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Gaumond L, Lamarche C, Beauchemin S, Henley N, Elftouh N, Gerarduzzi C, Laurin LP. Identification of inflammatory biomarkers in IgA nephropathy using the NanoString technology: a validation study in Caucasians. Inflamm Res 2024; 73:447-457. [PMID: 38291238 PMCID: PMC10894174 DOI: 10.1007/s00011-023-01848-3] [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: 10/13/2023] [Revised: 12/16/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
OBJECTIVE AND DESIGN Immunoglobulin A nephropathy (IgAN) is a kidney disease characterized by the accumulation of IgA deposits in the glomeruli of the kidney, leading to inflammation and damage to the kidney. The inflammatory markers involved in IgAN remain to be defined. Gene expression analysis platforms, such as the NanoString nCounter system, are promising screening and diagnostic tools, especially in oncology. Still, their role as a diagnostic and prognostic tool in IgAN remains scarce. In this study, we aimed to validate the use of NanoString technology to identify potential inflammatory biomarkers involved in the progression of IgAN. SUBJECTS A total of 30 patients with biopsy-proven IgAN and 7 cases of antineutrophil cytoplasmic antibody (ANCA)-associated pauci-immune glomerulonephritis were included for gene expression measurement. For the immunofluorescence validation experiments, a total of 6 IgAN patients and 3 controls were included. METHODS Total RNA was extracted from formalin-fixed paraffin-embedded kidney biopsy specimens, and a customized 48-plex human gene CodeSet was used to study 29 genes implicated in different biological pathways. Comparisons in gene expression were made between IgAN and ANCA-associated pauci-immune glomerulonephritis patients to delineate an expression profile specific to IgAN. Gene expression was compared between patients with low and moderate risk of progression. Genes for which RNA expression was associated with disease progression were analyzed for protein expression by immunofluorescence and compared with controls. RESULTS IgAN patients had a distinct gene expression profile with decreased expression in genes IL-6, INFG, and C1QB compared to ANCA patients. C3 and TNFRSF1B were identified as potential biomarkers for IgAN progression in patients early in their disease course. Protein expression for those 2 candidate genes was upregulated in IgAN patients compared to controls. Expression of genes implicated in fibrosis (PTEN, CASPASE 3, TGM2, TGFB1, IL2, and TNFRSF1B) was more pronounced in IgAN patients with severe fibrosis compared to those with none. CONCLUSIONS Our findings validate our NanoString mRNA profiling by examining protein expression levels of two candidate genes, C3 and TNFRSF1B, in IgAN patients and controls. We also identified several upregulated mRNA transcripts implicated in the development of fibrosis that may be considered fibrotic markers within IgAN patients.
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Affiliation(s)
- Laurence Gaumond
- Division of Nephrology, Maisonneuve-Rosemont Hospital, 5415 Boulevard de l'Assomption, Montreal, QC, H1T 2M4, Canada
| | - Caroline Lamarche
- Division of Nephrology, Maisonneuve-Rosemont Hospital, 5415 Boulevard de l'Assomption, Montreal, QC, H1T 2M4, Canada
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
- Department of Medicine, University of Montreal, Montreal, QC, Canada
| | | | - Nathalie Henley
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - Naoual Elftouh
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - Casimiro Gerarduzzi
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.
- Department of Medicine, University of Montreal, Montreal, QC, Canada.
| | - Louis-Philippe Laurin
- Division of Nephrology, Maisonneuve-Rosemont Hospital, 5415 Boulevard de l'Assomption, Montreal, QC, H1T 2M4, Canada.
- Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.
- Department of Medicine, University of Montreal, Montreal, QC, Canada.
