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Goida J, Pilmane M. The presence and distribution of various genes in postnatal CLP-affected palatine tissue. Maxillofac Plast Reconstr Surg 2024; 46:1. [PMID: 38227085 DOI: 10.1186/s40902-024-00412-1] [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: 09/13/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Worldwide cleft lip with or without a cleft palate (CL/P) is the most common craniofacial birth defect. Apart from changes in facial appearance, additionally affected individuals often suffer from various associated comorbidities requiring complex multidisciplinary treatment with overall high expenses. Understanding the complete pathogenetic mechanisms of CL/P might aid in developing new preventative strategies and therapeutic approaches, help with genetic counselling, and improve quality of life. Many genes have been associated with the development of orofacial clefts; however, the majority require further research. Based on the role of PAX7, PAX9, SHH, SOX3, WNT3A, and WNT9B in orofacial development, the intention was to use chromogenic in situ hybridization to detect the six genes in postnatal CLP-affected palatine tissue and compare their distribution within the tissue samples. RESULTS Statistically significant differences in the distribution of PAX7, PAX9, WNT3A, and WNT9B were observed. In total, 19 pairs of moderate to very strong positive correlations were noted. CONCLUSIONS Changes in the cleft-affected palatine epithelium primarily seem to be associated with the PAX7 gene; however, PAX9, WNT3A, WNT9B, and SOX3 role seems to be more limited. Whilst connective tissue changes seem to depend on PAX7 only, SHH seems to participate individually and indistinctly. Numerous positive correlations reflect the complicating interactions of the pathways and their components in the orofacial cleft morphopathogenesis.
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Affiliation(s)
- Jana Goida
- Institute of Anatomy and Anthropology, Riga Stradins University, Riga, LV-1010, Latvia.
| | - Mara Pilmane
- Institute of Anatomy and Anthropology, Riga Stradins University, Riga, LV-1010, Latvia
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet 2023; 142:1531-1541. [PMID: 37676273 DOI: 10.1007/s00439-023-02596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287714. [PMID: 37034635 PMCID: PMC10081436 DOI: 10.1101/2023.03.24.23287714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205,USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
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Pilmane M, Jain N, Nadzina E, Fedirko P, Sumeraga G. Immunohistochemical evaluation of the cleft-affected scar tissue three decades post-corrective surgery: A rare case report. ACTA OTO-LARYNGOLOGICA CASE REPORTS 2022. [DOI: 10.1080/23772484.2022.2146586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Mara Pilmane
- Department of Morphology, Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Nityanand Jain
- Department of Morphology, Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Elina Nadzina
- Department of Morphology, Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Pavlo Fedirko
- Institute of Radiation Hygiene and Epidemiology, State Institution – National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Gunta Sumeraga
- Department of Otorhinolaryngology, Riga Stradiņš University, Riga, Latvia
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