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Dai Y, Itai T, Pei G, Yan F, Chu Y, Jiang X, Weinberg SM, Mukhopadhyay N, Marazita ML, Simon LM, Jia P, Zhao Z. DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. HGG ADVANCES 2024; 5:100312. [PMID: 38796699 PMCID: PMC11193024 DOI: 10.1016/j.xhgg.2024.100312] [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: 02/08/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
Orofacial clefts (OFCs) are among the most common human congenital birth defects. Previous multiethnic studies have identified dozens of associated loci for both cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP). Although several nearby genes have been highlighted, the "casual" variants are largely unknown. Here, we developed DeepFace, a convolutional neural network model, to assess the functional impact of variants by SNP activity difference (SAD) scores. The DeepFace model is trained with 204 epigenomic assays from crucial human embryonic craniofacial developmental stages of post-conception week (pcw) 4 to pcw 10. The Pearson correlation coefficient between the predicted and actual values for 12 epigenetic features achieved a median range of 0.50-0.83. Specifically, our model revealed that SNPs significantly associated with OFCs tended to exhibit higher SAD scores across various variant categories compared to less related groups, indicating a context-specific impact of OFC-related SNPs. Notably, we identified six SNPs with a significant linear relationship to SAD scores throughout developmental progression, suggesting that these SNPs could play a temporal regulatory role. Furthermore, our cell-type specificity analysis pinpointed the trophoblast cell as having the highest enrichment of risk signals associated with OFCs. Overall, DeepFace can harness distal regulatory signals from extensive epigenomic assays, offering new perspectives for prioritizing OFC variants using contextualized functional genomic features. We expect DeepFace to be instrumental in accessing and predicting the regulatory roles of variants associated with OFCs, and the model can be extended to study other complex diseases or traits.
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Affiliation(s)
- Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Toshiyuki Itai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fangfang Yan
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yan Chu
- Center for Secure Artificial Intelligence for Healthcare, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoqian Jiang
- Center for Secure Artificial Intelligence for Healthcare, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Nandita Mukhopadhyay
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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2
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Dynamic enhancer landscapes in human craniofacial development. Nat Commun 2024; 15:2030. [PMID: 38448444 PMCID: PMC10917818 DOI: 10.1038/s41467-024-46396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Laura E Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, 3010, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Lucile Packard Children's Hospital, Stanford University, Stanford, CA, 94304, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA, 94110, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Octant Inc., Emeryville, CA, 94608, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, CA, USA.
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Wilderman A, D'haene E, Baetens M, Yankee TN, Winchester EW, Glidden N, Roets E, Van Dorpe J, Janssens S, Miller DE, Galey M, Brown KM, Stottmann RW, Vergult S, Weaver KN, Brugmann SA, Cox TC, Cotney J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nat Commun 2024; 15:136. [PMID: 38167838 PMCID: PMC10762089 DOI: 10.1038/s41467-023-44506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.
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Affiliation(s)
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Emma Wentworth Winchester
- Graduate Program UConn Health, Farmington, CT, USA
- University of Connecticut School of Dental Medicine, Farmington, CT, USA
| | - Nicole Glidden
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ellen Roets
- Department of Obstetrics, Women's Clinic, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Miranda Galey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kari M Brown
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - K Nicole Weaver
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy C Cox
- Department of Oral & Craniofacial Sciences, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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4
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Cui X, Zhu G, Han M, Li X, Lou S, Xing C, Xu S, Pan Y, Wang L. Genetic variants in BCL-2 family genes influence the risk of non-syndromic cleft lip with or without cleft palate. Birth Defects Res 2024; 116:e2288. [PMID: 38108593 DOI: 10.1002/bdr2.2288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/30/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND The BCL-2 family is crucial for cell death regulation and is involved in development, tissue homeostasis, and immunity. This study aimed to investigate the association between genetic variants in BCL-2 family genes and non-syndromic cleft lip with or without cleft palate (NSCL/P) risk. METHODS A two-stage case-control study was conducted in this association study. Gene-based analysis using Multi-marker Analysis of GenoMic Annotation was performed in the first stage cohort, which included 565 cases and 1269 controls. A logistic regression model was employed to assess the effect of single nucleotide polymorphisms (SNPs) on susceptibility to NSCL/P. Candidate SNPs were replicated by extra dbGaP case-parent trios. Haploreg, RegulomeDB, and UCSC Genome Browser were used to identify enhancer effects of promising SNPs. Bulk RNA sequencing data obtained from the Gene Expression Omnibus was used to identify co-expressed genes. Single-cell RNA sequencing dataset was used to infer the cell population of the candidate gene. The "Monocle" package was used to analyze the pseudotime cell trajectories. RESULTS Rs3943258 located in the enhancer region was associated with the risk of NSCL/P (Pmeta = 5.66 × 10-04 ) and exhibited an eQTL effect for BCL2 (P = 3.96 × 10-02 ). Co-expression and pathway enrichment analysis revealed that genes related to Bcl2 were significantly enriched in the PI3K-Akt signaling pathway, MAPK signaling pathway, and Wnt signaling pathway. Five cell clusters were identified in single-cell RNA sequencing, and Bcl2 was mainly located in the mesenchyme. CONCLUSION The rs3943258 located within BCL2 was probably related to NSCL/P susceptibility.
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Affiliation(s)
- Xing Cui
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Minxuan Han
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaofeng Li
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Changyue Xing
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Shuangbo Xu
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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5
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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6
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Robinson K, Mosley TJ, Rivera-González KS, Jabbarpour CR, Curtis SW, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Cutler DJ, Epstein MP, Gowans LJ, Hecht JT, Murray JC, Shaw GM, Uribe LM, Weinberg SM, Brand H, Marazita ML, Lipinski RJ, Leslie EJ. Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate. HGG ADVANCES 2023; 4:100234. [PMID: 37719664 PMCID: PMC10502411 DOI: 10.1016/j.xhgg.2023.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Cleft palate (CP) is one of the most common craniofacial birth defects; however, there are relatively few established genetic risk factors associated with its occurrence despite high heritability. Historically, CP has been studied as a single phenotype, although it manifests across a spectrum of defects involving the hard and/or soft palate. We performed a genome-wide association study using transmission disequilibrium tests of 435 case-parent trios to evaluate broad risks for any cleft palate (ACP) (n = 435), and subtype-specific risks for any cleft soft palate (CSP), (n = 259) and any cleft hard palate (CHP) (n = 125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p = 4.24 × 10-8) associated with CHP. One gene at this locus, angiopoietin-like 2 (ANGPTL2), plays a role in osteoblast differentiation. It is expressed both in craniofacial tissue of human embryos and developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p < 5 × 10-6), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios for the 20 loci were most similar across all 3 groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either subtype. We also found nominal evidence of replication (p < 0.05) for 22 SNPs previously associated with orofacial clefts. Our study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks.
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Affiliation(s)
- Kelsey Robinson
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Trenell J. Mosley
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Kenneth S. Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christopher R. Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Wasiu Lanre Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos 101017, Nigeria
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Azeez Butali
- Department of Oral Biology, Radiology, and Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, PR 00925, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | | | - Lord J.J. Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School University of Texas Health at Houston, Houston, TX 77030, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Lina Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA 52242, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet 2023; 142:1531-1541. [PMID: 37676273 DOI: 10.1007/s00439-023-02596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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8
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Tseng KC, Crump JG. Craniofacial developmental biology in the single-cell era. Development 2023; 150:dev202077. [PMID: 37812056 PMCID: PMC10617621 DOI: 10.1242/dev.202077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The evolution of a unique craniofacial complex in vertebrates made possible new ways of breathing, eating, communicating and sensing the environment. The head and face develop through interactions of all three germ layers, the endoderm, ectoderm and mesoderm, as well as the so-called fourth germ layer, the cranial neural crest. Over a century of experimental embryology and genetics have revealed an incredible diversity of cell types derived from each germ layer, signaling pathways and genes that coordinate craniofacial development, and how changes to these underlie human disease and vertebrate evolution. Yet for many diseases and congenital anomalies, we have an incomplete picture of the causative genomic changes, in particular how alterations to the non-coding genome might affect craniofacial gene expression. Emerging genomics and single-cell technologies provide an opportunity to obtain a more holistic view of the genes and gene regulatory elements orchestrating craniofacial development across vertebrates. These single-cell studies generate novel hypotheses that can be experimentally validated in vivo. In this Review, we highlight recent advances in single-cell studies of diverse craniofacial structures, as well as potential pitfalls and the need for extensive in vivo validation. We discuss how these studies inform the developmental sources and regulation of head structures, bringing new insights into the etiology of structural birth anomalies that affect the vertebrate head.
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Affiliation(s)
- Kuo-Chang Tseng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
| | - J. Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
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9
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Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun 2023; 14:4623. [PMID: 37532691 PMCID: PMC10397224 DOI: 10.1038/s41467-023-40363-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/- 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.
