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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 2024; 61:1480-1492. [PMID: 37161276 DOI: 10.1177/10556656231172296] [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: 05/11/2023] 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.
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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
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Davies AJV, Humphries K, Lewis SJ, Ho K, Sandy JR, Wren Y. The Cleft Collective: protocol for a longitudinal prospective cohort study. BMJ Open 2024; 14:e084737. [PMID: 38969383 PMCID: PMC11227803 DOI: 10.1136/bmjopen-2024-084737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/07/2024] [Indexed: 07/07/2024] Open
Abstract
INTRODUCTION Cleft lip and/or palate (CL/P) affects 1 in 700 live births globally. Children born with CL/P and their families face various challenges throughout the child's development. Extant research is often limited by small numbers and single-centre data. The Cleft Collective, a national cohort study in the UK, aims to build a resource, available to collaborators across the globe, to understand causes, best treatments and long-term outcomes for those born with CL/P, ultimately seeking to enhance their quality of life through improved understanding and care. METHODS AND ANALYSIS A longitudinal prospective cohort study of children born with CL/P and their families. Recruitment occurs across the UK and started in November 2013. Recruitment will continue until September 2027 with an estimated final sample of 4822 children born with CL/P (1157 cleft lip including/excluding the alveolus; 2112 cleft palate only; 1042 unilateral cleft lip and palate and 511 bilateral cleft lip and palate). Biological samples are collected from all recruited members of the family. Parental and child questionnaires are collected at key time points throughout the child's development. Surgical data are collected at the time of surgical repair of the child's cleft. Consent is obtained to link to external data sources. Nested substudies can be hosted within the cohort. Regular engagement with participants takes place through birthday cards for the children, social media posts and newsletters. Patient and Public Involvement is conducted through the Cleft Lip And Palate Association and Cleft Collective Patient Consultation Group who provide insightful and essential guidance to the Cleft Collective throughout planning and conducting research. ETHICS AND DISSEMINATION The Cleft Collective was ethically approved by the National Research Ethics Service committee South West-Central Bristol (REC13/SW/0064). Parental informed consent is required for participation. Findings from the Cleft Collective are disseminated through peer-reviewed publications, conference presentations, newsletters and social media.
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Affiliation(s)
- Amy J V Davies
- Bristol Dental School, The Cleft Collective, University of Bristol Faculty of Health Sciences, Bristol, UK
| | - Kerry Humphries
- Bristol Dental School, The Cleft Collective, University of Bristol Faculty of Health Sciences, Bristol, UK
| | - Sarah J Lewis
- Bristol Medical School, University of Bristol Faculty of Health Sciences, Bristol, UK
| | - Karen Ho
- Bristol Bioresource Laboratories, University of Bristol Faculty of Health Sciences, Bristol, UK
| | - Jonathan R Sandy
- Bristol Dental School, The Cleft Collective, University of Bristol Faculty of Health Sciences, Bristol, UK
| | - Yvonne Wren
- Bristol Dental School, The Cleft Collective, University of Bristol Faculty of Health Sciences, Bristol, UK
- Bristol Speech and Language Therapy Research Unit, North Bristol NHS Trust, Westbury on Trym, Bristol, UK
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Fell M, Fitzsimons KJ, Hamilton MJ, Medina J, Butterworth S, Park MH, Van der Meulen J, Lewis S, Chong D, Russell CJ. Cleft lip Sidedness and the Association with Additional Congenital Malformations. Cleft Palate Craniofac J 2024:10556656241261918. [PMID: 38870388 DOI: 10.1177/10556656241261918] [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: 06/15/2024] Open
Abstract
OBJECTIVE To investigate the association between the sidedness of orofacial clefts and additional congenital malformations. DESIGN Linkage of a national registry of cleft births to national administrative data of hospital admissions. SETTING National Health Service, England. PARTICIPANTS 2007 children born with cleft lip ± alveolus (CL ± A) and 2724 with cleft lip and palate (CLP) born between 2000 and 2012. MAIN OUTCOME MEASURE The proportion of children with ICD-10 codes for additional congenital malformations by the sidedness (left, right or bilateral) of orofacial clefts. RESULTS For CL ± A phenotypes, there was no evidence for a difference in the prevalence of additional anomalies between left (22%, reference), right (22%, aOR 1.02, 95% CI 0.80 to 1.28; P = .90) and bilateral clefts (23%, aOR 1.09, 95% CI 0.75 to 1.57; P = .66). For CLP phenotypes, there was evidence of a lower prevalence of additional malformations in left (23%, reference) compared to right (32%, aOR 1.54, 95% CI 1.25 to 1.91; P < .001) and bilateral clefts (33%, aOR 1.64, 95% CI 1.35 to 1.99; P < .001). CONCLUSIONS The prevalence of additional congenital malformations was similar across sidedness subtypes with CL ± A phenotypes but was different for sidedness subtypes within CLP cases. These data support the hypothesis that CL ± A has a different underlying aetiology from CLP and that within the CLP phenotype, right sided CLP may lie closer in aetiology to bilateral CLP than it does to left sided CLP.
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Affiliation(s)
- Matthew Fell
- Spires Cleft Centre, John Radcliffe Hospital, Oxford, UK
- The Cleft Collective, Bristol Dental School, University of Bristol, Bristol, UK
| | - Kate J Fitzsimons
- Cleft Registry and Audit Network, Clinical Effectiveness Unit, The Royal College of Surgeons of England, London UK
| | - Mark J Hamilton
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow UK
| | - Jibby Medina
- Cleft Registry and Audit Network, Clinical Effectiveness Unit, The Royal College of Surgeons of England, London UK
| | - Sophie Butterworth
- Cleft Registry and Audit Network, Clinical Effectiveness Unit, The Royal College of Surgeons of England, London UK
| | - Min Hae Park
- Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London UK
| | - Jan Van der Meulen
- Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London UK
| | - Sarah Lewis
- The Cleft Collective, Bristol Dental School, University of Bristol, Bristol, UK
| | - David Chong
- The Royal Children's Hospital, Melbourne, Australia
| | - Craig Jh Russell
- Royal Hospital for Children, Queen Elizabeth University Hospital, Glasgow, UK
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Wang L, Sun H, Cao L, Wang J. Role of HOXA1-4 in the development of genetic and malignant diseases. Biomark Res 2024; 12:18. [PMID: 38311789 PMCID: PMC10840290 DOI: 10.1186/s40364-024-00569-x] [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: 10/30/2023] [Accepted: 01/20/2024] [Indexed: 02/06/2024] Open
Abstract
The HOXA genes, belonging to the HOX family, encompass 11 members (HOXA1-11) and exert critical functions in early embryonic development, as well as various adult processes. Furthermore, dysregulation of HOXA genes is implicated in genetic diseases, heart disease, and various cancers. In this comprehensive overview, we primarily focused on the HOXA1-4 genes and their associated functions and diseases. Emphasis was placed on elucidating the impact of abnormal expression of these genes and highlighting their significance in maintaining optimal health and their involvement in the development of genetic and malignant diseases. Furthermore, we delved into their regulatory mechanisms, functional roles, and underlying biology and explored the therapeutic potential of targeting HOXA1-4 genes for the treatment of malignancies. Additionally, we explored the utility of HOXA1-4 genes as biomarkers for monitoring cancer recurrence and metastasis.
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Affiliation(s)
- Lumin Wang
- Gastroenterology Department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China.
| | - Haifeng Sun
- The Third Department of Medical Oncology, Shaanxi Provincial Cancer Hospital Affiliated to Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Li Cao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Jinhai Wang
- Gastroenterology Department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China.
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Fell M, Bradley D, Chadha A, Butterworth S, Davies A, Russell C, Richard B, Wren Y, Lewis S, Chong D. Sidedness in Unilateral Orofacial Clefts: A Systematic Scoping Review. Cleft Palate Craniofac J 2023:10556656231221027. [PMID: 38092732 DOI: 10.1177/10556656231221027] [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: 06/27/2024] Open
Abstract
OBJECTIVE An overview of the literature relating to the sidedness of unilateral cleft lip with or without cleft palate to map current knowledge on the cause and impact of directional asymmetry. DESIGN Scoping review with a systematic search of Medline and Embase from inception to May 2023. PATIENTS, PARTICIPANTS Humans born with a left or right unilateral cleft lip with or without a cleft palate. MAIN OUTCOME MEASURES Cleft sidedness as a co-occurrence, an outcome or an exposure. RESULTS Forty studies were eligible for inclusion and confirmed the predilection for the occurrence of left sided cleft lips; 12 studies reported cleft sidedness co-occurring with another phenotype, 11 studies report sidedness as an outcome and 17 studies as an exposure. Phenotypes which were reported to co-occur with either left or right sided clefts included congenital dental anomalies, handedness and additional congenital anomalies. Variables investigated as a potential cause of left or right sided clefts as an outcome included chromosomal anomalies, genetic variants and environmental factors. Outcomes investigated in relation to cleft sidedness as an exposure included facial anatomical features, facial growth, educational attainment, functional and psychological characteristics. More studies showed worse outcomes in right sided clefts versus left sided clefts than vice versa, although studies were inconsistent, and a quality assessment was not performed. CONCLUSIONS The field of cleft sidedness research is expanding and there are promising early findings to differentiate cause and outcome by sidedness of the cleft.
