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Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. CELL GENOMICS 2024; 4:100465. [PMID: 38190101 PMCID: PMC10794848 DOI: 10.1016/j.xgen.2023.100465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/07/2023] [Accepted: 11/19/2023] [Indexed: 01/09/2024]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.
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Affiliation(s)
- Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ruben Methorst
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Medical Scientist Training Program, Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
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2
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Bonaglia MC, Salvo E, Sironi M, Bertuzzo S, Errichiello E, Mattina T, Zuffardi O. Case Report: Decrypting an interchromosomal insertion associated with Marfan's syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants. Front Genet 2023; 14:1244983. [PMID: 37811140 PMCID: PMC10551147 DOI: 10.3389/fgene.2023.1244983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient's neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.
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Affiliation(s)
| | - Eliana Salvo
- Cytogenetics Laboratory, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Teresa Mattina
- Medical Genetics Unit, University of Catania, Catania, Italy
- Clinic G.B. Morgagni, Catania, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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Ye Z, Mo C, Liu S, Gao S, Feng L, Zhao B, Canida T, Wu YC, Hatch KS, Ma Y, Mitchell BD, Hong L, Kochunov P, Chen C, Zhao B, Chen S, Ma T. Deciphering the causal relationship between blood pressure and regional white matter integrity: A two-sample Mendelian randomization study. J Neurosci Res 2023; 101:1471-1483. [PMID: 37330925 PMCID: PMC10444533 DOI: 10.1002/jnr.25205] [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: 11/10/2022] [Revised: 04/30/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Elevated arterial blood pressure (BP) is a common risk factor for cerebrovascular and cardiovascular diseases, but no causal relationship has been established between BP and cerebral white matter (WM) integrity. In this study, we performed a two-sample Mendelian randomization (MR) analysis with individual-level data by defining two nonoverlapping sets of European ancestry individuals (genetics-exposure set: N = 203,111; mean age = 56.71 years, genetics-outcome set: N = 16,156; mean age = 54.61 years) from UK Biobank to evaluate the causal effects of BP on regional WM integrity, measured by fractional anisotropy of diffusion tensor imaging. Two BP traits: systolic and diastolic blood pressure were used as exposures. Genetic variant was carefully selected as instrumental variable (IV) under the MR analysis assumptions. We existing large-scale genome-wide association study summary data for validation. The main method used was a generalized version of inverse-variance weight method while other MR methods were also applied for consistent findings. Two additional MR analyses were performed to exclude the possibility of reverse causality. We found significantly negative causal effects (FDR-adjusted p < .05; every 10 mmHg increase in BP leads to a decrease in FA value by .4% ~ 2%) of BP traits on a union set of 17 WM tracts, including brain regions related to cognitive function and memory. Our study extended the previous findings of association to causation for regional WM integrity, providing insights into the pathological processes of elevated BP that might chronically alter the brain microstructure in different regions.
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Affiliation(s)
- Zhenyao Ye
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Chen Mo
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Song Liu
- School of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Si Gao
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Li Feng
- Department of Nutrition and Food Science, College of Agriculture & Natural Resources, University of Maryland, College Park, Maryland, United States of America
| | - Boao Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, Maryland, United States of America
| | - Travis Canida
- Department of Mathematics, The college of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Yu-Chia Wu
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, Maryland, United States of America
| | - Kathryn S Hatch
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Yizhou Ma
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - L.Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Chixiang Chen
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Bingxin Zhao
- Department of Statistics, Purdue University, West Lafayette, Indiana, United States of America
| | - Shuo Chen
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, Maryland, United States of America
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Khaing ZZ, Chandrasekaran A, Katta A, Reed MJ. The Brain and Spinal Microvasculature in Normal Aging. J Gerontol A Biol Sci Med Sci 2023; 78:1309-1319. [PMID: 37093786 PMCID: PMC10395569 DOI: 10.1093/gerona/glad107] [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: 12/08/2022] [Indexed: 04/25/2023] Open
Abstract
Changes in the brain and spinal cord microvasculature during normal aging contribute to the "sensitive" nature of aged central nervous system tissue to ischemic insults. In this review, we will examine alterations in the central nervous system microvasculature during normal aging, which we define as aging without a dominant pathology such as neurodegenerative processes, vascular injury or disease, or trauma. We will also discuss newer technologies to improve the study of central nervous system microvascular structure and function. Microvasculature within the brain and spinal cord will be discussed separately as anatomy and physiology differ between these compartments. Lastly, we will identify critical areas for future studies as well as key unanswered questions.