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Tang Y, Wang Y, Wang S, Wang R, Xu J, Peng Y, Ding L, Zhao J, Zhou G, Sun S, Zhang Z. Methylation and transcriptomic expression profiles of HUVEC in the oxygen and glucose deprivation model and its clinical implications in AMI patients. Front Genet 2023; 14:1293393. [PMID: 38145212 PMCID: PMC10740152 DOI: 10.3389/fgene.2023.1293393] [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: 09/13/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
The obstructed coronary artery undergoes a series of pathological changes due to ischemic-hypoxic shocks during acute myocardial infarction (AMI). However, the altered DNA methylation levels in endothelial cells under these conditions and their implication for the etiopathology of AMI have not been investigated in detail. This study aimed to explore the relationship between DNA methylation and pathologically altered gene expression profile in human umbilical vein endothelial cells (HUVECs) subjected to oxygen-glucose deprivation (OGD), and its clinical implications in AMI patients. The Illumina Infinium MethylationEPIC BeadChip assay was used to explore the genome-wide DNA methylation profile using the Novaseq6000 platform for mRNA sequencing in 3 pairs of HUVEC-OGD and control samples. GO and KEGG pathway enrichment analyses, as well as correlation, causal inference test (CIT), and protein-protein interaction (PPI) analyses identified 22 hub genes that were validated by MethylTarget sequencing as well as qRT-PCR. ELISA was used to detect four target molecules associated with the progression of AMI. A total of 2,524 differentially expressed genes (DEGs) and 22,148 differentially methylated positions (DMPs) corresponding to 6,642 differentially methylated genes (DMGs) were screened (|Δβ|>0.1 and detection p < 0.05). After GO, KEGG, correlation, CIT, and PPI analyses, 441 genes were filtered. qRT-PCR confirmed the overexpression of VEGFA, CCL2, TSP-1, SQSTM1, BCL2L11, and TIMP3 genes, and downregulation of MYC, CD44, BDNF, GNAQ, RUNX1, ETS1, NGFR, MME, SEMA6A, GNAI1, IFIT1, and MEIS1. DNA fragments BDNF_1_ (r = 0.931, p < 0.0001) and SQSTM1_2_NEW (r = 0.758, p = 0.0043) were positively correlated with the expressions of corresponding genes, and MYC_1_ (r = -0.8245, p = 0.001) was negatively correlated. Furthermore, ELISA confirmed TNFSF10 and BDNF were elevated in the peripheral blood of AMI patients (p = 0.0284 and p = 0.0142, respectively). Combined sequencing from in vitro cellular assays with clinical samples, aiming to establish the potential causal chain of the causal factor (DNA methylation) - mediator (mRNA)-cell outcome (endothelial cell ischemic-hypoxic injury)-clinical outcome (AMI), our study identified promising OGD-specific genes, which provided a solid basis for screening fundamental diagnostic and prognostic biomarkers of coronary endothelial cell injury of AMI. Moreover, it furnished the first evidence that during ischemia and hypoxia, the expression of BNDF was regulated by DNA methylation in endothelial cells and elevated in peripheral blood.
