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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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2
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Slavec L, Geršak K, Eberlinc A, Hovnik T, Lovrečić L, Mlinarič-Raščan I, Karas Kuželički N. A Comprehensive Genetic Analysis of Slovenian Families with Multiple Cases of Orofacial Clefts Reveals Novel Variants in the Genes IRF6, GRHL3, and TBX22. Int J Mol Sci 2023; 24:ijms24054262. [PMID: 36901693 PMCID: PMC10002089 DOI: 10.3390/ijms24054262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Although the aetiology of non-syndromic orofacial clefts (nsOFCs) is usually multifactorial, syndromic OFCs (syOFCs) are often caused by single mutations in known genes. Some syndromes, e.g., Van der Woude syndrome (VWS1; VWS2) and X-linked cleft palate with or without ankyloglossia (CPX), show only minor clinical signs in addition to OFC and are sometimes difficult to differentiate from nsOFCs. We recruited 34 Slovenian multi-case families with apparent nsOFCs (isolated OFCs or OFCs with minor additional facial signs). First, we examined IRF6, GRHL3, and TBX22 by Sanger or whole exome sequencing to identify VWS and CPX families. Next, we examined 72 additional nsOFC genes in the remaining families. Variant validation and co-segregation analysis were performed for each identified variant using Sanger sequencing, real-time quantitative PCR and microarray-based comparative genomic hybridization. We identified six disease-causing variants (three novel) in IRF6, GRHL3, and TBX22 in 21% of families with apparent nsOFCs, suggesting that our sequencing approach is useful for distinguishing syOFCs from nsOFCs. The novel variants, a frameshift variant in exon 7 of IRF6, a splice-altering variant in GRHL3, and a deletion of the coding exons of TBX22, indicate VWS1, VWS2, and CPX, respectively. We also identified five rare variants in nsOFC genes in families without VWS or CPX, but they could not be conclusively linked to nsOFC.
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Affiliation(s)
- Lara Slavec
- Research Unit, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ksenija Geršak
- Research Unit, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Department of Gynaecology and Obstetrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Eberlinc
- Department of Maxillofacial and Oral Surgery, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Tinka Hovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Department of Gynaecology and Obstetrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Irena Mlinarič-Raščan
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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3
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Alvizi L, Brito LA, Kobayashi GS, Bischain B, da Silva CBF, Ramos SLG, Wang J, Passos-Bueno MR. m ir152 hypomethylation as a mechanism for non-syndromic cleft lip and palate. Epigenetics 2022; 17:2278-2295. [PMID: 36047706 PMCID: PMC9665146 DOI: 10.1080/15592294.2022.2115606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/06/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP), the most common human craniofacial malformation, is a complex disorder given its genetic heterogeneity and multifactorial component revealed by genetic, epidemiological, and epigenetic findings. Epigenetic variations associated with NSCLP have been identified; however, functional investigation has been limited. Here, we combined a reanalysis of NSCLP methylome data with genetic analysis and used both in vitro and in vivo approaches to dissect the functional effects of epigenetic changes. We found a region in mir152 that is frequently hypomethylated in NSCLP cohorts (21-26%), leading to mir152 overexpression. mir152 overexpression in human neural crest cells led to downregulation of spliceosomal, ribosomal, and adherens junction genes. In vivo analysis using zebrafish embryos revealed that mir152 upregulation leads to craniofacial cartilage impairment. Also, we suggest that zebrafish embryonic hypoxia leads to mir152 upregulation combined with mir152 hypomethylation and also analogous palatal alterations. We therefore propose that mir152 hypomethylation, potentially induced by hypoxia in early development, is a novel and frequent predisposing factor to NSCLP.
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Affiliation(s)
- Lucas Alvizi
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | - Luciano Abreu Brito
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | | | - Bárbara Bischain
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | | | | | - Jaqueline Wang
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
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4
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Dąbrowska J, Biedziak B, Szponar-Żurowska A, Budner M, Jagodziński PP, Płoski R, Mostowska A. Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing. Mol Genet Genomics 2022; 297:1315-1327. [PMID: 35778651 DOI: 10.1007/s00438-022-01919-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/12/2022] [Indexed: 01/02/2023]
Abstract
For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.
