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Van der Auwera S, Ameling S, Wittfeld K, Frenzel S, Bülow R, Nauck M, Völzke H, Völker U, Grabe HJ. Circulating microRNA miR-425-5p Associated with Brain White Matter Lesions and Inflammatory Processes. Int J Mol Sci 2024; 25:887. [PMID: 38255959 PMCID: PMC10815886 DOI: 10.3390/ijms25020887] [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: 12/20/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
White matter lesions (WML) emerge as a consequence of vascular injuries in the brain. While they are commonly observed in aging, associations have been established with neurodegenerative and neurological disorders such as dementia or stroke. Despite substantial research efforts, biological mechanisms are incomplete and biomarkers indicating WMLs are lacking. Utilizing data from the population-based Study of Health in Pomerania (SHIP), our objective was to identify plasma-circulating micro-RNAs (miRNAs) associated with WMLs, thus providing a foundation for a comprehensive biological model and further research. In linear regression models, direct association and moderating factors were analyzed. In 648 individuals, we identified hsa-miR-425-5p as directly associated with WMLs. In subsequent analyses, hsa-miR-425-5p was found to regulate various genes associated with WMLs with particular emphasis on the SH3PXD2A gene. Furthermore, miR-425-5p was found to be involved in immunological processes. In addition, noteworthy miRNAs associated with WMLs were identified, primarily moderated by the factors of sex or smoking status. All identified miRNAs exhibited a strong over-representation in neurodegenerative and neurological diseases. We introduced hsa-miR-425-5p as a promising candidate in WML research probably involved in immunological processes. Mir-425-5p holds the potential as a biomarker of WMLs, shedding light on potential mechanisms and pathways in vascular dementia.
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Affiliation(s)
- Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Greifswald, Germany
| | - Sabine Ameling
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Robin Bülow
- Institute for Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Matthias Nauck
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Henry Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; (M.N.)
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Greifswald, Germany
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Patel KK, Venkatesan C, Abdelhalim H, Zeeshan S, Arima Y, Linna-Kuosmanen S, Ahmed Z. Genomic approaches to identify and investigate genes associated with atrial fibrillation and heart failure susceptibility. Hum Genomics 2023; 17:47. [PMID: 37270590 DOI: 10.1186/s40246-023-00498-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/31/2023] [Indexed: 06/05/2023] Open
Abstract
Atrial fibrillation (AF) and heart failure (HF) contribute to about 45% of all cardiovascular disease (CVD) deaths in the USA and around the globe. Due to the complex nature, progression, inherent genetic makeup, and heterogeneity of CVDs, personalized treatments are believed to be critical. To improve the deciphering of CVD mechanisms, we need to deeply investigate well-known and identify novel genes that are responsible for CVD development. With the advancements in sequencing technologies, genomic data have been generated at an unprecedented pace to foster translational research. Correct application of bioinformatics using genomic data holds the potential to reveal the genetic underpinnings of various health conditions. It can help in the identification of causal variants for AF, HF, and other CVDs by moving beyond the one-gene one-disease model through the integration of common and rare variant association, the expressed genome, and characterization of comorbidities and phenotypic traits derived from the clinical information. In this study, we examined and discussed variable genomic approaches investigating genes associated with AF, HF, and other CVDs. We collected, reviewed, and compared high-quality scientific literature published between 2009 and 2022 and accessible through PubMed/NCBI. While selecting relevant literature, we mainly focused on identifying genomic approaches involving the integration of genomic data; analysis of common and rare genetic variants; metadata and phenotypic details; and multi-ethnic studies including individuals from ethnic minorities, and European, Asian, and American ancestries. We found 190 genes associated with AF and 26 genes linked to HF. Seven genes had implications in both AF and HF, which are SYNPO2L, TTN, MTSS1, SCN5A, PITX2, KLHL3, and AGAP5. We listed our conclusion, which include detailed information about genes and SNPs associated with AF and HF.
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Affiliation(s)
- Kush Ketan Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Cynthia Venkatesan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ, USA
| | - Yuichiro Arima
- Developmental Cardiology Laboratory, International Research Center for Medical Sciences, Kumamoto University, 2-2-1 Honjo, Kumamoto City, Kumamoto, Japan
| | - Suvi Linna-Kuosmanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Zeeshan Ahmed
- Department of Genetics and Genome Sciences, UConn Health, 400 Farmington Ave, Farmington, CT, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, 125 Paterson St, New Brunswick, NJ, USA.