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Affiliation(s)
- Zin Z Khaing
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | | | - Anjali Katta
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | - May J Reed
- Department of Medicine, Division of Gerontology and Geriatric Medicine, University of Washington, Seattle, Washington, USA
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5
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Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.09.23285622. [PMID: 36824883 PMCID: PMC9949190 DOI: 10.1101/2023.02.09.23285622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary arteries and 19% exhibited cell-type-specific expression. Colocalization analysis with GWAS identified subgroups of eGenes unique to CAD and blood pressure. Fine-mapping highlighted additional eGenes of interest, including TBX20 and IL5 . Splicing (s)QTLs for 1,690 genes were also identified, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing events to accurately identify disease-relevant gene expression. Our work provides the first human coronary artery eQTL resource from a patient sample and exemplifies the necessity of diverse study populations and multi-omic approaches to characterize gene regulation in critical disease processes. Study Design Overview
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6
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Li Q, Dibus M, Casey A, Yee CSK, Vargas SO, Luo S, Rosen SM, Madden JA, Genetti CA, Brabek J, Brownstein CA, Kazerounian S, Raby BA, Schmitz-Abe K, Kennedy JC, Fishman MP, Mullen MP, Taylor JM, Rosel D, Agrawal PB. A homozygous stop-gain variant in ARHGAP42 is associated with childhood interstitial lung disease, systemic hypertension, and immunological findings. PLoS Genet 2021; 17:e1009639. [PMID: 34232960 PMCID: PMC8289122 DOI: 10.1371/journal.pgen.1009639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/19/2021] [Accepted: 06/02/2021] [Indexed: 11/18/2022] Open
Abstract
ARHGAP42 encodes Rho GTPase activating protein 42 that belongs to a member of the GTPase Regulator Associated with Focal Adhesion Kinase (GRAF) family. ARHGAP42 is involved in blood pressure control by regulating vascular tone. Despite these findings, disorders of human variants in the coding part of ARHGAP42 have not been reported. Here, we describe an 8-year-old girl with childhood interstitial lung disease (chILD), systemic hypertension, and immunological findings who carries a homozygous stop-gain variant (c.469G>T, p.(Glu157Ter)) in the ARHGAP42 gene. The family history is notable for both parents with hypertension. Histopathological examination of the proband lung biopsy showed increased mural smooth muscle in small airways and alveolar septa, and concentric medial hypertrophy in pulmonary arteries. ARHGAP42 stop-gain variant in the proband leads to exon 5 skipping, and reduced ARHGAP42 levels, which was associated with enhanced RhoA and Cdc42 expression. This is the first report linking a homozygous stop-gain variant in ARHGAP42 with a chILD disorder, systemic hypertension, and immunological findings in human patient. Evidence of smooth muscle hypertrophy on lung biopsy and an increase in RhoA/ROCK signaling in patient cells suggests the potential mechanistic link between ARHGAP42 deficiency and the development of chILD disorder.
