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Woronowicz KC, Esin EV, Markevich GN, Martinez CS, McMenamin SK, Daane JM, Harris MP, Shkil FN. Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation. Development 2024; 151:dev203002. [PMID: 39417576 DOI: 10.1242/dev.203002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 10/01/2024] [Indexed: 10/19/2024]
Abstract
Recent adaptive radiations provide experimental opportunities to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetic analyses as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, charr species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotskoe represent the most extensive radiation described for the genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages within the clade. We find that changes in genes associated with thyroid signaling and craniofacial development provided a foundational shift in evolution to the lake. The thyroid axis is further implicated in subsequent lineage partitioning events. These results delineate a genetic scenario for the diversification of specialized lineages and highlight a common axis of change biasing the generation of specific forms during adaptive radiation.
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Affiliation(s)
- Katherine C Woronowicz
- Department of Orthopedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Evgeny V Esin
- Laboratory of Lower Vertebrate Ecology, Severtsov Institute, Moscow 119071, Russian Federation
| | - Grigorii N Markevich
- Laboratory of Lower Vertebrate Ecology, Severtsov Institute, Moscow 119071, Russian Federation
| | | | | | - Jacob M Daane
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Matthew P Harris
- Department of Orthopedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Fedor N Shkil
- Laboratory of Evolutionary Morphology, Severtsov Institute, Moscow 119071, Russian Federation
- Laboratory of Postembryonic Development, Koltzov Institute, Moscow 119071, Russian Federation
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Spineli-Silva S, Monlleó IL, Félix TM, Gil-da-Silva-Lopes VL, Vieira TP. Overlapping Spectrum of Craniofacial Microsomia Phenotype in Cat-Eye Syndrome. Cleft Palate Craniofac J 2024; 61:1578-1585. [PMID: 37183441 DOI: 10.1177/10556656231174435] [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] [Indexed: 05/16/2023] Open
Abstract
This study reports three patients with Cat-eye Syndrome (CES), two of which present a previous clinical diagnosis of Craniofacial microsomia (CFM). Chromosomal microarray analysis (CMA) revealed a tetrasomy of 1,7 Mb at the 22q11.2q11.21 region, which is the typical region triplicated in the CES, in all patients. The most frequent craniofacial features found in individuals with CFM and CES are preauricular tags and/or pits and mandibular hypoplasia. We reinforce that the candidate genes for CFM features, particularly ear malformation, preauricular tags/pits, and facial asymmetry, can be in the proximal region of the 22q11.2 region.
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Affiliation(s)
- Samira Spineli-Silva
- Laboratory of Human Cytogenetics and Cytogenomics, Department of Translational Medicine, School of Medical Sciences, State University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Isabella L Monlleó
- Faculty of Medicine, Federal University of Alagoas (UFAL), Maceió, Alagoas, Brazil
- Clinical Genetics Service, University Hospital, Federal University of Alagoas (UFAL), Maceió, Alagoas, Brazil
| | - Têmis M Félix
- Medical Genetics Service, Clinical Hospital of Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Vera L Gil-da-Silva-Lopes
- Laboratory of Human Cytogenetics and Cytogenomics, Department of Translational Medicine, School of Medical Sciences, State University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Társis P Vieira
- Laboratory of Human Cytogenetics and Cytogenomics, Department of Translational Medicine, School of Medical Sciences, State University of Campinas (Unicamp), Campinas, São Paulo, Brazil
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Petrin AL, Machado-Paula LA, Hinkle A, Hovey L, Awotoye W, Chimenti M, Darbro B, Ribeiro-Bicudo LA, Dabdoub SM, Peter T, Breheny P, Murray J, Van Otterloo E, Rengasamy Venugopalan S, Moreno-Uribe LM. Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.07.24301824. [PMID: 38370836 PMCID: PMC10871465 DOI: 10.1101/2024.02.07.24301824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Oculoauriculovertebral Spectrum (OAVS) encompasses abnormalities on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular and vertebral anomalies. We present genetic findings on a three-generation family affected with macrostomia, preauricular tags and uni- or bilateral ptosis following an autosomal dominant pattern. Methods We generated whole genome sequencing data for the proband, affected parent and unaffected paternal grandparent followed by Sanger sequencing on 23 family members for the top 10 candidate genes: KCND2, PDGFRA, CASP9, NCOA3, WNT10A, SIX1, MTF1, KDR/VEGFR2, LRRK1, and TRIM2 We performed parent and sibling-based transmission disequilibrium tests and burden analysis via a penalized linear mixed model, for segregation and mutation burden respectively. Next, via bioinformatic tools we predicted protein function, mutation pathogenicity and pathway enrichment to investigate the biological relevance of mutations identified. Results Rare missense mutations in SIX1, KDR/VEGFR2, and PDGFRA showed the best segregation with the OAV phenotypes in this family. When considering any of the 3 OAVS phenotypes as an outcome, SIX1 had the strongest associations in parent-TDTs and sib-TDTs (p=0.025, p=0.052) (unadjusted p-values). Burden analysis identified SIX1 (RC=0.87) and PDGFRA (RC=0.98) strongly associated with OAVS severity. Using phenotype-specific outcomes, sib-TDTs identified SIX1 with uni- or bilateral ptosis (p=0.049) and ear tags (p=0.01), and PDGFRA and KDR/VEGFR2 with ear tags (both p<0.01). Conclusion SIX1, PDGFRA, and KDR/VEGFR2 are strongly associated to OAVS phenotypes. SIX1 has been previously associated with OAVS ear malformations and is co-expressed with EYA1 during ear development. Efforts to strengthen the genotype-phenotype co-relation underlying the OAVS are key to discover etiology, family counseling and prevention.
