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Ge B, Lin Y, Shi B, Jia Z. Integrating transcriptomics and genomics to identify fibroblast growth factor/receptor candidate genes for non-syndromic orofacial cleft in Chinese. Arch Oral Biol 2023; 153:105750. [PMID: 37348362 DOI: 10.1016/j.archoralbio.2023.105750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
OBJECTIVES The objective of this study was to explore the relationship between fibroblast growth factor/receptor (FGF/FGFR) and non-syndromic orofacial cleft (NSOC) in individuals of Han Chinese. DESIGN Initially, we performed RNA-Seq between non-syndromic cleft lip only (NSCLO) or non-syndromic cleft palate only (NSCPO) and control groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out to evaluate the functions of differentially expressed genes (DEGs) of FGF/FGFR. Then, we selected the most significant DEG FGFR2 and performed an association analysis in Chinese. Linkage disequilibrium (LD) and haplotype analyses were performed with HaploView and PLINK. Additional bioinformatics functional prediction for the notable single nucleotide polymorphisms was performed with HaploReg V4.1 and 3DSNP. RESULTS Finally, we identified 32 mRNAs related to FGF/FGFR via RNA-Seq and chose FGFR2 in the subsequent association analysis. Results indicated that the single nucleotide polymorphism (SNP) rs2288336 in FGFR2 contributed significantly to both non-syndromic cleft lip with or without cleft palate (NSCL/P) and NSCLO, with p values of 5.00E-05 (OR = 0.79, 95% CI: 0.70-0.88) and 1.38E-04 (OR = 0.76, 95% CI: 0.65-0.87), respectively. In addition, rs3793893 in FGFR2 was found to be associated with NSCLO, with a p value of 1.02E-04 (OR = 0.67, 95% CI: 0.55-0.82). CONCLUSIONS Our research demonstrated that FGFR2 is significantly more involved in NSOC than other FGF/FGFRs in Chinese and further identified rs2288336 and rs3793893 in FGFR2 associated with NSOC subtypes, which provide further evidence for the genetic etiology of NSOC in Han Chinese.
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Affiliation(s)
- Bin Ge
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, China
| | - Yansong Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, China.
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, China.
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Dąbrowska J, Biedziak B, Bogdanowicz A, Mostowska A. Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing. J Clin Med 2023; 12:2051. [PMID: 36902838 PMCID: PMC10004578 DOI: 10.3390/jcm12052051] [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: 12/17/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Non-syndromic cleft palate (ns-CP) has a genetically heterogeneous aetiology. Numerous studies have suggested a crucial role of rare coding variants in characterizing the unrevealed component of genetic variation in ns-CP called the "missing heritability". Therefore, this study aimed to detect low-frequency variants that are implicated in ns-CP aetiology in the Polish population. For this purpose, coding regions of 423 genes associated with orofacial cleft anomalies and/or involved with facial development were screened in 38 ns-CP patients using the next-generation sequencing technology. After multistage selection and prioritisation, eight novel and four known rare variants that may influence an individual's risk of ns-CP were identified. Among detected alternations, seven were located in novel candidate genes for ns-CP, including COL17A1 (c.2435-1G>A), DLG1 (c.1586G>C, p.Glu562Asp), NHS (c.568G>C, p.Val190Leu-de novo variant), NOTCH2 (c.1997A>G, p.Tyr666Cys), TBX18 (c.647A>T, p.His225Leu), VAX1 (c.400G>A, p.Ala134Thr) and WNT5B (c.716G>T, p.Arg239Leu). The remaining risk variants were identified within genes previously linked to ns-CP, confirming their contribution to this anomaly. This list included ARHGAP29 (c.1706G>A, p.Arg569Gln), FLNB (c.3605A>G, Tyr1202Cys), IRF6 (224A>G, p.Asp75Gly-de novo variant), LRP6 (c.481C>A, p.Pro161Thr) and TP63 (c.353A>T, p.Asn118Ile). In summary, this study provides further insights into the genetic components contributing to ns-CP aetiology and identifies novel susceptibility genes for this craniofacial anomaly.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Agnieszka Bogdanowicz
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
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3
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Lansdon LA, Dickinson A, Arlis S, Liu H, Hlas A, Hahn A, Bonde G, Long A, Standley J, Tyryshkina A, Wehby G, Lee NR, Daack-Hirsch S, Mohlke K, Girirajan S, Darbro BW, Cornell RA, Houston DW, Murray JC, Manak JR. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Am J Hum Genet 2023; 110:71-91. [PMID: 36493769 PMCID: PMC9892779 DOI: 10.1016/j.ajhg.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology, University of Missouri - Kansas City School of Medicine, Kansas City, MO 64108, USA
| | | | - Sydney Arlis
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Arman Hlas
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Alyssa Hahn
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Abby Long
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | | | - George Wehby
- College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Nanette R Lee
- Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | | | - Karen Mohlke
- University of North Carolina, Chapel Hill, NC 27514, USA
| | | | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Robert A Cornell
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas W Houston
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - J Robert Manak
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA.
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4
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Biedziak B, Dąbrowska J, Szponar-Żurowska A, Bukowska-Olech E, Jamsheer A, Mojs E, Mulle J, Płoski R, Mostowska A. Identification of a new familial case of 3q29 deletion syndrome associated with cleft lip and palate via whole-exome sequencing. Am J Med Genet A 2023; 191:205-219. [PMID: 36317839 DOI: 10.1002/ajmg.a.63015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/22/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022]
Abstract
Many unbalanced large copy number variants reviewed in the paper are associated with syndromic orofacial clefts, including a 1.6 Mb deletion on chromosome 3q29. The current report presents a new family with this recurrent deletion identified via whole-exome sequencing and confirmed by array comparative genomic hybridization. The proband exhibited a more severe clinical phenotype than his affected mother, comprising right-sided cleft lip/alveolus and cleft palate, advanced dental caries, heart defect, hypospadias, psychomotor, and speech delay, and an intellectual disability. Data analysis from the 3q29 registry revealed that the 3q29 deletion increases the risk of clefting by nearly 30-fold. No additional rare and pathogenic nucleotide variants were identified that could explain the clefting phenotype and observed intrafamilial phenotypic heterogeneity. These data suggest that the 3q29 deletion may be the primary risk factor for clefting, with additional genomic variants located outside the coding sequences, methylation changes, or environmental exposure serving as modifiers of this risk. Additional studies, including whole-genome sequencing or methylation analyses, should be performed to identify genetic factors underlying the phenotypic variation associated with the recurrent 3q29 deletion.
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Affiliation(s)
- Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewa Mojs
- Department of Clinical Psychology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jennifer Mulle
- Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
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Askarian S, Gholami M, Khalili-Tanha G, Tehrani NC, Joudi M, Khazaei M, Ferns GA, Hassanian SM, Avan A, Joodi M. The genetic factors contributing to the risk of cleft lip-cleft palate and their clinical utility. Oral Maxillofac Surg 2022:10.1007/s10006-022-01052-3. [PMID: 35426585 DOI: 10.1007/s10006-022-01052-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
Abstract
Cleft lip and cleft palate (CL/P) are among the most common congenital malformations in neonates and have syndromic or nonsyndromic forms. Nonsyndromic forms of malformation are being reported to be associated with chromosomal DNA modification by teratogenic exposure and to complex genetic contributions of multiple genes. Syndromic forms are shown to be related to chromosomal aberrations or monogenic diseases. There is a growing body of data illustrating the association of several genes with risk of developing this malformation, including genetic defects in T-box transcription factor-22 (TBX22), interferon regulatory factor-6 (IRF6), and poliovirus receptor-like-1 (PVRL1), responsible for X-linked cleft palate, cleft lip/palate-ectodermal dysplasia syndrome, and Van der Woude and popliteal pterygium syndromes, respectively. Genetic variants in MTR, PCYT1A, ASS1, SLC 25A13, GSTM1, GSTT1, SUMO1 BHMT1, and BHMT2 are being reported to be linked with CL/P risk. The etiology of nonsyndromic CLP is still remained to be unknown, although mutations in candidate genes have been found. Here, we provide an overview about the potential variants to be associated with CL/P for identification of the relative risk of CLP with respect to the basis of genetic background and environmental factors (e.g., dietary factors, alcohol use).
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Affiliation(s)
- Saeedeh Askarian
- Department of Medical Biotechnology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran.,Department of Physiology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Masoumeh Gholami
- Department of Physiology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Ghazaleh Khalili-Tanha
- Metabolic syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negin Chaeichi Tehrani
- Metabolic syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Joudi
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton & Sussex Medical School, Falmer, Brighton, BN1 9PH, Sussex, UK
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran. .,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Marjan Joodi
- Endoscopic and Minimally Invasive Surgery Research Center, Sarvar Children's Hospital, Mashhad, Iran. .,Department of Pediatric Surgery, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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6
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Lecaudey LA, Singh P, Sturmbauer C, Duenser A, Gessl W, Ahi EP. Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris. BMC Genomics 2021; 22:506. [PMID: 34225643 PMCID: PMC8256507 DOI: 10.1186/s12864-021-07775-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on an example of lip hypertrophy in the benthivorous Lake Tangnayika cichlid, Gnathochromis permaxillaris, considered to be a morphological adaptation to extract invertebrates out of the uppermost layer of mud bottom. We investigate the molecular and regulatory basis of lip hypertrophy in G. permaxillaris using a comparative transcriptomic approach. RESULTS We identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in lip formation in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression of foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation, and its function has been associated with hypertrophy of upper lip in human. CONCLUSION Our results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates. In the future, we advocate integrating gene regulatory networks of various craniofacial phenotypes to understand how they collectively govern trophic and behavioural adaptations.
