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Beccacece L, Abondio P, Giorgetti A, Bini C, Pelletti G, Luiselli D, Pelotti S. A Genome-Wide Analysis of a Sudden Cardiac Death Cohort: Identifying Novel Target Variants in the Era of Molecular Autopsy. Genes (Basel) 2023; 14:1265. [PMID: 37372445 DOI: 10.3390/genes14061265] [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: 05/19/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Sudden cardiac death (SCD) is an unexpected natural death due to cardiac causes, usually happening within one hour of symptom manifestation or in individuals in good health up to 24 h before the event. Genomic screening has been increasingly applied as a useful approach to detecting the genetic variants that potentially contribute to SCD and helping the evaluation of SCD cases in the post-mortem setting. Our aim was to identify the genetic markers associated with SCD, which might enable its target screening and prevention. In this scope, a case-control analysis through the post-mortem genome-wide screening of 30 autopsy cases was performed. We identified a high number of novel genetic variants associated with SCD, of which 25 polymorphisms were consistent with a previous link to cardiovascular diseases. We ascertained that many genes have been already linked to cardiovascular system functioning and diseases and that the metabolisms most implicated in SCD are the lipid, cholesterol, arachidonic acid, and drug metabolisms, suggesting their roles as potential risk factors. Overall, the genetic variants pinpointed herein might be useful markers of SCD, but the novelty of these results requires further investigations.
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Affiliation(s)
- Livia Beccacece
- Computational Genomics Lab, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Paolo Abondio
- aDNA Lab, Department of Cultural Heritage, University of Bologna, Ravenna Campus, 48121 Ravenna, Italy
| | - Arianna Giorgetti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy
| | - Carla Bini
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy
| | - Guido Pelletti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy
| | - Donata Luiselli
- aDNA Lab, Department of Cultural Heritage, University of Bologna, Ravenna Campus, 48121 Ravenna, Italy
| | - Susi Pelotti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy
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2
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Scapoli C, Ziliotto N, Lunghi B, Menegatti E, Salvi F, Zamboni P, Baroni M, Mascoli F, Bernardi F, Marchetti G. Combination of Genomic and Transcriptomic Approaches Highlights Vascular and Circadian Clock Components in Multiple Sclerosis. Int J Mol Sci 2021; 23:ijms23010310. [PMID: 35008743 PMCID: PMC8745220 DOI: 10.3390/ijms23010310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 12/17/2022] Open
Abstract
Aiming at exploring vascular components in multiple sclerosis (MS) with brain outflow disturbance, we combined transcriptome analysis in MS internal jugular vein (IJV) wall with WES in MS families with vertical transmission of disease. Main results were the differential expression in IJV wall of 16 MS-GWAS genes and of seven genes (GRIN2A, GRIN2B, IL20RB, IL26, PER3, PITX2, and PPARGC1A) not previously indicated by GWAS but encoding for proteins functionally interacting with MS candidate gene products. Strikingly, 22/23 genes have been previously associated with vascular or neuronal traits/diseases, nine encoded for transcriptional factors/regulators and six (CAMK2G, GRIN2A, GRIN2B, N1RD1, PER3, PPARGC1A) for circadian entrainment/rhythm components. Among the WES low-frequency (MAF ≤ 0.04) SNPs (n = 7) filtered in the 16 genes, the NR1D1 rs17616365 showed significantly different MAF in the Network for Italian Genomes affected cohort than in the 1000 Genome Project Tuscany samples. This pattern was also detected in five nonintronic variants (GRIN2B rs1805482, PER3 rs2640909, PPARGC1A rs2970847, rs8192678, and rs3755863) in genes coding for functional partners. Overall, the study proposes specific markers and low-frequency variants that might help (i) to understand perturbed biological processes in vascular tissues contributing to MS disease, and (ii) to characterize MS susceptibility genes for functional association with disease-pathways.
