Gene Interactions Provide Evidence for Signaling Pathways Involved in Cleft Lip/Palate in Humans

Abstract

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect that has a complex etiology. Genome-wide association studies have recently identified new loci associated with NSCL/P, but these loci have not been analyzed in a Mexican Mestizo population. A complex etiology implies the presence of genetic interactions, but there is little available information regarding this in NSCL/P, and no signaling pathway has been clearly implicated in humans. Here, we analyzed the associations of 24 single nucleotide polymorphisms (SNPs) with NSCL/P in a Mexican Mestizo population (133 cases, 263 controls). The multifactorial dimensionality reduction method was used to examine gene-gene and gene-folic acid consumption interactions for the 24 SNPs analyzed in this study and for 2 additional SNPs that had previously been genotyped in the same study population. Six SNPs located in paired box 7, ventral anterior homeobox 1, sprouty RTK signaling antagonist 2, bone morphogenetic protein 4, and tropomyosin 1 genes were associated with higher risks of NSCL/P (P = 0.0001 to 0.04); 2 SNPs, 1 each in netrin 1 and V-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B, were associated with a lower risk of NSCL/P (P = 0.013 to 0.03); and 2 SNPs, 1 each in ATP binding cassette subfamily A member 4 (ABCA4) and noggin, showed associations with NSCL/P that approached the threshold of significance (P = 0.056 to 0.07). In addition, 6 gene-gene interactions (P = 0.0001 to 0.001) and an ABCA4-folic acid consumption interaction (P < 0.0001) were identified. On the basis of these results, combined with those of previous association studies in the literature and biological characterizations of murine models, we propose an interaction network in which interferon regulatory factor 6 plays a central role in the etiology of NSCL/P.

Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models

“…Analysis of Irf6 expression and function in mouse and chick developmental models suggests that Irf6 might play a role in tissue fusion events during palatogenesis (Knight et al, 2006; Velazquez-Aragon et al, 2016). The Wnt target p63 (also known as TP63), a key regulator of proliferation and differentiation (Truong et al, 2006), inhibits the Wnt signaling output by repressing Wnt/β-catenin responsive elements in target genes (Katoh et al, 2016).…”

PBX‐WNT‐P63‐IRF6pathway in nonsyndromic cleft lip and palate

“…More recently, whole‐exome sequencing (WES) studies have confirmed the role of variants in known NSCLP genes ( IRF6 , CDH1 , CRISPLD2 , FGFR2 , and PAX7) and identified novel candidate genes ( CTNND1 , PLEKHA7 , PLEKHA5 , and ESRP2 ) (Bureau et al, ; Cox et al, ; Pengelly et al, ). Furthermore, there is increasing evidence supporting an additive role for gene–gene interactions in NSCLP, with modifier phenotypic effects (Carlson et al, ; Chiquet et al, ; Li et al, ; D. Liu et al, ; Velazquez‐Aragon et al, ; Zhou et al, ).…”

Genetic variants of MGMT, RHPN2, and FAM49A contributed to susceptibility of nonsyndromic orofacial clefts in a Chinese population

“…Furthermore, gene‐gene (G × G) and gene‐environment (G × E) interactions are being increasingly used to elucidate the etiology of NSOC . For example, using a multifactorial dimensionality reduction method, Velázquez et a found evidence of a G × G interaction for BMP4‐VAX1 and a G × E ABCA4‐folic acid consumption interaction . Multifactor dimensionality reduction (MDR) is a nonparametric and model‐free approach, which was applied to assess G × G interactions for the above six SNPs.…”

“…11 For example, using a multifactorial dimensionality reduction method, Velázquez et a found evidence of a G × G interaction for BMP4-VAX1 and a G × E ABCA4-folic acid consumption interaction. 12 Multifactor dimensionality reduction (MDR) is a nonparametric and model-free approach, 13 which was applied to assess G × G interactions for the above six SNPs. The bridge PCR products were sequenced on the Illumina X-10 (Illumina Technologies Corporation, California,USA) sequencing platform, and the operation flow was carried out according to the standard SOP.…”