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Bard AM, Clark LV, Cosgun E, Aldinger KA, Timms A, Quina LA, Ferres JML, Jardine D, Haas EA, Becker TM, Pagan CM, Santani A, Martinez D, Barua S, McNutt Z, Nesbitt A, Mitchell EA, Ramirez JM. Known pathogenic gene variants and new candidates detected in sudden unexpected infant death using whole genome sequencing. Am J Med Genet A 2024:e63596. [PMID: 38895864 DOI: 10.1002/ajmg.a.63596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/13/2024] [Accepted: 03/08/2024] [Indexed: 06/21/2024]
Abstract
The purpose of this study is to gain insights into potential genetic factors contributing to the infant's vulnerability to Sudden Unexpected Infant Death (SUID). Whole Genome Sequencing (WGS) was performed on 144 infants that succumbed to SUID, and 573 healthy adults. Variants were filtered by gnomAD allele frequencies and predictions of functional consequences. Variants of interest were identified in 88 genes, in 64.6% of our cohort. Seventy-three of these have been previously associated with SIDS/SUID/SUDP. Forty-three can be characterized as cardiac genes and are related to cardiomyopathies, arrhythmias, and other conditions. Variants in 22 genes were associated with neurologic functions. Variants were also found in 13 genes reported to be pathogenic for various systemic disorders and in two genes associated with immunological function. Variants in eight genes are implicated in the response to hypoxia and the regulation of reactive oxygen species (ROS) and have not been previously described in SIDS/SUID/SUDP. Seventy-two infants met the triple risk hypothesis criteria. Our study confirms and further expands the list of genetic variants associated with SUID. The abundance of genes associated with heart disease and the discovery of variants associated with the redox metabolism have important mechanistic implications for the pathophysiology of SUID.
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Affiliation(s)
- Angela M Bard
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lindsay V Clark
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Erdal Cosgun
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
- AI for Good Research Lab, Microsoft, Redmond, Washington, USA
- Microsoft Genomics Team, Redmond, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew Timms
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lely A Quina
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Juan M Lavista Ferres
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
- AI for Good Research Lab, Microsoft, Redmond, Washington, USA
- Microsoft Genomics Team, Redmond, Washington, USA
| | - David Jardine
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elisabeth A Haas
- Department of Research, Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Tatiana M Becker
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Chelsea M Pagan
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | | | | | | | | | | | - Edwin A Mitchell
- Department of Paediatrics, University of Auckland, Auckland, New Zealand
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington, USA
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de Wagenaar NP, van den Bersselaar LM, Odijk HJHM, Stefens SJM, Reinhardt DP, Roos-Hesselink JW, Kanaar R, Verhagen JMA, Brüggenwirth HT, van de Laar IMBH, van der Pluijm I, Essers J. Functional analysis of cell lines derived from SMAD3-related Loeys-Dietz syndrome patients provides insights into genotype-phenotype relation. Hum Mol Genet 2024; 33:1090-1104. [PMID: 38538566 PMCID: PMC11153339 DOI: 10.1093/hmg/ddae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 06/07/2024] Open
Abstract
RATIONALE Pathogenic (P)/likely pathogenic (LP) SMAD3 variants cause Loeys-Dietz syndrome type 3 (LDS3), which is characterized by arterial aneurysms, dissections and tortuosity throughout the vascular system combined with osteoarthritis. OBJECTIVES Investigate the impact of P/LP SMAD3 variants with functional tests on patient-derived fibroblasts and vascular smooth muscle cells (VSMCs), to optimize interpretation of SMAD3 variants. METHODS A retrospective analysis on clinical data from individuals with a P/LP SMAD3 variant and functional analyses on SMAD3 patient-derived VSMCs and SMAD3 patient-derived fibroblasts, differentiated into myofibroblasts. RESULTS Individuals with dominant negative (DN) SMAD3 variant in the MH2 domain exhibited more major events (66.7% vs. 44.0%, P = 0.054), occurring at a younger age compared to those with haploinsufficient (HI) variants. The age at first major event was 35.0 years [IQR 29.0-47.0] in individuals with DN variants in MH2, compared to 46.0 years [IQR 40.0-54.0] in those with HI variants (P = 0.065). Fibroblasts carrying DN SMAD3 variants displayed reduced differentiation potential, contrasting with increased differentiation potential in HI SMAD3 variant fibroblasts. HI SMAD3 variant VSMCs showed elevated SMA expression and altered expression of alternative MYH11 isoforms. DN SMAD3 variant myofibroblasts demonstrated reduced extracellular matrix formation compared to control cell lines. CONCLUSION Distinguishing between P/LP HI and DN SMAD3 variants can be achieved by assessing differentiation potential, and SMA and MYH11 expression. The differences between DN and HI SMAD3 variant fibroblasts and VSMCs potentially contribute to the differences in disease manifestation. Notably, myofibroblast differentiation seems a suitable alternative in vitro test system compared to VSMCs.
