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Diniz BL, Deconte D, Gadelha KA, Glaeser AB, Guaraná BB, de Moura AÁ, Rosa RFM, Zen PRG. Congenital Heart Defects and 22q11.2 Deletion Syndrome: A 20-Year Update and New Insights to Aid Clinical Diagnosis. J Pediatr Genet 2023; 12:113-122. [PMID: 37090828 PMCID: PMC10118709 DOI: 10.1055/s-0043-1763258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/16/2023] [Indexed: 02/19/2023]
Abstract
Congenital heart defects (CHDs) are one of the most prevalent clinical features described in individuals diagnosed with 22q11.2 deletion syndrome (22q11.2DS). Therefore, cardiac malformations may be the main finding to refer for syndrome investigation, especially in individuals with a mild phenotype. Nowadays, different cytogenetic methodologies have emerged and are used routinely in research laboratories. Hence, choosing an efficient technology and providing an accurate interpretation of clinical findings is crucial for 22q11.2DS patient's diagnosis. This systematic review provides an update of the last 20 years of research on 22q11.2DS patients with CHD and the investigation process behind each diagnosis. A search was performed in PubMed, Embase, and LILACS using all entry terms to DiGeorge syndrome, CHDs, and cytogenetic analysis. After screening, 60 papers were eligible for review. We present a new insight of ventricular septal defect as a possible pivotal cardiac finding in individuals with 22q11.2DS. Also, we describe molecular technologies and cardiac evaluation as valuable tools in order to guide researchers in future investigations.
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Affiliation(s)
- Bruna Lixinski Diniz
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Desirée Deconte
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Kerolainy Alves Gadelha
- Underdegree Program in Biomedicine, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Andressa Barreto Glaeser
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Bruna Baierle Guaraná
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
- Department of Internal Medicine, Clinical Genetics Service, Federal University of Health Sciences of Porto Alegre (UFCSPA) and Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Andreza Ávila de Moura
- Underdegree Program in Biomedicine, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Rafael Fabiano Machado Rosa
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
- Department of Internal Medicine, Clinical Genetics Service, Federal University of Health Sciences of Porto Alegre (UFCSPA) and Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Paulo Ricardo Gazzola Zen
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
- Department of Internal Medicine, Clinical Genetics Service, Federal University of Health Sciences of Porto Alegre (UFCSPA) and Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
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Salerno N, Panuccio G, Sabatino J, Leo I, Torella M, Sorrentino S, De Rosa S, Torella D. Cellular and Molecular Mechanisms Underlying Tricuspid Valve Development and Disease. J Clin Med 2023; 12:jcm12103454. [PMID: 37240563 DOI: 10.3390/jcm12103454] [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: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Tricuspid valve (TV) disease is highly prevalent in the general population. For ages considered "the forgotten valve" because of the predominant interest in left-side valve disease, the TV has now received significant attention in recent years, with significant improvement both in diagnosis and in management of tricuspid disease. TV is characterized by complex anatomy, physiology, and pathophysiology, in which the right ventricle plays a fundamental role. Comprehensive knowledge of molecular and cellular mechanisms underlying TV development, TV disease, and tricuspid regurgitation-related right-ventricle cardiomyopathy is necessary to enhance TV disease understanding to improve the ability to risk stratify TR patients, while also predicting valve dysfunction and/or response to tricuspid regurgitation treatment. Scientific efforts are still needed to eventually decipher the complete picture describing the etiopathogenesis of TV and TV-associated cardiomyopathy, and future advances to this aim may be achieved by combining emerging diagnostic imaging modalities with molecular and cellular studies. Overall, basic science studies could help to streamline a new coherent hypothesis underlying both the development of TV during embryogenesis and TV-associated disease and its complications in adult life, providing the conceptual basis for the ultimate and innovative field of valve repair and regeneration using tissue-engineered heart valves.
