Medicine, Cancer Center, and Genomic Sciences & Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jue-Sheng Ong
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matthew F Buas
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Aaron P Thrift
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Thomas L Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - David C Whiteman
- Cancer Control, Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rebecca Claire Fitzgerald
- Medical Research Council (MRC) Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Janusz Jankowski
- Comprehensive Clinical Trials Unit, University College London, London, UK
| | - Michael Vieth
- Institute of Pathology, Friedrich-Alexander-Universiät Erlangen-Nürnberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Andreas Mayr
- Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), Medical Faculty, University of Bonn, Bonn, Germany
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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17
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Went M, Sud A, Mills C, Hyde A, Culliford R, Law P, Vijayakrishnan J, Gockel I, Maj C, Schumacher J, Palles C, Kaiser M, Houlston R. Risk factors for eight common cancers revealed from a phenome-wide Mendelian randomisation analysis of 378,142 cases and 485,715 controls. Res Sq 2023:rs.3.rs-2587058. [PMID: 36993383 PMCID: PMC10055507 DOI: 10.21203/rs.3.rs-2587058/v1] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
For many cancers there are few well-established risk factors. Summary data from genome-wide association studies (GWAS) can be used in a Mendelian randomisation (MR) phenome-wide association study (PheWAS) to identify causal relationships. We performed a MR-PheWAS of breast, prostate, colorectal, lung, endometrial, oesophageal, renal, and ovarian cancers, comprising 378,142 cases and 485,715 controls. To derive a more comprehensive insight into disease aetiology we systematically mined the literature space for supporting evidence. We evaluated causal relationships for over 3,000 potential risk factors. In addition to identifying well-established risk factors (smoking, alcohol, obesity, lack of physical activity), we provide evidence for specific factors, including dietary intake, sex steroid hormones, plasma lipids and telomere length as determinants of cancer risk. We also implicate molecular factors including plasma levels of IL-18, LAG-3, IGF-1, CT-1, and PRDX1 as risk factors. Our analyses highlight the importance of risk factors that are common to many cancer types but also reveal aetiological differences. A number of the molecular factors we identify have the potential to be biomarkers. Our findings should aid public health prevention strategies to reduce cancer burden. We provide a R/Shiny app (https://mrcancer.shinyapps.io/mrcan/) to visualise findings.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Haemato-oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, Sutton, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Abi Hyde
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | | | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Carlo Maj
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Haemato-oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, Sutton, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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18
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Begg TJA, Schmidt A, Kocher A, Larmuseau MHD, Runfeldt G, Maier PA, Wilson JD, Barquera R, Maj C, Szolek A, Sager M, Clayton S, Peltzer A, Hui R, Ronge J, Reiter E, Freund C, Burri M, Aron F, Tiliakou A, Osborn J, Behar DM, Boecker M, Brandt G, Cleynen I, Strassburg C, Prüfer K, Kühnert D, Meredith WR, Nöthen MM, Attenborough RD, Kivisild T, Krause J. Genomic analyses of hair from Ludwig van Beethoven. Curr Biol 2023; 33:1431-1447.e22. [PMID: 36958333 DOI: 10.1016/j.cub.2023.02.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 05/29/2022] [Revised: 10/11/2022] [Accepted: 02/13/2023] [Indexed: 03/25/2023]
Abstract
Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.
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Affiliation(s)
- Tristan James Alexander Begg
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
| | - Axel Schmidt
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Arthur Kocher
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Maarten H D Larmuseau
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Laboratory of Human Genetic Genealogy, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ARCHES - Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, 2000 Antwerp, Belgium; Histories vzw, 9000 Gent, Belgium
| | | | | | - John D Wilson
- Austrian Academy of Sciences, 1030 Vienna, Austria; University of Vienna, 1010 Vienna, Austria
| | - Rodrigo Barquera
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Carlo Maj
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | | | - Stephen Clayton
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Alexander Peltzer
- Quantitative Biology Center (QBiC) University of Tübingen, Tübingen, Germany
| | - Ruoyun Hui
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; Alan Turing Institute, 2QR, John Dodson House, London NW1 2DB, UK
| | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Marta Burri
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Franziska Aron
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Anthi Tiliakou
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Joanna Osborn
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Guido Brandt
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Isabelle Cleynen
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Strassburg
- Department of Internal Medicine I, University Hospital Bonn, 53127 Bonn, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - William Rhea Meredith
- American Beethoven Society, San Jose State University, San Jose, CA 95192, USA; Ira F. Brilliant Center for Beethoven Studies, San Jose State University, San Jose, CA 95192, USA; School of Music and Dance, San Jose State University, San Jose, CA 95192, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Robert David Attenborough
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; School of Archaeology & Anthropology, Australian National University, Canberra, ACT 0200, Australia
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
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19
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Hassanin E, Spier I, Bobbili DR, Aldisi R, Klinkhammer H, David F, Dueñas N, Hüneburg R, Perne C, Brunet J, Capella G, Nöthen MM, Forstner AJ, Mayr A, Krawitz P, May P, Aretz S, Maj C. Clinically relevant combined effect of polygenic background, rare pathogenic germline variants, and family history on colorectal cancer incidence. BMC Med Genomics 2023; 16:42. [PMID: 36872334 PMCID: PMC9987090 DOI: 10.1186/s12920-023-01469-z] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/21/2023] [Indexed: 03/07/2023] Open
Abstract
BACKGROUND AND AIMS Summarised in polygenic risk scores (PRS), the effect of common, low penetrant genetic variants associated with colorectal cancer (CRC), can be used for risk stratification. METHODS To assess the combined impact of the PRS and other main factors on CRC risk, 163,516 individuals from the UK Biobank were stratified as follows: 1. carriers status for germline pathogenic variants (PV) in CRC susceptibility genes (APC, MLH1, MSH2, MSH6, PMS2), 2. low (< 20%), intermediate (20-80%), or high PRS (> 80%), and 3. family history (FH) of CRC. Multivariable logistic regression and Cox proportional hazards models were applied to compare odds ratios and to compute the lifetime incidence, respectively. RESULTS Depending on the PRS, the CRC lifetime incidence for non-carriers ranges between 6 and 22%, compared to 40% and 74% for carriers. A suspicious FH is associated with a further increase of the cumulative incidence reaching 26% for non-carriers and 98% for carriers. In non-carriers without FH, but high PRS, the CRC risk is doubled, whereas a low PRS even in the context of a FH results in a decreased risk. The full model including PRS, carrier status, and FH improved the area under the curve in risk prediction (0.704). CONCLUSION The findings demonstrate that CRC risks are strongly influenced by the PRS for both a sporadic and monogenic background. FH, PV, and common variants complementary contribute to CRC risk. The implementation of PRS in routine care will likely improve personalized risk stratification, which will in turn guide tailored preventive surveillance strategies in high, intermediate, and low risk groups.
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Affiliation(s)
- Emadeldin Hassanin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.,European Reference Network on Genetic Tumour Rsik Syndromes (ERNGENTURIS) - Project ID No 739547, Nijmegen, The Netherlands
| | - Dheeraj R Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Rana Aldisi
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany.,Medical Faculty, Institute for Medical Biometry, Informatics and Epidemiology, University Bonn, Bonn, Germany
| | - Friederike David
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Nuria Dueñas
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Robert Hüneburg
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.,Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Claudia Perne
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Joan Brunet
- European Reference Network on Genetic Tumour Rsik Syndromes (ERNGENTURIS) - Project ID No 739547, Nijmegen, The Netherlands.,Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology-IDBIGI, 17007, Girona, Spain
| | - Gabriel Capella
- European Reference Network on Genetic Tumour Rsik Syndromes (ERNGENTURIS) - Project ID No 739547, Nijmegen, The Netherlands.,Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Markus M Nöthen
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.,Centre for Human Genetics, University of Marburg, Marburg, Germany.,Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
| | - Andreas Mayr
- Medical Faculty, Institute for Medical Biometry, Informatics and Epidemiology, University Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany. .,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany. .,European Reference Network on Genetic Tumour Rsik Syndromes (ERNGENTURIS) - Project ID No 739547, Nijmegen, The Netherlands.
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
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20
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Chen Y, Hysi P, Maj C, Heilmann-Heimbach S, Spector TD, Liu F, Kayser M. Genetic prediction of male pattern baldness based on large independent datasets. Eur J Hum Genet 2023; 31:321-328. [PMID: 36336714 PMCID: PMC9995341 DOI: 10.1038/s41431-022-01201-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: 05/03/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic prediction of male pattern baldness (MPB) is important in science and society. Previous genetic MPB prediction models were limited by sparse marker coverage, small sample size, and/or data dependency in the different analytical steps. Here, we present novel models for genetic prediction of MPB based on a large set of markers and large independent subsample sets drawn among 187,435 European subjects. We selected 117 SNP predictors within 85 distinct loci from a list of 270 previously MPB-associated SNPs in 55,573 males of the UK Biobank Study (UKBB). Based on these 117 SNPs with and without age as additional predictor, we trained, by use of different methods, prediction models in a non-overlapping subset of 104,694 UKBB males and tested them in a non-overlapping subset of 26,177 UKBB males. Estimates of prediction accuracy were similar between methods with AUC ranges of 0.725-0.728 for severe, 0.631-0.635 for moderate, 0.598-0.602 for slight, and 0.708-0.711 for no hair loss with age, and slightly lower without, while prediction of any versus no hair loss gave 0.690-0.711 with age and slightly lower without. External validation in an early-onset enriched MPB dataset from the Bonn Study (N = 991) showed improved prediction accuracy without considering age such as AUC of 0.830 for no vs. any hair loss. Because of the large number of markers and the large independent datasets used for the different analytical steps, the newly presented genetic prediction models are the most reliable ones currently available for MPB or any other human appearance trait.
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Affiliation(s)
- Yan Chen
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pirro Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics (IGSB), University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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21
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Ishorst N, Henschel L, Thieme F, Drichel D, Sivalingam S, Mehrem SL, Fechtner AC, Fazaal J, Welzenbach J, Heimbach A, Maj C, Borisov O, Hausen J, Raff R, Hoischen A, Dixon M, Rada-Iglesias A, Bartusel M, Rojas-Martinez A, Aldhorae K, Braumann B, Kruse T, Kirschneck C, Spanier G, Reutter H, Nowak S, Gölz L, Knapp M, Buness A, Krawitz P, Nöthen MM, Nothnagel M, Becker T, Ludwig KU, Mangold E. Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. Mol Genet Genomic Med 2023; 11:e2109. [PMID: 36468602 PMCID: PMC10009911 DOI: 10.1002/mgg3.2109] [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: 08/08/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.
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Affiliation(s)
- Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Sarah L Mehrem
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Ariane C Fechtner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jonas Hausen
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Ruth Raff
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Dixon
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico.,Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Khalid Aldhorae
- Department of Orthodontics, College of Dentistry, Thamar University, Thamar, Yemen.,Department of Orthodontics, College of Dentistry, University of Ibn al-Nafis for Medical Sciences, Sanaa, Yemen
| | - Bert Braumann
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Teresa Kruse
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | | | - Gerrit Spanier
- Department of Cranio-Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Erlangen-Nürnberg, Erlangen, Germany.,Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,University Hospital Cologne, Cologne, Germany
| | - Tim Becker
- Institute of Community Medicine, University of Greifswald, Greifswald, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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22
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Klinkhammer H, Staerk C, Maj C, Krawitz PM, Mayr A. A statistical boosting framework for polygenic risk scores based on large-scale genotype data. Front Genet 2023; 13:1076440. [PMID: 36704342 PMCID: PMC9871367 DOI: 10.3389/fgene.2022.1076440] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Polygenic risk scores (PRS) evaluate the individual genetic liability to a certain trait and are expected to play an increasingly important role in clinical risk stratification. Most often, PRS are estimated based on summary statistics of univariate effects derived from genome-wide association studies. To improve the predictive performance of PRS, it is desirable to fit multivariable models directly on the genetic data. Due to the large and high-dimensional data, a direct application of existing methods is often not feasible and new efficient algorithms are required to overcome the computational burden regarding efficiency and memory demands. We develop an adapted component-wise L 2-boosting algorithm to fit genotype data from large cohort studies to continuous outcomes using linear base-learners for the genetic variants. Similar to the snpnet approach implementing lasso regression, the proposed snpboost approach iteratively works on smaller batches of variants. By restricting the set of possible base-learners in each boosting step to variants most correlated with the residuals from previous iterations, the computational efficiency can be substantially increased without losing prediction accuracy. Furthermore, for large-scale data based on various traits from the UK Biobank we show that our method yields competitive prediction accuracy and computational efficiency compared to the snpnet approach and further commonly used methods. Due to the modular structure of boosting, our framework can be further extended to construct PRS for different outcome data and effect types-we illustrate this for the prediction of binary traits.
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Affiliation(s)
- Hannah Klinkhammer
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Christian Staerk
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Peter Michael Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
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23
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Namba S, Saito Y, Kogure Y, Masuda T, Bondy ML, Gharahkhani P, Gockel I, Heider D, Hillmer A, Jankowski J, MacGregor S, Maj C, Melin B, Ostrom QT, Palles C, Schumacher J, Tomlinson I, Whiteman DC, Okada Y, Kataoka K. Common Germline Risk Variants Impact Somatic Alterations and Clinical Features across Cancers. Cancer Res 2023; 83:20-27. [PMID: 36286845 PMCID: PMC9811159 DOI: 10.1158/0008-5472.can-22-1492] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/20/2022] [Accepted: 10/21/2022] [Indexed: 02/03/2023]
Abstract
Aggregation of genome-wide common risk variants, such as polygenic risk score (PRS), can measure genetic susceptibility to cancer. A better understanding of how common germline variants associate with somatic alterations and clinical features could facilitate personalized cancer prevention and early detection. We constructed PRSs from 14 genome-wide association studies (median n = 64,905) for 12 cancer types by multiple methods and calibrated them using the UK Biobank resources (n = 335,048). Meta-analyses across cancer types in The Cancer Genome Atlas (n = 7,965) revealed that higher PRS values were associated with earlier cancer onset and lower burden of somatic alterations, including total mutations, chromosome/arm somatic copy-number alterations (SCNA), and focal SCNAs. This contrasts with rare germline pathogenic variants (e.g., BRCA1/2 variants), showing heterogeneous associations with somatic alterations. Our results suggest that common germline cancer risk variants allow early tumor development before the accumulation of many somatic alterations characteristic of later stages of carcinogenesis. SIGNIFICANCE Meta-analyses across cancers show that common germline risk variants affect not only cancer predisposition but the age of cancer onset and burden of somatic alterations, including total mutations and copy-number alterations.
