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Genetic variation of folate-mediated onecarbon transfer pathway predicts susceptibility
to choline deficiency in humans
Article in Proceedings of the National Academy of Sciences · November 2005
DOI: 10.1073/pnas.0504285102 · Source: PubMed
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Genetic variation of folate-mediated one-carbon
transfer pathway predicts susceptibility
to choline deficiency in humans
Martin Kohlmeier, Kerry-Ann da Costa, Leslie M. Fischer, and Steven H. Zeisel*
Department of Nutrition, School of Public Health and School of Medicine, University of North Carolina, Chapel Hill, NC 27599
Choline is a required nutrient, and some humans deplete quickly
when fed a low-choline diet, whereas others do not. Endogenous
choline synthesis can spare some of the dietary requirement and
requires one-carbon groups derived from folate metabolism. We
examined whether major genetic variants of folate metabolism
modify susceptibility of humans to choline deficiency. Fifty-four
adult men and women were fed diets containing adequate choline
and folate, followed by a diet containing almost no choline, with
or without added folate, until they were clinically judged to be
choline-deficient, or for up to 42 days. Criteria for clinical choline
deficiency were a more than five times increase in serum creatine
kinase activity or a >28% increase of liver fat after consuming the
low-choline diet that resolved when choline was returned to the
diet. Choline deficiency was observed in more than half of the
participants, usually within less than a month. Individuals who
were carriers of the very common 5,10-methylenetetrahydrofolate
dehydrogenase-1958A gene allele were more likely than noncarriers to develop signs of choline deficiency (odds ratio, 7.0; 95%
confidence interval, 2.0 –25; P < 0.01) on the low-choline diet unless
they were also treated with a folic acid supplement. The effects of
the C677T and A1298C polymorphisms of the 5,10-methylene
tetrahydrofolate reductase gene and the A80C polymorphism of
the reduced folate carrier 1 gene were not statistically significant.
The most remarkable finding was the strong association in premenopausal women of the 5,10-methylenetetrahydrofolate dehydrogenase-1958A gene allele polymorphism with 15 times increased susceptibility to developing organ dysfunction on a lowcholine diet.
genetic polymorphism 兩 methylene tetrahydrofolate dehydrogenase 兩
methylene tetrahydrofolate reductase 兩 reduced folate carrier 兩
nutrient requirement
C
holine or its metabolites are needed for the structural
integrity and signaling functions of cell membranes; it is the
major source of methyl groups in the diet (one of choline’s
metabolites, betaine, participates in the methylation of homocysteine to form methionine), and it directly affects cholinergic
neurotransmission, transmembrane signaling, and lipid transport兾metabolism (1). Choline is a required nutrient, and the
Institute of Medicine and the National Academy of Sciences of
the USA set an adequate intake level for choline of 550 mg兾day
for men and 425 mg兾day for women (2).
One of the clinical consequences of dietary choline deficiency
can be the development of fatty liver (hepatosteatosis) (3, 4),
because a lack of phosphatidylcholine limits the export of excess
triglyceride from liver (5, 6). Also, choline deficiency induces
hepatocyte apoptosis with leakage of alanine aminotransferase
from liver into blood (4, 7, 8). Some people, when deprived of
choline, develop muscle damage and increased creatine kinase
(CK) activity in blood (9). This effect may be attributable to
impaired membrane stability as a consequence of diminished
availability of phosphatidylcholine. The health significance of
this rise in CK activity is unknown, but the rise is certainly an
important surrogate marker for choline depletion status.
