Examining cleft lip and palate as a lifelong disease: genetic investigation of causes and outcomes

Beth Noelle Davidson

doi:10.17077/etd.6iqrbv7q

Nonsyndromic cleft lip and/or palate (NS CL/P) is a common birth defect with estimated birth prevalence of 1/1000 worldwide. NS CL/P etiology may be explained by the action of as few as two or as many as 14 different genes (Schliekelman et al. 2002) as well as several environmental factors (e.g. smoking and folic acid) (Shi et al. 2008; Wehby et al. 2010). Convincing genetic and/or biologic evidence exists for the contribution of many genes: IRF6, 8q24, FGFR2, FOXE1, BMP4, TGFβ3, MSX1, MAFB , PAX7, ABCA4, and VAX1, to NS CL/P (Dixon et al. 2011). Clefts place substantial burdens on families and society with the estimated costs of cleft care and surgical repair around $100,000 in the United States (Jugessur et al. 2009). The health burden of NS CL/P does not end after the last surgery - impaired social development, surgical morbidity, and cancer are all reported in older children and adults with NS CL/P. Genes involved in clefting during development may be involved in other processes throughout life. We hypothesize that non-coding variation of the FGFR2 gene is associated with NS CL/P and these variants correlate with levels of gene expression. We investigate links between clefting, wound healing, and genes implicated in cancer in NS CL/P families. Analysis of family genotype data with the Transmission Disequilibrium Test (TDT), demonstrated suggestive association for two non-coding SNPs, rs2912770 with CL/P (p = 0.002 -USA) and rs2114684 with cleft palate (p = 0.002 - USA and all populations) but not for SNPs located within intron 2 - where genome wide association (GWA) signals overlap in both NS CL/P and breast cancer studies. Studies of foreskin tissue supported correlation of rs2912770 genotype with level of FGFR2 expression, though the magnitude of the effect was modest and did not remain significant after correction for multiple comparisons. Transcriptome array analysis suggested novel regions of regulated transcription, but their function as novel exons was not validated by real-time PCR (RT-PCR). As we expanded our focus from FGFR2, we examined association of cleft candidate genes with wound healing complications (WHC) with case-control and TDT analysis. Allelic and genotypic case-control analysis suggests association of rs2981582 with WHCs (p < 0.08). TDT analysis revealed WHC potential association with rs6478437 located upstream of the ( FOXE1) gene (p = 0.04). This study has medical implications, as the identification of children at high-risk for WHCs prior to surgical treatment and interventions may prevent post-surgical wound healing complications. We finally examined NS CL/P association with genes that had prior evidence for a role in clefting and cancer. In this analysis, we observed TDT association of rs4746409, located in intron 4 of the zinc finger 365 ( ZNF365) gene (p = 0.0003). Interestingly, this gene and SNP were tested due to suggestive association with breast cancer (Turnbull et al. 2010) and NS CL/P from GWA analyses (Beaty et al. 2010), which strengthens the connection between NSCL/P and breast cancer risk. Identification of NS CL/P patients at increased cancer risk could save lives and extend healthy life for current cleft patients as the field continues to seek ways to intervene and prevent cleft lip and palate from occurring.

Examining cleft lip and palate as a lifelong disease: genetic investigation of causes and outcomes

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