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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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Samii A, Aslani S, Imani D, Razi B, Samaneh Tabaee S, Jamialahmadi T, Sahebkar A. MTHFR gene polymorphisms and susceptibility to myocardial infarction: Evidence from meta-analysis and trial sequential analysis. IJC HEART & VASCULATURE 2023; 49:101293. [PMID: 38035258 PMCID: PMC10687297 DOI: 10.1016/j.ijcha.2023.101293] [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: 08/04/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Background This meta-analysis aimed to provide a comprehensive assessment of the association between Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms, specifically C677T and A1298C, and the susceptibility to myocardial infarction (MI). Methods A systematic literature search was conducted in MEDLINE, Web of Science, and Scopus until April 2023 to identify studies investigating the relationship between MTHFR gene polymorphisms (C677T and A1298C) and the risk of MI. Results The analysis included 66 studies involving 16,860 cases and 20,403 controls for the C677T polymorphism and 18 studies comprising 3162 cases and 3632 controls for the A1298C polymorphism. Significant associations were observed between the C677T polymorphism and MI risk in various genetic models: dominant (OR = 1.16, 95 % CI = 1.06-1.28, P = 0.008), recessive (OR = 1.20, 95 % CI = 1.12-1.28, P < 0.001), allelic (OR = 1.13, 95 % CI = 1.06-1.21, P < 0.001), TT vs. CC (OR = 1.19, 95 % CI = 1.05-1.36, P < 0.001), and CT vs. CC (OR = 1.11, 95 % CI = 1.02-1.21, P = 0.01). Furthermore, an overall analysis indicated a marginally significant association between the A1298C polymorphism and MI risk in the recessive model (OR = 1.27, 95 % CI = 1.06-1.51, P = 0.008), allelic model (OR = 1.18, 95 % CI = 1.01-1.39, P = 0.03), and CC vs. AA model (OR = 1.22, 95 % CI = 1.01-1.47, P = 0.04). Meta-regression analysis revealed that none of the potential factors contributed to the observed heterogeneity. Conclusions This meta-analysis revealed an association between MTHFR gene C677T and A1298C polymorphisms and the risk of MI.
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Affiliation(s)
- Amir Samii
- Department of Hematology and Blood Transfusion, School of Allied Medical Science, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Aslani
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Danyal Imani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahman Razi
- Department of Hematology and Blood Transfusion, Faculty of Medical Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Seyedeh Samaneh Tabaee
- Noncommunicable Disease Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
- Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Tannaz Jamialahmadi
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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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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Zhan C, Tang T, Wu E, Zhang Y, He M, Wu R, Bi C, Wang J, Zhang Y, Shen B. From multi-omics approaches to personalized medicine in myocardial infarction. Front Cardiovasc Med 2023; 10:1250340. [PMID: 37965091 PMCID: PMC10642346 DOI: 10.3389/fcvm.2023.1250340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe complications such as arrhythmia, cardiac rupture, heart failure, and sudden death. Despite being a research hotspot, the etiological mechanism of MI remains unclear. The emergence and widespread use of omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and other omics, have provided new opportunities for exploring the molecular mechanism of MI and identifying a large number of disease biomarkers. However, a single-omics approach has limitations in understanding the complex biological pathways of diseases. The multi-omics approach can reveal the interaction network among molecules at various levels and overcome the limitations of the single-omics approaches. This review focuses on the omics studies of MI, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and other omics. The exploration extended into the domain of multi-omics integrative analysis, accompanied by a compilation of diverse online resources, databases, and tools conducive to these investigations. Additionally, we discussed the role and prospects of multi-omics approaches in personalized medicine, highlighting the potential for improving diagnosis, treatment, and prognosis of MI.