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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, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Margareta Budner
- Eastern Poland Burn Treatment and Reconstructive Center, Leczna, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, 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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5
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Alade A, Awotoye W, Butali A. Genetic and Epigenetic Studies in Nonsyndromic Oral Clefts. Oral Dis 2022; 28:1339-1350. [PMID: 35122708 DOI: 10.1111/odi.14146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The etiology of non-syndromic oral clefts (NSOFC) is complex with genetics, genomics, epigenetics and stochastics factors playing a role. Several approaches have been applied to understand the etiology of non-syndromic oral clefts. These include linkage, candidate gene association studies, genome-wide association studies, whole genome sequencing, copy number variations and epigenetics. In this review we shared these approaches, genes and loci reported in some studies.
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Affiliation(s)
- Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA.,Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
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Machado RA, Martelli-Junior H, Reis SRDA, Küchler EC, Scariot R, das Neves LT, Coletta RD. Identification of Novel Variants in Cleft Palate-Associated Genes in Brazilian Patients With Non-syndromic Cleft Palate Only. Front Cell Dev Biol 2021; 9:638522. [PMID: 34307341 PMCID: PMC8297955 DOI: 10.3389/fcell.2021.638522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 12/17/2022] Open
Abstract
The identification of genetic risk factors for non-syndromic oral clefts is of great importance for better understanding the biological processes related to this heterogeneous and complex group of diseases. Herein we applied whole-exome sequencing to identify potential variants related to non-syndromic cleft palate only (NSCPO) in the multiethnic Brazilian population. Thirty NSCPO samples and 30 sex- and genetic ancestry-matched healthy controls were pooled (3 pools with 10 samples for each group) and subjected to whole-exome sequencing. After filtering, the functional affects, individually and through interactions, of the selected variants and genes were assessed by bioinformatic analyses. As a group, 399 variants in 216 genes related to palatogenesis/cleft palate, corresponding to 6.43%, were exclusively identified in the NSCPO pools. Among those genes are 99 associated with syndromes displaying cleft palate in their clinical spectrum and 92 previously related to cleft lip palate. The most significantly biological processes and pathways overrepresented in the NSCPO-identified genes were associated with the folic acid metabolism, highlighting the interaction between LDL receptor-related protein 6 (LRP6) and 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) that interconnect two large networks. This study yields novel data on characterization of specific variants and complex processes and pathways related to NSCPO, including many variants in genes of the folate/homocysteine pathway, and confirms that variants in genes related to syndromic cleft palate and cleft lip-palate may cause NSCPO.
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Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP), Piracicaba, Brazil.,Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
| | - Hercílio Martelli-Junior
- Stomatology Clinic, School of Dental, State University of Montes Claros, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, School of Dental, UNIFENAS - Universidade José do Rosario Vellano, Alfenas, Brazil
| | | | | | - Rafaela Scariot
- Department of Oral and Maxillofacial Surgery, School of Health Science, Federal University of Paraná, Curitiba, Brazil
| | - Lucimara Teixeira das Neves
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil.,Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo (FOB), Bauru, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP), Piracicaba, Brazil
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7