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Affiliation(s)
- Tara N Yankee
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Sungryong Oh
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | | | - Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Jennifer VanOudenhove
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Justin Cotney
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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10
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Kaucka M. Cis-regulatory landscapes in the evolution and development of the mammalian skull. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220079. [PMID: 37183897 PMCID: PMC10184250 DOI: 10.1098/rstb.2022.0079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Extensive morphological variation found in mammals reflects the wide spectrum of their ecological adaptations. The highest morphological diversity is present in the craniofacial region, where geometry is mainly dictated by the bony skull. Mammalian craniofacial development represents complex multistep processes governed by numerous conserved genes that require precise spatio-temporal control. A central question in contemporary evolutionary biology is how a defined set of conserved genes can orchestrate formation of fundamentally different structures, and therefore how morphological variability arises. In principle, differential gene expression patterns during development are the source of morphological variation. With the emergence of multicellular organisms, precise regulation of gene expression in time and space is attributed to cis-regulatory elements. These elements contribute to higher-order chromatin structure and together with trans-acting factors control transcriptional landscapes that underlie intricate morphogenetic processes. Consequently, divergence in cis-regulation is believed to rewire existing gene regulatory networks and form the core of morphological evolution. This review outlines the fundamental principles of the genetic code and genomic regulation interplay during development. Recent work that deepened our comprehension of cis-regulatory element origin, divergence and function is presented here to illustrate the state-of-the-art research that uncovered the principles of morphological novelty. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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11
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Li Y, Xiong Z, Zhang M, Hysi PG, Qian Y, Adhikari K, Weng J, Wu S, Du S, Gonzalez-Jose R, Schuler-Faccini L, Bortolini MC, Acuna-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Wang J, Tan J, Yuan Z, Jin L, Uitterlinden AG, Ghanbari M, Ikram MA, Nijsten T, Zhu X, Lei Z, Jia P, Ruiz-Linares A, Spector TD, Wang S, Kayser M, Liu F. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci. PLoS Genet 2023; 19:e1010786. [PMID: 37459304 PMCID: PMC10351707 DOI: 10.1371/journal.pgen.1010786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/16/2023] [Indexed: 07/20/2023] Open
Abstract
Human ear morphology, a complex anatomical structure represented by a multidimensional set of correlated and heritable phenotypes, has a poorly understood genetic architecture. In this study, we quantitatively assessed 136 ear morphology traits using deep learning analysis of digital face images in 14,921 individuals from five different cohorts in Europe, Asia, and Latin America. Through GWAS meta-analysis and C-GWASs, a recently introduced method to effectively combine GWASs of many traits, we identified 16 genetic loci involved in various ear phenotypes, eight of which have not been previously associated with human ear features. Our findings suggest that ear morphology shares genetic determinants with other surface ectoderm-derived traits such as facial variation, mono eyebrow, and male pattern baldness. Our results enhance the genetic understanding of human ear morphology and shed light on the shared genetic contributors of different surface ectoderm-derived phenotypes. Additionally, gene editing experiments in mice have demonstrated that knocking out the newly ear-associated gene (Intu) and a previously ear-associated gene (Tbx15) causes deviating mouse ear morphology.
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Affiliation(s)
- Yi Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Manfei Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Yu Qian
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Beijing No.8 High School, Beijing, China
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, United Kingdom
| | - Jun Weng
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
| | - Sijie Wu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- University of Chinese Academy of Sciences, China
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Argentina
| | | | | | - Victor Acuna-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM-Instituto Nacional de Medicina Genomica, Mexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular), Universidad de Antioquia, Medellin, Colombia
| | | | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, China
| | - Li Jin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Fudan-Taizhou Institute of Health Sciences, China
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC, University Medical Center, the Netherlands
| | - Xiangyu Zhu
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Zhen Lei
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Aix-Marseille Universite, CNRS, EFS, ADES, France
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
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12
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Cell Type- and Tissue-specific Enhancers in Craniofacial Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546603. [PMID: 37425964 PMCID: PMC10327103 DOI: 10.1101/2023.06.26.546603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development1-3. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined histone modification and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. We used transgenic mouse reporter assays to determine the in vivo activity patterns of human face enhancers predicted from these data. Across 16 in vivo validated human enhancers, we observed a rich diversity of craniofacial subregions in which these enhancers are active in vivo. To annotate the cell type specificities of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating these data across species, we find that the majority (56%) of human craniofacial enhancers are functionally conserved in mice, providing cell type- and embryonic stage-resolved predictions of their in vivo activity profiles. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we demonstrate the utility of these data for predicting the in vivo cell type specificity of enhancers. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Laura E. Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Cailyn H. Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Lucile Packard Children’s Hospital, Stanford University, Stanford, CA 94304
| | - Matthew J. Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A. Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Catherine S. Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Riana D. Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA 94110
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E. Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Octant Inc., Emeryville, CA 94608, USA
| | - Len A. Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, California, USA
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13
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Li Q, Chen J, Faux P, Delgado ME, Bonfante B, Fuentes-Guajardo M, Mendoza-Revilla J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Wu S, Du S, Giardina A, Paria SS, Khokan MR, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Rojas W, Rothhammer F, Navarro N, Wang S, Adhikari K, Ruiz-Linares A. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape. Commun Biol 2023; 6:481. [PMID: 37156940 PMCID: PMC10167347 DOI: 10.1038/s42003-023-04838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.
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Affiliation(s)
- Qing Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
| | - Jieyi Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Miguel Eduardo Delgado
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, República Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Buenos Aires, República Argentina
| | - Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, 75015, France
| | - J Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City, 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Sijie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrea Giardina
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Soumya Subhra Paria
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Mahfuzur Rahman Khokan
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica, 1000000, Chile
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, Dijon, 21000, France
- EPHE, PSL University, Paris, 75014, France
| | - Sijia Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China.
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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14
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Xu X, Lin J, Li X, Shao Q, Cui X, Zhu G, Lou S, Zhong W, Liu L, Pan Y. Genetic Variants in Mammalian STE20-like Protein Kinase 2 were associated with risk of NSCL/P. Gene 2023; 873:147459. [PMID: 37141954 DOI: 10.1016/j.gene.2023.147459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
AIM Mammalian STE20-like protein kinase 2 (MST2) plays an important role in apoptosis and the development of many disorders. Here, we aim to explore if genetic variants in MST2 are associated with the risk of non-syndromic cleft lip with or without palate (NSCL/P). MATERIALS AND METHODS The association study was performed in a two-stage study of 1,069 cases and 1,724 controls to evaluate the association between genetic variants in the MST2 and NSCL/P risk. The potential function of the candidate single nucleotide polymorphism (SNP) was predicted using HaploReg, RegulomeDB, and public craniofacial histone chromatin immunoprecipitation sequencing (ChIP-seq) data. Haploview was used to perform the haplotype of risk alleles. The expression quantitative trait loci (eQTL) effect was assessed using the Genotype-Tissue Expression (GTEx) project. Gene expression in mouse embryo tissue was performed using data downloaded from GSE67985. The potential role of candidate gene in the development of NSCL/P was assessed by correlation and enrichment analysis. RESULTS Among SNPs in MST2, rs2922070 C allele (Pmeta = 2.93E-04) and rs6988087 T allele (Pmeta = 1.57E-03) were linked with significantly increased risk of NSCL/P. Rs2922070, rs6988087 and their high linkage disequilibrium (LD) SNPs constituted a risk haplotype of NSCL/P. Individuals carrying 3-4 risk alleles had an elevated risk of NSCL/P compared to those who carried less risk alleles (P = 2.00E-04). The eQTL analysis revealed a significant association between these two variants and MST2 in muscle tissue of the body. The MST2 expressed during mouse craniofacial development and over-expressed in the human orbicularis oris muscle (OOM) of NSCL/P patients compared to controls. MST2 was involved in the development of NSCL/P by regulating the mRNA surveillance pathway, the MAPK signaling pathway, the neurotrophin signaling pathway, the FoxO signaling pathway and the VEGF signaling pathway. CONCLUSION MST2 was associated with the development of NSCL/P.
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Affiliation(s)
- Xinze Xu
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Junyan Lin
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Xiaofeng Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Qinghua Shao
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Xing Cui
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Guirong Zhu
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Shu Lou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Weijie Zhong
- Department of Stomatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China Suzhou, 215127, China; Department of Stomatology, Medical Center of Soochow University, Suzhou, 215127, China.
| | - Luwei Liu
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China.
| | - Yongchu Pan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210000, China; Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210000, China.
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15
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Robinson K, Mosley TJ, Rivera-González KS, Jabbarpour CR, Curtis SW, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Cutler DJ, Epstein MP, Gowans LJ, Hecht JT, Murray JC, Shaw GM, Uribe LM, Weinberg SM, Brand H, Marazita ML, Lipinski RJ, Leslie EJ. Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.01.23286642. [PMID: 37066311 PMCID: PMC10104215 DOI: 10.1101/2023.03.01.23286642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Orofacial clefts (OFCs) are the most common craniofacial birth defects and are often categorized into two etiologically distinct groups: cleft lip with or without cleft palate (CL/P) and isolated cleft palate (CP). CP is highly heritable, but there are still relatively few established genetic risk factors associated with its occurrence compared to CL/P. Historically, CP has been studied as a single phenotype despite manifesting across a spectrum of defects involving the hard and/or soft palate. We performed GWAS using transmission disequilibrium tests using 435 case-parent trios to evaluate broad risks for any cleft palate (ACP, n=435), as well as subtype-specific risks for any cleft soft palate (CSP, n=259) and any cleft hard palate (CHP, n=125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p=4.24×10 -8 ) associated with CHP. One gene at this locus, angiopoietin-like 2 ( ANGPTL2 ), plays a role in osteoblast differentiation. It is expressed in craniofacial tissue of human embryos, as well as in the developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p<5×10 -6 ), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios (ORs) for each of the 20 loci were most similar across all three groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either the CSP or CHP groups. We also found nominal evidence of replication (p<0.05) for 22 SNPs previously associated with cleft palate (including CL/P). Interestingly, most SNPs associated with CL/P cases were found to convey the opposite effect in those replicated in our dataset for CP only. Ours is the first study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks.
