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Gürünlüoğlu K, Dündar M, Unver T, Akpınar N, Gokce IK, Gürünlüoğlu S, Demircan M, Koc A. Global gene expression profiling in congenital diaphragmatic hernia (CDH) patients. Funct Integr Genomics 2022; 22:359-369. [PMID: 35260975 DOI: 10.1007/s10142-022-00837-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 02/03/2023]
Abstract
Congenital diaphragmatic hernia (CDH) is an anomaly characterized by a defect in the diaphragm, leading to the passage of intra-abdominal organs into the thoracic cavity. Herein, the presented work analyzes the global gene expression profiles in nine CDH and one healthy newborn. All of the patients had left posterolateral (Bochdalek) diaphragmatic hernia, operated via an abdominal approach, and stomach and bowels in the thorax cavity. Some patients also had additional anomalies. A total of 560 differentially regulated genes were measured. Among them, 11 genes showed significant changes in expression associated with lung tissue, vascular structure development, and vitamin A metabolism, which are typical ontologies related to CDH etiology. Among them, SLC25A24 and RAB3IL1 are involved in angiogenesis, HIF1A and FOXC2-AS1 are related with the alveolus, MAGI2-AS3 is associated with the diaphragm, LHX4 and DHH are linked with the lung, and BRINP1, FZD9, WNT4, and BLOC1S1-RDH5 are involved in retinol. Besides, the expression levels of some previously claimed genes with CDH etiology also showed diverse expression patterns in different patients. All these indicated that CDH is a complex, multigenic anomaly, requiring holistic approaches for its elucidation.
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Affiliation(s)
- Kubilay Gürünlüoğlu
- Department of Pediatric Surgery, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Muhammed Dündar
- Department of Medical Genetics, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Turgay Unver
- Ficus Biotechnology Ostim OSB Mah, Inonu University, 100. Yıl Blv. No:55 Yenimahalle, Malatya, Turkey
| | - Necmettin Akpınar
- Department of Pediatric Surgery, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Ismail Kürşad Gokce
- Department of Pediatrics and Division of Neonatology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Semra Gürünlüoğlu
- Department of Pathology, Malatya Education and Research Hospital, Malatya, Turkey
| | - Mehmet Demircan
- Department of Pediatric Surgery, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Ahmet Koc
- Department of Medical Genetics, Faculty of Medicine, Inonu University, Malatya, Turkey.
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Collyer J, Xu F, Munkhsaikhan U, Alberson NF, Orgil BO, Zhang W, Czosek RJ, Lu L, Jefferies JL, Towbin JA, Purevjav E. Combining whole exome sequencing with in silico analysis and clinical data to identify candidate variants in pediatric left ventricular noncompaction. Int J Cardiol 2022; 347:29-37. [PMID: 34752814 DOI: 10.1016/j.ijcard.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Understanding the overall variant burden in pediatric patients with left ventricular noncompaction (LVNC) has clinical implications. Whole exome sequencing (WES) allows detection of coding variants in both candidate cardiomyopathy genes and those included on commercial panels. Other lines of evidence, including in silico analysis, are necessary to reduce the overwhelming number of variants to those most likely having a phenotypic impact. METHODS Five families, including five pediatric probands with LVNC, 5 other affected, and 10 unaffected family members, had WES performed, followed by bioinformatics filtering and Sanger sequencing. Review of the HGMD, variant classification by ACMG guidelines, and clinical information were used to further refine complex genotypes. RESULTS One nonsense and eleven missense variants were identified. In Family 1, affected siblings carried digenic heterozygous variants: E1350K-MYH7 and A276V-ANKRD1. The proband also carried heterozygous W143X-NRG1. Four affected members of Family 2 carried K184Q-MYH7 while unaffected members did not. In Family 3, homozygous A161T-MYH7 and heterozygous P4935T-OBSCN variants were identified in the proband with the latter being absent in his unaffected brother. In Family 4, proband's father and half-sibling have mild hypertrabeculation and carry T3796I-PLEC. The proband, carrying T3796I-PLEC and V2878A-OBSCN, demonstrated higher trabeculation burden. The proband in Family 5 carried four variants, R3247W-PLEC, C92Y-ERG, T1233M-NCOR2, and E54K-HIST1H4B. Application of ACMG criteria and clinical data revealed that W143X-NRG1, P4935T-OBSCN, and V2878A-OBSCN likely have no phenotypic role. CONCLUSIONS We report nine variants, including novel T3796I-PLEC and biallelic A161T-MYH7, likely contributing to phenotypes ranging from asymptomatic hypertrabeculation to severe LVNC with heart failure.