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Das D, Podder S. Deregulation of ceRNA Networks in Frontal Cortex and Choroid Plexus of Brain during SARS-CoV-2 Infection Aggravates Neurological Manifestations: An Insight from Bulk and Single-Cell Transcriptomic Analyses. Adv Biol (Weinh) 2022; 6:e2101310. [PMID: 35661455 PMCID: PMC9348399 DOI: 10.1002/adbi.202101310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/20/2022] [Indexed: 01/28/2023]
Abstract
Although transcriptomic studies of SARS-CoV-2-infected brains have depicted variability in gene expression, the landscape of deregulated cell-specific regulatory circuits has not been elucidated yet. Hence, bulk and single-cell RNA-seq data are analyzed to gain detailed insights. Initially, two ceRNA networks with 19 and 3 differentially expressed (DE) hub lncRNAs are reconstructed in SARS-CoV-2 infected Frontal Cortex (FC) and Choroid Plexus (CP), respectively. Functional and pathway enrichment analyses of downstream mRNAs of deregulated ceRNA axes demonstrate impairment of neurological processes. Mapping of hub lncRNA-mRNA pairs from bulk RNA-seq with snRNA-seq data has indicated that NORAD, NEAT1, and STXBP5-AS1 are downregulated across 4, 4, and 2 FC cell types, respectively. At the same time, MIRLET7BHG and MALAT1 are upregulated in excitatory neurons of FC and neurons of CP, respectively. Here, it is hypothesized that downregulation of NORAD, NEAT1, and STXBP5-AS1, and upregulation of MIRLET7BHG and MALAT1 might deregulate respectively 51, 6, and 37, and 31 and 19 mRNAs in cell types of FC and CP. Afterward, 13 therapeutic miRNAs are traced that might safeguard against deregulated lncRNA-mRNA pairs of NORAD, NEAT1, and MIRLET7BHG in FC. This study helps to explain the plausible mechanism of post-COVID neurological manifestation and also to devise therapeutics against it.
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Affiliation(s)
- Deepyaman Das
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
| | - Soumita Podder
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
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Pérez RF, Alba-Linares JJ, Tejedor JR, Fernández AF, Calero M, Román-Domínguez A, Borrás C, Viña J, Ávila J, Medina M, Fraga MF. Blood DNA methylation patterns in older adults with evolving dementia. J Gerontol A Biol Sci Med Sci 2022; 77:1743-1749. [PMID: 35299244 PMCID: PMC9434456 DOI: 10.1093/gerona/glac068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
Dementia and cognitive disorders are major aging-associated pathologies. The prevalence and severity of these conditions are influenced by both genetic and environmental factors. Reflecting this, epigenetic alterations have been associated with each of these processes, especially at the level of DNA methylation, and such changes may help explain the observed interindividual variability in the development of the 2 pathologies. However, the importance of epigenetic alterations in explaining their etiology is unclear because little is known about the timing of when they appear. Here, using Illumina MethylationEPIC arrays, we have longitudinally analyzed the peripheral blood methylomes of cognitively healthy older adults (>70 year), some of whom went on to develop dementia while others stayed healthy. We have characterized 34 individuals at the prediagnosis stage and at a 4-year follow-up in the postdiagnosis stage (total n = 68). Our results show multiple DNA methylation alterations linked to dementia status, particularly at the level of differentially methylated regions. These loci are associated with several dementia-related genes, including PON1, AP2A2, MAGI2, POT1, ITGAX, PACSIN1, SLC2A8, and EIF4E. We also provide validation of the previously reported epigenetic alteration of HOXB6 and PM20D1. Importantly, we show that most of these regions are already altered in the prediagnosis stage of individuals who go on to develop dementia. In conclusion, our observations suggest that dementia-associated epigenetic patterns that have specific biological features are already present before diagnosis, and thus may be important in the design of epigenetic biomarkers for disease detection based on peripheral tissues.
