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Rraku E, Kerstjens-Frederikse WS, Swertz MA, Dijkhuizen T, van Ravenswaaij-Arts CMA, Engwerda A. The phenotypic spectrum of terminal and subterminal 6p deletions based on a social media-derived cohort and literature review. Orphanet J Rare Dis 2023; 18:68. [PMID: 36964621 PMCID: PMC10039519 DOI: 10.1186/s13023-023-02670-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/11/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Terminal 6p deletions are rare, and information on their clinical consequences is scarce, which impedes optimal management and follow-up by clinicians. The parent-driven Chromosome 6 Project collaborates with families of affected children worldwide to better understand the clinical effects of chromosome 6 aberrations and to support clinical guidance. A microarray report is required for participation, and detailed phenotype information is collected directly from parents through a multilingual web-based questionnaire. Information collected from parents is then combined with case data from literature reports. Here, we present our findings on 13 newly identified patients and 46 literature cases with genotypically well-characterised terminal and subterminal 6p deletions. We provide phenotype descriptions for both the whole group and for subgroups based on deletion size and HI gene content. RESULTS The total group shared a common phenotype characterised by ocular anterior segment dysgenesis, vision problems, brain malformations, congenital defects of the cardiac septa and valves, mild to moderate hearing impairment, eye movement abnormalities, hypotonia, mild developmental delay and dysmorphic features. These characteristics were observed in all subgroups where FOXC1 was included in the deletion, confirming a dominant role for this gene. Additional characteristics were seen in individuals with terminal deletions exceeding 4.02 Mb, namely complex heart defects, corpus callosum abnormalities, kidney abnormalities and orofacial clefting. Some of these additional features may be related to the loss of other genes in the terminal 6p region, such as RREB1 for the cardiac phenotypes and TUBB2A and TUBB2B for the cerebral phenotypes. In the newly identified patients, we observed previously unreported features including gastrointestinal problems, neurological abnormalities, balance problems and sleep disturbances. CONCLUSIONS We present an overview of the phenotypic characteristics observed in terminal and subterminal 6p deletions. This reveals a common phenotype that can be highly attributable to haploinsufficiency of FOXC1, with a possible additional effect of other genes in the 6p25 region. We also delineate the developmental abilities of affected individuals and report on previously unrecognised features, showing the added benefit of collecting information directly from parents. Based on our overview, we provide recommendations for clinical surveillance to support clinicians, patients and families.
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Affiliation(s)
- Eleana Rraku
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Conny M A van Ravenswaaij-Arts
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
- ATN/Jonx, Groningen, The Netherlands.
| | - Aafke Engwerda
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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Copy number variation-associated lncRNAs may contribute to the etiologies of congenital heart disease. Commun Biol 2023; 6:189. [PMID: 36806749 PMCID: PMC9938258 DOI: 10.1038/s42003-023-04565-z] [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: 06/23/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Copy number variations (CNVs) have long been recognized as pathogenic factors for congenital heart disease (CHD). Few CHD associated CNVs could be interpreted as dosage effect due to disruption of coding sequences. Emerging evidences have highlighted the regulatory roles of long noncoding RNAs (lncRNAs) in cardiac development. Whereas it remains unexplored whether lncRNAs within CNVs (CNV-lncRNAs) could contribute to the etiology of CHD associated CNVs. Here we constructed coexpression networks involving CNV-lncRNAs within CHD associated CNVs and protein coding genes using the human organ developmental transcriptomic data, and showed that CNV-lncRNAs within 10 of the non-syndromic CHD associated CNVs clustered in the most significant heart correlated module, and had highly correlated coexpression with multiple key CHD genes. HSALNG0104472 within 15q11.2 region was identified as a hub CNV-lncRNA with heart-biased expression and validated experimentally. Our results indicated that HSALNG0104472 should be a main effector responsible for cardiac defects of 15q11.2 deletion through regulating cardiomyocytes differentiation. Our findings suggested that CNV-lncRNAs could potentially contribute to the pathologies of a maximum proportion of 68.4% (13/19) of non-syndromic CHD associated CNVs. These results indicated that explaining the pathogenesis of CHD associated CNVs should take account of the noncoding regions.
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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4
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Jimenez Y, Paulsen C, Turner E, Iturra S, Cuevas O, Lay-son G, Repetto GM, Rojas M, Calderon JF. Exome Sequencing Identifies Genetic Variants Associated with Extreme Manifestations of the Cardiovascular Phenotype in Marfan Syndrome. Genes (Basel) 2022; 13:genes13061027. [PMID: 35741789 PMCID: PMC9223058 DOI: 10.3390/genes13061027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/06/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
Marfan Syndrome (MFS) is an autosomal dominant condition caused by variants in the fibrillin-1 (FBN1) gene. Cardinal features of MFS include ectopia lentis (EL), musculoskeletal features and aortic root aneurysm and dissection. Although dissection of the ascending aorta is the main cause of mortality in MFS, the clinical course differs considerably in age of onset and severity, even among individuals who share the same causative variant, suggesting the existence of additional genetic variants that modify the severity of the cardiovascular phenotype in MFS. We recruited MFS patients and classified them into severe (n = 8) or mild aortic phenotype (n = 14) according to age of presentation of the first aorta-related incident. We used Exome Sequencing to identify the genetic variants associated with the severity of aortic manifestations and we performed linkage analysis where suitable. We found five genes associated with severe aortic phenotype and three genes that could be protective for this phenotype in MFS. These genes regulate components of the extracellular matrix, TGFβ pathway and other signaling pathways that are involved in the maintenance of the ECM or angiogenesis. Further studies will be required to understand the functional effect of these variants and explore novel, personalized risk management and, potentially, therapies for these patients.