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Affiliation(s)
- Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Osaka, Japan
- StemRIM Institute of Regeneration-Inducing Medicine, Osaka University, Osaka, Japan
| | - Melissa L. Bondy
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California
| | - Puya Gharahkhani
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Axel Hillmer
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Janusz Jankowski
- Office of Vice President Research and Innovation, Laucala Bay Campus, University of South Pacific, Suva, Fiji
- Institute for Clinical Trials, University College London, Holborn, London
| | - Stuart MacGregor
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Quinn T. Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, North Carolina
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - David C. Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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24
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Balestra C, Maj C, Müller E, Mayr A. Redundancy-aware unsupervised ranking based on game theory: Ranking pathways in collections of gene sets. PLoS One 2023; 18:e0282699. [PMID: 36893181 PMCID: PMC9997904 DOI: 10.1371/journal.pone.0282699] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 03/10/2023] Open
Abstract
In Genetics, gene sets are grouped in collections concerning their biological function. This often leads to high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation of their biological meaning. In Data Mining, it is often argued that techniques to reduce the dimensionality of data could increase the maneuverability and consequently the interpretability of large data. In the past years, moreover, we witnessed an increasing consciousness of the importance of understanding data and interpretable models in the machine learning and bioinformatics communities. On the one hand, there exist techniques aiming to aggregate overlapping gene sets to create larger pathways. While these methods could partly solve the large size of the collections' problem, modifying biological pathways is hardly justifiable in this biological context. On the other hand, the representation methods to increase interpretability of collections of gene sets that have been proposed so far have proved to be insufficient. Inspired by this Bioinformatics context, we propose a method to rank sets within a family of sets based on the distribution of the singletons and their size. We obtain sets' importance scores by computing Shapley values; Making use of microarray games, we do not incur the typical exponential computational complexity. Moreover, we address the challenge of constructing redundancy-aware rankings where, in our case, redundancy is a quantity proportional to the size of intersections among the sets in the collections. We use the obtained rankings to reduce the dimension of the families, therefore showing lower redundancy among sets while still preserving a high coverage of their elements. We finally evaluate our approach for collections of gene sets and apply Gene Sets Enrichment Analysis techniques to the now smaller collections: As expected, the unsupervised nature of the proposed rankings allows for unremarkable differences in the number of significant gene sets for specific phenotypic traits. In contrast, the number of performed statistical tests can be drastically reduced. The proposed rankings show a practical utility in bioinformatics to increase interpretability of the collections of gene sets and a step forward to include redundancy-awareness into Shapley values computations.
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Affiliation(s)
- Chiara Balestra
- Department of Computer Science, TU Dortmund, Dortmund, Germany
- Department of Medical Biometry, Informatics and Epidemiology (IMBIE), University Hospital Bonn, Bonn, Germany
- * E-mail:
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics IGSB, University Hospital Bonn, Bonn, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Emmanuel Müller
- Department of Computer Science, TU Dortmund, Dortmund, Germany
| | - Andreas Mayr
- Department of Medical Biometry, Informatics and Epidemiology (IMBIE), University Hospital Bonn, Bonn, Germany
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25
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Groen in ’t Woud S, Maj C, Renkema KY, Westland R, Galesloot T, van Rooij IALM, Vermeulen SH, Feitz WFJ, Roeleveld N, Schreuder MF, van der Zanden LFM. A Genome-Wide Association Study into the Aetiology of Congenital Solitary Functioning Kidney. Biomedicines 2022; 10:biomedicines10123023. [PMID: 36551779 PMCID: PMC9775328 DOI: 10.3390/biomedicines10123023] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
Congenital solitary functioning kidney (CSFK) is a birth defect that occurs in 1:1500 children and predisposes them to kidney injury. Its aetiology is likely multifactorial. In addition to known monogenic causes and environmental risk factors, common genetic variation may contribute to susceptibility to CSFK. We performed a genome-wide association study among 452 patients with CSFK and two control groups of 669 healthy children and 5363 unaffected adults. Variants in two loci reached the genome-wide significance threshold of 5 × 10-8, and variants in 30 loci reached the suggestive significance threshold of 1 × 10-5. Of these, an identified locus with lead single nucleotide variant (SNV) rs140804918 (odds ratio 3.1, p-value = 1.4 × 10-8) on chromosome 7 was most promising due to its close proximity to HGF, a gene known to be involved in kidney development. Based on their known molecular functions, both KCTD20 and STK38 could explain the suggestive significant association with lead SNV rs148413365 on chromosome 6. Our findings need replication in an independent cohort of CSFK patients before they can be established definitively. However, our analysis suggests that common variants play a role in CSFK aetiology. Future research could enhance our understanding of the molecular mechanisms involved.
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Affiliation(s)
- Sander Groen in ’t Woud
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Department of Paediatric Nephrology, Radboudumc Amalia Children’s Hospital, 6500 HB Nijmegen, The Netherlands
| | - Carlo Maj
- Centre for Human Genetics, University of Marburg, 35037 Marburg, Germany
| | - Kirsten Y. Renkema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Rik Westland
- Department of Pediatric Nephrology, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Tessel Galesloot
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Iris A. L. M. van Rooij
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Sita H. Vermeulen
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Wout F. J. Feitz
- Division of Pediatric Urology, Department of Urology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children’s Hospital, 6500 HB Nijmegen, The Netherlands
| | - Nel Roeleveld
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Michiel F. Schreuder
- Radboud Institute for Molecular Life Sciences, Department of Paediatric Nephrology, Radboudumc Amalia Children’s Hospital, 6500 HB Nijmegen, The Netherlands
- Correspondence: (M.F.S.); (L.F.v.d.Z.); Tel.: +31-24-3619132 (L.F.v.d.Z.); Fax: +31-24-3613505 (L.F.v.d.Z.)
| | - Loes F. M. van der Zanden
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Correspondence: (M.F.S.); (L.F.v.d.Z.); Tel.: +31-24-3619132 (L.F.v.d.Z.); Fax: +31-24-3613505 (L.F.v.d.Z.)
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26
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Cattane N, Courtin C, Mombelli E, Maj C, Mora C, Etain B, Bellivier F, Marie-Claire C, Cattaneo A. Transcriptomics and miRNomics data integration in lymphoblastoid cells highlights the key role of immune-related functions in lithium treatment response in Bipolar disorder. BMC Psychiatry 2022; 22:665. [PMID: 36303132 PMCID: PMC9615157 DOI: 10.1186/s12888-022-04286-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bipolar Disorder (BD) is a complex mental disease characterized by recurrent episodes of mania and depression. Lithium (Li) represents the mainstay of BD pharmacotherapy, despite the narrow therapeutic index and the high variability in treatment response. However, although several studies have been conducted, the molecular mechanisms underlying Li therapeutic effects remain unclear. METHODS In order to identify molecular signatures and biological pathways associated with Li treatment response, we conducted transcriptome and miRNome microarray analyses on lymphoblastoid cell lines (LCLs) from 20 patients diagnosed with BD classified as Li responders (n = 11) or non-responders (n = 9). RESULTS We found 335 mRNAs and 77 microRNAs (miRNAs) significantly modulated in BD responders versus non-responders. Interestingly, pathway and network analyses on these differentially expressed molecules suggested a modulatory effect of Li on several immune-related functions. Indeed, among the functional molecular nodes, we found NF-κB and TNF. Moreover, networks related to these molecules resulted overall inhibited in BD responder patients, suggesting anti-inflammatory properties of Li. From the integrative analysis between transcriptomics and miRNomics data carried out using miRComb R package on the same samples from patients diagnosed with BD, we found 97 significantly and negatively correlated mRNA-miRNA pairs, mainly involved in inflammatory/immune response. CONCLUSIONS Our results highlight that Li exerts modulatory effects on immune-related functions and that epigenetic mechanisms, especially miRNAs, can influence the modulation of different genes and pathways involved in Li response. Moreover, our data suggest the potentiality to integrate data coming from different high-throughput approaches as a tool to prioritize genes and pathways.
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Affiliation(s)
- Nadia Cattane
- grid.419422.8Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Cindie Courtin
- grid.7429.80000000121866389Université Paris Cité, INSERM UMR-S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeN, F-75006 Paris, France
| | - Elisa Mombelli
- grid.419422.8Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Carlo Maj
- grid.411097.a0000 0000 8852 305XInstitute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany
| | - Cristina Mora
- grid.419422.8Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Bruno Etain
- grid.7429.80000000121866389Université Paris Cité, INSERM UMR-S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeN, F-75006 Paris, France ,Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP Nord_Université Paris Cité, F-75010 Paris, France ,grid.484137.d0000 0005 0389 9389Fondation FondaMental, Créteil, France
| | - Frank Bellivier
- grid.7429.80000000121866389Université Paris Cité, INSERM UMR-S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeN, F-75006 Paris, France ,Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP Nord_Université Paris Cité, F-75010 Paris, France ,grid.484137.d0000 0005 0389 9389Fondation FondaMental, Créteil, France
| | - Cynthia Marie-Claire
- grid.7429.80000000121866389Université Paris Cité, INSERM UMR-S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeN, F-75006 Paris, France
| | - Annamaria Cattaneo
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy. .,Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy.
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27
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Chan MMY, Sadeghi-Alavijeh O, Lopes FM, Hilger AC, Stanescu HC, Voinescu CD, Beaman GM, Newman WG, Zaniew M, Weber S, Ho YM, Connolly JO, Wood D, Maj C, Stuckey A, Kousathanas A, Kleta R, Woolf AS, Bockenhauer D, Levine AP, Gale DP. Diverse ancestry whole-genome sequencing association study identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves. eLife 2022; 11:74777. [PMID: 36124557 PMCID: PMC9512401 DOI: 10.7554/elife.74777] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
Posterior urethral valves (PUV) are the commonest cause of end-stage renal disease in children, but the genetic architecture of this rare disorder remains unknown. We performed a sequencing-based genome-wide association study (seqGWAS) in 132 unrelated male PUV cases and 23,727 controls of diverse ancestry, identifying statistically significant associations with common variants at 12q24.21 (p=7.8 × 10-12; OR 0.4) and rare variants at 6p21.1 (p=2.0 × 10-8; OR 7.2), that were replicated in an independent European cohort of 395 cases and 4151 controls. Fine mapping and functional genomic data mapped these loci to the transcription factor TBX5 and planar cell polarity gene PTK7, respectively, the encoded proteins of which were detected in the developing urinary tract of human embryos. We also observed enrichment of rare structural variation intersecting with candidate cis-regulatory elements, particularly inversions predicted to affect chromatin looping (p=3.1 × 10-5). These findings represent the first robust genetic associations of PUV, providing novel insights into the underlying biology of this poorly understood disorder and demonstrate how a diverse ancestry seqGWAS can be used for disease locus discovery in a rare disease.
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Affiliation(s)
- Melanie MY Chan
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | | | - Filipa M Lopes
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Alina C Hilger
- Children's Hospital, University of BonnBonnGermany
- Institute of Human Genetics, University of BonnBonnGermany
| | - Horia C Stanescu
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | - Catalin D Voinescu
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | - Glenda M Beaman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Evolution and Genomic Sciences, School of Biological Sciences, University of ManchesterManchesterUnited Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Evolution and Genomic Sciences, School of Biological Sciences, University of ManchesterManchesterUnited Kingdom
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona GóraZielona GoraPoland
| | - Stefanie Weber
- Department of Pediatric Nephrology, University of MarburgMarburgGermany
| | - Yee Mang Ho
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - John O Connolly
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Department of Adolescent Urology, University College London Hospitals NHS Foundation TrustLondonUnited Kingdom
| | - Dan Wood
- Department of Adolescent Urology, University College London Hospitals NHS Foundation TrustLondonUnited Kingdom
| | - Carlo Maj
- Center for Human Genetics, University of MarburgMarburgGermany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of BonnBonnGermany
| | - Alexander Stuckey
- Genomics England, Queen Mary University of LondonLondonUnited Kingdom
| | | | | | - Robert Kleta
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Nephrology Department, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUnited Kingdom
| | - Adrian S Woolf
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Detlef Bockenhauer
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Nephrology Department, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUnited Kingdom
| | - Adam P Levine
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Research Department of Pathology, University College LondonLondonUnited Kingdom
| | - Daniel P Gale
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
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28
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Koutsouleris N, Pantelis C, Velakoulis D, McGuire P, Dwyer DB, Urquijo-Castro MF, Paul R, Dong S, Popovic D, Oeztuerk O, Kambeitz J, Salokangas RKR, Hietala J, Bertolino A, Brambilla P, Upthegrove R, Wood SJ, Lencer R, Borgwardt S, Maj C, Nöthen M, Degenhardt F, Polyakova M, Mueller K, Villringer A, Danek A, Fassbender K, Fliessbach K, Jahn H, Kornhuber J, Landwehrmeyer B, Anderl-Straub S, Prudlo J, Synofzik M, Wiltfang J, Riedl L, Diehl-Schmid J, Otto M, Meisenzahl E, Falkai P, Schroeter ML. Exploring Links Between Psychosis and Frontotemporal Dementia Using Multimodal Machine Learning: Dementia Praecox Revisited. JAMA Psychiatry 2022; 79:907-919. [PMID: 35921104 PMCID: PMC9350851 DOI: 10.1001/jamapsychiatry.2022.2075] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/12/2022] [Indexed: 12/04/2022]
Abstract
Importance The behavioral and cognitive symptoms of severe psychotic disorders overlap with those seen in dementia. However, shared brain alterations remain disputed, and their relevance for patients in at-risk disease stages has not been explored so far. Objective To use machine learning to compare the expression of structural magnetic resonance imaging (MRI) patterns of behavioral-variant frontotemporal dementia (bvFTD), Alzheimer disease (AD), and schizophrenia; estimate predictability in patients with bvFTD and schizophrenia based on sociodemographic, clinical, and biological data; and examine prognostic value, genetic underpinnings, and progression in patients with clinical high-risk (CHR) states for psychosis or recent-onset depression (ROD). Design, Setting, and Participants This study included 1870 individuals from 5 cohorts, including (1) patients with bvFTD (n = 108), established AD (n = 44), mild cognitive impairment or early-stage AD (n = 96), schizophrenia (n = 157), or major depression (n = 102) to derive and compare diagnostic patterns and (2) patients with CHR (n = 160) or ROD (n = 161) to test patterns' prognostic relevance and progression. Healthy individuals (n = 1042) were used for age-related and cohort-related data calibration. Data were collected from January 1996 to July 2019 and analyzed between April 2020 and April 2022. Main Outcomes and Measures Case assignments based on diagnostic patterns; sociodemographic, clinical, and biological data; 2-year functional outcomes and genetic separability of patients with CHR and ROD with high vs low pattern expression; and pattern progression from baseline to follow-up MRI scans in patients with nonrecovery vs preserved recovery. Results Of 1870 included patients, 902 (48.2%) were female, and the mean (SD) age was 38.0 (19.3) years. The bvFTD pattern comprising prefrontal, insular, and limbic volume reductions was more expressed in patients with schizophrenia (65 of 157 [41.2%]) and major depression (22 of 102 [21.6%]) than the temporo-limbic AD patterns (28 of 157 [17.8%] and 3 of 102 [2.9%], respectively). bvFTD expression was predicted by high body mass index, psychomotor slowing, affective disinhibition, and paranoid ideation (R2 = 0.11). The schizophrenia pattern was expressed in 92 of 108 patients (85.5%) with bvFTD and was linked to the C9orf72 variant, oligoclonal banding in the cerebrospinal fluid, cognitive impairment, and younger age (R2 = 0.29). bvFTD and schizophrenia pattern expressions forecasted 2-year psychosocial impairments in patients with CHR and were predicted by polygenic risk scores for frontotemporal dementia, AD, and schizophrenia. Findings were not associated with AD or accelerated brain aging. Finally, 1-year bvFTD/schizophrenia pattern progression distinguished patients with nonrecovery from those with preserved recovery. Conclusions and Relevance Neurobiological links may exist between bvFTD and psychosis focusing on prefrontal and salience system alterations. Further transdiagnostic investigations are needed to identify shared pathophysiological processes underlying the neuroanatomical interface between the 2 disease spectra.