www.pnas.org兾cgi兾doi兾10.1073兾pnas.0504285102
Little is understood about the factors that influence dietary
requirements for choline in humans. Endogenous production of
choline during phosphatidylcholine biosynthesis (through the
methylation of phosphatidylethanolamine by phosphatidylethanolamine N-methyltransferase) is most active in liver but has
been identified in many other tissues, including the brain and the
mammary gland (10–12). This synthesis of choline provides
some but not all of the choline required to sustain normal organ
function in humans (4). The use of choline as a methyl-group
donor also influences the dietary requirement for choline. The
metabolism of choline, methionine, and methylfolate are closely
interrelated and intersect at the formation of methionine from
homocysteine (Fig. 1). Betaine:homocysteine methyltransferase
catalyzes the remethylation of homocysteine by using the choline
metabolite betaine as the methyl donor (13, 14). In an alternative
pathway, 5-methyltetrahydrofolate:homocysteine S-methyltransferase (also known as methionine synthase) regenerates
methionine by using a methyl group derived de novo from the
one-carbon pool (15). Perturbing the metabolism of one of the
methyl donors results in compensatory changes in the other
methyl donors because of the intermingling of these metabolic
pathways (16–19). Rats ingesting a low-choline diet showed
diminished tissue concentrations of methionine and Sadenosylmethionine (SAM) (19) and of total folate (17). Humans deprived of dietary choline have difficulty removing
homocysteine after a methionine load and develop elevated
plasma homocysteine concentrations (20). Methotrexate, which
is widely used in the treatment of cancer, psoriasis, and rheumatoid arthritis, limits the availability of methyl groups by
competitively inhibiting dihydrofolate reductase, a key enzyme
in intracellular folate metabolism. Rats treated with methotrexate have diminished pools of all choline metabolites in liver (21).
Choline supplementation reverses the fatty liver caused by
methotrexate administration (22–24). Genetically modified mice
with defective 5,10-methylene tetrahydrofolate reductase
(MTHFR) activity become choline-deficient (25), an important
observation because many humans have genetic polymorphisms
that alter the activity of this enzyme (26, 27). Thus, common
SNPs in genes of folate metabolism could increase the demands
for choline as a methyl-group donor, thereby increasing dietary
requirements for this essential nutrient.
In this study, we examine whether SNPs in genes of folate
metabolism increase the susceptibility of humans to developing
signs of organ dysfunction when fed a low-choline diet.
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: THF, tetrahydrofolate; MTHFD1, cytosolic 5,10-methylene tetrahydrofolate
dehydrogenase; MTHFR, 5,10-methylene tetrahydrofolate reductase; RFC1, reduced folate
carrier 1; SAH, S-adenosylhomocysteine; SAM, S-adenosylmethionine; CI, confidence interval; CK, creatine kinase.
*To whom correspondence should be addressed. E-mail: steven㛭zeisel@unc.edu.
© 2005 by The National Academy of Sciences of the USA
PNAS 兩 November 1, 2005 兩 vol. 102 兩 no. 44 兩 16025–16030
MEDICAL SCIENCES
Edited by Bruce N. Ames, University of California, Berkeley, CA, and approved September 14, 2005 (received for review May 25, 2005)
Fig. 1. Three polymorphic genes are critical for folate-mediated one-carbon transfer. THF, tetrahydrofolate; MTHFR, 5,10-methylene tetrahydrofolate
reductase; MTHFD1, cytosolic 5,10-methylene tetrahydrofolate dehydrogenase; RFC1, reduced folate carrier 1.
Methods
Subjects. Healthy adults were recruited by advertising. Both
males (n ⫽ 31) and females (n ⫽ 31) were included, with ages
ranging from 18 to 70 years. Inclusion was contingent on
age-typical good state of health as determined by physical
examination and standard clinical laboratory tests. Of the originally recruited 62 subjects, 58 completed at least the initial
baseline phase and the depletion phase. Of these 58, 1 subject
was excluded because of a 9-kg weight loss during the study, and
3 subjects were excluded because they did not comply with diet
restrictions, leaving 54 subjects included in all analyses. Subject
characteristics were as follows: 28 women and 26 men; 34
Caucasians, 14 African-Americans, 3 Asians, and 3 of other
ethnicity; mean age was 38.7 ⫾ 15.4 (SD) years; mean body mass
index was 25.0 ⫾ 3.7 kg兾m2. The ethnicity of the participants
reflects the local population characteristics of the Raleigh–
Durham–Chapel Hill area of North Carolina. The criteria for
subject selection and all details of the clinical protocol were
approved by the institutional review board of the University of
North Carolina at Chapel Hill.