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Affiliation(s)
- Yanireth Jimenez
- Doctorado en Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 8320000, Chile; (Y.J.); (M.R.)
| | - Cesar Paulsen
- Servicio de Cirugía Cardiovascular, Instituto Nacional del Tórax, Santiago 7500808, Chile; (C.P.); (E.T.); (S.I.); (O.C.)
| | - Eduardo Turner
- Servicio de Cirugía Cardiovascular, Instituto Nacional del Tórax, Santiago 7500808, Chile; (C.P.); (E.T.); (S.I.); (O.C.)
| | - Sebastian Iturra
- Servicio de Cirugía Cardiovascular, Instituto Nacional del Tórax, Santiago 7500808, Chile; (C.P.); (E.T.); (S.I.); (O.C.)
| | - Oscar Cuevas
- Servicio de Cirugía Cardiovascular, Instituto Nacional del Tórax, Santiago 7500808, Chile; (C.P.); (E.T.); (S.I.); (O.C.)
- Departamento de Cirugía Cardiovascular, Clínica Alemana, Universidad del Desarrollo, Santiago 8320000, Chile
| | - Guillermo Lay-son
- Unidad de Genética, División de Pediatría, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile;
| | - Gabriela M. Repetto
- Programa de Enfermedades Poco Frecuentes, Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 8320000, Chile;
| | - Marcelo Rojas
- Doctorado en Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 8320000, Chile; (Y.J.); (M.R.)
| | - Juan F. Calderon
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 8320000, Chile
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago 8320000, Chile
- Correspondence: ; Tel.: +56-22-578-5778
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Bhatt AB, Lantin-Hermoso MR, Daniels CJ, Jaquiss R, Landis BJ, Marino BS, Rathod RH, Vincent RN, Keller BB, Villafane J. Isolated Coarctation of the Aorta: Current Concepts and Perspectives. Front Cardiovasc Med 2022; 9:817866. [PMID: 35694677 PMCID: PMC9174545 DOI: 10.3389/fcvm.2022.817866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Current management of isolated CoA, localized narrowing of the aortic arch in the absence of other congenital heart disease, is a success story with improved prenatal diagnosis, high survival and improved understanding of long-term complication. Isolated CoA has heterogenous presentations, complex etiologic mechanisms, and progressive pathophysiologic changes that influence outcome. End-to-end or extended end-to-end anastomosis are the favored surgical approaches for isolated CoA in infants and transcatheter intervention is favored for children and adults. Primary stent placement is the procedure of choice in larger children and adults. Most adults with treated isolated CoA thrive, have normal daily activities, and undergo successful childbirth. Fetal echocardiography is the cornerstone of prenatal counseling and genetic testing is recommended. Advanced 3D imaging identifies aortic complications and myocardial dysfunction and guides individualized therapies including re-intervention. Adult CHD program enrollment is recommended. Longer follow-up data are needed to determine the frequency and severity of aneurysm formation, myocardial dysfunction, and whether childhood lifestyle modifications reduce late-onset complications.
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Affiliation(s)
- Ami B. Bhatt
- Departments of Internal Medicine and Pediatrics and Division of Cardiology, Harvard Medical School, Boston, MA, United States
| | - Maria R. Lantin-Hermoso
- Section of Cardiology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Curt J. Daniels
- Departments of Pediatrics and Internal Medicine, The Ohio State University Medical Center, Columbus, OH, United States
| | - Robert Jaquiss
- Department of Cardiovascular and Thoracic Surgery and Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Benjamin John Landis
- Department of Pediatrics and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bradley S. Marino
- Department of Pediatric Cardiology, Cleveland Clinic Children's, Cleveland, OH, United States
| | - Rahul H. Rathod
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Robert N. Vincent
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Bradley B. Keller
- Cincinnati Children's Heart Institute and the Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Bradley B. Keller
| | - Juan Villafane
- Cincinnati Children's Heart Institute and the Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States
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Quttainah M, Raveendran VV, Saleh S, Parhar R, Aljoufan M, Moorjani N, Al-Halees ZY, AlShahid M, Collison KS, Westaby S, Al-Mohanna F. Transcriptomal Insights of Heart Failure from Normality to Recovery. Biomolecules 2022; 12:biom12050731. [PMID: 35625658 PMCID: PMC9138767 DOI: 10.3390/biom12050731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Current management of heart failure (HF) is centred on modulating the progression of symptoms and severity of left ventricular dysfunction. However, specific understandings of genetic and molecular targets are needed for more precise treatments. To attain a clearer picture of this, we studied transcriptome changes in a chronic progressive HF model. Fifteen sheep (Ovis aries) underwent supracoronary aortic banding using an inflatable cuff. Controlled and progressive induction of pressure overload in the LV was monitored by echocardiography. Endomyocardial biopsies were collected throughout the development of LV failure (LVF) and during the stage of recovery. RNA-seq data were analysed using the PANTHER database, Metascape, and DisGeNET to annotate the gene expression for functional ontologies. Echocardiography revealed distinct clinical differences between the progressive stages of hypertrophy, dilatation, and failure. A unique set of transcript expressions in each stage was identified, despite an overlap of gene expression. The removal of pressure overload allowed the LV to recover functionally. Compared to the control stage, there were a total of 256 genes significantly changed in their expression in failure, 210 genes in hypertrophy, and 73 genes in dilatation. Gene expression in the recovery stage was comparable with the control stage with a well-noted improvement in LV function. RNA-seq revealed the expression of genes in each stage that are not reported in cardiovascular pathology. We identified genes that may be potentially involved in the aetiology of progressive stages of HF, and that may provide future targets for its management.