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Affiliation(s)
- Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Max-Planck Institute of Psychiatry, Munich, Germany
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Australia
| | - Dennis Velakoulis
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Australia
| | - Philip McGuire
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Dominic B. Dwyer
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
| | | | - Riya Paul
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
| | - Sen Dong
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
| | - David Popovic
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
| | - Oemer Oeztuerk
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
| | - Joseph Kambeitz
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | | | - Jarmo Hietala
- Department of Psychiatry, University of Turku, Turku, Finland
| | - Alessandro Bertolino
- Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Paolo Brambilla
- Department of Neurosciences and Mental Health, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rachel Upthegrove
- Institute of Mental Health, University of Birmingham, Birmingham, United Kingdom
- Early Intervention Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, United Kingdom
| | - Stephen J. Wood
- School of Psychology, University of Birmingham, Birmingham, United Kingdom
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Australia
- Orygen, Melbourne, Australia
| | - Rebekka Lencer
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
- Institute for Translational Psychiatry, University Muenster, Muenster, Germany
| | - Stefan Borgwardt
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
- Department of Psychiatry, University Psychiatric Clinics (UPK), University of Basel, Basel, Switzerland
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Markus Nöthen
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Maryna Polyakova
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
| | - Karsten Mueller
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Arno Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Adrian Danek
- Department of Neurology, Ludwig Maximilian University Munich, Munich, Germany
| | - Klaus Fassbender
- Department of Neurology, Saarland University Hospital, Homburg, Germany
| | - Klaus Fliessbach
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Holger Jahn
- Department of Psychiatry and Psychotherapy, University Hospital Hamburg, Hamburg, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | | | - Johannes Prudlo
- Department of Neurology, University Medicine Rostock, Rostock, Germany
| | - Matthis Synofzik
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Jens Wiltfang
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department of Psychiatry and Psychotherapy, Medical University Göttingen, Göttingen, Germany
| | - Lina Riedl
- Department of Psychiatry and Psychotherapy, Technical University of Munich, Munich, Germany
| | - Janine Diehl-Schmid
- Department of Psychiatry and Psychotherapy, Technical University of Munich, Munich, Germany
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Eva Meisenzahl
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, Ludwig Maximilian University, Munich, Germany
| | - Matthias L. Schroeter
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
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Maj C, Staerk C, Borisov O, Klinkhammer H, Wai Yeung M, Krawitz P, Mayr A. Statistical learning for sparser fine-mapped polygenic models: The prediction of LDL-cholesterol. Genet Epidemiol 2022; 46:589-603. [PMID: 35938382 DOI: 10.1002/gepi.22495] [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: 08/24/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022]
Abstract
Polygenic risk scores quantify the individual genetic predisposition regarding a particular trait. We propose and illustrate the application of existing statistical learning methods to derive sparser models for genome-wide data with a polygenic signal. Our approach is based on three consecutive steps. First, potentially informative loci are identified by a marginal screening approach. Then, fine-mapping is independently applied for blocks of variants in linkage disequilibrium, where informative variants are retrieved by using variable selection methods including boosting with probing and stochastic searches with the Adaptive Subspace method. Finally, joint prediction models with the selected variants are derived using statistical boosting. In contrast to alternative approaches relying on univariate summary statistics from genome-wide association studies, our three-step approach enables to select and fit multivariable regression models on large-scale genotype data. Based on UK Biobank data, we develop prediction models for LDL-cholesterol as a continuous trait. Additionally, we consider a recent scalable algorithm for the Lasso. Results show that statistical learning approaches based on fine-mapping of genetic signals result in a competitive prediction performance compared to classical polygenic risk approaches, while yielding sparser risk models.
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Affiliation(s)
- Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany.,Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Christian Staerk
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany.,Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Ming Wai Yeung
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany.,Department of Cardiology, University of Groningen, Groningen, The Netherlands
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
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Freff J, Beins EC, Bröker L, Schwarte K, Leite Dantas R, Maj C, Arolt V, Dannlowski U, Nöthen MM, Baune BT, Forstner AJ, Alferink J. Chemokine receptor 4 expression on blood T lymphocytes predicts severity of major depressive disorder. J Affect Disord 2022; 310:343-353. [PMID: 35526724 DOI: 10.1016/j.jad.2022.05.003] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Chemokines and their receptors regulate inflammatory processes in major depressive disorder (MDD). Here, we characterize the expression pattern of the C-C chemokine receptor 4 (CCR4) and its ligands CCL17 and CCL22 in MDD and its clinical relevance in predicting disease severity. METHODS Expression of CCR4 on peripheral blood lymphocytes and serum CCL17/CCL22 levels were measured using multiparameter flow cytometry and multiplex assays in 33 depressed inpatients at baseline (T0) and after 6-week multimodal treatment (T1) compared with 21 healthy controls (HC). Using stratified and correlation analysis, we examined the associations of CCR4-CCL17/CCL22 expression with depression severity and symptoms according to standard clinical rating scales and questionnaires. Additionally, we assessed whether polygenic risk score (PRS) for psychiatric disorders and chronotype are associated with disease status or CCR4-CCL17/CCL22 expression. Regression analysis was performed to assess the capacity of CCR4 and PRS in predicting disease severity. RESULTS Compared with HC, MDD patients showed significantly decreased CCR4 expression on T cells (T0 and T1), whereas CCL17/CCL22 serum levels were increased. Stratified and correlation analysis revealed an association of CCR4 expression on CD4+ T cells with depression severity as well as Beck Depression Inventory-II items including loss of pleasure, agitation and cognitive deficits. CCR4 expression levels on CD4+ T cells together with cross-disorder and chronotype PRS significantly predicted disease severity. LIMITATIONS This exploratory study with small sample size warrants future studies. CONCLUSIONS This newly identified CCR4-CCL17/CCL22 signature and its predictive capacity for MDD severity suggest its potential functional involvement in the pathophysiology of MDD.
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Affiliation(s)
- Jana Freff
- Department of Psychiatry, University of Münster, Münster, Germany; Cells in Motion Interfaculty Cluster, University of Münster, Münster, Germany.
| | - Eva C Beins
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.
| | - Lisa Bröker
- Department of Psychiatry, University of Münster, Münster, Germany; Cells in Motion Interfaculty Cluster, University of Münster, Münster, Germany.
| | - Kathrin Schwarte
- Department of Psychiatry, University of Münster, Münster, Germany.
| | - Rafael Leite Dantas
- Department of Psychiatry, University of Münster, Münster, Germany; Cells in Motion Interfaculty Cluster, University of Münster, Münster, Germany.
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany; Centre for Human Genetics, University of Marburg, Marburg, Germany.
| | - Volker Arolt
- Department of Psychiatry, University of Münster, Münster, Germany.
| | - Udo Dannlowski
- Institute for Translational Psychiatry, University of Münster, Münster, Germany.
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.
| | - Bernhard T Baune
- Department of Psychiatry, University of Münster, Münster, Germany; Department of Psychiatry, University of Melbourne, Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia.
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany; Centre for Human Genetics, University of Marburg, Marburg, Germany; Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany.
| | - Judith Alferink
- Department of Psychiatry, University of Münster, Münster, Germany; Cells in Motion Interfaculty Cluster, University of Münster, Münster, Germany.
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Mathey CM, Maj C, Scheer AB, Fazaal J, Wedi B, Wieczorek D, Amann PM, Löffler H, Koch L, Schöffl C, Dickel H, Ganjuur N, Hornung T, Forkel S, Greve J, Wurpts G, Hallberg P, Bygum A, Von Buchwald C, Karawajczyk M, Steffens M, Stingl J, Hoffmann P, Heilmann-Heimbach S, Mangold E, Ludwig KU, Rasmussen ER, Wadelius M, Sachs B, Nöthen MM, Forstner AJ. Molecular Genetic Screening in Patients With ACE Inhibitor/Angiotensin Receptor Blocker-Induced Angioedema to Explore the Role of Hereditary Angioedema Genes. Front Genet 2022; 13:914376. [PMID: 35923707 PMCID: PMC9339951 DOI: 10.3389/fgene.2022.914376] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Angioedema is a relatively rare but potentially life-threatening adverse reaction to angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs). As with hereditary forms of angioedema (HAE), this adverse reaction is mediated by bradykinin. Research suggests that ACEi/ARB-induced angioedema has a multifactorial etiology. In addition, recent case reports suggest that some ACEi/ARB-induced angioedema patients may carry pathogenic HAE variants. The aim of the present study was to investigate the possible association between ACEi/ARB-induced angioedema and HAE genes via systematic molecular genetic screening in a large cohort of ACEi/ARB-induced angioedema cases. Targeted re-sequencing of five HAE-associated genes (SERPING1, F12, PLG, ANGPT1, and KNG1) was performed in 212 ACEi/ARB-induced angioedema patients recruited in Germany/Austria, Sweden, and Denmark, and in 352 controls from a German cohort. Among patients, none of the identified variants represented a known pathogenic variant for HAE. Moreover, no significant association with ACEi/ARB-induced angioedema was found for any of the identified common [minor allele frequency (MAF) >5%] or rare (MAF < 5%) variants. However, several non-significant trends suggestive of possible protective effects were observed. The lowest p-value for an individual variant was found in PLG (rs4252129, p.R523W, p = 0.057, p.adjust > 0.999, Fisher’s exact test). Variant p.R523W was found exclusively in controls and has previously been associated with decreased levels of plasminogen, a precursor of plasmin which is part of a pathway directly involved in bradykinin production. In addition, rare, potentially functional variants (MAF < 5%, Phred-scaled combined annotation dependent depletion score >10) showed a nominally significant enrichment in controls both: 1) across all five genes; and 2) in the F12 gene alone. However, these results did not withstand correction for multiple testing. In conclusion, our results suggest that HAE-associated mutations are, at best, a rare cause of ACEi/ARB-induced angioedema. Furthermore, we were unable to identify a significant association between ACEi/ARB-induced angioedema and other variants in the investigated genes. Further studies with larger sample sizes are warranted to draw more definite conclusions concerning variants with limited effect sizes, including protective variants.