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Affiliation(s)
- Raúl Fernández Pérez
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Agustín Fernández Fernández
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Miguel Calero
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Aurora Román-Domínguez
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia and CIBERFES-ISCIII, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - Consuelo Borrás
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia and CIBERFES-ISCIII, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - José Viña
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia and CIBERFES-ISCIII, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - Jesús Ávila
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Centro de Biología Molecular Severo Ochoa (CBMSO) CSIC-UAM, Madrid, Spain
| | - Miguel Medina
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Mario Fernández Fraga
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
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Bernstein HG, Keilhoff G, Dobrowolny H, Lendeckel U, Steiner J. From putative brain tumor marker to high cognitive abilities: Emerging roles of a disintegrin and metalloprotease (ADAM) 12 in the brain. J Chem Neuroanat 2020; 109:101846. [PMID: 32622867 DOI: 10.1016/j.jchemneu.2020.101846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/15/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022]
Abstract
ADAM (a disintergin and metalloprotease) 12 is a member of the large family of multidomain metalloprotease-disintegrins, which possess cell-binding and metalloprotease properties. The enzyme is responsible for the shedding of a number of membrane-bound proteins (heparin-binding-EGF, insulin-like growth factor 2-binding proteins 3 and 5, oxytocinase, glycoprotein non-metastatic melanoma protein B and basigin). In rat and human CNS, ADAM12 is predominantly localized in white and gray matter oligodendrocytes. In addition it can be detected in astrocytes, neurons and endothelial cells. Its function in healthy brain is not well established yet, but prominent roles in CNS development, myelination and high cognitive abilities are discussed. There is increasing evidence that ADAM12 is involved in numerous major diseases of the CNS, which are summarized in the present review (brain tumors, multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer´s disease, stroke, schizophrenia, autism and bipolar disorder).
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Affiliation(s)
| | - Gerburg Keilhoff
- Institute of Biochemistry and Cell Biology, Faculty of Medicine, Otto-von-Guericke University, Magdeburg, Germany
| | - Henrik Dobrowolny
- Department of Psychiatry, Otto-von-Guericke University, Magdeburg, Germany
| | - Uwe Lendeckel
- Institute of Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Germany
| | - Johann Steiner
- Department of Psychiatry, Otto-von-Guericke University, Magdeburg, Germany
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6
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Edea Z, Jeoung YH, Shin SS, Ku J, Seo S, Kim IH, Kim SW, Kim KS. Genome-wide association study of carcass weight in commercial Hanwoo cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:327-334. [PMID: 29103288 PMCID: PMC5838337 DOI: 10.5713/ajas.17.0276] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/12/2017] [Accepted: 10/22/2017] [Indexed: 12/25/2022]
Abstract
Objective The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10−6 (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. Conclusion This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | | | - Sung-Sub Shin
- Korea Institute for Animal products Quality Evaluation, Sejong 30100, Korea
| | - Jaeul Ku
- Biomedical Research Center, Turbosoft Inc. Cheongju 28161, Korea
| | - Sungbo Seo
- Biomedical Research Center, Turbosoft Inc. Cheongju 28161, Korea
| | - Il-Hoi Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Sang-Wook Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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7
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Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nat Genet 2017; 49:946-952. [PMID: 28416818 DOI: 10.1038/ng.3843] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/20/2017] [Indexed: 12/14/2022]
Abstract
Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death. Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups. To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery.
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Juiz NA, Cayo NM, Burgos M, Salvo ME, Nasser JR, Búa J, Longhi SA, Schijman AG. Human Polymorphisms in Placentally Expressed Genes and Their Association With Susceptibility to Congenital Trypanosoma cruzi Infection. J Infect Dis 2015; 213:1299-306. [PMID: 26597259 DOI: 10.1093/infdis/jiv561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND It is currently unclear why only a proportion of children born to Trypanosoma cruzi-infected mothers acquire the infection. We have examined the association of 11 single-nucleotide polymorphisms (SNPs) located in genes coding for placental expression enzymes as genetic markers of susceptibility to congenital T. cruzi infection (hereafter, "congenital infection"): rs2014683 and rs1048988 in ALPP; rs11244787 and rs1871054 in ADAM12; rs243866, rs243865, rs17859821, rs243864, and rs2285053 in MMP2; and rs3918242 and rs2234681 in MMP9. METHODS Two groups of children born to mothers seropositive for T. cruzi were compared: 101 had congenital infection, and 116 were uninfected. Novel high-resolution melting and capillary electrophoresis genotyping techniques were designed and used. RESULTS Logistic regression analysis showed that mutations in rs11244787 and rs1871054 (in ADAM12) and rs243866, rs17859821, and rs2285053 (in MMP2) were associated with susceptibility to congenital infection. Multifactor dimensionality reduction revealed that genotyping results for rs11244787, rs1871054, rs243866, rs17859821 and rs243864 sites would be a good predictor of congenital infection. CONCLUSIONS Our results suggest an important role of human polymorphisms in proteins involved in extracellular matrix remodeling and the immune response during congenital infection. To our knowledge, this is the first study demonstrating the association between mutations in placentally expressed genes and susceptibility to congenital infection.