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Affiliation(s)
- Mohammed Quttainah
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.Q.); (V.V.R.); (S.S.); (R.P.); (K.S.C.)
| | - Vineesh Vimala Raveendran
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.Q.); (V.V.R.); (S.S.); (R.P.); (K.S.C.)
| | - Soad Saleh
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.Q.); (V.V.R.); (S.S.); (R.P.); (K.S.C.)
| | - Ranjit Parhar
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.Q.); (V.V.R.); (S.S.); (R.P.); (K.S.C.)
| | - Mansour Aljoufan
- Heart Centre, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.A.); (Z.Y.A.-H.); (M.A.)
| | - Narain Moorjani
- Department of Cardiothoracic Surgery, Papworth Hospital, University of Cambridge, Cambridge CB23 3RE, UK;
| | - Zohair Y. Al-Halees
- Heart Centre, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.A.); (Z.Y.A.-H.); (M.A.)
| | - Maie AlShahid
- Heart Centre, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.A.); (Z.Y.A.-H.); (M.A.)
| | - Kate S. Collison
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.Q.); (V.V.R.); (S.S.); (R.P.); (K.S.C.)
| | - Stephen Westaby
- Oxford Heart Centre, John Radcliffe Hospital, Oxford OX9 3DU, UK;
| | - Futwan Al-Mohanna
- Department of Cell Biology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia; (M.Q.); (V.V.R.); (S.S.); (R.P.); (K.S.C.)
- Correspondence:
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7
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Zebrafish foxc1a controls ventricular chamber maturation by directly regulating wwtr1 and nkx2.5 expression. J Genet Genomics 2021; 49:559-568. [PMID: 34923164 DOI: 10.1016/j.jgg.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022]
Abstract
Chamber maturation is a significant process in cardiac development. Disorders of this crucial process lead to a range of congenital heart defects. Foxc1a is a critical transcription factor reported to regulate the specification of cardiac progenitor cells. However, little is known about the role of Foxc1a in modulating chamber maturation. Previously, we reported that foxc1a-null zebrafish embryos exhibit disrupted heart structures and functions. In this study, we observed that ventricle structure and cardiomyocyte proliferation were abolished during chamber maturation in foxc1a-null zebrafish embryos. To observe the endogenous localization of Foxc1a in the hearts of living embryos, we inserted eyfp at the foxc1a genomic locus using TALEN. Analysis of the knockin zebrafish showed that foxc1a was widely expressed in ventricular cardiomyocytes during chamber development. Cardiac RNA sequencing analysis revealed downregulated expression of the Hippo signaling effector wwtr1. Dual-luciferase and chromatin immunoprecipitation assays revealed that Foxc1a could bind directly to three sites in the wwtr1 promoter region. Furthermore, wwtr1 mRNA overexpression was sufficient to reverse the ventricle defects during chamber maturation. Conditional overexpression of nkx2.5 also partially rescued the ventricular defects during chamber development. These findings demonstrate that wwtr1 and nkx2.5 are direct targets of Foxc1a during ventricular chamber maturation.
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Zhang X, Wang B, You G, Xiang Y, Fu Q, Yu Y, Zhang X. Copy number variation analysis in Chinese children with complete atrioventricular canal and single ventricle. BMC Med Genomics 2021; 14:243. [PMID: 34627233 PMCID: PMC8502261 DOI: 10.1186/s12920-021-01090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is one of the most common birth defects. Copy number variations (CNVs) have been proved to be important genetic factors that contribute to CHD. Here we screened genome-wide CNVs in Chinese children with complete atrioventricular canal (CAVC) and single ventricle (SV), since there were scarce researches dedicated to these two types of CHD. METHODS We screened CNVs in 262 sporadic CAVC cases and 259 sporadic SV cases respectively, using a customized SNP array. The detected CNVs were annotated and filtered using available databases. RESULTS Among 262 CAVC patients, we identified 6 potentially-causative CNVs in 43 individuals (16.41%, 43/262), including 2 syndrome-related CNVs (7q11.23 and 8q24.3 deletion). Surprisingly, 90.70% CAVC patients with detected CNVs (39/43) were found to carry duplications of 21q11.2-21q22.3, which were recognized as trisomy 21 (Down syndrome, DS). In CAVC with DS patients, the female to male ratio was 1.6:1.0 (24:15), and the rate of pulmonary hypertension (PH) was 41.03% (16/39). Additionally, 6 potentially-causative CNVs were identified in the SV patients (2.32%, 6/259), and none of them was trisomy 21. Most CNVs identified in our cohort were classified as rare (< 1%), occurring just once among CAVC or SV individuals except the 21q11.2-21q22.3 duplication (14.89%) in CAVC cohort. CONCLUSIONS Our study identified 12 potentially-causative CNVs in 262 CAVC and 259 SV patients, representing the largest cohort of these two CHD types in Chinese population. The results provided strong correlation between CAVC and DS, which also showed sex difference and high incidence of PH. The presence of potentially-causative CNVs suggests the etiology of complex CHD is incredibly diverse, and CHD candidate genes remain to be discovered.