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Affiliation(s)
- Matthew Fell
- Spires Cleft Centre, John Radcliffe Hospital, Oxford, UK
- The Cleft Collective, Bristol Dental School, University of Bristol, Bristol, UK
| | | | - Ambika Chadha
- Cleft.Net.East, University of Cambridge NHS Hospitals Trust, Cambridge, UK
- Department of Perinatal Imaging and Health, Kings College London & South Thames Cleft Service, St. Thomas Hospital, London, UK
| | - Sophie Butterworth
- Cleft Registry and Audit Network, Clinical Excellence Unit, The Royal College of Surgeons of England, London, UK
| | - Amy Davies
- The Cleft Collective, Bristol Dental School, University of Bristol, Bristol, UK
| | - Craig Russell
- Cleft Care Scotland, Royal Hospital for Children, Queen Elizabeth University Hospital, Glasgow, UK
| | - Bruce Richard
- West Midlands Cleft Service, Birmingham Women and Children's Hospital, Birmingham, UK
| | - Yvonne Wren
- The Cleft Collective, Bristol Dental School, University of Bristol, Bristol, UK
- Speech and language therapy research unit, North Bristol NHS Trust, Bristol, UK
| | - Sarah Lewis
- The Cleft Collective, Bristol Dental School, University of Bristol, UK
| | - David Chong
- Plastic and Maxillofacial Surgery, The Royal Children's Hospital, Melbourne, Australia
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Yu Z, Wang G, Song S, Zhang Y, Wu Y, Zhang Y, Duan W, Liu X. Associations between the proliferation of palatal mesenchymal cells, Tgfβ2 promoter methylation, Meg3 expression, and Smad signaling in atRA-induced cleft palate. Reprod Toxicol 2023; 122:108486. [PMID: 37866657 DOI: 10.1016/j.reprotox.2023.108486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
All-trans retinoic acid (atRA) is a teratogen that can induce cleft palate formation. During palatal development, murine embryonic palate mesenchymal (MEPM) cell proliferation is required for the appropriate development of the palatal frame, with Meg3 serving as a key regulator of the proliferative activity of these cells and the associated epithelial-mesenchymal transition process. DNA methylation and signaling via the TGFβ/Smad pathway are key in regulating embryonic development. Here, the impact of atRA on MEPM cell proliferation and associations between Tgfβ2 promoter methylation, Meg3, and signaling via the Smad pathway were explored using C57BL/6 N mice treated with atRA (100 mg/kg) to induce fetal cleft palate formation. Immunohistochemistry and BrdU assays were used to detect MEPM proliferation and DNA methylation assays were performed to detect Tgfβ2 promoter expression. These analyses revealed that atRA suppressed MEPM cell proliferation, promoted the upregulation of Meg3, and reduced the levels of Smad2 and Tgfβ2 expression phosphorylation, whereas Tgfβ2 promoter methylation was unaffected. RNA immunoprecipitation experiments indicated that the TgfβI receptor is directly targeted by Meg3, suggesting that the ability of atRA to induce cleft palate may be mediated through the Tgfβ/Smad signaling pathway.
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Affiliation(s)
- Zengli Yu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China; School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guoxu Wang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaixing Song
- School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yaxin Zhang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yang Wu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Yuwei Zhang
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Wenjing Duan
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Xiaozhuan Liu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China.
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Parham MJ, Simpson AE, Moreno TA, Maricevich RS. Updates in Cleft Care. Semin Plast Surg 2023; 37:240-252. [PMID: 38098682 PMCID: PMC10718659 DOI: 10.1055/s-0043-1776733] [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: 12/17/2023]
Abstract
Cleft lip and/or palate is a congenital malformation with a wide range of presentations, and its effective treatment necessitates sustained, comprehensive care across an affected child's life. Early diagnosis, ideally through prenatal imaging or immediately postbirth, is paramount. Access to longitudinal care and long-term follow-up with a multidisciplinary approach, led by the recommendations of the American Cleft Palate Association, is the best way to ensure optimal outcomes. Multiple specialties including plastic surgery, otolaryngology, speech therapy, orthodontists, psychologists, and audiologists all may be indicated in the care of the child. Primary repair of the lip, nose, and palate are generally conducted during infancy. Postoperative care demands meticulous oversight to detect potential complications. If necessary, revisional surgeries should be performed before the child begin primary school. As the child matures, secondary procedures like alveolar bone grafting and orthognathic surgery may be requisite. The landscape of cleft care has undergone significant transformation since early surgical correction, with treatment plans now tailored to the specific type and severity of the cleft. The purpose of this text is to outline the current standards of care in children born with cleft lip and/or palate and to highlight ongoing advancements in the field.
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Affiliation(s)
- Matthew J. Parham
- Division of Plastic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
- Division of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | - Arren E. Simpson
- Division of Plastic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
- Division of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | - Tanir A. Moreno
- Division of Plastic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
- Division of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | - Renata S. Maricevich
- Division of Plastic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
- Division of Plastic Surgery, Texas Children's Hospital, Houston, Texas
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Kini U. Genetics and orofacial clefts: a clinical perspective. Br Dent J 2023; 234:947-952. [PMID: 37349452 PMCID: PMC10287552 DOI: 10.1038/s41415-023-5994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Orofacial clefts (OFCs) are the most common congenital craniofacial anomaly seen in humans. Most OFCs are sporadic and isolated - these are thought to be multifactorial in origin. Chromosomal and monogenic variants account for the syndromic forms and for some of the non-syndromic inherited forms. This review discusses the importance of genetic testing and the current clinical strategy to deliver a genomics service that is of direct benefit to patients and their families.
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Affiliation(s)
- Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals, UK; Spires Cleft Service, Oxford University Hospitals, UK; NDCLS, Radcliffe Department of Medicine, University of Oxford, United Kingdom.
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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.
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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
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Xu X, Zhang Y, Pan Z, Zhang X, Liu X, Tang L, Zhang X, Zhou F, Cheng H. Genome-wide DNA methylation of Munro's microabscess reveals the epigenetic regulation in the pathogenesis of psoriasis. Front Immunol 2022; 13:1057839. [PMID: 36569916 PMCID: PMC9773074 DOI: 10.3389/fimmu.2022.1057839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction Munro's microabscess is a typical pathological feature in the early psoriatic lesion, mainly characterized by the accumulation of neutrophils in the epidermis. DNA methylation microenvironment of Munro's microabscess and the crosstalk with transcription and its effect on neutrophils have not yet been revealed. Methods Performed genome-wide DNA methylation analysis and further differential methylation analysis of psoriatic skin lesions with and without Munro's microabscess from two batch samples consisting of 114 former samples in the discovery stage and 21 newly-collected samples in the validation stage. Utilized GO, MEME, and other tools to conduct downstream analysis on differentially methylated sites (DMSs). Correlation analysis of methylation level and transcriptome data was also conducted. Results We observed 647 overlapping DMSs associated with Munro's microabscess. Subsequently, GO pathway analysis revealed that DNA methylation might affect the physical properties associated with skin cells through focal adhesion and cellsubstrate junction and was likely to recruit neutrophils in the epidermis. Via the MEME tool, used to investigate the possible binding transcription factors (TFs) of 20 motifs around the 647 DMSs, it was found that DNA methylation regulated the binding of AP1 family members and the recruitment of neutrophils in the epidermis through the TGF-beta pathway and the TH17 pathway. Meanwhile, combined with our earlier transcriptome data, we found DNA methylation would regulate the expressions of CFDP, SIRT6, SMG6, TRAPPC9, HSD17B7, and KIAA0415, indicating these genes would potentially promote the process of Munro's microabscess. Discussion In conclusion, DNA methylation may affect the course of psoriasis by regulating the progression of Munro's microabscess in psoriatic skin lesions.
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Affiliation(s)
- Xiaoqing Xu
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Yuxi Zhang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Zhaobing Pan
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Xiaojing Zhang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Xiaonan Liu
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Lili Tang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Xiaoguang Zhang
- Department of Dermatology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China,*Correspondence: Hui Cheng, ; Fusheng Zhou, ; Xiaoguang Zhang,
| | - Fusheng Zhou
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China,*Correspondence: Hui Cheng, ; Fusheng Zhou, ; Xiaoguang Zhang,
| | - Hui Cheng
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China,*Correspondence: Hui Cheng, ; Fusheng Zhou, ; Xiaoguang Zhang,
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Alvizi L, Brito LA, Kobayashi GS, Bischain B, da Silva CBF, Ramos SLG, Wang J, Passos-Bueno MR. m ir152 hypomethylation as a mechanism for non-syndromic cleft lip and palate. Epigenetics 2022; 17:2278-2295. [PMID: 36047706 PMCID: PMC9665146 DOI: 10.1080/15592294.2022.2115606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/06/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP), the most common human craniofacial malformation, is a complex disorder given its genetic heterogeneity and multifactorial component revealed by genetic, epidemiological, and epigenetic findings. Epigenetic variations associated with NSCLP have been identified; however, functional investigation has been limited. Here, we combined a reanalysis of NSCLP methylome data with genetic analysis and used both in vitro and in vivo approaches to dissect the functional effects of epigenetic changes. We found a region in mir152 that is frequently hypomethylated in NSCLP cohorts (21-26%), leading to mir152 overexpression. mir152 overexpression in human neural crest cells led to downregulation of spliceosomal, ribosomal, and adherens junction genes. In vivo analysis using zebrafish embryos revealed that mir152 upregulation leads to craniofacial cartilage impairment. Also, we suggest that zebrafish embryonic hypoxia leads to mir152 upregulation combined with mir152 hypomethylation and also analogous palatal alterations. We therefore propose that mir152 hypomethylation, potentially induced by hypoxia in early development, is a novel and frequent predisposing factor to NSCLP.
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Affiliation(s)
- Lucas Alvizi
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | - Luciano Abreu Brito
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | | | - Bárbara Bischain
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | | | | | - Jaqueline Wang
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Universidade de São Paulo, Brasil
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12
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Fitriasari S, Trainor PA. Gene-environment interactions in the pathogenesis of common craniofacial anomalies. Curr Top Dev Biol 2022; 152:139-168. [PMID: 36707210 DOI: 10.1016/bs.ctdb.2022.10.005] [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: 12/03/2022]
Abstract
Craniofacial anomalies often exhibit phenotype variability and non-mendelian inheritance due to their multifactorial origin, involving both genetic and environmental factors. A combination of epidemiologic studies, genome-wide association, and analysis of animal models have provided insight into the effects of gene-environment interactions on craniofacial and brain development and the pathogenesis of congenital disorders. In this chapter, we briefly summarize the etiology and pathogenesis of common craniofacial anomalies, focusing on orofacial clefts, hemifacial microsomia, and microcephaly. We then discuss how environmental risk factors interact with genes to modulate the incidence and phenotype severity of craniofacial anomalies. Identifying environmental risk factors and dissecting their interaction with different genes and modifiers is central to improved strategies for preventing craniofacial anomalies.
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Affiliation(s)
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, United States; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, United States.
