Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models

Orofacial clefting (OFC) is a frequent congenital anomaly and can occur either in the context of underlying syndromes or in isolation (nonsyndromic). The two common OFC phenotypes are cleft lip with/without cleft palate (CL/P) and cleft palate only (CPO). In this study, we searched for penetrant CL/P genes, by evaluating de novo copy number variants (CNV) from an exome sequencing dataset of 50 nonsyndromic patient-parent trios. We detected a heterozygous 86 kb de novo deletion affecting exons 4-11 of ZFHX4, a gene previously associated with OFC. Genetic and phenotypic data from our in-house and the AGORA cohort (710 and 229 individuals with nonsyndromic CL/P) together with literature and database reviews demonstrate that ZFHX4 variants can lead to both nonsyndromic and syndromic forms not only of CL/P but also CPO. Expression analysis in published single-cell RNA-sequencing data (mouse embryo, zebrafish larva) at relevant time-points support an important role of Zfhx4/zfhx4 in craniofacial development. To characterize the role of zfhx4 in zebrafish craniofacial development, we knocked out/down the zebrafish orthologue. Cartilage staining of the zfhx4 CRISPR F0 knockout and morpholino knockdown at 4 days post-fertilization showed an underdeveloped and abnormally shaped ethmoid plate and cartilaginous jaw (resembling micrognathia). While there is evidence for the dominant inheritance of ZFHX4 variants in OFC, we here present a patient with a possible recessive inheritance. In conclusion, ZFHX4 has a highly heterogeneous phenotypic spectrum and variable mode of inheritance. Our data highlight that ZFHX4 should be considered in genetic testing in patients with nonsyndromic clefting.

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Publication Details

Journal
European Journal of Human Genetics
Published
2024-12-19
DOI
https://doi.org/10.1038/s41431-024-01775-9
Citations
5
Primary Topic
Cleft Lip and Palate Research
Type
article
Field-Weighted Citation Impact
2.75

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article

Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models

Enrico Mingardo, Jessica Lambertz, Iris A.L.M. van Rooij, Katta M. Girisha et al.
5 citations
European Journal of Human Genetics
Cleft Lip and Palate Research
2.75
article

Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models

Enrico Mingardo, Jessica Lambertz, Iris A.L.M. van Rooij, Katta M. Girisha, Anna Siewert, Tobias Lindenberg, Stefanie Nowak, Edwin M. Ongkosuwito, Teresa Kruse, Dmitriy Drichel, Sabrina K. Henne, Jeshurun C. Kalanithy, Carola Greve, Gregor Hagelueken, Matthias Geyer, Elisabeth Mangold, Kerstin U. Ludwig, Shruti Pande, Michael J. Dixon, Nina Ishorst, Benjamin Odermatt, Franziska Degenhardt, Carine Carels, Öznur Yılmaz, Selina Hölzel, Khadija Channab, Berina Zametica, Duygu Kibris
article en
5 citations

Abstract

Orofacial clefting (OFC) is a frequent congenital anomaly and can occur either in the context of underlying syndromes or in isolation (nonsyndromic). The two common OFC phenotypes are cleft lip with/without cleft palate (CL/P) and cleft palate only (CPO). In this study, we searched for penetrant CL/P genes, by evaluating de novo copy number variants (CNV) from an exome sequencing dataset of 50 nonsyndromic patient-parent trios. We detected a heterozygous 86 kb de novo deletion affecting exons 4-11 of ZFHX4, a gene previously associated with OFC. Genetic and phenotypic data from our in-house and the AGORA cohort (710 and 229 individuals with nonsyndromic CL/P) together with literature and database reviews demonstrate that ZFHX4 variants can lead to both nonsyndromic and syndromic forms not only of CL/P but also CPO. Expression analysis in published single-cell RNA-sequencing data (mouse embryo, zebrafish larva) at relevant time-points support an important role of Zfhx4/zfhx4 in craniofacial development. To characterize the role of zfhx4 in zebrafish craniofacial development, we knocked out/down the zebrafish orthologue. Cartilage staining of the zfhx4 CRISPR F0 knockout and morpholino knockdown at 4 days post-fertilization showed an underdeveloped and abnormally shaped ethmoid plate and cartilaginous jaw (resembling micrognathia). While there is evidence for the dominant inheritance of ZFHX4 variants in OFC, we here present a patient with a possible recessive inheritance. In conclusion, ZFHX4 has a highly heterogeneous phenotypic spectrum and variable mode of inheritance. Our data highlight that ZFHX4 should be considered in genetic testing in patients with nonsyndromic clefting.

European Journal of Human GeneticsVol. 33(5)
University of Bonn (DE), Radboud University Nijmegen (NL), Manipal Academy of Higher Education (IN), University of Cologne (DE), University Hospital Bonn (DE), Radboud University Medical Center (NL), University of Manchester (GB), LOEWE Centre for Translational Biodiversity Genomics (DE), University Hospital Cologne (DE), University of Bayreuth (DE), University of Duisburg-Essen (DE), Kasturba Medical College, Manipal (IN), KU Leuven (BE)
Wellcome Trust, Newcastle University, Department of Biotechnology, Ministry of Science and Technology, India, Deutsche Forschungsgemeinschaft, Else Kröner-Fresenius-Stiftung, Rheinische Friedrich-Wilhelms-Universität Bonn, The Wellcome Trust DBT India Alliance, Fakultet Medicinskih Nauka, Univerziteta U Kragujevcu, Faculty of Medical Sciences, Newcastle University
Life below water
Openalex Percentile: Top 9%
Cleft Lip and Palate Research
2.75
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