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Affiliation(s)
- Xingyu Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoling You
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Ray T, Ryusaki T, Ray PS. Therapeutically Targeting Cancers That Overexpress FOXC1: A Transcriptional Driver of Cell Plasticity, Partial EMT, and Cancer Metastasis. Front Oncol 2021; 11:721959. [PMID: 34540690 PMCID: PMC8446626 DOI: 10.3389/fonc.2021.721959] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 12/28/2022] Open
Abstract
Metastasis accounts for more than 90% of cancer related mortality, thus the most pressing need in the field of oncology today is the ability to accurately predict future onset of metastatic disease, ideally at the time of initial diagnosis. As opposed to current practice, what would be desirable is that prognostic, biomarker-based detection of metastatic propensity and heightened risk of cancer recurrence be performed long before overt metastasis has set in. Without such timely information it will be impossible to formulate a rational therapeutic treatment plan to favorably alter the trajectory of disease progression. In order to help inform rational selection of targeted therapeutics, any recurrence/metastasis risk prediction strategy must occur with the paired identification of novel prognostic biomarkers and their underlying molecular regulatory mechanisms that help drive cancer recurrence/metastasis (i.e. recurrence biomarkers). Traditional clinical factors alone (such as TNM staging criteria) are no longer adequately prognostic for this purpose in the current molecular era. FOXC1 is a pivotal transcription factor that has been functionally implicated to drive cancer metastasis and has been demonstrated to be an independent predictor of heightened metastatic risk, at the time of initial diagnosis. In this review, we present our viewpoints on the master regulatory role that FOXC1 plays in mediating cancer stem cell traits that include cellular plasticity, partial EMT, treatment resistance, cancer invasion and cancer migration during cancer progression and metastasis. We also highlight potential therapeutic strategies to target cancers that are, or have evolved to become, “transcriptionally addicted” to FOXC1. The potential role of FOXC1 expression status in predicting the efficacy of these identified therapeutic approaches merits evaluation in clinical trials.
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Affiliation(s)
- Tania Ray
- R&D Division, Onconostic Technologies (OT), Inc., Champaign, IL, United States
| | | | - Partha S Ray
- R&D Division, Onconostic Technologies (OT), Inc., Champaign, IL, United States
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10
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Magouliotis DE, Fergadi MP, Christodoulidis G, Svokos AA, Svokos KA, Bareka M, Athanasiou T. In-depth bioinformatic study of the cadherin 5 interactome in patients with thoracic aortic aneurysm unveils 8 novel biomarkers. Eur J Cardiothorac Surg 2021; 61:11-18. [PMID: 34293135 DOI: 10.1093/ejcts/ezab338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/25/2021] [Accepted: 06/12/2021] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVES Thoracic aortic aneurysm (TAA) is characterized by the dilation of the aorta and is associated with poor prognosis if not diagnosed and treated early. In this context, the identification of biomarkers regarding the TAA diagnosis, monitoring and prognosis is crucial. The purpose of the current study was to investigate the differential gene expression profile of the cadherin 5 (CDH5 or VE-Cadherin) gene network in patients with TAA, to propose novel biomarkers. METHODS In silico techniques were used to construct the interactome of the CDH5 network, identify the differentially expressed genes (DEGs) in TAA as compared to healthy controls, and uncover the related molecular functions and the regulating miRNAs. RESULTS Transcriptomic data of one microarray dataset were included, incorporating 43 TAA and 43 control samples. Eight DEGs were identified; 7 were up-regulated and 1 was down-regulated. A molecular signature of 8 genes (CDH5; Calcitonin Receptor-Like Receptor-CALCRL; Activin A Receptor-Like Type 1-ACVRL1, Tryptophanyl-TRNA Synthetase 1-WARS; Junction Plakoglobin-JUP, Protein Tyrosine Phosphatase Receptor Type J-PTPRJ, Purinergic Receptor P2X 4-P2RX4, Kinase Insert Domain Receptor-KDR) were identified as biomarkers associated with TAA. PTPRJ was associated with excellent discrimination and calibration in predicting TAA presentation. Positive correlations were reported regarding the expression of CDH5-CALCRL, CDH5-ACVRL1, CDH5-WARS and CDH5-PTPRJ. Finally, gene set enrichment analysis indicated the molecular functions and miRNA families (hsa-miR-296-5p, hsa-miR-6836-5p, hsa-miR-6132, hsa-miR-27a-5p and hsa-miR-6773-5p) relevant to the 8 biomarkers. CONCLUSIONS These outcomes propose an 8-gene molecular panel associated with TAA.
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Affiliation(s)
- Dimitrios E Magouliotis
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, UCL, London, UK
- Department of Cardiothoracic Surgery, University of Thessaly, Biopolis, Larissa, Greece
| | - Maria P Fergadi
- Department of Radiology, University of Thessaly, Biopolis, Larissa, Greece
| | | | - Alexis A Svokos
- Department of Obstetrics and Gynecology, Geisinger Medical Center, Danville, PA, USA
| | - Konstantina A Svokos
- Department of Neurosurgery, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Metaxia Bareka
- Department of Anesthesiology, University of Thessaly, Biopolis, Larissa, Greece
| | - Thanos Athanasiou
- Department of Surgery and Cancer, Imperial College London, St Mary's Hospital, London, UK
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11
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Affiliation(s)
- Lisa K Hornberger
- Fetal and Neonatal Cardiology Program, Division of Cardiology, Department of Pediatrics, Stollery Children's Hospital, Lois Hole Hospital for Women, Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Luke G Eckersley
- Fetal and Neonatal Cardiology Program, Division of Cardiology, Department of Pediatrics, Stollery Children's Hospital, Lois Hole Hospital for Women, Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
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12
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Abstract
Congenital heart disease is the most common congenital defect observed in newborns. Within the spectrum of congenital heart disease are left‐sided obstructive lesions (LSOLs), which include hypoplastic left heart syndrome, aortic stenosis, bicuspid aortic valve, coarctation of the aorta, and interrupted aortic arch. These defects can arise in isolation or as a component of a defined syndrome; however, nonsyndromic defects are often observed in multiple family members and associated with high sibling recurrence risk. This clear evidence for a heritable basis has driven a lengthy search for disease‐causing variants that has uncovered both rare and common variants in genes that, when perturbed in cardiac development, can result in LSOLs. Despite advancements in genetic sequencing platforms and broadening use of exome sequencing, the currently accepted LSOL‐associated genes explain only 10% to 20% of patients. Further, the combinatorial effects of common and rare variants as a cause of LSOLs are emerging. In this review, we highlight the genes and variants associated with the different LSOLs and discuss the strengths and weaknesses of the present genetic associations. Furthermore, we discuss the research avenues needed to bridge the gaps in our current understanding of the genetic basis of nonsyndromic congenital heart disease.