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Affiliation(s)
- Natalia A Juiz
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
| | - Nelly M Cayo
- Instituto de Biología de la Altura, Universidad Nacional de Jujuy
| | - Marianela Burgos
- Servicio de Obstetricia, Departamento Materno Infantil, Hospital Nacional Profesor Alejandro Posadas
| | - Miriam E Salvo
- Servicio de Obstetricia, Departamento Materno Infantil, Hospital Nacional Profesor Alejandro Posadas
| | - Julio R Nasser
- Laboratorio de Química Biológica, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Argentina
| | - Jacqueline Búa
- Instituto Nacional de Parasitología Dr Mario Fatala Chaben, ANLIS, Buenos Aires
| | - Silvia A Longhi
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
| | - Alejandro G Schijman
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
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9
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Puig-Oliveras A, Ballester M, Corominas J, Revilla M, Estellé J, Fernández AI, Ramayo-Caldas Y, Folch JM. A co-association network analysis of the genetic determination of pig conformation, growth and fatness. PLoS One 2014; 9:e114862. [PMID: 25503799 PMCID: PMC4263716 DOI: 10.1371/journal.pone.0114862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/14/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Several QTLs have been identified for major economically relevant traits in livestock, such as growth and meat quality, revealing the complex genetic architecture of these traits. The use of network approaches considering the interactions of multiple molecules and traits provides useful insights into the molecular underpinnings of complex traits. Here, a network based methodology, named Association Weight Matrix, was applied to study gene interactions and pathways affecting pig conformation, growth and fatness traits. RESULTS The co-association network analysis underpinned three transcription factors, PPARγ, ELF1, and PRDM16 involved in mesoderm tissue differentiation. Fifty-four genes in the network belonged to growth-related ontologies and 46 of them were common with a similar study for growth in cattle supporting our results. The functional analysis uncovered the lipid metabolism and the corticotrophin and gonadotrophin release hormone pathways among the most important pathways influencing these traits. Our results suggest that the genes and pathways here identified are important determining either the total body weight of the animal and the fat content. For instance, a switch in the mesoderm tissue differentiation may determinate the age-related preferred pathways being in the puberty stage those related with the miogenic and osteogenic lineages; on the contrary, in the maturity stage cells may be more prone to the adipocyte fate. Hence, our results demonstrate that an integrative genomic co-association analysis is a powerful approach for identifying new connections and interactions among genes. CONCLUSIONS This work provides insights about pathways and key regulators which may be important determining the animal growth, conformation and body proportions and fatness traits. Molecular information concerning genes and pathways here described may be crucial for the improvement of genetic breeding programs applied to pork meat production.
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Affiliation(s)
- Anna Puig-Oliveras
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Maria Ballester
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Jordi Corominas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Manuel Revilla
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Jordi Estellé
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), 78350, Jouy-en-Josas, France
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, 78350, Jouy-en-Josas, France
- Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 78350, Jouy-en-Josas, France
| | - Ana I. Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Yuliaxis Ramayo-Caldas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), 78350, Jouy-en-Josas, France
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, 78350, Jouy-en-Josas, France
- Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 78350, Jouy-en-Josas, France
| | - Josep M. Folch
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
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Transcriptional analysis of apoptotic cerebellar granule neurons following rescue by gastric inhibitory polypeptide. Int J Mol Sci 2014; 15:5596-622. [PMID: 24694544 PMCID: PMC4013584 DOI: 10.3390/ijms15045596] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/04/2014] [Accepted: 03/17/2014] [Indexed: 12/31/2022] Open
Abstract
Apoptosis triggered by exogenous or endogenous stimuli is a crucial phenomenon to determine the fate of neurons, both in physiological and in pathological conditions. Our previous study established that gastric inhibitory polypeptide (Gip) is a neurotrophic factor capable of preventing apoptosis of cerebellar granule neurons (CGNs), during its pre-commitment phase. In the present study, we conducted whole-genome expression profiling to obtain a comprehensive view of the transcriptional program underlying the rescue effect of Gip in CGNs. By using DNA microarray technology, we identified 65 genes, we named survival related genes, whose expression is significantly de-regulated following Gip treatment. The expression levels of six transcripts were confirmed by real-time quantitative polymerase chain reaction. The proteins encoded by the survival related genes are functionally grouped in the following categories: signal transduction, transcription, cell cycle, chromatin remodeling, cell death, antioxidant activity, ubiquitination, metabolism and cytoskeletal organization. Our data outline that Gip supports CGNs rescue via a molecular framework, orchestrated by a wide spectrum of gene actors, which propagate survival signals and support neuronal viability.