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Affiliation(s)
- A L Petrin
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - L A Machado-Paula
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - A Hinkle
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - L Hovey
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - W Awotoye
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - M Chimenti
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - B Darbro
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | | | - S M Dabdoub
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - T Peter
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - P Breheny
- College of Public Health, University of Iowa, Iowa City, IA, USA
| | - J Murray
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - E Van Otterloo
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | | | - L M Moreno-Uribe
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
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Niu X, Zhang F, Gu W, Zhang B, Chen X. FBLN2 is associated with Goldenhar syndrome and is essential for cranial neural crest cell development. Ann N Y Acad Sci 2024; 1537:113-128. [PMID: 38970771 DOI: 10.1111/nyas.15183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 07/08/2024]
Abstract
Goldenhar syndrome, a rare craniofacial malformation, is characterized by developmental anomalies in the first and second pharyngeal arches. Its etiology is considered to be heterogenous, including both genetic and environmental factors that remain largely unknown. To further elucidate the genetic cause in a five-generation Goldenhar syndrome pedigree and exploit the whole-exome sequencing (WES) data of this pedigree, we generated collapsed haplotype pattern markers based on WES and employed rare variant nonparametric linkage analysis. FBLN2 was identified as a candidate gene via analysis of WES data across the significant linkage region. A fbln2 knockout zebrafish line was established by CRISPR/Cas9 to examine the gene's role in craniofacial cartilage development. fbln2 was expressed specifically in the mandible during the zebrafish early development, while fbln2 knockout zebrafish exhibited craniofacial malformations with abnormal chondrocyte morphologies. Functional studies revealed that fbln2 knockout caused abnormal chondrogenic differentiation, apoptosis, and proliferation of cranial neural crest cells (CNCCs), and downregulated the bone morphogenic protein (BMP) signaling pathway in the zebrafish model. This study demonstrates the role of FBLN2 in CNCC development and BMP pathway regulation, and highlights FBLN2 as a candidate gene for Goldenhar syndrome, which may have implications for the selection of potential screening targets and the development of treatments for conditions like microtia-atresia.
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Affiliation(s)
- Xiaomin Niu
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Fuyu Zhang
- 8-Year MD Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Wei Gu
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Xiaowei Chen
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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Woronowicz KC, Esin EV, Markevich GN, Martinez CS, McMenamin SK, Daane JM, Harris MP, Shkil FN. Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.24.529919. [PMID: 38712299 PMCID: PMC11071292 DOI: 10.1101/2023.02.24.529919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Recent adaptive radiations provide evolutionary case studies, which provide the context to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetics as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotske represent the most extensive radiation described for the charr genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages with little evidence of hybridization. We also find that specific selection on thyroid signaling and craniofacial genes forms a genomic basis for the radiation. Thyroid hormone is further implicated in subsequent lineage partitioning events. These results delineate a clear genetic basis for the diversification of specialized lineages, and highlight the role of developmental mechanisms in shaping the forms generated during adaptive radiation.
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Affiliation(s)
- Katherine C Woronowicz
- Department of Orthopaedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Evgeny V Esin
- AN Severtsov Institute of Ecology and Evolution, RAS; Leninskiy-33, 119071 Moscow, Russian Federation
| | - Grigorii N Markevich
- Kronotsky Nature Biosphere Reserve; Ryabikova-48, 68400 Yelizovo, Russian Federation
| | | | | | - Jacob M Daane
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204
| | - Matthew P Harris
- Department of Orthopaedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Fedor N Shkil
- AN Severtsov Institute of Ecology and Evolution, RAS; Leninskiy-33, 119071 Moscow, Russian Federation
- NK Koltzov Institute of Developmental Biology, RAS; Vavilova-26, 119334 Moscow, Russian Federation
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Xing X, Zeng Z, Wang Y, Pan B, Huang X. Identification of potential molecular mechanism related to craniofacial dysmorphism caused by FOXI3 deficiency. Mol Genet Genomic Med 2024; 12:e2411. [PMID: 38433559 PMCID: PMC10910234 DOI: 10.1002/mgg3.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Hemifacial macrosomia (HFM, OMIM 164210) is a complex and highly heterogeneous disease. FORKHEAD BOX I3 (FOXI3) is a susceptibility gene for HFM, and mice with loss of function of Foxi3 did exhibit a phenotype similar to craniofacial dysmorphism. However, the specific pathogenesis of HFM caused by FOXI3 deficiency remains unclear till now. METHOD In this study, we first constructed a Foxi3 deficiency (Foxi3-/- ) mouse model to verify the craniofacial phenotype of Foxi3-/- mice, and then used RNAseq data for gene differential expression analysis to screen candidate pathogenic genes, and conducted gene expression verification analysis using quantitative real-time PCR. RESULTS By observing the phenotype of Foxi3-/- mice, we found that craniofacial dysmorphism was present. The results of comprehensive bioinformatics analysis suggested that the craniofacial dysmorphism caused by Foxi3 deficiency may be involved in the PI3K-Akt signaling pathway. Quantitative real-time PCR results showed that the expression of PI3K-Akt signaling pathway-related gene Akt2 was significantly increased in Foxi3-/- mice. CONCLUSION The craniofacial dysmorphism caused by the deficiency of Foxi3 may be related to the expression of Akt2 and PI3K-Akt signaling pathway. This study laid a foundation for understanding the function of FOXI3 and the pathogenesis and treatment of related craniofacial dysmorphism caused by FOXI3 dysfunction.