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13
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Modifiable Risk Factors of Non-Syndromic Orofacial Clefts: A Systematic Review. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9121846. [PMID: 36553290 PMCID: PMC9777067 DOI: 10.3390/children9121846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
OFCs (orofacial clefts) are among the most frequent congenital defects, but their etiology has yet to be clarified. OFCs affect different structures and functions with social, psychological and economic implications in children and their families. Identifying modifiable risk factors is mandatory to prevent the occurrence of non-syndromic OFCs (NSOFCs). PubMed, Cochrane Library, Scopus and Web of Science were searched from 1 January 2012 to 25 May 2022 and a total of 7668 publications were identified. Studies focusing on the risk factors of NSOFCs were selected, leading to 62 case-control and randomized clinical trials. Risk factors were categorized into non-modifiable and modifiable. The first group includes genetic polymorphisms, gender of the newborn, ethnicity, and familiarity. Within the second group, risk factors that can only be modified before conception (consanguinity, parental age at conception, socio-economical and educational level, area of residency and climate), and risk factors modifiable before and after conception (weight, nutritional state, acute and chronic diseases, psychophysical stress, licit and illicit drugs, alcohol, smoke, pollutants and contaminants) have been distinguished. This study provides a wide overview of the risk factors of NSOFCs, focusing on modifiable ones, to suggest new perspectives in education, prevention, medical interventions and clinical research.
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14
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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.
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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
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15
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Epigenetic Effect of Maternal Methyl-Group Donor Intake on Offspring’s Health and Disease. Life (Basel) 2022; 12:life12050609. [PMID: 35629277 PMCID: PMC9145757 DOI: 10.3390/life12050609] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/02/2022] [Accepted: 04/15/2022] [Indexed: 01/16/2023] Open
Abstract
Maternal exposure to some dietary and environmental factors during embryonic development can affect offspring’s phenotype and, furthermore, the risk of developing diseases later in life. One potential mechanism responsible for this early programming may be the modification of the epigenome, such as DNA methylation. Methyl-group donors are essential for DNA methylation and are shown to have an important role in fetal development and later health. The main goal of the present review is to summarize the available literature data on the epigenetic effect (DNA methylation) of maternal methyl-group donor availability on reproductivity, perinatal outcome, and later health of the offspring. In our literature search, we found evidence for the association between alterations in DNA methylation patterns caused by different maternal methyl-group donor (folate, choline, methionine, betaine) intake and reproductivity, birth weight, neural tube defect, congenital heart defect, cleft lip and palate, brain development, and the development of obesity and associated non-communicable diseases in later life. We can conclude that maternal methyl-group donor availability could affect offspring’s health via alterations in DNA methylation and may be a major link between early environmental exposure and the development of diseases in the offspring. However, still, further studies are necessary to confirm the associations and causal relationships.
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16
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Fitzsimons KJ, Hamilton MJ, van der Meulen J, Medina J, Wahedally M, Park MH, Russell C. Range and Frequency of Congenital Malformations Among Children With Cleft Lip and/or Palate. Cleft Palate Craniofac J 2022:10556656221089160. [PMID: 35382604 DOI: 10.1177/10556656221089160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To assess the range and frequency of additional congenital malformations identified among children born alive with CL/P. Analysis of patient-level data from a national registry of cleft births linked to national administrative data of hospital admissions. National Health Service, England. Children born between 2000 and 2012 receiving cleft care in English NHS hospitals. The proportion of children with ICD-10 codes for additional congenital malformations, according to cleft type. The study included 9403 children. Of these 2114 (22.5%) had CL±A, 4509 (48.0%) had CP, 1896 (20.2%) had UCLP, and 884 (9.4%) had BCLP. A total of 3653 (38.8%) children had additional congenital malformations documented in their hospital admission records. The prevalence of additional congenital malformations was greatest among children with CP (53.0%), followed by those with BCLP (33.5%), UCLP (26.3%), and then CL±A (22.2%) (P < .001). Among those with UCLP, children with right-sided clefts were more likely to have additional malformations than those with left-sided clefts (31.6% vs 23.0%, P < .001). Malformations of the skeletal system and circulatory system were most common, affecting 10.5% and 10.2% of the included children, respectively. A total of 16.8% of children had additional congenital malformations affecting 2 or more structural systems. Congenital malformations are common among children born alive with a cleft, affecting over half of some cleft subgroups. Given the frequency of certain structural malformations, clinicians should consider standardized screening for these children. Establishing good links with pediatric and genetic services is recommended.
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Affiliation(s)
- K J Fitzsimons
- Clinical Effectiveness Unit, 14211Royal College of Surgeons of England, London, UK
| | - M J Hamilton
- West of Scotland Centre for Genomic Medicine, 473300Queen Elizabeth University Hospital, Glasgow, UK
| | - J van der Meulen
- Department of Health Services Research and Policy, 4906London School of Hygiene and Tropical Medicine, London, UK
| | - J Medina
- Clinical Effectiveness Unit, 14211Royal College of Surgeons of England, London, UK
| | - Mah Wahedally
- Clinical Effectiveness Unit, 14211Royal College of Surgeons of England, London, UK
| | - M H Park
- Department of Health Services Research and Policy, 4906London School of Hygiene and Tropical Medicine, London, UK
| | - Cjh Russell
- 59842Royal Hospital for Children, 473300Queen Elizabeth University Hospital, Glasgow, UK
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17
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Tran C, Crawford AA, Hamilton A, French CE, Wren Y, Sandy J, Sharp G. Maternal Stressful Life Events During the Periconceptional Period and Orofacial Clefts: A Systematic Review and Meta-Analysis. Cleft Palate Craniofac J 2022; 59:1253-1263. [PMID: 35014881 DOI: 10.1177/10556656211045553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To assess whether women who experience stressful life events during the periconceptional period are at higher risk of giving birth to a baby with an orofacial cleft (OFC). DESIGN Systematic review and meta-analysis of studies reporting the proportion of babies born with OFC to mothers exposed and unexposed to population-level or personal-level stressful life events during the periconceptional period. Six electronic databases were searched from inception to August 2020. Risk of bias was assessed using the Newcastle-Ottawa scale. Odds ratios (ORs) for the odds of OFC in babies of exposed mothers relative to unexposed controls were extracted and/or calculated. Random effects meta-analysis was undertaken, stratified by cleft subtype. RESULTS Of 12 eligible studies, 8 examined experience of personal events and 4 examined population-level events. Studies demonstrated low-moderate risk of bias and there was indication of publication bias. There was some evidence that personal stressful life events were associated with greater odds of cleft lip and/or palate (six studies, OR 1.63, 95% confidence interval (CI) 1.16, 2.30, P = 0.001) and cleft palate only (six studies, OR 1.45, 95% CI 1.02, 2.06, P = 0.04). Population-level events were associated with higher odds of OFC in studies that did not specify subtype (three studies, OR 1.64, 95% CI 1.19, 2.25, P = 0.002), but subtype stratified analyses were underpowered. Heterogeneity was high. CONCLUSIONS Limited evidence indicated a weak positive association between maternal stressful life events during the periconceptional period and risk of OFC in the offspring, but further studies with greater consistency in research design are needed.
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Affiliation(s)
- Christina Tran
- Bristol Dental School, Faculty of Health Sciences, 152331University of Bristol, Bristol, UK
| | - Andrew A Crawford
- Population Health Sciences, 152331Bristol Medical School, University of Bristol, Bristol, UK
| | - Alexander Hamilton
- 152331Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Clare E French
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK.,Population Health Sciences, 152331Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Yvonne Wren
- Bristol Dental School, Faculty of Health Sciences, 152331University of Bristol, Bristol, UK
| | - Jonathan Sandy
- Bristol Dental School, Faculty of Health Sciences, 152331University of Bristol, Bristol, UK
| | - Gemma Sharp
- Population Health Sciences, 152331Bristol Medical School, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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18
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as epigenetic regulators of orofacial development. Differentiation 2022; 124:1-16. [DOI: 10.1016/j.diff.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 11/03/2022]
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19
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Fell M, Russell C, Medina J, Gillgrass T, Chummun S, Cobb ARM, Sandy J, Wren Y, Wills A, Lewis SJ. The impact of changing cigarette smoking habits and smoke-free legislation on orofacial cleft incidence in the United Kingdom: Evidence from two time-series studies. PLoS One 2021; 16:e0259820. [PMID: 34818369 PMCID: PMC8612573 DOI: 10.1371/journal.pone.0259820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Both active and passive cigarette smoking have previously been associated with orofacial cleft aetiology. We aimed to analyse the impact of declining active smoking prevalence and the implementation of smoke-free legislation on the incidence of children born with a cleft lip and/or palate within the United Kingdom. METHODS AND FINDINGS We conducted regression analysis using national administrative data in the United Kingdom between 2000-2018. The main outcome measure was orofacial cleft incidence, reported annually for England, Wales and Northern Ireland and separately for Scotland. First, we conducted an ecological study with longitudinal time-series analysis using smoking prevalence data for females over 16 years of age. Second, we used a natural experiment design with interrupted time-series analysis to assess the impact of smoke-free legislation. Over the study period, the annual incidence of orofacial cleft per 10,000 live births ranged from 14.2-16.2 in England, Wales and Northern Ireland and 13.4-18.8 in Scotland. The proportion of active smokers amongst females in the United Kingdom declined by 37% during the study period. Adjusted regression analysis did not show a correlation between the proportion of active smokers and orofacial cleft incidence in either dataset, although we were unable to exclude a modest effect of the magnitude seen in individual-level observational studies. The data in England, Wales and Northern Ireland suggested an 8% reduction in orofacial cleft incidence (RR 0.92, 95%CI 0.85 to 0.99; P = 0.024) following the implementation of smoke-free legislation. In Scotland, there was weak evidence for an increase in orofacial cleft incidence following smoke-free legislation (RR 1.16, 95%CI 0.94 to 1.44; P = 0.173). CONCLUSIONS These two ecological studies offer a novel insight into the influence of smoking in orofacial cleft aetiology, adding to the evidence base from individual-level studies. Our results suggest that smoke-free legislation may have reduced orofacial cleft incidence in England, Wales and Northern Ireland.