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Affiliation(s)
- Qifei Li
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michal Dibus
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy, Czech Republic
| | - Alicia Casey
- Division of Pulmonary Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christina S. K. Yee
- Division of Immunology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sara O. Vargas
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shiyu Luo
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Samantha M. Rosen
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jill A. Madden
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Casie A. Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jan Brabek
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy, Czech Republic
| | - Catherine A. Brownstein
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shideh Kazerounian
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin A. Raby
- Division of Pulmonary Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Klaus Schmitz-Abe
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - John C. Kennedy
- Division of Pulmonary Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Martha P. Fishman
- Division of Pulmonary Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mary P. Mullen
- Department of Cardiology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joan M. Taylor
- Dept. Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Daniel Rosel
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy, Czech Republic
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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Tseng CC, Wong MC, Liao WT, Chen CJ, Lee SC, Yen JH, Chang SJ. Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases. Int J Mol Sci 2021; 22:ijms22084187. [PMID: 33919522 PMCID: PMC8073710 DOI: 10.3390/ijms22084187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.
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Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Man-Chun Wong
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan;
| | - Su-Chen Lee
- Laboratory Diagnosis of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu 30010, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung 81148, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
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8
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Abstract
The blood-brain barrier (BBB) protects the central nervous system (CNS) from unregulated exposure to the blood and its contents. The BBB also controls the blood-to-brain and brain-to-blood permeation of many substances, resulting in nourishment of the CNS, its homeostatic regulation and communication between the CNS and peripheral tissues. The cells forming the BBB communicate with cells of the brain and in the periphery. This highly regulated interface changes with healthy aging. Here, we review those changes, starting with morphology and disruption. Transporter changes include those for amyloid beta peptide, glucose and drugs. Brain fluid dynamics, pericyte health and basement membrane and glycocalyx compositions are all altered with healthy aging. Carrying the ApoE4 allele leads to an acceleration of most of the BBB's age-related changes. We discuss how alterations in the BBB that occur with healthy aging reflect adaptation to the postreproductive phase of life and may affect vulnerability to age-associated diseases.
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Bonaglia MC, Bertuzzo S, Ciaschini AM, Discepoli G, Castiglia L, Romaniello R, Zuffardi O, Fichera M. Targeted next-generation sequencing identifies the disruption of the SHANK3 and RYR2 genes in a patient carrying a de novo t(1;22)(q43;q13.3) associated with signs of Phelan-McDermid syndrome. Mol Cytogenet 2020; 13:22. [PMID: 32536973 PMCID: PMC7291734 DOI: 10.1186/s13039-020-00490-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background It has been known for more than 30 years that balanced translocations, especially if de novo, can associate with congenital malformations and / or neurodevelopmental disorders, following the disruption of a disease gene or its cis-regulatory elements at one or both breakpoints. Case presentation We describe a 10-year-old girl with a non-specific neurodevelopmental disorder characterized by moderate intellectual disability (ID), gross motor clumsiness, social and communication deficits. She carries a de novo reciprocal translocation between chromosomes 1q43 and 22q13.3, the latter suggesting the involvement of SHANK3. Indeed, its haploinsufficiency associates with Phelan-McDermid Syndrome, whose main symptoms are characterized by global developmental delay and absent or severely delayed expressive speech. A deep molecular approach, including next-generation sequencing of SHANK3 locus, allowed demonstrating the breakage of RYR2 and SHANK3 on the derivative chromosomes 1 and 22 respectively, and the formation of two fusion genes SHANK3-RYR2 and RYR2-SHANK3 with concomitant cryptic deletion of 3.6 and 4.1 kilobases at translocation junction of both derivatives chromosomes 22 and 1, respectively. Conclusions Although the interruption of SHANK3 accounts for the patient’s psychomotor retardation and autism-like behavior, we do not exclude that the interruption of RYR2 may also have a role on her disorder, or result in further pathogenicity in the future. Indeed, RYR2 that has a well-established role in the etiology of two autosomal dominant adulthood cardiac disorders (#600996 and #604772) is also expressed in the brain (cerebellum, hippocampus, and cerebral cortex) and about half of RYR2 mutation carriers present late onset primary generalized epilepsy without cardiac arrhythmogenic disorders. Moreover, RYR2 variants have also been sporadically reported in individuals with early onset schizophrenia or ID, and its constraint values suggest intolerance to loss-of-function. This study not only confirms the usefulness of the molecular mapping of de novo balanced rearrangements in symptomatic individuals, but also underscores the need for long-term clinical evaluation of the patients, for better evaluating the pathogenicity of the chromosomal breakpoints.