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Affiliation(s)
- Lauren E Parker
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC
| | - Andrew P Landstrom
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC.,Department of Cell Biology Duke University School of Medicine Durham NC
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13
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Varshney A, Chahal G, Santos L, Stolper J, Hallab JC, Nim HT, Nikolov M, Yip A, Ramialison M. Human Cardiac Transcription Factor Networks. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11597-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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14
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Duddu S, Chakrabarti R, Ghosh A, Shukla PC. Hematopoietic Stem Cell Transcription Factors in Cardiovascular Pathology. Front Genet 2020; 11:588602. [PMID: 33193725 PMCID: PMC7596349 DOI: 10.3389/fgene.2020.588602] [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: 07/29/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Transcription factors as multifaceted modulators of gene expression that play a central role in cell proliferation, differentiation, lineage commitment, and disease progression. They interact among themselves and create complex spatiotemporal gene regulatory networks that modulate hematopoiesis, cardiogenesis, and conditional differentiation of hematopoietic stem cells into cells of cardiovascular lineage. Additionally, bone marrow-derived stem cells potentially contribute to the cardiovascular cell population and have shown potential as a therapeutic approach to treat cardiovascular diseases. However, the underlying regulatory mechanisms are currently debatable. This review focuses on some key transcription factors and associated epigenetic modifications that modulate the maintenance and differentiation of hematopoietic stem cells and cardiac progenitor cells. In addition to this, we aim to summarize different potential clinical therapeutic approaches in cardiac regeneration therapy and recent discoveries in stem cell-based transplantation.
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Affiliation(s)
| | | | | | - Praphulla Chandra Shukla
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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15
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Abstract
Aortic coarctation is a discrete narrowing of the thoracic aorta. In addition to anatomic obstruction, it can be considered an aortopathy with abnormal vascular properties characterized by stiffness and impaired relaxation. There are surgical and transcatheter techniques to address the obstruction but, despite relief, patients with aortic coarctation are at risk for hypertension, aortic complications, and abnormalities with left ventricular performance. This review covers the etiology, pathophysiology, diagnosis, and management of adults with aortic coarctation, with emphasis on multimodality imaging characteristics and lifelong surveillance to identify long-term complications.
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Affiliation(s)
- Yuli Y Kim
- Philadelphia Adult Congenital Heart Center, Perelman School of Medicine at the University of Pennsylvania, Penn Medicine and Children's Hospital of Philadelphia, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
| | - Lauren Andrade
- Philadelphia Adult Congenital Heart Center, Perelman School of Medicine at the University of Pennsylvania, Penn Medicine and Children's Hospital of Philadelphia, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Stephen C Cook
- Adult Congenital Heart Disease Program, Congenital Heart Center, Helen DeVos Children's Hospital, Frederik Meijer Heart & Vascular Institute, Pediatrics and Human Development, Michigan State University, 25 Michigan Street NE Suite 4200, Grand Rapids, MI 49503, USA
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16
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Bjornsson T, Thorolfsdottir RB, Sveinbjornsson G, Sulem P, Norddahl GL, Helgadottir A, Gretarsdottir S, Magnusdottir A, Danielsen R, Sigurdsson EL, Adalsteinsdottir B, Gunnarsson SI, Jonsdottir I, Arnar DO, Helgason H, Gudbjartsson T, Gudbjartsson DF, Thorsteinsdottir U, Holm H, Stefansson K. A rare missense mutation in MYH6 associates with non-syndromic coarctation of the aorta. Eur Heart J 2019; 39:3243-3249. [PMID: 29590334 PMCID: PMC6127890 DOI: 10.1093/eurheartj/ehy142] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
Aims Coarctation of the aorta (CoA) accounts for 4–8% of congenital heart defects (CHDs) and confers substantial morbidity despite treatment. It is increasingly recognized as a highly heritable condition. The aim of the study was to search for sequence variants that affect the risk of CoA. Methods and results We performed a genome-wide association study of CoA among Icelanders (120 cases and 355 166 controls) based on imputed variants identified through whole-genome sequencing. We found association with a rare (frequency = 0.34%) missense mutation p.Arg721Trp in MYH6 (odds ratio = 44.2, P = 5.0 × 10−22), encoding the alpha-heavy chain subunit of cardiac myosin, an essential sarcomere protein. Approximately 20% of individuals with CoA in Iceland carry this mutation. We show that p.Arg721Trp also associates with other CHDs, in particular bicuspid aortic valve. We have previously reported broad effects of p.Arg721Trp on cardiac electrical function and strong association with sick sinus syndrome and atrial fibrillation. Conclusion Through a population approach, we found that a rare missense mutation p.Arg721Trp in the sarcomere gene MYH6 has a strong effect on the risk of CoA and explains a substantial fraction of the Icelanders with CoA. This is the first mutation associated with non-familial or sporadic form of CoA at a population level. The p.Arg721Trp in MYH6 causes a cardiac syndrome with highly variable expressivity and emphasizes the importance of sarcomere integrity for cardiac development and function.