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Affiliation(s)
- Xiao‐Liang Xing
- School of Basic MedicineNingxia Medical UniversityYinchuanNingxiaChina
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese MedicineHunan University of MedicineChangshaChina
| | - Ziqiang Zeng
- School of Basic MedicineNingxia Medical UniversityYinchuanNingxiaChina
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese MedicineHunan University of MedicineChangshaChina
| | - Yana Wang
- School of Basic MedicineNingxia Medical UniversityYinchuanNingxiaChina
| | - Bo Pan
- Department of Auricular Reconstruction, Plastic Surgery HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xueshuang Huang
- School of Basic MedicineNingxia Medical UniversityYinchuanNingxiaChina
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese MedicineHunan University of MedicineChangshaChina
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Chen X, Ma J, Zhang T. Genetics and Epigenetics in the Genesis and Development of Microtia. J Craniofac Surg 2024; 35:00001665-990000000-01343. [PMID: 38345940 PMCID: PMC11045557 DOI: 10.1097/scs.0000000000010004] [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: 07/24/2023] [Accepted: 12/03/2023] [Indexed: 04/28/2024] Open
Abstract
Microtia is a congenital malformation of the external and middle ear associated with varying degrees of severity that range from mild structural abnormalities to the absence of the external ear and auditory canal. Globally, it is the second most common congenital craniofacial malformation and is typically caused by inherited defects, external factors, or the interaction between genes and external factors. Epigenetics notably represents a bridge between genetics and the environment. This review has devoted attention to the current proceedings of the genetics and epigenetics of microtia and related syndromes.
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Affiliation(s)
- Xin Chen
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital, Fudan University
| | - Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital, Fudan University
| | - Tianyu Zhang
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital, Fudan University
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China
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Zhao H, Du C, Yang G, Wang Y. Diagnosis, treatment, and research status of rare diseases related to birth defects. Intractable Rare Dis Res 2023; 12:148-160. [PMID: 37662624 PMCID: PMC10468410 DOI: 10.5582/irdr.2023.01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Rare diseases are diseases that occur at low prevalence, and most of them are chronic and serious diseases that are often life-threatening. Currently, there is no unified definition for rare diseases. The diagnosis, treatment, and research of rare diseases have become the focus of medicine and biopharmacology, as well as the breakthrough point of clinical and basic research. Birth defects are the hard-hit area of rare diseases and the frontiers of its research. Since most of these defects have a genetic basis, early screening and diagnosis have important scientific value and social significance for the prevention and control of such diseases. At present, there is no effective treatment for most rare diseases, but progress in prenatal diagnosis and screening can prevent the occurrence of diseases and help prevent and treat rare diseases. This article discusses the progress in genetic-related birth defects and rare diseases.
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Affiliation(s)
- Hongjuan Zhao
- Department of Gynecology and Obstetrics, Shandong Provincial Third Hospital, Shandong University, Ji'nan, China
| | - Chen Du
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University Affiliated Hospital, Hohhot, China
| | - Guang Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University Affiliated Hospital, Hohhot, China
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Exploration of Novel Genetic Evidence and Clinical Significance Into Hemifacial Microsomia Pathogenesis. J Craniofac Surg 2023; 34:834-838. [PMID: 36745106 DOI: 10.1097/scs.0000000000009167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/24/2022] [Indexed: 02/07/2023] Open
Abstract
The authors browsed through past genetic findings in hemifacial microsomia along with our previously identified mutations in ITGB4 and PDE4DIP from whole genome sequencing of hemifacial microsomia patients. Wondering whether these genes influence mandibular bone modeling by regulation on osteogenesis, the authors approached mechanisms of hemifacial microsomia through this investigation into gene knockdown effects in vitro. MC3T3E1 cells were divided into 5 groups: the negative control group without osteogenesis induction or siRNA, the positive control group with only osteogenesis induction, and 3 gene silenced groups with both osteogenesis induction and siRNA. Validation of transfection was through fluorescence microscopy and quantitative real-time Polymerase chain reaction on knockdown efficiency. Changes in expression levels of the 3 genes during osteogenesis and impact of Itgb4 and Pde4dip knockdown on osteogenesis were examined by quantitative real-time Polymerase chain reaction, alkaline phosphatase, and alizarin red staining. Elevation of osteogenic genes Alpl, Col1a1, Bglap, Spp1, and Runx2 verified successful osteogenesis. Both genes were upregulated under osteogenic induction, while they had different trends over time. Intracellular fluorophores under microscope validated successful transfection and si-m-Itgb4_003, si-m-Pde4dip_002 had satisfactory knockdown effects. During osteogenesis, Pde4dip knockdown enhanced Spp1 expression (1.95±0.13 folds, P =0.045). The authors speculated that these genes may have different involvements in osteogenesis. Stimulated expression of Spp1 by Pde4dip knockdown may suggest that Pde4dip inhibits osteogenesis.