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Affiliation(s)
| | - Trenell J Mosley
- Department of Human Genetics, Emory University, Atlanta, GA
- Current address: Chief Officer for Scientific Workforce Diversity Office, National Institutes of Health, Bethesda, MD
| | - Kenneth S Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Christopher R Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA
| | - Wasiu Lanre Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD
| | - Azeez Butali
- Department of Oral Biology, Radiology, and Medicine, University of Iowa, Iowa City, IA
| | - Carmen J Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA
| | | | - Lord Jj Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School University of Texas Health at Houston, Houston, TX
| | | | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Lina Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Robert J Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
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16
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Fan L, Ma L, Zhu G, Yao S, Li X, Yu X, Pan Y, Wang L. A Genome-wide association study of premolar agenesis in a chinese population. Oral Dis 2023; 29:1102-1114. [PMID: 34878701 DOI: 10.1111/odi.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/14/2021] [Accepted: 11/28/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Premolar agenesis is a common subtype of tooth agenesis. Although a genome-wide study (GWAS) has identified some variants involved in tooth agenesis in Europeans, the genetic mutation related to premolar agenesis in the Chinese population remains unclear. MATERIALS AND METHODS We present a GWAS in 218 premolar agenesis cases and 1,222 controls using the Illumina Infinium® Global Screening Array. 5,585,618 single nucleotide polymorphisms (SNPs) were used for tests of associations with premolar agenesis. RESULTS Four independent SNPs on chromosome 2 were identified as susceptibility loci, including rs147680216, rs79743039, rs60540881, and rs6738629. The genome-wide significant SNP rs147680216 (p = 6.09 × 10-9 ) was predicted to change the structure of the WNT10A protein and interact with hedgehog signaling pathway components. Meta-analysis showed that the rs147680216 A allele significantly increased the risk of tooth agenesis (p = 0.000). The other three SNPs with nominal significance are novel susceptibility loci. Of them, rs6738629 (p = 5.40 × 10-6 ) acts as a potential transcriptional regulator of GCC2, a gene playing a putative role in dental and craniofacial development. CONCLUSION Our GWAS indicates that rs147680216 and additional three novel susceptibility loci on chromosome 2 are associated with the risk of premolar agenesis in the Chinese population.
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Affiliation(s)
- Liwen Fan
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Siyue Yao
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaofeng Li
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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17
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287714. [PMID: 37034635 PMCID: PMC10081436 DOI: 10.1101/2023.03.24.23287714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205,USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
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18
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Suratannon N, Ittiwut C, Dik WA, Ittiwut R, Meesilpavikkai K, Israsena N, Ingrungruanglert P, Dalm VASH, van Daele PLA, Sanpavat A, Chaijitraruch N, Schrijver B, Buranapraditkun S, Porntaveetus T, Swagemakers SMA, IJspeert H, Palaga T, Suphapeetiporn K, van der Spek PJ, Hirankarn N, Chatchatee P, Martin van Hagen P, Shotelersuk V. A germline STAT6 gain-of-function variant is associated with early-onset allergies. J Allergy Clin Immunol 2023; 151:565-571.e9. [PMID: 36216080 DOI: 10.1016/j.jaci.2022.09.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND The signal transducer and activator of transcription 6 (STAT6) signaling pathway plays a central role in allergic inflammation. To date, however, there have been no descriptions of STAT6 gain-of-function variants leading to allergies in humans. OBJECTIVE We report a STAT6 gain-of-function variant associated with early-onset multiorgan allergies in a family with 3 affected members. METHODS Exome sequencing and immunophenotyping of T-helper cell subsets were conducted. The function of the STAT6 protein was analyzed by Western blot, immunofluorescence, electrophoretic mobility shift assays, and luciferase assays. Gastric organoids obtained from the index patient were used to study downstream effector cytokines. RESULTS We identified a heterozygous missense variant (c.1129G>A;p.Glu377Lys) in the DNA binding domain of STAT6 that was de novo in the index patient's father and was inherited by 2 of his 3 children. Severe atopic dermatitis and food allergy were key presentations. Clinical heterogeneity was observed among the affected individuals. Higher levels of peripheral blood TH2 lymphocytes were detected. The mutant STAT6 displayed a strong preference for nuclear localization, increased DNA binding affinity, and spontaneous transcriptional activity. Moreover, gastric organoids showed constitutive activation of STAT6 downstream signaling molecules. CONCLUSIONS A germline STAT6 gain-of-function variant results in spontaneous activation of the STAT6 signaling pathway and is associated with an early-onset and severe allergic phenotype in humans. These observations enhance our knowledge of the molecular mechanisms underlying allergic diseases and will potentially contribute to novel therapeutic interventions.
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Affiliation(s)
- Narissara Suratannon
- Center of Excellence for Allergy and Clinical Immunology, Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Willem A Dik
- Laboratory Medical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Rungnapa Ittiwut
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Kornvalee Meesilpavikkai
- Center of Excellence in Immunology and Immune-mediated Diseases, Immunology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nipan Israsena
- Center of Excellence for Stem Cell and Cell Therapy, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Praewphan Ingrungruanglert
- Center of Excellence for Stem Cell and Cell Therapy, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Virgil A S H Dalm
- Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Paul L A van Daele
- Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Anapat Sanpavat
- Department of Pathology, Faculty of Medicine, Thai Pediatric Gastroenterology, Hepatology and Immunology Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Nataruks Chaijitraruch
- Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Organ Transplantation, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Benjamin Schrijver
- Laboratory Medical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Supranee Buranapraditkun
- Cellular Immunology Laboratory Allergy and Clinical Immunology Unit, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Sigrid M A Swagemakers
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Erasmus Center for Data Analytics, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hanna IJspeert
- Laboratory Medical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Tanapat Palaga
- Center of Excellence in Immunology and Immune-mediated Diseases, Immunology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Peter J van der Spek
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Erasmus Center for Data Analytics, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Immunology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Pantipa Chatchatee
- Center of Excellence for Allergy and Clinical Immunology, Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
| | - P Martin van Hagen
- Center of Excellence for Allergy and Clinical Immunology, Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands; Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center), Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
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19
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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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20
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Zieger HK, Weinhold L, Schmidt A, Holtgrewe M, Juranek SA, Siewert A, Scheer AB, Thieme F, Mangold E, Ishorst N, Brand FU, Welzenbach J, Beule D, Paeschke K, Krawitz PM, Ludwig KU. Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations. HGG ADVANCES 2022; 4:100166. [PMID: 36589413 PMCID: PMC9795529 DOI: 10.1016/j.xhgg.2022.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a highly heritable facial disorder. To date, systematic investigations of the contribution of rare variants in non-coding regions to nsCL/P etiology are sparse. Here, we re-analyzed available whole-genome sequence (WGS) data from 211 European case-parent trios with nsCL/P and identified 13,522 de novo mutations (DNMs) in nsCL/P cases, 13,055 of which mapped to non-coding regions. We integrated these data with DNMs from a reference cohort, with results of previous genome-wide association studies (GWASs), and functional and epigenetic datasets of relevance to embryonic facial development. A significant enrichment of nsCL/P DNMs was observed at two GWAS risk loci (4q28.1 (p = 8 × 10-4) and 2p21 (p = 0.02)), suggesting a convergence of both common and rare variants at these loci. We also mapped the DNMs to 810 position weight matrices indicative of transcription factor (TF) binding, and quantified the effect of the allelic changes in silico. This revealed a nominally significant overrepresentation of DNMs (p = 0.037), and a stronger effect on binding strength, for DNMs located in the sequence of the core binding region of the TF Musculin (MSC). Notably, MSC is involved in facial muscle development, together with a set of nsCL/P genes located at GWAS loci. Supported by additional results from single-cell transcriptomic data and molecular binding assays, this suggests that variation in MSC binding sites contributes to nsCL/P etiology. Our study describes a set of approaches that can be applied to increase the added value of WGS data.
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Affiliation(s)
- Hanna K. Zieger
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Leonie Weinhold
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
| | - Stefan A. Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Annika B. Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Fabian U. Brand
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Peter M. Krawitz
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany,Corresponding author
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21
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Winchester EW, Hardy A, Cotney J. Integration of multimodal data in the developing tooth reveals candidate regulatory loci driving human odontogenic phenotypes. FRONTIERS IN DENTAL MEDICINE 2022; 3:1009264. [PMID: 37034481 PMCID: PMC10078798 DOI: 10.3389/fdmed.2022.1009264] [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: 12/02/2022] Open
Abstract
Human odontogenic aberrations such as abnormal tooth number and delayed tooth eruption can occur as a symptom of rare syndromes or, more commonly, as nonsyndromic phenotypes. These phenotypes can require extensive and expensive dental treatment, posing a significant burden. While many dental phenotypes are heritable, most nonsyndromic cases have not been linked to causal genes. We demonstrate the novel finding that common sequence variants associated with human odontogenic phenotypes are enriched in developmental craniofacial enhancers conserved between human and mouse. However, the bulk nature of these samples obscures if this finding is due to the tooth itself or the surrounding tissues. We therefore sought to identify enhancers specifically active in the tooth anlagen and quantify their contribution to the observed genetic enrichments. We systematically identified 22,001 conserved enhancers active in E13.5 mouse incisors using ChIP-seq and machine learning pipelines and demonstrated biologically relevant enrichments in putative target genes, transcription factor binding motifs, and in vivo activity. Multi-tissue comparisons of human and mouse enhancers revealed that these putative tooth enhancers had the strongest enrichment of odontogenic phenotype-associated variants, suggesting a role for dysregulation of tooth developmental enhancers in human dental phenotypes. The large number of these regions genome-wide necessitated prioritization of enhancer loci for future investigations. As enhancers modulate gene expression, we prioritized regions based on enhancers' putative target genes. We predicted these target genes and prioritized loci by integrating chromatin state, bulk gene expression and coexpression, GWAS variants, and cell type resolved gene expression to generate a prioritized list of putative odontogenic phenotype-driving loci active in the developing tooth. These genomic regions are of particular interest for downstream experiments determining the role of specific dental enhancer:gene pairs in odontogenesis.