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Affiliation(s)
- Matthew Fell
- Cleft Collective, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Craig Russell
- Scottish Cleft Service, Royal Hospital for Children, Glasgow, United Kingdom
| | - Jibby Medina
- Clinical Effectiveness Unit, Royal College of Surgeons of England, London, United Kingdom
| | - Toby Gillgrass
- Scottish Cleft Service, Royal Hospital for Children, Glasgow, United Kingdom
| | - Shaheel Chummun
- South West Cleft Service, University Hospitals Bristol and Weston NHS Trust, Bristol, United Kingdom
| | - Alistair R. M. Cobb
- South West Cleft Service, University Hospitals Bristol and Weston NHS Trust, Bristol, United Kingdom
| | - Jonathan Sandy
- Cleft Collective, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Yvonne Wren
- Cleft Collective, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Andrew Wills
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Sarah J. Lewis
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
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20
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Southby L, Harding S, Phillips V, Wren Y, Joinson C. Speech input processing in children born with cleft palate: A systematic literature review with narrative synthesis. INTERNATIONAL JOURNAL OF LANGUAGE & COMMUNICATION DISORDERS 2021; 56:668-693. [PMID: 34125466 PMCID: PMC8362211 DOI: 10.1111/1460-6984.12633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/31/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Speech development requires intact and adequately functioning oral anatomy and cognitive 'speech processing' skills. There is evidence that speech input processing skills are associated with speech output problems in children not born with a cleft. Children born with cleft palate ± lip (CP±L) are at high risk of developing disordered speech output. Less is known about their speech input processing skills and whether they are associated with cleft-related speech sound disorder (SSD). AIMS (1) To collate and evaluate studies reporting evidence regarding the speech input processing skills of children born with cleft palate in comparison with data from typically developing children or other comparison groups; and (2) to identify any available evidence regarding relationships between speech input processing skills and speech output in children born with CP±L. METHODS & PROCEDURES Potentially relevant studies published up to November 2019 were identified from the following databases: Medline via Ovid, Embase via Ovid, Cinahl via Ebscohost, PsycInfo via Ebscohost, BNI via ProQuest, AMED via Ovid, Cochrane Library and Scopus. Inclusion criteria were: peer-reviewed articles published in scientific journals, any design, published in English, participants born with a CP±L aged up to age 18 years who completed speech input processing assessments compared with normative data and/or a control or other comparison group. Critical Appraisal Skills Programme (CASP) checklists were used to quality appraise included studies. OUTCOMES & RESULTS Six studies were retained in the final review. There is some evidence that children born with CP±L perform less well than non-cleft controls on some speech input processing tasks and that specific input processing skills may be related to errors in the children's speech. Heterogeneity in relation to study groups and assessments used, as well as small sample sizes, limits generalization of findings. CONCLUSION & IMPLICATIONS There is limited evidence regarding the speech input processing skills of children born with CP±L. There are indications that children born with CP+/L may have difficulty in some aspects of speech input processing in comparison with children not born with a cleft, and that difficulties with some speech input processing tasks may be specific to errors in children's speech output. Further research is required to develop our understanding of these skills in this population and any associations with speech output. WHAT THIS PAPER ADDS What is already known on the subject Few studies have been published that examine aspects of speech input processing in children born with CP±L. Theoretical models of speech processing, and published studies, propose that speech input processing skills are associated with SSD in children who were not born with a cleft. However, it is less clear whether there is any association between speech input processing and cleft-related SSD. What this paper adds to existing knowledge This review systematically collates and evaluates the published, peer-reviewed evidence regarding speech input processing skills in children born with CP±L. The collated evidence indicates that some speech input processing skills differ between children with and without CP±L. There is some evidence, from a single study, that speech input processing of specific cleft speech characteristics (CSCs) may be associated with the presence of these CSCs in the speech output of some children born with CP±L. What are the potential or actual clinical implications of this work? While the evidence is currently limited, increasing our knowledge of speech input processing skills in children born with CP±L contributes to our clinical understanding of the nature of cleft-related SSD. The current evidence suggests that speech and language therapists should consider speech input processing skills when assessing children with cleft-related SSD to support intervention planning. Considering these skills in relation to literacy development in these children may also be important.
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Affiliation(s)
- Lucy Southby
- Cleft.NET.EastCambridge University Hospitals NHS Foundation TrustCambridgeUK
- Centre for Academic Child Health, Bristol Medical SchoolUniversity of BristolBristolUK
- Bristol Speech and Language Therapy Research UnitNorth Bristol NHS TrustBristolUK
| | - Sam Harding
- Bristol Speech and Language Therapy Research UnitNorth Bristol NHS TrustBristolUK
| | | | - Yvonne Wren
- Bristol Speech and Language Therapy Research UnitNorth Bristol NHS TrustBristolUK
- Bristol Dental SchoolUniversity of BristolBristolUK
| | - Carol Joinson
- Centre for Academic Child Health, Bristol Medical SchoolUniversity of BristolBristolUK
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21
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Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor J, Xu Z, Lie RT, Gjessing HK, Jugessur A. Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 2021; 3:lqab035. [PMID: 33987535 PMCID: PMC8092375 DOI: 10.1093/nargab/lqab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is the most widely studied epigenetic mark in humans and plays an essential role in normal biological processes as well as in disease development. More focus has recently been placed on understanding functional aspects of methylation, prompting the development of methods to investigate the relationship between heterogeneity in methylation patterns and disease risk. However, most of these methods are limited in that they use simplified models that may rely on arbitrarily chosen parameters, they can only detect differentially methylated regions (DMRs) one at a time, or they are computationally intensive. To address these shortcomings, we present a wavelet-based method called 'Wavelet Screening' (WS) that can perform an epigenome-wide association study (EWAS) of thousands of individuals on a single CPU in only a matter of hours. By detecting multiple DMRs located near each other, WS identifies more complex patterns that can differentiate between different methylation profiles. We performed an extensive set of simulations to demonstrate the robustness and high power of WS, before applying it to a previously published EWAS dataset of orofacial clefts (OFCs). WS identified 82 associated regions containing several known genes and loci for OFCs, while other findings are novel and warrant replication in other OFCs cohorts.
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch and Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
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22
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Young JI, Slifer S, Hecht JT, Blanton SH. DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Non-syndromic Cleft Lip and Palate. Front Cell Dev Biol 2021; 9:656865. [PMID: 34055787 PMCID: PMC8149607 DOI: 10.3389/fcell.2021.656865] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP) is the most common craniofacial birth defect. The etiology of NSCLP is complex with multiple genes and environmental factors playing causal roles. Although studies have identified numerous genetic markers associated with NSCLP, the role of epigenetic variation remains relatively unexplored. Because of their identical DNA sequences, monozygotic (MZ) twins discordant for NSCLP are an ideal model for examining the potential contribution of DNA methylation to non-syndromic orofacial clefting. In this study, we compared the patterns of whole genome DNA methylation in six MZ twin pairs discordant for NSCLP. Differentially methylated positions (DMPs) and regions (DMRs) were identified in NSCLP candidate genes, including differential methylation in MAFB and ZEB2 in two independent MZ twin pairs. In addition to DNA methylation differences in NSCLP candidate genes, we found common differential methylation in genes belonging to the Hippo signaling pathway, implicating this mechanosensory pathway in the etiology of NSCLP. The results of this novel approach using MZ twins discordant for NSCLP suggests that differential methylation is one mechanism contributing to NSCLP, meriting future studies on the role of DNA methylation in familial and sporadic NSCLP.
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Affiliation(s)
- Juan I. Young
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Susan Slifer
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Jacqueline T. Hecht
- McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Susan H. Blanton
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
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23
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Vieira AR, Furtado PGC, Filho VVL, Pereira JAT, Tenório IS, Luna AM, Filgueiras VM, Lacerda RHW. Orofacial Cleft Frequency Differences Depending on Geographic Origin: Coast vs. Inland. FRONTIERS IN DENTAL MEDICINE 2021. [DOI: 10.3389/fdmed.2021.670948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objective: Cleft lip and/or palate is the most common congenital anomaly in a human face, with a multifactorial and complex etiology. Although many studies have been developed, the role of the environment is still unclear. This study aims to test the hypothesis that differences in lifestyle and environment change the reproductive risks of orofacial clefts.Methods: A total of 2,422 medical records of individuals born with cleft lip and/or palate in a reference center in the northeast of Brazil over a period of 30 years were analyzed. Data on the cleft type, geographic origin of the patient (coast or inland), presence of associated congenital anomalies or syndromes, maternal age, and maternal parity were recorded. Differences in frequencies between the cleft types were compared based on geographic origin, maternal age, and parity. Chi-square, Student's t, Kruskal–Wallis, and logistic regression were used to analyze the interference of covariables on the cleft type.Results: The distribution of cleft types was significantly different between the coastal and inland areas (chi-square test, p < 0.0001). A higher frequency of cleft lip with or without palate was observed the inland area (chi-square test, p = 0.0006), while cleft palate only (chi-square test, p = 0.003) and rare facial clefts (chi-square test, p = 0.004) were more frequent in the coastal area. No difference was found in the distribution of maternal age (t-test, p > 0.05) between the two geographic areas, but parity was higher inland (t-test, p = 0.04). Logistic regression suggested that parity explained just a small portion of the differences in frequency between cleft types of the coast vs. inland.Conclusion: Frequency of orofacial cleft types differs by geographic area in this region of the South American continent.
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Maden SK, Thompson RF, Hansen KD, Nellore A. Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. NAR Genom Bioinform 2021; 3:lqab025. [PMID: 33937763 PMCID: PMC8061458 DOI: 10.1093/nargab/lqab025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus. We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain and one-third were from cancer patients. About 19% of samples failed at least one of Illumina's 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via the recountmethylation R/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.
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Affiliation(s)
- Sean K Maden
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
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25
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Shi X, Wang Q, Sun C, Guo Q, Song T. Study on the role of methylation in nonsyndromic cleft lip with or without cleft palate using a monozygotic twin model. Int J Pediatr Otorhinolaryngol 2021; 143:110659. [PMID: 33667834 DOI: 10.1016/j.ijporl.2021.110659] [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: 11/08/2020] [Accepted: 02/19/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The research on the etiology of nonsyndromic cleft lip with or without cleft palate(NSCL/P) is challenging, and DNA methylation has an impact on the formation of cleft lip and palate. SUBJECTS In this study, one of a pair of monozygotic twins (T1) had nonsyndromic cleft lip (NSCL), and one of a pair of monozygotic twins (T2) had nonsyndromic cleft lip and palate (NSCLP). We determined the methylation profiles of more than 850,000 CpGs in the DNA of the blood samples from the two pairs of monozygotic twins. RESULT Methylation data indicated that 1184 differentially methylated CpG sites were found in the T1 group (651 hypermethylated and 533 hypomethylated) and 8099 differentially methylated CpG sites in the T2 group (1713 hypermethylated and 6386 hypomethylated) compared with the healthy twin.The common difference was 107 methylation sites.GO enrichment analysis showed that regulation of smooth muscle cell migration and actin cytoskeleton reorganization were the most prominent classes.KEGG pathway enrichment analysis showed that the TGF-β signaling pathway, Notch signaling pathway and Wnt signaling pathway are relevant to the formation of NSCL/P.Two selected genes (NTN1 and PLEKHA7) are involved in the formation of NSCL/P. CONCLUSION These findings provide some support for the hypothesis that abnormal DNA methylation may influence the formation of clefts.