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Affiliation(s)
- Nadia Salerno
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy
| | - Giuseppe Panuccio
- Department of Medical and Surgical Sciences, Magna Graecia University, 88100 Catanzaro, Italy
| | - Jolanda Sabatino
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy
| | - Isabella Leo
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy
| | - Michele Torella
- Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Sabato Sorrentino
- Department of Medical and Surgical Sciences, Magna Graecia University, 88100 Catanzaro, Italy
| | - Salvatore De Rosa
- Department of Medical and Surgical Sciences, Magna Graecia University, 88100 Catanzaro, Italy
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy
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Gavril EC, Popescu R, Nucă I, Ciobanu CG, Butnariu LI, Rusu C, Pânzaru MC. Different Types of Deletions Created by Low-Copy Repeats Sequences Location in 22q11.2 Deletion Syndrome: Genotype-Phenotype Correlation. Genes (Basel) 2022; 13:2083. [PMID: 36360320 PMCID: PMC9690028 DOI: 10.3390/genes13112083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 09/19/2023] Open
Abstract
The most frequent microdeletion, 22q11.2 deletion syndrome (22q11.2DS), has a wide and variable phenotype that causes difficulties in diagnosis. 22q11.2DS is a contiguous gene syndrome, but due to the existence of several low-copy-number repeat sequences (LCR) it displays a high variety of deletion types: typical deletions LCR A-D-the most common (~90%), proximal deletions LCR A-B, central deletions (LCR B, C-D) and distal deletions (LCR D-E, F). METHODS We conducted a retrospective study of 59 22q11.2SD cases, with the aim of highlighting phenotype-genotype correlations. All cases were tested using MLPA combined kits: SALSA MLPA KIT P245 and P250 (MRC Holland). RESULTS most cases (76%) presented classic deletion LCR A-D with various severity and phenotypic findings. A total of 14 atypical new deletions were identified: 2 proximal deletions LCR A-B, 1 CES (Cat Eye Syndrome region) to LCR B deletion, 4 nested deletions LCR B-D and 1 LCR C-D, 3 LCR A-E deletions, 1 LCR D-E, and 2 small single gene deletions: delDGCR8 and delTOP3B. CONCLUSIONS This study emphasizes the wide phenotypic variety and incomplete penetrance of 22q11.2DS. Our findings contribute to the genotype-phenotype data regarding different types of 22q11.2 deletions and illustrate the usefulness of MLPA combined kits in 22q11.2DS diagnosis.
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Affiliation(s)
- Eva-Cristiana Gavril
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigații Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Irina Nucă
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigații Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Cristian-Gabriel Ciobanu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Lăcrămioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Cristina Rusu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Department of Medical Genetics “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Dong W, Kaymakcalan H, Jin SC, Diab NS, Tanıdır C, Yalcin ASY, Ercan‐Sencicek AG, Mane S, Gunel M, Lifton RP, Bilguvar K, Brueckner M. Mutation spectrum of congenital heart disease in a consanguineous Turkish population. Mol Genet Genomic Med 2022; 10:e1944. [PMID: 35481623 PMCID: PMC9184665 DOI: 10.1002/mgg3.1944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUNDS While many studies agree that consanguinity increases the rate of congenital heart disease (CHD), few genome analyses have been conducted with consanguineous CHD cohorts. METHODS We recruited 73 CHD probands from consanguineous families in Turkey and used whole-exome sequencing (WES) to identify genetic lesions in these patients. RESULTS On average, each patient had 6.95 rare damaging homozygous variants, 0.68 of which are loss-of-function (LoF) variants. Seven patients (9.6%) carried damaging homozygous variants in five causal CHD genes. Six of those patients exhibited laterality defects (six HTX and one D-TGA). Three additional patients (4.1%) harbored other types of CHD-associated genomic alterations, which overall explained 13.7% (10/73) of the cohort. The contribution from recessive variants in our cohort is higher than 1.8% reported from a cohort of 2871 CHD subjects where 5.6% of subjects met the criteria for consanguinity. CONCLUSIONS Our WES screen of a Turkish consanguineous population with structural CHD revealed its unique genetic architecture. Six of seven damaging homozygous variants in CHD causal genes occur in the setting of laterality defects implies a strong contribution from consanguinity to these defects specifically. Our study thus provided valuable information about the genetic landscape of CHD in consanguineous families in Turkey.