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Celse T, Tingaud-Sequeira A, Dieterich K, Siegfried G, Lecaignec C, Bouneau L, Fannemel M, Salaun G, Laffargue F, Martinez G, Satre V, Vieville G, Bidart M, Soussi Zander C, Turesson AC, Splitt M, Reboul D, Chiesa J, Khau Van Kien P, Godin M, Gruchy N, Goel H, Palmer E, Demetriou K, Shalhoub C, Rooryck-Thambo C, Coutton C. OTX2 duplications: a recurrent cause of oculo-auriculo-vertebral spectrum. J Med Genet 2022; 60:620-626. [DOI: 10.1136/jmg-2022-108678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022]
Abstract
BackgroundOculo-auriculo-vertebral spectrum (OAVS) is the second most common cause of head and neck malformations in children after orofacial clefts. OAVS is clinically heterogeneous and characterised by a broad range of clinical features including ear anomalies with or without hearing loss, hemifacial microsomia, orofacial clefts, ocular defects and vertebral abnormalities. Various genetic causes were associated with OAVS and copy number variations represent a recurrent cause of OAVS, but the responsible gene often remains elusive.MethodsWe described an international cohort of 17 patients, including 10 probands and 7 affected relatives, presenting with OAVS and carrying a 14q22.3 microduplication detected using chromosomal microarray analysis. For each patient, clinical data were collected using a detailed questionnaire addressed to the referring clinicians. We subsequently studied the effects ofOTX2overexpression in a zebrafish model.ResultsWe defined a 272 kb minimal common region that only overlaps with theOTX2gene. Head and face defects with a predominance of ear malformations were present in 100% of patients. The variability in expressivity was significant, ranging from simple chondromas to severe microtia, even between intrafamilial cases. Heterologous overexpression ofOTX2in zebrafish embryos showed significant effects on early development with alterations in craniofacial development.ConclusionsOur results indicate that properOTX2dosage seems to be critical for the normal development of the first and second branchial arches. Overall, we demonstrated thatOTX2genomic duplications are a recurrent cause of OAVS marked by auricular malformations of variable severity.
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The Enigmatic Etiology of Oculo-Auriculo-Vertebral Spectrum (OAVS): An Exploratory Gene Variant Interaction Approach in Candidate Genes. Life (Basel) 2022; 12:life12111723. [PMID: 36362878 PMCID: PMC9693117 DOI: 10.3390/life12111723] [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: 09/26/2022] [Revised: 10/12/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
The clinical diagnosis of oculo-auriculo-vertebral spectrum (OAVS) is established when microtia is present in association with hemifacial hypoplasia (HH) and/or ocular, vertebral, and/or renal malformations. Genetic and non-genetic factors have been associated with microtia/OAVS. Although the etiology remains unknown in most patients, some cases may have an autosomal dominant, autosomal recessive, or multifactorial inheritance. Among the possible genetic factors, gene−gene interactions may play important roles in the etiology of complex diseases, but the literature lacks related reports in OAVS patients. Therefore, we performed a gene−variant interaction analysis within five microtia/OAVS candidate genes (HOXA2, TCOF1, SALL1, EYA1 and TBX1) in 49 unrelated OAVS Mexican patients (25 familial and 24 sporadic cases). A statistically significant intergenic interaction (p-value < 0.001) was identified between variants p.(Pro1099Arg) TCOF1 (rs1136103) and p.(Leu858=) SALL1 (rs1965024). This intergenic interaction may suggest that the products of these genes could participate in pathways related to craniofacial alterations, such as the retinoic acid (RA) pathway. The absence of clearly pathogenic variants in any of the analyzed genes does not support a monogenic etiology for microtia/OAVS involving these genes in our patients. Our findings could suggest that in addition to high-throughput genomic approaches, future gene−gene interaction analyses could contribute to improving our understanding of the etiology of microtia/OAVS.
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Carter S, Fellows BJ, Gibson K, Bicknell LS. Extending the PAX1 spectrum: a dominantly inherited variant causes oculo-auriculo-vertebral syndrome. Eur J Hum Genet 2022; 30:1178-1181. [PMID: 35879406 PMCID: PMC9553880 DOI: 10.1038/s41431-022-01154-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/17/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
Oculo-auriculo-vertebral syndrome (OAVS) is a clinically heterogeneous disorder, with both genetic and environmental contributors. Multiple genes have been associated with OAVS and common molecular pathways, such as retinoic acid and the PAX-SIX-EYA-DACH (PSED) network, are being implicated in the disease pathophysiology. Biallelic homozygous nonsense or hypomorphic missense mutations in PAX1 cause otofaciocervical syndrome type 2 (OTFCS2), a similar but more severe multi-system disorder that can be accompanied by severe combined immunodeficiency due to thymic aplasia. Here we have identified a multi-generational family with mild features of OAVS segregating a heterozygous frameshift in PAX1. The four base duplication is expected to result in nonsense-mediated decay, and therefore cause a null allele. While there was full penetrance of the variant, expressivity of facial and ear features were variable. Our findings indicate there can be monoallelic and biallelic disorders associated with PAX1, and further implicate the PSED network in OAVS.