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Affiliation(s)
- Carina M. Mathey
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Annika B. Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Bettina Wedi
- Department of Dermatology and Allergy, Comprehensive Allergy Center, Hannover Medical School, Hannover, Germany
| | - Dorothea Wieczorek
- Department of Dermatology and Allergy, Comprehensive Allergy Center, Hannover Medical School, Hannover, Germany
| | - Philipp M. Amann
- Department of Dermatology, SLK Hospital Heilbronn, Heilbronn, Germany
| | - Harald Löffler
- Department of Dermatology, SLK Hospital Heilbronn, Heilbronn, Germany
| | - Lukas Koch
- Department of Dermatology and Venereology, Medical University Graz, Graz, Austria
| | - Clemens Schöffl
- Department of Dermatology and Venereology, Medical University Graz, Graz, Austria
| | - Heinrich Dickel
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, University Medical Center, Ruhr University Bochum, Bochum, Germany
| | - Nomun Ganjuur
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, University Medical Center, Ruhr University Bochum, Bochum, Germany
| | - Thorsten Hornung
- Department of Dermatology and Allergy, University Hospital of Bonn, Bonn, Germany
| | - Susann Forkel
- Department of Dermatology, Venereology and Allergology, University Medical Center Göttingen, Göttingen, Germany
| | - Jens Greve
- Department of Otorhinolaryngology—Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Gerda Wurpts
- Department of Dermatology and Allergy, Aachen Comprehensive Allergy Center, University Hospital RWTH Aachen, Aachen, Germany
| | - Pär Hallberg
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anette Bygum
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Christian Von Buchwald
- Department of Otorhinolaryngology—Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Julia Stingl
- Institute for Clinical Pharmacology, RWTH Aachen University, Aachen, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Eva R. Rasmussen
- Department of Otorhinolaryngology—Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bernhardt Sachs
- Department of Dermatology and Allergy, Aachen Comprehensive Allergy Center, University Hospital RWTH Aachen, Aachen, Germany
- Research Division, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Andreas J. Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
- *Correspondence: Andreas J. Forstner,
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Degenhardt F, Ellinghaus D, Juzenas S, Lerga-Jaso J, Wendorff M, Maya-Miles D, Uellendahl-Werth F, ElAbd H, Rühlemann MC, Arora J, Özer O, Lenning OB, Myhre R, Vadla MS, Wacker EM, Wienbrandt L, Blandino Ortiz A, de Salazar A, Garrido Chercoles A, Palom A, Ruiz A, Garcia-Fernandez AE, Blanco-Grau A, Mantovani A, Zanella A, Holten AR, Mayer A, Bandera A, Cherubini A, Protti A, Aghemo A, Gerussi A, Ramirez A, Braun A, Nebel A, Barreira A, Lleo A, Teles A, Kildal AB, Biondi A, Caballero-Garralda A, Ganna A, Gori A, Glück A, Lind A, Tanck A, Hinney A, Carreras Nolla A, Fracanzani AL, Peschuck A, Cavallero A, Dyrhol-Riise AM, Ruello A, Julià A, Muscatello A, Pesenti A, Voza A, Rando-Segura A, Solier A, Schmidt A, Cortes B, Mateos B, Nafria-Jimenez B, Schaefer B, Jensen B, Bellinghausen C, Maj C, Ferrando C, de la Horra C, Quereda C, Skurk C, Thibeault C, Scollo C, Herr C, Spinner CD, Gassner C, Lange C, Hu C, Paccapelo C, Lehmann C, Angelini C, Cappadona C, Azuure C, Bianco C, Cea C, Sancho C, Hoff DAL, Galimberti D, Prati D, Haschka D, Jiménez D, Pestaña D, Toapanta D, Muñiz-Diaz E, Azzolini E, Sandoval E, Binatti E, Scarpini E, Helbig ET, Casalone E, Urrechaga E, Paraboschi EM, Pontali E, Reverter E, Calderón EJ, Navas E, Solligård E, Contro E, Arana-Arri E, Aziz F, Garcia F, García Sánchez F, Ceriotti F, Martinelli-Boneschi F, Peyvandi F, Kurth F, Blasi F, Malvestiti F, Medrano FJ, Mesonero F, Rodriguez-Frias F, Hanses F, Müller F, Hemmrich-Stanisak G, Bellani G, Grasselli G, Pezzoli G, Costantino G, Albano G, Cardamone G, Bellelli G, Citerio G, Foti G, Lamorte G, Matullo G, Baselli G, Kurihara H, Neb H, My I, Kurth I, Hernández I, Pink I, de Rojas I, Galván-Femenia I, Holter JC, Afset JE, Heyckendorf J, Kässens J, Damås JK, Rybniker J, Altmüller J, Ampuero J, Martín J, Erdmann J, Banales JM, Badia JR, Dopazo J, Schneider J, Bergan J, Barretina J, Walter J, Hernández Quero J, Goikoetxea J, Delgado J, Guerrero JM, Fazaal J, Kraft J, Schröder J, Risnes K, Banasik K, Müller KE, Gaede KI, Garcia-Etxebarria K, Tonby K, Heggelund L, Izquierdo-Sanchez L, Bettini LR, Sumoy L, Sander LE, Lippert LJ, Terranova L, Nkambule L, Knopp L, Gustad LT, Garbarino L, Santoro L, Téllez L, Roade L, Ostadreza M, Intxausti M, Kogevinas M, Riveiro-Barciela M, Berger MM, Schaefer M, Niemi MEK, Gutiérrez-Stampa MA, Carrabba M, Figuera Basso ME, Valsecchi MG, Hernandez-Tejero M, Vehreschild MJGT, Manunta M, Acosta-Herrera M, D'Angiò M, Baldini M, Cazzaniga M, Grimsrud MM, Cornberg M, Nöthen MM, Marquié M, Castoldi M, Cordioli M, Cecconi M, D'Amato M, Augustin M, Tomasi M, Boada M, Dreher M, Seilmaier MJ, Joannidis M, Wittig M, Mazzocco M, Ciccarelli M, Rodríguez-Gandía M, Bocciolone M, Miozzo M, Imaz Ayo N, Blay N, Chueca N, Montano N, Braun N, Ludwig N, Marx N, Martínez N, Cornely OA, Witzke O, Palmieri O, Faverio P, Preatoni P, Bonfanti P, Omodei P, Tentorio P, Castro P, Rodrigues PM, España PP, Hoffmann P, Rosenstiel P, Schommers P, Suwalski P, de Pablo R, Ferrer R, Bals R, Gualtierotti R, Gallego-Durán R, Nieto R, Carpani R, Morilla R, Badalamenti S, Haider S, Ciesek S, May S, Bombace S, Marsal S, Pigazzini S, Klein S, Pelusi S, Wilfling S, Bosari S, Volland S, Brunak S, Raychaudhuri S, Schreiber S, Heilmann-Heimbach S, Aliberti S, Ripke S, Dudman S, Wesse T, Zheng T, Bahmer T, Eggermann T, Illig T, Brenner T, Pumarola T, Feldt T, Folseraas T, Gonzalez Cejudo T, Landmesser U, Protzer U, Hehr U, Rimoldi V, Monzani V, Skogen V, Keitel V, Kopfnagel V, Friaza V, Andrade V, Moreno V, Albrecht W, Peter W, Poller W, Farre X, Yi X, Wang X, Khodamoradi Y, Karadeniz Z, Latiano A, Goerg S, Bacher P, Koehler P, Tran F, Zoller H, Schulte EC, Heidecker B, Ludwig KU, Fernández J, Romero-Gómez M, Albillos A, Invernizzi P, Buti M, Duga S, Bujanda L, Hov JR, Lenz TL, Asselta R, de Cid R, Valenti L, Karlsen TH, Cáceres M, Franke A. Detailed stratified GWAS analysis for severe COVID-19 in four European populations. Hum Mol Genet 2022; 31:3945-3966. [PMID: 35848942 PMCID: PMC9703941 DOI: 10.1093/hmg/ddac158] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 01/14/2022] [Revised: 06/11/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022] Open
Abstract
Given the highly variable clinical phenotype of Coronavirus disease 2019 (COVID-19), a deeper analysis of the host genetic contribution to severe COVID-19 is important to improve our understanding of underlying disease mechanisms. Here, we describe an extended genome-wide association meta-analysis of a well-characterized cohort of 3255 COVID-19 patients with respiratory failure and 12 488 population controls from Italy, Spain, Norway and Germany/Austria, including stratified analyses based on age, sex and disease severity, as well as targeted analyses of chromosome Y haplotypes, the human leukocyte antigen region and the SARS-CoV-2 peptidome. By inversion imputation, we traced a reported association at 17q21.31 to a ~0.9-Mb inversion polymorphism that creates two highly differentiated haplotypes and characterized the potential effects of the inversion in detail. Our data, together with the 5th release of summary statistics from the COVID-19 Host Genetics Initiative including non-Caucasian individuals, also identified a new locus at 19q13.33, including NAPSA, a gene which is expressed primarily in alveolar cells responsible for gas exchange in the lung.
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Affiliation(s)
- Frauke Degenhardt
- To whom correspondence should be addressed. (Frauke Degenhardt) and (Andre Franke)
| | | | | | | | | | | | | | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Jatin Arora
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA,Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
| | - Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Ole Bernt Lenning
- Research Department, Stavanger University Hospital, Stavanger, Norway,Randaberg Municipality, Stavanger, Norway
| | - Ronny Myhre
- Division of Health Data and Digitalization, Department of Genetics and Bioinformatics (HDGB), Norwegian Institute of Public Health, Oslo, Norway
| | - May Sissel Vadla
- Randaberg Municipality, Stavanger, Norway,Department of Quality and Health Technology, Faculty of Health Sciences, University of Stavanger, Stavanger, Norway
| | - Eike M Wacker
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Lars Wienbrandt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Aaron Blandino Ortiz
- Department of Intensive Care, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Adolfo de Salazar
- Ibs.Granada Instituto de Investigación Biosanitaria, Granada, Spain,Microbiology Unit. Hospital Universitario Clinico San Cecilio, Granada, Spain
| | - Adolfo Garrido Chercoles
- Clinical Biochemistry Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, San Sebastian, Spain
| | - Adriana Palom
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain,Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Agustín Ruiz
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain,CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | | | - Albert Blanco-Grau
- Department of Biochemistry, University Hospital Vall d’Hebron, Barcelona, Spain
| | - Alberto Mantovani
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Alberto Zanella
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Aleksander Rygh Holten
- Department of Acute Medicine, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alena Mayer
- Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Alessandra Bandera
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Alessandro Protti
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Alessio Aghemo
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Alessio Gerussi
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy,Division of Gastroenterology, School of Medicine and Surgery, Center for Autoimmune Liver Diseases, University of Milano-Bicocca, Milan, Italy
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany,Department of Psychiatry, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
| | - Alice Braun
- Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Ana Barreira
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ana Lleo
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Ana Teles
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Anders Benjamin Kildal
- Department of Anesthesiology and Intensive Care, University Hospital of North Norway, Tromsø, Norway
| | - Andrea Biondi
- Pediatric Departement, Centro Tettamanti-European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM/Ospedale, San Gerardo, Italy
| | | | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Andrea Gori
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy,Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Andreas Glück
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Andreas Lind
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Anja Tanck
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anna Carreras Nolla
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Anna Ludovica Fracanzani
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Anna Peschuck
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | | | - Anne Ma Dyrhol-Riise
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Infectious diseases, Oslo University Hospital, Oslo, Norway
| | | | - Antonio Julià
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | | | - Antonio Pesenti
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Voza
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Ariadna Rando-Segura
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain,Universitat Autònoma de Barcelona, Bellatera, Spain
| | - Aurora Solier
- Department of Respiratory Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), University of Alcalá, Madrid, Spain
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Beatriz Cortes
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Beatriz Mateos
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Gastroenterology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Beatriz Nafria-Jimenez
- Clinical Biochemistry Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, San Sebastian, Spain
| | - Benedikt Schaefer
- Department of Medicine I, Gastroenterology, Hepatology and Endocrinology, Medical University of Innsbruck, Innsbruck, Austria,Christian Doppler Laboratory of Iron and Phosphate Biology at the Department of Medicine I, Medical University of Innsbruck, Innsbruck, Austria
| | - Björn Jensen
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Germany
| | - Carla Bellinghausen
- Department of Respiratory Medicine and Allergology, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, Medical Faculty University of Bonn, Bonn, Germany
| | - Carlos Ferrando
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain,Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Carmen de la Horra
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Carmen Quereda
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | | | | | - Chiara Scollo
- Department of Transfusion Medicine and Haematology Laboratory, San Gerardo Hospital, Monza, Italy
| | - Christian Herr
- Department of Internal Medicine V—Pneumology, Allergology and Intensive Care Medicine, University Hospital Saarland, Homburg, Germany
| | - Christoph D Spinner
- Department of Internal Medicine II, School of Medicine, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
| | - Christoph Gassner
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,Institute of Translational Medicine, Private University in the Principality of Liechtenstein (UFL), Triesen, Liechtenstein
| | - Christoph Lange
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany,Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany,Clinical Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
| | - Cinzia Hu
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cinzia Paccapelo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Clara Lehmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,German Center for Infection Research (DZIF), Cologne, Germany
| | | | - Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Clinton Azuure
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | | | - Cristiana Bianco
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Cea
- Department of Biochemistry, University Hospital Vall d’Hebron, Barcelona, Spain
| | - Cristina Sancho
- Osakidetza Basque Health Service, Basurto University Hospital, Respiratory Service, Bilbao, Spain
| | - Dag Arne Lihaug Hoff
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway,Department of Medicine, Møre and Romsdal Hospital Trust, Ålesund, Norway
| | - Daniela Galimberti
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Prati
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - David Haschka
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - David Jiménez
- Department of Respiratory Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), University of Alcalá, Madrid, Spain
| | - David Pestaña
- Department of Anesthesiology and Critical Care, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - David Toapanta
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Eduardo Muñiz-Diaz
- Immunohematology Department, Banc de Sang i Teixits, Autonomous University of Barcelona, Barcelona, Spain
| | - Elena Azzolini
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Elena Sandoval
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Eleonora Binatti
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy,Division of Gastroenterology, School of Medicine and Surgery, Center for Autoimmune Liver Diseases, University of Milano-Bicocca, Milan, Italy
| | - Elio Scarpini
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Elisabetta Casalone
- Department of Medical Sciences, Università degli Studi di Torino, Turin, Italy
| | - Eloisa Urrechaga
- Osakidetza Basque Health Service, Galdakao Hospital, Respiratory Service, Galdakao, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Elvezia Maria Paraboschi
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Emanuele Pontali
- Department of Infectious Diseases, E.O. Ospedali Galliera, Genova, Italy
| | - Enric Reverter
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Enrique J Calderón
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Enrique Navas
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Erik Solligård
- Geminicenter for Sepsis Research, Institute of Circulation and Medical Imaging (ISB), NTNU, Trondheim, Norway,Clinic of Anesthesia and Intensive Care, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ernesto Contro
- Accident and Emergency and Emergency Medicine Unit, San Gerardo Hospital, Monza, Italy
| | | | - Fátima Aziz
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Federico Garcia
- Ibs.Granada Instituto de Investigación Biosanitaria, Granada, Spain,Microbiology Unit. Hospital Universitario Clinico San Cecilio, Granada, Spain,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Félix García Sánchez
- Histocompatibilidad y Biologia Molecular, Centro de Transfusion de Madrid, Madrid, Spain
| | | | - Filippo Martinelli-Boneschi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy,Neurology Unit, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Flora Peyvandi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - Florian Kurth
- Charite Universitätsmedizin Berlin, Berlin, Germany,Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Department of Medicine I, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Francesco Blasi
- Respiratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | | | - Francisco J Medrano
- Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Consejo Superior de Investigaciones Científicas, Sevilla, Spain,Internal Medicine Department, Virgen del Rocio University Hospital, Sevilla, Spain
| | - Francisco Mesonero
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Gastroenterology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain,Department of Biochemistry, University Hospital Vall d’Hebron, Barcelona, Spain,Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain,Universitat Autònoma de Barcelona, Bellatera, Spain,Biochemistry Department, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Frank Hanses
- Emergency Department, University Hospital Regensburg, Regensburg, Germany,Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Regensburg, Germany
| | - Fredrik Müller
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Giacomo Bellani
- Department Emergency, Anesthesia and Intensive Care, San Gerardo Hospital, Monza, Italy,School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Giacomo Grasselli
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gianni Pezzoli
- Fondazione Grigioni per il Morbo di Parkinson and Parkinson Institute, ASST Gaetano Pini-CTO, Milan, Italy
| | - Giorgio Costantino
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Giuseppe Bellelli
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy,Acute Geriatric Unit, San Gerardo Hospital, Monza, Italy
| | - Giuseppe Citerio
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy,Neurointensive Care Unit, San Gerardo Hospital, Monza, Italy
| | - Giuseppe Foti
- Department Emergency, Anesthesia and Intensive Care, San Gerardo Hospital, Monza, Italy,School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Giuseppe Lamorte
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, Università degli Studi di Torino, Turin, Italy
| | - Guido Baselli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Holger Neb
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ilaria My
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Isabel Hernández