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Affiliation(s)
- Yuning Tang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yongxiang Wang
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Shengxiang Wang
- School of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Runqing Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
| | - Jin Xu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yu Peng
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Liqiong Ding
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jing Zhao
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Gang Zhou
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Shougang Sun
- Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zheng Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
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Iversen PL, Kipshidze N, Kipshidze N, Dangas G, Ramacciotti E, Kakabadze Z, Fareed J. A novel therapeutic vaccine targeting the soluble TNFα receptor II to limit the progression of cardiovascular disease: AtheroVax™. Front Cardiovasc Med 2023; 10:1206541. [PMID: 37534280 PMCID: PMC10392828 DOI: 10.3389/fcvm.2023.1206541] [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: 04/15/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
The burden of atherosclerotic cardiovascular disease contributes to a large proportion of morbidity and mortality, globally. Vaccination against atherosclerosis has been proposed for over 20 years targeting different mediators of atherothrombosis; however, these have not been adequately evaluated in human clinical trials to assess safety and efficacy. Inflammation is a driver of atherosclerosis, but inflammatory mediators are essential components of the immune response. Only pathogenic forms of sTNFR2 are acted upon while preserving the membrane-bound (wild-type) TNFR2 contributions to a non-pathogenic immune response. We hypothesize that the inhibition of sTNRF2 will be more specific and offer long-term treatment options. Here we describe pre-clinical findings of an sTNFR2-targeting peptide vaccine (AtheroVax™) in a mouse model. The multiple pathways to synthesis of the soluble TNFRII receptor (sTNFRII) were identified as sTNFRII(PC), sTNFRII(Δ7), and sTNFRII(Δ7,9). The sTNFRII(Δ7) peptide, NH2-DFALPVEKPLCLQR-COOH is specific to sTNFR2 based on an mRNA splice-variant in which exon 6 is joined to exon 8. The role of sTNFRII(Δ7) as a mediator of prolonged TNFα activity by preventing degradation and clearance was investigated. Inflammation is a critical driver of onset, progression and expansion of atherosclerosis. The TNFα ligand represents a driver of inflammation that is mediated by a splice variant of TNFR2, referred to as sTNFRII(Δ7). The multiple forms of TNFRII, both membrane bound and soluble, are associated with distinctly different phenotypes. sTNFRII(PC) and sTNFRII(Δ7) are not equivalent to etanercept because they lack a clearance mechanism. The unique peptide associated with sTNFRII(Δ7) contains a linear B-cell epitope with amino acids from both exon 6 and exon 8 supporting the vaccine design. Animal studies to evaluate the vaccine are ongoing, and results will be forthcoming. We describe a peptide vaccine targeting sTNFR2 in limiting the progression of atherosclerosis. A therapeutic vaccine limiting the progression of atherosclerosis will greatly contribute to the reduction in morbidity and mortality from cardiovascular disease. It is likely the vaccine will be used in combination with the current standards of care and lifestyle modifications.
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Affiliation(s)
- Patrick L. Iversen
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | | | - Nodar Kipshidze
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - George Dangas
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Zurab Kakabadze
- Head Department of Clinical Anatomy, Tbilisi State Medical University, Tbilisi, Georgia
| | - Jawed Fareed
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL, United States
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Picher-Martel V, Boutej H, Vézina A, Cordeau P, Kaneb H, Julien JP, Genge A, Dupré N, Kriz J. Distinct Plasma Immune Profile in ALS Implicates sTNFR-II in pAMPK/Leptin Homeostasis. Int J Mol Sci 2023; 24:ijms24065065. [PMID: 36982140 PMCID: PMC10049559 DOI: 10.3390/ijms24065065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a clinically highly heterogeneous disease with a survival rate ranging from months to decades. Evidence suggests that a systemic deregulation of immune response may play a role and affect disease progression. Here, we measured 62 different immune/metabolic mediators in plasma of sporadic ALS (sALS) patients. We show that, at the protein level, the majority of immune mediators including a metabolic sensor, leptin, were significantly decreased in the plasma of sALS patients and in two animal models of the disease. Next, we found that a subset of patients with rapidly progressing ALS develop a distinct plasma assess immune–metabolic molecular signature characterized by a differential increase in soluble tumor necrosis factor receptor II (sTNF-RII) and chemokine (C-C motif) ligand 16 (CCL16) and further decrease in the levels of leptin, mostly dysregulated in male patients. Consistent with in vivo findings, exposure of human adipocytes to sALS plasma and/or sTNF-RII alone, induced a significant deregulation in leptin production/homeostasis and was associated with a robust increase in AMP-activated protein kinase (AMPK) phosphorylation. Conversely, treatment with an AMPK inhibitor restored leptin production in human adipocytes. Together, this study provides evidence of a distinct plasma immune profile in sALS which affects adipocyte function and leptin signaling. Furthermore, our results suggest that targeting the sTNF-RII/AMPK/leptin pathway in adipocytes may help restore assess immune–metabolic homeostasis in ALS.