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Affiliation(s)
- Laurène Alicia Lecaudey
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4 Canada
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Anna Duenser
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
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Pilmane M, Jain N, Vitenberga-Verza Z. Expression Analysis of FGF/FGFR and FOX Family Proteins in Mucosal Tissue Obtained from Orofacial Cleft-Affected Children. BIOLOGY 2021; 10:423. [PMID: 34068496 PMCID: PMC8151933 DOI: 10.3390/biology10050423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/02/2023]
Abstract
Orofacial clefts affect hundreds of thousands of children worldwide annually and are usually corrected by a series of surgeries extending to childhood. The underlying mechanisms that lead to clefts are still unknown, mainly because of the multifactorial etiology and the myriad of interactions between genes and environmental factors. In the present study, we investigated the role and expression of candidate genes belonging to the FGF/FGFR signaling pathway and FOX family in tissue material obtained from 12 pediatric patients undergoing cleft correction surgery. The expression was investigated using immunohistochemistry (IHC) and chromogenic in-situ hybridization (CISH) in three cell/tissue types-epithelial cells, connective tissue, and endothelial cells. We found elevated expression of FGFR1 in epithelial cells while no expression was observed in endothelial cells. Further, our results elucidate the potential pathogenetic role of FGFR1 in cellular proliferation, local site inflammation, and fibrosis in cleft patients. Along with bFGF (also called FGF2), FGFR1 could play a pro-inflammatory role in clefts. Over-amplification of FGFR2 in some patients, along with bFGF, could potentially suggest roles for these genes in angiogenesis. Additionally, increased expression of FOXE1 (also called TTF2) contributes to local site inflammation. Finally, zero to low amplification of FOXO1 could suggest its potential role in inducing oxidative stress in the endothelium along with reduced epithelial apoptosis.
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Affiliation(s)
| | - Nityanand Jain
- Department of Morphology, Institute of Anatomy and Anthropology, Riga Stradinš University, LV-1007 Riga, Latvia; (M.P.); (Z.V.-V.)
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8
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Lustosa-Mendes E, Santos APD, Vieira TP, Ribeiro EM, Rezende AA, Fett-Conte AC, Cavalcanti DP, Félix TM, Monlleó IL, Gil-da-Silva-Lopes VL. Identification of genomic imbalances in oral clefts. J Pediatr (Rio J) 2021; 97:321-328. [PMID: 32707036 PMCID: PMC9432012 DOI: 10.1016/j.jped.2020.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE This article presents a clinical and cytogenomic approach that focuses on the diagnosis of syndromic oral clefts (OCs). METHODS The inclusion criteria were individuals with OC presenting four or more minor signs and no major defects (non-syndromic oral clefts [NSOCs]) as well as individuals with OC presenting at least another major defect, regardless of the number of minor signs (syndromic oral clefts [SOCs]). The exclusion criteria included NSOC with less than four minor signs, SOC with known etiology, as well as atypical oral clefts. RESULTS Of 1647 individuals with OC recorded in the Brazilian Database of Craniofacial Anomalies, 100 individuals were selected for chromosome microarray analysis (CMA). Among these, 44 individuals were clinically classified as NSOC and 56 as SOC. CMA was performed for both groups, and abnormal CMA was identified in 9%, all previously classified as SCO. The clinical and CMA data analyses showed a significant predominance of abnormal CMA in individuals classified as SOC (p = 0.0044); prematurity, weight, length, and head circumference at birth were significantly lower in the group with abnormal CMA. Besides, minor signs were significantly higher in this group (p = 0.0090). CONCLUSION The rigorous selection of cases indicates that the significant variables could help in early recognition of SOC. This study reinforces the importance of applying the CMA technique to establish the diagnosis of SOC. This is an important and universal issue in clinical practice for intervention, care, and genetic counseling.
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Affiliation(s)
- Elaine Lustosa-Mendes
- Universidade de Campinas (Unicamp), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil; Centro de Atendimento Integral ao Fissurado Labio-Palatal, Hospital do Trabalhador (CAIF-HT), Curitiba, PR, Brazil
| | - Ana P Dos Santos
- Universidade de Campinas (Unicamp), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil
| | - Társis P Vieira
- Universidade de Campinas (Unicamp), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil
| | - Erlane M Ribeiro
- Hospital Infantil Albert Sabin (HIAS), Serviço de Genética Médica, Fortaleza, CE, Brazil
| | - Adriana A Rezende
- Universidade Federal do Rio Grande do Norte (UFRN), Hospital Universitário Onofre Lopes (HUOL), Empresa Brasileira de Serviços Hospitalares (EBSERH), Natal, RN, Brazil
| | - Agnes C Fett-Conte
- Faculdade de Medicina de São José do Rio Preto (FAMERP/FUNFARME), Departamento de Biologia Molecular, São José do Rio Preto, SP, Brazil
| | - Denise P Cavalcanti
- Universidade de Campinas (Unicamp), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Programa Genético Perinatal, Campinas, SP, Brazil
| | - Têmis M Félix
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Isabella L Monlleó
- Universidade Federal de Alagoas (UFAL), Faculdade de Medicina, Setor de Genética Médica, Hospital Universitário, Serviço de Genética Clínica, Maceió, AL, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Universidade de Campinas (Unicamp), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.
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9
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Gil-da-Silva-Lopes VL, Tacla MA, Sgardioli IC, Vieira TP, Monlleó IL. Brazil's Craniofacial Project: Different approaches on orofacial clefts and 22q11.2 deletion syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:912-927. [PMID: 33166033 DOI: 10.1002/ajmg.c.31852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
This article reports the present situation of Brazilian health care in genetics for Orofacial Cleft (OFC) and 22q11.2 Deletions Syndrome (22q11.2 DS) based on research conducted by Brazil's Craniofacial Project (BCFP). Established in 2003, BCFP is a voluntary and cooperative network aiming to investigate the health care of people with these diseases and other craniofacial anomalies. The initiatives and research results are presented in four sections: (a) a comprehensive report of the Brazilian public health system in craniofacial genetics; (b) multicentric studies developed on OFC and 22q11.2 DS; (c) education strategies focused on addressing these conditions for both population and health-care professionals; and (d) the nosology through the Brazilian Database on Craniofacial Anomalies (BDCA). Since 2006, BDCA uses a standardized method with detailed clinical data collection, which allows for conducting studies on nosology, genotype-phenotype correlations, and natural history; data can also contribute to public policies. Currently, the BDCA stores data on 1,724 individuals, including 1,351 (78.36%) who were primarily admitted due to OFC and 373 (21.63%) with clinical suspicion of 22q11.2 DS. Chromosomal abnormalities/genomic imbalances were represented by 92/213 (43.19%) individuals with syndromic OFC, including 43 with 22q11.2 DS, which indicates the need for chromosomal microarray analysis in this group. The nosologic diversity reinforces that monitoring clinical is the best strategy for etiological investigation. BCFP's methodology has introduced the possibility of increasing scientific knowledge and genetic diagnosis of OFC and 22q11.2 DS to in turn improve health care and policies for this group of diseases.
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Affiliation(s)
- Vera Lúcia Gil-da-Silva-Lopes
- Faculty of Medical Sciences, Department of Medical Genetics and Genomic Medicine, University of Campinas (Unicamp), Campinas, Sao Paulo, Brazil
| | - Milena Atique Tacla
- Faculty of Medical Sciences, Department of Medical Genetics and Genomic Medicine, University of Campinas (Unicamp), Sao Paulo, Brazil
| | - Ilária Cristina Sgardioli
- Faculty of Medical Sciences, Department of Medical Genetics and Genomic Medicine, University of Campinas (Unicamp), Campinas, Sao Paulo, Brazil
| | - Társis Paiva Vieira
- Faculty of Medical Sciences, Department of Medical Genetics and Genomic Medicine, University of Campinas (Unicamp), Campinas, Sao Paulo, Brazil
| | - Isabella Lopes Monlleó
- Faculty of Medicine, Clinical Genetics Service, University Hospital, Medical Genetics Sector, Federal University of Alagoas-UFAL, Maceió, Alagoas, Brazil
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10
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Degen M, Girousi E, Feldmann J, Parisi L, La Scala GC, Schnyder I, Schaller A, Katsaros C. A Novel Van der Woude Syndrome-Causing IRF6 Variant Is Subject to Incomplete Non-sense-Mediated mRNA Decay Affecting the Phenotype of Keratinocytes. Front Cell Dev Biol 2020; 8:583115. [PMID: 33117810 PMCID: PMC7552806 DOI: 10.3389/fcell.2020.583115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/03/2020] [Indexed: 01/02/2023] Open
Abstract
Van der Woude syndrome (VWS) is a genetic syndrome that leads to typical phenotypic traits, including lower lip pits and cleft lip/palate (CLP). The majority of VWS-affected patients harbor a pathogenic variant in the gene encoding for the transcription factor interferon regulatory factor 6 (IRF6), a crucial regulator of orofacial development, epidermal differentiation and tissue repair. However, most of the underlying mechanisms leading from pathogenic IRF6 gene variants to phenotypes observed in VWS remain poorly understood and elusive. The availability of one VWS individual within our cohort of CLP patients allowed us to identify a novel VWS-causing IRF6 variant and to functionally characterize it. Using VWS patient-derived keratinocytes, we reveal that most of the mutated IRF6_VWS transcripts are subject to a non-sense-mediated mRNA decay mechanism, resulting in IRF6 haploinsufficiency. While moderate levels of IRF6_VWS remain detectable in the VWS keratinocytes, our data illustrate that the IRF6_VWS protein, which lacks part of its protein-binding domain and its whole C-terminus, is noticeably less stable than its wild-type counterpart. Still, it maintains transcription factor function. As we report and characterize a so far undescribed VWS-causing IRF6 variant, our results shed light on the physiological as well as pathological role of IRF6 in keratinocytes. This acquired knowledge is essential for a better understanding of the molecular mechanisms leading to VWS and CLP.
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Affiliation(s)
- Martin Degen
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Eleftheria Girousi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Julia Feldmann
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Ludovica Parisi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Giorgio C La Scala
- Division of Pediatric Surgery, Department of Pediatrics, University Hospital of Geneva, Geneva, Switzerland
| | - Isabelle Schnyder
- University Clinic for Pediatric Surgery, Bern University Hospital, Bern, Switzerland
| | - André Schaller
- Division of Human Genetics, Bern University Hospital, Bern, Switzerland
| | - Christos Katsaros
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
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11
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Microdeletion of the entire IRF6 gene in a Subsaharian African's family with Van der Woude syndrome. Clin Dysmorphol 2020; 29:24-27. [PMID: 30946036 DOI: 10.1097/mcd.0000000000000272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microdeletion of the entire interferon regulatory factory 6 (IRF 6) gene is a rare cause of Van der Woude syndrome (VDW) with only few cases reported in medical literature. Its occurrence in multiple affected members of a family is exceptional. The aim of this presentation was to describe a Central African family with typical VDW phenotype carrying an IRF6 gene deletion. Here we reported phenotype features of members of a Central African family with VDW syndrome consisting of labioalveolar cleft, depressions of the lower lip with labial fistulae (lip pits), submucosal clefts and cleft palate. Mutation analysis by means of multiplex ligation-dependent probe amplification and chromosomal microarray revealed a 374.070 kb, deletion encompassing the entire IRF6 gene in four affected family members. Microdeletion of the entire IRF6 gene causes the classical VDW syndrome phenotype.