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain,CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Isabell Pink
- Department of Pneumology, Hannover Medical School, Hannover, Germany
| | - Itziar de Rojas
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain,CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Iván Galván-Femenia
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Jan Cato Holter
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jan Egil Afset
- Osakidetza Basque Health Service, Basurto University Hospital, Respiratory Service, Bilbao, Spain,Department of Medical Microbiology, Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway
| | - Jan Heyckendorf
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany,Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany,Clinical Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
| | - Jan Kässens
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Jan Kristian Damås
- Department of Infectious Diseases, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway,Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,German Centre for Infection Research (DZIF), Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Javier Ampuero
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany,German Research Center for Cardiovascular Research, Lübeck, Germany,University Heart Center Lübeck, Lübeck, Germany
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Joan Ramon Badia
- Respiratory ICU, Institut Clínic Respiratory, Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Joaquin Dopazo
- Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,Bioinformatics Area, Fundación Progreso y Salud, and Institute of Biomedicine of Sevilla (IBIS), Sevilla, Spain
| | - Jochen Schneider
- Department of Internal Medicine V—Pneumology, Allergology and Intensive Care Medicine, University Hospital Saarland, Homburg, Germany
| | - Jonas Bergan
- Department of Research, Ostfold Hospital Trust, Gralum, Norway
| | - Jordi Barretina
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Jörn Walter
- Department of Genetics & Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jose Hernández Quero
- Ibs.Granada Instituto de Investigación Biosanitaria, Granada, Spain,Department of Infectious Diseases, Hospital Universitario Clinico San Cecilio, Granada, Spain
| | - Josune Goikoetxea
- Infectious Diseases Service, Osakidetza, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Juan Delgado
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Juan M Guerrero
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Kraft
- Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Kari Risnes
- Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway,Department of Research, St. Olav Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karl Erik Müller
- Medical Department, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Karoline I Gaede
- Research Center Borstel, BioMaterialBank Nord, Borstel, Germany,German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany,Popgen 2.0 Network (P2N), Kiel, Germany
| | - Koldo Garcia-Etxebarria
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Kristian Tonby
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Infectious diseases, Oslo University Hospital, Oslo, Norway
| | - Lars Heggelund
- Medical Department, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Laura Izquierdo-Sanchez
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain,Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Laura Rachele Bettini
- Pediatric Departement, Centro Tettamanti-European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM/Ospedale, San Gerardo, Italy
| | - Lauro Sumoy
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | | | | | | | - Lindokuhle Nkambule
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Stanley Center for Psychiatric Research & Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa Knopp
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Germany
| | - Lise Tuset Gustad
- Geminicenter for Sepsis Research, Institute of Circulation and Medical Imaging (ISB), NTNU, Trondheim, Norway,Clinic of Medicine and Rehabilitation, Levanger Hospital, Nord-Trondelag Hospital Trust, Levanger, Norway
| | | | - Luigi Santoro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luis Téllez
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Gastroenterology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Luisa Roade
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain,Department of Respiratory Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | | | - Maider Intxausti
- Osakidetza Basque Health Service, Basurto University Hospital, Respiratory Service, Bilbao, Spain
| | - Manolis Kogevinas
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,ISGlobal, Barcelona, Spain,Universitat Pompeu Fabra (UPF), Barcelona, Spain,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain,Universitat Autònoma de Barcelona, Bellatera, Spain
| | - Marc M Berger
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Mari E K Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - María A Gutiérrez-Stampa
- Osakidetza, OSI Donostialdea, Altza Primary Care, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Maria Carrabba
- Internal Medicine Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria E Figuera Basso
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Maria Grazia Valsecchi
- Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | | | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Manunta
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Mariella D'Angiò
- Pediatric Departement, Centro Tettamanti-European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM/Ospedale, San Gerardo, Italy
| | - Marina Baldini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marina Cazzaniga
- Phase 1 Research Centre, ASST Monza, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Marit M Grimsrud
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Division of Surgery, Inflammatory Diseases and Transplantation, Research Institute for Internal Medicine, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway,Division of Surgery, Inflammatory Diseases and Transplantation, Department of Transplantation Medicine, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Marta Marquié
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain,CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | | | - Mattia Cordioli
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Maurizio Cecconi
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Mauro D'Amato
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain,Gastrointestinal Genetics Lab, CIC bioGUNE—BRTA, Derio, Spain,Department of Medicine and Surgery, LUM University, Casamassima, Italy
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,German Center for Infection Research (DZIF), Cologne, Germany
| | - Melissa Tomasi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mercè Boada
- Research Center and Memory Clinic, Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain,CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Michael Dreher
- Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, Aachen, Germany
| | - Michael J Seilmaier
- Munich Clinic Schwabing, Academic Teaching Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Michael Joannidis
- Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Medical University Innsbruck, Innsbruck, Austria
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | | | | | - Miguel Rodríguez-Gandía
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Gastroenterology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | | | - Monica Miozzo
- University of Milan, Milan, Italy,Internal Medicine Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Natale Imaz Ayo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Natalia Blay
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Natalia Chueca
- Microbiology Unit. Hospital Universitario Clinico San Cecilio, Granada, Spain
| | - Nicola Montano
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nicole Braun
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Center of Human and Molecular Biology, University Hospital Saarland, Homburg/Saar, Germany
| | - Nikolaus Marx
- Department of Internal Medicine I, RWTH Aachen University Hospital, Aachen, Germany
| | - Nilda Martínez
- Department of Anesthesiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,German Center for Infection Research (DZIF), Cologne, Germany,Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Orazio Palmieri
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Paola Faverio
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy,Pulmonary Unit, San Gerardo Hospital, Monza, Italy
| | | | - Paolo Bonfanti
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy,Infectious Diseases Unit, San Gerardo Hospital, Monza, Italy
| | - Paolo Omodei
- Humanitas Clinical and Research Center, IRCCS, Milan, Italy
| | | | - Pedro Castro
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
| | - Pedro M Rodrigues
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain,Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Pedro Pablo España
- Osakidetza Basque Health Service, Galdakao Hospital, Respiratory Service, Galdakao, Spain
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,German Center for Infection Research (DZIF), Cologne, Germany
| | | | - Raúl de Pablo
- Department of Intensive Care, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d'Hebron University Hospital, SODIR-VHIR research group, Barcelona, Spain
| | - Robert Bals
- Department of Internal Medicine V—Pneumology, Allergology and Intensive Care Medicine, University Hospital Saarland, Homburg, Germany
| | - Roberta Gualtierotti
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Rocío Gallego-Durán
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
| | - Rosa Nieto
- Department of Respiratory Diseases, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), University of Alcalá, Madrid, Spain
| | - Rossana Carpani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Rubén Morilla
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | | | - Sammra Haider
- Department of Medicine, Møre & Romsdal Hospital Trust, Molde, Norway
| | - Sandra Ciesek
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany,German Centre for Infection Research (DZIF), Frankfurt am Main, Germany
| | - Sandra May
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Sara Bombace
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Sara Marsal
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Sara Pigazzini
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sebastian Klein
- Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Medical University Innsbruck, Innsbruck, Austria
| | - Serena Pelusi
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sibylle Wilfling
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Regensburg, Germany,Zentrum für Humangenetik Regensburg, Regensburg, Germany,Department of Neurology, Bezirksklinikum Regensburg, University of Regensburg, Regensburg, Germany
| | - Silvano Bosari
- University of Milan, Milan, Italy,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonja Volland
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Soumya Raychaudhuri
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA,Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA,Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefano Aliberti
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | - Susanne Dudman
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tanja Wesse
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | | | - Thomas Bahmer
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Thorsten Brenner
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Tomas Pumarola
- Department of Microbiology, University Hospital Vall d’Hebron, Barcelona, Spain,Autonoma University of Barcelona, Barcelona, Spain
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Germany
| | - Trine Folseraas
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Division of Surgery, Inflammatory Diseases and Transplantation, Research Institute for Internal Medicine, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway,Division of Surgery, Inflammatory Diseases and Transplantation, Department of Transplantation Medicine, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway,Division for Cancer Medicine, Surgery and Transplantation, Section for Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | | | - Ulf Landmesser
- Berlin Institute of Health, Charite Universitätsmedizin Berlin, Berlin Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany,German Center for Infection Research (DZIF), Munich, Germany
| | - Ute Hehr
- Zentrum für Humangenetik Regensburg, Regensburg, Germany
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Valter Monzani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Vegard Skogen
- Department of Infectious Diseases, University Hospital of North Norway, Tromsø, Norway,Faculty of Health Sciences, UIT The Arctic University of Norway, Norway
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Germany
| | - Verena Kopfnagel
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Vicente Friaza
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Victor Andrade
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Victor Moreno
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,Catalan Institute of Oncology (ICO), Barcelona, Spain,Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain,Universitat de Barcelona (UB), Barcelona, Spain
| | - Wolfgang Albrecht
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Wolfgang Peter
- Stefan-Morsch-Stiftung, Birkenfeld, Germany,Faculty of Medicine and University Hospital Cologne, Institute for Transfusion Medicine, University of Cologne, Cologne, Germany
| | | | - Xavier Farre
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Xiaoli Yi
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Xiaomin Wang
- Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Anna Latiano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Siegfried Goerg
- Institute of Transfusionsmedicine, University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,Institute of Immunology, Christian-Albrechts-University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Philipp Koehler
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Heinz Zoller
- Department of Medicine I, Gastroenterology, Hepatology and Endocrinology, Medical University of Innsbruck, Innsbruck, Austria,Christian Doppler Laboratory of Iron and Phosphate Biology at the Department of Medicine I, Medical University of Innsbruck, Innsbruck, Austria
| | - Eva C Schulte
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany,Institute of Psychiatric Phenomics and Genomics, University Medical Center, University of Munich, Munich, Germany,Department of Psychiatry, University Medical Center, University of Munich, Munich, Germany
| | | | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Javier Fernández
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain,European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain
| | - Manuel Romero-Gómez
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain,Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain,University of Sevilla, Sevilla, Spain,Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain
| | - Agustín Albillos
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Gastroenterology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University of Alcalá, Madrid, Spain
| | - Pietro Invernizzi
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy,Division of Gastroenterology, School of Medicine and Surgery, Center for Autoimmune Liver Diseases, University of Milano-Bicocca, Milan, Italy
| | - Maria Buti
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain,Universitat Autònoma de Barcelona, Bellatera, Spain
| | - Stefano Duga
- IRCCS Humanitas Research Hospital, Milan, Italy,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute—Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | | | | | | | | | | | | | | | - Andre Franke
- To whom correspondence should be addressed. (Frauke Degenhardt) and (Andre Franke)
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Dwyer DB, Buciuman MO, Ruef A, Kambeitz J, Sen Dong M, Stinson C, Kambeitz-Ilankovic L, Degenhardt F, Sanfelici R, Antonucci LA, Lalousis PA, Wenzel J, Urquijo-Castro MF, Popovic D, Oeztuerk OF, Haas SS, Weiske J, Hauke D, Neufang S, Schmidt-Kraepelin C, Ruhrmann S, Penzel N, Lichtenstein T, Rosen M, Chisholm K, Riecher-Rössler A, Egloff L, Schmidt A, Andreou C, Hietala J, Schirmer T, Romer G, Michel C, Rössler W, Maj C, Borisov O, Krawitz PM, Falkai P, Pantelis C, Lencer R, Bertolino A, Borgwardt S, Noethen M, Brambilla P, Schultze-Lutter F, Meisenzahl E, Wood SJ, Davatzikos C, Upthegrove R, Salokangas RKR, Koutsouleris N. Clinical, Brain, and Multilevel Clustering in Early Psychosis and Affective Stages. JAMA Psychiatry 2022; 79:677-689. [PMID: 35583903 PMCID: PMC9118078 DOI: 10.1001/jamapsychiatry.2022.1163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Indexed: 12/13/2022]
Abstract
Importance Approaches are needed to stratify individuals in early psychosis stages beyond positive symptom severity to investigate specificity related to affective and normative variation and to validate solutions with premorbid, longitudinal, and genetic risk measures. Objective To use machine learning techniques to cluster, compare, and combine subgroup solutions using clinical and brain structural imaging data from early psychosis and depression stages. Design, Setting, and Participants A multisite, naturalistic, longitudinal cohort study (10 sites in 5 European countries; including major follow-up intervals at 9 and 18 months) with a referred patient sample of those with clinical high risk for psychosis (CHR-P), recent-onset psychosis (ROP), recent-onset depression (ROD), and healthy controls were recruited between February 1, 2014, to July 1, 2019. Data were analyzed between January 2020 and January 2022. Main Outcomes and Measures A nonnegative matrix factorization technique separately decomposed clinical (287 variables) and parcellated brain structural volume (204 gray, white, and cerebrospinal fluid regions) data across CHR-P, ROP, ROD, and healthy controls study groups. Stability criteria determined cluster number using nested cross-validation. Validation targets were compared across subgroup solutions (premorbid, longitudinal, and schizophrenia polygenic risk scores). Multiclass supervised machine learning produced a transferable solution to the validation sample. Results There were a total of 749 individuals in the discovery group and 610 individuals in the validation group. Individuals included those with CHR-P (n = 287), ROP (n = 323), ROD (n = 285), and healthy controls (n = 464), The mean (SD) age was 25.1 (5.9) years, and 702 (51.7%) were female. A clinical 4-dimensional solution separated individuals based on positive symptoms, negative symptoms, depression, and functioning, demonstrating associations with all validation targets. Brain clustering revealed a subgroup with distributed brain volume reductions associated with negative symptoms, reduced performance IQ, and increased schizophrenia polygenic risk scores. Multilevel results distinguished between normative and illness-related brain differences. Subgroup results were largely validated in the external sample. Conclusions and Relevance The results of this longitudinal cohort study provide stratifications beyond the expression of positive symptoms that cut across illness stages and diagnoses. Clinical results suggest the importance of negative symptoms, depression, and functioning. Brain results suggest substantial overlap across illness stages and normative variation, which may highlight a vulnerability signature independent from specific presentations. Premorbid, longitudinal, and genetic risk validation suggested clinical importance of the subgroups to preventive treatments.