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Affiliation(s)
- Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Anna Maria Ciaschini
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | - Giancarlo Discepoli
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | | | - Romina Romaniello
- Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, 23842 Lecco, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Marco Fichera
- Oasi Research Institute-IRCCS, Troina, Italy.,Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
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Molecular Regulation of the RhoGAP GRAF3 and Its Capacity to Limit Blood Pressure In Vivo. Cells 2020; 9:cells9041042. [PMID: 32331391 PMCID: PMC7226614 DOI: 10.3390/cells9041042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
Anti-hypertensive therapies are usually prescribed empirically and are often ineffective. Given the prevalence and deleterious outcomes of hypertension (HTN), improved strategies are needed. We reported that the Rho-GAP GRAF3 is selectively expressed in smooth muscle cells (SMC) and controls blood pressure (BP) by limiting the RhoA-dependent contractility of resistance arterioles. Importantly, genetic variants at the GRAF3 locus controls BP in patients. The goal of this study was to validate GRAF3 as a druggable candidate for future anti-HTN therapies. Importantly, using a novel mouse model, we found that modest induction of GRAF3 in SMC significantly decreased basal and vasoconstrictor-induced BP. Moreover, we found that GRAF3 protein toggles between inactive and active states by processes controlled by the mechano-sensing kinase, focal adhesion kinase (FAK). Using resonance energy transfer methods, we showed that agonist-induced FAK-dependent phosphorylation at Y376GRAF3 reverses an auto-inhibitory interaction between the GAP and BAR-PH domains. Y376 is located in a linker between the PH and GAP domains and is invariant in GRAF3 homologues and a phosphomimetic E376GRAF3 variant exhibited elevated GAP activity. Collectively, these data provide strong support for the future identification of allosteric activators of GRAF3 for targeted anti-hypertensive therapies.
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11
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Cabrera CP, Ng FL, Nicholls HL, Gupta A, Barnes MR, Munroe PB, Caulfield MJ. Over 1000 genetic loci influencing blood pressure with multiple systems and tissues implicated. Hum Mol Genet 2019; 28:R151-R161. [PMID: 31411675 PMCID: PMC6872427 DOI: 10.1093/hmg/ddz197] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/12/2022] Open
Abstract
High blood pressure (BP) remains the major heritable and modifiable risk factor for cardiovascular disease. Persistent high BP, or hypertension, is a complex trait with both genetic and environmental interactions. Despite swift advances in genomics, translating new discoveries to further our understanding of the underlying molecular mechanisms remains a challenge. More than 500 loci implicated in the regulation of BP have been revealed by genome-wide association studies (GWAS) in 2018 alone, taking the total number of BP genetic loci to over 1000. Even with the large number of loci now associated to BP, the genetic variance explained by all loci together remains low (~5.7%). These genetic associations have elucidated mechanisms and pathways regulating BP, highlighting potential new therapeutic and drug repurposing targets. A large proportion of the BP loci were discovered and reported simultaneously by multiple research groups, creating a knowledge gap, where the reported loci to date have not been investigated in a harmonious way. Here, we review the BP-associated genetic variants reported across GWAS studies and investigate their potential impact on the biological systems using in silico enrichment analyses for pathways, tissues, gene ontology and genetic pleiotropy.
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Affiliation(s)
- Claudia P Cabrera
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Fu Liang Ng
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Hannah L Nicholls
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ajay Gupta
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael R Barnes
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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