1
|
Sun B, Reynolds K, Saha SK, Zhang S, McMahon M, Zhou CJ. Ezh2-dependent methylation in oral epithelia promotes secondary palatogenesis. Birth Defects Res 2023; 115:1851-1865. [PMID: 37435868 PMCID: PMC10784412 DOI: 10.1002/bdr2.2216] [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: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND In addition to genomic risk variants and environmental influences, increasing evidence suggests epigenetic modifications are important for orofacial development and their alterations can contribute to orofacial clefts. Ezh2 encodes a core catalytic component of the Polycomb repressive complex responsible for addition of methyl marks to Histone H3 as a mechanism of repressing target genes. The role of Ezh2 in orofacial clefts remains unknown. AIMS To investigate the epithelial role of Ezh2-dependent methylation in secondary palatogenesis. METHODS We used conditional gene-targeting methods to ablate Ezh2 in the surface ectoderm-derived oral epithelium of mouse embryos. We then performed single-cell RNA sequencing combined with immunofluorescence and RT-qPCR to investigate gene expression in conditional mutant palate. We also employed double knockout analyses of Ezh1 and Ezh2 to address if they have synergistic roles in palatogenesis. RESULTS We found that conditional inactivation of Ezh2 in oral epithelia results in partially penetrant cleft palate. Double knockout analyses revealed that another family member Ezh1 is dispensable in orofacial development, and it does not have synergistic roles with Ezh2 in palatogenesis. Histochemistry and single-cell RNA-seq analyses revealed dysregulation of cell cycle regulators in the palatal epithelia of Ezh2 mutant mouse embryos disrupts palatogenesis. CONCLUSION Ezh2-dependent histone H3K27 methylation represses expression of cell cycle regulator Cdkn1a and promotes proliferation in the epithelium of the developing palatal shelves. Loss of this regulation may perturb movement of the palatal shelves, causing a delay in palate elevation which may result in failure of the secondary palate to close altogether.
Collapse
Affiliation(s)
| | | | - Subbroto Kuma Saha
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Shuwen Zhang
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Moira McMahon
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Chengji J Zhou
- Institute for Pediatric Regenerative Medicine of Shriners Hospital for Children – Northern California & Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| |
Collapse
|
2
|
Enkhmandakh B, Joshi P, Robson P, Vijaykumar A, Mina M, Shin DG, Bayarsaihan D. Single-cell Transcriptome Landscape of DNA Methylome Regulators Associated with Orofacial Clefts in the Mouse Dental Pulp. Cleft Palate Craniofac J 2023:10556656231172296. [PMID: 37161276 DOI: 10.1177/10556656231172296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
OBJECTIVE Significant evidence links epigenetic processes governing the dynamics of DNA methylation and demethylation to an increased risk of syndromic and nonsyndromic cleft lip and/or cleft palate (CL/P). Previously, we characterized mesenchymal stem/stromal cells (MSCs) at different stages of osteogenic differentiation in the mouse incisor dental pulp. The main objective of this research was to characterize the transcriptional landscape of regulatory genes associated with DNA methylation and demethylation at a single-cell resolution. DESIGN We used single-cell RNA sequencing (scRNA-seq) data to characterize transcriptome in individual subpopulations of MSCs in the mouse incisor dental pulp. SETTINGS The biomedical research institution. PATIENTS/PARTICIPANTS This study did not include patients. INTERVENTIONS This study collected and analyzed data on the single-cell RNA expssion in the mouse incisor dental pulp. MAIN OUTCOME MEASURE(S) Molecular regulators of DNA methylation/demethylation exhibit differential transcriptional landscape in different subpopulations of osteogenic progenitor cells. RESULTS scRNA-seq analysis revealed that genes encoding DNA methylation and demethylation enzymes (DNA methyltransferases and members of the ten-eleven translocation family of methylcytosine dioxygenases), methyl-DNA binding domain proteins, as well as transcription factors and chromatin remodeling proteins that cooperate with DNA methylation machinery are differentially expressed within distinct subpopulations of MSCs that undergo different stages of osteogenic differentiation. CONCLUSIONS These findings suggest some mechanistic insights into a potential link between epigenetic alterations and multifactorial causes of CL/P phenotypes.