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Cacabelos R, Martínez R, Fernández-Novoa L, Carril JC, Lombardi V, Carrera I, Corzo L, Tellado I, Leszek J, McKay A, Takeda M. Genomics of Dementia: APOE- and CYP2D6-Related Pharmacogenetics. Int J Alzheimers Dis 2012; 2012:518901. [PMID: 22482072 PMCID: PMC3312254 DOI: 10.1155/2012/518901] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/12/2011] [Indexed: 01/05/2023] Open
Abstract
Dementia is a major problem of health in developed societies. Alzheimer's disease (AD), vascular dementia, and mixed dementia account for over 90% of the most prevalent forms of dementia. Both genetic and environmental factors are determinant for the phenotypic expression of dementia. AD is a complex disorder in which many different gene clusters may be involved. Most genes screened to date belong to different proteomic and metabolomic pathways potentially affecting AD pathogenesis. The ε4 variant of the APOE gene seems to be a major risk factor for both degenerative and vascular dementia. Metabolic factors, cerebrovascular disorders, and epigenetic phenomena also contribute to neurodegeneration. Five categories of genes are mainly involved in pharmacogenomics: genes associated with disease pathogenesis, genes associated with the mechanism of action of a particular drug, genes associated with phase I and phase II metabolic reactions, genes associated with transporters, and pleiotropic genes and/or genes associated with concomitant pathologies. The APOE and CYP2D6 genes have been extensively studied in AD. The therapeutic response to conventional drugs in patients with AD is genotype specific, with CYP2D6-PMs, CYP2D6-UMs, and APOE-4/4 carriers acting as the worst responders. APOE and CYP2D6 may cooperate, as pleiotropic genes, in the metabolism of drugs and hepatic function. The introduction of pharmacogenetic procedures into AD pharmacological treatment may help to optimize therapeutics.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Rocío Martínez
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Lucía Fernández-Novoa
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Juan C. Carril
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Valter Lombardi
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Iván Carrera
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Lola Corzo
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Iván Tellado
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Jerzy Leszek
- Department of Psychiatry, Medical University of Wroclaw, Pasteura 10, 50-229 Wroclaw, Poland
| | - Adam McKay
- EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, 15165 Bergondo, Spain
| | - Masatoshi Takeda
- Department of Psychiatry and Behavioral Sciences, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
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Future Trends in the Pharmacogenomics of Brain Disorders and Dementia: Influence of APOE and CYP2D6 Variants. Pharmaceuticals (Basel) 2010. [PMCID: PMC4034082 DOI: 10.3390/ph3103040] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
About 80% of functional genes in the human genome are expressed in the brain and over 1,200 different genes have been associated with the pathogenesis of CNS disorders and dementia. Pharmacogenetic studies of psychotropic drug response have focused on determining the relationship between variations in specific candidate genes and the positive and adverse effects of drug treatment. Approximately, 18% of neuroleptics are substrates of CYP1A2 enzymes, 40% of CYP2D6, and 23% of CYP3A4; 24% of antidepressants are substrates of CYP1A2 enzymes, 5% of CYP2B6, 38% of CYP2C19, 85% of CYP2D6, and 38% of CYP3A4; 7% of benzodiazepines are substrates of CYP2C19 enzymes, 20% of CYP2D6, and 95% of CYP3A4. 10-20% of Western populations are defective in genes of the CYP superfamily; and the pharmacogenomic response of psychotropic drugs also depends on genetic variants associated with dementia. Prospective studies with anti-dementia drugs or with multifactorial strategies have revealed that the therapeutic response to conventional drugs in Alzheimer’s disease is genotype-specific. The disease-modifying effects (cognitive performance, biomarker modification) of therapeutic intervention are APOE-dependent, with APOE-4 carriers acting as the worst responders (APOE-3/3 > APOE-3/4 > APOE-4/4). APOE-CYP2D6 interactions also influence the therapeutic outcome in patients with dementia.
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