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Affiliation(s)
| | - Alexis Hardy
- Master of Genetics Program, Paris Diderot University,
Paris, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of
Connecticut School of Medicine, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut,
Storrs, CT, United States
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22
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Xiao Y, Jiao S, He M, Lin D, Zuo H, Han J, Sun Y, Cao G, Chen Z, Liu H. Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants. Int J Oral Sci 2022; 14:43. [PMID: 36008388 PMCID: PMC9411193 DOI: 10.1038/s41368-022-00194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts (OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability, suggesting there are more associations under the current stringent statistical threshold. In this study, we obtained an integrated epigenomic dataset based on the chromatin conformation of a human oral epithelial cell line (HIOEC) using RNA-seq, ATAC-seq, H3K27ac ChIP-seq, and DLO Hi-C. Presumably, this epigenomic dataset could reveal the missing functional variants located in the oral epithelial cell active enhancers/promoters along with their risk target genes, despite relatively less-stringent statistical association with OFC. Taken a non-syndromic cleft palate only (NSCPO) GWAS data of the Chinese Han population as an example, 3664 SNPs that cannot reach the strict significance threshold were subjected to this functional identification pipeline. In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epithelium-expressed genes were screened. Gapped k-mer machine learning based on enhancers interacting with epithelium-expressed genes along with in vivo and in vitro reporter assays were employed as functional validation. Among all the potential SNPs, we chose and confirmed that the risk alleles of rs560789 and rs174570 reduced the epithelial-specific enhancer activity by preventing the binding of transcription factors related to epithelial development. In summary, we established chromatin conformation datasets of human oral epithelial cells and provided a framework for testing and understanding how regulatory variants impart risk for clefts.
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Affiliation(s)
- Yao Xiao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China.,Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shengbo Jiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Huanyan Zuo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Jiahao Han
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zhi Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China.
| | - Huan Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China. .,Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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23
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Dąbrowska J, Biedziak B, Szponar-Żurowska A, Budner M, Jagodziński PP, Płoski R, Mostowska A. Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing. Mol Genet Genomics 2022; 297:1315-1327. [PMID: 35778651 DOI: 10.1007/s00438-022-01919-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/12/2022] [Indexed: 01/02/2023]
Abstract
For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Margareta Budner
- Eastern Poland Burn Treatment and Reconstructive Center, Leczna, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland.
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24
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Hammond NL, Dixon MJ. Revisiting the embryogenesis of lip and palate development. Oral Dis 2022; 28:1306-1326. [PMID: 35226783 PMCID: PMC10234451 DOI: 10.1111/odi.14174] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/13/2022]
Abstract
Clefts of the lip and palate (CLP), the major causes of congenital facial malformation globally, result from failure of fusion of the facial processes during embryogenesis. With a prevalence of 1 in 500-2500 live births, CLP causes major morbidity throughout life as a result of problems with facial appearance, feeding, speaking, obstructive apnoea, hearing and social adjustment and requires complex, multi-disciplinary care at considerable cost to healthcare systems worldwide. Long-term outcomes for affected individuals include increased mortality compared with their unaffected siblings. The frequent occurrence and major healthcare burden imposed by CLP highlight the importance of dissecting the molecular mechanisms driving facial development. Identification of the genetic mutations underlying syndromic forms of CLP, where CLP occurs in association with non-cleft clinical features, allied to developmental studies using appropriate animal models is central to our understanding of the molecular events underlying development of the lip and palate and, ultimately, how these are disturbed in CLP.
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Affiliation(s)
- Nigel L. Hammond
- Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Michael J. Dixon
- Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
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25
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Hirsch N, Dahan I, D'haene E, Avni M, Vergult S, Vidal-García M, Magini P, Graziano C, Bonora E, Nardone AM, Brancati F, Fernández-Jaén A, Rory OJ, Hallgrimsson B, Birnbaum RY. HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations. Genome Res 2022; 32:1242-1253. [PMID: 35710300 PMCID: PMC9341515 DOI: 10.1101/gr.276196.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the Histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3'-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or Ctcf site (CtcfΔ/Δ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior\posterior limb expression patterns of Shh pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/- mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a Ctcf site and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9INV/+) in mice that does not disrupt HDAC9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidated essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence It suggests that SVs, encompassing protein-coding sequence could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.
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Affiliation(s)
| | | | | | | | | | | | - Pamela Magini
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero Universitaria di Bologna
| | - Claudio Graziano
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero Universitaria di Bologna
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26
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Quiat D, Kim SW, Zhang Q, Morton SU, Pereira AC, DePalma SR, Willcox JAL, McDonough B, DeLaughter DM, Gorham JM, Curran JJ, Tumblin M, Nicolau Y, Artunduaga MA, Quintanilla-Dieck L, Osorno G, Serrano L, Hamdan U, Eavey RD, Seidman CE, Seidman JG. An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations. Proc Natl Acad Sci U S A 2022; 119:e2203928119. [PMID: 35584116 PMCID: PMC9173816 DOI: 10.1073/pnas.2203928119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/12/2022] [Indexed: 01/14/2023] Open
Abstract
Microtia is a congenital malformation that encompasses mild hypoplasia to complete loss of the external ear, or pinna. Although the contribution of genetic variation and environmental factors to microtia remains elusive, Amerindigenous populations have the highest reported incidence. Here, using both transmission disequilibrium tests and association studies in microtia trios (parents and affected child) and microtia cohorts enrolled in Latin America, we map an ∼10-kb microtia locus (odds ratio = 4.7; P = 6.78e-18) to the intergenic region between Roundabout 1 (ROBO1) and Roundabout 2 (ROBO2) (chr3: 78546526 to 78555137). While alleles at the microtia locus significantly increase the risk of microtia, their penetrance is low (<1%). We demonstrate that the microtia locus contains a polymorphic complex repeat element that is expanded in affected individuals. The locus is located near a chromatin loop region that regulates ROBO1 and ROBO2 expression in induced pluripotent stem cell–derived neural crest cells. Furthermore, we use single nuclear RNA sequencing to demonstrate ROBO1 and ROBO2 expression in both fibroblasts and chondrocytes of the mature human pinna. Because the microtia allele is enriched in Amerindigenous populations and is shared by some East Asian subjects with craniofacial malformations, we propose that both populations share a mutation that arose in a common ancestor prior to the ancient migration of Eurasian populations into the Americas and that the high incidence of microtia among Amerindigenous populations reflects the population bottleneck that occurred during the migration out of Eurasia.
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Affiliation(s)
- Daniel Quiat
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Sarah U. Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, 05508-060, Brazil
| | | | | | | | | | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Justin J. Curran
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | | | | | - Lourdes Quintanilla-Dieck
- Department of Otolaryngology Head and Neck Surgery, Oregon Health & Science University, Portland, OR 97239
| | - Gabriel Osorno
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | | | | | - Roland D. Eavey
- Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA 02115
- HHMI, Chevy Chase, MD 20815
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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27
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Naqvi S, Hoskens H, Wilke F, Weinberg SM, Shaffer JR, Walsh S, Shriver MD, Wysocka J, Claes P. Decoding the Human Face: Challenges and Progress in Understanding the Genetics of Craniofacial Morphology. Annu Rev Genomics Hum Genet 2022; 23:383-412. [PMID: 35483406 PMCID: PMC9482780 DOI: 10.1146/annurev-genom-120121-102607] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Variations in the form of the human face, which plays a role in our individual identities and societal interactions, have fascinated scientists and artists alike. Here, we review our current understanding of the genetics underlying variation in craniofacial morphology and disease-associated dysmorphology, synthesizing decades of progress on Mendelian syndromes in addition to more recent results from genome-wide association studies of human facial shape and disease risk. We also discuss the various approaches used to phenotype and quantify facial shape, which are of particular importance due to the complex, multipartite nature of the craniofacial form. We close by discussing how experimental studies have contributed and will further contribute to our understanding of human genetic variation and then proposing future directions and applications for the field.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA; , .,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Hanne Hoskens
- Center for Processing Speech and Images, Department of Electrical Engineering, KU Leuven, Leuven, Belgium; , .,Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Franziska Wilke
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA; ,
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; , .,Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; , .,Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA; ,
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA; , .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Peter Claes
- Center for Processing Speech and Images, Department of Electrical Engineering, KU Leuven, Leuven, Belgium; , .,Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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28
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Zhang M, Wu S, Du S, Qian W, Chen J, Qiao L, Yang Y, Tan J, Yuan Z, Peng Q, Liu Y, Navarro N, Tang K, Ruiz-Linares A, Wang J, Claes P, Jin L, Li J, Wang S. Genetic variants underlying differences in facial morphology in East Asian and European populations. Nat Genet 2022; 54:403-411. [PMID: 35393595 DOI: 10.1038/s41588-022-01038-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 01/19/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Facial morphology-a conspicuous feature of human appearance-is highly heritable. Previous studies on the genetic basis of facial morphology were performed mainly in European-ancestry cohorts (EUR). Applying a data-driven phenotyping and multivariate genome-wide scanning protocol to a large collection of three-dimensional facial images of individuals with East Asian ancestry (EAS), we identified 244 variants in 166 loci (62 new) associated with typical-range facial variation. A newly proposed polygenic shape analysis indicates that the effects of the variants on facial shape in EAS can be generalized to EUR. Based on this, we further identified 13 variants related to differences between facial shape in EUR and EAS populations. Evolutionary analyses suggest that the difference in nose shape between EUR and EAS populations is caused by a directional selection, due mainly to a local adaptation in Europeans. Our results illustrate the underlying genetic basis for facial differences across populations.