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12
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Zhou T, Thung KH, Liu M, Shen D. Brain-Wide Genome-Wide Association Study for Alzheimer's Disease via Joint Projection Learning and Sparse Regression Model. IEEE Trans Biomed Eng 2019; 66:165-175. [PMID: 29993426 PMCID: PMC6342004 DOI: 10.1109/tbme.2018.2824725] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Brain-wide and genome-wide association (BW-GWA) study is presented in this paper to identify the associations between the brain imaging phenotypes (i.e., regional volumetric measures) and the genetic variants [i.e., single nucleotide polymorphism (SNP)] in Alzheimer's disease (AD). The main challenges of this study include the data heterogeneity, complex phenotype-genotype associations, high-dimensional data (e.g., thousands of SNPs), and the existence of phenotype outliers. Previous BW-GWA studies, while addressing some of these challenges, did not consider the diagnostic label information in their formulations, thus limiting their clinical applicability. To address these issues, we present a novel joint projection and sparse regression model to discover the associations between the phenotypes and genotypes. Specifically, to alleviate the negative influence of data heterogeneity, we first map the genotypes into an intermediate imaging-phenotype-like space. Then, to better reveal the complex phenotype-genotype associations, we project both the mapped genotypes and the original imaging phenotypes into a diagnostic-label-guided joint feature space, where the intraclass projected points are constrained to be close to each other. In addition, we use l2,1-norm minimization on both the regression loss function and the transformation coefficient matrices, to reduce the effect of phenotype outliers and also to encourage sparse feature selections of both the genotypes and phenotypes. We evaluate our method using AD neuroimaging initiative dataset, and the results show that our proposed method outperforms several state-of-the-art methods in term of the average root-mean-square error of genome-to-phenotype predictions. Besides, the associated SNPs and brain regions identified in this study have also been shown in the previous AD-related studies, thus verifying the effectiveness and potential of our proposed method in AD pathogenesis study.
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Affiliation(s)
- Tao Zhou
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ()
| | - Kim-Han Thung
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ()
| | - Mingxia Liu
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA ()
| | - Dinggang Shen
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599 USA, and also with the Department of Brain and Cognitive Engineering, Korea University, Seoul 02841, Republic of Korea ()
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13
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Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, Mitrotti A, Fasel DA, Batourina E, Sampson MG, Bodria M, Werth M, Kao C, Martino J, Capone VP, Vivante A, Shril S, Kil BH, Marasà M, Zhang JY, Na YJ, Lim TY, Ahram D, Weng PL, Heinzen EL, Carrea A, Piaggio G, Gesualdo L, Manca V, Masnata G, Gigante M, Cusi D, Izzi C, Scolari F, van Wijk JAE, Saraga M, Santoro D, Conti G, Zamboli P, White H, Drozdz D, Zachwieja K, Miklaszewska M, Tkaczyk M, Tomczyk D, Krakowska A, Sikora P, Jarmoliński T, Borszewska-Kornacka MK, Pawluch R, Szczepanska M, Adamczyk P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Dobson MG, Darlow JM, Puri P, Barton DE, Furth SL, Warady BA, Gucev Z, Lozanovski VJ, Tasic V, Pisani I, Allegri L, Rodas LM, Campistol JM, Jeanpierre C, Alam S, Casale P, Wong CS, Lin F, Miranda DM, Oliveira EA, Simões-E-Silva AC, Barasch JM, Levy B, Wu N, Hildebrandt F, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Zhang F, Hakonarson H, Papaioannou VE, Mendelsohn CL, Gharavi AG, Sanna-Cherchi S. The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Nat Genet 2018; 51:117-127. [PMID: 30578417 PMCID: PMC6668343 DOI: 10.1038/s41588-018-0281-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/18/2018] [Indexed: 12/18/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2,824 cases and 21,498 controls. Affected individuals carried a significant burden of rare exonic (i.e. affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs; vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1-p16.3, and 22q11.2 were specific for KA; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.,Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Alejandra Perez
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Qingxue Liu
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - David A Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ekaterina Batourina
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Max Werth
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Charlly Kao
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Valentina P Capone
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Young-Ji Na
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dina Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alba Carrea
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Daniele Cusi
- National Research Council of Italy, Inst. Biomedical Technologies Milano Bio4dreams Scientific Unit, Milano, Italy
| | - Claudia Izzi
- Dipartimento Ostetrico-Ginecologico e Seconda Divisione di Nefrologia ASST, Spedali Civili e Presidio di Montichiari, Brescia, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia, Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia.,School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria "G. Martino", Messina, Italy
| | - Pasquale Zamboli
- Division of Nephrology, University of Campania "Luigi Vanvitell", Naples, Italy
| | - Hope White
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology, Jagiellonian University Medical College, Krakow, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Anna Krakowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, Lublin, Poland
| | | | - Maria K Borszewska-Kornacka
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Robert Pawluch
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Mark G Dobson
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - John M Darlow
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Hospital Tallaght, Dublin, Ireland
| | - David E Barton
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,University College Dublin UCD School of Medicine, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Susan L Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Division of Nephrology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Bradley A Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Division of Nephrology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Zoran Gucev
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Vladimir J Lozanovski
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia.,University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Lida M Rodas
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Josep M Campistol
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pasquale Casale
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Mount Sinai Medical Center, Kravis Children's Hospital, New York, NY, USA
| | - Craig S Wong
- Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque, NM, USA
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Débora M Miranda
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo A Oliveira
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Cristina Simões-E-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jonathan M Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, all at Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA.
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
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14
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Chromosomal Abnormalities in Syndromic Orofacial Clefts: Report of Three Children. Case Rep Genet 2018; 2018:1928918. [PMID: 30271639 PMCID: PMC6151207 DOI: 10.1155/2018/1928918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/01/2018] [Accepted: 08/27/2018] [Indexed: 11/29/2022] Open
Abstract
This case series of three children reports clinical features and chromosomal abnormalities seen in a craniofacial clinic. All presented with orofacial cleft, developmental or intellectual disability, and dysmorphism. Emanuel syndrome or supernumerary der (22)t(11; 22), the prototype of complex small supernumerary marker disorders, was seen in one child. Duplication 4q27q35.2 with concomitant deletion 21q22.2q22.3 and duplication 12p13.33p13.32 with concomitant deletion 18q22.3q23 seen in the remaining two children are not reported in literature. Maternal balanced translocation was established in both of these children.
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15
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Guo W, Zhu X, Yan L, Qiao J. The present and future of whole-exome sequencing in studying and treating human reproductive disorders. J Genet Genomics 2018; 45:517-525. [DOI: 10.1016/j.jgg.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
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16
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Funato N, Yanagisawa H. Deletion of the T-box transcription factor gene, Tbx1, in mice induces differential expression of genes associated with cleft palate in humans. Arch Oral Biol 2018; 95:149-155. [PMID: 30121012 DOI: 10.1016/j.archoralbio.2018.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/27/2018] [Accepted: 08/06/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVE We examined the function of the T-box transcription factor 1 (TBX1) in palatogenesis. DESIGN Tbx1-knockout mice were histologically examined by hematoxylin and eosin staining. Next, secondary palatal shelves dissected from wild type or Tbx1-knockout mice embryos at embryonic day 13.5 were investigated with microarray analysis, gene ontology analysis, and real-time quantitative polymerase chain reaction. We performed gene profiling of developing palatal shelves from wild type and Tbx1-knockout embryos. We also analyzed the association of mouse genes linked to cleft palate with biological processes and compared the results with those of our ontology analysis of dysregulated genes in Tbx1-knockout palatal shelves. RESULTS Histological analysis of Tbx1-knockout palate with complete cleft palate at postnatal day 1 showed aplasia of secondary palates associated with a small mandible and a small tongue compared to wild type littermates. Gene ontology analysis indicated that genes associated with development of the nervous system, muscle, and biomineral tissue were dysregulated in Tbx1-knockout palatal shelves. Furthermore, in Tbx1-knockout palatal shelves, genes associated with human cleft palate, specifically, myosin heavy chain 3 (Myh3) and nebulin (Neb), were downregulated and gamma-aminobutyric acid type A receptor beta 3 subunit (Gabrb3) was upregulated. CONCLUSIONS Our findings demonstrate that TBX1 maintains normal growth and development of palatal shelves, mediated through the regulation of genes involved in muscle cell differentiation, nervous system development, and biomineral tissue development. Multiple factors in Tbx1-knockout mice may lead to various subtypes of cleft palate.
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Affiliation(s)
- Noriko Funato
- Department of Signal Gene Regulation, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan; Research Core, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.
| | - Hiromi Yanagisawa
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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17
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da Silva HPV, Oliveira GHDM, Ururahy MAG, Bezerra JF, de Souza KSC, Bortolin RH, Luchessi AD, Silbiger VN, Lima VMGDM, Leite GCP, Brito MEF, Ribeiro EM, Gil-da-Silva-Lopes VL, de Rezende AA. Application of high-resolution array platform for genome-wide copy number variation analysis in patients with nonsyndromic cleft lip and palate. J Clin Lab Anal 2018; 32:e22428. [PMID: 29512191 DOI: 10.1002/jcla.22428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/09/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Although more than 14 loci may be involved in the development of nonsyndromic cleft lip and palate (NSCLP), the etiology has not been fully elucidated due to genetic and environmental risk factor interactions. Despite advances in identifying genes associated with the NSCLP development using traditional genetic mapping strategies of candidate genes, genome-wide studies, and epidemiologic and linkage analysis, microarray techniques have become important complementary tools in the search for potential causative oral clefts genes in genetic studies. Microarray hybridization enables scanning of the whole genome and detecting copy number variants (CNVs). Although common benign CNVs are often smaller, with sizes smaller than 20 kb, here we reveal small exonic CNVs based on the importance of the encompassed genes in cleft lip and palate phenotype. METHODS Microarray hybridization analysis was performed in 15 individuals with NSCLP. RESULTS We identified 11 exonic CNVs affecting at least one exon of the candidate genes. Thirteen candidate genes (COL11A1-1p21; IRF6-1q32.3; MSX1-4p16.2; TERT-5p15.33; MIR4457-5p15.33; CLPTM1L-5p15.33; ESR1-6q25.1; GLI3-7p13; FGFR-8p11.23; TBX1-22q11.21; OFD-Xp22; PHF8-Xp11.22; and FLNA-Xq28) overlapped with the CNVs identified. CONCLUSIONS Considering the importance to NSCLP, the microdeletions that encompass MSX1, microduplications over TERT, MIR4457, CLPTM1L, and microduplication of PHF8 have been identified as small CNVs related to sequence variants associated with oral clefts susceptibility. Our findings represent a preliminary study on the clinical significance of small CNVs and their relationship with genes implicated in NSCLP.