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Affiliation(s)
- Vincent Picher-Martel
- CERVO Brain Research Centre, Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec City, QC G1J 2G3, Canada
- CHU de Québec, Department of Medicine, Université Laval, Québec City, QC G1J 1Z4, Canada
| | - Hejer Boutej
- CERVO Brain Research Centre, Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec City, QC G1J 2G3, Canada
| | - Alexandre Vézina
- CERVO Brain Research Centre, Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec City, QC G1J 2G3, Canada
| | - Pierre Cordeau
- CERVO Brain Research Centre, Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec City, QC G1J 2G3, Canada
| | - Hannah Kaneb
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jean-Pierre Julien
- CERVO Brain Research Centre, Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec City, QC G1J 2G3, Canada
| | - Angela Genge
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nicolas Dupré
- CHU de Québec, Department of Medicine, Université Laval, Québec City, QC G1J 1Z4, Canada
| | - Jasna Kriz
- CERVO Brain Research Centre, Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec City, QC G1J 2G3, Canada
- Correspondence: ; Tel.: +1-418-663-5000 (ext. 6732)
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Jeong A, Eze IC, Vienneau D, de Hoogh K, Keidel D, Rothe T, Burdet L, Holloway JW, Jarvis D, Kronenberg F, Lovison G, Imboden M, Probst-Hensch N. Residential greenness-related DNA methylation changes. ENVIRONMENT INTERNATIONAL 2022; 158:106945. [PMID: 34689037 DOI: 10.1016/j.envint.2021.106945] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/10/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Residential greenness has been associated with health benefits, but its biological mechanism is largely unknown. Investigation of greenness-related DNA methylation profiles can contribute to mechanistic understanding of the health benefits of residential greenness. OBJECTIVE To identify DNA methylation profiles associated with greenness in the immediate surroundings of the residence. METHODS We analyzed genome-wide DNA methylation in 1938 blood samples (982 participants) from the Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults (SAPALDIA). We estimated residential greenness based on normalized difference vegetation index at 30 × 30 m cell (green30) and 500 m buffer (green500) around the residential address. We conducted epigenome-wide association study (EWAS) to identify differentially methylated CpGs and regions, and enrichment tests by comparing to the CpGs that previous EWAS identified as associated with allergy, physical activity, and allostatic load-relevant biomarkers. RESULTS We identified no genome-wide significant CpGs, but 163 and 56 differentially methylated regions for green30 and green500, respectively. Green30-related DNA methylation profiles showed enrichments in allergy, physical activity, and allostatic load, while green500-related methylation was enriched in allergy and allostatic load. CONCLUSIONS Residential greenness may have health impacts through allergic sensitization, stress coping, or behavioral changes. Exposure to more proximal greenness may be more health-relevant.
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Affiliation(s)
- Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland.
| | - Ikenna C Eze
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland
| | - Danielle Vienneau
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland
| | - Kees de Hoogh
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland
| | - Dirk Keidel
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland
| | | | - Luc Burdet
- Hôpital Intercantonal de la Broye, Payerne, Switzerland
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Debbie Jarvis
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK; Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gianfranco Lovison
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland; Department of Economics, Business and Statistics, University of Palermo, Italy
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Public Health, University of Basel, Switzerland.