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Affiliation(s)
- Dominic B Dwyer
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Madalina-Octavia Buciuman
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Anne Ruef
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Joseph Kambeitz
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Mark Sen Dong
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Caedyn Stinson
- Max-Planck School of Cognition, Leipzig, Germany.,Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Lana Kambeitz-Ilankovic
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rachele Sanfelici
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Max-Planck Institute of Psychiatry, Munich, Germany
| | - Linda A Antonucci
- Department of Education, Psychology, Communication, University of Bari Aldo Moro, Bari, Italy
| | - Paris Alexandros Lalousis
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, United Kingdom
| | - Julian Wenzel
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | | | - David Popovic
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Oemer Faruk Oeztuerk
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Shalaila S Haas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Johanna Weiske
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Daniel Hauke
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland.,Early Intervention Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom.,Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Susanne Neufang
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Stephan Ruhrmann
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Nora Penzel
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Theresa Lichtenstein
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Marlene Rosen
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Katharine Chisholm
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, United Kingdom.,Department of Psychology, Aston University, Birmingham, United Kingdom
| | | | - Laura Egloff
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland
| | - André Schmidt
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland
| | - Christina Andreou
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland
| | - Jarmo Hietala
- Department of Psychiatry, University of Turku, Turku, Finland
| | - Timo Schirmer
- GE Healthcare GmbH (previously GE Global Research GmbH), Munich, Germany
| | - Georg Romer
- Department of Child and Adolescent Psychiatry, University of Münster, Münster, Germany
| | - Chantal Michel
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland
| | - Wulf Rössler
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zurich, Zurich, Switzerland
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Max-Planck Institute of Psychiatry, Munich, Germany
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, University of Melbourne & Melbourne Health, Melbourne, Victoria, Australia
| | - Rebekka Lencer
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany.,Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Alessandro Bertolino
- Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Stefan Borgwardt
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland.,Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Markus Noethen
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Paolo Brambilla
- Department of Neurosciences and Mental Health, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Frauke Schultze-Lutter
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany.,University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland.,Department of Psychology, Faculty of Psychology, Airlangga University, Surabaya, Indonesia
| | | | - Stephen J Wood
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia.,Orygen, the National Centre of Excellence for Youth Mental Health, Melbourne, Victoria, Australia
| | - Christos Davatzikos
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rachel Upthegrove
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, United Kingdom.,Early Intervention Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Max-Planck Institute of Psychiatry, Munich, Germany.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
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Aldisi R, Hassanin E, Sivalingam S, Buness A, Klinkhammer H, Mayr A, Fröhlich H, Krawitz P, Maj C. GenRisk: A tool for comprehensive genetic risk modeling. Bioinformatics 2022; 38:2651-2653. [PMID: 35266528 PMCID: PMC9048672 DOI: 10.1093/bioinformatics/btac152] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/04/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Summary The genetic architecture of complex traits can be influenced by both many common regulatory variants with small effect sizes and rare deleterious variants in coding regions with larger effect sizes. However, the two kinds of genetic contributions are typically analyzed independently. Here, we present GenRisk, a python package for the computation and the integration of gene scores based on the burden of rare deleterious variants and common-variants-based polygenic risk scores. The derived scores can be analyzed within GenRisk to perform association tests or to derive phenotype prediction models by testing multiple classification and regression approaches. GenRisk is compatible with VCF input file formats. Availability and implementation GenRisk is an open source publicly available python package that can be downloaded or installed from Github (https://github.com/AldisiRana/GenRisk). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rana Aldisi
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Emadeldin Hassanin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany.,Core Unit for Bioinformatics Analysis, University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany.,Core Unit for Bioinformatics Analysis, University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany.,Bonn-Aachen International Center for IT (b-it), University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany.,Centre for Human Genetics, University of Marburg, Marburg, Germany
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Hassanin E, May P, Aldisi R, Spier I, Forstner AJ, Nöthen MM, Aretz S, Krawitz P, Bobbili DR, Maj C. Breast and prostate cancer risk: The interplay of polygenic risk, rare pathogenic germline variants, and family history. Genet Med 2022; 24:576-585. [PMID: 34906469 DOI: 10.1016/j.gim.2021.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 06/06/2021] [Revised: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
PURPOSE We aimed to investigate to what extent polygenic risk scores (PRS), rare pathogenic germline variants (PVs), and family history jointly influence breast cancer and prostate cancer risk. METHODS A total of 200,643 individuals from the UK Biobank were categorized as follows: (1) heterozygotes or nonheterozygotes for PVs in moderate to high-risk cancer genes, (2) PRS strata, and (3) with or without a family history of cancer. Multivariable logistic regression and Cox proportional hazards models were used to compute the odds ratio across groups and the cumulative incidence through life. RESULTS Cumulative incidence by age 70 years among the nonheterozygotes across PRS strata ranged from 9% to 32% and from 9% to 35% for breast cancer and prostate cancer, respectively. Among the PV heterozygotes it ranged from 20% to 48% in moderate-risk genes and from 51% to 74% in high-risk genes for breast cancer, and it ranged from 30% to 59% in prostate cancer risk genes. Family history was always associated with an increased cancer odds ratio. CONCLUSION PRS alone provides a meaningful risk gradient leading to a cancer risk stratification comparable to PVs in moderate risk genes, whereas acts as a risk modifier when considering high-risk genes. Including family history along with PV and PRS further improves cancer risk stratification.
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Affiliation(s)
- Emadeldin Hassanin
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rana Aldisi
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Centre for Human Genetics, Philipps-University Marburg, Marburg, Germany; Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Dheeraj Reddy Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany.
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Maj C, Salvi E, Citterio L, Borisov O, Simonini M, Glorioso V, Barlassina C, Glorioso N, Thijs L, Kuznetsova T, Cappuccio FP, Zhang ZY, Staessen JA, Cusi D, Lanzani C, Manunta P. Dissecting the Polygenic Basis of Primary Hypertension: Identification of Key Pathway-Specific Components. Front Cardiovasc Med 2022; 9:814502. [PMID: 35252394 PMCID: PMC8888857 DOI: 10.3389/fcvm.2022.814502] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/13/2021] [Accepted: 01/19/2022] [Indexed: 12/11/2022] Open
Abstract
Introduction and Objectives Genome-wide association studies have identified a high number of genetic loci associated with hypertension suggesting the presence of an underlying polygenic architecture. In this study, we aimed to dissect the polygenic component of primary hypertension searching also for pathway-specific components. Methods The polygenic risk score (PRS) models, based on the UK biobank genetic signals for hypertension status, were obtained on a target Italian case/control cohort including 561 cases and 731 hyper-normal controls from HYPERGENES, and were then applied to an independent validation cohort composed by multi-countries European-based samples including 1,284 cases and 960 hyper-normal controls. Results The resulting genome-wide PRS was capable of stratifying the individuals for hypertension risk by comparing between individuals in the last PRS decile and the median decile: we observed an odds ratio (OR) of 3.62, CI = [2.01, 6.32] (P = 9.01E-07) and 3.22, 95% CI = [2.06, 5.10] (P = 6.47E-08) in the target and validation cohorts, respectively. The relatively high case/control ORs across PRS quantiles corroborates the presence of strong polygenic components which could be driven by an enrichment of risk alleles within the cases but also by potential enrichment of protective alleles in the old normotensive controls. Moreover, novel pathway-specific PRS revealed an enrichment of the polygenic signal attributable to specific biological pathways. Among those the most significantly associated with hypertension status was the calcium signaling pathway together with other mainly related such as the phosphatidylinositol/inositol phosphate pathways. Conclusions The development of pathway-specific PRS could prioritize biological mechanisms, according to their contribution to the genetic susceptibility, whose regulations might be a potential pharmacological preventive target.
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Affiliation(s)
- Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- *Correspondence: Carlo Maj
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Lorena Citterio
- Genomics of Renal Diseases and Hypertension Unit, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Marco Simonini
- Genomics of Renal Diseases and Hypertension Unit, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Valeria Glorioso
- Department of Statistics and Quantitative Methods, University of Milano-Bicocca, Milan, Italy
| | | | - Nicola Glorioso
- Department of Clinical and Experimental Medicine, Hypertension and Related Diseases Centre, University of Sassari, Sassari, Italy
| | - Lutgarde Thijs
- Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Tatiana Kuznetsova
- Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Francesco P. Cappuccio
- Warwick Medical School, and UHCW NHS Trust, University of Warwick, Coventry, United Kingdom
| | - Zhen-Yu Zhang
- Research Unit Hypertension and Cardiovascular Epidemiology, KU Leuven Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Jan A. Staessen
- Research Institute Alliance for the Promotion of Preventive Medicine (APPREMED), Mechelen, Belgium
- Biomedical Science Group, Faculty of Medicine, University of Leuven, Leuven, Belgium
| | - Daniele Cusi
- Institute of Biomedical Technologies Milano National Research Council of Italy (CNR), Milano, Italy
- Bio4Dreams Scientific Unit, Bio4Dreams-Business Nursery for Life Sciences, Milano, Italy
| | - Chiara Lanzani
- Genomics of Renal Diseases and Hypertension Unit, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Manunta
- Genomics of Renal Diseases and Hypertension Unit, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
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van der Zanden LFM, Maj C, Borisov O, van Rooij IALM, Quaedackers JSLT, Steffens M, Schierbaum L, Schneider S, Waffenschmidt L, Kiemeney LALM, de Wall LLL, Heilmann S, Hofmann A, Gehlen J, Schumacher J, Szczepanska M, Taranta-Janusz K, Kroll P, Krzemien G, Szmigielska A, Schreuder MF, Weber S, Zaniew M, Roeleveld N, Reutter H, Feitz WFJ, Hilger AC. Genome-wide association study in patients with posterior urethral valves. Front Pediatr 2022; 10:988374. [PMID: 36238604 PMCID: PMC9552614 DOI: 10.3389/fped.2022.988374] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Congenital lower urinary tract obstructions (LUTO) are most often caused by posterior urethral valves (PUV), a male limited anatomical obstruction of the urethra affecting 1 in 4,000 male live births. Little is known about the genetic background of PUV. Here, we report the largest genome-wide association study (GWAS) for PUV in 4 cohorts of patients and controls. The final meta-analysis included 756 patients and 4,823 ethnicity matched controls and comprised 5,754,208 variants that were genotyped or imputed and passed quality control in all 4 cohorts. No genome-wide significant locus was identified, but 33 variants showed suggestive significance (P < 1 × 10-5). When considering only loci with multiple variants residing within < 10 kB of each other showing suggestive significance and with the same effect direction in all 4 cohorts, 3 loci comprising a total of 9 variants remained. These loci resided on chromosomes 13, 16, and 20. The present GWAS and meta-analysis is the largest genetic study on PUV performed to date. The fact that no genome-wide significant locus was identified, can be explained by lack of power or may indicate that common variants do not play a major role in the etiology of PUV. Nevertheless, future studies are warranted to replicate and validate the 3 loci that yielded suggestive associations.
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Affiliation(s)
- Loes F M van der Zanden
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Iris A L M van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Luca Schierbaum
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sophia Schneider
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Lea Waffenschmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Lambertus A L M Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Liesbeth L L de Wall
- Division of Pediatric Urology, Department of Urology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children's Hospital, Nijmegen, Netherlands
| | - Stefanie Heilmann
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Aybike Hofmann
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, Regensburg, Germany
| | - Jan Gehlen
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | | | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Zabrze, Poland
| | | | - Pawel Kroll
- Neurourology Unit, Pediatric Surgery and Urology Clinic, Poznań, Poland
| | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children's Hospital, Nijmegen, Netherlands
| | - Stefanie Weber
- University Children Hospital Marburg, Philipps University Marburg, Marburg, Germany
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Heiko Reutter
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Wout F J Feitz
- Division of Pediatric Urology, Department of Urology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children's Hospital, Nijmegen, Netherlands
| | - Alina C Hilger
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.,Research Center on Rare Kidney Diseases, University Hospital Erlangen, Erlangen, Germany
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38
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Henne SK, Hochfeld LM, Maj C, Nöthen MM, Heilmann-Heimbach S. Systematic investigation of a potential epidemiological and genetic association between male androgenetic alopecia and COVID-19. Skin Health Dis 2021; 1:e72. [PMID: 34901950 PMCID: PMC8646653 DOI: 10.1002/ski2.72] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022]
Abstract
Background Male androgenetic alopecia (AGA) has been implicated as a putative risk factor in severe COVID‐19 based on high incidences of advanced AGA in male hospitalized COVID‐19 patients. Research further suggests that androgen signalling, which plays a central role in AGA aetiology, promotes SARS‐CoV‐2 infection and is associated with severe COVID‐19 symptoms in men. Objectives We aimed to systematically investigate a potential association between AGA and COVID‐19 both on an epidemiological and a genetic level in a large single‐population cohort. Methods We performed regression, genetic correlation and polygenic risk score (PRS) analyses using data from the UK Biobank and published GWAS data on AGA and COVID‐19. Results Our analyses did not reveal any significant epidemiological or genome‐wide genetic association between AGA and severe COVID‐19. Pathway‐based PRS analyses however revealed a significant association in specific pathways, namely vitamin metabolism, natural killer cell‐mediated cytotoxicity, WNT signalling and aryl hydrocarbon receptor signalling. Limitations We restricted our analyses to the white British population and used self‐reported AGA status. Sample size may be a limitation in our regression and PRS analyses. Conclusions Our data yield no evidence for an epidemiological association between AGA and COVID‐19 but suggest that a shared genetic basis for both traits exists in specific pathways.
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Affiliation(s)
- S K Henne
- Institute of Human Genetics School of Medicine & University Hospital Bonn University of Bonn Bonn Germany
| | - L M Hochfeld
- Institute of Human Genetics School of Medicine & University Hospital Bonn University of Bonn Bonn Germany
| | - C Maj
- Institute for Genomic Statistics and Bioinformatics University of Bonn Bonn Germany
| | - M M Nöthen
- Institute of Human Genetics School of Medicine & University Hospital Bonn University of Bonn Bonn Germany
| | - S Heilmann-Heimbach
- Institute of Human Genetics School of Medicine & University Hospital Bonn University of Bonn Bonn Germany
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39
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Schmidt A, Peters S, Knaus A, Sabir H, Hamsen F, Maj C, Fazaal J, Sivalingam S, Savchenko O, Mantri A, Holzinger D, Neudorf U, Müller A, Ludwig KU, Krawitz PM, Engels H, Nöthen MM, Bagci S. TBK1 and TNFRSF13B mutations and an autoinflammatory disease in a child with lethal COVID-19. NPJ Genom Med 2021; 6:55. [PMID: 34210994 PMCID: PMC8249618 DOI: 10.1038/s41525-021-00220-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 02/02/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
Among children, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are typically mild. Here, we describe the case of a 3.5-year-old girl with an unusually severe presentation of coronavirus disease (COVID-19). The child had an autoinflammatory disorder of unknown etiology, which had been treated using prednisolone and methotrexate, and her parents were half cousins of Turkish descent. After 5 days of nonspecific viral infection symptoms, tonic-clonic seizures occurred followed by acute cardiac insufficiency, multi-organ insufficiency, and ultimate death. Trio exome sequencing identified a homozygous splice-variant in the gene TBK1, and a homozygous missense variant in the gene TNFRSF13B. Heterozygous deleterious variants in the TBK1 gene have been associated with severe COVID-19, and the variant in the TNFRSF13B gene has been associated with common variable immunodeficiency (CVID). We suggest that the identified variants, the autoinflammatory disorder and its treatment, or a combination of these factors probably predisposed to lethal COVID-19 in the present case.
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Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Hemmen Sabir
- Neonatology and Pediatric Intensive Care, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frauke Hamsen
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Bonn, Germany
| | - Oleksandr Savchenko
- Department of Diagnostic and Interventional Radiology, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Aakash Mantri
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Neudorf
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Andreas Müller
- Neonatology and Pediatric Intensive Care, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
| | - Soyhan Bagci
- Neonatology and Pediatric Intensive Care, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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40
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Thieme F, Henschel L, Hammond NL, Ishorst N, Hausen J, Adamson AD, Biedermann A, Bowes J, Zieger HK, Maj C, Kruse T, Buness A, Hoischen A, Gilissen C, Kreusch T, Jäger A, Gölz L, Braumann B, Aldhorae K, Rojas-Martinez A, Krawitz PM, Mangold E, Dixon MJ, Ludwig KU. Extending the allelic spectrum at noncoding risk loci of orofacial clefting. Hum Mutat 2021; 42:1066-1078. [PMID: 34004033 DOI: 10.1002/humu.24219] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 11/08/2022]
Abstract
Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.
