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White A, Poorvu T, Estroff J, U Morton S, H Wojcik M. Prenatal Diagnosis of a Heterotaxy Syndrome. Neoreviews 2024; 25:e594-e600. [PMID: 39217136 DOI: 10.1542/neo.25-9-e594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 09/04/2024]
Affiliation(s)
| | - Tabitha Poorvu
- Department of Radiology, Maternal Fetal Care Center, Boston Children's Hospital, Boston, MA
- Division of Genetics and Genomics
| | - Judy Estroff
- Department of Radiology, Maternal Fetal Care Center, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Sarah U Morton
- Division of Newborn Medicine
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Monica H Wojcik
- Division of Newborn Medicine
- Department of Radiology, Maternal Fetal Care Center, Boston Children's Hospital, Boston, MA
- Division of Genetics and Genomics
- Department of Pediatrics, Harvard Medical School, Boston, MA
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2
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Alaamery M, Albesher N, Alhabshan F, Barnett P, Salim Kabbani M, Chaikhouni F, Ilgun A, Mook ORF, Alsaif H, Christoffels VM, van Tintelen P, Wilde AAM, Houweling AC, Massadeh S, Postma AV. TGFBR1 Variants Can Associate with Non-Syndromic Congenital Heart Disease without Aortopathy. J Cardiovasc Dev Dis 2023; 10:455. [PMID: 37998513 PMCID: PMC10672196 DOI: 10.3390/jcdd10110455] [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: 10/11/2023] [Revised: 10/31/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Congenital heart diseases (CHD) are the most common congenital malformations in newborns and remain the leading cause of mortality among infants under one year old. Molecular diagnosis is crucial to evaluate the recurrence risk and to address future prenatal diagnosis. Here, we describe two families with various forms of inherited non-syndromic CHD and the genetic work-up and resultant findings. METHODS Next-generation sequencing (NGS) was employed in both families to uncover the genetic cause. In addition, we performed functional analysis to investigate the consequences of the identified variants in vitro. RESULTS NGS identified possible causative variants in both families in the protein kinase domain of the TGFBR1 gene. These variants occurred on the same amino acid, but resulted in differently substituted amino acids (p.R398C/p.R398H). Both variants co-segregate with the disease, are extremely rare or unique, and occur in an evolutionary highly conserved domain of the protein. Furthermore, both variants demonstrated a significantly altered TGFBR1-smad signaling activity. Clinical investigation revealed that none of the carriers had (signs of) aortopathy. CONCLUSION In conclusion, we describe two families, with various forms of inherited non-syndromic CHD without aortopathies, associated with unique/rare variants in TGFBR1 that display altered TGF-beta signaling. These findings highlight involvement of TGFBR1 in CHD, and warrant consideration of potential causative TGFBR1 variants also in CHD patients without aortopathies.
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Affiliation(s)
- Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard—Health Affairs, Riyadh 11481, Saudi Arabia
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Nour Albesher
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fahad Alhabshan
- Department of Cardiac Sciences, Ministry of the National Guard—Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Phil Barnett
- Department of Medical Biology, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (P.B.); (A.I.)
| | - Mohamed Salim Kabbani
- Department of Cardiac Sciences, Ministry of the National Guard—Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Farah Chaikhouni
- Department of Cardiac Sciences, Ministry of the National Guard—Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (P.B.); (A.I.)
| | - Olaf R. F. Mook
- Department of Human Genetics, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (O.R.F.M.); (A.C.H.)
| | - Hessa Alsaif
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (P.B.); (A.I.)
| | - Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, 3584 CS Utrecht, The Netherlands;
| | - Arthur A. M. Wilde
- Department of Cardiology, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands;
| | - Arjan C. Houweling
- Department of Human Genetics, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (O.R.F.M.); (A.C.H.)
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard—Health Affairs, Riyadh 11481, Saudi Arabia
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Alex V. Postma
- Department of Medical Biology, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (P.B.); (A.I.)
- Department of Human Genetics, Amsterdam University Medical Centre, 1105 AZ Amsterdam, The Netherlands; (O.R.F.M.); (A.C.H.)