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Affiliation(s)
- Xuheng Shi
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Qi Wang
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Changsheng Sun
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Qiang Guo
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Tao Song
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China.
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26
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Genetic variants in S-adenosyl-methionine synthesis pathway and nonsyndromic cleft lip with or without cleft palate in Chile. Pediatr Res 2021; 89:1020-1025. [PMID: 32492698 DOI: 10.1038/s41390-020-0994-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/25/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND The S-adenosyl-methionine (SAM) availability is crucial for DNA methylation, an epigenetic mechanism involved in nonsyndromic cleft lip with or without cleft palate (NSCL/P) expression. The aim of this study was to assess the association between single-nucleotide polymorphisms (SNPs) of genes involved in SAM synthesis and NSCL/P in a Chilean population. METHODS In 234 cases and 309 controls, 18 SNPs in AHCY, MTR, MTRR, and MAT2A were genotyped, and the association between them and the phenotype was evaluated based on additive (allele), dominant, recessive and haplotype models, by odds ratio (OR) computing. RESULTS Three deep intronic SNPs of MTR showed a protective effect on NSCL/P expression: rs10925239 (OR 0.68; p = 0.0032; q = 0.0192), rs10925254 (OR 0.66; p = 0.0018; q = 0.0162), and rs3768142 (OR 0.66; p = 0.0015; q = 0.0162). Annotations in expression database demonstrate that the protective allele of the three SNPs is associated with a reduction of MTR expression summed to the prediction by bioinformatic tools of its potentiality to modify splicing sites. CONCLUSIONS The protective effect against NSCL/P of these intronic MTR SNPs seems to be related to a decrease in MTR enzyme expression, modulating the SAM availability for proper substrate methylation. However, functional analyses are necessary to confirm our findings. IMPACT SAM synthesis pathway genetic variants are factors associated to NSCL/P. This article adds new evidence for folate related genes in NSCL/P in Chile. Its impact is to contribute with potential new markers for genetic counseling.
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27
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Yow M, Hermann NV, Wei Y, Karsten A, Kreiborg S. Dental Subphenotypes in Infants With Orofacial Clefts-A Longitudinal Population-Based Retrospective Radiographic Study of the Primary and Secondary Dentitions. Cleft Palate Craniofac J 2021; 58:1526-1535. [PMID: 33541114 DOI: 10.1177/1055665621990148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES To determine the developmental patterns of primary and secondary dentitions in infants with orofacial clefts. DESIGN Retrospective, longitudinal, population-based cohort study. MATERIALS Longitudinal records and radiographs of 192 nonsyndromic Northern European infants with isolated unilateral cleft lip (UCL, n = 111) and isolated cleft palate (CP, n = 81). METHODS Radiographic assessments of primary and secondary dentition anomalies and dental maturation, by gender and cleft severity for comparisons between the groups and with historical controls. RESULTS In infants with UCL, the frequencies of dental anomalies were high in both primary (38.7%) and secondary (18.0%) dentitions. Primary and secondary dentition anomalies were not observed in infants with CP and different in the UCL group (P = .003). Risk differences involved primary supernumerary teeth (P = .0001) and talon cusp formation (P = .0001), and secondary tooth agenesis (P = .001) of the maxillary lateral incisor on the side of the cleft lip. Delayed primary and secondary dental maturation occurred in the UCL and CP groups, greater in infants with UCL (P < .0001). Primary and secondary dental maturation featured sexual dimorphism with greater delay in males (UCL, P < .0001; CP, .0001 > P = .001). The effect of cleft severity on dental maturation was significant in infants with UCL (P = .0361) and CP (P = .0175) in the primary but not in the secondary dentition. CONCLUSIONS There were different dental anomalies in the primary and secondary dentitions in operated infants with UCL and no dental anomalies in unoperated infants with CP. Dental maturation was delayed in infants with UCL and CP with greater delay in males compared to females.
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Affiliation(s)
- Mimi Yow
- Department of Orthodontics, National Dental Centre, SingHealth Duke-NUS Oral Health Academic Programme, Second Hospital Avenue, Singapore.,Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Nuno V Hermann
- Department of Pediatric Dentistry and Clinical Genetics, School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Yuan Wei
- Singapore Clinical Research Institute (SCRI), Singapore
| | - Agneta Karsten
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Sven Kreiborg
- Department of Pediatric Dentistry and Clinical Genetics, School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Denmark
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28
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Yang W, Guo Y, Ni W, Tian T, Jin L, Liu J, Li Z, Ren A, Wang L. Hypermethylation of WNT3A gene and non-syndromic cleft lip and/or palate in association with in utero exposure to lead: A mediation analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111415. [PMID: 33091767 DOI: 10.1016/j.ecoenv.2020.111415] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVES We aim to investigate association between WNT3A methylation and risk of non-syndromic cleft lip and/or palate (NSCL/P), and examine mediating effect of WNT3A methylation on the association of NSCL/P and lead (Pb) exposure in fetuses. METHODS DNA methylation of WNT3A in umbilical cord blood was determined among 59 NSCL/P cases and 118 non-malformed controls. Mediation analysis was performed to evaluate the potential mediating effect of WNT3A methylation on association between concentrations of Pb in umbilical cord and risk for NSCL/P. Additionally, an animal experiment in which cleft palates were induced by lead acetate was conducted. RESULTS The overall average methylation level of WNT3A was significant higher in NSCL/P cases as compared to controls. The risk for NSCL/P was increased by 1.90-fold with hypermethylation of WNT3A. Significant correlation was observed between concentrations of Pb in umbilical cord and methylation level of WNT3A. The hypermethylation of WNT3A had a mediating effect by 9.32% of total effect of Pb on NSCL/P risk. Gender-specific association between WNT3A methylation and NSCL/P was observed in male fetuses, and the percentage of the mediating effect increased to 14.28%. Animal experiment of mice showed that maternal oral exposure to lead acetate may result in cleft palate in offspring. CONCLUSION Hypermethylation of WNT3A was associated with the risk for NSCL/P and may be partly explain the association between exposure to Pb and risk for NSCL/P. The teratogenic and fetotoxic effects of Pb were found in mice.
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Affiliation(s)
- Wenlei Yang
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Yingnan Guo
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Wenli Ni
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Tian Tian
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Lei Jin
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Jufen Liu
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Zhiwen Li
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Aiguo Ren
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Linlin Wang
- Institute of Reproductive and Child Health, NHC Key Laboratory of Reproductive Health, Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China.
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29
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Deep orofacial phenotyping of population-based infants with isolated cleft lip and isolated cleft palate. Sci Rep 2020; 10:21666. [PMID: 33303814 PMCID: PMC7730196 DOI: 10.1038/s41598-020-78602-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/24/2020] [Indexed: 11/24/2022] Open
Abstract
Isolated orofacial clefts (OFC) are common with poorly understood aetiology. Heterogeneous phenotypes and subphenotypes confound aetiological variant findings. To improve OFC phenome understanding, population-based, consecutive, pre-treatment infants with isolated unilateral cleft lip (UCL, n = 183) and isolated cleft palate (CP, n = 83) of similar ancestry were grouped for deep phenotyping. Subphenotypes stratified by gender and cleft severity were evaluated for primary dental malformations and maturation using radiographs. We found that cleft severity and tooth agenesis were inadequate to distinguish heterogeneity in infants with UCL and CP. Both groups featured slow dental maturity, significantly slower in males and the UCL phenotype. In 32.8% of infants with UCL, supernumerary maxillary lateral incisors were present on the cleft lip side, but not in infants with CP, suggesting a cleft dental epithelium and forme fruste cleft dentoalveolus of the UCL subphenotype. The findings underscored the importance of deep phenotyping to disclose occult OFC subphenotypes.
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30
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Xu F, He L, Zhan X, Chen J, Xu H, Huang X, Li Y, Zheng X, Lin L, Chen Y. DNA methylation-based lung adenocarcinoma subtypes can predict prognosis, recurrence, and immunotherapeutic implications. Aging (Albany NY) 2020; 12:25275-25293. [PMID: 33234739 PMCID: PMC7803536 DOI: 10.18632/aging.104129] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023]
Abstract
The marked heterogeneity of lung adenocarcinoma (LUAD) makes its diagnosis and treatment difficult. In addition, the aberrant DNA methylation profile contributes to tumor heterogeneity and alters the immune response. We used DNA methylation array data from publicly available databases to establish a predictive model for LUAD prognosis. Thirty-three methylation sites were identified as specific prognostic biomarkers, independent of patients' clinical characteristics. These methylation profiles were used to identify potential drug candidates and study the immune microenvironment of LUAD and response to immunotherapy. When compared with the high-risk group, the low-risk group had a lower recurrence rate and favorable prognosis. The tumor microenvironment differed between the two groups as reflected by the higher number of resting dendritic cells and a lower number of monocytes and resting mast cells in the low-risk group. Moreover, low-risk patients reported higher immune and stromal scores, lower tumor purity, and higher expression of HLA genes. Low-risk patients responded well to immunotherapy due to higher expression of immune checkpoint molecules and lower stemness index. Thus, our model predicted a favorable prognosis and increased overall survival for patients in the low-risk methylation group. Further, this model could provide potential drug targets to develop effective immunotherapies for LUAD.