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Affiliation(s)
- Weilai Dong
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
- Laboratory of Human Genetics and GenomicsThe Rockefeller UniversityNew YorkNew YorkUSA
| | | | - Sheng Chih Jin
- Department of GeneticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Nicholas S. Diab
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
| | - Cansaran Tanıdır
- Department of PediatricsMehmet Akif Ersoy HospitalIstanbulTurkey
| | | | - A. Gulhan Ercan‐Sencicek
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
- Biomedical research and translational medicineMasonic Medical Research InstituteUticaNew YorkUSA
| | - Shrikant Mane
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
| | - Murat Gunel
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
| | - Richard P. Lifton
- Laboratory of Human Genetics and GenomicsThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Kaya Bilguvar
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
- Department of GeneticsYale Center for Genomic AnalysisNew HavenConnecticutUSA
| | - Martina Brueckner
- Department of GeneticsYale School of MedicineNew HavenConnecticutUSA
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Zhou XY, Zheng HY, Han L, Wang Y, Zhang L, Shu XM, Zhang ML, Liu GN, Ding LS. Copy Number Variations Analysis Identifies QPRT as a Candidate Gene Associated With Susceptibility for Solitary Functioning Kidney. Front Genet 2021; 12:575830. [PMID: 34079576 PMCID: PMC8165445 DOI: 10.3389/fgene.2021.575830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/06/2021] [Indexed: 01/03/2023] Open
Abstract
Background The lack of understanding of molecular pathologies of the solitary functioning kidney makes improving and strengthening the continuity of care between pediatric and adult nephrological patients difficult. Copy number variations (CNVs) account for a molecular cause of solitary functioning kidney, but characterization of the pathogenic genes remains challenging. Methods In our prospective cohort study, 99 fetuses clinically diagnosed with a solitary functioning kidney were enrolled and evaluated using chromosomal microarray analysis (CMA). The genetic drivers for the pathogenic CNVs were analyzed. We characterized QPRT localization in fetal kidneys using immunohistochemistry and its expression in adult kidneys using quantitative RT-PCR. Further, QPRT was knocked down using siRNA in human embryonic kidney (HEK293T) cells, and the cell cycle and proliferation were tested. Results Besides one Triple X syndrome and one Down syndrome, we identified a total of 45 CNVs out of 34 subjects. Among the 14 pathogenic CNVs, CNV 16p11.2 reached the highest number of records with the phenotype of kidney anomalies in the Decipher database. Among the 26 genes within the 16p11.2 region, as a key enzyme for nicotinamide adenine dinucleotide (NAD+) biosynthesis, QPRT was distinctly localized in renal tubules but was barely observed in renal interstitial and glomeruli in fetal kidneys. The loss of QPRT prevented cells’ efficient transition into S phase, affected cell-cycle progression, and abrogated proliferation of human embryonic kidney cells. Conclusion Our data suggest that QPRT is a candidate gene associated with susceptibility for solitary functioning kidney. The CNVs discovered in our study exhibit great potential for future applications in genetic counseling and pregnancy management.
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Affiliation(s)
- Xiao Y Zhou
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Hao Y Zheng
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Han
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yan Wang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Xiao M Shu
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Mu L Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Guan N Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Lian S Ding
- Department of Neurosurgery, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
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Onur P, Shaver M, Iqbal MA. Interstitial 20p13 microdeletion including PRNP and adjacent genes in a fetus with congenital abnormalities-First case report. Clin Case Rep 2021; 9:e04082. [PMID: 34084500 PMCID: PMC8142463 DOI: 10.1002/ccr3.4082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/31/2021] [Accepted: 02/22/2021] [Indexed: 11/11/2022] Open
Abstract
We present a prenatal case with congenital anomalies that revealed a 759 kb microdeletion at 20p13 possibly implicating PRNP and adjacent genes.