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Affiliation(s)
| | | | | | - Patrick Sulem
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland
| | | | | | | | | | - Ragnar Danielsen
- Department of Medicine, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Emil L Sigurdsson
- Department of Family Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland.,Department of Development, Primary Health Care of the Capital Area, Alfabakki 16, Reykjavik, Iceland
| | - Berglind Adalsteinsdottir
- Department of Cardiology, Haukeland University Hospital, Jonas Lies vei 83, Bergen, Norway.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| | - Sverrir I Gunnarsson
- Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, 600 Highland Ave, Madison, WI, USA
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland.,Department of Immunology, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - David O Arnar
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| | - Hrodmar Helgason
- Children's Hospital, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Tomas Gudbjartsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland.,Department of Cardiothoracic Surgery, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Hjardarhagi 4, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
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17
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Fotiou E, Williams S, Martin-Geary A, Robertson DL, Tenin G, Hentges KE, Keavney B. Integration of Large-Scale Genomic Data Sources With Evolutionary History Reveals Novel Genetic Loci for Congenital Heart Disease. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 12:442-451. [PMID: 31613678 PMCID: PMC6798745 DOI: 10.1161/circgen.119.002694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Supplemental Digital Content is available in the text. Most cases of congenital heart disease (CHD) are sporadic and nonsyndromic, with poorly understood etiology. Rare genetic variants have been found to affect the risk of sporadic, nonsyndromic CHD, but individual studies to date are of only moderate sizes, and none to date has incorporated the ohnolog status of candidate genes in the analysis. Ohnologs are genes retained from ancestral whole-genome duplications during evolution; multiple lines of evidence suggest ohnologs are overrepresented among dosage-sensitive genes. We integrated large-scale data on rare variants with evolutionary information on ohnolog status to identify novel genetic loci predisposing to CHD.
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Affiliation(s)
- Elisavet Fotiou
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester
| | - Simon Williams
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester
| | - Alexandra Martin-Geary
- Division of Evolution and Genomic science (A.M.-G., D.L.R., K.E.H.), University of Manchester
| | - David L Robertson
- Division of Evolution and Genomic science (A.M.-G., D.L.R., K.E.H.), University of Manchester.,MRC-University of Glasgow Centre for Virus Research (D.L.R.)
| | - Gennadiy Tenin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester
| | - Kathryn E Hentges
- Division of Evolution and Genomic science (A.M.-G., D.L.R., K.E.H.), University of Manchester
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester.,Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester (B.K.)
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18
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Zhang SP, Yang RH, Shang J, Gao T, Wang R, Peng XD, Miao X, Pan L, Yuan WJ, Lin L, Hu QK. FOXC1 up-regulates the expression of toll-like receptors in myocardial ischaemia. J Cell Mol Med 2019; 23:7566-7580. [PMID: 31517441 PMCID: PMC6815849 DOI: 10.1111/jcmm.14626] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/20/2019] [Accepted: 08/06/2019] [Indexed: 01/01/2023] Open
Abstract
Myocardial ischaemia (MI) remains a major cause of death and disability worldwide. Accumulating evidence suggests a significant role for innate immunity, in which the family of toll‐like receptors (TLRs) acts as an essential player. We previously reported and reviewed the changes of Tlr expression in models of MI. However, the underlying mechanisms regulating Tlr expression in MI remain unclear. The present study first screened transcription factors (TFs) that potentially regulate Tlr gene transcription based on in silico analyses followed by experimental verification, using both in vivo and in vitro models. Forkhead box C1 (FOXC1) was identified as a putative TF, which was highly responsive to MI. Next, by focusing on two representative TLR subtypes, an intracellular subtype TLR3 and a cell‐surface subtype TLR4, the regulation of FOXC1 on Tlr expression was investigated. The overexpression or knockdown of FoxC1 was observed to up‐ or down‐regulate Tlr3/4 mRNA and protein levels, respectively. A dual‐luciferase assay showed that FOXC1 trans‐activated Tlr3/4 promoter, and a ChIP assay showed direct binding of FOXC1 to Tlr3/4 promoter. Last, a functional study of FOXC1 was performed, which revealed the pro‐inflammatory effects of FOXC1 and its destructive effects on infarct size and heart function in a mouse model of MI. The present study for the first time identified FOXC1 as a novel regulator of Tlr expression and described its function in MI.
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Affiliation(s)
- Shao-Ping Zhang
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China.,Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ruo-Han Yang
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan, China.,Department of Pharmacy, First People's Hospital, Guangyuan, China
| | - Jia Shang
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China.,Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Ting Gao
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China.,Department of Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Wang
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China.,Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Xiao-Dong Peng
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Xiao Miao
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lei Pan
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen-Jun Yuan
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China.,Department of Physiology, Second Military Medical University, Shanghai, China
| | - Li Lin
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China.,Department of Physiology, Second Military Medical University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University, Shanghai, China
| | - Qi-Kuan Hu
- Department of Physiology, Institute of Basic Medicine, Ningxia Medical University, Yinchuan, China
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19
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Liu Y, Chang X, Glessner J, Qu H, Tian L, Li D, Nguyen K, Sleiman PMA, Hakonarson H. Association of Rare Recurrent Copy Number Variants With Congenital Heart Defects Based on Next-Generation Sequencing Data From Family Trios. Front Genet 2019; 10:819. [PMID: 31552105 PMCID: PMC6746959 DOI: 10.3389/fgene.2019.00819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/07/2019] [Indexed: 01/17/2023] Open