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Affiliation(s)
- Chiara Scapoli
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (C.S.); (B.L.); (M.B.)
| | - Nicole Ziliotto
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20072 Milan, Italy;
| | - Barbara Lunghi
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (C.S.); (B.L.); (M.B.)
| | - Erica Menegatti
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121 Ferrara, Italy; (E.M.); (P.Z.)
| | - Fabrizio Salvi
- Center for Immunological and Rare Neurological Diseases, IRCCS of Neurological Sciences, Bellaria Hospital, 40139 Bologna, Italy;
| | - Paolo Zamboni
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121 Ferrara, Italy; (E.M.); (P.Z.)
| | - Marcello Baroni
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (C.S.); (B.L.); (M.B.)
| | - Francesco Mascoli
- Unit of Vascular and Endovascular Surgery, S. Anna University-Hospital, 44124 Ferrara, Italy;
| | - Francesco Bernardi
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (C.S.); (B.L.); (M.B.)
- Correspondence: ; Tel.: +39-0532-974425
| | - Giovanna Marchetti
- Department of Neuroscience and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy;
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Mertens JC, Blanc-Guillemaud V, Claesen K, Cardona P, Hendriks D, Tyl B, Molina CA. Carboxypeptidase U (TAFIa) Is Rapidly Activated and Deactivated Following Thrombolysis and Thrombectomy in Stroke Patients. Transl Stroke Res 2021; 13:959-969. [PMID: 34796454 DOI: 10.1007/s12975-021-00962-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/29/2022]
Abstract
The antifibrinolytic enzyme carboxypeptidase U (CPU, TAFIa, CPB2) is an appealing target for the treatment of acute ischemic stroke (AIS). Increased insights in CPU activation and inactivation during thrombolysis (rtPA) with or without endovascular thrombectomy (EVT) are required to develop CPU inhibitors as profibrinolytic agents with optimal benefits/risks. Therefore, CPU kinetics during ischemic stroke treatment were evaluated. AIS patients with documented cerebral artery occlusion receiving rtPA (N = 20) or rtPA + EVT (N = 16) were included. CPU activation during thrombolysis was measured by an ultrasensitive HPLC-based CPU activity method and by an ELISA measuring both CPU and inactivated CPU (CPU + CPUi). Intravenous blood samples were collected at admission and throughout the first 24 h. Additional in situ blood samples were collected in the rtPA + EVT cohort proximal from the thrombus. The NIHSS score was determined at baseline and 24 h. CPU activity and CPU + CPUi levels increased upon rtPA administration and reached peak values at the end of thrombolysis (1 h). High inter-individual variability was observed in both groups. CPU activity decreased rapidly within 3 h, while CPU + CPUi levels were still elevated at 7 h. CPU activity or CPU + CPUi levels were similar in in situ and peripheral samples. No correlation between CPU or CPU + CPUi and NIHSS or thrombus localization was found. The CPU system was rapidly activated and deactivated following thrombolysis and thrombectomy in stroke patients, suggesting that a CPU inhibitor would have to be administered during rtPA infusion and over the next few hours. The high CPU generation variability suggests that some patients may not respond to the treatment. EudraCT number 2017-002760-41.
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Affiliation(s)
- Joachim C Mertens
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | - Vanessa Blanc-Guillemaud
- Cardiovascular and Metabolic Diseases Center for Therapeutic Innovation, Institut de Recherches Internationales Servier, Suresnes Cedex, France.