Clinical Studies. The participants stayed at the University of North
Carolina at Chapel Hill General Clinical Research Center for the
entire duration of the study and could leave only for brief periods
under the direct supervision of study staff. All foods were
prepared in-house to protocol specifications (28). Total food
intake was adjusted to be isocaloric and to provide adequate
intake levels of macro- and micronutrients. Individual energy
requirements were estimated by using the Harris–Benedict
equation, and individual adjustments were made during the first
week on the basal diet, if necessary, to achieve participants’
satiety. Once individual needs had been determined, daily
energy intakes were kept at a constant level, ranging between 35
and 45 kcal兾kg of body weight. The diets, which provided 0.8
g兾kg high biologic value protein, with 30% energy coming from
fat and the remaining energy from carbohydrate, met or exceeded the estimated average requirement for methionine plus
cysteine and the recommended dietary allowances for vitamin
B12 and all other vitamins except folic acid (diets contained 100
g兾day folate, see below). During the initial 10 days (baseline),
the participants consumed normal foods containing 550 mg of
choline per 70 kg of body weight per day, which approximates the
current adequate intake level (550 mg兾day for men and 425
mg兾day for women; ref. 2) and 400 g of folic acid per day as a
16026 兩 www.pnas.org兾cgi兾doi兾10.1073兾pnas.0504285102
supplement (General Nutrition Center, Pittsburgh). The actual
choline content of a sampling of duplicate portions was assayed
by our laboratory (29). Subjects were then switched to a cholinedepletion diet containing ⬍50 mg of choline per 70 kg of body
weight per day by eliminating choline-rich foods, as confirmed by
analysis of duplicate food portions (32, 33). Details of diet
formulations were previously published (28). Furthermore, participants were randomly assigned to receive either placebo or 400
g of folic acid per day as a supplement in addition to the amount
of folate consumed with food (100 g兾day). Diets were well
tolerated.
Periodic determinations of urinary choline and betaine concentrations were used to confirm compliance with the dietary
restrictions. Subjects remained on this depletion diet until they
developed signs of organ dysfunction associated with choline
deficiency, or for 42 days if they did not. Humans were deemed
to have signs of organ dysfunction associated with choline
deficiency if they had more than a 5-fold increase of serum CK
activity while on the choline depletion diet and if this increased
CK resolved when they were returned to the repletion diet (9),
or if they had an increase of liver fat content by 28% or more
while on the choline depletion diet and if this increased liver fat
resolved when they were returned to the repletion or ad libitum
diet (20). After the depletion period, subjects were repleted by
gradually increasing choline intake and were maintained at a
final level of ⬎550 mg of choline per day for at least 3 days.
Change in liver fat content was estimated by MRI with a
clinical MR system (Vision 41.5-T, Siemens, Iselin, NJ) using a
modified ‘‘In and Out of Phase’’ procedure (20, 30). This
approach utilizes the differences in transverse magnetization
intensity after an ultrabrief time interval [fast low-angle shot
(FLASH); echo time (TE) ⫽ 2.2 msec and 4.5 msec, with a flip
angle of 80°, and relaxation time (TR) ⫽ 140 msec]. Processing
of successive FLASH MRI images with software from Siemens
Medical Solutions (Malvern, PA) was used to estimate fat
content. Organ content was derived from measurements across
five liver slices per subject and standardized by relating the
results to the similarly measured fat content of spleen. We
assumed that spleen signal would be largely invariant and used
this value to calculate the outcome variable liver-to-spleen fat
ratio.
Fasting blood samples were taken every 3–4 days throughout
the study, and in particular, after 10 days on the 550 mg兾day
choline diet (baseline), at the end of the low-choline diet
(depletion phase), and after consuming a repletion diet with
Kohlmeier et al.