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Affiliation(s)
- Manfei Zhang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Computer Science, Fudan University, Shanghai, China
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Qian
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Computer Science, Fudan University, Shanghai, China
| | - Jieyi Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lu Qiao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS-EPHE, Université Bourgogne Franche-Comté, Dijon, France.,Ecole Pratique des Hautes Etudes, PSL University, Paris, France
| | - Kun Tang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrés Ruiz-Linares
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China. .,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Fudan-Taizhou Institute of Health Sciences, Taizhou, China.
| | - Jiarui Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium. .,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
| | - Sijia Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China. .,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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29
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Rajagopal R, Baltazar MT, Carmichael PL, Dent MP, Head J, Li H, Muller I, Reynolds J, Sadh K, Simpson W, Spriggs S, White A, Kukic P. Beyond AOPs: A Mechanistic Evaluation of NAMs in DART Testing. FRONTIERS IN TOXICOLOGY 2022; 4:838466. [PMID: 35295212 PMCID: PMC8915803 DOI: 10.3389/ftox.2022.838466] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
New Approach Methodologies (NAMs) promise to offer a unique opportunity to enable human-relevant safety decisions to be made without the need for animal testing in the context of exposure-driven Next Generation Risk Assessment (NGRA). Protecting human health against the potential effects a chemical may have on embryo-foetal development and/or aspects of reproductive biology using NGRA is particularly challenging. These are not single endpoint or health effects and risk assessments have traditionally relied on data from Developmental and Reproductive Toxicity (DART) tests in animals. There are numerous Adverse Outcome Pathways (AOPs) that can lead to DART, which means defining and developing strict testing strategies for every AOP, to predict apical outcomes, is neither a tenable goal nor a necessity to ensure NAM-based safety assessments are fit-for-purpose. Instead, a pragmatic approach is needed that uses the available knowledge and data to ensure NAM-based exposure-led safety assessments are sufficiently protective. To this end, the mechanistic and biological coverage of existing NAMs for DART were assessed and gaps to be addressed were identified, allowing the development of an approach that relies on generating data relevant to the overall mechanisms involved in human reproduction and embryo-foetal development. Using the knowledge of cellular processes and signalling pathways underlying the key stages in reproduction and development, we have developed a broad outline of endpoints informative of DART. When the existing NAMs were compared against this outline to determine whether they provide comprehensive coverage when integrated in a framework, we found them to generally cover the reproductive and developmental processes underlying the traditionally evaluated apical endpoint studies. The application of this safety assessment framework is illustrated using an exposure-led case study.
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30
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Cesario J, Ha S, Kim J, Kataria N, Jeong J. Candidate positive targets of LHX6 and LHX8 transcription factors in the developing upper jaw. Gene Expr Patterns 2022; 43:119227. [PMID: 34861428 PMCID: PMC8930537 DOI: 10.1016/j.gep.2021.119227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/02/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022]
Abstract
Craniofacial development is controlled by a large number of genes, which interact with one another to form a complex gene regulatory network (GRN). Key components of GRN are signaling molecules and transcription factors. Therefore, identifying targets of core transcription factors is an important part of the overall efforts toward building a comprehensive and accurate model of GRN. LHX6 and LHX8 are transcription factors expressed in the oral mesenchyme of the first pharyngeal arch (PA1), and they are crucial regulators of palate and tooth development. Previously, we performed genome-wide transcriptional profiling and chromatin immunoprecipitation to identify target genes of LHX6 and LHX8 in PA1, and described a set of genes repressed by LHX. However, there has not been any discussion of the genes positively regulated by LHX6 and LHX8. In this paper, we revisited the above datasets to identify candidate positive targets of LHX in PA1. Focusing on those with known connections to craniofacial development, we performed RNA in situ hybridization to confirm the changes in expression in Lhx6;Lhx8 mutant. We also confirmed the binding of LHX6 to several putative enhancers near the candidate target genes. Together, we have uncovered novel connections between Lhx and other important regulators of craniofacial development, including Eya1, Barx1, Rspo2, Rspo3, and Wnt11.
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Affiliation(s)
| | | | | | | | - Juhee Jeong
- Department of Molecular Pathobiology, New York University College of Dentistry, 345 E. 24th Street, New York, NY, 10010, USA.
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31
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Ruff KLM, Hollstein R, Fazaal J, Thieme F, Gehlen J, Mangold E, Knapp M, Welzenbach J, Ludwig KU. Allele-specific transcription factor binding in a cellular model of orofacial clefting. Sci Rep 2022; 12:1807. [PMID: 35110662 PMCID: PMC8810875 DOI: 10.1038/s41598-022-05876-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a frequent congenital malformation with multifactorial etiology. While recent genome-wide association studies (GWAS) have identified several nsCL/P risk loci, the functional effects of the associated non-coding variants are largely unknown. Furthermore, additional risk loci remain undetected due to lack of power. As genetic variants might alter binding of transcription factors (TF), we here hypothesized that the integration of data from TF binding sites, expression analyses and nsCL/P GWAS might help to (i) identify functionally relevant variants at GWAS loci, and (ii) highlight novel risk variants that have been previously undetected. Analysing the craniofacial TF TFAP2A in human embryonic palatal mesenchyme (HEPM) cells, we identified 2845 TFAP2A ChIP-seq peaks, several of which were located near nsCL/P candidate genes (e.g. MSX1 and SPRY2). Comparison with independent data suggest that 802 of them might be specific to craniofacial development, and genes near these peaks are enriched in processes relevant to nsCL/P. Integration with nsCL/P GWAS data, however, did not show robust evidence for co-localization of common nsCL/P risk variants with TFAP2A ChIP-seq peaks. This data set represents a new resource for the analyses of craniofacial processes, and similar approaches with additional cell lines and TFs could be applied to generate further insights into nsCL/P etiology.
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Affiliation(s)
- Katharina L M Ruff
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Ronja Hollstein
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julia Fazaal
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Frederic Thieme
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Elisabeth Mangold
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute for Medical Biometry, Informatics and Epidemiology IMBIE, University of Bonn, Bonn, Germany
| | - Julia Welzenbach
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany.
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32
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Zyner KG, Simeone A, Flynn SM, Doyle C, Marsico G, Adhikari S, Portella G, Tannahill D, Balasubramanian S. G-quadruplex DNA structures in human stem cells and differentiation. Nat Commun 2022; 13:142. [PMID: 35013231 PMCID: PMC8748810 DOI: 10.1038/s41467-021-27719-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
The establishment of cell identity during embryonic development involves the activation of specific gene expression programmes and is underpinned by epigenetic factors including DNA methylation and histone post-translational modifications. G-quadruplexes are four-stranded DNA secondary structures (G4s) that have been implicated in transcriptional regulation and cancer. Here, we show that G4s are key genomic structural features linked to cellular differentiation. We find that G4s are highly abundant in human embryonic stem cells and are lost during lineage specification. G4s are prevalent in enhancers and promoters. G4s that are found in common between embryonic and downstream lineages are tightly linked to transcriptional stabilisation of genes involved in essential cellular functions as well as transitions in the histone post-translational modification landscape. Furthermore, the application of small molecules that stabilise G4s causes a delay in stem cell differentiation, keeping cells in a more pluripotent-like state. Collectively, our data highlight G4s as important epigenetic features that are coupled to stem cell pluripotency and differentiation.
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Affiliation(s)
- Katherine G Zyner
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Angela Simeone
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sean M Flynn
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Colm Doyle
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Giovanni Marsico
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Santosh Adhikari
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Guillem Portella
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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33
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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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34
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Stüssel LG, Hollstein R, Laugsch M, Hochfeld LM, Welzenbach J, Schröder J, Thieme F, Ishorst N, Romero RO, Weinhold L, Hess T, Gehlen J, Mostowska A, Heilmann-Heimbach S, Mangold E, Rada-Iglesias A, Knapp M, Schaaf CP, Ludwig KU. MiRNA-149 as a Candidate for Facial Clefting and Neural Crest Cell Migration. J Dent Res 2021; 101:323-330. [PMID: 34528480 DOI: 10.1177/00220345211038203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nonsyndromic cleft lip with or without palate (nsCL/P) ranks among the most common human birth defects and has a multifactorial etiology. Human neural crest cells (hNCC) make a substantial contribution to the formation of facial bone and cartilage and are a key cell type in terms of nsCL/P etiology. Based on increasing evidence for the role of noncoding regulatory mechanisms in nsCL/P, we investigated the role of hNCC-expressed microRNAs (miRNA) in cleft development. First, we conducted a systematic analysis of miRNAs expressed in human-induced pluripotent stem cell-derived hNCC using Affymetrix microarrays on cell lines established from 4 unaffected donors. These analyses identified 152 candidate miRNAs. Based on the hypothesis that candidate miRNA loci harbor genetic variation associated with nsCL/P risk, the genomic locations of these candidates were cross-referenced with data from a previous genome-wide association study of nsCL/P. Associated variants were reanalyzed in independent nsCL/P study populations. Jointly, the results suggest that miR-149 is implicated in nsCL/P etiology. Second, functional follow-up included in vitro overexpression and inhibition of miR-149 in hNCC and subsequent analyses at the molecular and phenotypic level. Using 3'RNA-Seq, we identified 604 differentially expressed (DE) genes in hNCC overexpressing miR-149 compared with untreated cells. These included TLR4 and JUNB, which are established targets of miR-149, and NOG, BMP4, and PAX6, which are reported nsCL/P candidate genes. Pathway analyses revealed that DE genes were enriched in pathways including regulation of cartilage development and NCC differentiation. At the cellular level, distinct hNCC migration patterns were observed in response to miR-149 overexpression. Our data suggest that miR-149 is involved in the etiology of nsCL/P via its role in hNCC migration.