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Affiliation(s)
| | | | | | - João Felipe Bezerra
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | | | | | | | - Adriana Augusto de Rezende
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
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18
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Rojnueangnit K, Mikhail FM, Cui X, Yu S, Robin NH. Predictor(s) of Abnormal Array Comparative Genomic Hybridization Results in Patients with Cleft Lip and/or Palate. Cleft Palate Craniofac J 2018; 52:724-31. [DOI: 10.1597/14-088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objectives Cleft lip and/or cleft palate (CL/P) occurs either as an isolated anomaly or as one manifestation of genetic syndromes. Chromosomal abnormalities from karyotype analysis are commonly seen in cases of nonisolated CL/P. This study was designed to evaluate the usefulness of clinical array comparative genomic hybridization (aCGH) testing in patients with CL/P. Our objectives were to identify the clinical phenotypes that are predicative of an abnormal aCGH result, correlate aCGH results with language outcome, and analyze the data in the abnormal aCGH results group. Methods Nonisolated CL/P patients who had clinical aCGH testing performed between 2009 and 2012 in the University of Alabama at Birmingham cytogenetics lab were enrolled. The demographic data, clinical phenotypes, and speech outcome were collected. Results Two hundred forty-five nonisolated CL/P patients were studied, with 62 having an abnormal aCGH result compared to 183 patients with a normal aCGH result. The presence of developmental delay/intellectual disability (DD/ID), dysmorphic features, congenital anomalies, and/or family history of DD/ID were significantly higher in the abnormal aCGH group ( P < .05). Neither the aCGH results nor the type of CL/P correlated with speech outcome. Finally, analysis of the abnormal aCGH result group revealed that DD/ID had a strong positive association with the copy number variation pathogenicity and the number of genes involved. Conclusions This study demonstrated the diagnostic value of clinical aCGH testing in CL/P patients who present with DD/ID, dysmorphic features, other congenital anomalies, and/or family history of DD/ID.
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Affiliation(s)
- Kitiwan Rojnueangnit
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Fady M. Mikhail
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiangqin Cui
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Shaohua Yu
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H. Robin
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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19
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Sanna-Cherchi S, Westland R, Ghiggeri GM, Gharavi AG. Genetic basis of human congenital anomalies of the kidney and urinary tract. J Clin Invest 2018; 128:4-15. [PMID: 29293093 DOI: 10.1172/jci95300] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The clinical spectrum of congenital anomalies of the kidney and urinary tract (CAKUT) encompasses a common birth defect in humans that has significant impact on long-term patient survival. Overall, data indicate that approximately 20% of patients may have a genetic disorder that is usually not detected based on standard clinical evaluation, implicating many different mutational mechanisms and pathogenic pathways. In particular, 10% to 15% of CAKUT patients harbor an unsuspected genomic disorder that increases risk of neurocognitive impairment and whose early recognition can impact clinical care. The emergence of high-throughput genomic technologies is expected to provide insight into the common and rare genetic determinants of diseases and offer opportunities for early diagnosis with genetic testing.
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Affiliation(s)
- Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, Netherlands
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genoa, Italy
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
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20
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Lansdon LA, Darbro BW, Petrin AL, Hulstrand AM, Standley JM, Brouillette RB, Long A, Mansilla MA, Cornell RA, Murray JC, Houston DW, Manak JR. Identification of Isthmin 1 as a Novel Clefting and Craniofacial Patterning Gene in Humans. Genetics 2018; 208:283-296. [PMID: 29162626 PMCID: PMC5753863 DOI: 10.1534/genetics.117.300535] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/20/2017] [Indexed: 12/26/2022] Open
Abstract
Orofacial clefts are one of the most common birth defects, affecting 1-2 per 1000 births, and have a complex etiology. High-resolution array-based comparative genomic hybridization has increased the ability to detect copy number variants (CNVs) that can be causative for complex diseases such as cleft lip and/or palate. Utilizing this technique on 97 nonsyndromic cleft lip and palate cases and 43 cases with cleft palate only, we identified a heterozygous deletion of Isthmin 1 in one affected case, as well as a deletion in a second case that removes putative 3' regulatory information. Isthmin 1 is a strong candidate for clefting, as it is expressed in orofacial structures derived from the first branchial arch and is also in the same "synexpression group" as fibroblast growth factor 8 and sprouty RTK signaling antagonist 1a and 2, all of which have been associated with clefting. CNVs affecting Isthmin 1 are exceedingly rare in control populations, and Isthmin 1 scores as a likely haploinsufficiency locus. Confirming its role in craniofacial development, knockdown or clustered randomly interspaced short palindromic repeats/Cas9-generated mutation of isthmin 1 in Xenopus laevis resulted in mild to severe craniofacial dysmorphologies, with several individuals presenting with median clefts. Moreover, knockdown of isthmin 1 produced decreased expression of LIM homeobox 8, itself a gene associated with clefting, in regions of the face that pattern the maxilla. Our study demonstrates a successful pipeline from CNV identification of a candidate gene to functional validation in a vertebrate model system, and reveals Isthmin 1 as both a new human clefting locus as well as a key craniofacial patterning gene.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics
- Department of Biology
- Interdisciplinary Graduate Program in Genetics
| | - Benjamin W Darbro
- Department of Pediatrics
- Interdisciplinary Graduate Program in Genetics
| | - Aline L Petrin
- Department of Pediatrics
- College of Dentistry, University of Iowa, Iowa 52242 and
| | | | | | | | | | | | - Robert A Cornell
- Interdisciplinary Graduate Program in Genetics
- Department of Anatomy and Cell Biology, and
| | - Jeffrey C Murray
- Department of Pediatrics
- Department of Biology
- Department of Anatomy and Cell Biology, and
- Interdisciplinary Graduate Program in Genetics
- College of Dentistry, University of Iowa, Iowa 52242 and
| | | | - J Robert Manak
- Department of Pediatrics,
- Department of Biology
- Interdisciplinary Graduate Program in Genetics
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21
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Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play. Int J Mol Sci 2017; 18:ijms18040796. [PMID: 28398236 PMCID: PMC5412380 DOI: 10.3390/ijms18040796] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 01/13/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most frequent form of malformation at birth and represent the cause of 40–50% of pediatric and 7% of adult end-stage renal disease worldwide. The pathogenesis of CAKUT is based on the disturbance of normal nephrogenesis, secondary to environmental and genetic causes. Often CAKUT is the first clinical manifestation of a complex systemic disease, so an early molecular diagnosis can help the physician identify other subtle clinical manifestations, significantly affecting the management and prognosis of patients. The number of sporadic CAKUT cases explained by highly penetrant mutations in a single gene may have been overestimated over the years and a genetic diagnosis is missed in most cases, hence the importance of identifying new genetic approaches which can help unraveling the vast majority of unexplained CAKUT cases. The aim of our review is to clarify the current state of play and the future perspectives of the genetic bases of CAKUT.
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22
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Tan EC, Lim HW, Lim ECP, Lee ST. A Novel Interferon Regulatory Factor 6 Mutation in an Asian Family With Van der Woude Syndrome. Cleft Palate Craniofac J 2016; 54:442-445. [PMID: 27243668 DOI: 10.1597/15-327] [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] [Indexed: 02/05/2023] Open
Abstract
Van der Woude syndrome (VWS) is a rare autosomal dominant genetic disorder characterized by orofacial clefting and lip pits. Mutations in the transcription factor interferon regulatory factor 6 gene (IRF6) have been identified in individuals with VWS. We performed direct sequencing of the gene for molecular investigation of a proband with Bangladeshi-Malay ancestry. A novel transition mutation (c.113T>C), which resulted in an amino acid substitution (p.Ile38Thr) in the deoxyribonucleic acid-binding domain was detected. Testing of family members showed that the mutation segregated with the VWS phenotype for members of her immediate family. Although there is some phenotypic variability, all of the affected members are of the female gender.