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Yin S, Wang C, Wei J, Jin L, Liu J, Wang L, Li Z, Yin C, Ren A. Selected essential trace elements in maternal serum and risk for fetal orofacial clefts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136542. [PMID: 31945535 DOI: 10.1016/j.scitotenv.2020.136542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Disturbances in the homeostasis of essential trace elements (ETEs) may interfere with embryonic organogenesis. However, the effect of ETEs on the development of orofacial clefts (OFCs) remains unclear. OBJECTIVES This study examined associations between concentrations of iron (Fe), zinc (Zn), selenium (Se), cuprum (Cu), cobalt (Co), and molybdenum (Mo) in maternal serum and risk for OFCs in offspring. METHODS A total of 130 cases of OFCs and 260 nonmalformed controls were included in this study. Concentrations of Fe, Zn, Se, Cu, Co, and Mo in maternal serum were detected by inductively coupled plasma mass spectrometry. We examined associations between levels of the six ETEs in maternal serum and risk for OFCs for each element separately using multilevel mixed-effects logistic regression and for all elements collectively using Bayesian kernel machine regression (BKMR). RESULTS Higher concentrations of Mo and Co in maternal serum were associated with a decreased risk for OFCs in a dose-dependent manner, with odds ratios and 95% confidence intervals of 0.37 (0.20-0.66) for the second tertile of Mo, 0.28 (0.15-0.54) for the third tertile of Mo, 0.54 (0.29-1.00) for the second tertile of Co, and 0.47 (0.25-0.87) for the third tertile of Co, with the lowest tertile as the referent. When all six ETEs were considered together, increased levels of ETEs were associated with a decreased risk for OFCs. In addition, Mo showed a protective effect against risk for OFCs when the other ETEs were fixed at their 25th, 50th, or 75th percentile, whereas the protective effect of Co turned to a null effect in the BKMR model. No association was observed between levels of Fe, Zn, Se, or Cu and risk for OFCs in either statistical model. CONCLUSION Elevated concentrations of Mo in maternal serum were associated with a reduced risk for OFCs.
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Affiliation(s)
- Shengju Yin
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Chengrong Wang
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Beijing Obstetrics and Genecology Hospital, Capital Medical University, Beijing 100026, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Jing Wei
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Lei Jin
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Jufen Liu
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Linlin Wang
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Zhiwen Li
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing 100191, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Chenghong Yin
- Beijing Obstetrics and Genecology Hospital, Capital Medical University, Beijing 100026, China.
| | - Aiguo Ren
- Beijing Obstetrics and Genecology Hospital, Capital Medical University, Beijing 100026, China; Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China.
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Hall EG, Wenger LW, Wilson NR, Undurty-Akella SS, Standley J, Augustine-Akpan EA, Kousa YA, Acevedo DS, Goering JP, Pitstick L, Natsume N, Paroya SM, Busch TD, Ito M, Mori A, Imura H, Schultz-Rogers LE, Klee EW, Babovic-Vuksanovic D, Kroc SA, Adeyemo WL, Eshete MA, Bjork BC, Suzuki S, Murray JC, Schutte BC, Butali A, Saadi I. SPECC1L regulates palate development downstream of IRF6. Hum Mol Genet 2020; 29:845-858. [PMID: 31943082 PMCID: PMC7104672 DOI: 10.1093/hmg/ddaa002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 12/23/2022] Open
Abstract
SPECC1L mutations have been identified in patients with rare atypical orofacial clefts and with syndromic cleft lip and/or palate (CL/P). These mutations cluster in the second coiled-coil and calponin homology domains of SPECC1L and severely affect the ability of SPECC1L to associate with microtubules. We previously showed that gene-trap knockout of Specc1l in mouse results in early embryonic lethality. We now present a truncation mutant mouse allele, Specc1lΔC510, that results in perinatal lethality. Specc1lΔC510/ΔC510 homozygotes showed abnormal palate rugae but did not show cleft palate. However, when crossed with a gene-trap allele, Specc1lcGT/ΔC510 compound heterozygotes showed a palate elevation delay with incompletely penetrant cleft palate. Specc1lcGT/ΔC510 embryos exhibit transient oral epithelial adhesions at E13.5, which may delay shelf elevation. Consistent with oral adhesions, we show periderm layer abnormalities, including ectopic apical expression of adherens junction markers, similar to Irf6 hypomorphic mutants and Arhgap29 heterozygotes. Indeed, SPECC1L expression is drastically reduced in Irf6 mutant palatal shelves. Finally, we wanted to determine if SPECC1L deficiency also contributed to non-syndromic (ns) CL/P. We sequenced 62 Caucasian, 89 Filipino, 90 Ethiopian, 90 Nigerian and 95 Japanese patients with nsCL/P and identified three rare coding variants (p.Ala86Thr, p.Met91Iso and p.Arg546Gln) in six individuals. These variants reside outside of SPECC1L coiled-coil domains and result in milder functional defects than variants associated with syndromic clefting. Together, our data indicate that palate elevation is sensitive to deficiency of SPECC1L dosage and function and that SPECC1L cytoskeletal protein functions downstream of IRF6 in palatogenesis.