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Affiliation(s)
- Feng Xu
- Department of Respiratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Lulu He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xueqin Zhan
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiexin Chen
- Department of Endocrinology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Huan Xu
- Department of Rheumatology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaoling Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yangyi Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaohe Zheng
- Department of Respiratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ling Lin
- Department of Rheumatology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yongsong Chen
- Department of Endocrinology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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31
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Cáceres-Rojas G, Salamanca C, Krause BJ, Recabarren AS, Recabarren PA, Pantoja R, Leiva N, Pardo R, Santos JL, Suazo J. Nonsyndromic orofacial clefts in Chile: LINE-1 methylation and MTHFR variants. Epigenomics 2020; 12:1783-1791. [PMID: 33147056 DOI: 10.2217/epi-2020-0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate the risk of nonsyndromic orofacial clefts (NSOFCs) associated with LINE-1 methylation, as a marker of global DNA methylation, and the effect of MTHFR functional variants on this variable. Patients & methods: LINE-1 methylation was evaluated by bisulfite modification coupled to DNA pyrosequencing in 95 NSOFC cases and 95 controls. In these subjects, MTHFR genotypes for variants c.C677T (rs1801133) and c.A1298C (rs1801131) were obtained. Results: Middle levels (second tertile) of LINE-1 methylation increase the risk of NSOFCs. In addition, LINE-1 methylation depends on c.A1298C genotypes in controls but not in cases. Conclusion: A nonlinear association between global DNA methylation and NSOFCs was detected in this Chilean population, which appears to be influenced by MTHFR functional variants.
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Affiliation(s)
- Gabriela Cáceres-Rojas
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Carlos Salamanca
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile.,Research Centre in Dental Sciences (CICO), Dental School, Universidad de La Frontera, Chile.,Universidad Adventista de Chile, Chillán, Chile
| | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | - Andrea S Recabarren
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Pamela A Recabarren
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Roberto Pantoja
- Maxillofacial Surgery Service, Cleft Lip & Palate Unit, Hospital Clínico San Borja-Arriaran. Santiago de Chile, Chile.,Department of Oral & Maxillofacial Surgery, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Noemi Leiva
- Unit of Maxillofacial Malformations, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Rosa Pardo
- Section of Genetics, Hospital Clínico Universidad de Chile, Santiago, Chile.,Unit of Neonatology, Hospital Clínico Universidad de Chile, Santiago, Chile.,Unit of Genetics, Hospital Dr Sótero del Río, Santiago, Chile
| | - José Luis Santos
- Department of Nutrition, Diabetes & Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José Suazo
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
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32
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Howe LJ, Hemani G, Lesseur C, Gaborieau V, Ludwig KU, Mangold E, Brennan P, Ness AR, St Pourcain B, Davey Smith G, Lewis SJ. Evaluating shared genetic influences on nonsyndromic cleft lip/palate and oropharyngeal neoplasms. Genet Epidemiol 2020; 44:924-933. [PMID: 32710482 PMCID: PMC8240308 DOI: 10.1002/gepi.22343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/12/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022]
Abstract
It has been hypothesised that nonsyndromic cleft lip/palate (nsCL/P) and cancer may share aetiological risk factors. Population studies have found inconsistent evidence for increased incidence of cancer in nsCL/P cases, but several genes (e.g., CDH1, AXIN2) have been implicated in the aetiologies of both phenotypes. We aimed to evaluate shared genetic aetiology between nsCL/P and oral cavity/oropharyngeal cancers (OC/OPC), which affect similar anatomical regions. Using a primary sample of 5,048 OC/OPC cases and 5,450 controls of European ancestry and a replication sample of 750 cases and 336,319 controls from UK Biobank, we estimate genetic overlap using nsCL/P polygenic risk scores (PRS) with Mendelian randomization analyses performed to evaluate potential causal mechanisms. In the primary sample, we found strong evidence for an association between a nsCL/P PRS and increased odds of OC/OPC (per standard deviation increase in score, odds ratio [OR]: 1.09; 95% confidence interval [CI]: 1.04, 1.13; p = .000053). Although confidence intervals overlapped with the primary estimate, we did not find confirmatory evidence of an association between the PRS and OC/OPC in UK Biobank (OR 1.02; 95% CI: 0.95, 1.10; p = .55). Mendelian randomization analyses provided evidence that major nsCL/P risk variants are unlikely to influence OC/OPC. Our findings suggest possible shared genetic influences on nsCL/P and OC/OPC.
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Affiliation(s)
- Laurence J. Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
- Institute of Cardiovascular ScienceUniversity College LondonLondonUK
- Max Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
| | - Corina Lesseur
- Section of GeneticsInternational Agency for Research on CancerLyonFrance
| | - Valérie Gaborieau
- Section of GeneticsInternational Agency for Research on CancerLyonFrance
| | | | | | - Paul Brennan
- Section of GeneticsInternational Agency for Research on CancerLyonFrance
| | - Andy R. Ness
- NIHR Bristol Biomedical Research CentreUniversity Hospitals BristolBristolUK
- Weston NHS Foundation TrustUniversity of BristolBristolUK
| | - Beate St Pourcain
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
- Max Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
| | - Sarah J. Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
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33
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Association between Breastfeeding and DNA Methylation over the Life Course: Findings from the Avon Longitudinal Study of Parents and Children (ALSPAC). Nutrients 2020; 12:nu12113309. [PMID: 33137917 PMCID: PMC7692466 DOI: 10.3390/nu12113309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/25/2022] Open
Abstract
Background: Breastfeeding is associated with short and long-term health benefits. Long-term effects might be mediated by epigenetic mechanisms, yet the literature on this topic is scarce. We performed the first epigenome-wide association study of infant feeding, comparing breastfed vs non-breastfed children. We measured DNA methylation in children from peripheral blood collected in childhood (age 7 years, N = 640) and adolescence (age 15–17 years, N = 709) within the Accessible Resource for Integrated Epigenomic Studies (ARIES) project, part of the larger Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Cord blood methylation (N = 702) was used as a negative control for potential pre-natal residual confounding. Results: Two differentially-methylated sites presented directionally-consistent associations with breastfeeding at ages 7 and 15–17 years, but not at birth. Twelve differentially-methylated regions in relation to breastfeeding were identified, and for three of them there was evidence of directional concordance between ages 7 and 15–17 years, but not between birth and age 7 years. Conclusions: Our findings indicate that DNA methylation in childhood and adolescence may be predicted by breastfeeding, but further studies with sufficiently large samples for replication are required to identify robust associations.
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34
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Martinelli M, Palmieri A, Carinci F, Scapoli L. Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors. Front Cell Dev Biol 2020; 8:592271. [PMID: 33195260 PMCID: PMC7606870 DOI: 10.3389/fcell.2020.592271] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
The epithelial and mesenchymal cells involved in early embryonic facial development are guided by complex regulatory mechanisms. Any factor perturbing the growth, approach and fusion of the frontonasal and maxillary processes could result in orofacial clefts that represent the most common craniofacial malformations in humans. The rarest and, probably for this reason, the least studied form of cleft involves only the secondary palate, which is posterior to the incisive foramen. The etiology of cleft palate only is multifactorial and involves both genetic and environmental risk factors. The intention of this review is to give the reader an overview of the efforts made by researchers to shed light on the underlying causes of this birth defect. Most of the scientific papers suggesting potential environmental and genetic causes of non-syndromic cleft palate are summarized in this review, including genome-wide association and gene–environment interaction studies.
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Affiliation(s)
- Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Francesco Carinci
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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35
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Sandy J, Davies A, Humphries K, Ireland T, Wren Y. Cleft lip and palate: Care configuration, national registration, and research strategies. J World Fed Orthod 2020; 9:S40-S44. [PMID: 33023731 PMCID: PMC7532935 DOI: 10.1016/j.ejwf.2020.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 11/24/2022]
Abstract
A child born with a cleft lip and palate will face 20 years or more of hospital care and surgery. This is a global problem with approximately 10 million people affected worldwide. Various models of care exist around the condition, and the best configurations of services within an economy need to be optimized. We provide examples of how centralized care can improve outcomes and provide an opportunity to establish national registries, and then emphasize the opportunities for building research platforms of relevance. The default of any cleft service should be to centralize care and enable cleft teams with a sufficient volume of patients to develop proficiency and measure the quality of outcomes. The latter needs to be benchmarked against the better centers in Europe. Two areas of concern for those with cleft are morbidity/mortality and educational attainment. These two issues are placed in context within the literature and wider approaches using population genetics. Orthodontists have always played a key role in developing these initiatives and are core members of cleft teams with major responsibilities for these children and their families. Cleft lip and palate affects about 10 million people worldwide. Centralised care can improve outcome and establish national registries. Orthodontists have played a key role in developing these initiatives. No strong evidence of an association between clefting and cancer. Proper care can positively influence lives of children born with a cleft.
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Affiliation(s)
- Jonathan Sandy
- The Cleft Collective, University of Bristol, Bristol, United Kingdom.
| | - Amy Davies
- The Cleft Collective, University of Bristol, Bristol, United Kingdom
| | - Kerry Humphries
- The Cleft Collective, University of Bristol, Bristol, United Kingdom
| | - Tony Ireland
- The Cleft Collective, University of Bristol, Bristol, United Kingdom
| | - Yvonne Wren
- The Cleft Collective, University of Bristol, Bristol, United Kingdom
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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.
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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
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Kruse T, Mangold E, Braumann B. Impact of Maternal Smoking on Nonsyndromic Clefts: Sex-Specific Associations With Side and Laterality. Cleft Palate Craniofac J 2020; 58:181-188. [PMID: 32844678 DOI: 10.1177/1055665620951099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE To compare the incidence of right-sided versus left-sided, and unilateral versus bilateral, nonsyndromic clefting in the affected offspring of smoking and nonsmoking mothers. DESIGN Self-report data on periconceptual and first trimester smoking behavior were collected from 842 mothers of children with nonsyndromic orofacial clefting. Differences in the incidence of left- versus right-sided clefts, and of unilateral versus bilateral clefts, were analyzed between the children of smoking and nonsmoking mothers. SETTING Interviews and clinical examinations took place at 8 specialist centers in Germany. PATIENTS AND PARTICIPANTS Children with nonsyndromic clefts were recruited during the course of surgical or orthodontic treatment, or within the context of the annual control consultation. Patients with cleft palate only or missing data were excluded. The final cohort comprised 842 patients (540 males and 302 females) with unilateral or bilateral clefts. The respective mothers were interviewed. MAIN OUTCOME MEASURE Side and laterality of nonsyndromic clefts were the main outcome measures. RESULTS Children of smoking mothers more often had right-sided clefts than children of nonsmoking mothers (42% right-sided clefts in children of smoking mothers vs 31% of nonsmoking mothers). Children of smoking mothers more often had bilateral clefts than children of nonsmoking mothers (35% bilateral clefts in children of smoking mothers vs 29% of nonsmoking mothers). Sex-specific analyses confirmed substantially and statistically significant associations only for girls. CONCLUSIONS The results suggest that maternal smoking is a sex-specific, exogenous determinant of laterality and side in nonsyndromic clefts.
