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Thromb Haemost 2023; 123(04): 438-452
DOI: 10.1055/s-0043-1760844
Stroke, Systemic or Venous Thromboembolism

Multiallelic Copy Number Variation in ORM1 is Associated with Plasma Cell-Free DNA Levels as an Intermediate Phenotype for Venous Thromboembolism

Laura Martin-Fernandez 
1   Genomics of Complex Diseases Unit, Research Institute Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
2   Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain
3   Fundación Española de Trombosis y Hemostasia (FETH), Madrid, Spain
4   Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
,
Iris Garcia-Martínez 
2   Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain
4   Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
,
Sonia Lopez 
1   Genomics of Complex Diseases Unit, Research Institute Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
,
Angel Martinez-Perez 
1   Genomics of Complex Diseases Unit, Research Institute Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
,
Noelia Vilalta
5   Hemostasis and Thrombosis Unit, Department of Hematology, Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
,
Melania Plaza
5   Hemostasis and Thrombosis Unit, Department of Hematology, Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
,
Carla Moret
5   Hemostasis and Thrombosis Unit, Department of Hematology, Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
,
Ana Viñuela
6   Biosciences Institute, Faculty of Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
,
Andrew A. Brown
7   Population Health and Genomics, University of Dundee, Dundee, Scotland, United Kingdom
,
Nikolaos I. Panousis
8   Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, South Cambridgeshire, United Kingdom
9   Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
,
Alfonso Buil
10   Institute of Biological Psychiatry, Mental Health Sct. Hans Hospital, Roskilde, Denmark
,
Emmanouil T. Dermitzakis
9   Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
,
Irene Corrales
2   Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain
4   Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
11   Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto Carlos III (ISCIII), Madrid, Spain
,
Juan Carlos Souto
5   Hemostasis and Thrombosis Unit, Department of Hematology, Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
,
Francisco Vidal 
2   Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain
4   Transfusional Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
11   Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto Carlos III (ISCIII), Madrid, Spain
,
Jose Manuel Soria
1   Genomics of Complex Diseases Unit, Research Institute Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
› Author Affiliations Funding This study was supported by grants of the Spanish Government Instituto de Salud Carlos III and Fondo de Investigación Sanitaria (ISCIII-FIS) (PI14/00582, PI20/00325, J.M.S. and S.L.; PI21/01772, J.C.S.), the Grupo Consolidado Generalitat de Catalunya (SGR 1736, J.M.S.), the CERCA Programme/Generalitat de Catalunya, the Fundación Española de Trombosis y Hemostasia (FETH, L.M.-F.), and the nonprofit association Activa'TT por la Salud. CIBERCV is an initiative of the ISCIII, and is co-financed by the European Regional Development Fund (ERDF), “A way to make Europe.”
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Abstract

Venous thromboembolism (VTE) is a common disease with high heritability. However, only a small portion of the genetic variance of VTE can be explained by known genetic risk factors. Neutrophil extracellular traps (NETs) have been associated with prothrombotic activity. Therefore, the genetic basis of NETs could reveal novel risk factors for VTE. A recent genome-wide association study of plasma cell-free DNA (cfDNA) levels in the Genetic Analysis of Idiopathic Thrombophilia 2 (GAIT-2) Project showed a significant associated locus near ORM1. We aimed to further explore this candidate region by next-generation sequencing, copy number variation (CNV) quantification, and expression analysis using an extreme phenotype sampling design involving 80 individuals from the GAIT-2 Project. The RETROVE study with 400 VTE cases and 400 controls was used to replicate the results. A total of 105 genetic variants and a multiallelic CNV (mCNV) spanning ORM1 were identified in GAIT-2. Of these, 17 independent common variants, a region of 22 rare variants, and the mCNV were significantly associated with cfDNA levels. In addition, eight of these common variants and the mCNV influenced ORM1 expression. The association of the mCNV and cfDNA levels was replicated in RETROVE (p-value = 1.19 × 10−6). Additional associations between the mCNV and thrombin generation parameters were identified. Our results reveal that increased mCNV dosages in ORM1 decreased gene expression and upregulated cfDNA levels. Therefore, the mCNV in ORM1 appears to be a novel marker for cfDNA levels, which could contribute to VTE risk.

Keywords

cell-free DNA - neutrophil extracellular traps - α-1-acid glycoprotein - venous thrombosis - genetics

Supplementary Material



Publication History

Received: 02 June 2022

Accepted: 20 November 2022

Article published online:
25 January 2023

© 2023. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 

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