Polymorphisms in SLC44A1 are associated with cognitive improvement in children diagnosed with fetal alcohol spectrum disorder: an exploratory study of oral choline supplementation

Abstract

Background: The essential nutrient choline provides one-carbon units for metabolite synthesis and epigenetic regulation in tissues including brain. Dietary choline intake is often inadequate, and higher intakes are associated with improved cognitive function.

Objective: Choline supplements confer cognitive improvement for those diagnosed with fetal alcohol spectrum disorder (FASD), a common set of neurodevelopmental impairments; however, the effect sizes have been modest. In this retrospective analysis, we report that genetic polymorphisms affecting choline utilization are associated with cognitive improvement following choline intervention.

Methods: Fifty-two children from the upper midwestern United States and diagnosed with FASD, ages 2-5 y, were randomly assigned to receive choline (500 mg/d; n = 26) or placebo (n = 26) for 9 mo, and were genotyped for 384 choline-related single nucleotide polymorphisms (SNPs). Memory and cognition were assessed at enrollment, study terminus, and at 4-y follow-up for a subset.

Results: When stratified by intervention (choline vs. placebo), 14-16 SNPs within the cellular choline transporter gene solute carrier family 44 member 1 (SLC44A1) were significantly associated with performance in an elicited imitation sequential memory task, wherein the effect alleles were associated with the greatest pre-/postintervention improvement. Of these, rs3199966 is a structural variant (S644A) and rs2771040 is a single-nucleotide variant within the 3' untranslated region of the plasma membrane isoform. An additive genetic model best explained the genotype associations. Lesser associations were observed for cognitive outcome and polymorphisms in flavin monooxygenase-3 (FMO3), methylenetetrahydrofolate dehydrogenase-1 (MTHFD1), fatty acid desaturase-2 (FADS2), and adiponectin receptor 1 (ADIPOR1).

Conclusions: These SLC44A1 variants were previously associated with greater vulnerability to choline deficiency. Our data potentially support the use of choline supplements to improve cognitive function in individuals diagnosed with FASD who carry these effect alleles. Although these findings require replication in both retrospective and prospective confirmatory trials, they emphasize the need to incorporate similar genetic analyses of choline-related polymorphisms in other FASD-choline trials, and to test for similar associations within the general FASD population. This trial was registered at www.clinicaltrials.gov as NCT01149538.

Keywords: SLC44A1; choline; fetal alcohol spectrum disorder; nutrigenomics; precision nutrition; rs2771040; rs3199966; single nucleotide polymorphism (SNP).

FIGURE 1

CONSORT flow diagram of the randomized postnatal choline intervention trial. CONSORT, Consolidated Standards of Reporting Trials.

FIGURE 2

PCA of genotypes and population characteristics. PCA (FactoMineR, v2.3) was used to examine the genomic separation of all 52 participants based on race, sex, treatment, diagnostic category, or age. No significant associations between genotype and any of these population characteristics were observed in the PCA. (A) Self-identified race vs. genotype. Red circles, Native American (n = 10); blue triangles, Asian (n = 2); green squares, Black or African-American (n = 13); purple crosses, multiracial (n = 7); yellow crossed squares, White or Caucasian (n = 19); orange crossed squares, unknown (n = 1). (B) Sex vs. genotype. Red circles, female (n = 33); blue triangles, male (n = 19). (C) Treatment vs. genotype. Red circles, choline-treated (n = 26); blue triangles, placebo-treated (n = 26). (D) Diagnostic category vs. genotype. Red circles, alcohol-related neurodevelopmental disorder (n = 23); blue triangles, FAS (n = 9); green squares, partial FAS (n = 20). (E) Age vs. genotype. Red circles, 3 y or younger (n = 12); blue triangles, older than 3 y (n = 40). The largest symbol for each population characteristic represents the group mean for that characteristic, and the ellipse is the 95% CI surrounding that group mean. Dim1, dimension1; Dim2, dimension 2; FAS, fetal alcohol syndrome; PCA, principal components analysis.

FIGURE 3

Change in cognitive performance for participants, stratified by intervention and effect allele status. Comparison of individual cognitive performance in the delta_pairs_imm (A) and delta_adjpairs_imm (B) outcomes at baseline (0 mo) and postintervention (9 mo), stratified by whether the participant carried the effect alleles (solid symbols) and received the choline (●) or placebo (▓) intervention, or did not carry the effect alleles (open symbols) and received either the choline (○) or placebo (□) intervention. delta_pairs_imm is the change in Elicited Imitation immediate memory task performance (for pairs of items regardless of sequence order) between baseline (0 mo) and 9 mo, and delta_adjpairs_imm is the change in Elicited Imitation immediate memory task performance (for pairs of adjacent items placed in the correct sequence order) between baseline (0 mo) and 9 mo; for both, higher scores indicate greater positive change (improvement). Carriers receiving choline (solid circles) all reside at or above the regression line that indicates no change in performance (R = 1.00). Because most of the effect alleles were in linkage disequilibrium, all carriers held at least 6 effect alleles. Presented are the 44 of 52 participants who completed this task at baseline and study conclusion; sample sizes are choline carrier, n = 10 of 11 participants: choline not carrier, n = 12 of 15 participants; placebo carrier, n = 5 of 5 participants; placebo not carrier, n = 17 of 21 participants.