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Pulido-Perez P, Torres-Rasgado E, Pérez-Fuentes R, Rosales-Encina JL, Rodríguez-Antolín J, Romero JR. Disordered glycemic control in women with type 2 diabetes is associated with increased TNF receptor-2 levels. J Diabetes Complications 2021; 35:107974. [PMID: 34210601 DOI: 10.1016/j.jdiacomp.2021.107974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/12/2021] [Accepted: 06/12/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Evidence implicates tumor necrosis factor (TNF) in the pathophysiology of Type 2 Diabetes (T2D) through unclear mechanisms. We hypothesized that disordered glycemic control leads to TNF activation and increases in soluble-TNF (sTNF) and its receptors-1 (sTNFR1) and -2 (sTNFR2). METHODS We characterized 265 T2D and non-diabetic Latin American subjects and assessed the relationship between the TNF system and fasting plasma glucose (FPG), hemoglobin-A1C (A1C), insulin (FPI), C-peptide and HOMA-Beta. RESULTS sTNF and sTNFR2 but not sTNFR1 levels were higher in T2D than non-diabetics (P<0.0001). In T2D, sTNFR2 was associated with A1C and C-peptide (R2=0.354, b=0.504, P<0.0001; b=0.167, P=0.049). Also, T2D patients with disordered glycemic control had increased sTNFR2 levels that correlated with FPG (Rho:0.393, P<0.001), A1C (Rho:0.451, P<0.001) and HOMA-Beta (Rho:-0.308, P=0.005); events not observed in T2D patients with adequate glycemic control. Furthermore, sex-based comparative analyses of T2D patients showed that women compared to men had higher sTNFR2 levels (P=0.017) that correlated with FPG, A1C, FPI and HOMA-Beta. CONCLUSIONS Disordered glycemic control is associated with sTNF and sTNFR2. sTNFR2 levels were higher in T2D women than men. Thus, increased sTNFR2 levels may be an important biomarker for disordered glucose and inflammatory complications in T2D patients and women in particular.
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Affiliation(s)
- Patricia Pulido-Perez
- Doctorate in Biological Science, Autonomous University of Tlaxcala, Mexico; Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA; Center for Biomedical Research East, Mexican Social Security Institute of Puebla, Mexico; Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, National Polytechnic Institute, Mexico
| | - Enrique Torres-Rasgado
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA; Center for Biomedical Research East, Mexican Social Security Institute of Puebla, Mexico; Faculty of Medicine, Autonomous University of Puebla, Mexico.
| | - Ricardo Pérez-Fuentes
- Center for Biomedical Research East, Mexican Social Security Institute of Puebla, Mexico; Faculty of Medicine, Autonomous University of Puebla, Mexico
| | - José Luis Rosales-Encina
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, National Polytechnic Institute, Mexico
| | | | - Jose R Romero
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
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Kornej J, Hanger VA, Trinquart L, Ko D, Preis SR, Benjamin EJ, Lin H. New biomarkers from multiomics approaches: improving risk prediction of atrial fibrillation. Cardiovasc Res 2021; 117:1632-1644. [PMID: 33751041 PMCID: PMC8208748 DOI: 10.1093/cvr/cvab073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/07/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Atrial fibrillation (AF) is a common cardiac arrhythmia leading to many adverse outcomes and increased mortality. Yet the molecular mechanisms underlying AF remain largely unknown. Recent advances in high-throughput technologies make large-scale molecular profiling possible. In the past decade, multiomics studies of AF have identified a number of potential biomarkers of AF. In this review, we focus on the studies of multiomics profiles with AF risk. We summarize recent advances in the discovery of novel biomarkers for AF through multiomics studies. We also discuss limitations and future directions in risk assessment and discovery of therapeutic targets for AF.
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Affiliation(s)
- Jelena Kornej
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, 73 Mt Wayte Ave, Framingham, MA 01702, USA
- Section of Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Ludovic Trinquart
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Darae Ko
- Section of Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sarah R Preis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Emelia J Benjamin
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, 73 Mt Wayte Ave, Framingham, MA 01702, USA
- Section of Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Section of Preventive Medicine & Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Honghuang Lin
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, 73 Mt Wayte Ave, Framingham, MA 01702, USA
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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8
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Lent S, Cardenas A, Rifas-Shiman SL, Perron P, Bouchard L, Liu CT, Hivert MF, Dupuis J. Detecting differentially methylated regions with multiple distinct associations. Epigenomics 2021; 13:451-464. [PMID: 33641349 DOI: 10.2217/epi-2020-0344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aim: We evaluated five methods for detecting differentially methylated regions (DMRs): DMRcate, comb-p, seqlm, GlobalP and dmrff. Materials & methods: We used a simulation study and real data analysis to evaluate performance. Additionally, we evaluated the use of an ancestry-matched reference cohort to estimate correlations between CpG sites in cord blood. Results: Several methods had inflated Type I error, which increased at more stringent significant levels. In power simulations with 1-2 causal CpG sites with the same direction of effect, dmrff was consistently among the most powerful methods. Conclusion: This study illustrates the need for more thorough simulation studies when evaluating novel methods. More work must be done to develop methods with well-controlled Type I error that do not require individual-level data.