| | - Karen Claesen
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | - Pere Cardona
- Department of Neurology, Hospital de Bellvitge, Hospitalet de Llobregat-Barcelona, Spain
| | - Dirk Hendriks
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | - Benoit Tyl
- Cardiovascular and Metabolic Diseases Center for Therapeutic Innovation, Institut de Recherches Internationales Servier, Suresnes Cedex, France
| | - Carlos A Molina
- Stroke Unit, Neurology Department, Vall d'Hebron University Hospital, Barcelona, Spain.,Departament de Medicina, Universitat Autónoma de Barcelona, Barcelona, Spain
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Olsson Lindvall M, Angerfors A, Andersson B, Nilsson S, Davila Lopez M, Hansson L, Stanne TM, Jern C. Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals. Thromb Haemost 2020; 121:573-583. [PMID: 33202445 PMCID: PMC8116175 DOI: 10.1055/s-0040-1720980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
DNA methylation has become increasingly recognized in the etiology of complex diseases, including thrombotic disorders. Blood is often collected in epidemiological studies for genotyping and has recently also been used to examine DNA methylation in epigenome-wide association studies. DNA methylation patterns are often tissue-specific, thus, peripheral blood may not accurately reflect the methylation pattern in the tissue of relevance. Here, we collected paired liver and blood samples concurrently from 27 individuals undergoing liver surgery. We performed targeted bisulfite sequencing for a set of 35 hemostatic genes primarily expressed in liver to analyze DNA methylation levels of >10,000 cytosine-phosphate-guanine (CpG) dinucleotides. We evaluated whether DNA methylation in blood could serve as a proxy for DNA methylation in liver at individual CpGs. Approximately 30% of CpGs were nonvariable and were predominantly hypo- (<25%) or hypermethylated (>70%) in both tissues. While blood can serve as a proxy for liver at these CpGs, the low variability renders these unlikely to explain phenotypic differences. We therefore focused on CpG sites with variable methylation levels in liver. The level of blood-liver tissue correlation varied widely across these variable CpGs; moderate correlations (0.5 ≤ r < 0.75) were detected for 6% and strong correlations (r ≥ 0.75) for a further 4%. Our findings indicate that it is essential to study the concordance of DNA methylation between blood and liver at individual CpGs. This paired blood-liver dataset is intended as a resource to aid interpretation of blood-based DNA methylation results.
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Affiliation(s)
- Martina Olsson Lindvall
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Annelie Angerfors
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Bioinformatics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Tara M Stanne
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Christina Jern
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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5
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Harshfield EL, Sims MC, Traylor M, Ouwehand WH, Markus HS. The role of haematological traits in risk of ischaemic stroke and its subtypes. Brain 2020; 143:210-221. [PMID: 31755939 PMCID: PMC6935746 DOI: 10.1093/brain/awz362] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/05/2019] [Accepted: 09/25/2019] [Indexed: 12/13/2022] Open
Abstract
Thrombosis and platelet activation play a central role in stroke pathogenesis, and antiplatelet and anticoagulant therapies are central to stroke prevention. However, whether haematological traits contribute equally to all ischaemic stroke subtypes is uncertain. Furthermore, identification of associations with new traits may offer novel treatment opportunities. The aim of this research was to ascertain causal relationships between a wide range of haematological traits and ischaemic stroke and its subtypes. We obtained summary statistics from 27 published genome-wide association studies of haematological traits involving over 375 000 individuals, and genetic associations with stroke from the MEGASTROKE Consortium (n = 67 000 stroke cases). Using two-sample Mendelian randomization we analysed the association of genetically elevated levels of 36 blood cell traits (platelets, mature/immature red cells, and myeloid/lymphoid/compound white cells) and 49 haemostasis traits (including clotting cascade factors and markers of platelet function) with risk of developing ischaemic (AIS), cardioembolic (CES), large artery (LAS), and small vessel stroke (SVS). Several factors on the intrinsic clotting pathway were significantly associated (P < 3.85 × 10-4) with CES and LAS, but not with SVS (e.g. reduced factor VIII activity with AIS/CES/LAS; raised factor VIII antigen with AIS/CES; and increased factor XI activity with AIS/CES). On the common pathway, increased gamma (γ') fibrinogen was significantly associated with AIS/CES. Furthermore, elevated plateletcrit was significantly associated with AIS/CES, eosinophil percentage of white cells with LAS, and thrombin-activatable fibrinolysis inhibitor activation peptide antigen with AIS. We also conducted a follow-up analysis in UK Biobank, which showed that amongst individuals with atrial fibrillation, those with genetically lower levels of factor XI are at reduced risk of AIS compared to those with normal levels of factor XI. These results implicate components of the intrinsic and common pathways of the clotting cascade, as well as several other haematological traits, in the pathogenesis of CES and possibly LAS, but not SVS. The lack of associations with SVS suggests thrombosis may be less important for this stroke subtype. Plateletcrit and factor XI are potentially tractable new targets for secondary prevention of ischaemic stroke, while factor VIII and γ' fibrinogen require further population-based studies to ascertain their possible aetiological roles.