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Affiliation(s)
- Shannon Carter
- grid.414299.30000 0004 0614 1349Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand
| | - Bridget J. Fellows
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kate Gibson
- grid.414299.30000 0004 0614 1349Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand
| | - Louise S. Bicknell
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, New Zealand
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[Genetic characteristics of microtia-associated syndromes in neonates]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:614-619. [PMID: 35762425 PMCID: PMC9250400 DOI: 10.7499/j.issn.1008-8830.2203008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microtia is the second most common maxillofacial birth defect in neonates and has an prevalence rate of 3.06/10 000 in China, and 20%-60% of microtia cases is associated with a certain type of syndrome. This article elaborates on the clinical phenotypes and genetic characteristics of three microtia-associated syndromes (MASs) with high prevalence, high incidence rate of ear deformity, and definite genetic etiology, i.e., oculo-auriculo-vertebral spectrum, branchio-oto-renal spectrum disorder, and Treacher-Collins syndrome, and summarizes another three common MASs, so as to provide a reference for the genetic diagnosis of neonatal MAS.
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14
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Tingaud-Sequeira A, Trimouille A, Sagardoy T, Lacombe D, Rooryck-Thambo C. Oculo-auriculo-vertebral spectrum: new genes and literature review on a complex disease. J Med Genet 2022; 59:417-427. [PMID: 35110414 DOI: 10.1136/jmedgenet-2021-108219] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/30/2021] [Indexed: 12/23/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) or Goldenhar syndrome is due to an abnormal development of first and second branchial arches derivatives during embryogenesis and is characterised by hemifacial microsomia associated with auricular, ocular and vertebral malformations. The clinical and genetic heterogeneity of this spectrum with incomplete penetrance and variable expressivity, render its molecular diagnosis difficult. Only a few recurrent CNVs and genes have been identified as causatives in this complex disorder so far. Prenatal environmental causal factors have also been hypothesised. However, most of the patients remain without aetiology. In this review, we aim at updating clinical diagnostic criteria and describing genetic and non-genetic aetiologies, animal models as well as novel diagnostic tools and surgical management, in order to help and improve clinical care and genetic counselling of these patients and their families.
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Affiliation(s)
- Angèle Tingaud-Sequeira
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France
| | - Aurélien Trimouille
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France.,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
| | - Thomas Sagardoy
- CHU de Bordeaux, Service d'oto-rhino-laryngologie, de chirurgie cervico-faciale et d'ORL pédiatrique, 33076 Bordeaux, France
| | - Didier Lacombe
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France.,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
| | - Caroline Rooryck-Thambo
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France .,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
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15
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Abstract
The field of craniofacial malformations is comprehensive and does not allow to discuss all craniofacial malformations which have been described as single entities. Many of the syndromes with craniofacial malformations are ultrarare. In this review we have chosen craniofacial malformation syndromes which are of relevance for the pediatrician, especially neonatologist: different types of craniosynostoses, oculo-auriculo-vertebral spectrum, Pierre Robin sequence and Treacher Collins syndrome. These syndromes will be described in detail. Diagnostic and therapeutic options will be discussed.
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Affiliation(s)
- Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | - Jeanne Amiel
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, AP-HP, Paris, France
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany.
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16
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Peusner KD, Bell NM, Hirsch JC, Beraneck M, Popratiloff A. Understanding the Pathophysiology of Congenital Vestibular Disorders: Current Challenges and Future Directions. Front Neurol 2021; 12:708395. [PMID: 34589045 PMCID: PMC8475631 DOI: 10.3389/fneur.2021.708395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
In congenital vestibular disorders (CVDs), children develop an abnormal inner ear before birth and face postnatal challenges to maintain posture, balance, walking, eye-hand coordination, eye tracking, or reading. Only limited information on inner ear pathology is acquired from clinical imaging of the temporal bone or studying histological slides of the temporal bone. A more comprehensive and precise assessment and determination of the underlying mechanisms necessitate analyses of the disorders at the cellular level, which can be achieved using animal models. Two main criteria for a suitable animal model are first, a pathology that mirrors the human disorder, and second, a reproducible experimental outcome leading to statistical power. With over 40 genes that affect inner ear development, the phenotypic abnormalities resulting from congenital vestibular disorders (CVDs) are highly variable. Nonetheless, there is a large subset of CVDs that form a common phenotype of a sac-like inner ear with the semicircular canals missing or dysplastic, and discrete abnormalities in the vestibular sensory organs. We have focused the review on this subset, but to advance research on CVDs we have added other CVDs not forming a sac-like inner ear. We have included examples of animal models used to study these CVDs. Presently, little is known about the central pathology resulting from CVDs at the cellular level in the central vestibular neural network, except for preliminary studies on a chick model that show significant loss of second-order, vestibular reflex projection neurons.