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Affiliation(s)
- Frederic Thieme
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nigel L Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nina Ishorst
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jonas Hausen
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Antony D Adamson
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Angelika Biedermann
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Hanna K Zieger
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Carlo Maj
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Andreas Buness
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany.,Department of Orthodontics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Bert Braumann
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Khalid Aldhorae
- Department of Orthodontics, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey, Mexico
| | - Peter M Krawitz
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Kerstin U Ludwig
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
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41
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Maj C, Chiarenza GA, Faraone SV, Miriam C, Gennarelli M, Bonvicini C, Scassellati C. Intermediate lengths of the C9ORF72 hexanucleotide repeat expansion may synergistically contribute to attention deficit hyperactivity disorder in child and his father: case report. Neurocase 2021; 27:138-146. [PMID: 33730968 DOI: 10.1080/13554794.2021.1887275] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We have summarized the abstract section as follows: "We report a son and his father affected by Attention Deficit Hyperactivity Disorder (ADHD). They belonged to a larger cohort (116 ADHD children, 20 related parents, 77 controls) wholly genotyped forC9ORF72 expansion. Ten ADHD susceptibility genes were further investigated in the family. We revealed that son and father shared an intermediateC9ORF72 expansion and common variants inCDH23, ITGAE and MTRR. Bioinformatics highlighted aC9ORF72-MTRR interaction. This case-report underlines that in relatives with ADHD, carrying variants in ADHD susceptibility genes, the intermediateC9ORF72 repeats might have a potentially pathogenetic synergistic effect, supporting the multifactorial polygenic aetiopathogenetic profile of disease".
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Affiliation(s)
- Carlo Maj
- Genetics Unit, IRCCS Istituto Centro San Giovanni Di Dio Fatebenefratelli, Brescia, Italy.,Istitute for Genomic Statistics and Bioinformatics, Bonn, Germany
| | | | - Stephen V Faraone
- Department of Biomedicine, K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway; Department of Biomedicine, K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Ciani Miriam
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni Di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni Di Dio Fatebenefratelli, Brescia, Italy.,Section of Biology and Genetic, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Cristian Bonvicini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni Di Dio Fatebenefratelli, Brescia, Italy
| | - Catia Scassellati
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni Di Dio Fatebenefratelli, Brescia, Italy
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42
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Koutsouleris N, Dwyer DB, Degenhardt F, Maj C, Urquijo-Castro MF, Sanfelici R, Popovic D, Oeztuerk O, Haas SS, Weiske J, Ruef A, Kambeitz-Ilankovic L, Antonucci LA, Neufang S, Schmidt-Kraepelin C, Ruhrmann S, Penzel N, Kambeitz J, Haidl TK, Rosen M, Chisholm K, Riecher-Rössler A, Egloff L, Schmidt A, Andreou C, Hietala J, Schirmer T, Romer G, Walger P, Franscini M, Traber-Walker N, Schimmelmann BG, Flückiger R, Michel C, Rössler W, Borisov O, Krawitz PM, Heekeren K, Buechler R, Pantelis C, Falkai P, Salokangas RKR, Lencer R, Bertolino A, Borgwardt S, Noethen M, Brambilla P, Wood SJ, Upthegrove R, Schultze-Lutter F, Theodoridou A, Meisenzahl E. Multimodal Machine Learning Workflows for Prediction of Psychosis in Patients With Clinical High-Risk Syndromes and Recent-Onset Depression. JAMA Psychiatry 2021; 78:195-209. [PMID: 33263726 PMCID: PMC7711566 DOI: 10.1001/jamapsychiatry.2020.3604] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
IMPORTANCE Diverse models have been developed to predict psychosis in patients with clinical high-risk (CHR) states. Whether prediction can be improved by efficiently combining clinical and biological models and by broadening the risk spectrum to young patients with depressive syndromes remains unclear. OBJECTIVES To evaluate whether psychosis transition can be predicted in patients with CHR or recent-onset depression (ROD) using multimodal machine learning that optimally integrates clinical and neurocognitive data, structural magnetic resonance imaging (sMRI), and polygenic risk scores (PRS) for schizophrenia; to assess models' geographic generalizability; to test and integrate clinicians' predictions; and to maximize clinical utility by building a sequential prognostic system. DESIGN, SETTING, AND PARTICIPANTS This multisite, longitudinal prognostic study performed in 7 academic early recognition services in 5 European countries followed up patients with CHR syndromes or ROD and healthy volunteers. The referred sample of 167 patients with CHR syndromes and 167 with ROD was recruited from February 1, 2014, to May 31, 2017, of whom 26 (23 with CHR syndromes and 3 with ROD) developed psychosis. Patients with 18-month follow-up (n = 246) were used for model training and leave-one-site-out cross-validation. The remaining 88 patients with nontransition served as the validation of model specificity. Three hundred thirty-four healthy volunteers provided a normative sample for prognostic signature evaluation. Three independent Swiss projects contributed a further 45 cases with psychosis transition and 600 with nontransition for the external validation of clinical-neurocognitive, sMRI-based, and combined models. Data were analyzed from January 1, 2019, to March 31, 2020. MAIN OUTCOMES AND MEASURES Accuracy and generalizability of prognostic systems. RESULTS A total of 668 individuals (334 patients and 334 controls) were included in the analysis (mean [SD] age, 25.1 [5.8] years; 354 [53.0%] female and 314 [47.0%] male). Clinicians attained a balanced accuracy of 73.2% by effectively ruling out (specificity, 84.9%) but ineffectively ruling in (sensitivity, 61.5%) psychosis transition. In contrast, algorithms showed high sensitivity (76.0%-88.0%) but low specificity (53.5%-66.8%). A cybernetic risk calculator combining all algorithmic and human components predicted psychosis with a balanced accuracy of 85.5% (sensitivity, 84.6%; specificity, 86.4%). In comparison, an optimal prognostic workflow produced a balanced accuracy of 85.9% (sensitivity, 84.6%; specificity, 87.3%) at a much lower diagnostic burden by sequentially integrating clinical-neurocognitive, expert-based, PRS-based, and sMRI-based risk estimates as needed for the given patient. Findings were supported by good external validation results. CONCLUSIONS AND RELEVANCE These findings suggest that psychosis transition can be predicted in a broader risk spectrum by sequentially integrating algorithms' and clinicians' risk estimates. For clinical translation, the proposed workflow should undergo large-scale international validation.
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Affiliation(s)
- Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany,Max-Planck Institute of Psychiatry, Munich, Germany,Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Dominic B. Dwyer
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | | | - Rachele Sanfelici
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany,Max-Planck School of Cognition, Leipzig, Germany
| | - David Popovic
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Oemer Oeztuerk
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Shalaila S. Haas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Johanna Weiske
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Anne Ruef
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Lana Kambeitz-Ilankovic
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Linda A. Antonucci
- Department of Education, Psychology, and Communication, University of Bari Aldo Moro, Bari, Italy
| | - Susanne Neufang
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Stephan Ruhrmann
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Nora Penzel
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Joseph Kambeitz
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Theresa K. Haidl
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Marlene Rosen
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Katharine Chisholm
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
| | - Anita Riecher-Rössler
- Department of Psychiatry, Psychiatric University Hospital, University of Basel, Switzerland
| | - Laura Egloff
- Department of Psychiatry, Psychiatric University Hospital, University of Basel, Switzerland
| | - André Schmidt
- Department of Psychiatry, Psychiatric University Hospital, University of Basel, Switzerland
| | - Christina Andreou
- Department of Psychiatry, Psychiatric University Hospital, University of Basel, Switzerland
| | - Jarmo Hietala
- Department of Psychiatry, University of Turku, Turku, Finland
| | - Timo Schirmer
- GE Healthcare GmbH (previously GE Global Research GmbH), Munich, Germany
| | - Georg Romer
- Department of Child and Adolescent Psychiatry, University of Münster, Münster, Germany
| | - Petra Walger
- Department of Child and Adolescent Psychiatry, Psychotherapy and Psychosomatics, LVR Clinic Düsseldorf, Düsseldorf, Germany
| | - Maurizia Franscini
- Department of Child and Adolescent Psychiatry and Psychotherapy, University of Zürich, Zürich, Switzerland
| | - Nina Traber-Walker
- Department of Child and Adolescent Psychiatry and Psychotherapy, University of Zürich, Zürich, Switzerland
| | - Benno G. Schimmelmann
- University Hospital of Child and Adolescent Psychiatry, University Hospital Hamburg-Eppendorf, Hamburg, Germany,University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland
| | - Rahel Flückiger
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland
| | - Chantal Michel
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland
| | - Wulf Rössler
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zurich, Zurich, Switzerland
| | - Oleg Borisov
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M. Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Karsten Heekeren
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zurich, Zurich, Switzerland,Department of Psychiatry and Psychotherapy I, LVR Hospital Cologne, Cologne, Germany
| | - Roman Buechler
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zurich, Zurich, Switzerland,Department of Neuroradiology, University Hospital of Zurich, Zurich, Switzerland
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, University of Melbourne and Melbourne Health, Melbourne, Australia
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany,Max-Planck Institute of Psychiatry, Munich, Germany
| | | | - Rebekka Lencer
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany,Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Alessandro Bertolino
- Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Stefan Borgwardt
- Department of Psychiatry, Psychiatric University Hospital, University of Basel, Switzerland,Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Markus Noethen
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Paolo Brambilla
- Department of Neurosciences and Mental Health, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Stephen J. Wood
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Australia,Orygen, the National Centre of Excellence for Youth Mental Health, Melbourne, Australia
| | - Rachel Upthegrove
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
| | - Frauke Schultze-Lutter
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany,Department of Psychology and Mental Health, Faculty of Psychology, Airlangga University, Surabaya, Indonesia
| | - Anastasia Theodoridou
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zurich, Zurich, Switzerland
| | - Eva Meisenzahl
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
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Dong J, Maj C, Tsavachidis S, Ostrom QT, Gharahkhani P, Anderson LA, Wu AH, Ye W, Bernstein L, Borisov O, Schröder J, Chow WH, Gammon MD, Liu G, Caldas C, Pharoah PD, Risch HA, May A, Gerges C, Anders M, Venerito M, Schmidt T, Izbicki JR, Hölscher AH, Schumacher B, Vashist Y, Neuhaus H, Rösch T, Knapp M, Krawitz P, Böhmer A, Iyer PG, Reid BJ, Lagergren J, Shaheen NJ, Corley DA, Gockel I, Fitzgerald RC, Cook MB, Whiteman DC, Vaughan TL, Schumacher J, Thrift AP. Sex-Specific Genetic Associations for Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterology 2020; 159:2065-2076.e1. [PMID: 32918910 PMCID: PMC9057456 DOI: 10.1053/j.gastro.2020.08.052] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/04/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Esophageal adenocarcinoma (EA) and its premalignant lesion, Barrett's esophagus (BE), are characterized by a strong and yet unexplained male predominance (with a male-to-female ratio in EA incidence of up to 6:1). Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for these conditions. However, potential sex differences in genetic associations with BE/EA remain largely unexplored. METHODS Given strong genetic overlap, BE and EA cases were combined into a single case group for analysis. These were compared with population-based controls. We performed sex-specific GWAS of BE/EA in 3 separate studies and then used fixed-effects meta-analysis to provide summary estimates for >9 million variants for male and female individuals. A series of downstream analyses were conducted separately in male and female individuals to identify genes associated with BE/EA and the genetic correlations between BE/EA and other traits. RESULTS We included 6758 male BE/EA cases, 7489 male controls, 1670 female BE/EA cases, and 6174 female controls. After Bonferroni correction, our meta-analysis of sex-specific GWAS identified 1 variant at chromosome 6q11.1 (rs112894788, KHDRBS2-MTRNR2L9, PBONF = .039) that was statistically significantly associated with BE/EA risk in male individuals only, and 1 variant at chromosome 8p23.1 (rs13259457, PRSS55-RP1L1, PBONF = 0.057) associated, at borderline significance, with BE/EA risk in female individuals only. We also observed strong genetic correlations of BE/EA with gastroesophageal reflux disease in male individuals and obesity in female individuals. CONCLUSIONS The identified novel sex-specific variants associated with BE/EA could improve the understanding of the genetic architecture of the disease and the reasons for the male predominance.
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Affiliation(s)
- Jing Dong
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas; Division of Hematology and Oncology, Department of Medicine, Cancer Center, and Genomic Sciences & Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Germany
| | - Spiridon Tsavachidis
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Quinn T Ostrom
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lesley A Anderson
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland & Aberdeen Center for Health Data Science, University of Aberdeen, Scotland
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, California
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Wong-Ho Chow
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Geoffrey Liu
- Pharmacogenomic Epidemiology, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Paul D Pharoah
- Department of Oncology, University of Cambridge, Cambridge, UK; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Andrea May
- Department of Medicine II, Sana Klinikum, Offenbach, Germany
| | - Christian Gerges
- Department of Internal Medicine II, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Mario Anders
- Department of Gastroenterology and Interdisciplinary Endoscopy, Vivantes Wenckebach-Klinikum, Berlin, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Arnulf H Hölscher
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Brigitte Schumacher
- Department of Internal Medicine and Gastroenterology, Elisabeth Hospital, Essen, Germany
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Horst Neuhaus
- Department of Internal Medicine II, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Germany
| | - Anne Böhmer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brian J Reid
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jesper Lagergren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Nicholas J Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, California; San Francisco Medical Center, Kaiser Permanente Northern California, San Francisco, California
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Rebecca C Fitzgerald
- Medical Research Council (MRC) Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - David C Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thomas L Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Aaron P Thrift
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas.