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Affiliation(s)
- Eric L Harshfield
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Matthew C Sims
- Department of Haematology, University of Cambridge, Cambridge, UK
- Oxford Haemophilia and Thrombosis Centre, Oxford University Hospitals NHS Foundation Trust, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Matthew Traylor
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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6
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Mave V, Chandrasekaran P, Chavan A, Shivakumar SVBY, Danasekaran K, Paradkar M, Thiruvengadam K, Kinikar A, Murali L, Gaikwad S, Hanna LE, Kulkarni V, Pattabiraman S, Suryavanshi N, Thomas B, Kohli R, Sivaramakrishnan GN, Pradhan N, Bhanu B, Kagal A, Golub J, Gandhi N, Gupte A, Gupte N, Swaminathan S, Gupta A. Infection free "resisters" among household contacts of adult pulmonary tuberculosis. PLoS One 2019; 14:e0218034. [PMID: 31318864 PMCID: PMC6638997 DOI: 10.1371/journal.pone.0218034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/23/2019] [Indexed: 02/01/2023] Open
Abstract
Despite substantial exposure to infectious pulmonary tuberculosis (TB) cases, some household contacts (HHC) never acquire latent TB infection (LTBI). Characterizing these “resisters” can inform who to study immunologically for the development of TB vaccines. We enrolled HHCs of culture-confirmed adult pulmonary TB in India who underwent LTBI testing using tuberculin skin test (TST) and QuantiFERON TB Gold Test-in-tube (QFT-GIT) at baseline and, if negative by both (<5mm TST and <0.35IU/mL QFT-GIT), underwent follow-up testing at 4–6 and/or 12 months. We defined persons with persistently negative LTBI tests at both baseline and followup as pLTBI- and resisters as those who had a high exposure to TB using a published score and remained pLTBI-. We calculated the proportion of resisters overall and resisters with complete absence of response to LTBI tests (0mm TST and/or QFT-GIT <0.01 IU/ml). Using random effects Poisson regression, we assessed factors associated with pLTBI-. Of 799 HHCs in 355 households, 67 (8%) were pLTBI- at 12 months; 52 (6.5%) pLTBI- in 39 households were resisters. Complete absence of response to LTBI tests was found in 27 (53%) resisters. No epidemiological characteristics were associated with the pLTBI- phenotype. LTBI free resisters among HHC exist but are uncommon and are without distinguishing epidemiologic characteristics. Assessing the genetic and immunologic features of such resister individuals is likely to elucidate mechanisms of protective immunity to TB.
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Affiliation(s)
- Vidya Mave
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | | | - Amol Chavan
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | | | | | - Mandar Paradkar
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | | | - Aarti Kinikar
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Lakshmi Murali
- District Tuberculosis Officer, State Tuberculosis Office, Thiruvallur, Tamil Nadu, India
| | - Sanjay Gaikwad
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | | | - Vandana Kulkarni
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | | | - Nishi Suryavanshi
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Beena Thomas
- National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Rewa Kohli
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | | | - Neeta Pradhan
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Brindha Bhanu
- National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Anju Kagal
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Jonathan Golub
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Neel Gandhi
- Emory University, Atlanta, Georgia, United States of America
| | - Akshay Gupte
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Nikhil Gupte
- Byramjee Jeejeebhoy Government Medical College- Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | | | - Amita Gupta
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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