Abstract
Congenital heart defects (CHDs) are a common birth defect, affecting approximately 1% of newborn children in the United States. As previously reported, a significant number of CHDs are potentially attributed to altered copy number variants (CNVs). However, as many genomic variants are rare, a large-scale CNV triad study is necessary to characterize the genetic architecture of CHD. We used whole-exome sequencing (WES) data generated by the Pediatric Cardiac Genomics Consortium (PCGC), including a discovery dataset of 2,103 individuals from 760 nuclear family trios and an independent replication set of 4,808 individuals from 1,712 trios. The candidate targets uncovered were further validated through different platforms, including the Omni single-nucleotide polymorphism (SNP) array chip in 1,860 individuals and the whole-genome sequencing (WGS) data in 33 trios. The genes harboring CNVs of interest were then investigated for expression alternations based on cardiac tissue RNA-Seq data. We identified multiple CNVs in the WES data that associated with specific sub-phenotypes of CHD in approximately 2,400 families, including 98 de novo CNV regions. We identified five CNV loci harboring LIMS1, GCC2, RANBP2, TTC3, and MAP3K7CL, respectively, where those genes are highly expressed in human heart and/or mouse embryo heart at 15 days. Five novel CNV loci were uncovered, demonstrating altered expression of the respective candidate genes involved. To our knowledge, this is the largest trio-based WES study of CHD and, in addition to uncovering novel CHD targets, presents an extensive resource with the potential to provide important insights to the architecture and impact of CNVs in CHD.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xiao Chang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joseph Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Huiqi Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lifeng Tian
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kenny Nguyen
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
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20
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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21
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Jetten AM. GLIS1-3 transcription factors: critical roles in the regulation of multiple physiological processes and diseases. Cell Mol Life Sci 2018; 75:3473-3494. [PMID: 29779043 PMCID: PMC6123274 DOI: 10.1007/s00018-018-2841-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Krüppel-like zinc finger proteins form one of the largest families of transcription factors. They function as key regulators of embryonic development and a wide range of other physiological processes, and are implicated in a variety of pathologies. GLI-similar 1-3 (GLIS1-3) constitute a subfamily of Krüppel-like zinc finger proteins that act either as activators or repressors of gene transcription. GLIS3 plays a critical role in the regulation of multiple biological processes and is a key regulator of pancreatic β cell generation and maturation, insulin gene expression, thyroid hormone biosynthesis, spermatogenesis, and the maintenance of normal kidney functions. Loss of GLIS3 function in humans and mice leads to the development of several pathologies, including neonatal diabetes and congenital hypothyroidism, polycystic kidney disease, and infertility. Single nucleotide polymorphisms in GLIS3 genes have been associated with increased risk of several diseases, including type 1 and type 2 diabetes, glaucoma, and neurological disorders. GLIS2 plays a critical role in the kidney and GLIS2 dysfunction leads to nephronophthisis, an end-stage, cystic renal disease. In addition, GLIS1-3 have regulatory functions in several stem/progenitor cell populations. GLIS1 and GLIS3 greatly enhance reprogramming efficiency of somatic cells into induced embryonic stem cells, while GLIS2 inhibits reprogramming. Recent studies have obtained substantial mechanistic insights into several physiological processes regulated by GLIS2 and GLIS3, while a little is still known about the physiological functions of GLIS1. The localization of some GLIS proteins to the primary cilium suggests that their activity may be regulated by a downstream primary cilium-associated signaling pathway. Insights into the upstream GLIS signaling pathway may provide opportunities for the development of new therapeutic strategies for diabetes, hypothyroidism, and other diseases.
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Affiliation(s)
- Anton M Jetten
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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22
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Thomford NE, Dzobo K, Yao NA, Chimusa E, Evans J, Okai E, Kruszka P, Muenke M, Awandare G, Wonkam A, Dandara C. Genomics and Epigenomics of Congenital Heart Defects: Expert Review and Lessons Learned in Africa. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:301-321. [PMID: 29762087 PMCID: PMC6016577 DOI: 10.1089/omi.2018.0033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHD) are structural malformations found at birth with a prevalence of 1%. The clinical trajectory of CHD is highly variable and thus in need of robust diagnostics and therapeutics. Major surgical interventions are often required for most CHDs. In Africa, despite advances in life sciences infrastructure and improving education of medical scholars, the limited clinical data suggest that CHD detection and correction are still not at par with the rest of the world. But the toll and genetics of CHDs in Africa has seldom been systematically investigated. We present an expert review on CHD with lessons learned on Africa. We found variable CHD phenotype prevalence in Africa across countries and populations. There are important gaps and paucity in genomic studies of CHD in African populations. Among the available genomic studies, the key findings in Africa were variants in GATA4 (P193H), MTHFR 677TT, and MTHFR 1298CC that were associated with atrial septal defect, ventricular septal defect (VSD), Tetralogy of Fallot (TOF), and patent ductus arteriosus phenotypes and 22q.11 deletion, which is associated with TOF. There were no data on epigenomic association of CHD in Africa, however, other studies have shown an altered expression of miR-421 and miR-1233-3p to be associated with TOF and hypermethylation of CpG islands in the promoter of SCO2 gene also been associated with TOF and VSD in children with non-syndromic CHD. These findings signal the urgent need to develop and implement genetic and genomic research on CHD to identify the hereditary and genome-environment interactions contributing to CHD. These projected studies would also offer comparisons on CHD pathophysiology between African and other populations worldwide. Genomic research on CHD in Africa should be developed in parallel with next generation technology policy research and responsible innovation frameworks that examine the social and political factors that shape the emergence and societal embedding of new technologies.