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Affiliation(s)
- Everett G Hall
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Luke W Wenger
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nathan R Wilson
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sraavya S Undurty-Akella
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Eno-Abasi Augustine-Akpan
- Department of Oral Pathology, Radiology and Medicine/Dow Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - Youssef A Kousa
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Diana S Acevedo
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jeremy P Goering
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Lenore Pitstick
- Department of Biochemistry, Midwestern University, Downers Grove, IL 60515, USA
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Shahnawaz M Paroya
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Tamara D Busch
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Masaaki Ito
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Akihiro Mori
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Hideto Imura
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos, PMB 12003, Nigeria
| | - Mekonen A Eshete
- Department of Plastic and Reconstructive Surgery, Addis Ababa University, Addis Ababa, PO Box 26493, Ethiopia
| | - Bryan C Bjork
- Department of Biochemistry, Midwestern University, Downers Grove, IL 60515, USA
| | - Satoshi Suzuki
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Jeffrey C Murray
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Brian C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine/Dow Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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9
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Cárdenas-Nieto D, Forero-Castro M, Esteban-Pérez C, Martínez-Lozano J, Briceño-Balcázar I. The 22q11.2 Microdeletion in Pediatric Patients with Cleft Lip, Palate, or Both and Congenital Heart Disease: A Systematic Review. J Pediatr Genet 2020; 9:1-8. [PMID: 31976137 DOI: 10.1055/s-0039-1698804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is present in approximately 5 to 8% of patients with cleft lip, palate, or both (CL/P) and 75 to 80% of patients with congenital heart disease (CHD). In a literature review, we consider this association of 22q11.2DS in pediatric patients with CL/P and CHD. Early diagnosis of 22q11.2DS in pediatric patients with CL/P and CHD helps to optimize a multidisciplinary treatment approach for 22q11DS. Early diagnosis, thereby, can improve quality of life for these patients and awareness of other potential clinical implications that may require attention throughout the patient's life.
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Affiliation(s)
- Diana Cárdenas-Nieto
- Programa de Maestría en Ciencias Biológicas, Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia.,Escuela de Ciencias Biológicas, Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Maribel Forero-Castro
- Escuela de Ciencias Biológicas, Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Clara Esteban-Pérez
- Escuela de Ciencias Biológicas, Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Julio Martínez-Lozano
- Facultad de Medicina, Grupo de investigación en Genética Humana, Universidad de La Sabana, Chía, Colombia
| | - Ignacio Briceño-Balcázar
- Facultad de Medicina, Grupo de investigación en Genética Humana, Universidad de La Sabana, Chía, Colombia
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10
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Demeer B, Revencu N, Helaers R, Gbaguidi C, Dakpe S, François G, Devauchelle B, Bayet B, Vikkula M. Likely Pathogenic Variants in One Third of Non-Syndromic Discontinuous Cleft Lip and Palate Patients. Genes (Basel) 2019; 10:genes10100833. [PMID: 31652620 PMCID: PMC6826364 DOI: 10.3390/genes10100833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/14/2019] [Accepted: 10/19/2019] [Indexed: 12/19/2022] Open
Abstract
Oral clefts are composed of cleft of the lip, cleft of the lip and palate, or cleft of the palate, and they are associated with a wide range of expression and severity. When cleft of the palate is associated with cleft of the lip with preservation of the primary palate, it defines an atypical phenotype called discontinuous cleft. Although this phenotype may represent 5% of clefts of the lip and/or palate (CLP), it is rarely specifically referred to and its pathophysiology is unknown. We conducted whole exome sequencing (WES) and apply a candidate gene approach to non-syndromic discontinuous CLP individuals in order to identify genes and deleterious variants that could underlie this phenotype. We discovered loss-of-function variants in two out of the seven individuals, implicating FGFR1 and DLG1 genes, which represents almost one third of this cohort. Whole exome sequencing of clinically well-defined subgroups of CLP, such as discontinuous cleft, is a relevant approach to study CLP etiopathogenesis. It could facilitate more accurate clinical, epidemiological and fundamental research, ultimately resulting in better diagnosis and care of CLP patients. Non-syndromic discontinuous cleft lip and palate seems to have a strong genetic basis.