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Affiliation(s)
- John Collyer
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States of America; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States of America
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America; School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Undral Munkhsaikhan
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States of America; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States of America
| | - Neely F Alberson
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States of America; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States of America
| | - Buyan-Ochir Orgil
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States of America; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States of America
| | - Wenying Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America; Laboratory of Genetics and Genomics, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - Richard J Czosek
- Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - John L Jefferies
- Division of Adult Cardiovascular Diseases, University of Tennessee Health Science Center, Memphis, TN, United States of America; Pediatric Cardiology, Le Bonheur Children's Hospital, Memphis, TN, United States of America; Pediatric Cardiology, St. Jude Children's Research Hospital, Memphis, TN, United States of America
| | - Jeffrey A Towbin
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States of America; Pediatric Cardiology, Le Bonheur Children's Hospital, Memphis, TN, United States of America; Pediatric Cardiology, St. Jude Children's Research Hospital, Memphis, TN, United States of America
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States of America; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States of America.
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Mäder G, Freitas LB. Biogeographical, ecological, and phylogenetic analyses clarifying the evolutionary history of Calibrachoa in South American grasslands. Mol Phylogenet Evol 2019; 141:106614. [PMID: 31518694 DOI: 10.1016/j.ympev.2019.106614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022]
Abstract
Calibrachoa is a charismatic South American genus of Solanaceae, closely related to Petunia, which encompasses approximately 30 species. Studies that were based solely on plastid molecular markers indicated the monophyly of the genus and distributed its species in two subgenera; to date no phylogeny has included a broad morphological variants and nuclear markers. Here, we present a phylogenetic analysis based on eight plastid and eight nuclear markers that cover the most extensive geographic distribution for the genus. We use this phylogeny to infer the biogeographic history of the genus and to understand the primary drivers for species diversification. Our results yield a fully supported tree where monophyly is confirmed to genus and subgenera. The species of Stimomphis subgenus that were previously considered uncertain, here emerge in four highly supported clades. The hypothesis of niche conservatism is confirmed, and adaptive radiation explains the species diversification. The lowlands are the most likely ancestral area of the genus, subgenera, and two clades of Stimomphis subgenus. Our results constitute an excellent starting point for further evolutionary and taxonomic studies and explain several uncertain evolutionary relationships in the group and the evolution of their distribution.
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Affiliation(s)
- Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil.
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Abstract
The gene/mutation discovery approaches for inherited retinal diseases (RDs) in the dog model have seen considerable development over the past 25 years. Initial attempts were focused on candidate genes, followed by genome-wide approaches including linkage analysis and DNA-chip-based genome-wide association study. Combined, there are as many as 32 mutations in 27 genes that have been associated with canine retinal diseases to date. More recently, next-generation sequencing has become one of the key methods of choice. With increasing knowledge of the molecular basis of RDs and follow-up surveys in different subpopulations, the conventional understanding of RDs as simple Mendelian traits is being challenged. Modifiers and involvement of multiple genes that alter the disease expression are complicating the prediction of the disease course. In this chapter, advances in the gene/mutation discovery approaches for canine RDs are reviewed, and a multigenic form of canine RD is discussed using a form of canine cone-rod dystrophy as an example.
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Affiliation(s)
- Keiko Miyadera
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Simpson S, Edwards J, Emes RD, Cobb MA, Mongan NP, Rutland CS. A predictive model for canine dilated cardiomyopathy-a meta-analysis of Doberman Pinscher data. PeerJ 2015; 3:e842. [PMID: 25834770 PMCID: PMC4380154 DOI: 10.7717/peerj.842] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/27/2015] [Indexed: 11/20/2022] Open
Abstract
Dilated cardiomyopathy is a prevalent and often fatal disease in humans and dogs. Indeed dilated cardiomyopathy is the third most common form of cardiac disease in humans, reported to affect approximately 36 individuals per 100,000 individuals. In dogs, dilated cardiomyopathy is the second most common cardiac disease and is most prevalent in the Irish Wolfhound, Doberman Pinscher and Newfoundland breeds. Dilated cardiomyopathy is characterised by ventricular chamber enlargement and systolic dysfunction which often leads to congestive heart failure. Although multiple human loci have been implicated in the pathogenesis of dilated cardiomyopathy, the identified variants are typically associated with rare monogenic forms of dilated cardiomyopathy. The potential for multigenic interactions contributing to human dilated cardiomyopathy remains poorly understood. Consistent with this, several known human dilated cardiomyopathy loci have been excluded as common causes of canine dilated cardiomyopathy, although canine dilated cardiomyopathy resembles the human disease functionally. This suggests additional genetic factors contribute to the dilated cardiomyopathy phenotype.This study represents a meta-analysis of available canine dilated cardiomyopathy genetic datasets with the goal of determining potential multigenic interactions relating the sex chromosome genotype (XX vs. XY) with known dilated cardiomyopathy associated loci on chromosome 5 and the PDK4 gene in the incidence and progression of dilated cardiomyopathy. The results show an interaction between known canine dilated cardiomyopathy loci and an unknown X-linked locus. Our study is the first to test a multigenic contribution to dilated cardiomyopathy and suggest a genetic basis for the known sex-disparity in dilated cardiomyopathy outcomes.
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Affiliation(s)
- Siobhan Simpson
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Jennifer Edwards
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK ; Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Malcolm A Cobb
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK ; Department of Pharmacology, Weill Cornell Medical College , New York, NY , USA
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
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