Evidence for Craniofacial Enhancer Variation Underlying Nonsyndromic Cleft Lip and Palate

Authors

Vershanna E Morris
S Shahrukh Hashmi
Lisha Zhu
Lorena Maili
Christian Urbina
Steven Blackwell
Matthew R Greives
Edward P Buchanan
John B Mulliken
Susan H Blanton
W Jim Zheng
Jacqueline T Hecht
Ariadne Letra

Publication Date

10-1-2020

Journal

Human Genetics

Abstract

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect for which only ~ 20% of the underlying genetic variation has been identified. Variants in noncoding regions have been increasingly suggested to contribute to the missing heritability. In this study, we investigated whether variation in craniofacial enhancers contributes to NSCLP. Candidate enhancers were identified using VISTA Enhancer Browser and previous publications. Prioritization was based on patterning defects in knockout mice, deletion/duplication of craniofacial genes in animal models and results of whole exome/whole genome sequencing studies. This resulted in 20 craniofacial enhancers to be investigated. Custom amplicon-based sequencing probes were designed and used for sequencing 380 NSCLP probands (from multiplex and simplex families of non-Hispanic white (NHW) and Hispanic ethnicities) using Illumina MiSeq. The frequencies of identified variants were compared to ethnically matched European (CEU) and Los Angeles Mexican (MXL) control genomes and used for association analyses. Variants in mm427/MSX1 and hs1582/SPRY1 showed genome-wide significant association with NSCLP (p ≤ 6.4 × 10-11). In silico analysis showed that these enhancer variants may disrupt important transcription factor binding sites. Haplotypes involving these enhancers and also mm435/ABCA4 were significantly associated with NSCLP, especially in NHW (p ≤ 6.3 × 10-7). Importantly, groupwise burden analysis showed several enhancer combinations significantly over-represented in NSCLP individuals, revealing novel NSCLP pathways and supporting a polygenic inheritance model. Our findings support the role of craniofacial enhancer sequence variation in the etiology of NSCLP.

Keywords

ATP-Binding Cassette Transporters, Animals, Asymptomatic Diseases, Cleft Lip, Cleft Palate, Embryo, Mammalian, Enhancer Elements, Genetic, Female, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Variation, High-Throughput Nucleotide Sequencing, Hispanic or Latino, Humans, MSX1 Transcription Factor, Male, Membrane Proteins, Mice, Multifactorial Inheritance, Pedigree, Phosphoproteins, United States, White People, enhancer, variation, nonsyndromic cleft lip/palate, network, gene

DOI

10.1007/s00439-020-02169-9

PMID

32318854

PMCID

PMC7487053

PubMedCentral® Posted Date

10-1-2021

PubMedCentral® Full Text Version

Post-print

Recommended Citation

Morris, Vershanna E; Hashmi, S Shahrukh; Zhu, Lisha; Maili, Lorena; Urbina, Christian; Blackwell, Steven; Greives, Matthew R; Buchanan, Edward P; Mulliken, John B; Blanton, Susan H; Zheng, W Jim; Hecht, Jacqueline T; and Letra, Ariadne, "Evidence for Craniofacial Enhancer Variation Underlying Nonsyndromic Cleft Lip and Palate" (2020). Faculty, Staff and Student Publications. 82.
https://digitalcommons.library.tmc.edu/uthdb_docs/82

Published Open-Access

yes