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Affiliation(s)
- Bénédicte Demeer
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, 80054 Amiens, France.
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
| | - Nicole Revencu
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Raphael Helaers
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
| | - Cica Gbaguidi
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Stéphanie Dakpe
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Geneviève François
- Department of Pediatrics, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Bernard Devauchelle
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Bénédicte Bayet
- Centre Labiopalatin, Division of Plastic Surgery, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
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11
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Reynolds K, Kumari P, Sepulveda Rincon L, Gu R, Ji Y, Kumar S, Zhou CJ. Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models. Dis Model Mech 2019; 12:12/2/dmm037051. [PMID: 30760477 PMCID: PMC6398499 DOI: 10.1242/dmm.037051] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diverse signaling cues and attendant proteins work together during organogenesis, including craniofacial development. Lip and palate formation starts as early as the fourth week of gestation in humans or embryonic day 9.5 in mice. Disruptions in these early events may cause serious consequences, such as orofacial clefts, mainly cleft lip and/or cleft palate. Morphogenetic Wnt signaling, along with other signaling pathways and transcription regulation mechanisms, plays crucial roles during embryonic development, yet the signaling mechanisms and interactions in lip and palate formation and fusion remain poorly understood. Various Wnt signaling and related genes have been associated with orofacial clefts. This Review discusses the role of Wnt signaling and its crosstalk with cell adhesion molecules, transcription factors, epigenetic regulators and other morphogenetic signaling pathways, including the Bmp, Fgf, Tgfβ, Shh and retinoic acid pathways, in orofacial clefts in humans and animal models, which may provide a better understanding of these disorders and could be applied towards prevention and treatments.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Priyanka Kumari
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Lessly Sepulveda Rincon
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Ran Gu
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Santosh Kumar
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA .,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
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12
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Liu H, Busch T, Eliason S, Anand D, Bullard S, Gowans LJJ, Nidey N, Petrin A, Augustine-Akpan EA, Saadi I, Dunnwald M, Lachke SA, Zhu Y, Adeyemo A, Amendt B, Roscioli T, Cornell R, Murray J, Butali A. Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate. Birth Defects Res 2018; 109:27-37. [PMID: 28029220 PMCID: PMC5388577 DOI: 10.1002/bdra.23596] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/21/2016] [Accepted: 10/01/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Recent advances in genomics methodologies, in particular the availability of next-generation sequencing approaches have made it possible to identify risk loci throughout the genome, in particular the exome. In the current study, we present findings from an exome study conducted in five affected individuals of a multiplex family with cleft palate only. METHODS The GEnome MINIng (GEMINI) pipeline was used to functionally annotate the single nucleotide polymorphisms, insertions and deletions. Filtering methods were applied to identify variants that are clinically relevant and present in affected individuals at minor allele frequencies (≤1%) in the 1000 Genomes Project single nucleotide polymorphism database, Exome Aggregation Consortium, and Exome Variant Server databases. The bioinformatics tool Systems Tool for Craniofacial Expression-Based Gene Discovery was used to prioritize cleft candidates in our list of variants, and Sanger sequencing was used to validate the presence of identified variants in affected and unaffected relatives. RESULTS Our analyses approach narrowed the candidates down to the novel missense variant in ARHGAP29 (GenBank: NM_004815.3, NP_004806.3;c.1654T>C [p.Ser552Pro]. A functional assay in zebrafish embryos showed that the encoded protein lacks the activity possessed by its wild-type counterpart, and migration assays revealed that keratinocytes transfected with wild-type ARHGAP29 migrated faster than counterparts transfected with the p.Ser552Pro ARHGAP29 variant or empty vector (control). CONCLUSION These findings reveal ARHGAP29 to be a regulatory protein essential for proper development of the face, identifies an amino acid that is key for this, and provides a potential new diagnostic tool.Birth Defects Research 109:27-37, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Huan Liu