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23
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Rincic M, Rados M, Krsnik Z, Gotovac K, Borovecki F, Liehr T, Brecevic L. Complex intrachromosomal rearrangement in 1q leading to 1q32.2 microdeletion: a potential role of SRGAP2 in the gyrification of cerebral cortex. Mol Cytogenet 2016; 9:19. [PMID: 26900403 PMCID: PMC4761178 DOI: 10.1186/s13039-016-0221-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/30/2016] [Indexed: 12/13/2022] Open
Abstract
Background Van der Woude syndrome (MIM: 119300, VWS) is a dominantly inherited and the most common orofacial clefting syndrome; it accounts for ~2 % of all cleft lip and palate cases. Intellectual disability (ID) is characterized by significant limitations, both in intellectual functioning (cognitive deficit) and in adaptive behavior as expressed in conceptual, social and practical adaptive skills. Karyotyping has been the first standard test for the detection of genetic imbalance in patients with ID for more than 35 years. Advances in genetic diagnosis have laid chromosomal microarrays (CMA) as a new standard and first first-line test for diagnosis of patients with ID, as well as other conditions, such as autism spectrum disorders or multiple congenital anomalies. Case Presentation The present case was initially studied due to unexplained cognitive deficit. Physical examination at the age of 18 years revealed cleft palate, lower lip pits and hypodontia, accompanied with other dysmorphic features and absence of speech. Brain MRI uncovered significantly reduced overall volume of gray matter and cortical gyrification. Banding cytogenetics revealed an indistinct intrachromosomal rearrangement in the long arm of one chromosome 1, and subsequent microarray analyses identified a 5.56 Mb deletion in 1q32.1-1q32.3, encompassing 52 genes; included were the entire IRF6 gene (whose mutations/deletions underlay VWS) and SRGAP2, a gene with an important role in neuronal migration during development of cerebral cortex. Besides, a duplication in 3q26.32 (1.9 Mb in size) comprising TBL1XR1 gene was identified. Multicolor banding for chromosome 1 and molecular cytogenetics applying a battery of locus-specific probes covering 1q32.1 to 1q44 characterized a four breakpoint-insertional-rearrangement-event, resulting in 1q32.1-1q32.3 deletion. Conclusions Considering that the human-specific three-fold segmental duplication of SRGAP2 gene evolutionary corresponds to the beginning of neocortical expansion, we hypothesize that aberrations in SRGAP2 are strong candidates underlying specific brain abnormalities, namely reduced volume of grey matter and reduced gyrification. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0221-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martina Rincic
- Croatian Institute for Brain Research, School of Medicine University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Milan Rados
- Croatian Institute for Brain Research, School of Medicine University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Zeljka Krsnik
- Croatian Institute for Brain Research, School of Medicine University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Kristina Gotovac
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, and University Hospital Center Zagreb, Šalata 2, 10 000 Zagreb, Croatia
| | - Fran Borovecki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, and University Hospital Center Zagreb, Šalata 2, 10 000 Zagreb, Croatia ; Department of Neurology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, D-07743 Jena, Germany
| | - Lukrecija Brecevic
- Croatian Institute for Brain Research, School of Medicine University of Zagreb, Salata 12, 10000 Zagreb, Croatia
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Mohamad Shah NS, Salahshourifar I, Sulong S, Wan Sulaiman WA, Halim AS. Discovery of candidate genes for nonsyndromic cleft lip palate through genome-wide linkage analysis of large extended families in the Malay population. BMC Genet 2016; 17:39. [PMID: 26868259 PMCID: PMC4751652 DOI: 10.1186/s12863-016-0345-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts are one of the most common birth defects worldwide. It occurs as a result of genetic or environmental factors. This study investigates the genetic contribution to nonsyndromic cleft lip and/or palate through the analysis of family pedigrees. Candidate genes associated with the condition were identified from large extended families from the Malay population. RESULTS A significant nonparametric linkage (NPL) score was detected in family 100. Other suggestive NPL and logarithm of the odds (LOD) scores were attained from families 50, 58, 99 and 100 under autosomal recessive mode. Heterogeneity LOD (HLOD) score ≥ 1 was determined for all families, confirming genetic heterogeneity of the population and indicating that a proportion of families might be linked to each other. Several candidate genes in linkage intervals were determined; LPHN2 at 1p31, SATB2 at 2q33.1-q35, PVRL3 at 3q13.3, COL21A1 at 6p12.1, FOXP2 at 7q22.3-q33, FOXG1 and HECTD1 at 14q12 and TOX3 at 16q12.1. CONCLUSIONS We have identified several novel and known candidate genes for nonsyndromic cleft lip and/or palate through genome-wide linkage analysis. Further analysis of the involvement of these genes in the condition will shed light on the disease mechanism. Comprehensive genetic testing of the candidate genes is warranted.
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Affiliation(s)
| | - Iman Salahshourifar
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Isfahan, Iran.
| | - Sarina Sulong
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Ahmad Sukari Halim
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia.
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Wang H, Qiu T, Shi J, Liang J, Wang Y, Quan L, Zhang Y, Zhang Q, Tao K. Gene expression profiling analysis contributes to understanding the association between non-syndromic cleft lip and palate, and cancer. Mol Med Rep 2016; 13:2110-6. [PMID: 26795696 PMCID: PMC4768957 DOI: 10.3892/mmr.2016.4802] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 12/18/2015] [Indexed: 12/30/2022] Open
Abstract
The present study aimed to investigate the molecular mechanisms underlying non-syndromic cleft lip, with or without cleft palate (NSCL/P), and the association between this disease and cancer. The GSE42589 data set was downloaded from the Gene Expression Omnibus database, and contained seven dental pulp stem cell samples from children with NSCL/P in the exfoliation period, and six controls. Differentially expressed genes (DEGs) were screened using the RankProd method, and their potential functions were revealed by pathway enrichment analysis and construction of a pathway interaction network. Subsequently, cancer genes were obtained from six cancer databases, and the cancer-associated protein-protein interaction network for the DEGs was visualized using Cytoscape. In total, 452 upregulated and 1,288 downregulated DEGs were screened. The upregulated DEGs were significantly enriched in the arachidonic acid metabolism pathway, including PTGDS, CYP4F2 and PLA2G16; and transforming growth factor (TGF)-β signaling pathway, including SMAD3 and TGFB2. The downregulated DEGs were distinctly involved in the pathways of DNA replication, including MCM2 and POLA1; cell cycle, including CDK1 and STAG1; and viral carcinogenesis, including PIK3CA and HIST1H2BF. Furthermore, the pathways of cell cycle and viral carcinogenesis, with higher degrees of interaction were found to interact with other pathways, including DNA replication, transcriptional misregulation in cancer, and the TGF-β signaling pathway. Additionally, TP53, CDK1, SMAD3, PIK3R1 and CASP3, with higher degrees, interacted with the cancer genes. In conclusion, the DEGs for NSCL/P were implicated predominantly in the TGF-β signaling pathway, the cell cycle and in viral carcinogenesis. The TP53, CDK1, SMAD3, PIK3R1 and CASP3 genes were found to be associated, not only with NSCL/P, but also with cancer. These results may contribute to a better understanding of the molecular mechanisms of NSCL/P.
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Affiliation(s)
- Hongyi Wang
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Tao Qiu
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Jie Shi
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Jiulong Liang
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Yang Wang
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Liangliang Quan
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Yu Zhang
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Qian Zhang
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
| | - Kai Tao
- Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, Shenyang, Liaoning 110016, P.R. China
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Arias Urueña L, Briceño Balcazar I, Martinez Lozano J, Collins A, Uricoechea Patiño DA. Clinical Aspects associated with Syndromic forms of Orofacial Clefts in a Colombian population. Colomb Med (Cali) 2015; 46:162-7. [PMID: 26848196 PMCID: PMC4732505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
OBJECTIVES To present descriptive epidemiology of Orofacial Clefts and to determine the association of syndromic forms with antenatal high-risk conditions, preterm birth, and comorbidities among nested-series of cases. METHODS A study of nested-series of cases was conducted. Frequencies of cleft type, associated congenital anomalies, syndromic, non-syndromic and multiple malformation forms, and distribution of Orofacial Clefts according to sex and affected-side were determined. Odds ratios were calculated as measures of association between syndromic forms and antenatal high-risk conditions, preterm birth and comorbidities. A total of three hundred and eleven patients with Orofacial Clefts were assessed in a 12-month period. RESULTS The most frequent type of Orofacial Clefts was cleft lip and palate, this type of cleft was more frequent in males, whereas cleft palate occurred more often in females. The most common cases occurred as non-syndromic forms. Aarskog-Scott syndrome showed the highest frequency amongst syndromic forms. Hypertensive disorders in pregnancy, developmental dysplasia of the hip, central nervous diseases and respiratory failure showed significant statistical associations (p <0.05) with syndromic forms. CONCLUSIONS These data provide an epidemiological reference of Orofacial Clefts in Colombia. Novel associations between syndromic forms and clinical variables are determined. In order to investigate causality relationships between these variables further studies must be carried out.
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Affiliation(s)
| | - Ignacio Briceño Balcazar
- Medical School. Universidad de La Sabana, Bogota, Colombia, Pontificia Universidad Javeriana. Bogota, Colombia
| | | | - Andrew Collins
- Genetic Epidemiology and Bioinformatics. University of Southampton. Southampton, UK
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27
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Twigg SRF, Wilkie AOM. New insights into craniofacial malformations. Hum Mol Genet 2015; 24:R50-9. [PMID: 26085576 PMCID: PMC4571997 DOI: 10.1093/hmg/ddv228] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/15/2015] [Indexed: 12/13/2022] Open
Abstract
Development of the human skull and face is a highly orchestrated and complex three-dimensional morphogenetic process, involving hundreds of genes controlling the coordinated patterning, proliferation and differentiation of tissues having multiple embryological origins. Craniofacial malformations that occur because of abnormal development (including cleft lip and/or palate, craniosynostosis and facial dysostoses), comprise over one-third of all congenital birth defects. High-throughput sequencing has recently led to the identification of many new causative disease genes and functional studies have clarified their mechanisms of action. We present recent findings in craniofacial genetics and discuss how this information together with developmental studies in animal models is helping to increase understanding of normal craniofacial development.
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Affiliation(s)
- Stephen R F Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
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28
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Westland R, Verbitsky M, Vukojevic K, Perry BJ, Fasel DA, Zwijnenburg PJG, Bökenkamp A, Gille JJP, Saraga-Babic M, Ghiggeri GM, D'Agati VD, Schreuder MF, Gharavi AG, van Wijk JAE, Sanna-Cherchi S. Copy number variation analysis identifies novel CAKUT candidate genes in children with a solitary functioning kidney. Kidney Int 2015; 88:1402-1410. [PMID: 26352300 PMCID: PMC4834924 DOI: 10.1038/ki.2015.239] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 05/28/2015] [Accepted: 06/12/2015] [Indexed: 12/29/2022]
Abstract
Copy number variations associate with different developmental phenotypes and represent a major cause of congenital anomalies of the kidney and urinary tract (CAKUT). Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult. Here we studied the role of rare copy number variations in 80 patients from the KIMONO-study cohort for which pathogenic mutations in three genes commonly implicated in CAKUT were excluded. In total, 13 known or novel genomic imbalances in 11 of 80 patients were absent or extremely rare in 23,362 population controls. To identify the most likely genetic drivers for the CAKUT phenotype underlying these rare copy number variations, we used a systematic in silico approach based on frequency in a large dataset of controls, annotation with publicly available databases for developmental diseases, tolerance and haploinsufficiency scores, and gene expression profile in the developing kidney and urinary tract. Five novel candidate genes for CAKUT were identified that showed specific expression in the human and mouse developing urinary tract. Among these genes, DLG1 and KIF12 are likely novel susceptibility genes for CAKUT in humans. Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes. Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.