Table 1. Effect of genotype on susceptibility to organ dysfunction in humans eating
low-choline diets
Polymorphism
MTHFR 677
MTHFR 1298
MTHFD1 1958
RFC1 80
Genotype (n)
% subjects with signs of
choline deficiency
CC (28)
CT (22)
TT (4)
AA (28)
AC (22)
CC (4)
GG (20)
GA (28)
AA (6)
AA (19)
AG (20)
GG (15)
61
73
75
64
68
75
40
82
83
56
70
73
P
Odds ratio and 95% CI
0.63
CC vs. CT兾TT
Odds ratio, 1.76
95% CI, 0.56–5.6
AA vs AC兾CC
Odds ratio, 1.25
95% CI, 0.40–3.9
GG vs GA兾AA
Odds ratio, 7.0
95% CI, 2.0–25
AA vs AG兾GG
Odds ratio, 1.82
95% CI, 0.56–5.9
0.90
0.007
0.59
Significance was calculated with 2⫻3 Fisher’s exact test. Application of Bonferroni’s correction for multiple
testing lowers the threshold for statistical significance to 0.0125.
Laboratory Analyses. Plasma folate concentrations in fasted sam-
ples were measured by using a microbiological assay (31). Serum
was analyzed by using a dry-slide colorimetric method for CK
activity by the McClendon Clinical Laboratories at University of
North Carolina Hospitals, which is both Clinical Laboratory
Improvement Act (CLIA)- and College of American Pathologists (CAP)-accredited. Total plasma homocysteine concentration was measured in fasted samples by using a HPLC method
(20, 32). SAM and SAH levels in plasma were measured by
HPLC with fluorescence detection after conversion into their
fluorescent isoindoles (33).
Genotyping. Genomic DNA was prepared according to manu-
facturer’s instructions from peripheral blood with a commercial
extraction kit (PureGene, Gentra Systems) and diluted to a
standard concentration of 1 g兾ml. The polymorphic sites of
MTHFR (MTHFR-C677T and -A1298C), cytosolic C-1-THF
synthase (MTHFD1-G1958A), and reduced folate carrier 1
(RFC1-G80A) were studied (Fig. 1). The targeted DNA sequences were amplified by multiplex PCR, purified, and then
analyzed with matrix-assisted laser desorption兾ionization timeof-flight mass spectrometry (34). For all subjects, duplicate
samples were genotyped. In the few instances of amplification
failure, new DNA was prepared from backup blood samples.
Statistical Analysis. Genotype-related differences in dichotomous
outcomes were calculated with two-sided Fisher’s exact probability test (http:兾兾faculty.vassar.edu兾lowry兾webtext.html) to determine statistical significance (GraphPad, San Diego). Odds
ratios for depletion by presence vs. absence of the predominant
alleles were calculated as the odds to deplete for subjects with the
allele divided by odds for subjects without the allele (35).
Statistical significance of odds ratios was again calculated by
using two-sided Fisher’s exact probability test. The statistical
significance of group differences for continuous variables was
assessed with Student’s t test, and differences between subjects
on different diets were assessed by using pair t tests. A twosample t test based on the differences between homocysteine
concentrations in subjects on the two diets was used to compare
the clinically depleted and not-depleted groups (GraphPad).
Kohlmeier et al.
Results
Genetic Variation. The distribution of the polymorphic variants of
MTHFR and cytosolic MTHFD1 (Table 1) largely agreed with
that of larger North European populations [Norwegian Colorectal Cancer Prevention study (NORCCAP)] that were analyzed previously with the same genotyping methodology (K.
Meyer and P. M. Ueland, personal communication). Within our
group, however, fewer African-Americans than Caucasians had
the variant allele MTHFD1 1958A (allele frequency 0.18 vs.
0.50). The RFC1 80G allele was slightly underrepresented in our
subjects (0.47 vs. 0.58), but we considered this the reference
allele, nonetheless. The difference is mostly attributable to the
presence of many non-Caucasians in our regionally representative population sample.
Folate Status. Twenty-six participants were assigned to receive
placebo, and 28 subjects received an additional 400 g of folic
acid per day as a supplement. Average serum folate concentration at the end of the depletion phase was lower in subjects with
the lower folate intake (22.1 ⫾ 1.3 nmol兾liter vs. 28.3 ⫾ 1.2
nmol兾liter; P ⬍ 0.01 by Student’s t test). None of the investigated
polymorphisms had a statistically significant effect on serum
folate concentrations at any time point.
Signs of Organ Dysfunction Associated with Choline Deficiency.