- Department of Anatomy and Cell Biology, Iowa City, U.S.A
| | - Tamara Busch
- Department of Pediatrics, University of Iowa, Iowa City, U.S.A
| | - Steven Eliason
- Department of Anatomy and Cell Biology, Iowa City, U.S.A
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Steven Bullard
- Department of Internal Medicine, University of Iowa, Iowa City, U.S.A
| | - Lord J J Gowans
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, U.S.A
| | - Nichole Nidey
- Department of Pediatrics, University of Iowa, Iowa City, U.S.A
| | - Aline Petrin
- Department of Pediatrics, University of Iowa, Iowa City, U.S.A
| | | | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center Kansas City, KS, USA
| | | | - Salil A Lachke
- Department of Internal Medicine, University of Iowa, Iowa City, U.S.A.,Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Ying Zhu
- Newcastle GOLD Service, Hunter Genetics, Waratah, NSW, Australia
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, U.S.A
| | - Brad Amendt
- Department of Anatomy and Cell Biology, Iowa City, U.S.A.,Dows Research Institute, University of Iowa, Iowa City, U.S.A
| | - Tony Roscioli
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia.,The Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Robert Cornell
- Department of Anatomy and Cell Biology, Iowa City, U.S.A
| | - Jeffrey Murray
- Department of Pediatrics, University of Iowa, Iowa City, U.S.A
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, U.S.A.,Dows Research Institute, University of Iowa, Iowa City, U.S.A
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13
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Mostowska A, Gaczkowska A, Żukowski K, Ludwig K, Hozyasz K, Wójcicki P, Mangold E, Böhmer A, Heilmann-Heimbach S, Knapp M, Zadurska M, Biedziak B, Budner M, Lasota A, Daktera-Micker A, Jagodziński P. Common variants inDLG1locus are associated with non-syndromic cleft lip with or without cleft palate. Clin Genet 2018; 93:784-793. [DOI: 10.1111/cge.13141] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Affiliation(s)
- A. Mostowska
- Department of Biochemistry and Molecular Biology; Poznan University of Medical Sciences; Poznan Poland
| | - A. Gaczkowska
- Department of Biochemistry and Molecular Biology; Poznan University of Medical Sciences; Poznan Poland
| | - K. Żukowski
- Department of Animal Genetics and Breeding; National Research Institute of Animal Production; Balice Poland
| | - K.U. Ludwig
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - K.K. Hozyasz
- Department of Pediatrics; Institute of Mother and Child; Warsaw Poland
| | - P. Wójcicki
- Plastic Surgery Clinic of Medical University in Wroclaw; Wroclaw Poland
- Department of Plastic Surgery in Specialist Medical Center in Polanica Zdroj; Polanica Zdroj Poland
| | - E. Mangold
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - A.C. Böhmer
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - S. Heilmann-Heimbach
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - M. Knapp
- Institute for Medical Biometry, Informatics and Epidemiology; University of Bonn; Bonn Germany
| | - M. Zadurska
- Department of Orthodontics; Medical University of Warsaw; Warsaw Poland
| | - B. Biedziak
- Department of Dental Surgery, Division of Facial Malformation; Poznan University of Medical Sciences; Poznan Poland
| | - M. Budner
- Eastern Poland Burn Treatment and Reconstructive Center; Leczna Poland
| | - A. Lasota
- Department of Jaw Orthopedics; Medical University of Lublin; Lublin Poland
| | - A. Daktera-Micker
- Department of Dental Surgery, Division of Facial Malformation; Poznan University of Medical Sciences; Poznan Poland
| | - P.P. Jagodziński
- Department of Biochemistry and Molecular Biology; Poznan University of Medical Sciences; Poznan Poland
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14