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Affiliation(s)
- Nathalie P de Wagenaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Cardiology and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisa M van den Bersselaar
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hanny J H M Odijk
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Sanne J M Stefens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Dieter P Reinhardt
- Faculty of Medicine and Health Sciences, McGill University, 3640 University Street, Montreal, QC H3A 0C7, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, 3640 University Street, Montreal, QC H3A 0C7, Canada
| | - Jolien W Roos-Hesselink
- Department of Cardiology and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Vascular Surgery, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Vascular Surgery, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Radiotherapy, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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Bard AM, Clark LV, Cosgun E, Aldinger KA, Timms A, Quina LA, Lavista Ferres JM, Jardine D, Haas EA, Becker TM, Pagan CM, Santani A, Martinez D, Barua S, McNutt Z, Nesbitt A, Mitchell EA, Ramirez JM. Known pathogenic gene variants and new candidates detected in Sudden Unexpected Infant Death using Whole Genome Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.11.23295207. [PMID: 37745463 PMCID: PMC10516094 DOI: 10.1101/2023.09.11.23295207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Purpose To gain insights into potential genetic factors contributing to the infant's vulnerability to Sudden Unexpected Infant Death (SUID). Methods Whole Genome Sequencing (WGS) was performed on 145 infants that succumbed to SUID, and 576 healthy adults. Variants were filtered by gnomAD allele frequencies and predictions of functional consequences. Results Variants of interest were identified in 86 genes, 63.4% of our cohort. Seventy-one of these have been previously associated with SIDS/SUID/SUDP. Forty-three can be characterized as cardiac genes and are related to cardiomyopathies, arrhythmias, and other conditions. Variants in 22 genes were associated with neurologic functions. Variants were also found in 13 genes reported to be pathogenic for various systemic disorders. Variants in eight genes are implicated in the response to hypoxia and the regulation of reactive oxygen species (ROS) and have not been previously described in SIDS/SUID/SUDP. Seventy-two infants met the triple risk hypothesis criteria (Figure 1). Conclusion Our study confirms and further expands the list of genetic variants associated with SUID. The abundance of genes associated with heart disease and the discovery of variants associated with the redox metabolism have important mechanistic implications for the pathophysiology of SUID.
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Hao X, Cheng S, Jiang B, Xin S. Applying multi-omics techniques to the discovery of biomarkers for acute aortic dissection. Front Cardiovasc Med 2022; 9:961991. [PMID: 36588568 PMCID: PMC9797526 DOI: 10.3389/fcvm.2022.961991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Acute aortic dissection (AAD) is a cardiovascular disease that manifests suddenly and fatally. Due to the lack of specific early symptoms, many patients with AAD are often overlooked or misdiagnosed, which is undoubtedly catastrophic for patients. The particular pathogenic mechanism of AAD is yet unknown, which makes clinical pharmacological therapy extremely difficult. Therefore, it is necessary and crucial to find and employ unique biomarkers for Acute aortic dissection (AAD) as soon as possible in clinical practice and research. This will aid in the early detection of AAD and give clear guidelines for the creation of focused treatment agents. This goal has been made attainable over the past 20 years by the quick advancement of omics technologies and the development of high-throughput tissue specimen biomarker screening. The primary histology data support and add to one another to create a more thorough and three-dimensional picture of the disease. Based on the introduction of the main histology technologies, in this review, we summarize the current situation and most recent developments in the application of multi-omics technologies to AAD biomarker discovery and emphasize the significance of concentrating on integration concepts for integrating multi-omics data. In this context, we seek to offer fresh concepts and recommendations for fundamental investigation, perspective innovation, and therapeutic development in AAD.
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Affiliation(s)
- Xinyu Hao
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China
| | - Shuai Cheng
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China
| | - Bo Jiang
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China
| | - Shijie Xin
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China,*Correspondence: Shijie Xin,
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Engström K, Vánky F, Rehnberg M, Trinks C, Jonasson J, Green A, Gunnarsson C. Novel SMAD3 p.Arg386Thr genetic variant co-segregating with thoracic aortic aneurysm and dissection. Mol Genet Genomic Med 2020; 8:e1089. [PMID: 32022471 PMCID: PMC7196476 DOI: 10.1002/mgg3.1089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
Background Pathogenic variants in the SMAD3 gene affecting the TGF‐β/SMAD3 signaling pathway with aortic vessel involvement cause Loeys‐Dietz syndrome 3, also known as aneurysms–osteoarthritis syndrome. Methods Description of clinical history of a family in Sweden using clinical data, DNA sequencing, bioinformatics, and pedigree analysis. Results We report a novel SMAD3 variant, initially classified as a genetic variant of uncertain clinical significance (VUS), and later found to be co‐segregating with aortic dissection in the family. The index patient presented with a dissecting aneurysm of the aorta including the ascending, descending, and abdominal parts. Genotype analysis revealed a heterozygous missense SMAD3 variant: NM_005902.3(SMAD3): c.11576G > C (p.Arg386Thr). The same variant was also identified in a 30 years old formalin‐fixed paraffin‐embedded block of tissue from a second cousin, who died at 26 years of age from a dissecting aneurysm of the aorta. Conclusion A “variant of uncertain significance” according to the ACMG guidelines has always a scope for reappraisal. Genetic counselling to relatives, and the offering of surveillance service is important to families with aortic aneurysm disease. The report also highlight the potential use of FFPE analysis from deceased relatives to help in the interpretation of variants.
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Affiliation(s)
- Karolina Engström
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Farkas Vánky
- Department of Cardiothoracic and Vascular Surgery and Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Malin Rehnberg
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Cecilia Trinks
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jon Jonasson
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Anna Green
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Cecilia Gunnarsson
- Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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