Genome-wide pathway analysis of folate-responsive genes to unravel the pathogenesis of orofacial clefting in man

BACKGROUND: A cleft of the lip with or without the palate (CLP) is a frequent congenital malformation with a heterogeneous etiology, for which folic acid supplementation has a protective effect. To gain more insight into the molecular pathways affected by natural folate, we examined gene expression profiles of cultured B‐lymphoblasts from CLP patients before and after the addition of 5‐methyltetrahydrofolate (5‐mTHF) to the cultures. METHODS: Immortalized B‐lymphoblasts from five children with CLP were cultured in folate‐deficient medium for 5 days. 5‐mTHF was added to a concentration of 30 nM. Gene expression patterns were then evaluated before and after supplementation using Human Genome U133 Plus 2.0 arrays. Data analysis was performed with Omniviz and the GEPAS analysis suite. Differential genes were categorized into biological pathways with Ingenuity Pathway systems. Differential expression was validated by quantitative RT‐PCR. RESULTS: Using supervised clustering, with a false discovery rate