Twelve subjects responded to the low-choline diet with an
increase in serum CK activity, all but 1 within a month on the
depletion diet. A significant increase in liver fat content was
observed in another 24 participants, usually within a month on
the depletion diet. In six of these participants, however, it took
up to 42 days to accumulate the additional 28% or more of liver
fat. Eighteen subjects did not show signs of organ dysfunction in
response to the low-choline diet. Daily supplementation with
folic acid did little to affect the likelihood of developing signs of
choline deficiency [odds ratio, absence over presence of signs of
choline deficiency in subjects with supplementation vs. without
supplementation 0.8, 95% confidence interval (CI), 0.26–2.5].
Methionine Metabolism. Homocysteine concentrations during
both baseline and choline-depletion conditions were measured
in 54 subjects, and methionine load tests were completed in 52
of these participants at the end of the baseline and depletion diet
phases. Homocysteine concentration increased by 19% with the
low-choline regime (P ⬍ 0.001, paired t test). Supplementation
with 400 g兾day folic acid blunted this increase, compared with
placebo (15% vs. 23% increase, P ⬍ 0.05, Student’s t test).
PNAS 兩 November 1, 2005 兩 vol. 102 兩 no. 44 兩 16027
MEDICAL SCIENCES
137–550 mg兾day choline (repletion phase). The metabolic response to an oral challenge with 100 mg L-methionine兾kg was
determined initially and after depletion. Blood for homocysteine, SAM, and S-adenosylhomocysteine (SAH) measurements
was obtained before and 4 h after methionine ingestion (20).
However, there was no significant interaction between fasting
plasma homocysteine concentration and clinical status (P ⫽
0.113, Student’s t test), because there was a similar increase of
this measure in subjects judged to be clinically depleted (by 1.4
mol兾liter; 95% CI, 1.1–1.7) as in subjects without clinical signs
of choline deficiency (0.9 mol兾liter; 95% CI, 0.5–1.4). None of
the polymorphic variants had a statistically significant influence
on plasma homocysteine concentrations, at either baseline or
depletion. The expected rise of plasma homocysteine concentration after methionine loading was observed on both diets. The
rise in homocysteine concentration in response to the methionine challenge in subjects eating the 550-mg choline diet was
significantly less in subjects without the RFC1 80G allele than in
the carriers of this allele (P ⫽ 0.02, Student’s t test). None of the
other polymorphic variations were predictive for the metabolic
response to methionine or the change of this response with
choline depletion.
As was previously reported in a pilot study (20), the rise in
plasma homocysteine concentration after a methionine load was
greater in individuals developing signs of choline deficiency
when ingesting a low-choline diet than in those that did not. In
this study, after a methionine load at the end of the depletion
phase, plasma homocysteine concentrations in the group with
signs of choline deficiency rose 6.9 mol兾liter above that which
was previously observed after a methionine load on the 550-mg
choline diet (95% CI, 4.4–9.3, P ⫽ 0.0001). For subjects without
signs of deficiency, plasma homocysteine did not increase significantly after the same methionine load (1.6 mol兾liter; 95%
CI, ⫺1.7–4.9, P ⫽ 0.318).
SAM and SAH concentrations were assessed in 26 individuals
with MTHFD1 1958GA兾AA genotype and in 15 individuals with
MTHFD1 1958GG genotype. Concentrations did not change
significantly upon switching from baseline to a low-choline diet.
On both the baseline and the low-choline diets, SAM and SAH
concentrations increased greatly after oral methionine load, as
expected. The postloading concentration of SAH increased from
28.8 ⫾ 12.8 nmol兾liter on the baseline diet to 34.7 ⫾ 12.8
nmol兾liter on the low-choline diet (P ⬍ 0.05). No statistically
significant change of postloading SAM concentrations in response to the low-choline diet was observed. Although SAM
concentrations at depletion did not differ significantly between
MTHFD1 1958 genotype groups, SAH concentrations were
significantly lower in participants with the GG genotype than in
those with the GA and AA genotypes, both with and without
methionine loading (Fig. 2). The same pattern of genotype-SAH
concentration was observed while subjects were on the baseline
diet, but the contrasts did not reach statistical significance.