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Affiliation(s)
- Teresa Kruse
- Department of Orthodontics, 14309University of Cologne, Cologne, Germany.,Center for Rare Diseases Cologne, 14309University of Cologne, Cologne, Germany
| | | | - Bert Braumann
- Department of Orthodontics, 14309University of Cologne, Cologne, Germany.,Center for Rare Diseases Cologne, 14309University of Cologne, Cologne, Germany
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38
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Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations. Hum Genet 2020; 140:457-475. [PMID: 32778951 DOI: 10.1007/s00439-020-02214-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/30/2020] [Indexed: 01/02/2023]
Abstract
Copy number variation (CNV) related disorders tend to show complex phenotypic profiles that do not match known diseases. This makes it difficult to ascertain their underlying molecular basis. A potential solution is to compare the affected genomic regions for multiple patients that share a pathological phenotype, looking for commonalities. Here, we present a novel approach to associate phenotypes with functional systems, in terms of GO categories and KEGG and Reactome pathways, based on patient data. The approach uses genomic and phenomic data from the same patients, finding shared genomic regions between patients with similar phenotypes. These regions are mapped to genes to find associated functional systems. We applied the approach to analyse patients in the DECIPHER database with de novo CNVs, finding functional systems associated with most phenotypes, often due to mutations affecting related genes in the same genomic region. Manual inspection of the ten top-scoring phenotypes found multiple FunSys connections supported by the previous studies for seven of them. The workflow also produces reports focussed on the genes and FunSys connected to the different phenotypes, alongside patient-specific reports, which give details of the associated genes and FunSys for each individual in the cohort. These can be run in "confidential" mode, preserving patient confidentiality. The workflow presented here can be used to associate phenotypes with functional systems using data at the level of a whole cohort of patients, identifying important connections that could not be found when considering them individually. The full workflow is available for download, enabling it to be run on any patient cohort for which phenotypic and CNV data are available.
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39
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Ji Y, Garland MA, Sun B, Zhang S, Reynolds K, McMahon M, Rajakumar R, Islam MS, Liu Y, Chen Y, Zhou CJ. Cellular and developmental basis of orofacial clefts. Birth Defects Res 2020; 112:1558-1587. [PMID: 32725806 DOI: 10.1002/bdr2.1768] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/11/2022]
Abstract
During craniofacial development, defective growth and fusion of the upper lip and/or palate can cause orofacial clefts (OFCs), which are among the most common structural birth defects in humans. The developmental basis of OFCs includes morphogenesis of the upper lip, primary palate, secondary palate, and other orofacial structures, each consisting of diverse cell types originating from all three germ layers: the ectoderm, mesoderm, and endoderm. Cranial neural crest cells and orofacial epithelial cells are two major cell types that interact with various cell lineages and play key roles in orofacial development. The cellular basis of OFCs involves defective execution in any one or several of the following processes: neural crest induction, epithelial-mesenchymal transition, migration, proliferation, differentiation, apoptosis, primary cilia formation and its signaling transduction, epithelial seam formation and disappearance, periderm formation and peeling, convergence and extrusion of palatal epithelial seam cells, cell adhesion, cytoskeleton dynamics, and extracellular matrix function. The latest cellular and developmental findings may provide a basis for better understanding of the underlying genetic, epigenetic, environmental, and molecular mechanisms of OFCs.
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Affiliation(s)
- 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, School of Medicine, University of California at Davis, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| | - 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, School of Medicine, University of California at Davis, 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, School of Medicine, University of California at Davis, 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, School of Medicine, University of California at Davis, 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, School of Medicine, University of California at Davis, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| | - Moira McMahon
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, School of Medicine, University of California at Davis, Sacramento, California, USA
| | - Ratheya Rajakumar
- 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, School of Medicine, University of California at Davis, Sacramento, California, USA
| | - Mohammad S Islam
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, School of Medicine, University of California at Davis, Sacramento, California, USA
| | - Yue Liu
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, School of Medicine, University of California at Davis, Sacramento, California, USA
| | - YiPing Chen
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana, 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, School of Medicine, University of California at Davis, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
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Romanowska J, Haaland ØA, Jugessur A, Gjerdevik M, Xu Z, Taylor J, Wilcox AJ, Jonassen I, Lie RT, Gjessing HK. Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk. Clin Epigenetics 2020; 12:109. [PMID: 32678018 PMCID: PMC7367265 DOI: 10.1186/s13148-020-00881-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Current technology allows rapid assessment of DNA sequences and methylation levels at a single-site resolution for hundreds of thousands of sites in the human genome, in thousands of individuals simultaneously. This has led to an increase in epigenome-wide association studies (EWAS) of complex traits, particularly those that are poorly explained by previous genome-wide association studies (GWAS). However, the genome and epigenome are intertwined, e.g., DNA methylation is known to affect gene expression through, for example, genomic imprinting. There is thus a need to go beyond single-omics data analyses and develop interaction models that allow a meaningful combination of information from EWAS and GWAS. RESULTS We present two new methods for genetic association analyses that treat offspring DNA methylation levels as environmental exposure. Our approach searches for statistical interactions between SNP alleles and DNA methylation (G ×Me) and between parent-of-origin effects and DNA methylation (PoO ×Me), using case-parent triads or dyads. We use summarized methylation levels over nearby genomic region to ease biological interpretation. The methods were tested on a dataset of parent-offspring dyads, with EWAS data on the offspring. Our results showed that methylation levels around a SNP can significantly alter the estimated relative risk. Moreover, we show how a control dataset can identify false positives. CONCLUSIONS The new methods, G ×Me and PoO ×Me, integrate DNA methylation in the assessment of genetic relative risks and thus enable a more comprehensive biological interpretation of genome-wide scans. Moreover, our strategy of condensing DNA methylation levels within regions helps overcome specific disadvantages of using sparse chip-based measurements. The methods are implemented in the freely available R package Haplin ( https://cran.r-project.org/package=Haplin ), enabling fast scans of multi-omics datasets.
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Affiliation(s)
- Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway.
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway.
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway.
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, N-0473, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, N-0473, Norway
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Jack Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Allen J Wilcox
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Inge Jonassen
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
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41
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Maternal Folic Acid Supplementation Mediates Offspring Health via DNA Methylation. Reprod Sci 2020; 27:963-976. [PMID: 32124397 DOI: 10.1007/s43032-020-00161-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 10/24/2022]
Abstract
The clinical significance of periconceptional folic acid supplementation (FAS) in the prevention of neonatal neural tube defects (NTDs) has been recognized for decades. Epidemiological data and experimental findings have consistently been indicating an association between folate deficiency in the first trimester of pregnancy and poor fetal development as well as offspring health (i.e., NTDs, isolated orofacial clefts, neurodevelopmental disorders). Moreover, compelling evidence has suggested adverse effects of folate overload during perinatal period on offspring health (i.e., immune diseases, autism, lipid disorders). In addition to several single-nucleotide polymorphisms (SNPs) in genes related to folate one-carbon metabolism (FOCM), folate concentrations in maternal serum/plasma/red blood cells must be considered when counseling FAS. Epigenetic information encoded by 5-methylcytosines (5mC) plays a critical role in fetal development and offspring health. S-adenosylmethionine (SAM), a methyl donor for 5mC, could be derived from FOCM. As such, folic acid plays a double-edged sword role in offspring health via mediating DNA methylation. However, the underlying epigenetic mechanism is still largely unclear. In this review, we summarized the link across DNA methylation, maternal FAS, and offspring health to provide more evidence for clinical guidance in terms of precise FAS dosage and time point. Future studies are, therefore, required to set up the reference intervals of folate concentrations at different trimesters of pregnancy for different populations and to clarify the epigenetic mechanism for specific offspring diseases.
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42
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Lakkakula BV, Sengupta S, Agrawal J, Singh S, Mendhey P, Jangde P, Sharma A, Pande PA, Krishan P, Shukla P, Momin S, Nagaraju GP, Pattnaik S. Maternal and infant MTHFR gene polymorphisms and non-syndromic oral cleft susceptibility: An updated meta-analysis. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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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.
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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
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44
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Khan MFJ, Little J, Aleotti V, Mossey PA, Steegers-Theunissen RPM, Autelitano L, Meazzini MC, Ravaei A, Rubini M. LINE-1 methylation in cleft lip tissues: Influence of infant MTHFR c.677C>T genotype. Oral Dis 2019; 25:1668-1671. [PMID: 31161688 DOI: 10.1111/odi.13136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/06/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate the influence of MTHFR c.677C>T genotype on LINE-1 methylation in lateral and medial tissues from cleft lip (CL). METHODS Forty-five consecutive non-syndromic cleft lip with or without cleft palate (nsCL/P) cases were included in the study. Genomic DNA was extracted from tissues at both sides of cleft lip, and LINE-1 methylation was detected by bisulfite conversion and pyrosequencing. MTHFR c.677C>T genotyping was carried out using the TaqMan genotyping assay. RESULTS LINE-1 methylation level was significantly higher on medial side of cleft lip compared with lateral side (p = 0.001). This difference was not significantly influenced by the case's sex or cleft type. However, MTHFR c.677C>T genotyping revealed that the difference in LINE-1 methylation across cleft lip was restricted to carriers of C allele of MTHFR c.677C>T and was not apparent in TT homozygous cases (p = 0.027). CONCLUSION This integrated analysis supports the previous finding of differences in DNA methylation across the two sides of cleft lip and further suggests a possible role of MTHFR c.677C>T genotype in establishing this difference.