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Cattaneo A, Suderman M, Cattane N, Mazzelli M, Begni V, Maj C, D'Aprile I, Pariante CM, Luoni A, Berry A, Wurst K, Hommers L, Domschke K, Cirulli F, Szyf M, Menke A, Riva MA. Long-term effects of stress early in life on microRNA-30a and its network: Preventive effects of lurasidone and potential implications for depression vulnerability. Neurobiol Stress 2020; 13:100271. [PMID: 33344724 PMCID: PMC7739180 DOI: 10.1016/j.ynstr.2020.100271] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 08/24/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Exposure to early life stress can interfere with neurodevelopmental trajectories to increase the vulnerability for psychiatric disorders later in life. With this respect, epigenetic mechanisms play a key role for the long-lasting changes in brain functions that may elicit and sustain psychopathologic outcomes. Here, we investigated DNA methylation changes as possible epigenetic mechanism mediating the effect of prenatal stress (PNS), an experimental paradigm associated with behavioral and molecular alterations relevant for psychiatric disorders. We identified 138 genes as being differentially methylated in the prefrontal cortex (PFC) and in the hippocampus (HIP) of male and female adult rats exposed to PNS. Among these genes, miR-30a and Neurod1 emerged as potential players for the negative outcomes associated with PNS exposure. Indeed, in addition to showing consistent methylation differences in both brain regions and in both sexes, and interacting with each other, they are both involved in Axon guidance and Neurotrophin signaling, which are important to neurodevelopmental disorders. We also found a significant reduction in the expression of a panel of genes (CAMK2A, c-JUN, LIMK1, MAP2K1, MAP2K2, PIK3CA and PLCG1) that belong to these two biological pathways and are also validated targets of miR-30a, pointing to a down-regulation of these pathways as a consequence of PNS exposure. Interestingly, we also found that miR-30a levels were significantly upregulated in depressed patients exposed to childhood trauma, as compared to control individuals. Importantly, we also found that a sub-chronic treatment with the atypical antipsychotic drug, lurasidone, during adolescence was able to prevent the up-regulation of miR-30a and normalized the expression of its target genes in response to PNS exposure. Our results demonstrate that miR-30a undergoes epigenetic changes following early life stress exposure and suggest that this miRNA could play a key role in producing broad and long-lasting alterations in neuroplasticity-related pathways, contributing to the etiology of psychiatric disorders. MiR-30a and Neurod1 undergo epigenetic changes following PNS exposure. MiR-30 and Neurod1 are involved in Axon guidance and Neurotrophin signaling, two important pathways for neurodevelopment. We found lower expression levels of a panel of genes targeted by miR-30a. MiR-30a was significantly up-regulated in depressed patients exposed to childhood trauma. A chronic treatment with lurasidone during adolescence prevented the up-regulation of miR-30a following PNS exposure.
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Affiliation(s)
- Annamaria Cattaneo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133, Milan, Italy.,Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BSB 1TH, UK
| | - Nadia Cattane
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Monica Mazzelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133, Milan, Italy.,Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133, Milan, Italy
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany
| | - Ilari D'Aprile
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Carmine M Pariante
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, United Kingdom
| | - Alessia Luoni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133, Milan, Italy
| | - Alessandra Berry
- Section of Behavioural Neurosciences, Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Katharina Wurst
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital, Würzburg, Germany
| | - Leif Hommers
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital, Würzburg, Germany.,Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Francesca Cirulli
- Section of Behavioural Neurosciences, Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade #1311, Montreal, Quebec, Canada, H3G 1Y6
| | - Andreas Menke
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital, Würzburg, Germany.,Interdisciplinary Center for Clinical Research, University Hospital of Würzburg, Germany.,Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco A Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133, Milan, Italy
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Scassellati C, Ciani M, Maj C, Geroldi C, Zanetti O, Gennarelli M, Bonvicini C. Behavioral and Psychological Symptoms of Dementia (BPSD): Clinical Characterization and Genetic Correlates in an Italian Alzheimer's Disease Cohort. J Pers Med 2020; 10:jpm10030090. [PMID: 32823921 PMCID: PMC7563608 DOI: 10.3390/jpm10030090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/25/2020] [Revised: 08/05/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The occurrence of Behavioral and Psychological Symptoms of Dementia (BPSD) in Alzheimer's Disease (AD) patients hampers the clinical management and exacerbates the burden for caregivers. The definition of the clinical distribution of BPSD symptoms, and the extent to which symptoms are genetically determined, are still open to debate. Moreover, genetic factors that underline BPSD symptoms still need to be identified. PURPOSE To characterize our Italian AD cohort according to specific BPSD symptoms as well as to endophenotypes. To evaluate the associations between the considered BPSD traits and COMT, MTHFR, and APOE genetic variants. METHODS AD patients (n = 362) underwent neuropsychological examination and genotyping. BPSD were assessed with the Neuropsychiatric Inventory scale. RESULTS APOE and MTHFR variants were significantly associated with specific single BPSD symptoms. Furthermore, "Psychosis" and "Hyperactivity" resulted in the most severe endophenotypes, with APOE and MTHFR implicated as both single risk factors and "genexgene" interactions. CONCLUSIONS We strongly suggest the combined use of both BPSD single symptoms/endophenotypes and the "genexgene" interactions as valid strategies for expanding the knowledge about the BPSD aetiopathogenetic mechanisms.
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Affiliation(s)
- Catia Scassellati
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy; (C.S.); (C.M.); (M.G.)
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy;
| | - Carlo Maj
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy; (C.S.); (C.M.); (M.G.)
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, 53127 Bonn, Germany
| | - Cristina Geroldi
- Alzheimer’s Research Unit-Memory Clinic, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy; (C.G.); (O.Z.)
| | - Orazio Zanetti
- Alzheimer’s Research Unit-Memory Clinic, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy; (C.G.); (O.Z.)
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy; (C.S.); (C.M.); (M.G.)
- Section of Biology and Genetic, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Cristian Bonvicini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy;
- Correspondence:
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46
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Maj C, Tosato S, Zanardini R, Lasalvia A, Favaro A, Leuci E, De Girolamo G, Ruggeri M, Gennarelli M, Bocchio-Chiavetto L. Correlations between immune and metabolic serum markers and schizophrenia/bipolar disorder polygenic risk score in first-episode psychosis. Early Interv Psychiatry 2020; 14:507-511. [PMID: 31749237 DOI: 10.1111/eip.12906] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/09/2019] [Accepted: 10/31/2019] [Indexed: 01/01/2023]
Abstract
AIMS There is a strong interest in identifying the biological mechanisms involved in the genetic risk for psychotic disorders. In this study, we evaluated the correlation between serum concentrations of specific molecular markers and the genetic component for schizophrenia and bipolar disorder. METHODS We analysed the association between the polygenic risk score (PRS) and the serum levels of different inflammatory/metabolic markers in a sample of 81 first-episode psychosis patients (FEP) with a diagnosis of schizophrenia or bipolar disorder and 33 controls. RESULTS A positive correlation of schizophrenia and bipolar disorder PRS with the inflammatory marker C-C Motif Chemokine Ligand 4 serum concentration (ρ = 0.42, P = 1.56 × 10-04 and ρ = 0.40, P = 1.65 × 10-03 , respectively) and a negative correlation with the serum ghrelin content (ρ = - 0.35, P = 4.27 × 10-03 and ρ = - 0.45, P = 6.05 × 10-04 , respectively) were observed. CONCLUSION These findings provide new insight into the biological underpinnings of the PRS component, thus supporting a role of the genetic liability on the inflammatory and metabolic alterations that characterize psychosis onset.
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Affiliation(s)
- Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany.,Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Sarah Tosato
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Psychiatry, University of Verona, Italy
| | - Roberta Zanardini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Antonio Lasalvia
- UOC Psichiatria, Azienda Ospedaliera Universitaria Integrata (AOUI) di Verona, Verona, Italy
| | - Angela Favaro
- Department of Neurosciences, University of Padua and Azienda Ospedaliera, Padua, Italy
| | | | - Giovanni De Girolamo
- Psychiatric Epidemiology and Evaluation Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Mirella Ruggeri
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Psychiatry, University of Verona, Italy
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Italy
| | | | - Luisella Bocchio-Chiavetto
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Faculty of Psychology, eCampus University, Novedrate (Como), Italy
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Wienbergen H, Fach A, Erdmann J, Katalinic A, Eisemann N, Krawitz P, Maj C, Borisov O, Munz M, Noethen M, Meyer-Saraei R, Osteresch R, Schmucker J, Linke A, Eitel I, Hambrecht R, Langer H. New technologies for intensive prevention programs after myocardial infarction: rationale and design of the NET-IPP trial. Clin Res Cardiol 2020; 110:153-161. [DOI: 10.1007/s00392-020-01695-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
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Mazzelli M, Maj C, Mariani N, Mora C, Begni V, Pariante CM, Riva MA, Cattaneo A, Cattane N. The Long-Term Effects of Early Life Stress on the Modulation of miR-19 Levels. Front Psychiatry 2020; 11:389. [PMID: 32499725 PMCID: PMC7243913 DOI: 10.3389/fpsyt.2020.00389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/17/2020] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs), one of the major small non-coding RNA classes, have been proposed as regulatory molecules in neurodevelopment and stress response. Although alterations in miRNAs profiles have been implicated in several psychiatric and neurodevelopmental disorders, the contribution of individual miRNAs in brain development and function is still unknown. Recent studies have identified miR-19 as a key regulator of brain trajectories, since it drives the differentiation of neural stem cells into mature neurons. However, no findings are available on how vulnerability factors for these disorders, such as early life stress (ELS), can modulate the expression of miR-19 and its target genes. To reach our aim, we investigated miR-19 modulation in human hippocampal progenitor stem cells (HPCs) treated with cortisol during 3 days of proliferation and harvested immediately after the end of the treatment or after 20 days of differentiation into mature neurons. We also analyzed the long-term expression changes of miR-19 and of its validated target genes, involved in neurodevelopment and inflammation, in the hippocampus of adult rats exposed or not to prenatal stress (PNS). Interestingly, we observed a significant downregulation of miR-19 levels both in proliferating (FC = −1.59, p-value = 0.022 for miR-19a; FC = −1.79, p-value = 0.016 for miR-19b) as well as differentiated HPCs (FC = −1.28, p-value = 0.065 for miR-19a; FC = −1.75, p-value = 0.047 for miR-19b) treated with cortisol. Similarly, we found a long-term decrease of miR-19 levels in the hippocampus of adult PNS rats (FC = −1.35, p-value = 0.025 for miR-19a; FC = −1.43, p-value = 0.032 for miR-19b). Among all the validated target genes, we observed a significant increase of NRCAM (FC = 1.20, p-value = 0.027), IL4R (FC = 1.26, p-value = 0.046), and RAPGEF2 (FC = 1.23, p-value = 0.020).We suggest that ELS can cause a long-term downregulation of miR-19 levels, which may be responsible of alterations in neurodevelopmental pathways and in immune/inflammatory processes, leading to an enhanced risk for mental disorders later in life. Intervention strategies targeting miR-19 may prevent alterations in these pathways, reducing the ELS-related effects.
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Affiliation(s)
- Monica Mazzelli
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany
| | - Nicole Mariani
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Cristina Mora
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Carmine M Pariante
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Marco A Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Annamaria Cattaneo
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Nadia Cattane
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
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Bonvicini C, Scassellati C, Benussi L, Di Maria E, Maj C, Ciani M, Fostinelli S, Mega A, Bocchetta M, Lanzi G, Giacopuzzi E, Ferraboli S, Pievani M, Fedi V, Defanti CA, Giliani S, Frisoni GB, Ghidoni R, Gennarelli M. Next Generation Sequencing Analysis in Early Onset Dementia Patients. J Alzheimers Dis 2020; 67:243-256. [PMID: 30530974 PMCID: PMC6398561 DOI: 10.3233/jad-180482] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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] [Indexed: 12/13/2022]
Abstract
Background: Early onset dementias (EOD) are rare neurodegenerative dementias that present before 65 years. Genetic factors have a substantially higher pathogenetic contribution in EOD patients than in late onset dementia. Objective: To identify known and/or novel rare variants in major candidate genes associated to EOD by high-throughput sequencing. Common-risk variants of apolipoprotein E (APOE) and prion protein (PRNP) genes were also assessed. Methods: We studied 22 EOD patients recruited in Memory Clinics, in the context of studies investigating genetic forms of dementia. Two methodological approaches were applied for the target-Next Generation Sequencing (NGS) analysis of these patients. In addition, we performed progranulin plasma dosage, C9Orf72 hexanucleotide repeat expansion analysis, and APOE genotyping. Results: We detected three rare known pathogenic mutations in the GRN and PSEN2 genes and eleven unknown-impact mutations in the GRN, VCP, MAPT, FUS, TREM2, and NOTCH3 genes. Six patients were carriers of only common risk variants (APOE and PRNP), and one did not show any risk mutation/variant. Overall, 69% (n = 9) of our early onset Alzheimer’s disease (EAOD) patients, compared with 34% (n = 13) of sporadic late onset Alzheimer’s disease (LOAD) patients and 27% (n = 73) of non-affected controls (ADNI, whole genome data), were carriers of at least two rare/common risk variants in the analyzed candidate genes panel, excluding the full penetrant mutations. Conclusion: This study suggests that EOD patients without full penetrant mutations are characterized by higher probability to carry polygenic risk alleles that patients with LOAD forms. This finding is in line with recently reported evidence, thus suggesting that the genetic risk factors identified in LOAD might modulate the risk also in EOAD.
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Affiliation(s)
- Cristian Bonvicini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Catia Scassellati
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Emilio Di Maria
- Department of Health Sciences, University of Genova and Division of Medical Genetics, Galliera Hospital, Genova, Italy
| | - Carlo Maj
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Institute for Genomic Statistics and Bioinformatics, Bonn, Germany
| | - Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Silvia Fostinelli
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Anna Mega
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Martina Bocchetta
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Gaetana Lanzi
- A. Nocivelli' Institute for Molecular Medicine Spedali Civili and University of Brescia, Brescia, Italy
| | - Edoardo Giacopuzzi
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sergio Ferraboli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Michela Pievani
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Carlo Alberto Defanti
- Fondazione Europea Ricerca Biomedica, Centro di Eccellenza Alzheimer, Ospedale Briolini Gazzaniga, Bergamo, Italy
| | - Silvia Giliani
- A. Nocivelli' Institute for Molecular Medicine Spedali Civili and University of Brescia, Brescia, Italy
| | | | - Giovanni Battista Frisoni
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Laboratory of Neuroimaging of Aging (LANVIE), University Hospitals and University of Geneva, Geneva, Switzerland; Department of Internal Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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50
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Mazzelli M, Maj C, Mariani N, Mora C, Begni V, Pariante CM, Riva MA, Cattaneo A, Cattane N. Corrigendum: The Long-Term Effects of Early Life Stress on the Modulation of miR-19 Levels. Front Psychiatry 2020; 11:643932. [PMID: 33679461 PMCID: PMC7928271 DOI: 10.3389/fpsyt.2020.643932] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 12/24/2020] [Indexed: 12/05/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fpsyt.2020.00389.].
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Affiliation(s)
- Monica Mazzelli
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany
| | - Nicole Mariani
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Cristina Mora
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Carmine M Pariante
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Marco A Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Annamaria Cattaneo
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Nadia Cattane
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
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