Among the examined polymorphisms, the MTHFD1 G1958A
variant was the best predictor of susceptibility to choline depletion (Table 1). In light of the small subject numbers in several of
the cells, the carriers of what are usually the minor alleles were
grouped together for calculating odds ratios. Again, the
MTHFD1 polymorphism was the only one of the four variants
with a distinct impact on risk of developing clinical signs of
choline deficiency. A higher percentage of the 34 carriers of the
1958A allele showed signs of choline deficiency in response to
the low-choline diet (odds ratio, 7.0; two-sided, P ⫽ 0.0025;
Table 2). This genotypic difference was largely attributable to
the fact that none of the young women with MTHFD1 1958GG
genotype showed deficiency signs, whereas seven of the eight
young women carriers of the GA or AA genotypes did so. The
corresponding differences were not seen in men (odds ratio, 3.0;
P ⫽ 0.33) and postmenopausal women (odds ratio, 1.0; P ⫽ 0.99).
However, because only four postmenopausal women had the
MTHFD1 1958-GG genotype, the power to detect an odds ratio
of 7.0 (the average for all subjects) at the usual level of
significance was only 0.13. With the eight male carriers of the GG
genotype, the corresponding statistical power also was very low.
16028 兩 www.pnas.org兾cgi兾doi兾10.1073兾pnas.0504285102
Fig. 2. Increase in SAH concentrations after a methionine load was lower in
MTFD1 1958 GG individuals. Subjects were treated with a low-choline diet as
described in Methods. Blood for SAM and SAH measurements was obtained
before (fasting) and 4 h after an oral methionine load (Met-load; 100 mg of
L-methionine per kg of body weight) from 26 individuals with MTHFD1 1958
GA兾AA genotype and from 15 individuals with MTHFD1 1958 GG genotype.
Values are presented as mean ⫾ standard error. Solid bars indicate means of
individuals with the MTHFD1 1958 GA or AA genotypes, and open bars
correspond to means from those with the GG genotype. *, P ⬍ 0.05; **, P ⬍
0.01 different from other genotype by one-way ANOVA.
Thus, the study was clearly underpowered for the detection of an
effect smaller than the one observed in the young women.
In regard to folate supplementation, the MTHFD1 1958A
allele-related difference in susceptibility to developing organ
dysfunction when eating a low-choline diet was greatest in the
group getting folate only from the diet (no supplement; odds
ratio, 35; two-sided, P ⫽ 0.001; Table 2) and was much smaller
and statistically not significant in the folate-supplemented group
(odds ratio, 2.5; two-sided, P ⫽ 0.41; Table 2). None of the other
polymorphisms showed a similarly strong or consistent relationship to choline-depletion susceptibility, with or without folate
supplementation. Power calculations based on Fisher’s exact test
indicate that, for an odds ratio of 1.5, ⬎200 subjects with the least
frequent genotype would be needed to give the study a power of
0.8 at the usual level of statistical significance.
Discussion
In this investigation of healthy subjects, more than half of the
participants developed signs of organ dysfunction when consuming low-choline diets. This report focuses on the impact of
genetic variants of folate metabolism on susceptibility to clinical
choline deficiency. The most remarkable finding was the strong
association of the MTHFD1 G1958A polymorphism with susceptibility to developing signs of organ dysfunction associated
with choline deficiency, particularly in comparison to the very
weak association with variation in the MTHFR gene. Presence
of the MTHFD1 1958A allele made it much more likely that
subjects developed signs of choline deficiency.
Choline-deficient individuals were found to have impaired
capacity to handle a methionine load, developing elevated
plasma SAH and homocysteine concentrations. This finding
confirms our earlier report in a limited number of subjects (20)
and highlights the importance of alternative folate-mediated
pathways for homocysteine remethylation. The observation of
higher SAH concentrations in carriers of the MTHFD1 1958A
allele, compared with noncarriers, is particularly informative,
because accumulation of this metabolite has been found to be a
more sensitive indicator of disturbed methionine regeneration
than is elevated homocysteine concentration (36). SAH is a
potent inhibitor of phosphatidylethanolamine methyltransferase, which catalyzes the endogenous formation of choline
moiety in liver (10). Phosphatidylethanolamine methyltransKohlmeier et al.