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Liu D, Schwender H, Wang M, Wang H, Wang P, Zhu H, Zhou Z, Li J, Wu T, Beaty TH. Gene-gene interaction between MSX1 and TP63 in Asian case-parent trios with nonsyndromic cleft lip with or without cleft palate. Birth Defects Res 2018; 110:317-324. [PMID: 29341488 DOI: 10.1002/bdr2.1139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/27/2017] [Accepted: 09/06/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P). METHODS A total of 130 single-nucleotide polymorphisms (SNPs) in or near SUMO1, MSX1, and TP63 was analyzed among 1,038 Asian NSCL/P trios ascertained through an international consortium. Conditional logistic regression models were used to explore gene-gene (G × G) and gene-environment (G × E) interaction involving maternal environmental tobacco smoke and multivitamin supplementation. Bonferroni correction was used for G × E analysis and permutation tests were used for G × G analysis. RESULTS While transmission disequilibrium tests and gene-environment interaction analysis showed no significant results, we did find signals of gene-gene interaction between SNPs near MSX1 and TP63. Three pairwise interactions yielded significant p values in permutation tests (rs884690 and rs9290890 with p = 9.34 × 10-5 and empirical p = 1.00 × 10-4 , rs1022136 and rs4687098 with p = 2.41 × 10-4 and empirical p = 2.95 × 10-4 , rs6819546 and rs9681004 with p = 5.15 × 10-4 and empirical p = 3.02 × 10-4 ). CONCLUSION Gene-gene interaction between MSX1 and TP63 may influence the risk of NSCL/P in Asian populations. Our study provided additional understanding of the genetic etiology of NSCL/P and underlined the importance of considering gene-gene interaction in the etiology of this common craniofacial malformation.
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Affiliation(s)
- Dongjing Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Department of Statistics and Information, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, Maryland
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15
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Hoebel AK, Drichel D, van de Vorst M, Böhmer AC, Sivalingam S, Ishorst N, Klamt J, Gölz L, Alblas M, Maaser A, Keppler K, Zink AM, Dixon MJ, Dixon J, Hemprich A, Kruse T, Graf I, Dunsche A, Schmidt G, Daratsianos N, Nowak S, Aldhorae KA, Nöthen MM, Knapp M, Thiele H, Gilissen C, Reutter H, Hoischen A, Mangold E, Ludwig KU. Candidate Genes for Nonsyndromic Cleft Palate Detected by Exome Sequencing. J Dent Res 2017; 96:1314-1321. [PMID: 28767323 DOI: 10.1177/0022034517722761] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nonsyndromic cleft palate only (nsCPO) is a facial malformation that has a livebirth prevalence of 1 in 2,500. Research suggests that the etiology of nsCPO is multifactorial, with a clear genetic component. To date, genome-wide association studies have identified only 1 conclusive common variant for nsCPO, that is, a missense variant in the gene grainyhead-like-3 ( GRHL3). Thus, the underlying genetic causes of nsCPO remain largely unknown. The present study aimed at identifying rare variants that might contribute to nsCPO risk, via whole-exome sequencing (WES), in multiply affected Central European nsCPO pedigrees. WES was performed in 2 affected first-degree relatives from each family. Variants shared between both individuals were analyzed for their potential deleterious nature and a low frequency in the general population. Genes carrying promising variants were annotated for 1) reported associations with facial development, 2) multiple occurrence of variants, and 3) expression in mouse embryonic palatal shelves. This strategy resulted in the identification of a set of 26 candidate genes that were resequenced in 132 independent nsCPO cases and 623 independent controls of 2 different ethnicities, using molecular inversion probes. No rare loss-of-function mutation was identified in either WES or resequencing step. However, we identified 2 or more missense variants predicted to be deleterious in each of 3 genes ( ACACB, PTPRS, MIB1) in individuals from independent families. In addition, the analyses identified a novel variant in GRHL3 in 1 patient and a variant in CREBBP in 2 siblings. Both genes underlie different syndromic forms of CPO. A plausible hypothesis is that the apparently nonsyndromic clefts in these 3 patients might represent hypomorphic forms of the respective syndromes. In summary, the present study identified rare variants that might contribute to nsCPO risk and suggests candidate genes for further investigation.