Collapse
Affiliation(s)
- Badam Enkhmandakh
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Pujan Joshi
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Single Cell Biology Laboratory, Farmington, CT, USA
| | - Anushree Vijaykumar
- Department of Craniofacial Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Mina Mina
- Department of Craniofacial Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Dong-Guk Shin
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Institute for System Genomics, University of Connecticut, Storrs, CT, USA
| |
Collapse
|
3
|
Petrin AL, Zeng E, Thomas MA, Moretti-Ferreira D, Marazita ML, Xie XJ, Murray JC, Moreno-Uribe LM. DNA methylation differences in monozygotic twins with Van der Woude syndrome. FRONTIERS IN DENTAL MEDICINE 2023; 4:1120948. [PMID: 36936396 PMCID: PMC10019782 DOI: 10.3389/fdmed.2023.1120948] [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] [Indexed: 02/19/2023] Open
Abstract
Introduction Van der Woude Syndrome (VWS) is an autosomal dominant disorder responsible for 2% of all syndromic orofacial clefts (OFCs) with IRF6 being the primary causal gene (70%). Cases may present with lip pits and either cleft lip, cleft lip with cleft palate, or cleft palate, with marked phenotypic discordance even among individuals carrying the same mutation. This suggests that genetic or epigenetic modifiers may play additional roles in the syndrome's etiology and variability in expression. We report the first DNA methylation profiling of 2 pairs of monozygotic twins with VWS. Our goal is to explore epigenetic contributions to VWS etiology and variable phenotypic expressivity by comparing DNAm profiles in both twin pairs. While the mutations that cause VWS in these twins are known, the additional mechanism behind their phenotypic risk and variability in expression remains unclear. Methods We generated whole genome DNAm data for both twin pairs. Differentially methylated positions (DMPs) were selected based on: (1) a coefficient of variation in DNAm levels in unaffected individuals < 20%, and (2) intra-twin pair absolute difference in DNAm levels >5% (delta beta > | 0.05|). We then divided the DMPs in two subgroups for each twin pair for further analysis: (1) higher methylation levels in twin A (Twin A > Twin B); and (2) higher methylation levels in twin B (Twin B >Twin A). Results and Discussion Gene ontology analysis revealed a list of enriched genes that showed significant differential DNAm, including clef-associated genes. Among the cleft-associated genes, TP63 was the most significant hit (p=7.82E-12). Both twin pairs presented differential DNAm levels in CpG sites in/near TP63 (Twin 1A > Twin 1B and Twin 2A < Twin 2B). The genes TP63 and IRF6 function in a biological regulatory loop to coordinate epithelial proliferation and differentiation in a process that is critical for palatal fusion. The effects of the causal mutations in IRF6 can be further impacted by epigenetic dysregulation of IRF6 itself, or genes in its pathway. Our data shows evidence that changes in DNAm is a plausible mechanism that can lead to markedly distinct phenotypes, even among individuals carrying the same mutation.
Collapse
Affiliation(s)
- A. L. Petrin
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
- CORRESPONDENCE A. L. Petrin
| | - E. Zeng
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - M. A. Thomas
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - D. Moretti-Ferreira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - M. L. Marazita
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - X. J. Xie
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - J. C. Murray
- Carver College of Medicine, University of Iowa, Iowa, IA, United States
| | - L. M. Moreno-Uribe
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| |
Collapse
|
4
|
Charoenvicha C, Sirimaharaj W, Khwanngern K, Chattipakorn N, Chattipakorn SC. Alterations in DNA Methylation in Orofacial Clefts. Int J Mol Sci 2022; 23:ijms232112727. [PMID: 36361518 PMCID: PMC9654384 DOI: 10.3390/ijms232112727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Orofacial clefts are among the most common craniofacial anomalies with multifactorial etiologies, including genetics and environments. DNA methylation, one of the most acknowledged mechanisms of epigenetics, is involved in the development of orofacial clefts. DNA methylation has been examined in patients with non-syndromic cleft lip with cleft palate (nsCL/P) from multiple specimens, including blood, saliva, lip, and palate, as well as experimental studies in mice. The results can be reported in two different trends: hypomethylation and hypermethylation. Both hypomethylation and hypermethylation can potentially increase the risk of nsCL/P depending on the types of specimens and the specific regions on each gene and chromosome. This is the most up-to-date review, intending to summarize evidence of the alterations of DNA methylation in association with the occurrence of orofacial clefts. To make things straightforward to understand, we have systematically categorized the data into four main groups: human blood, human tissues, animal models, and the factors associated with DNA methylation. With this review, we are moving closer to the core of DNA methylation associated with nsCL/P development; we hope this is the initial step to find a genetic tool for early detection and prevention of the occurrence of nsCL/P.
Collapse
Affiliation(s)
- Chirakan Charoenvicha
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Clinical Surgical Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wimon Sirimaharaj
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Krit Khwanngern
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Siriporn C. Chattipakorn
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +011-66-53-944-451; Fax: +011-66-53-222-844
| |
Collapse
|
5
|
Garland MA, Sun B, Zhang S, Reynolds K, Ji Y, Zhou CJ. Role of epigenetics and miRNAs in orofacial clefts. Birth Defects Res 2020; 112:1635-1659. [PMID: 32926553 DOI: 10.1002/bdr2.1802] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/17/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022]
Abstract
Orofacial clefts (OFCs) have multiple etiologies and likely result from an interplay between genetic and environmental factors. Within the last decade, studies have implicated specific epigenetic modifications and noncoding RNAs as additional facets of OFC etiology. Altered gene expression through DNA methylation and histone modification offer novel insights into how specific genes contribute to distinct OFC subtypes. Epigenetics research has also provided further evidence that cleft lip only (CLO) is a cleft subtype with distinct etiology. Polymorphisms or misexpression of genes encoding microRNAs, as well as their targets, contribute to OFC risk. The ability to experimentally manipulate epigenetic changes and noncoding RNAs in animal models, such as zebrafish, Xenopus, mice, and rats, has offered novel insights into the mechanisms of various OFC subtypes. Although much remains to be understood, recent advancements in our understanding of OFC etiology may advise future strategies of research and preventive care.
Collapse
Affiliation(s)
- Michael A Garland
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA
| | - Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| |
Collapse
|
6
|
Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
Collapse
Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| |
Collapse
|