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Affiliation(s)
- Pelin Onur
- Pathology and Laboratory MedicineUniversity of Rochester Medical CenterRochesterNYUSA
| | - Mary Shaver
- Pathology and Laboratory MedicineUniversity of Rochester Medical CenterRochesterNYUSA
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Osumi K, Suga K, Ono A, Goji A, Mori T, Kinoshita Y, Sugano M, Toda Y, Urushihara M, Nakagawa R, Hayabuchi Y, Imoto I, Kagami S. Molecular diagnosis of an infant with TSC2/ PKD1 contiguous gene syndrome. Hum Genome Var 2020; 7:21. [PMID: 32695431 PMCID: PMC7363882 DOI: 10.1038/s41439-020-0108-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 12/02/2022] Open
Abstract
A 1-month-old Japanese infant with cardiac rhabdomyoma was diagnosed with TSC2/PKD1 contiguous gene syndrome by targeted panel sequencing with subsequent quantitative polymerase chain reaction that revealed gross monoallelic deletion, including parts of two genes: exons 19-42 of TSC2 and exons 2-46 of PKD1. Early molecular diagnosis can help to detect bilateral renal cyst formation and multidisciplinary follow-up of this multisystem disease.
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Affiliation(s)
- Keita Osumi
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Kenichi Suga
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Akemi Ono
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Aya Goji
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Tatsuo Mori
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Yukiko Kinoshita
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Mikio Sugano
- Department of Cardiovascular Surgery, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima, Japan
| | - Yoshihiro Toda
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Maki Urushihara
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Ryuji Nakagawa
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Yasunobu Hayabuchi
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
| | - Issei Imoto
- Department of Preventive Medicine, Division of Molecular Genetics, Aichi Cancer Center Research Institute, Nagoya, Aichi Japan
- Department of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Shoji Kagami
- Department of Pediatrics, Tokushima University Hospital, Kuramotocho, Tokushima, Tokushima Japan
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Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect, found in up to 2% of the population and associated with a 30% lifetime risk of complications. BAV is inherited as an autosomal dominant trait with incomplete penetrance and variable expressivity due to a complex genetic architecture that involves many interacting genes. In this review, we highlight the current state of knowledge about BAV genetics, principles and methods for BAV gene discovery, clinical applications of BAV genetics, and important future directions.
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Du Q, de la Morena MT, van Oers NSC. The Genetics and Epigenetics of 22q11.2 Deletion Syndrome. Front Genet 2020; 10:1365. [PMID: 32117416 PMCID: PMC7016268 DOI: 10.3389/fgene.2019.01365] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.
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Affiliation(s)
- Qiumei Du
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - M. Teresa de la Morena
- Department of Pediatrics, The University of Washington and Seattle Children’s Hospital, Seattle, WA, United States
| | - Nicolai S. C. van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Genetics of Congenital Heart Disease. Biomolecules 2019; 9:biom9120879. [PMID: 31888141 PMCID: PMC6995556 DOI: 10.3390/biom9120879] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
Congenital heart disease (CHD) is one of the most common birth defects. Studies in animal models and humans have indicated a genetic etiology for CHD. About 400 genes have been implicated in CHD, encompassing transcription factors, cell signaling molecules, and structural proteins that are important for heart development. Recent studies have shown genes encoding chromatin modifiers, cilia related proteins, and cilia-transduced cell signaling pathways play important roles in CHD pathogenesis. Elucidating the genetic etiology of CHD will help improve diagnosis and the development of new therapies to improve patient outcomes.