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Affiliation(s)
- L G Stüssel
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - R Hollstein
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - M Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - L M Hochfeld
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - J Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - J Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - F Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - N Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - R Olmos Romero
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - L Weinhold
- Institute of Medical Biometry Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - T Hess
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.,Center of Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - J Gehlen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.,Center of Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - A Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - S Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - E Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - A Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Institute of Biomedicine and Biotechnology, University of Cantabria, Santander, Spain
| | - M Knapp
- Institute of Medical Biometry Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - C P Schaaf
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - K U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
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35
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Liu C, Lee MK, Naqvi S, Hoskens H, Liu D, White JD, Indencleef K, Matthews H, Eller RJ, Li J, Mohammed J, Swigut T, Richmond S, Manyama M, Hallgrímsson B, Spritz RA, Feingold E, Marazita ML, Wysocka J, Walsh S, Shriver MD, Claes P, Weinberg SM, Shaffer JR. Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations. PLoS Genet 2021; 17:e1009695. [PMID: 34411106 PMCID: PMC8375984 DOI: 10.1371/journal.pgen.1009695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 07/02/2021] [Indexed: 12/16/2022] Open
Abstract
Facial morphology is highly variable, both within and among human populations, and a sizable portion of this variation is attributable to genetics. Previous genome scans have revealed more than 100 genetic loci associated with different aspects of normal-range facial variation. Most of these loci have been detected in Europeans, with few studies focusing on other ancestral groups. Consequently, the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown. We therefore investigated the genetic basis of facial morphology in an East African cohort. We applied an open-ended data-driven phenotyping approach to a sample of 2,595 3D facial images collected on Tanzanian children. This approach segments the face into hierarchically arranged, multivariate features that capture the shape variation after adjusting for age, sex, height, weight, facial size and population stratification. Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10−8) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. Two of these associations were in highly conserved regions showing craniofacial-specific enhancer activity during embryological development (5q31.1 and 12q21.31). Six of the 20 loci surpassed a stricter threshold accounting for multiple phenotypes with study-wide significance (p < 6.25 × 10−10). Cross-population comparisons indicated 10 association signals were shared with Europeans (seven sharing the same associated SNP), and facilitated fine-mapping of causal variants at previously reported loci. Taken together, these results may point to both shared and population-specific components to the genetic architecture of facial variation. Genetic factors play an important role in shaping human facial features. Over the last decade, studies have identified numerous genes associated with various facial traits. The vast majority of these studies have focused on European or Asian populations, while African populations have been underrepresented. Increasing the diversity of these analyses can reveal novel associations and cross-population analyses can help deepen our understanding of known genetic associations. We therefore performed a genome scan of 3D facial features in African children from Tanzania and then compared our results to Europeans. We found 20 regions of the genome associated with facial shape in Tanzanian children, 10 of which were also present in Europeans, indicating evidence for a partly shared genetic basis for human facial shape across populations. In addition, about half of the genetic associations observed in Tanzanians were not present in Europeans, and some of the shared signals differed between populations in the specific genetic variants associated or specific facial traits affected. These results shed light on the shared and population-specific genetic contributors to normal-range facial variation.
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Affiliation(s)
- Chenxing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Myoung Keun Lee
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hanne Hoskens
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dongjing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Julie D. White
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Karlijne Indencleef
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Harold Matthews
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Jiarui Li
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Mange Manyama
- Anatomy in Radiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Benedikt Hallgrímsson
- Department of Anatomy and Cell Biology, Alberta Children´s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mary L. Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Peter Claes
- Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Processing Speech & Images, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Seth M. Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SMW); (JRS)
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SMW); (JRS)
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Smits JJ, de Bruijn SE, Lanting CP, Oostrik J, O'Gorman L, Mantere T, Cremers FPM, Roosing S, Yntema HG, de Vrieze E, Derks R, Hoischen A, Pegge SAH, Neveling K, Pennings RJE, Kremer H. Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. Hum Genet 2021; 141:465-484. [PMID: 34410491 PMCID: PMC9035008 DOI: 10.1007/s00439-021-02336-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype–phenotype correlation, a significant part of cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, we first determined the presence of the previously described EVA-associated haplotype (Caucasian EVA (CEVA)), characterized by 12 single nucleotide variants located upstream of SLC26A4. We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12). Short- and long-read whole genome sequencing and optical genome mapping could not prioritize any of the variants present within the CEVA haplotype as the likely pathogenic defect. Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases, who are now genetically explained. No deep-intronic or structural variants were identified in any of the M1 subjects. With this study, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases. For pinpointing the pathogenic effect of the CEVA haplotype, additional analyses are required addressing defect(s) at the RNA, protein, or epigenetic level.
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Affiliation(s)
- Jeroen J Smits
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelis P Lanting
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sjoert A H Pegge
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J E Pennings
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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37
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Ray D, Venkataraghavan S, Zhang W, Leslie EJ, Hetmanski JB, Weinberg SM, Murray JC, Marazita ML, Ruczinski I, Taub MA, Beaty TH. Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios. PLoS Genet 2021; 17:e1009584. [PMID: 34242216 PMCID: PMC8270211 DOI: 10.1371/journal.pgen.1009584] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Based on epidemiologic and embryologic patterns, nonsyndromic orofacial clefts- the most common craniofacial birth defects in humans- are commonly categorized into cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which are traditionally considered to be etiologically distinct. However, some evidence of shared genetic risk in IRF6, GRHL3 and ARHGAP29 regions exists; only FOXE1 has been recognized as significantly associated with both CL/P and CP in genome-wide association studies (GWAS). We used a new statistical approach, PLACO (pleiotropic analysis under composite null), on a combined multi-ethnic GWAS of 2,771 CL/P and 611 CP case-parent trios. At the genome-wide significance threshold of 5 × 10-8, PLACO identified 1 locus in 1q32.2 (IRF6) that appears to increase risk for one OFC subgroup but decrease risk for the other. At a suggestive significance threshold of 10-6, we found 5 more loci with compelling candidate genes having opposite effects on CL/P and CP: 1p36.13 (PAX7), 3q29 (DLG1), 4p13 (LIMCH1), 4q21.1 (SHROOM3) and 17q22 (NOG). Additionally, we replicated the recognized shared locus 9q22.33 (FOXE1), and identified 2 loci in 19p13.12 (RAB8A) and 20q12 (MAFB) that appear to influence risk of both CL/P and CP in the same direction. We found locus-specific effects may vary by racial/ethnic group at these regions of genetic overlap, and failed to find evidence of sex-specific differences. We confirmed shared etiology of the two OFC subtypes comprising CL/P, and additionally found suggestive evidence of differences in their pathogenesis at 2 loci of genetic overlap. Our novel findings include 6 new loci of genetic overlap between CL/P and CP; 3 new loci between pairwise OFC subtypes; and 4 loci not previously implicated in OFCs. Our in-silico validation showed PLACO is robust to subtype-specific effects, and can achieve massive power gains over existing approaches for identifying genetic overlap between disease subtypes. In summary, we found suggestive evidence for new genetic regions and confirmed some recognized OFC genes either exerting shared risk or with opposite effects on risk to OFC subtypes.
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Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
| | - Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wanying Zhang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Seth M. Weinberg
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
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38
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Welzenbach J, Hammond NL, Nikolić M, Thieme F, Ishorst N, Leslie EJ, Weinberg SM, Beaty TH, Marazita ML, Mangold E, Knapp M, Cotney J, Rada-Iglesias A, Dixon MJ, Ludwig KU. Integrative approaches generate insights into the architecture of non-syndromic cleft lip with or without cleft palate. HGG ADVANCES 2021; 2:100038. [PMID: 35047836 PMCID: PMC8756534 DOI: 10.1016/j.xhgg.2021.100038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common congenital facial malformation with a multifactorial etiology. Genome-wide association studies (GWASs) have identified multiple genetic risk loci. However, functional interpretation of these loci is hampered by the underrepresentation in public resources of systematic functional maps representative of human embryonic facial development. To generate novel insights into the etiology of nsCL/P, we leveraged published GWAS data on nsCL/P as well as available chromatin modification and expression data on mid-facial development. Our analyses identified five novel risk loci, prioritized candidate target genes within associated regions, and highlighted distinct pathways. Furthermore, the results suggest the presence of distinct regulatory effects of nsCL/P risk variants throughout mid-facial development and shed light on its regulatory architecture. Our integrated data provide a platform to advance hypothesis-driven molecular investigations of nsCL/P and other human facial defects.
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Affiliation(s)
- Julia Welzenbach
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nigel L. Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Miloš Nikolić
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics, and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
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39
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Ni P, Su Z. Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. NAR Genom Bioinform 2021; 3:lqab052. [PMID: 34159315 PMCID: PMC8210889 DOI: 10.1093/nargab/lqab052] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/01/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
cis-regulatory modules(CRMs) formed by clusters of transcription factor (TF) binding sites (TFBSs) are as important as coding sequences in specifying phenotypes of humans. It is essential to categorize all CRMs and constituent TFBSs in the genome. In contrast to most existing methods that predict CRMs in specific cell types using epigenetic marks, we predict a largely cell type agonistic but more comprehensive map of CRMs and constituent TFBSs in the gnome by integrating all available TF ChIP-seq datasets. Our method is able to partition 77.47% of genome regions covered by available 6092 datasets into a CRM candidate (CRMC) set (56.84%) and a non-CRMC set (43.16%). Intriguingly, the predicted CRMCs are under strong evolutionary constraints, while the non-CRMCs are largely selectively neutral, strongly suggesting that the CRMCs are likely cis-regulatory, while the non-CRMCs are not. Our predicted CRMs are under stronger evolutionary constraints than three state-of-the-art predictions (GeneHancer, EnhancerAtlas and ENCODE phase 3) and substantially outperform them for recalling VISTA enhancers and non-coding ClinVar variants. We estimated that the human genome might encode about 1.47M CRMs and 68M TFBSs, comprising about 55% and 22% of the genome, respectively; for both of which, we predicted 80%. Therefore, the cis-regulatory genome appears to be more prevalent than originally thought.