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Affiliation(s)
- Kenna D Peusner
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Nina M Bell
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - June C Hirsch
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Mathieu Beraneck
- Université de Paris, Integrative Neuroscience and Cognition Center, CNRS UMR 8002, Paris, France
| | - Anastas Popratiloff
- The George Washington University Nanofabrication and Imaging Center, Washington, DC, United States
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17
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Güleray N, Koşukcu C, Oğuz S, Ürel Demir G, Taşkıran EZ, Kiper PÖŞ, Utine GE, Alanay Y, Boduroğlu K, Alikaşifoğlu M. Investigation of Genetic Causes in a Developmental Disorder: Oculoauriculovertebral Spectrum. Cleft Palate Craniofac J 2021; 59:1114-1124. [PMID: 34410171 DOI: 10.1177/10556656211038115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Oculoauriculovertebral spectrum (OAVS) is a genetically and clinically heterogeneous disorder that occurs due to a developmental field defect of the first and second pharyngeal arches. Even though recent whole exome sequencing studies (WES) have led to identification of several genes associated with this spectrum in a subset of individuals, complete pathogenesis of OAVS remains unsolved. In this study, molecular genetic etiology of OAVS was systematically investigated. DESIGN/SETTING/PATIENTS A cohort of 23 Turkish patients with OAVS, referred to Hacettepe University Hospital, Department of Pediatric Genetics from 2008 to 2018, was included in this study. Minimal diagnostic criteria for OAVS were considered as unilateral microtia or hemifacial microsomia with preauricular skin tag. The cohort was clinically reevaluated for craniofacial and extracranial findings. Molecular etiology was investigated using candidate gene sequencing following copy number variant (CNV) analysis. WES was also performed for 2 of the selected patients. RESULTS Patients in the study cohort presented similar demographic and phenotypic characteristics to previously described patients in the literature except for a higher frequency of bilaterality, cardiac findings, and intellectual disability/developmental delay. CNV analysis revealed a possible genetic etiology for 3 patients (13%). Additional WES in 1 of the 2 patients uncovered a novel heterozygous nonsense variant in Elongation factor Tu GTP-binding domain-containing 2 (EFTUD2) causing mandibulofacial dysostosis with microcephaly (MFDM), which clinically overlaps with OAVS. CONCLUSION Detailed clinical evaluation for any patient with OAVS is recommended due to a high rate of accompanying systemic findings. We further expand the existing genetic heterogeneity of OAVS by identifying several CNVs and a phenotypically overlapping disorder, MFDM.
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Affiliation(s)
- Naz Güleray
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Can Koşukcu
- Department of Bioinformatics, Hacettepe University Institute of Health Sciences, Ankara, Turkey
| | - Sümeyra Oğuz
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Gizem Ürel Demir
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ekim Z Taşkıran
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | | | - Gülen Eda Utine
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yasemin Alanay
- Department of Pediatric Genetics, Acıbadem University Faculty of Medicine, Istanbul, Turkey
| | - Koray Boduroğlu
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Mehmet Alikaşifoğlu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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18
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Guida V, Sparascio FP, Bernardini L, Pancheri F, Melis D, Cocciadiferro D, Pagnoni M, Puzzo M, Goldoni M, Barone C, Hozhabri H, Putotto C, Giuffrida MG, Briuglia S, Palumbo O, Bianca S, Stanzial F, Benedicenti F, Kariminejad A, Forzano F, Baghernajad Salehi L, Mattina T, Brancati F, Castori M, Carella M, Fadda MT, Iannetti G, Dallapiccola B, Digilio MC, Marino B, Tartaglia M, De Luca A. Copy number variation analysis implicates novel pathways in patients with oculo-auriculo-vertebral-spectrum and congenital heart defects. Clin Genet 2021; 100:268-279. [PMID: 33988253 DOI: 10.1111/cge.13994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/22/2021] [Accepted: 05/08/2021] [Indexed: 12/19/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder of craniofacial morphogenesis. Its etiology is unclear, but assumed to be complex and heterogeneous, with contribution of both genetic and environmental factors. We assessed the occurrence of copy number variants (CNVs) in a cohort of 19 unrelated OAVS individuals with congenital heart defect. Chromosomal microarray analysis identified pathogenic CNVs in 2/19 (10.5%) individuals, and CNVs classified as variants of uncertain significance in 7/19 (36.9%) individuals. Remarkably, two subjects had small intragenic CNVs involving DACH1 and DACH2, two paralogs coding for key components of the PAX-SIX-EYA-DACH network, a transcriptional regulatory pathway controlling developmental processes relevant to OAVS and causally associated with syndromes characterized by craniofacial involvement. Moreover, a third patient showed a large duplication encompassing DMBX1/OTX3, encoding a transcriptional repressor of OTX2, another transcription factor functionally connected to the DACH-EYA-PAX network. Among the other relevant CNVs, a deletion encompassing HSD17B6, a gene connected with the retinoic acid signaling pathway, whose dysregulation has been implicated in craniofacial malformations, was also identified. Our findings suggest that CNVs affecting gene dosage likely contribute to the genetic heterogeneity of OAVS, and implicate the PAX-SIX-EYA-DACH network as novel pathway involved in the etiology of this developmental trait.