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Affiliation(s)
- Rik Westland
- Division of Nephrology, Columbia University, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Miguel Verbitsky
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Katarina Vukojevic
- Division of Nephrology, Columbia University, New York, New York, USA.,Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split, Croatia
| | - Brittany J Perry
- Division of Nephrology, Columbia University, New York, New York, USA
| | - David A Fasel
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Arend Bökenkamp
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Johan J P Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Mirna Saraga-Babic
- Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split, Croatia
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Vivette D D'Agati
- Department of Pathology, Columbia University, New York, New York, USA
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
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Mehrotra D. Genomic expression in non syndromic cleft lip and palate patients: A review. J Oral Biol Craniofac Res 2015; 5:86-91. [PMID: 26258020 DOI: 10.1016/j.jobcr.2015.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022] Open
Abstract
Cleft lip and palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications, affecting one in seven hundred live births. Genetic causes of non syndromic cleft lip and/or palate (NSCLP) include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. Development of the orofacial clefts in an individual will depend on the interaction of several moderately effecting genes with environmental factors. Several candidate genes have been genotyped in different population types, using case parent trio or case control design; also genes have been sequenced and SNPs have been reported. Quantitative and molecular analysis have shown linkage and association studies to be more relevant. Recent literature search shows genome wide association studies using microarray. The aim of this paper was to review the approaches to identify genes associated with NSCLP and to analyze their differential expressions. Although no major gene has been confirmed, a lot of research is ongoing to provide an understanding of the pathophysiology of the orofacial clefts.
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Affiliation(s)
- D Mehrotra
- Professor, Department of Oral & Maxillofacial Surgery, King George Medical University, Lucknow, India
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Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I. A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts. ACTA ACUST UNITED AC 2015; 103:276-83. [PMID: 25776870 DOI: 10.1002/bdra.23362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND DNA copy number variants play an important part in the development of common birth defects such as oral clefts. Individual patients with multiple birth defects (including oral clefts) have been shown to carry small and large chromosomal deletions. METHODS We investigated the role of polymorphic copy number deletions by comparing transmission rates of deletions from parents to offspring in case-parent trios of European ancestry ascertained through a cleft proband with trios ascertained through a normal offspring. DNA copy numbers in trios were called using the joint hidden Markov model in the freely available PennCNV software. All statistical analyses were performed using Bioconductor tools in the open source environment R. RESULTS We identified a 67 kb region in the gene MGAM on chromosome 7q34, and a 206 kb region overlapping genes ADAM3A and ADAM5 on chromosome 8p11, where deletions are more frequently transmitted to cleft offspring than control offspring. CONCLUSIONS These genes or nearby regulatory elements may be involved in the etiology of oral clefts.
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Affiliation(s)
- Samuel G Younkin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore
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31
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Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS, Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FWB, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet 2015; 96:397-411. [PMID: 25704602 PMCID: PMC4375420 DOI: 10.1016/j.ajhg.2015.01.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/09/2015] [Indexed: 11/21/2022] Open
Abstract
Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants are unknown. To address this, we selected 13 regions from GWASs and other studies, performed targeted sequencing in 1,409 Asian and European trios, and carried out a series of statistical and functional analyses. Within a cluster of strongly associated common variants near NOG, we found that one, rs227727, disrupts enhancer activity. We furthermore identified significant clusters of non-coding rare variants near NTN1 and NOG and found several rare coding variants likely to affect protein function, including four nonsense variants in ARHGAP29. We confirmed 48 de novo mutations and, based on best biological evidence available, chose two of these for functional assays. One mutation in PAX7 disrupted the DNA binding of the encoded transcription factor in an in vitro assay. The second, a non-coding mutation, disrupted the activity of a neural crest enhancer downstream of FGFR2 both in vitro and in vivo. This targeted sequencing study provides strong functional evidence implicating several specific variants as primary contributory risk alleles for nonsyndromic clefting in humans.
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Affiliation(s)
- Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Huan Liu
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA; State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 430072 Wuhan, China
| | - Karyn Meltz Steinberg
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Qunyuan Zhang
- Department of Statistical Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jenna C Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hang Wang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - David E Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Youssef A Kousa
- Department of Biochemistry and Molecular Biology, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ali Naji
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ferdouse Begum
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tamara Busch
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Rigdon
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alan F Scott
- Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, 5230 Odense, Denmark
| | - Andrew E Czeizel
- Foundation for the Community Control of Hereditary Diseases, Budapest 1148, Hungary
| | - Frederic W-B Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO 80045, USA
| | - Brian C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew C Lidral
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - George M Weinstock
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06117, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Emy Dorfman L, Leite JCL, Giugliani R, Riegel M. Microarray-based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances. J Pediatr (Rio J) 2015; 91:59-67. [PMID: 25203518 DOI: 10.1016/j.jped.2014.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/24/2014] [Accepted: 04/28/2014] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array-CGH) in DNA samples of neonates with congenital anomalies of unknown cause from a birth defects monitoring program at a public maternity hospital. METHODS A blind genomic analysis was performed retrospectively in 35 stored DNA samples of neonates born between July of 2011 and December of 2012. All potential DNA copy number variations detected (CNVs) were matched with those reported in public genomic databases, and their clinical significance was evaluated. RESULTS Out of a total of 35 samples tested, 13 genomic imbalances were detected in 12/35 cases (34.3%). In 4/35 cases (11.4%), chromosomal imbalances could be defined as pathogenic; in 5/35 (14.3%) cases, DNA CNVs of uncertain clinical significance were identified; and in 4/35 cases (11.4%), normal variants were detected. Among the four cases with results considered causally related to the clinical findings, two of the four (50%) showed causative alterations already associated with well-defined microdeletion syndromes. In two of the four samples (50%), the chromosomal imbalances found, although predicted as pathogenic, had not been previously associated with recognized clinical entities. CONCLUSIONS Array-CGH analysis allowed for a higher rate of detection of chromosomal anomalies, and this determination is especially valuable in neonates with congenital anomalies of unknown etiology, or in cases in which karyotype results cannot be obtained. Moreover, although the interpretation of the results must be refined, this method is a robust and precise tool that can be used in the first-line investigation of congenital anomalies, and should be considered for prospective/retrospective analyses of DNA samples by birth defect monitoring programs.
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Affiliation(s)
- Luiza Emy Dorfman
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Roberto Giugliani
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Mariluce Riegel
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil.
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Emy Dorfman L, Leite JCL, Giugliani R, Riegel M. Microarray‐based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2015. [DOI: 10.1016/j.jpedp.2014.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Investigation of genetic factors underlying typical orofacial clefts: mutational screening and copy number variation. J Hum Genet 2014; 60:17-25. [PMID: 25391604 DOI: 10.1038/jhg.2014.96] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/01/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022]
Abstract
Typical orofacial clefts (OFCs) comprise cleft lip, cleft palate and cleft lip and palate. The complex etiology has been postulated to involve chromosome rearrangements, gene mutations and environmental factors. A group of genes including IRF6, FOXE1, GLI2, MSX2, SKI, SATB2, MSX1 and FGF has been implicated in the etiology of OFCs. Recently, the role of the copy number variations (CNVs) has been studied in genetic defects and diseases. CNVs act by modifying gene expression, disrupting gene sequence or altering gene dosage. The aims of this study were to screen the above-mentioned genes and to investigate CNVs in patients with OFCs. The sample was composed of 23 unrelated individuals who were grouped according to phenotype (associated with other anomalies or isolated) and familial recurrence. New sequence variants in GLI2, MSX1 and FGF8 were detected in patients, but not in their parents, as well as in 200 control chromosomes, indicating that these were rare variants. CNV screening identified new genes that can influence OFC pathogenesis, particularly highlighting TCEB3 and KIF7, that could be further analyzed. The findings of the present study suggest that the mechanism underlying CNV associated with sequence variants may play a role in the etiology of OFC.
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Role of angiogenesis-related genes in cleft lip/palate: review of the literature. Int J Pediatr Otorhinolaryngol 2014; 78:1579-85. [PMID: 25176321 DOI: 10.1016/j.ijporl.2014.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Cleft lip and cleft palate (CLP) are the most common congenital craniofacial anomalies. They have a multifactorial etiology and result from an incomplete fusion of the facial buds. Two main mechanisms, acting alone or interacting with each other, were evidenced in this fusion defect responsible for CLP: defective tissue development and/or defective apoptosis in normal or defective tissues. The objective of this work was to study the implication and role of angiogenesis-related genes in the etiology of CL/P. METHODS Our methodological approach included a systematic and thorough analysis of the genes involved in CL/P (syndromic and non-syndromic forms) including previously identified genes but also genes that could potentially be angiogenesis-related (OMIM, Pub Med).We studied the interactions of these different genes and their relationships with potential environmental factors. RESULTS TGFβ, FGA, PDGFc, PDGFRa, FGF, FGFR1, FGFR2 growth factors as well as MMP and TIMP2 proteolytic enzymes are involved in the genesis of CLP (P>L). Furthermore, 18 genes involved in CLP also interact with angiogenesis-related genes. DISCUSSION Even if the main angiogenesis-related genes involved in CLP formation are genes participating in several biological activities and their implication might not be always related to angiogenesis defects, they nevertheless remain an undeniably important research pathway. Furthermore, their interactions with environmental factors make them good candidates in the field of CLP prevention.