Table 2. Effect of folate and sex on effect of MTHFD1 1958 SNP on susceptibility to organ
dysfunction in humans eating low-choline diets
Group
Premenopausal women
Postmenopausal women
Men
All subjects
Diet folate only
Diet folate plus folic acid
supplement
(400 g兾day)
Genotype (n)
% subjects with signs of
choline deficiency
GG (8)
GA兾AA (8)
GG (4)
GA兾AA (8)
GG (8)
GA兾AA (18)
GG (20)
GA兾AA (34)
GG (10)
GA兾AA (16)
GG (10)
0
88
75
75
63
83
40
82
30
94
50
GA兾AA (18)
72
P
0.000
0.99
0.33
0.007
0.00
0.41
Odds ratio and
95% CI
Odds ratio, 85*
95% CI, 3–2418
Odds ratio, 1.0
95% CI, 0.06–16
Odds ratio, 3.0
95% CI, 0.45–20
Odds ratio, 7.0
95% CI, 2.0–25
Odds ratio, 35
95% CI, 3.0–39
Odds ratio, 2.6
95% CI, 0.52–13
ferase activity is increased by estrogen (37), and this mechanism
probably explains why we observed that premenopausal women
were relatively resistant to developing signs of organ dysfunction
when fed a low-choline diet, compared with men. It is in these
premenopausal women that we observed the most significant
effect of the MTHFD1 1958A SNP on susceptibility to developing signs of choline deficiency (Table 2). We suggest that this
SNP restricts methyl-group availability enough so that SAM
availability for the phosphatidylethanolamine methyltransferase-catalyzed formation of choline moiety becomes limiting,
thereby eliminating this protective mechanism for females. Our
SAH data (Fig. 2) support this hypothesis. Alternatively, it is
possible that men and postmenopausal women are already so
susceptible to choline deficiency (80% show signs of organ
dysfunction on a low-choline diet) that a further increase in
susceptibility cannot be appreciated, given the small incremental
effect size. In premenopausal women, in contrast, where 60% of
the population was resistant to choline deficiency, there was
sufficient margin for detecting an increase in susceptibility
associated with the MTHFD1 1958A SNP.
Under standard conditions, serine provides the bulk of onecarbon groups (38). Cytosolic serine hydromethyltransferase (EC
2.1.2.1) transfers a one-carbon unit from serine to THF, and the
resulting 5,10-methylene-THF can then be reduced by MTHFR to
5-methyl-THF. An alternative source for the one-carbon unit is
derived from formate through mitochondrial or cytosolic reactions
that can be linked to free folate by formyl-THF synthetase (EC
6.3.4.3) and generate 10-formyl-THF in an ATP-dependent reaction. This distinct reaction is only one of three that are catalyzed by
the cytosolic enzyme C-1-THF synthase complex (all encoded by
the MTHFD1 gene sequence). Two additional reactions, mediated
by methylene-THF dehydrogenase (EC 1.5.1.5) and methenyl-THF
cyclohydrolase (EC 3.5.4.9), can then convert 10-formyl-THF to
5,10-methylene-THF (Fig. 1). Although the formation of 5-methylTHF is practically irreversible in vivo, the interconversion of
5,10-methylene-THF and 10-formyl-THF is closer to equilibrium
(39). Thus, 5,10-methylene-THF may be directed either toward
homocysteine remethylation or away from it. Both purine synthesis
and oxidative release of carbon dioxide and THF by 10-formylTHF dehydrogenase (EC 1.5.1.6) draw on the 10-formyl-THF pool.