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Affiliation(s)
- Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, 94704, USA
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School & Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA
| | - Patrice Perron
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Luigi Bouchard
- Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean, Hôpital de Chicoutimi, Saguenay, QC, G7H 5H6, Canada
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School & Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA.,Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
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Juvinao-Quintero DL, Marioni RE, Ochoa-Rosales C, Russ TC, Deary IJ, van Meurs JBJ, Voortman T, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA methylation of blood cells is associated with prevalent type 2 diabetes in a meta-analysis of four European cohorts. Clin Epigenetics 2021; 13:40. [PMID: 33622391 PMCID: PMC7903628 DOI: 10.1186/s13148-021-01027-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/11/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a heterogeneous disease with well-known genetic and environmental risk factors contributing to its prevalence. Epigenetic mechanisms related to changes in DNA methylation (DNAm), may also contribute to T2D risk, but larger studies are required to discover novel markers, and to confirm existing ones. RESULTS We performed a large meta-analysis of individual epigenome-wide association studies (EWAS) of prevalent T2D conducted in four European studies using peripheral blood DNAm. Analysis of differentially methylated regions (DMR) was also undertaken, based on the meta-analysis results. We found three novel CpGs associated with prevalent T2D in Europeans at cg00144180 (HDAC4), cg16765088 (near SYNM) and cg24704287 (near MIR23A) and confirmed three CpGs previously identified (mapping to TXNIP, ABCG1 and CPT1A). We also identified 77 T2D associated DMRs, most of them hypomethylated in T2D cases versus controls. In adjusted regressions among diabetic-free participants in ALSPAC, we found that all six CpGs identified in the meta-EWAS were associated with white cell-types. We estimated that these six CpGs captured 11% of the variation in T2D, which was similar to the variation explained by the model including only the common risk factors of BMI, sex, age and smoking (R2 = 10.6%). CONCLUSIONS This study identifies novel loci associated with T2D in Europeans. We also demonstrate associations of the same loci with other traits. Future studies should investigate if our findings are generalizable in non-European populations, and potential roles of these epigenetic markers in T2D etiology or in determining long term consequences of T2D.
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Affiliation(s)
- Diana L. Juvinao-Quintero
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA 02215 USA
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, 3000 CA The Netherlands
- Centro de Vida Saludable de La Universidad de Concepción, Victoria 580, Concepción, Chile
| | - Tom C. Russ
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ UK
- Edinburgh Dementia Prevention Research Group, University of Edinburgh, Edinburgh, EH16 4UX UK
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Ian J. Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Joyce B. J. van Meurs
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, 3000 CA The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, 3000 CA The Netherlands
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA 02215 USA
| | - Gemma C. Sharp
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Caroline L. Relton
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
- Bristol NIHR Biomedical Research Centre, Oakfield House, Oakfield Grove, Bristol, BS8 2BN UK
| | - Hannah R. Elliott
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
