1
|
Robinson K, Parrish R, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Gowans LJ, Hecht JT, Moreno L, Murray JC, Shaw GM, Weinberg SM, Brand H, Marazita ML, Cutler DJ, Epstein MP, Yang J, Leslie EJ. Genome-wide study of gene-by-sex interactions identifies risks for cleft palate. medRxiv 2024:2024.05.01.24306701. [PMID: 38746184 PMCID: PMC11092717 DOI: 10.1101/2024.05.01.24306701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Structural birth defects affect 3-4% of all live births and, depending on the type, tend to manifest in a sex-biased manner. Orofacial clefts (OFCs) are the most common craniofacial structural birth defects and are often divided into cleft lip with or without cleft palate (CL/P) and cleft palate only (CP). Previous studies have found sex-specific risks for CL/P, but these risks have yet to be evaluated in CP. CL/P is more common in males and CP is more frequently observed in females, so we hypothesized there would also be sex-specific differences for CP. Using a trio-based cohort, we performed sex-stratified genome-wide association studies (GWAS) based on proband sex followed by a genome-wide gene-by-sex (GxS) interaction testing. There were 13 loci significant for GxS interactions, with the top finding in LTBP1 (RR=3.37 [2.04 - 5.56], p=1.93x10 -6 ). LTBP1 plays a role in regulating TGF-B bioavailability, and knockdown in both mice and zebrafish lead to craniofacial anomalies. Further, there is evidence for differential expression of LTBP1 between males and females in both mice and humans. Therefore, we tested the association between the imputed genetically regulated gene expression of genes with significant GxS interactions and the CP phenotype. We found significant association for LTBP1 in cell cultured fibroblasts in female probands (p=0.0013) but not in males. Taken altogether, we show there are sex-specific risks for CP that are otherwise undetectable in a combined sex cohort, and LTBP1 is a candidate risk gene, particularly in females.
Collapse
|
2
|
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 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | |
Collapse
|