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Affiliation(s)
- Nicholas Ekow Thomford
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
- 2 School of Medical Sciences, University of Cape Coast , Cape Coast, Ghana
| | - Kevin Dzobo
- 3 ICGEB, Cape Town Component, University of Cape Town , Cape Town, South Africa
- 4 Division of Medical Biochemistry, IIDMM, Department of IBM, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Nana Akyaa Yao
- 5 National Cardiothoracic Centre, Korle Bu Teaching Hospital , Accra, Ghana
- 6 University of Ghana Medical School, University of Ghana , Accra, Ghana
| | - Emile Chimusa
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Jonathan Evans
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Emmanuel Okai
- 2 School of Medical Sciences, University of Cape Coast , Cape Coast, Ghana
- 7 Cape Coast Teaching Hospital , Cape Coast, Ghana
| | - Paul Kruszka
- 8 National Human Genome Research Institute, Medical Genetics Branch, National Institutes of Health , Bethesda, Maryland, USA
| | - Maximilian Muenke
- 8 National Human Genome Research Institute, Medical Genetics Branch, National Institutes of Health , Bethesda, Maryland, USA
| | - Gordon Awandare
- 9 Department of Biochemistry, WACCBIP, University of Ghana , Legon, Accra, Ghana
| | - Ambroise Wonkam
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Collet Dandara
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
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23
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Ovaert C, Busa T, Faure E, Missirian C, Philip N, Paoli F, Milh M, Macé L, Zaffran S. FOXC1 haploinsufficiency due to 6p25 deletion in a patient with rapidly progressing aortic valve disease. Am J Med Genet A 2017; 173:2489-2493. [PMID: 28657660 DOI: 10.1002/ajmg.a.38331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 05/15/2017] [Accepted: 05/24/2017] [Indexed: 01/12/2023]
Abstract
6p25 deletion is a rare but well-known entity. The main clinical features include an abnormal facial appearance, developmental delay, and ocular anomalies. Cardiac anomalies are frequently seen but remain poorly delineated. We describe a 4-year-old girl with 6p25.3 deletion, which includes the FOXC1 gene, typical dysmorphic features associated with developmental delay and oculo-motor anomalies. Aortic valve dysplasia was diagnosed early in life. The cardiac lesion progressed very rapidly between the age of 3 and 4 years requiring aortic valve replacement. Genomic analysis of blood and excised valve tissue showed down-regulation of FOXC1 but also FOXC2 expression in the diseased aortic valve. This allows us to speculate on the potential role of FOXC1 in aortic valve anomalies.
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Affiliation(s)
- Caroline Ovaert
- Department of Pediatric and Congenital Cardiology, Timone Enfant, AP-HM, Marseille, France.,Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France
| | - Tiffany Busa
- Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France.,Department of Clinical Genetics, Timone Enfant, AP-HM, Marseille, France
| | - Emilie Faure
- Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France
| | - Chantal Missirian
- Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France.,Department of Clinical Genetics, Timone Enfant, AP-HM, Marseille, France
| | - Nicole Philip
- Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France.,Department of Clinical Genetics, Timone Enfant, AP-HM, Marseille, France
| | - Florent Paoli
- Department of Pediatric and Congenital Cardiology, Timone Enfant, AP-HM, Marseille, France
| | - Mathieu Milh
- Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France.,Department of Pediatric Neurology, Timone Enfant, AP-HM, Marseille, France
| | - Loic Macé
- Department of Pediatric and Congenital Cardiology, Timone Enfant, AP-HM, Marseille, France
| | - Stephane Zaffran
- Faculté de Médecine, Inserm, GMGF, UMR_S910, Aix Marseille Université, Marseille, France
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[Genetics of congenital heart diseases]. Presse Med 2017; 46:612-619. [PMID: 28583745 DOI: 10.1016/j.lpm.2017.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/01/2017] [Accepted: 05/11/2017] [Indexed: 01/24/2023] Open
Abstract
Developmental genetics of congenital heart diseases has evolved from analysis of serial slices in embryos towards molecular genetics of cardiac morphogenesis with a dynamic view of cardiac development. Genetics of congenital heart diseases has also changed from formal genetic analysis of familial recurrences or population-based analysis to screening for mutations in candidates genes identified in animal models. Close cooperation between molecular embryologists, pathologists involved in heart development and pediatric cardiologists is crucial for further increase of knowledge in the field of cardiac morphogenesis and genetics of cardiac defects. The genetic model for congenital heart disease has to be revised to favor a polygenic origin rather than a monogenic one. The main mechanism is altered genic dosage that can account for heart diseases in chromosomal anomalies as well as in point mutations in syndromic and isolated congenital heart diseases. The use of big data grouping information from cardiac development, interactions between genes and proteins, epigenetic factors such as chromatin remodeling or DNA methylation is the current source for improving our knowledge in the field and to give clues for future therapies.
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Abstract
Coarctation of the aorta is a congenital cardiac defect that results in a variable degree of obstruction to the left side of the heart. It can present with either acute shock in the neonatal period as a critical lesion or it can appear more insidiously with hypertension or other findings later in life. This article summarises aspects of outpatient care of patients with this lesion, including clinical history and physical examination, ancillary testing, and issues associated with long-term follow-up and management. Increasing knowledge and experience with this group of patients have allowed for a higher level of evidence-based care over the long term.
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Abstract
Congenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD. These include de novo and inherited variants at established (chromosome 22q11.2), emerging (chromosome 1q21.1), and novel loci across the genome. Variable expression of rare CNVs provides support for the notion of a genetic spectrum of CHD that crosses traditional anatomic classification boundaries. Clinical genetic testing using genome-wide technologies (e.g., chromosomal microarray analysis) is increasingly employed in prenatal, paediatric and adult settings. CNV discoveries in CHD have translated to changes to clinical management, prognostication and genetic counselling. The convergence of findings at individual gene and at pathway levels is shedding light on the mechanisms that govern human cardiac morphogenesis. These clinical and research advances are helping to inform whole-genome sequencing, the next logical step in delineating the genetic architecture of CHD.
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Bouvagnet P. Unraveling De Novo Copy Number Variants in Congenital Heart Defects: The Bottom of the Iceberg Is Under Attack. ACTA ACUST UNITED AC 2016; 9:4-5. [PMID: 26884608 DOI: 10.1161/circgenetics.116.001360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Patrice Bouvagnet
- From Laboratoire Cardiogénétique, INMG, CNRS UMR 5310, INSERM U1217 and Université Lyon 1, Lyon, France and Laboratoire Cardiogénétique, Hospices Civils de Lyon, Lyon, France.
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