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Interplay of pro-inflammatory cytokines, pro-inflammatory microparticles and oxidative stress and recurrent ventricular arrhythmias in elderly patients after coronary stent implantations. Cytokine 2020; 137:155345. [PMID: 33137563 DOI: 10.1016/j.cyto.2020.155345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/09/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND The roles of pro-inflammatory microparticles, pro-inflammatory cytokines and oxidative stress were unknown in elderly patients with recurrent ventricular arrhythmias (VA). We evaluated whether cross talk between oxidative stress, pro-inflammatory microparticles, and pro-inflammatory cytokines play the roles in elderly patients with recurrent VA after coronary stenting. This research sought to investigate the effects of oxidative stress, pro-inflammatory microparticles, and pro-inflammatory cytokines on recurrent VA in elderly patients after coronary stenting. METHODS In this study, we included 613 consecutive elderly patients with recurrent ventricular arrhythmias induced by coronary reocclusions after coronary stenting. We measured CD31+ endothelial microparticle (CD31+EMP), CD62E+ endothelial microparticle (CD62E+EMP), high-sensitivity C-reactive protein (hs-CRP), aldosterone (ALD), malondialdehyde (MDA), tumor necrosis factor-α (TNF-α), soluble tumor necrosis factor receptor-1 (sTNFR-1) and soluble tumor necrosis factor receptor-2 (sTNFR-2) in elderly patients with recurrent VA and assessed impacts of pro-inflammatory microparticles, pro-inflammatory cytokines and oxidative stress on recurrent VA in elderly patients after coronary stenting. RESULTS The levels of CD31+EMP, CD62E+EMP, hs-CRP, ALD, MDA, TNF-α, sTNFR-1 and sTNFR-2 were increased in recurrent malignant ventricular arrhythmia, sustained ventricular tachycardia, multiple ventricular premature beat and left and right ventricular bundle branch block groups (P < 0.001) in elderly patients with coronary reocclusions after coronary stent implantation. Upregulation of pro-inflammatory microparticles, pro-inflammatory cytokines and oxidative stress markers induced recurrent VA in elderly patients after coronary stenting. CONCLUSIONS High levels of pro-inflammatory microparticles, pro-inflammatory cytokines and oxidative stress markers were associated with recurrent VA in elderly patients after coronary stenting. Our results suggested that the pro-inflammatory microparticles, pro-inflammatory cytokines and oxidative stress may simultaneously induce and aggravate recurrent VA in elderly patients after coronary stenting.
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Zaghlool SB, Kühnel B, Elhadad MA, Kader S, Halama A, Thareja G, Engelke R, Sarwath H, Al-Dous EK, Mohamoud YA, Meitinger T, Wilson R, Strauch K, Peters A, Mook-Kanamori DO, Graumann J, Malek JA, Gieger C, Waldenberger M, Suhre K. Epigenetics meets proteomics in an epigenome-wide association study with circulating blood plasma protein traits. Nat Commun 2020; 11:15. [PMID: 31900413 PMCID: PMC6941977 DOI: 10.1038/s41467-019-13831-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation and blood circulating proteins have been associated with many complex disorders, but the underlying disease-causing mechanisms often remain unclear. Here, we report an epigenome-wide association study of 1123 proteins from 944 participants of the KORA population study and replication in a multi-ethnic cohort of 344 individuals. We identify 98 CpG-protein associations (pQTMs) at a stringent Bonferroni level of significance. Overlapping associations with transcriptomics, metabolomics, and clinical endpoints suggest implication of processes related to chronic low-grade inflammation, including a network involving methylation of NLRC5, a regulator of the inflammasome, and associated pQTMs implicating key proteins of the immune system, such as CD48, CD163, CXCL10, CXCL11, LAG3, FCGR3B, and B2M. Our study links DNA methylation to disease endpoints via intermediate proteomics phenotypes and identifies correlative networks that may eventually be targeted in a personalized approach of chronic low-grade inflammation.
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Affiliation(s)
- Shaza B Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
- Computer Engineering Department, Virginia Tech, Blacksburg, VA, USA
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Mohamed A Elhadad
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Sara Kader
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Anna Halama
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Rudolf Engelke
- Proteomics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Hina Sarwath
- Proteomics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Eman K Al-Dous
- Genomics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | | | - Thomas Meitinger
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Rhine-Main, Max Planck Institute of Heart and Lung Research, Bad Nauheim, Germany
| | - Joel A Malek
- Genomics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar.
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