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Robinson K, Curtis SW, Leslie EJ. The heterogeneous genetic architectures of orofacial clefts. Trends Genet 2024; 40:410-421. [PMID: 38480105 DOI: 10.1016/j.tig.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 05/09/2024]
Abstract
Orofacial clefts (OFCs) are common, affecting 1:1000 live births. OFCs occur across a phenotypic spectrum - including cleft lip (CL), cleft lip and palate (CLP), or cleft palate (CP) - and can be further subdivided based on laterality, severity, or specific structures affected. Herein we review what is known about the genetic architecture underlying each of these subtypes, considering both shared and subtype-specific risks. While there are more known genetic similarities between CL and CLP than CP, recent research supports both shared and subtype-specific genetic risk factors within and between phenotypic classifications of OFCs. Larger sample sizes and deeper phenotyping data will be of increasing importance for the discovery of novel genetic risk factors for OFCs and various subtypes going forward.
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Affiliation(s)
- Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sarah W Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Shrestha P, Graff M, Gu Y, Wang Y, Avery CL, Ginnis J, Simancas-Pallares MA, Ferreira Zandoná AG, Ahn HS, Nguyen KN, Lin DY, Preisser JS, Slade GD, Marazita ML, North KE, Divaris K. Multi-ancestry Genome-Wide Association Study of Early Childhood Caries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.12.24303742. [PMID: 38562815 PMCID: PMC10984042 DOI: 10.1101/2024.03.12.24303742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Early childhood caries (ECC) is the most common non-communicable childhood disease. It is an important health problem with known environmental and social/behavioral influences that lacks evidence for specific associated genetic risk loci. To address this knowledge gap, we conducted a genome-wide association study of ECC in a multi-ancestry population of U.S. preschool-age children (n=6,103) participating in a community-based epidemiologic study of early childhood oral health. Calibrated examiners used ICDAS criteria to measure ECC with the primary trait using the dmfs index with decay classified as macroscopic enamel loss (ICDAS ≥3). We estimated heritability, concordance rates, and conducted genome-wide association analyses to estimate overall genetic effects; the effects stratified by sex, household water fluoride, and dietary sugar; and leveraged the combined gene/gene-environment effects using the 2-degree-of-freedom (2df) joint test. The common genetic variants explained 24% of the phenotypic variance (heritability) of the primary ECC trait and the concordance rate was higher with a higher degree of relatedness. We identified 21 novel non-overlapping genome-wide significant loci for ECC. Two loci, namely RP11-856F16 . 2 (rs74606067) and SLC41A3 (rs71327750) showed evidence of association with dental caries in external cohorts, namely the GLIDE consortium adult cohort (n=∼487,000) and the GLIDE pediatric cohort (n=19,000), respectively. The gene-based tests identified TAAR6 as a genome-wide significant gene. Implicated genes have relevant biological functions including roles in tooth development and taste. These novel associations expand the genomics knowledge base for this common childhood disease and underscore the importance of accounting for sex and pertinent environmental exposures in genetic investigations of oral health.
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Xu C, Xiang Y, Xu X, Zhou L, Li H, Dong X, Tang S. Clinical application of chromosomal microarray analysis for fetuses with craniofacial malformations. Mol Cytogenet 2020; 13:38. [PMID: 32863884 PMCID: PMC7448974 DOI: 10.1186/s13039-020-00502-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
Background The potential correlations between chromosomal abnormalities and craniofacial malformations (CFMs) remain a challenge in prenatal diagnosis. This study aimed to evaluate 118 fetuses with CFMs by applying chromosomal microarray analysis (CMA) and G-banded chromosome analysis. Results Of the 118 cases in this study, 39.8% were isolated CFMs (47/118) whereas 60.2% were non-isolated CFMs (71/118). The detection rate of chromosomal abnormalities in non-isolated CFM fetuses was significantly higher than that in isolated CFM fetuses (26/71 vs. 7/47, p = 0.01). Compared to the 16 fetuses (16/104; 15.4%) with pathogenic chromosomal abnormalities detected by karyotype analysis, CMA identified a total of 33 fetuses (33/118; 28.0%) with clinically significant findings. These 33 fetuses included cases with aneuploidy abnormalities (14/118; 11.9%), microdeletion/microduplication syndromes (9/118; 7.6%), and other pathogenic copy number variations (CNVs) only (10/118; 8.5%).We further explored the CNV/phenotype correlation and found a series of clear or suspected dosage-sensitive CFM genes including TBX1, MAPK1, PCYT1A, DLG1, LHX1, SHH, SF3B4, FOXC1, ZIC2, CREBBP, SNRPB, and CSNK2A1. Conclusion These findings enrich our understanding of the potential causative CNVs and genes in CFMs. Identification of the genetic basis of CFMs contributes to our understanding of their pathogenesis and allows detailed genetic counselling.