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Affiliation(s)
- Chaoying Zhan
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tong Tang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Erman Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengqiao He
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Rongrong Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Bi
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiao Wang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yingbo Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bairong Shen
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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Jian L, Zhang Z, Zhou Q, Duan X, Ge L. Red Cell Distribution Width/Albumin Ratio: A Predictor of In-Hospital All-Cause Mortality in Patients with Acute Myocardial Infarction in the ICU. Int J Gen Med 2023; 16:745-756. [PMID: 36872940 PMCID: PMC9983434 DOI: 10.2147/ijgm.s393393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/17/2023] [Indexed: 03/03/2023] Open
Abstract
Purpose Red cell distribution width (RDW) and albumin level are linked to adverse outcomes in patients with acute myocardial infarction (AMI). Nonetheless, it remains unknown whether the RDW/albumin ratio (RAR) is associated with the short-term prognosis of AMI. Using a large cohort, we aimed to explore the association between RAR and in-hospital all-cause mortality in intensive care unit (ICU) patients with AMI. Patients and Methods The patients' data analyzed in this retrospective cohort investigation were obtained from the eICU Collaborative Research Data Resource. RAR was calculated based on the serum albumin level and RDW. The primary outcome was in-hospital all-cause mortality. Receiver operating characteristic curve, multiple logistic regression model, and Kaplan-Meier survival analysis were performed to explore the prognostic value of RAR. Results We enrolled 2594 patients in this study. After correcting for confounding factors, the RAR was an independent predictor for in-hospital mortality in our model (odds ratio [OR] 1.27, 95% confidence interval [CI] 1.12, 1.43). A similar relationship was observed with mechanical ventilation use. RAR showed a better predictive value with an area under the curve (AUC) of 0.738 (cutoff, 4.776) for in-hospital all-cause mortality compared to RDW or albumin alone. Kaplan-Meier estimator curve analyses for RAR demonstrated that the group with RAR ≥4.776%/g/dL had poorer survival than the group with RAR <4.776%/g/dL (p< 0.0001). The subgroup analysis revealed no significant interaction between RAR and in-hospital all-cause mortality in all strata. Conclusion RAR was an independent risk factor for in-hospital all-cause mortality in ICU patients with AMI. Higher RAR values corresponded to higher mortality rates. RAR is a more accurate predictor of in-hospital all-cause mortality in patients with AMI in the ICU than albumin or RDW. Thus, RAR may be a potential biomarker of AMI.
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Affiliation(s)
- Linhao Jian
- Department of the First Clinical College, Jinan University, Guangzhou, 510632, People's Republic of China.,Department of Cardiology, The First People's Hospital of Changde, Changde City, 415003, People's Republic of China
| | - Zhixiang Zhang
- Department of Cardiology, The First People's Hospital of Changde, Changde City, 415003, People's Republic of China
| | - Quan Zhou
- Department of Science and Education, The First People's Hospital of Changde, Changde City, 415003, People's Republic of China
| | - Xiangjie Duan
- Department of Infectious Diseases, The First People's Hospital of Changde, Changde City, 415003, People's Republic of China
| | - Liangqing Ge
- Department of Cardiology, The First People's Hospital of Changde, Changde City, 415003, People's Republic of China
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Golestani A, Rahimi A, Moridi N, Anani-Sarab G, Salmani F, Dastjerdi K, Azdaki N, Sajjadi SM. Association of factor V Leiden R506Q, FXIIIVal34Leu, and MTHFR C677T polymorphisms with acute myocardial infarction. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Acute myocardial infarction (AMI) is a leading cause of death and morbidity around the world. Although the association between thrombophilia and AMI is well-established, controversial data are present on the association between thrombophilic polymorphisms and AMI. The aim of this study was to investigate the association of three thrombophilic polymorphisms including factor V Leiden (FVL), MTHFRC677T (methylenetetrahydrofolate reductase), and Coagulation factor XIIIVal34Leu with AMI in East of Iran.