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Affiliation(s)
- A K Hoebel
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - D Drichel
- 3 German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,4 Cologne Center for Genomics, Department of Statistical Genetics and Bioinformatics, University of Cologne, Cologne, Germany
| | - M van de Vorst
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A C Böhmer
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - S Sivalingam
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - N Ishorst
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - J Klamt
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - L Gölz
- 6 Department of Orthodontics, University of Bonn, Bonn, Germany
| | - M Alblas
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - A Maaser
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - K Keppler
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - A M Zink
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - M J Dixon
- 7 Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - J Dixon
- 7 Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - A Hemprich
- 8 Department of Oral and Maxillo-Facial Surgery, University of Leipzig, Leipzig, Germany
| | - T Kruse
- 9 Department of Orthodontics, University of Cologne, Cologne, Germany
| | - I Graf
- 9 Department of Orthodontics, University of Cologne, Cologne, Germany
| | - A Dunsche
- 10 Clinics Karlsruhe, Department of Oral and Maxillo-Facial Surgery, Karlsruhe, Germany
| | - G Schmidt
- 11 Department of Cleft Lip and Cleft Palate Surgery, Humboldt University of Berlin, Berlin, Germany
| | - N Daratsianos
- 6 Department of Orthodontics, University of Bonn, Bonn, Germany
| | - S Nowak
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - K A Aldhorae
- 12 Department of Orthodontics, College of Dentistry, Dhamar University, Dhamar, Yemen
| | - M M Nöthen
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - M Knapp
- 13 Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - H Thiele
- 14 Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - C Gilissen
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H Reutter
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,15 Department of Neonatology &Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - A Hoischen
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,16 Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,17 Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E Mangold
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - K U Ludwig
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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16
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Tian H, Feng J, Li J, Ho TV, Yuan Y, Liu Y, Brindopke F, Figueiredo JC, Magee W, Sanchez-Lara PA, Chai Y. Intraflagellar transport 88 (IFT88) is crucial for craniofacial development in mice and is a candidate gene for human cleft lip and palate. Hum Mol Genet 2017; 26:860-872. [PMID: 28069795 DOI: 10.1093/hmg/ddx002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/03/2016] [Indexed: 01/08/2023] Open
Abstract
Ciliopathies are pleiotropic human diseases resulting from defects of the primary cilium, and these patients often have cleft lip and palate. IFT88 is required for the assembly and function of the primary cilia, which mediate the activity of key developmental signaling pathways. Through whole exome sequencing of a family of three affected siblings with isolated cleft lip and palate, we discovered that they share a novel missense mutation in IFT88 (c.915G > C, p.E305D), suggesting this gene should be considered a candidate for isolated orofacial clefting. In order to evaluate the function of IFT88 in regulating craniofacial development, we generated Wnt1-Cre;Ift88fl/fl mice to eliminate Ift88 specifically in cranial neural crest (CNC) cells. Wnt1-Cre;Ift88fl/flpups died at birth due to severe craniofacial defects including bilateral cleft lip and palate and tongue agenesis, following the loss of the primary cilia in the CNC-derived palatal mesenchyme. Loss of Ift88 also resulted in a decrease in neural crest cell proliferation during early stages of palatogenesis as well as a downregulation of the Shh signaling pathway in the palatal mesenchyme. Importantly, Osr2KI-Cre;Ift88fl/flmice, in which Ift88 is lost specifically in the palatal mesenchyme, exhibit isolated cleft palate. Taken together, our results demonstrate that IFT88 has a highly conserved function within the primary cilia of the CNC-derived mesenchyme in the lip and palate region in mice and is a strong candidate as an orofacial clefting gene in humans.
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Affiliation(s)
- Hua Tian
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Department of Cariology and Endodontology, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jingyuan Li
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing 100050, China
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Liu
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Frederick Brindopke
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - William Magee
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Pedro A Sanchez-Lara
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Department of Pathology & Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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