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Li M, Chen F, Zhang Y, Xiong Y, Li Q, Huang H. Identification of Post-myocardial Infarction Blood Expression Signatures Using Multiple Feature Selection Strategies. Front Physiol 2020; 11:483. [PMID: 32581823 PMCID: PMC7287215 DOI: 10.3389/fphys.2020.00483] [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: 03/06/2020] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Myocardial infarction (MI) is a type of serious heart attack in which the blood flow to the heart is suddenly interrupted, resulting in injury to the heart muscles due to a lack of oxygen supply. Although clinical diagnosis methods can be used to identify the occurrence of MI, using the changes of molecular markers or characteristic molecules in blood to characterize the early phase and later trend of MI will help us choose a more reasonable treatment plan. Previously, comparative transcriptome studies focused on finding differentially expressed genes between MI patients and healthy people. However, signature molecules altered in different phases of MI have not been well excavated. We developed a set of computational approaches integrating multiple machine learning algorithms, including Monte Carlo feature selection (MCFS), incremental feature selection (IFS), and support vector machine (SVM), to identify gene expression characteristics on different phases of MI. 134 genes were determined to serve as features for building optimal SVM classifiers to distinguish acute MI and post-MI. Subsequently, functional enrichment analyses followed by protein-protein interaction analysis on 134 genes identified several hub genes (IL1R1, TLR2, and TLR4) associated with progression of MI, which can be used as new diagnostic molecules for MI.
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Affiliation(s)
- Ming Li
- Department of Cardiology, Eastern Hospital, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Fuli Chen
- Department of Cardiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Yaling Zhang
- Department of Nephrology, Eastern Hospital, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Yan Xiong
- Department of Cardiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Qiyong Li
- Department of Cardiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Hui Huang
- Department of Cardiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
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4
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Minhas R, Paterek A, Łapiński M, Bazała M, Korzh V, Winata CL. A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Dev Dyn 2019; 248:837-849. [PMID: 31194899 PMCID: PMC6771876 DOI: 10.1002/dvdy.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 01/15/2023] Open
Abstract
Background Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis. Results We identified two novel tetrapod‐teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue‐specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression. Conclusion This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression. Identified a novel enhancer near zebrafish zic3/zic6 locus. The novel enhancer drives tissue‐specific expression in the habenula. Zebrafish transgenic line generated in this study can be a useful resource for studying development of habenula.
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Affiliation(s)
- Rashid Minhas
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aleksandra Paterek
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Clinical Physiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Bazała
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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5
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Dugan SL, Panza E, Openshaw A, Botto LD, Camacho JA, Toydemir RM. Delineation of the 9q31 deletion syndrome: Genomic microarray characterization of two patients with overlapping deletions. Am J Med Genet A 2018; 176:2901-2906. [PMID: 30346094 DOI: 10.1002/ajmg.a.40664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/04/2018] [Accepted: 09/28/2018] [Indexed: 11/08/2022]
Abstract
Interstitial deletions of chromosome 9q31 are very rare. The deletions in most reported patients have been detected by conventional cytogenetics, with reported breakpoints ranging between 9q21 and 9q34. Therefore, an accurate description of a "9q31 deletion syndrome" could not be established. However, based on microarray studies, a small region of overlap has recently been proposed. We report clinical features of two unrelated individuals with overlapping 9q deletions identified by SNP microarray analysis. Patient 1 has a 9 Mb deletion, while Patient 2's deletion was 21.6 Mb. The clinical features common to our patients and those in the literature include developmental delay and short stature. Patient 2 shows additional features not reported in other 9q31 deletions, such as hearing loss, ventriculomegaly, cleft lip and palate, and small kidneys, which could be due to the larger size of the deletion, hence the influence of the genes in the region beyond the smallest region of overlap. Based on the comparison of these patients with the previously reported patients, we redefine the smallest region of overlap and characterize the clinical features of the 9q31 deletion syndrome.