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Affiliation(s)
- Chenyang Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China
| | - Yanbao Xiang
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China
| | - Xueqin Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China
| | - Lili Zhou
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China
| | - Huanzheng Li
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China
| | - Xueqin Dong
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China
| | - Shaohua Tang
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, China.,Key Laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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Yu J, Wu C, Wu Q, Huang J, Fu W, Xie X, Li W, Tang W, Xu C, Jin G. PCYT1A suppresses proliferation and migration via inhibiting mTORC1 pathway in lung adenocarcinoma. Biochem Biophys Res Commun 2020; 529:353-361. [PMID: 32703435 DOI: 10.1016/j.bbrc.2020.05.164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 12/26/2022]
Abstract
Lung cancer is one of most common malignant cancer worldwide. It is emerging that PCYT1A, a rate-limiting enzyme required for the biosynthesis of phosphatidylcholine, is associated with cancer progression. However, the biological functions and underlying molecular mechanisms of PCYT1A in lung adenocarcinoma is still unknown. Here we found that PCYT1A suppressed lung adenocarcinoma cancer cell proliferation and migration. Mechanically, PCYT1A served as a novel negative regulator of mTORC1 signaling. PCYT1A knockdown enhanced the malignant proliferation and migration of lung adenocarcinoma cells by activating mTORC1. The promoting effects of PCYT1A silencing on cell proliferation and migration could be abolished when mTORC1 signaling was inhibited by rapamycin or RAPTOR depletion. Importantly, PCYT1A high expression predicted longer survival of lung cancer patients. The expression of PCYT1A was also negatively correlated with mTORC1 activation in the clinical lung cancer samples. We therefore reveal that PCYT1A suppresses proliferation and migration by inhibiting the mTORC1 signaling pathway in lung adenocarcinoma. PCYT1A shows as a potential promising biomarker in lung adenocarcinoma.
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Affiliation(s)
- Jing Yu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China; Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), And Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Changtao Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), And Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China; Department of Colorectal and Anal Surgery, The First Affiliated Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Qi Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), And Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Jiafeng Huang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), And Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Wenjuan Fu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), And Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Xuemei Xie
- Department of Pathology, The Affiliated Hospital of North Sichuan Medical College, Nanchong, 637100, China
| | - Wen Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine University of Electronic Science and Technology of China, Chengdu, 610047, China
| | - Weizhong Tang
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Chuan Xu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China; Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine University of Electronic Science and Technology of China, Chengdu, 610047, China.
| | - Guoxiang Jin
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), And Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China.
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Boyce JO, Raj S, Sanchez K, Marazita ML, Morgan AT, Kilpatrick N. Speech Phenotyping in Unaffected Family Members of Individuals With Nonsyndromic Cleft Lip With or Without Palate. Cleft Palate Craniofac J 2019; 56:867-876. [PMID: 30696259 DOI: 10.1177/1055665618823936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Subclinical phenotypes of nonsyndromic cleft lip with or without cleft palate (CL ± P) may be identified from clinically "unaffected" relatives and could be associated with specific cleft-related gene mutations. It has been hypothesized that velopharyngeal insufficiency (VPI) may be a subclinical phenotype of interest in this population, but this has not been explored quantitatively with appropriate control cohorts. The aim of this case-control study was to compare VPI in at-risk clinically unaffected relatives of individuals with nonsyndromic CL ± P with a low-risk matched normative Australian cohort. PARTICIPANTS Clinically unaffected (ie, with no overt cleft) first-degree relatives of a proband with nonsyndromic CL ± P (n = 189) and noncleft controls (n = 207). MAIN OUTCOME MEASURE(S) Perceptual measures of VPI encompassing resonance, nasal emission, and articulation were evaluated using the Great Ormond Street Speech Assessment. Quantitative measures of VPI were obtained from the Nasometer II using standardized adult and pediatric speech stimuli. RESULTS Both perceptual and instrumental measures showed no significant difference (P > .01) between the VPI in unaffected relatives and the noncleft comparison group. Mean nasalance scores for both groups were calculated and reported according to speech stimuli, age, and sex. CONCLUSIONS Results suggest that VPI, measured through speech, is not a significant subclinical phenotype of nonsyndromic CL ± P. Therefore, further familial genetic investigations exploring VPI may not yield meaningful results. Exploration across multiple subclinical phenotypes in larger cohorts may enable researchers to better understand the multifaceted nature of this complex and heterogeneous anomaly.
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Affiliation(s)
- Jessica O Boyce
- 1 Department of Audiology and Speech Pathology, The University of Melbourne, Carlton, VIC, Australia.,2 Speech and Language Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Supriya Raj
- 3 Musculoskeletal Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Katherine Sanchez
- 1 Department of Audiology and Speech Pathology, The University of Melbourne, Carlton, VIC, Australia.,2 Speech and Language Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Mary L Marazita
- 4 Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,5 Department of Human Genetics, Graduate School of Public Health, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Angela T Morgan
- 1 Department of Audiology and Speech Pathology, The University of Melbourne, Carlton, VIC, Australia.,2 Speech and Language Group, Murdoch Children's Research Institute, Parkville, VIC, Australia.,6 Speech Pathology Department, Royal Children's Hospital, Parkville, VIC, Australia
| | - Nicky Kilpatrick
- 7 Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, VIC, Australia.,8 Facial Sciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
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