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Motahari Z, Moody SA, Maynard TM, LaMantia AS. In the line-up: deleted genes associated with DiGeorge/22q11.2 deletion syndrome: are they all suspects? J Neurodev Disord 2019; 11:7. [PMID: 31174463 PMCID: PMC6554986 DOI: 10.1186/s11689-019-9267-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND 22q11.2 deletion syndrome (22q11DS), a copy number variation (CNV) disorder, occurs in approximately 1:4000 live births due to a heterozygous microdeletion at position 11.2 (proximal) on the q arm of human chromosome 22 (hChr22) (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011). This disorder was known as DiGeorge syndrome, Velo-cardio-facial syndrome (VCFS) or conotruncal anomaly face syndrome (CTAF) based upon diagnostic cardiovascular, pharyngeal, and craniofacial anomalies (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011; Burn et al., J Med Genet 30:822-4, 1993) before this phenotypic spectrum was associated with 22q11.2 CNVs. Subsequently, 22q11.2 deletion emerged as a major genomic lesion associated with vulnerability for several clinically defined behavioral deficits common to a number of neurodevelopmental disorders (Fernandez et al., Principles of Developmental Genetics, 2015; Robin and Shprintzen, J Pediatr 147:90-6, 2005; Schneider et al., Am J Psychiatry 171:627-39, 2014). RESULTS The mechanistic relationships between heterozygously deleted 22q11.2 genes and 22q11DS phenotypes are still unknown. We assembled a comprehensive "line-up" of the 36 protein coding loci in the 1.5 Mb minimal critical deleted region on hChr22q11.2, plus 20 protein coding loci in the distal 1.5 Mb that defines the 3 Mb typical 22q11DS deletion. We categorized candidates based upon apparent primary cell biological functions. We analyzed 41 of these genes that encode known proteins to determine whether haploinsufficiency of any single 22q11.2 gene-a one gene to one phenotype correspondence due to heterozygous deletion restricted to that locus-versus complex multigenic interactions can account for single or multiple 22q11DS phenotypes. CONCLUSIONS Our 22q11.2 functional genomic assessment does not support current theories of single gene haploinsufficiency for one or all 22q11DS phenotypes. Shared molecular functions, convergence on fundamental cell biological processes, and related consequences of individual 22q11.2 genes point to a matrix of multigenic interactions due to diminished 22q11.2 gene dosage. These interactions target fundamental cellular mechanisms essential for development, maturation, or homeostasis at subsets of 22q11DS phenotypic sites.
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Affiliation(s)
- Zahra Motahari
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Sally Ann Moody
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Thomas Michael Maynard
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Anthony-Samuel LaMantia
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
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Copy number variation analysis in bicuspid aortic valve-related aortopathy identifies TBX20 as a contributing gene. Eur J Hum Genet 2019; 27:1033-1043. [PMID: 30820038 DOI: 10.1038/s41431-019-0364-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/08/2019] [Accepted: 02/02/2019] [Indexed: 12/26/2022] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect (CHD), affecting 1-2% of the population. BAV is associated with thoracic aortic aneurysms (TAAs). Deleterious copy number variations (CNVs) were found previously in up to 10% of CHD cases. This study aimed at unravelling the contribution of deleterious deletions or duplications in 95 unrelated BAV/TAA patients. Seven unique or rare CNVs were validated, harbouring protein-coding genes with a role in the cardiovascular system. Based on the presence of overlapping CNVs in patients with cardiovascular phenotypes in the DECIPHER database, the identification of similar CNVs in whole-exome sequencing data of 67 BAV/TAA patients and suggested topological domain involvement from Hi-C data, supportive evidence was obtained for two genes (DGCR6 and TBX20) of the seven initially validated CNVs. A rare variant burden analysis using next-generation sequencing data from 637 BAV/TAA patients was performed for these two candidate genes. This revealed a suggestive genetic role for TBX20 in BAV/TAA aetiology, further reinforced by segregation of a rare TBX20 variant with the phenotype within a BAV/TAA family. To conclude, our results do not confirm a significant contribution for deleterious CNVs in BAV/TAA as only one potentially pathogenic CNV (1.05%) was identified. We cannot exclude the possibility that BAV/TAA is occasionally attributed to causal CNVs though, or that certain CNVs act as genetic risk factors by creating a sensitised background for BAV/TAA. Finally, accumulative evidence for TBX20 involvement in BAV/TAA aetiology underlines the importance of this transcription factor in cardiovascular disease.