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Affiliation(s)
- Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesca Piceci Sparascio
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.,Department of Experimental Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Laura Bernardini
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Pancheri
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Daniela Melis
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Naples, Italy.,Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Dario Cocciadiferro
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.,Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mario Pagnoni
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Marianna Puzzo
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marina Goldoni
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Chiara Barone
- Medical Genetics, Referral Center for Rare Genetic Diseases, ARNAS Garibaldi, Catania, Italy
| | - Hossein Hozhabri
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Carolina Putotto
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Maria Grazia Giuffrida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Silvana Briuglia
- Department of Human Pathology of Adult and Childhood "Gaetano Barresi", Unit of Emergency Pediatrics, University of Messina, Messina, Italy
| | - Orazio Palumbo
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Sebastiano Bianca
- Medical Genetics, Referral Center for Rare Genetic Diseases, ARNAS Garibaldi, Catania, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Francesca Forzano
- Clinical Genetics Department, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | | | - Teresa Mattina
- Unit of Medical Genetics, University of Catania, Catania, Italy
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, Unit of Medical Genetics University of L'Aquila, L'Aquila, Italy
| | - Marco Castori
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Teresa Fadda
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Giorgio Iannetti
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Bruno Marino
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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19
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Zamariolli M, Burssed B, Moysés-Oliveira M, Colovati M, Bellucco FTDS, Dos Santos LC, Alvarez Perez AB, Bragagnolo S, Melaragno MI. Novel MYT1 variants expose the complexity of oculo-auriculo-vertebral spectrum genetic mechanisms. Am J Med Genet A 2021; 185:2056-2064. [PMID: 33880880 DOI: 10.1002/ajmg.a.62217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder characterized by anomalies mainly involving the structures derived from the first and second pharyngeal arches. The spectrum presents with heterogeneous clinical features and complex etiology with genetic factors not yet completely understood. To date, MYT1 is the most important gene unambiguously associated with the spectrum and with functional data confirmation. In this work, we aimed to identify new single nucleotide variants (SNVs) affecting MYT1 in a cohort of 73 Brazilian patients diagnosed with OAVS. In addition, we investigated copy number variations (CNVs) encompassing this gene or its cis-regulatory elements and compared the frequency of these events in patients versus a cohort of 455 Brazilian control individuals. A new SNV, predicted as likely deleterious, was identified in five unrelated patients with OAVS. All five patients presented hearing impairment and orbital asymmetry suggesting an association with the variant. CNVs near MYT1, located in its neighboring topologically associating domain (TAD), were found to be enriched in patients when compared to controls, indicating a possible involvement of this region with OAVS pathogenicity. Our findings highlight the genetic complexity of the spectrum that seems to involve more than one variant type and inheritance patterns.
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Affiliation(s)
- Malú Zamariolli
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bruna Burssed
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mileny Colovati
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Leonardo Caires Dos Santos
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Beatriz Alvarez Perez
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Silvia Bragagnolo
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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20
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Guida V, Calzari L, Fadda MT, Piceci-Sparascio F, Digilio MC, Bernardini L, Brancati F, Mattina T, Melis D, Forzano F, Briuglia S, Mazza T, Bianca S, Valente EM, Salehi LB, Prontera P, Pagnoni M, Tenconi R, Dallapiccola B, Iannetti G, Corsaro L, De Luca A, Gentilini D. Genome-Wide DNA Methylation Analysis of a Cohort of 41 Patients Affected by Oculo-Auriculo-Vertebral Spectrum (OAVS). Int J Mol Sci 2021; 22:ijms22031190. [PMID: 33530447 PMCID: PMC7866060 DOI: 10.3390/ijms22031190] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Oculo-auriculo-vertebral-spectrum (OAVS; OMIM 164210) is a rare disorder originating from abnormal development of the first and second branchial arch. The clinical phenotype is extremely heterogeneous with ear anomalies, hemifacial microsomia, ocular defects, and vertebral malformations being the main features. MYT1, AMIGO2, and ZYG11B gene variants were reported in a few OAVS patients, but the etiology remains largely unknown. A multifactorial origin has been proposed, including the involvement of environmental and epigenetic mechanisms. To identify the epigenetic mechanisms contributing to OAVS, we evaluated the DNA-methylation profiles of 41 OAVS unrelated affected individuals by using a genome-wide microarray-based methylation approach. The analysis was first carried out comparing OAVS patients with controls at the group level. It revealed a moderate epigenetic variation in a large number of genes implicated in basic chromatin dynamics such as DNA packaging and protein-DNA organization. The alternative analysis in individual profiles based on the searching for Stochastic Epigenetic Variants (SEV) identified an increased number of SEVs in OAVS patients compared to controls. Although no recurrent deregulated enriched regions were found, isolated patients harboring suggestive epigenetic deregulations were identified. The recognition of a different DNA methylation pattern in the OAVS cohort and the identification of isolated patients with suggestive epigenetic variations provide consistent evidence for the contribution of epigenetic mechanisms to the etiology of this complex and heterogeneous disorder.
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Affiliation(s)
- Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (F.P.-S.); (L.B.); (A.D.L.)
- Correspondence: (V.G.); (D.G.)
| | - Luciano Calzari
- Istituto Auxologico Italiano IRCCS, Bioinformatics and Statistical Genomics Unit, Cusano Milanino, 20095 Milano, Italy;
| | - Maria Teresa Fadda
- Department of Maxillofacial Surgery, Sapienza University of Rome, 00161 Rome, Italy; (M.T.F.); (M.P.); (G.I.)
| | - Francesca Piceci-Sparascio
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (F.P.-S.); (L.B.); (A.D.L.)
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (M.C.D.); (B.D.)
| | - Laura Bernardini
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (F.P.-S.); (L.B.); (A.D.L.)
