Folate deficiency in normal human fibroblasts leads to altered expression of genes primarily linked to cell signaling, the cytoskeleton and extracellular matrix

The molecular basis linking folate deficiency to certain health conditions and developmental defects is not fully understood. We examined the consequences of folate deficiency on global gene expression by microarray and compared transcript levels in normal human fibroblast cells (GM03349) grown in folate-deficient and -sufficient medium. The largest represented groups from the selected genes functioned in cell signaling, the cytoskeleton and the extracellular matrix and included the Wnt pathway genes DKK1, WISP1 and WNT5A. Twelve selected genes were further validated by qRT-PCR. Analysis of six genes at 4, 7, 10 and 14 days indicated that the relative differences in transcript levels between folate-sufficient and -deficient cells increases with time. Transcripts for 7 of the 12 selected genes were detected in the human lymphoblast cell line GM02257, and of these, changes in 4 genes corresponded to the results with fibroblast cells. Fibroblast cells were treated with the compounds homocysteine, methotrexate and the MEK1/2 inhibitor U0126, and relative transcript levels of six genes were determined. U0126 caused changes that more closely mimicked those detected in folate-deficient cells. The response of the DKK1 and TAGLN gene promoters to folate deficiency and compounds was examined in NIH3T3 cells using luciferase reporter plasmids. Promoter activity for both genes was decreased by folate deficiency and methotrexate and unaffected by homocysteine. U0126 caused a decrease in DKK1 promoter activity at 50 μM and had no effect on TAGLN promoter activity. These findings suggest an alternative mechanism for how folate deficiency leads to changes in gene expression and altered cell function.