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Peltekova IT, Hurteau-Millar J, Armour CM. Novel interstitial deletion of 10q24.3-25.1 associated with multiple congenital anomalies including lobar holoprosencephaly, cleft lip and palate, and hypoplastic kidneys. Am J Med Genet A 2014; 164A:3132-6. [DOI: 10.1002/ajmg.a.36740] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 07/31/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Iskra T. Peltekova
- Department of Developmental Pediatrics; Montréal Children's Hospital; Montreal Québec
| | - Julie Hurteau-Millar
- Division of Radiology; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - Christine M. Armour
- Division of Clinical Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
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Tickotsky N, Moskovitz M. Renal agenesis in Kallmann syndrome: a network approach. Ann Hum Genet 2014; 78:424-33. [PMID: 25227403 DOI: 10.1111/ahg.12079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/19/2014] [Indexed: 01/18/2023]
Abstract
Kallmann syndrome (KS) is defined by the combination of isolated hypogonadotrophic hypogonadism (IHH) and anosmia, with renal agenesis occurring in 30% of KS cases with KAL1 gene mutations. Unlike other KS-related disorders, renal agenesis cannot be directly associated with mutations in the KAL1 gene. We hypothesized that protein interaction networks may suggest a link between genes currently known to be associated with KS on the one hand and those associated with renal agenesis on the other hand. We created a STRING protein interaction network from KS-related genes and renal-agenesis-associated genes and analyzed it with Cytoscape 3.0.1 network software. The STRING protein interaction network provided a conceptual framework for current knowledge on the subject of renal morphogenesis in Kallmann syndrome. In addition, STRING and Cytoscape 3.0.1 software identified new potential KS renal-aplasia-associated genes (PAX2, BMP4, and SOX10). The use of protein-protein interaction networks and network analysis tools provided interesting insights and possible directions for future studies on the subject of renal aplasia in Kallmann syndrome.
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Affiliation(s)
| | - Moti Moskovitz
- Department of Pediatric Dentistry, Hebrew University, Hadassah School of Dental Medicine, Jerusalem, Israel
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Osoegawa K, Schultz K, Yun K, Mohammed N, Shaw GM, Lammer EJ. Haploinsufficiency of insulin gene enhancer protein 1 (ISL1) is associated with d-transposition of the great arteries. Mol Genet Genomic Med 2014; 2:341-51. [PMID: 25077177 PMCID: PMC4113275 DOI: 10.1002/mgg3.75] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/06/2014] [Accepted: 02/11/2014] [Indexed: 01/13/2023] Open
Abstract
Congenital heart defects are the most common malformation, and are the foremost causes of mortality in the first year of life. Among congenital heart defects, conotruncal defects represent about 20% and are severe malformations with significant morbidity. Insulin gene enhancer protein 1 (ISL1) has been considered a candidate gene for conotruncal heart defects based on its embryonic expression pattern and heart defects induced in Isl1 knockout mice. Nevertheless no mutation of ISL1 has been reported from any human subject with a heart defect. From a population base of 974,579 births during 1999–2004, we used multiplex ligation-dependent probe amplification to screen for microdeletions/duplications of ISL1 among 389 infants with tetralogy of Fallot or d-transposition of the great arteries (d-TGA). We also sequenced all exons of ISL1. We identified a novel 20-kb microdeletion encompassing the entire coding region of ISL1, but not including either flanking gene, from an infant with d-TGA. We confirmed that the deletion was caused by nonhomologous end joining mechanism. Sequencing of exons of ISL1 did not reveal any subject with a novel nonsynonymous mutation. This is the first report of an ISL1 mutation of a child with a congenital heart defect.
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Affiliation(s)
- Kazutoyo Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland Oakland, 94609, California ; Department of Pathology, Stanford University School of Medicine Palo Alto, California
| | - Kathleen Schultz
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland Oakland, 94609, California
| | - Kenneth Yun
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland Oakland, 94609, California
| | - Nebil Mohammed
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland Oakland, 94609, California
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine Stanford, California
| | - Edward J Lammer
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland Oakland, 94609, California
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Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I. A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk. BMC Genet 2014; 15:24. [PMID: 24528994 PMCID: PMC3929298 DOI: 10.1186/1471-2156-15-24] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 01/31/2014] [Indexed: 01/25/2023] Open
Abstract
Background Copy number variants (CNVs) may play an important part in the development of common birth defects such as oral clefts, and individual patients with multiple birth defects (including clefts) have been shown to carry small and large chromosomal deletions. In this paper we investigate de novo deletions defined as DNA segments missing in an oral cleft proband but present in both unaffected parents. We compare de novo deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios. Results We identified a genome-wide significant 62 kilo base (kb) non-coding region on chromosome 7p14.1 where de novo deletions occur more frequently among oral cleft cases than controls. We also observed wider de novo deletions among cleft lip and palate (CLP) cases than seen among cleft palate (CP) and cleft lip (CL) cases. Conclusions This study presents a region where de novo deletions appear to be involved in the etiology of oral clefts, although the underlying biological mechanisms are still unknown. Larger de novo deletions are more likely to interfere with normal craniofacial development and may result in more severe clefts. Study protocol and sample DNA source can severely affect estimates of de novo deletion frequencies. Follow-up studies are needed to further validate these findings and to potentially identify additional structural variants underlying oral clefts.
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Affiliation(s)
- Samuel G Younkin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA.
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Fakhouri WD, Rahimov F, Attanasio C, Kouwenhoven EN, Ferreira De Lima RL, Felix TM, Nitschke L, Huver D, Barrons J, Kousa YA, Leslie E, Pennacchio LA, Van Bokhoven H, Visel A, Zhou H, Murray JC, Schutte BC. An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects. Hum Mol Genet 2014; 23:2711-20. [PMID: 24442519 DOI: 10.1093/hmg/ddt664] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DNA variation in Interferon Regulatory Factor 6 (IRF6) causes Van der Woude syndrome (VWS), the most common syndromic form of cleft lip and palate (CLP). However, an etiologic variant in IRF6 has been found in only 70% of VWS families. To test whether DNA variants in regulatory elements cause VWS, we sequenced three conserved elements near IRF6 in 70 VWS families that lack an etiologic mutation within IRF6 exons. A rare mutation (350dupA) was found in a conserved IRF6 enhancer element (MCS9.7) in a Brazilian family. The 350dupA mutation abrogated the binding of p63 and E47 transcription factors to cis-overlapping motifs, and significantly disrupted enhancer activity in human cell cultures. Moreover, using a transgenic assay in mice, the 350dupA mutation disrupted the activation of MCS9.7 enhancer element and led to failure of lacZ expression in all head and neck pharyngeal arches. Interestingly, disruption of the p63 Motif1 and/or E47 binding sites by nucleotide substitution did not fully recapitulate the effect of the 350dupA mutation. Rather, we recognized that the 350dupA created a CAAAGT motif, a binding site for Lef1 protein. We showed that Lef1 binds to the mutated site and that overexpression of Lef1/β-Catenin chimeric protein repressed MCS9.7-350dupA enhancer activity. In conclusion, our data strongly suggest that 350dupA variant is an etiologic mutation in VWS patients and disrupts enhancer activity by a loss- and gain-of-function mechanism, and thus support the rationale for additional screening for regulatory mutations in patients with CLP.
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Abstract
Orofacial clefts comprise a range of congenital deformities and are the most common head and neck congenital malformation. Clefting has significant psychological and socio- economic effects on patient quality of life and require a multidisciplinary team approach for management. The complex interplay between genetic and environmental factors play a significant role in the incidence and cause of clefting. In this review, the embryology, classification, epidemiology, and etiology of cleft lip are discussed. The primary goals of surgical repair are to restore normal function, speech development, and facial esthetics. Different techniques are employed based on surgeon expertise and the unique patient presentations. Pre-surgical orthopedics are frequently employed prior to definitive repair to improve outcomes. Long term follow up and quality of life studies are discussed.
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Affiliation(s)
- Mahdi A Shkoukani
- Department of Otolaryngology, Wayne State University School of Medicine , Detroit, MI , USA
| | - Michael Chen
- Department of Otolaryngology, Wayne State University School of Medicine , Detroit, MI , USA
| | - Angela Vong
- Department of Otolaryngology, Wayne State University School of Medicine , Detroit, MI , USA
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Dauber A, Golzio C, Guenot C, Jodelka FM, Kibaek M, Kjaergaard S, Leheup B, Martinet D, Nowaczyk MJM, Rosenfeld JA, Zeesman S, Zunich J, Beckmann JS, Hirschhorn JN, Hastings ML, Jacquemont S, Katsanis N. SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant. Am J Hum Genet 2013; 93:798-811. [PMID: 24140112 DOI: 10.1016/j.ajhg.2013.09.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/10/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Copy-number variants (CNVs) represent a significant interpretative challenge, given that each CNV typically affects the dosage of multiple genes. Here we report on five individuals with coloboma, microcephaly, developmental delay, short stature, and craniofacial, cardiac, and renal defects who harbor overlapping microdeletions on 8q24.3. Fine mapping localized a commonly deleted 78 kb region that contains three genes: SCRIB, NRBP2, and PUF60. In vivo dissection of the CNV showed discrete contributions of the planar cell polarity effector SCRIB and the splicing factor PUF60 to the syndromic phenotype, and the combinatorial suppression of both genes exacerbated some, but not all, phenotypic components. Consistent with these findings, we identified an individual with microcephaly, short stature, intellectual disability, and heart defects with a de novo c.505C>T variant leading to a p.His169Tyr change in PUF60. Functional testing of this allele in vivo and in vitro showed that the mutation perturbs the relative dosage of two PUF60 isoforms and, subsequently, the splicing efficiency of downstream PUF60 targets. These data inform the functions of two genes not associated previously with human genetic disease and demonstrate how CNVs can exhibit complex genetic architecture, with the phenotype being the amalgam of both discrete dosage dysfunction of single transcripts and also of binary genetic interactions.
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Affiliation(s)
- Andrew Dauber
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02115, USA
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Khandelwal KD, van Bokhoven H, Roscioli T, Carels CE, Zhou H. Genomic approaches for studying craniofacial disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:218-31. [DOI: 10.1002/ajmg.c.31379] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Osoegawa K, Iovannisci DM, Lin B, Parodi C, Schultz K, Shaw GM, Lammer EJ. Identification of novel candidate gene loci and increased sex chromosome aneuploidy among infants with conotruncal heart defects. Am J Med Genet A 2013; 164A:397-406. [PMID: 24127225 DOI: 10.1002/ajmg.a.36291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 09/10/2013] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHDs) are common malformations, affecting four to eight per 1,000 total births. Conotruncal defects are an important pathogenetic subset of CHDs, comprising nearly 20% of the total. Although both environmental and genetic factors are known to contribute to the occurrence of conotruncal defects, the causes remain unknown for most. To identify novel candidate genes/loci, we used array comparative genomic hybridization to detect chromosomal microdeletions/duplications. From a population base of 974,579 total births born during 1999-2004, we screened 389 California infants born with tetralogy of Fallot or d-transposition of the great arteries. We found that 1.7% (5/288) of males with a conotruncal defect had sex chromosome aneuploidy, a sevenfold increased frequency (relative risk = 7.0; 95% confidence interval 2.9-16.9). We identified eight chromosomal microdeletions/duplications for conotruncal defects. From these duplications and deletions, we found five high priority candidate genes (GATA4, CRKL, BMPR1A, SNAI2, and ZFHX4). This is the initial report that sex chromosome aneuploidy is associated with conotruncal defects among boys. These chromosomal microduplications/deletions provide evidence that GATA4, SNAI2, and CRKL are highly dosage sensitive genes involved in outflow tract development. Genome wide screening for copy number variation can be productive for identifying novel genes/loci contributing to non-syndromic common malformations.
