Identification of Isthmin 1 as a Novel Clefting and Craniofacial Patterning Gene in Humans. Issue 1 (1st January 2018)

• Record Type: Journal Article
• Authors: Lansdon, Lisa A; Darbro, Benjamin W; Petrin, Aline L; Hulstrand, Alissa M; Standley, Jennifer M; Brouillette, Rachel B; Long, Abby; Mansilla, M Adela; Cornell, Robert A; Murray, Jeffrey C; Houston, Douglas W; Manak, J Robert
• Is Part Of: Genetics. Volume 208:Issue 1(2018)
• Page Start: 283
• Page End: 296
• Publication Date: 2018-01-01
• Subjects: branchial arches -- cleft lip and palate -- copy number variation -- craniofacial development -- Xenopus laevis; Genetics -- Periodicals; 576.5
• DOI: 10.1534/genetics.117.300535
• Languages: English
• ISSNs: 0016-6731

Abstract

Abstract: Orofacial clefts are one of the most common birth defects, affecting 1–2 per 1000 births, and have a complex etiology. High-resolution array-based comparative genomic hybridization has increased the ability to detect copy number variants (CNVs) that can be causative for complex diseases such as cleft lip and/or palate. Utilizing this technique on 97 nonsyndromic cleft lip and palate cases and 43 cases with cleft palate only, we identified a heterozygous deletion of Isthmin 1 in one affected case, as well as a deletion in a second case that removes putative 3′ regulatory information. Isthmin 1 is a strong candidate for clefting, as it is expressed in orofacial structures derived from the first branchial arch and is also in the same "synexpression group" as fibroblast growth factor 8 and sprouty RTK signaling antagonist 1a and 2, all of which have been associated with clefting. CNVs affecting Isthmin 1 are exceedingly rare in control populations, and Isthmin 1 scores as a likely haploinsufficiency locus. Confirming its role in craniofacial development, knockdown or clustered randomly interspaced short palindromic repeats/Cas9-generated mutation of isthmin 1 in Xenopus laevis resulted in mild to severe craniofacial dysmorphologies, with several individuals presenting with median clefts. Moreover, knockdown of isthmin 1 produced decreased expression of LIM homeobox 8, itself a gene associated with clefting, in regions of the face that pattern the maxilla. Our study demonstrates a successful pipeline from CNV identification of a candidate gene to functional validation in a vertebrate model system, and reveals Isthmin 1 as both a new human clefting locus as well as a key craniofacial patterning gene.