Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not

Abstract

Background: Some humans fed a low-choline diet develop hepatosteatosis, liver and muscle damage, and lymphocyte apoptosis. The risk of developing such organ dysfunction is increased by the presence of single-nucleotide polymorphisms (SNPs) in genes involved in folate and choline metabolism.

Objective: We investigated whether these changes that occur in the expression of many genes when humans are fed a low-choline diet differ between subjects who develop organ dysfunction and those who do not. We also investigated whether expression changes were dependent on the presence of the SNPs of interest.

Design: Thirty-three subjects aged 20-67 y were fed for 10 d a baseline diet containing the recommended adequate intake of choline. They then were fed a low-choline diet for up to 42 d or until they developed organ dysfunction. Blood was collected at the end of each phase, and peripheral lymphocytes were isolated and used for genotyping and for gene expression profiling with the use of microarray hybridization.

Results: Feeding a low-choline diet changed the expression of 259 genes, and the profiles of subjects who developed and those who did not develop signs of organ dysfunction differed. Group clustering and gene ontology analyses found that the diet-induced changes in gene expression profiles were significantly influenced by the SNPs of interest and that the gene expression phenotype of the variant gene carriers differed significantly even with the baseline diet.

Conclusion: These findings support our hypothesis that a person's susceptibility to organ dysfunction when fed a low-choline diet is modulated by specific SNPs in genes involved in folate and choline metabolism.

FIGURE 1

Cluster analysis. All comparison groups defined in Table 1 were subjected to cluster analysis (see Materials and Methods) to determine the distance of change between groups, as defined by the node structure indicated. ALL SUBJECTS, comparison of all subjects (the end of the depletion phase compared with the end of the baseline phase); SIGNS, the subjects who developed organ dysfunction when fed the low-choline diet; NO SIGNS, the subjects who did not develop organ dysfunction (comparing the end of the depletion phase with the end of the baseline phase). For each polymorphism, the gene symbol is indicated. The choline dehydrogenase single-nucleotide polymorphisms are indicated by the nucleotide replacement, and the sample is at the end of depletion phase. The notation “(B)” after the gene symbol indicates the sample after the baseline (adequate choline) phase; “(D)” after the gene symbol indicates the sample after the low-choline diet phase; “(W)” after the gene symbol indicates women only after the depletion phase. FOLATE compares subjects with and without folate supplementation at the end of the depletion phase. The number of arrays for each comparison is provided in Table 1. Red indicates overexpression, green indicates underexpression, and black indicates no change in gene expression.

FIGURE 2

Gene expression profiles across all groups. The computed change in expression is shown for each gene included in gene ontology (GO) classes pertaining to folate-thymidine metabolism, apoptosis, DNA damage-repair, cell cycle regulation-proliferation, immune-inflammatory response and lymphocyte differentiation-activation, epigenetic regulation, and telomere maintenance. ■, overexpression; , no change; □, underexpression within each comparison group (by significance analysis by microarray; the false discovery rate was <5%) as indicated in Table 1. ALL SUBJECTS, comparison of all subjects (the end of the depletion phrase compared with the end of the baseline phase); SIGNS, the subjects who developed organ dysfunction when fed the low-choline diet; NO SIGNS, the subjects who did not develop organ dysfunction (comparing the end of the depletion phase with the end of the baseline phase). For each polymorphism, the gene symbol is indicated. The choline dehydrogenase single-nucleotide polymorphisms are indicated by the nucleotide replacement, and the sample is at the end of depletion phase. The notation “(B)” after the gene symbol indicates the sample after the baseline (adequate choline) phase; “(D)” after the gene symbol indicates the sample after the low-choline diet phase; “(W)” after the gene symbol indicates women only after the depletion phase. FOLATE compares subjects with and without folate supplementation at the end of the depletion phase. The number of arrays for each comparison is provided in Table 1.