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Affiliation(s)
- Pengyu Ni
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
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40
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Curtis SW, Chang D, Sun MR, Epstein MP, Murray JC, Feingold E, Beaty TH, Weinberg SM, Marazita ML, Lipinski RJ, Carlson JC, Leslie EJ. FAT4 identified as a potential modifier of orofacial cleft laterality. Genet Epidemiol 2021; 45:721-735. [PMID: 34130359 DOI: 10.1002/gepi.22420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023]
Abstract
Orofacial clefts (OFCs) are common (1 in 700 births) congenital malformations that include a cleft lip (CL) and cleft lip and palate (CLP). These OFC subtypes are also heterogeneous themselves, with the CL occurring on the left, right, or both sides of the upper lip. Unilateral CL and CLP have a 2:1 bias towards left-sided clefts, suggesting a nonrandom process. Here, we performed a study of left- and right-sided clefts within the CL and CLP subtypes to better understand the genetic factors controlling cleft laterality. We conducted genome-wide modifier analyses by comparing cases that had right unilateral CL (RCL; N = 130), left unilateral CL (LCL; N = 216), right unilateral CLP (RCLP; N = 416), or left unilateral CLP (LCLP; N = 638), and identified a candidate region on 4q28, 400 kb downstream from FAT4, that approached genome-wide significance for LCL versus RCL (p = 8.4 × 10-8 ). Consistent with its potential involvement as a genetic modifier of CL, we found that Fat4 exhibits a specific domain of expression in the mesenchyme of the medial nasal processes that form the median upper lip. Overall, these results suggest that the epidemiological similarities in left- to right-sided clefts in CL and CLP are not reflected in the genetic association results.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Daniel Chang
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Miranda R Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert J Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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41
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Thieme F, Henschel L, Hammond NL, Ishorst N, Hausen J, Adamson AD, Biedermann A, Bowes J, Zieger HK, Maj C, Kruse T, Buness A, Hoischen A, Gilissen C, Kreusch T, Jäger A, Gölz L, Braumann B, Aldhorae K, Rojas-Martinez A, Krawitz PM, Mangold E, Dixon MJ, Ludwig KU. Extending the allelic spectrum at noncoding risk loci of orofacial clefting. Hum Mutat 2021; 42:1066-1078. [PMID: 34004033 DOI: 10.1002/humu.24219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 11/08/2022]
Abstract
Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.
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Affiliation(s)
- Frederic Thieme
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nigel L Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nina Ishorst
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jonas Hausen
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Antony D Adamson
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Angelika Biedermann
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Hanna K Zieger
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Carlo Maj
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Andreas Buness
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany.,Department of Orthodontics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Bert Braumann
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Khalid Aldhorae
- Department of Orthodontics, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey, Mexico
| | - Peter M Krawitz
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Kerstin U Ludwig
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
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42
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Naqvi S, Sleyp Y, Hoskens H, Indencleef K, Spence JP, Bruffaerts R, Radwan A, Eller RJ, Richmond S, Shriver MD, Shaffer JR, Weinberg SM, Walsh S, Thompson J, Pritchard JK, Sunaert S, Peeters H, Wysocka J, Claes P. Shared heritability of human face and brain shape. Nat Genet 2021; 53:830-839. [PMID: 33821002 PMCID: PMC8232039 DOI: 10.1038/s41588-021-00827-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023]
Abstract
Evidence from model organisms and clinical genetics suggests coordination between the developing brain and face, but the role of this link in common genetic variation remains unknown. We performed a multivariate genome-wide association study of cortical surface morphology in 19,644 individuals of European ancestry, identifying 472 genomic loci influencing brain shape, of which 76 are also linked to face shape. Shared loci include transcription factors involved in craniofacial development, as well as members of signaling pathways implicated in brain-face cross-talk. Brain shape heritability is equivalently enriched near regulatory regions active in either forebrain organoids or facial progenitors. However, we do not detect significant overlap between shared brain-face genome-wide association study signals and variants affecting behavioral-cognitive traits. These results suggest that early in embryogenesis, the face and brain mutually shape each other through both structural effects and paracrine signaling, but this interplay may not impact later brain development associated with cognitive function.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Departments of Genetics and Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Yoeri Sleyp
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Karlijne Indencleef
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jeffrey P Spence
- Departments of Genetics and Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rose Bruffaerts
- Department of Neurosciences, KU Leuven, Leuven, Belgium, Hasselt University, Hasselt, Belgium
- Neurology Department, University Hospitals Leuven, Leuven, Belgium, Hasselt University, Hasselt, Belgium
- Biomedical Research Institute Hasselt University Hasselt Belgium, Hasselt University, Hasselt, Belgium
| | - Ahmed Radwan
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Imaging and Pathology, Translational MRI, KU Leuven, Leuven, Belgium
| | - Ryan J Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, UK
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - James Thompson
- Department of Psychology, George Mason University, Fairfax, VA, USA
| | - Jonathan K Pritchard
- Departments of Genetics and Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefan Sunaert
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Imaging and Pathology, Translational MRI, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
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43
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Ewing AD, Cheetham SW, McGill JJ, Sharkey M, Walker R, West JA, West MJ, Summers KM. Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype. Am J Med Genet A 2021; 185:2070-2083. [PMID: 33960642 PMCID: PMC8251932 DOI: 10.1002/ajmg.a.62224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/17/2021] [Accepted: 04/02/2021] [Indexed: 01/20/2023]
Abstract
Basal cell nevus syndrome (also known as Gorlin Syndrome; MIM109400) is an autosomal dominant disorder characterized by recurrent pathological features such as basal cell carcinomas and odontogenic keratocysts as well as skeletal abnormalities. Most affected individuals have point mutations or small insertions or deletions within the PTCH1 gene on human chromosome 9, but there are some cases with more extensive deletion of the region, usually including the neighboring FANCC and/or ERCC6L2 genes. We report a 16‐year‐old patient with a deletion of approximately 400,000 bases which removes only PTCH1 and some non‐coding RNA genes but leaves FANCC and ERCC6L2 intact. In spite of the small amount of DNA for which he is haploid, his phenotype is more extreme than many individuals with longer deletions in the region. This includes early presentation with a large number of basal cell nevi and other skin lesions, multiple jaw keratocysts, and macrosomia. We found that the deletion was in the paternal chromosome, in common with other macrosomia cases. Using public databases, we have examined possible interactions between sequences within and outside the deletion and speculate that a regulatory relationship exists with flanking genes, which is unbalanced by the deletion, resulting in abnormal activation or repression of the target genes and hence the severity of the phenotype.
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Affiliation(s)
- Adam D Ewing
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Seth W Cheetham
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - James J McGill
- Department of Chemical Pathology, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Michael Sharkey
- Paddington Dermatology Specialist Clinic, Paddington, Queensland, Australia
| | - Rick Walker
- QLD Youth Cancer Service, Queensland Children's Hospital, South Brisbane, Queensland, Australia.,School of Clinical Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Jennifer A West
- Northside Clinical School, Prince Charles Hospital, The University of Queensland, Chermside, Queensland, Australia
| | - Malcolm J West
- Northside Clinical School, Prince Charles Hospital, The University of Queensland, Chermside, Queensland, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
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44
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Pettinato AM, Yoo D, VanOudenhove J, Chen YS, Cohn R, Ladha FA, Yang X, Thakar K, Romano R, Legere N, Meredith E, Robson P, Regnier M, Cotney JL, Murry CE, Hinson JT. Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. Cell Rep 2021; 35:109088. [PMID: 33951429 PMCID: PMC8161465 DOI: 10.1016/j.celrep.2021.109088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/11/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
Human cardiac regeneration is limited by low cardiomyocyte replicative rates and progressive polyploidization by unclear mechanisms. To study this process, we engineer a human cardiomyocyte model to track replication and polyploidization using fluorescently tagged cyclin B1 and cardiac troponin T. Using time-lapse imaging, in vitro cardiomyocyte replication patterns recapitulate the progressive mononuclear polyploidization and replicative arrest observed in vivo. Single-cell transcriptomics and chromatin state analyses reveal that polyploidization is preceded by sarcomere assembly, enhanced oxidative metabolism, a DNA damage response, and p53 activation. CRISPR knockout screening reveals p53 as a driver of cell-cycle arrest and polyploidization. Inhibiting sarcomere function, or scavenging ROS, inhibits cell-cycle arrest and polyploidization. Finally, we show that cardiomyocyte engraftment in infarcted rat hearts is enhanced 4-fold by the increased proliferation of troponin-knockout cardiomyocytes. Thus, the sarcomere inhibits cell division through a DNA damage response that can be targeted to improve cardiomyocyte replacement strategies.
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Affiliation(s)
- Anthony M Pettinato
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Dasom Yoo
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA
| | | | - Yu-Sheng Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Rachel Cohn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Feria A Ladha
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Xiulan Yang
- Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ketan Thakar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Robert Romano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nicolas Legere
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Emily Meredith
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Charles E Murry
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA; Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - J Travis Hinson
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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45
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Hoskens H, Liu D, Naqvi S, Lee MK, Eller RJ, Indencleef K, White JD, Li J, Larmuseau MHD, Hens G, Wysocka J, Walsh S, Richmond S, Shriver MD, Shaffer JR, Peeters H, Weinberg SM, Claes P. 3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies. PLoS Genet 2021; 17:e1009528. [PMID: 33983923 PMCID: PMC8118281 DOI: 10.1371/journal.pgen.1009528] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.