Result
There were no statistically significant differences between the patients and control groups in terms of the distributions of allelic and genotypic frequencies of FVL and FXIIIVal34Leu polymorphisms (P-value > 0.05). Subjects who carried CT genotype of MTHFR C677T polymorphism were at a 2.03-fold higher risk for AMI (P-value: 0.02, OR 1.76, 95% CI 1.07–2.75). Furthermore, patients with MTHFR 677CT (P-value < 0.001, β = - 0.90, 95% CI − 1.33, − 047) or 677CC (P-value < 0.001, β = - 1.04, 95% CI − 1.47, − 0.61) genotypes showed significantly Lower creatinine levels compared with patients having the MTHFR 677TT. No association was observed between the other remaining polymorphisms and AMI (P-value > 0.05).
Conclusion
Our findings showed that MTHFRC677T polymorphism could contribute to AMI susceptibility and increase creatinine levels in east Iran population. This was the first study to examine the association of these three polymorphisms with AMI in east Iran.
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Genetic Polymorphisms in a Familial Hypercholesterolemia Population from North-Eastern Europe. J Pers Med 2022; 12:jpm12030429. [PMID: 35330428 PMCID: PMC8949493 DOI: 10.3390/jpm12030429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Familial hypercholesterolemia (FH) is one of the most prevalent inherited metabolic disorders. The purpose of the study was to investigate the role in cardiovascular disease (CVD) of PAI-1, ACE, ApoB-100, MTHFR A1298C, and C677T. (2) Methods: From a group of 1499 patients, we included 52 patients diagnosed with FH phenotype and 17 patients in a control group. (3) Results: Most of the FH patients had multiple comorbidities compared to the control group, such as atherosclerosis (48.1% vs. 17.6%), atherosclerotic cardiovascular disease (ASCVD 32.7% vs. 11.8%), and metabolic syndrome (MetS, 40.4% vs. 11.8%). In total, 66.7% of the FH patients had PAI-1 4G/5G genotype and MetS. Between 4G/5G and 4G/4G, a statistically significant difference was observed (p = 0.013). FH patients with ApoB R3500Q polymorphism were correlated with ASCVD (p = 0.031). Both MTHFR C677T and A1298C polymorphisms had a significant correlation with gender, alcohol consumption, and smoking status. ACE polymorphism was associated with ATS in FH patients, statistically significant differences being observed between heterozygous and homozygous D genotype (p = 0.036) as well as between heterozygous and homozygous I genotype (p = 0.021). (4) Conclusions: A link between these polymorphisms was demonstrated in the FH group for ATS, ASCVD, and MetS.
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Argyrophilic Nucleolar Organizer Regions as New Biomarkers in ST-Elevation Myocardial Infarction. J Cardiovasc Dev Dis 2022; 9:jcdd9020058. [PMID: 35200711 PMCID: PMC8875583 DOI: 10.3390/jcdd9020058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/05/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022] Open
Abstract
(1) Background: ST-elevation myocardial infarction (STEMI) is an inflammatory disease in which neutrophils, macrophages, and lymphocytes accumulate in the ischemic myocardium and have important functions. Nucleolar-organizing regions (NORs) are the site of the ribosomal genes composed of ribosomal DNA and proteins. We aimed to evaluate AgNOR proteins, which have never been studied in patients with STEMI in the literature. (2) Methods: A total of 140 participants (75 with STEMI and 65 volunteers without any diagnosis of acute coronary syndrome) were included in this study. Echocardiography was carried out, and mean AgNOR number and total AgNOR area/total nuclear area (TAA/TNA) were evaluated for all individuals. (3) Results: The mean AgNOR number and TAA/TNA ratio were significantly higher in the STEMI group than the control (p < 0.001). Statistically significant relations between both TAA/TNA ratio and mean AgNOR number and interventricular septal thickness, fasting blood sugar, creatinine, HDL, hemoglobin (g/dL), WBC (µL/mL), monocytes, neutrophils, and neutrophil/lymphocyte ratio were detected (p < 0.05). Moreover, a statistically significant relation between LDL (mg/dL) and mean AgNOR number (p = 0.005) was detected. (4) Conclusion: Both AgNOR protein amounts increase depending on the hypoxia that occurs in STEMI. The AgNOR proteins may thus be promising markers in STEMI.
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