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, Unit of Medical Genetics University of L’Aquila, 67100 L’Aquila, Italy;
- IRCCS San Raffaele Pisana, 00163 Rome, Italy
| | - Teresa Mattina
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95131 Catania, Italy;
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84084 Salerno, Italy;
| | - Francesca Forzano
- Clinical Genetics Department, Guy’s & St Thomas’ NHS Foundation Trust, London SE1 7EH, UK;
| | | | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy;
| | - Sebastiano Bianca
- Centro di Consulenza Genetica e Teratologia della Riproduzione, Dipartimento Materno Infantile, ARNAS Garibaldi Nesima, 95123 Catania, Italy;
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy;
- IRCCS Mondino Foundation, 27100 Pavia, Italy
| | | | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, 06129 Perugia, Italy;
| | - Mario Pagnoni
- Department of Maxillofacial Surgery, Sapienza University of Rome, 00161 Rome, Italy; (M.T.F.); (M.P.); (G.I.)
| | - Romano Tenconi
- Department of Pediatrics, Clinical Genetics, Università di Padova, 35122 Padova, Italy;
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (M.C.D.); (B.D.)
| | - Giorgio Iannetti
- Department of Maxillofacial Surgery, Sapienza University of Rome, 00161 Rome, Italy; (M.T.F.); (M.P.); (G.I.)
| | - Luigi Corsaro
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (F.P.-S.); (L.B.); (A.D.L.)
| | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Bioinformatics and Statistical Genomics Unit, Cusano Milanino, 20095 Milano, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
- Correspondence: (V.G.); (D.G.)
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21
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Tingaud‐Sequeira A, Trimouille A, Marlin S, Lopez E, Berenguer M, Gherbi S, Arveiler B, Lacombe D, Rooryck C. Functional and genetic analyses of ZYG11B provide evidences for its involvement in OAVS. Mol Genet Genomic Med 2020; 8:e1375. [PMID: 32738032 PMCID: PMC7549578 DOI: 10.1002/mgg3.1375] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/30/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Oculo-Auriculo-Vertebral Spectrum (OAVS) or Goldenhar Syndrome is an embryonic developmental disorder characterized by hemifacial microsomia associated with auricular, ocular and vertebral malformations. The clinical heterogeneity of this spectrum and its incomplete penetrance limited the molecular diagnosis. In this study, we describe a novel causative gene, ZYG11B. METHODS A sporadic case of OAVS was analyzed by whole exome sequencing in trio strategy. The identified candidate gene, ZYG11B, was screened in 143 patients by next generation sequencing. Overexpression and immunofluorescence of wild-type and mutated ZYG11B forms were performed in Hela cells. Moreover, morpholinos were used for transient knockdown of its homologue in zebrafish embryo. RESULTS A nonsense de novo heterozygous variant in ZYG11B, (NM_024646, c.1609G>T, p.Glu537*) was identified in a single OAVS patient. This variant leads in vitro to a truncated protein whose subcellular localization is altered. Transient knockdown of the zebrafish homologue gene confirmed its role in craniofacial cartilages architecture and in notochord development. Moreover, ZYG11B expression regulates a cartilage master regulator, SOX6, and is regulated by Retinoic Acid, a known developmental toxic molecule leading to clinical features of OAVS. CONCLUSION Based on genetic, cellular and animal model data, we proposed ZYG11B as a novel rare causative gene for OAVS.
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Affiliation(s)
| | - Aurélien Trimouille
- Maladies Rares: Génétique et Métabolisme (MRGM)U 1211 INSERMUniv. BordeauxBordeauxFrance
- Service de Génétique MédicaleCentre de Référence Anomalies du Développement et Syndromes MalformatifsCHU de BordeauxBordeauxFrance
| | - Sandrine Marlin
- Département de GénétiqueCentre de Référence des Surdités GénétiquesInstitut ImagineHôpital Universitaire Necker‐Enfants‐MaladesParisFrance
- Institut ImagineU 1163 INSERMUniversité Paris DescartesParisFrance
| | - Estelle Lopez
- Maladies Rares: Génétique et Métabolisme (MRGM)U 1211 INSERMUniv. BordeauxBordeauxFrance
| | - Marie Berenguer
- Maladies Rares: Génétique et Métabolisme (MRGM)U 1211 INSERMUniv. BordeauxBordeauxFrance
| | - Souad Gherbi
- Département de GénétiqueCentre de Référence des Surdités GénétiquesInstitut ImagineHôpital Universitaire Necker‐Enfants‐MaladesParisFrance
| | - Benoit Arveiler
- Maladies Rares: Génétique et Métabolisme (MRGM)U 1211 INSERMUniv. BordeauxBordeauxFrance
- Service de Génétique MédicaleCentre de Référence Anomalies du Développement et Syndromes MalformatifsCHU de BordeauxBordeauxFrance
| | - Didier Lacombe
- Maladies Rares: Génétique et Métabolisme (MRGM)U 1211 INSERMUniv. BordeauxBordeauxFrance
- Service de Génétique MédicaleCentre de Référence Anomalies du Développement et Syndromes MalformatifsCHU de BordeauxBordeauxFrance
| | - Caroline Rooryck
- Maladies Rares: Génétique et Métabolisme (MRGM)U 1211 INSERMUniv. BordeauxBordeauxFrance
- Service de Génétique MédicaleCentre de Référence Anomalies du Développement et Syndromes MalformatifsCHU de BordeauxBordeauxFrance
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