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Downregulation of genes outside the deleted region in individuals with 22q11.2 deletion syndrome. Hum Genet 2019; 138:93-103. [PMID: 30627818 DOI: 10.1007/s00439-018-01967-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is caused by recurrent hemizygous deletions of chromosome 22q11.2. The phenotype of the syndrome is complex and varies widely among individuals. Little is known about the role of the different genes located in 22q11.2, and we hypothesized that genetic risk factors lying elsewhere in the genome might contribute to the phenotype. Here, we present the whole-genome gene expression data of 11 patients with approximately 3 Mb deletions. Apart from the hemizygous genes mapped to the 22q11.2 region, the TUBA8 and GNAZ genes, neighboring the deleted interval but in normal copy number, showed altered expression. When genes mapped to other chromosomes were considered in the gene expression analysis, a genome-wide dysregulation was observed, with increased or decreased expression levels. The enriched pathways of these genes were related to immune response, a deficiency that is frequently observed in 22q11.2DS patients. We also used the hypothesis-free weighted gene co-expression network analysis (WGCNA), which revealed the co-expression gene network modules with clear connection to mechanisms associated with 22q11.2DS such as immune response and schizophrenia. These findings, combined with the traditional gene expression profile, can be used for the identification of potential pathways and genes not previously considered to be related to the 22q11.2 deletion syndrome.
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Sato T, Migita O, Hata H, Okamoto A, Hata K. Analysis of chromosome microstructures in products of conception associated with recurrent miscarriage. Reprod Biomed Online 2018; 38:787-795. [PMID: 30926177 DOI: 10.1016/j.rbmo.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/31/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022]
Abstract
RESEARCH QUESTION The causes of almost half of all miscarriages are unknown. Genetic alterations undetectable by conventional methods may cause some cases of recurrent miscarriage. The study aimed to identify candidate genetic alterations associated with recurrent miscarriage. DESIGN Twenty-nine Japanese women with a history of recurrent miscarriage without any known underlying anatomical or medical causes were recruited. The products of conception were collected after miscarriage and showed either a normal karyotype or a failure of complete chromosomal Giemsa banding. Genomic DNA from the chorionic villi of the conception products was analysed using genome-wide single-nucleotide polymorphism (SNP) arrays. RESULTS In four cases, the products could not be analysed because of contaminating maternal-origin DNA, and chromosomal aneuploidies were observed in 10 cases. Thirty-three copy-number variations (CNV) were identified from the array data of 15 diploid cases. Causative CNV were identified by comparison with CNV observed in healthy, parous Japanese women. Twenty-four chromosomal regions with 26 CNV were identified as strong candidates for causing recurrent miscarriage, and these were all too small to detect by conventional chromosome analysis banding. Moreover, one novel CNV that caused complete deletion of a microRNA cluster region was detected. CONCLUSIONS High-resolution genome-wide SNP arrays are effective for detecting novel genetic factors causing recurrent miscarriage. A more appropriate reference CNV list may be necessary to more effectively enrich for CNV likely to cause recurrent miscarriage. The findings confirmed one non-coding RNA cluster as a strong candidate that may contribute to unexplained miscarriages. Gene expression-regulatory mechanisms may play important roles in the pathogenesis of miscarriages.
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Affiliation(s)
- Taisuke Sato
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; Department of Maternal-Fetal Biology, National Center Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Ohsuke Migita
- Department of Maternal-Fetal Biology, National Center Institute for Child Health and Development, Tokyo 157-8535, Japan; Department of Pediatrics, St. Marianna University School of Medicine, Kanagawa 216-8511, Japan
| | - Hiroka Hata
- Department of Maternal-Fetal Biology, National Center Institute for Child Health and Development, Tokyo 157-8535, Japan; Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kanagawa 216-8511, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Center Institute for Child Health and Development, Tokyo 157-8535, Japan.