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Affiliation(s)
- Sarah L Dugan
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Emanuele Panza
- Department of Human Genetics, University of Utah, Salt Lake City, Utah.,Department of Medical and Surgical Sciences, University of Bologna, Italy
| | | | - Lorenzo D Botto
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Jose A Camacho
- Department of Pediatrics, Miller Children's and Women's Hospital, Long Beach, California
| | - Reha M Toydemir
- Department of Pediatrics, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
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Tonni G, Lituania M, Chitayat D, Bonasoni MP, Keating S, Thompson M, Shannon P. Complete trisomy 9 with unusual phenotypic associations: Dandy-Walker malformation, cleft lip and cleft palate, cardiovascular abnormalities. Taiwan J Obstet Gynecol 2015; 53:592-7. [PMID: 25510707 DOI: 10.1016/j.tjog.2014.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Trisomy 9 is a rare chromosomal abnormality usually associated with first-trimester miscarriage; few fetuses survive until the second trimester. We report two new cases of complete trisomy 9 that both present unusual phenotypic associations, and we analyze the genetic pathway involved in this chromosomal abnormality. CASE REPORT The first fetus investigated showed Dandy-Walker malformation, cleft lip, and cleft palate) at the second trimester scan. Cardiovascular abnormalities were characterized by a right-sided, U-shaped aortic arch associated with a ventricular septal defect (VSD). Symmetrical intrauterine growth restriction and multicystic dysplastic kidney disease were associated findings. The second fetus showed a dysmorphic face, bilateral cleft lip, hypoplastic corpus callosum, and a Dandy-Walker malformation. Postmortem examination revealed cardiovascular abnormalities such as persistent left superior vena cava draining into the coronary sinus, membranous ventricular septal defect, overriding aorta, pulmonary valve with two cusps and three sinuses, and the origin of the left subclavian artery distal to the junction of ductus arteriosus and aortic arch. CONCLUSION Complete trisomy 9 may result in a wide spectrum of congenital abnormalities, and the presented case series contributes further details on the phenotype of this rare aneuploidy.
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Affiliation(s)
- Gabriele Tonni
- Department of Obstetrics and Gynecology, Prenatal Diagnostic Service, Guastalla Civil Hospital, Azienda Unità Sanitaria Locale Reggio Emilia, Reggio Emilia, Italy.
| | - Mario Lituania
- Preconceptional and Prenatal Diagnostic Center, Istituto di Ricerca a Carettere Clinico Scientifico Galliera Hospital, Genoa, Italy
| | - David Chitayat
- Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Maria Paola Bonasoni
- Pathology Service, Istituto di Ricerca a Carettere Clinico Scientifico Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Sarah Keating
- Department of Laboratory Medicine and Pathology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Megan Thompson
- Department of Laboratory Medicine and Pathology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Laboratory Medicine and Pathology, Mount Sinai Hospital, Toronto, Ontario, Canada
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van Engelen K, Baars MJ, Felix JP, Postma AV, Mulder BJ, Smets EM. The value of the clinical geneticist caring for adults with congenital heart disease: Diagnostic yield and patients' perspective. Am J Med Genet A 2013; 161A:1628-37. [DOI: 10.1002/ajmg.a.35973] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 02/26/2013] [Indexed: 02/07/2023]
Affiliation(s)
| | - Marieke J.H. Baars
- Department of Clinical Genetics; Academic Medical Center; Amsterdam; The; Netherlands
| | - Joyce P. Felix
- Department of Cardiology; Academic Medical Center; Amsterdam; The; Netherlands
| | | | | | - Ellen M.A. Smets
- Department of Medical Psychology; Academic Medical Center; Amsterdam; The; Netherlands
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Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE. Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy. ACTA ACUST UNITED AC 2013; 6:144-53. [PMID: 23418287 DOI: 10.1161/circgenetics.111.000062] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND- Familial dilated cardiomyopathy (DCM) is a genetically heterogeneous disease with >30 known genes. TTN truncating variants were recently implicated in a candidate gene study to cause 25% of familial and 18% of sporadic DCM cases. METHODS AND RESULTS- We used an unbiased genome-wide approach using both linkage analysis and variant filtering across the exome sequences of 48 individuals affected with DCM from 17 families to identify genetic cause. Linkage analysis ranked the TTN region as falling under the second highest genome-wide multipoint linkage peak, multipoint logarithm of odds, 1.59. We identified 6 TTN truncating variants carried by individuals affected with DCM in 7 of 17 DCM families (logarithm of odds, 2.99); 2 of these 7 families also had novel missense variants that segregated with disease. Two additional novel truncating TTN variants did not segregate with DCM. Nucleotide diversity at the TTN locus, including missense variants, was comparable with 5 other known DCM genes. The average number of missense variants in the exome sequences from the DCM cases or the ≈5400 cases from the Exome Sequencing Project was ≈23 per individual. The average number of TTN truncating variants in the Exome Sequencing Project was 0.014 per individual. We also identified a region (chr9q21.11-q22.31) with no known DCM genes with a maximum heterogeneity logarithm of odds score of 1.74. CONCLUSIONS- These data suggest that TTN truncating variants contribute to DCM cause. However, the lack of segregation of all identified TTN truncating variants illustrates the challenge of determining variant pathogenicity even with full exome sequencing.
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Affiliation(s)
- Nadine Norton
- Cardiovascular Division, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
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