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Affiliation(s)
- Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Dongjing Liu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Myoung Keun Lee
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Karlijne Indencleef
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Julie D. White
- Department of Anthropology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Jiarui Li
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Maarten H. D. Larmuseau
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
- Histories vzw, Mechelen, Belgium
| | - Greet Hens
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Mark D. Shriver
- Department of Anthropology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
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46
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Mukhopadhyay N, Feingold E, Moreno-Uribe L, Wehby G, Valencia-Ramirez LC, Muñeton CPR, Padilla C, Deleyiannis F, Christensen K, Poletta FA, Orioli IM, Hecht JT, Buxó CJ, Butali A, Adeyemo WL, Vieira AR, Shaffer JR, Murray JC, Weinberg SM, Leslie EJ, Marazita ML. Genome-Wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions. Front Cell Dev Biol 2021; 9:621482. [PMID: 33898419 PMCID: PMC8062975 DOI: 10.3389/fcell.2021.621482] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/15/2021] [Indexed: 01/20/2023] Open
Abstract
Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (~ 1/2,500), Asians have the highest prevalence (~1/500), Europeans and Latin Americans lie somewhere in the middle (~1/800 and 1/900, respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (~12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (<5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p = 6.27e-07), 10q22.2 (rs150952246, p = 3.14e-07), and 10q24.32 (rs118107597, p = 8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were (a) purely due to sample sizes, (b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.
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Affiliation(s)
- Nandita Mukhopadhyay
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Lina Moreno-Uribe
- Department of Orthodontics, The Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - George Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, United States
| | | | | | - Carmencita Padilla
- Department of Pediatrics, College of Medicine, Institute of Human Genetics, National Institutes of Health, University of the Philippines, Manila, Philippines
| | | | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Fernando A. Poletta
- CEMIC: Center for Medical Education and Clinical Research, Buenos Aires, Argentina
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Genética Médica Populacional INAGEMP, Porto Alegre, Brazil
| | - Jacqueline T. Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Carmen J. Buxó
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Alexandre R. Vieira
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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47
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Curtis SW, Chang D, Lee MK, Shaffer JR, Indencleef K, Epstein MP, Cutler DJ, Murray JC, Feingold E, Beaty TH, Claes P, Weinberg SM, Marazita ML, Carlson JC, Leslie EJ. The PAX1 locus at 20p11 is a potential genetic modifier for bilateral cleft lip. HGG ADVANCES 2021; 2:100025. [PMID: 33817668 PMCID: PMC8018676 DOI: 10.1016/j.xhgg.2021.100025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Nonsyndromic orofacial clefts (OFCs) are a common birth defect and are phenotypically heterogenous in the structure affected by the cleft - cleft lip (CL) and cleft lip and palate (CLP) - as well as other features, such as the severity of the cleft. Here, we focus on bilateral and unilateral clefts as one dimension of OFC severity, because the genetic architecture of these subtypes is not well understood. We tested for subtype-specific genetic associations in 44 bilateral CL (BCL) cases, 434 unilateral CL (UCL) cases, 530 bilateral CLP cases (BCLP), 1123 unilateral CLP (UCLP) cases, and unrelated controls (N = 1626), using a mixed-model approach. While no novel loci were found, the genetic architecture of UCL was distinct compared to BCL, with 44.03% of suggestive loci having different effects between the two subtypes. To further understand the subtype-specific genetic risk factors, we performed a genome-wide scan for modifiers and found a significant modifier locus on 20p11 (p=7.53×10-9), 300kb downstream of PAX1, that associated with higher odds of BCL vs. UCL, and replicated in an independent cohort (p=0.0018) with no effect in BCLP (p>0.05). We further found that this locus was associated with normal human nasal shape. Taken together, these results suggest bilateral and unilateral clefts may have different genetic architectures. Moreover, our results suggest BCL, the rarest form of OFC, may be genetically distinct from the other OFC subtypes. This expands our understanding of modifiers for OFC subtypes and further elucidates the genetic mechanisms behind the phenotypic heterogeneity in OFCs.
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Affiliation(s)
- Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Daniel Chang
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Karlijne Indencleef
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | | | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Peter Claes
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Jenna C. Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
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48
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Feng Z, Duren Z, Xiong Z, Wang S, Liu F, Wong WH, Wang Y. hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context. Commun Biol 2021; 4:442. [PMID: 33824393 PMCID: PMC8024315 DOI: 10.1038/s42003-021-01970-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into the developing craniofacial region, and subsequently differentiate into multiple cell types. The entire specification, delamination, migration, and differentiation process is highly regulated and abnormalities during this craniofacial development cause birth defects. To better understand the molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data and reconstruct the genome-wide human Regulatory network of CNCC (hReg-CNCC). Consensus optimization predicts high-quality regulations and reveals the architecture of upstream, core, and downstream transcription factors that are associated with functions of neural plate border, specification, and migration. hReg-CNCC allows us to annotate genetic variants of human facial GWAS and disease traits with associated cis-regulatory modules, transcription factors, and target genes. For example, we reveal the distal and combinatorial regulation of multiple SNPs to core TF ALX1 and associations to facial distances and cranial rare disease. In addition, hReg-CNCC connects the DNA sequence differences in evolution, such as ultra-conserved elements and human accelerated regions, with gene expression and phenotype. hReg-CNCC provides a valuable resource to interpret genetic variants as early as gastrulation during embryonic development. The network resources are available at https://github.com/AMSSwanglab/hReg-CNCC .
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Affiliation(s)
- Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China.,School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA.,Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA, USA
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Sijia Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China.
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA, USA.
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China. .,School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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49
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Bonfante B, Faux P, Navarro N, Mendoza-Revilla J, Dubied M, Montillot C, Wentworth E, Poloni L, Varón-González C, Jones P, Xiong Z, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Liu F, Weinberg SM, Shaffer JR, Stergiakouli E, Howe LJ, Hysi PG, Spector TD, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Thauvin-Robinet C, Faivre L, Costedoat C, Balding D, Cox T, Kayser M, Duplomb L, Yalcin B, Cotney J, Adhikari K, Ruiz-Linares A. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. SCIENCE ADVANCES 2021; 7:eabc6160. [PMID: 33547071 PMCID: PMC7864580 DOI: 10.1126/sciadv.abc6160] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/17/2020] [Indexed: 05/25/2023]
Abstract
To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.
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Affiliation(s)
- Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Morgane Dubied
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
| | - Charlotte Montillot
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Emma Wentworth
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Lauriane Poloni
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, UA, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Philip Jones
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Sagnik Palmal
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100864, China
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica 1000000, Chile
| | - Christel Thauvin-Robinet
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Timothy Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Laurence Duplomb
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Binnaz Yalcin
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Andrés Ruiz-Linares
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
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50
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Richmond S, Zhurov AI, Ali ABM, Pirttiniemi P, Heikkinen T, Harila V, Silinevica S, Jakobsone G, Urtane I. Exploring the midline soft tissue surface changes from 12 to 15 years of age in three distinct country population cohorts. Eur J Orthod 2021; 42:517-524. [PMID: 31748803 DOI: 10.1093/ejo/cjz080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Several studies have highlighted differences in the facial features in a White European population. Genetics appear to have a major influence on normal facial variation, and environmental factors are likely to have minor influences on face shape directly or through epigenetic mechanisms. AIM The aim of this longitudinal cohort study is to determine the rate of change in midline facial landmarks in three distinct homogenous population groups (Finnish, Latvian, and Welsh) from 12.8 to 15.3 years of age. This age range covers the pubertal growth period for the majority of boys and girls. METHODS A cohort of children aged 12 were monitored for facial growth in three countries [Finland (n = 60), Latvia (n = 107), and Wales (n = 96)]. Three-dimensional facial surface images were acquired (using either laser or photogrammetric methods) at regular intervals (6-12 months) for 4 years. Ethical approval was granted in each country. Nine midline landmarks were identified and the relative spatial positions of these surface landmarks were measured relative to the mid-endocanthion (men) over a 4-year period. RESULTS This study reports the children who attended 95 per cent of all scanning sessions (Finland 48 out of 60; Latvia 104 out of 107; Wales 50 out of 96). Considerable facial variation is seen for all countries and sexes. There are clear patterns of growth that show different magnitudes at different age groups for the different country groups, sexes, and facial parameters. The greatest single yearly growth rate (5.4 mm) was seen for Welsh males for men-pogonion distance at 13.6 years of age. Males exhibit greater rates of growth compared to females. These variations in magnitude and timings are likely to be influenced by genetic ancestry as a result of population migration. CONCLUSION The midline points are a simple and valid method to assess the relative spatial positions of facial surface landmarks. This study confirms previous reports on the subtle differences in facial shapes and sizes of male and female children in different populations and also highlights the magnitudes and timings of growth for various midline landmark distances to the men point.
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Affiliation(s)
- Stephen Richmond
- Orthodontic Department, Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Heath Park, Cardiff, UK
| | - Alexei I Zhurov
- Orthodontic Department, Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Heath Park, Cardiff, UK
| | - Azrul Bin Mohd Ali
- Orthodontic Department, Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Heath Park, Cardiff, UK
| | - Pertti Pirttiniemi
- Oral Development and Orthodontics, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Tuomo Heikkinen
- Oral Development and Orthodontics, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Virpi Harila
- Oral Development and Orthodontics, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Signe Silinevica
- Orthodontic Department, RSU Institute of Stomatology, Rīga, Latvia
| | | | - Ilga Urtane
- Orthodontic Department, RSU Institute of Stomatology, Rīga, Latvia
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