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Jaouadi A, Tabebi M, Abdelhedi F, Abid D, Kamoun F, Chabchoub I, Maatoug S, Doukali H, Belghuith N, Ksentini MA, Keskes LA, Triki C, Hachicha M, Kamoun S, Kamoun H. A novel TBX1 missense mutation in patients with syndromic congenital heart defects. Biochem Biophys Res Commun 2018; 499:563-569. [DOI: 10.1016/j.bbrc.2018.03.190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/25/2018] [Indexed: 10/17/2022]
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Shetty M, Srikanth A, Kadandale J, Hegde S. Pre- and Postnatal Diagnosis of 10p14 Deletion and 22q11.2 Deletion Syndrome and Significance of Non-Cardiac Markers. Cytogenet Genome Res 2016; 148:249-55. [DOI: 10.1159/000446162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 11/19/2022] Open
Abstract
Congenital heart defect (CHD) is the most common form of birth defects. There is a high association between increased nuchal translucency and CHD in fetuses, and CHD in the antenatal period has a high incidence of 22q11.2 deletion syndrome (22q11.2DS). Apart from 22q11.2DS, the BRUNOL3 gene at 10p14 is also associated with DiGeorge-like features. We studied a total of 110 pre- and postnatal CHD cases with FISH probes. 22q11.2DS was detected in 5 cases and 10p14 deletion in 1 case. Antenatally diagnosed cases of CHD should be investigated by karyotyping and 22q11.2DS testing. Cases with increased nuchal translucency, intrauterine growth retardation, and other non-cardiac malformations because of 22q11.2DS should be screened carefully for thymus dysgenesis. It is also advisable to screen patients referred for 22q11.2DS for a 10p14 deletion, therefore enabling appropriate parental counseling.
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Detection of 1p36 deletion by clinical exome-first diagnostic approach. Hum Genome Var 2016; 3:16006. [PMID: 28428889 PMCID: PMC5381605 DOI: 10.1038/hgv.2016.6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 11/29/2022] Open
Abstract
Although chromosome 1p36 deletion syndrome is considered clinically recognizable based on characteristic features, the clinical manifestations of patients during infancy are often not consistent with those observed later in life. We report a 4-month-old girl who showed multiple congenital anomalies and developmental delay, but no clinical signs of syndromic disease caused by a terminal deletion in 1p36.32-p36.33 that was first identified by targeted-exome sequencing for molecular diagnosis.
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Morita KI, Naruto T, Tanimoto K, Yasukawa C, Oikawa Y, Masuda K, Imoto I, Inazawa J, Omura K, Harada H. Simultaneous Detection of Both Single Nucleotide Variations and Copy Number Alterations by Next-Generation Sequencing in Gorlin Syndrome. PLoS One 2015; 10:e0140480. [PMID: 26544948 PMCID: PMC4636311 DOI: 10.1371/journal.pone.0140480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 09/25/2015] [Indexed: 11/18/2022] Open
Abstract
Gorlin syndrome (GS) is an autosomal dominant disorder that predisposes affected individuals to developmental defects and tumorigenesis, and caused mainly by heterozygous germline PTCH1 mutations. Despite exhaustive analysis, PTCH1 mutations are often unidentifiable in some patients; the failure to detect mutations is presumably because of mutations occurred in other causative genes or outside of analyzed regions of PTCH1, or copy number alterations (CNAs). In this study, we subjected a cohort of GS-affected individuals from six unrelated families to next-generation sequencing (NGS) analysis for the combined screening of causative alterations in Hedgehog signaling pathway-related genes. Specific single nucleotide variations (SNVs) of PTCH1 causing inferred amino acid changes were identified in four families (seven affected individuals), whereas CNAs within or around PTCH1 were found in two families in whom possible causative SNVs were not detected. Through a targeted resequencing of all coding exons, as well as simultaneous evaluation of copy number status using the alignment map files obtained via NGS, we found that GS phenotypes could be explained by PTCH1 mutations or deletions in all affected patients. Because it is advisable to evaluate CNAs of candidate causative genes in point mutation-negative cases, NGS methodology appears to be useful for improving molecular diagnosis through the simultaneous detection of both SNVs and CNAs in the targeted genes/regions.
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Affiliation(s)
- Kei-ichi Morita
- Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Naruto
- Department of Stress Science, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kousuke Tanimoto
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chisato Yasukawa
- Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yu Oikawa
- Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kiyoshi Masuda
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Issei Imoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Johji Inazawa
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Omura
- Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Oral Cancer Center, Tokyo General Hospital, Tokyo, Japan
| | - Hiroyuki Harada
- Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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