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Affiliation(s)
- Mohammad Faisal J Khan
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy.,Epidemiology Research Group, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven - University, Leuven, Belgium
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Valentina Aleotti
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Peter A Mossey
- Craniofacial Development at the World Health Organization-collaborating Centre for Oral and Craniofacial Research, Dental Hospital and School, University of Dundee, Dundee, UK
| | - Régine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, University Medical Center, Rotterdam, The Netherlands.,Division Neonatology Erasmus MC, Department of Pediatrics, University Medical Center, Rotterdam, The Netherlands
| | - Luca Autelitano
- Smile House, Regional Centre for Orofacial Clefts and Craniofacial Anomalies, Department of Cranio-Maxillo-Facial Surgery, San Paolo Hospital, University of Milan, Milan, Italy
| | - Maria C Meazzini
- Smile House, Regional Centre for Orofacial Clefts and Craniofacial Anomalies, Department of Cranio-Maxillo-Facial Surgery, San Paolo Hospital, University of Milan, Milan, Italy
| | - Amin Ravaei
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
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45
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Marini NJ, Asrani K, Yang W, Rine J, Shaw GM. Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate. Am J Med Genet A 2019; 179:1260-1269. [PMID: 31063268 PMCID: PMC6557678 DOI: 10.1002/ajmg.a.61183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 01/15/2023]
Abstract
Cleft lip with/without cleft palate (CLP) is a common craniofacial malformation with complex etiologies, reflecting both genetic and environmental factors. Most of the suspected genetic risk for CLP has yet to be identified. To further classify risk loci and estimate the contribution of rare variants, we sequenced the exons in 49 candidate genes in 323 CLP cases and 211 nonmalformed controls. Our findings indicated that rare, protein-altering variants displayed markedly higher burdens in CLP cases at relevant loci. First, putative loss-of-function mutations (nonsense, frameshift) were significantly enriched among cases: 13 of 323 cases (~4%) harbored such alleles within these 49 genes, versus one such change in controls (p = 0.01). Second, in gene-level analyses, the burden of rare alleles showed greater case-association for several genes previously implicated in cleft risk. For example, BHMT displayed a 10-fold increase in protein-altering variants in CLP cases (p = .03), including multiple case occurrences of a rare frameshift mutation (K400 fs). Other loci with greater rare, coding allele burdens in cases were in signaling pathways relevant to craniofacial development (WNT9B, BMP4, BMPR1B) as well as the methionine cycle (MTRR). We conclude that rare coding variants may confer risk for isolated CLP.
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Affiliation(s)
- Nicholas J Marini
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California, Berkeley, California
| | - Kripa Asrani
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California, Berkeley, California
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Jasper Rine
- California Institute for Quantitative Biosciences, Department of Molecular and Cellular Biology, University of California, Berkeley, California
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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46
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Abstract
This short review is an opportunity to focus on significant positive changes for those children born with some form of oro-facial clefting and who are treated in a centralised service within the National Health Service (NHS). There has also been an opportunity to provide a focus for research as part of this service model. Orthodontists have played a key role in all aspects of this and will continue to be central to further improvements in caring for cleft children.
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Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Wiemels J, Marini NJ. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk. Epigenetics 2019; 14:198-213. [PMID: 30870065 PMCID: PMC6557558 DOI: 10.1080/15592294.2019.1581591] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the VTRNA2-1 gene, which was also hypomethylated in cases (FWER p = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as WNT9B, MIR140 and LHX8. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
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Affiliation(s)
- Semira Gonseth
- a School of Public Health , University of California , Berkeley , CA , USA.,b Institute of Social and Preventive Medicine , Lausanne University Hospital , Lausanne , Switzerland
| | - Gary M Shaw
- c Department of Pediatrics , Stanford University School of Medicine , Stanford , CA , USA
| | - Ritu Roy
- d Cancer Research Institute , University of California , San Francisco , CA , USA
| | - Mark R Segal
- e Department of Epidemiology and Biostatistics , University of California , San Francisco , CA , USA
| | - Kripa Asrani
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Jasper Rine
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Joseph Wiemels
- g Center for Genetic Epidemiology , University of Southern California School of Medicine , Los Angeles , CA , USA
| | - Nicholas J Marini
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
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Xu Z, Lie RT, Wilcox AJ, Saugstad OD, Taylor JA. A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts. Clin Epigenetics 2019; 11:40. [PMID: 30832715 PMCID: PMC6399917 DOI: 10.1186/s13148-019-0638-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/20/2019] [Indexed: 01/08/2023] Open
Abstract
Background Isolated orofacial clefts are among the most common congenital birth defects. Although the underlying biological mechanisms remain largely unknown, clefts are thought to be complex disorders influenced by genetic, environmental, and potentially epigenetic factors. Methods In blood samples from 2- to 3-day-old infants (n = 747) collected in a nationwide population-based study of orofacial clefts in Norway, we measured DNA methylation profiles for more than 450,000 CpGs and then conducted epigenome-wide association analyses (EWAS). We tested methylation profile difference at each CpG between controls (n = 436) and each of the cleft subtypes (92 cleft lip only, CLO; 84 cleft palate only, CPO; 132 cleft lip and palate, CLP). We also compared controls to various combinations of case groups and compared case subtypes to each other. Finally, using the EWAS results, we searched for larger differentially methylated regions (DMRs) associated with orofacial clefts. Results In EWAS comparing controls to individual cleft subtypes, we found no significant associations at a Bonferroni P value threshold of 10−7. After pooling case groups, we found two significantly differentially methylated CpGs: cg09696939 near gene BICC1 is associated with CLO+CLP (P = 9.58 × 10−8); cg26985354 in gene CLASRP is associated with CPO+CLP (P = 7.38 × 10−8). In DMR analysis, we identified a total of 56 significant regions when comparing controls to individual cleft subtypes (10 for CLO, 6 for CPO, 41 for CLP). Only one DMR is shared among the three cleft groups. In combined case group analysis, we found 26 DMRs for CLP+CLO, 31 for CLP+CPO, and 37 when all subtypes are combined. Finally, in case-case comparisons of subtypes, we identified 10 DMRs when comparing CLP to CPO, 9 in CLP compared to CLO, and 13 in CLP compared to CPO. Conclusions We identified two individual CpGs and multiple DMRs that differ between controls and cleft case subtypes. Although we find some evidence for the possible role of DNA methylation in etiology of orofacial clefts, our study does not support previous reports of widespread differences in blood DNA methylation between babies with and without facial clefts. Electronic supplementary material The online version of this article (10.1186/s13148-019-0638-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Ola Didrik Saugstad
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA. .,Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Mail Drop A3-05, Research Triangle Park, NC, 27709, USA.
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Reynolds K, Kumari P, Sepulveda Rincon L, Gu R, Ji Y, Kumar S, Zhou CJ. Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models. Dis Model Mech 2019; 12:12/2/dmm037051. [PMID: 30760477 PMCID: PMC6398499 DOI: 10.1242/dmm.037051] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diverse signaling cues and attendant proteins work together during organogenesis, including craniofacial development. Lip and palate formation starts as early as the fourth week of gestation in humans or embryonic day 9.5 in mice. Disruptions in these early events may cause serious consequences, such as orofacial clefts, mainly cleft lip and/or cleft palate. Morphogenetic Wnt signaling, along with other signaling pathways and transcription regulation mechanisms, plays crucial roles during embryonic development, yet the signaling mechanisms and interactions in lip and palate formation and fusion remain poorly understood. Various Wnt signaling and related genes have been associated with orofacial clefts. This Review discusses the role of Wnt signaling and its crosstalk with cell adhesion molecules, transcription factors, epigenetic regulators and other morphogenetic signaling pathways, including the Bmp, Fgf, Tgfβ, Shh and retinoic acid pathways, in orofacial clefts in humans and animal models, which may provide a better understanding of these disorders and could be applied towards prevention and treatments.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Priyanka Kumari
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Lessly Sepulveda Rincon
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Ran Gu
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Santosh Kumar
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA .,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
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50
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Howe LJ, Richardson TG, Arathimos R, Alvizi L, Passos-Bueno MR, Stanier P, Nohr E, Ludwig KU, Mangold E, Knapp M, Stergiakouli E, Pourcain BS, Smith GD, Sandy J, Relton CL, Lewis SJ, Hemani G, Sharp GC. Evidence for DNA methylation mediating genetic liability to non-syndromic cleft lip/palate. Epigenomics 2019; 11:133-145. [PMID: 30638414 PMCID: PMC6462847 DOI: 10.2217/epi-2018-0091] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/18/2018] [Indexed: 12/26/2022] Open
Abstract
AIM To determine if nonsyndromic cleft lip with or without cleft palate (nsCL/P) genetic risk variants influence liability to nsCL/P through gene regulation pathways, such as those involving DNA methylation. MATERIALS & METHODS nsCL/P genetic summary data and methylation data from four studies were used in conjunction with Mendelian randomization and joint likelihood mapping to investigate potential mediation of nsCL/P genetic variants. RESULTS & CONCLUSION Evidence was found at VAX1 (10q25.3), LOC146880 (17q23.3) and NTN1 (17p13.1), that liability to nsCL/P and variation in DNA methylation might be driven by the same genetic variant, suggesting that genetic variation at these loci may increase liability to nsCL/P by influencing DNA methylation. Follow-up analyses using different tissues and gene expression data provided further insight into possible biological mechanisms.
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Affiliation(s)
- Laurence J Howe
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
- Institute of Cardiovascular Science, University College London, London, NW1 2DA, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
| | - Lucas Alvizi
- Centro de Pesquisas Sobre o Genoma Humano eCélulas-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Maria R Passos-Bueno
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
- Institute of Cardiovascular Science, University College London, London, NW1 2DA, UK
- Centro de Pesquisas Sobre o Genoma Humano eCélulas-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, WC1N 3JH, UK
- Institute of Public Health, Aarhus University, Aarhus, Denmark
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
- Institute of Medical Biometry, Informatics & Epidemiology, University of Bonn, 53127 Bonn, Germany
- Max Planck Institute for Psycholinguistics, Nijmegen, 6525 XD, Netherlands
- Donders Institute, 6525 EN Nijmegen, The Netherlands
- Bristol Dental School, University of Bristol, BS8 2BN, UK
| | - Philip Stanier
- Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, WC1N 3JH, UK
| | - Ellen Nohr
- Institute of Public Health, Aarhus University, Aarhus, Denmark
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics & Epidemiology, University of Bonn, 53127 Bonn, Germany
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
- Max Planck Institute for Psycholinguistics, Nijmegen, 6525 XD, Netherlands
- Donders Institute, 6525 EN Nijmegen, The Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
| | - Jonathan Sandy
- Bristol Dental School, University of Bristol, BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
| | - Sarah J Lewis
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
- Bristol Dental School, University of Bristol, BS8 2BN, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK
- Bristol Dental School, University of Bristol, BS8 2BN, UK
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