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Affiliation(s)
- Kazutoyo Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland, Oakland, California
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Leslie EJ, Marazita ML. Genetics of cleft lip and cleft palate. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:246-58. [PMID: 24124047 DOI: 10.1002/ajmg.c.31381] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Orofacial clefts are common birth defects and can occur as isolated, nonsyndromic events or as part of Mendelian syndromes. There is substantial phenotypic diversity in individuals with these birth defects and their family members: from subclinical phenotypes to associated syndromic features that is mirrored by the many genes that contribute to the etiology of these disorders. Identification of these genes and loci has been the result of decades of research using multiple genetic approaches. Significant progress has been made recently due to advances in sequencing and genotyping technologies, primarily through the use of whole exome sequencing and genome-wide association studies. Future progress will hinge on identifying functional variants, investigation of pathway and other interactions, and inclusion of phenotypic and ethnic diversity in studies.
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De novo 2.3 Mb microdeletion of 1q32.2 involving the Van der Woude Syndrome locus. Mol Cytogenet 2013; 6:31. [PMID: 23915469 PMCID: PMC3751720 DOI: 10.1186/1755-8166-6-31] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/04/2013] [Indexed: 11/29/2022] Open
Abstract
Background Van der Woude syndrome is the most common among syndromes which include cleft lip and/or cleft palate as one of the presentations. It is usually caused by mutations in the interferon regulatory factor 6 (IRF6) gene. Case presentation We previously reported on a patient with suspected deletion of the IRF6 gene. Using the Affymetrix Human SNP 6.0 Array, the interstitial deletion has been confirmed and found to be approximately 2.327–2.334 Mb within the 1q32.2 region. Although several known genes were deleted, the patient has no other phenotype apart from the orofacial presentations typical of VWS. The same deletion was not present in either parent and his two siblings were also phenotypically normal. Conclusions Other than IRF6, the genes which are deleted in this patient appear to be insensitive to copy number and haploinsufficiency. We compared the deletion in this patient with another case which was also mapped by high resolution array but had additional phenotypic features.
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Golzio C, Katsanis N. Genetic architecture of reciprocal CNVs. Curr Opin Genet Dev 2013; 23:240-8. [PMID: 23747035 DOI: 10.1016/j.gde.2013.04.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/22/2013] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
Abstract
Copy number variants (CNVs) represent a frequent type of lesion in human genetic disorders that typically affects numerous genes simultaneously. This has raised the challenge of understanding which genes within a CNV drive clinical phenotypes. Although CNVs can arise by multiple mechanisms, a subset is driven by local genomic architecture permissive to recombination events that can lead to both deletions and duplications. Phenotypic analyses of patients with such reciprocal CNVs have revealed instances in which the phenotype is either identical or mirrored; strikingly, molecular studies have shown that such phenotypes are often driven by reciprocal dosage defects of the same transcript. Here we explore how these observations can help the dissection of CNVs and inform the genetic architecture of CNV-induced disorders.
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Affiliation(s)
- Christelle Golzio
- Center for Human Disease Modeling, Duke University, Durham 27710, USA
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Wu-Chou YH, Lo LJ, Chen KTP, Chang CSF, Chen YR. A combined targeted mutation analysis of IRF6 gene would be useful in the first screening of oral facial clefts. BMC MEDICAL GENETICS 2013; 14:37. [PMID: 23510002 PMCID: PMC3606492 DOI: 10.1186/1471-2350-14-37] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/13/2013] [Indexed: 01/30/2023]
Abstract
Background Interferon Regulatory Factor 6 (IRF6) is a member of the IRF family of transcription factors. It has been suggested to be an important contributor to orofacial development since mutations of the IRF6 gene has been found in Van der Woude (VWS) and popliteal pterygium syndromes (PPS), two disorders that can present with isolated cleft lip and palate. The association between IRF6 gene and cleft lip and palate has also been independently replicated in many populations. Methods We screened a total of 155 Taiwanese patients with cleft lip with or without cleft palate (CL/P); 31 syndromic (including 19 VWS families), 44 non-syndromic families with at least two affected members, and 80 non-syndromic patients through a combined targeted, polymerase chain reaction (PCR)-based mutation analysis for the entire coding regions of IRF6 gene. Results We found 11 mutations in 57.89% (11/19) of the VWS patients and no IRF6 mutation in 44 of the non-syndromic multiplex families and 80 non-syndromic oral cleft patients. In this IRF6 gene screening, five of these mutations (c.290 A>G, p.Tyr97Cys; c.360-375 16 bp deletion, p.Gln120HisfsX24; c.411_412 insA, p.Glu136fsX3; c.871 A>C, p.Thr291Pro; c.969 G>A, and p.Trp323X) have not been reported in the literature previously. Exon deletion was not detected in this series of IRF6 gene screening. Conclusions Our results confirm the crucial role of IRF6 in the VWS patients and further work is needed to explore for its function in the non-syndromic oral cleft with vary clinical features.
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Affiliation(s)
- Yah-Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, No. 5, Fushing Street, Kweishan, Taoyuan, Taiwan.
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Widdershoven JC, Bowser M, Sheridan MB, McDonald-McGinn DM, Zackai EH, Solot CB, Kirschner RE, Beemer FA, Morrow BE, Devoto M, Emanuel BS. A candidate gene approach to identify modifiers of the palatal phenotype in 22q11.2 deletion syndrome patients. Int J Pediatr Otorhinolaryngol 2013; 77:123-7. [PMID: 23121717 PMCID: PMC4098838 DOI: 10.1016/j.ijporl.2012.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 10/06/2012] [Accepted: 10/09/2012] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Palatal anomalies are one of the identifying features of 22q11.2 deletion syndrome (22q11.2DS) affecting about one third of patients. To identify genetic variants that increase the risk of cleft or palatal anomalies in 22q11.2DS patients, we performed a candidate gene association study in 101 patients with 22q11.2DS genotyped with the Affymetrix genome-wide human SNP array 6.0. METHODS Patients from Children's Hospital of Philadelphia, USA and Wilhelmina Children's Hospital Utrecht, The Netherlands were stratified based on palatal phenotype (overt cleft, submucosal cleft, bifid uvula). SNPs in 21 candidate genes for cleft palate were analyzed for genotype-phenotype association. In addition, TBX1 sequencing was carried out. Quality control and association analyses were conducted using the software package PLINK. RESULTS Genotype and phenotype data of 101 unrelated patients (63 non-cleft subjects (62.4%), 38 cleft subjects (37.6%)) were analyzed. A Total of 39 SNPs on 10 genes demonstrated a p-value ≤0.05 prior to correction. The most significant SNPs were found on FGF10. However none of the SNPs remained significant after correcting for multiple testing. CONCLUSIONS Although these results are promising, analysis of additional samples will be required to confirm that variants in these regions influence risk for cleft palate or palatal anomalies in 22q11.2DS patients.
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Affiliation(s)
- Josine C.C. Widdershoven
- Department of Otolaryngology – Head and Neck Surgery, Maastricht University Medical Center, The Netherlands,Corresponding author at: Postbox 5800, 6202 AZ Maastricht, The Netherlands, Tel.: +31 433875400
| | - Mark Bowser
- Department of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, USA
| | - Molly B. Sheridan
- Department of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, USA
| | - Donna M. McDonald-McGinn
- Department of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, USA,University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Elaine H. Zackai
- Department of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, USA,University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Cynthia B. Solot
- Center for Childhood Communication, The Children's Seashore House of The Children's Hospital of Philadelphia, USA
| | | | - Frits A. Beemer
- Department of Medical Genetics, University Medical Center, Utrecht, The Netherlands
| | - Bernice E. Morrow
- Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, USA
| | - Marcella Devoto
- Department of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, USA
| | - Beverly S. Emanuel
- Department of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, USA,University of Pennsylvania School of Medicine, Philadelphia, USA
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Submicroscopic chromosomal copy number variations identified in children with hypoplastic left heart syndrome. Pediatr Cardiol 2012; 33:757-63. [PMID: 22349727 DOI: 10.1007/s00246-012-0208-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 12/13/2011] [Indexed: 01/03/2023]
Abstract
Hypoplastic left heart syndrome (HLHS), one of the most severe types of congenital heart disease (CHD), results in significant morbidity and mortality despite surgical palliation. The etiology of HLHS is unknown, but evidence supports genetic contributors. The authors hypothesized that submicroscopic chromosomal abnormalities exist in individuals with HLHS and are more frequent in those with additional birth defects. This study sought to determine the incidence and genomic location of submicroscopic chromosomal abnormalities in HLHS and potentially to identify novel genetic loci that may contribute to the disease. For this study, 43 children with HLHS were recruited and screened together with a control population of 16 subjects using array comparative genomic hybridization, also called chromosomal microarray, for chromosomal copy number variations (CNVs). A statistically greater number of CNVs were found in the HLHS group than in the control group (p < 0.03). The CNVs were predominantly small autosomal deletions and duplications (≤ 60,000 bp). The frequency of unique CNVs, those not previously reported in public databases, did not differ statistically between the HLHS subjects and the control subjects. No difference in the frequency of CNVs was noted between the patients with HLHS and additional anomalies and those with isolated HLHS. The identified CNVs did not harbor potential candidate genes for HLHS, but one microdeletion was located on chromosome 14q23, a genetic locus linked to left-sided CHD. The study data demonstrate that CNVs, specifically those relatively small in size, are more common in subjects with HLHS, but the frequency of large potentially disease-causing CNVs (>480,000 bp) did not differ between the HLHS and control populations.
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