The irreversible and nonproductive dissipation of an excess in
transferable one-carbon units is likely to be a significant regulatory
Kohlmeier et al.
factor, because the intrahepatic concentration of 10-formyl-THF
exceeds the half-maximal equilibrium constant Km of 10-formylTHF dehydrogenase (40). The 10-formyl-THF synthase activity of
C-1-THF synthase, on the other hand, can add to the 5,10methylene-THF pool by linking formate to free folate. The G-to-A
transition mutation at nucleotide 1958 in MTHFD1 causes an
arginine to glutamine substitution in the protein region responsible
for 10-formyl-THF dehydrogenase, which is far removed from the
region providing for the methenyl-THF cyclohydrolase and methylene-THF dehydrogenase activities. The MTHFD1 G1958A polymorphism may thus affect the delicately balanced flux between
5,10-methylene-THF and 10-formyl-THF and thereby influence
the availability of 5-methyl-THF for homocysteine remethylation.
The pattern of decreased SAM:SAH ratios among individuals with
an MTHFD1 1958A allele appears to be consistent with the view
that their one-carbon flux slightly tilts away from 5-methyl-THF
formation. The finding of increased susceptibility to developing
signs of choline deficiency coinciding with evidence of impaired
5-methyl-THF availability (increased SAH concentration) in carriers of an MTHFD1 1958A allele makes it less likely that the
association is due to just random chance. If a nearby gene locus in
strong linkage disequilibrium with the MTHFD1 1958A were
ultimately responsible for increased susceptibility to choline deficiency, this locus also would have to explain the observed shift in
methyl-group metabolism.
It is of particular interest that the gene-variant effect can be
overcome if humans are supplemented with folic acid. It may be
surprising that the development of choline deficiency signs was
strongly favored by the presence of the MTHFD1 1958A allele
but not by polymorphic variants of MTHFR or RFC1. A partial
explanation may be provided by a recent investigation of folatedependent homocysteine remethylation in young women (41).
This study found that the MTHFR 677TT genotype had little
detectable effect on remethylation flux. In comparison, the
MTHFD1 1958A polymorphism, which has not been extensively
investigated until now, may be a more potent determinant of the
rate at which one-carbon units become available for methylgroup transfer reactions, such as the synthesis of phosphatidylcholine from phosphatidylethanolamine.
Observations on genetically linked susceptibility to choline
deficiency are important because they can help the Institute of
Medicine refine their recommendations for dietary choline
PNAS 兩 November 1, 2005 兩 vol. 102 兩 no. 44 兩 16029
MEDICAL SCIENCES
The odds ratios were calculated as the odds of showing signs of deficiency for subjects without the MTHFD1
1958A allele divided by the odds of showing signs of deficiency for subjects with the A allele. Two-sided P and 95%
CI were calculated with Fisher’s exact test.
*The odds ratio for premenopausal women was calculated by adding a value of 0.5 to each cell for premenopausal
women; this value is an underestimate, because the value in the GG-YES cell was 0. Thus, in reality, the odds ratio
exceeds 85.
intake by taking into account the needs of sizeable population
groups with greater-than-average vulnerability to low choline
or folate intake. There also is a potential relevance for the
prevention of neural tube defects. One of the great successes
of nutrition science has been the identification of the role that
folate plays in normal neural tube closure; adequate dietary
folate intake by mothers during pregnancy can prevent ⬎50%
of neural tube defects in babies (42). The risk of having a child
with a neural tube defect increases in mothers with the
G1958A SNP in MTHFD1 (43). As discussed earlier, choline
and folate metabolism are highly interrelated. Inhibition of
choline uptake and metabolism was associated with the development of neural tube defects in mice (44, 45). Recent
evidence suggests that availability of choline also might impact
the risk of neural tube defects in humans: A retrospective
We thank Klaus Meyer and Per Magne Ueland (both of the University
of Bergen, Norway) for the SNP analyses; Conrad Wagner (Vanderbilt
University, Nashville) for the analysis of methionine metabolites; and
Lester Kwock for assistance with MRI studies. This work was supported
by National Institutes of Health Grants DK55865, DK56350, RR00046,
and ES10126.
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case-control study (400 cases and 400 controls) of periconceptional dietary intakes of choline in women in California
found that women in the lowest quartile for daily choline
intake had 4⫻ the risk of having a baby with a neural tube
defect than did women in the highest quartile for intake (46).
We suggest the need to focus future epidemiologic studies on
interactions among dietary choline intake, folate intake, and
MTHFD1 polymorphisms.
Kohlmeier et al.