Stroke is the third most common cause of death in many developed countries, and approximately 80% of stroke cases are ischemic in origin1,2. In South Korea, stroke is the most frequent cause of death after cancer and is more frequent than heart disease3,4. Stroke is a complex multifactorial and polygenic disease arising from a variety of gene-gene and gene-environment interactions5,6. Multiple factors, including hypertension (HTN), diabetes mellitus (DM), smoking, hyperlipidemia, and hyperhomocysteinemia, are associated with a higher risk of stroke1,7,8. In particular, hyperhomocysteinemia is considered an independent, potentially modifiable risk factor for ischemic stroke, and has been previously reported in several studies involving different ethnic groups9,10,11,12.

The 5, 10-methylenetetrahydrofolate reductase (MTHFR) protein performs a central reaction in folate metabolism. It irreversibly catalyzes the conversion of 5, 10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, the primary circulating form of folate13,14. In addition, MTHFR converts 5, 10-methylenetetrahydrofolate into 5-methyltetrahydrofolate and provides the methyl group for homocysteine (Hcy) in methionine synthesis. It has been reported that elevation of Hcy in the blood is associated with an increased risk for arteriosclerosis, myocardial infarction, venous thrombosis, stroke, and neural tube defects3,15. The effect of several polymorphic genes involved in folate metabolism, including MTHFR on ischemic stroke susceptibility and progression, has been reported. The MTHFR gene is critical for Hcy and folate metabolism, and polymorphic variants of the enzymes involved in Hcy and folate metabolism also play an important role in determining the susceptibility of an individual to disease16. Lower MTHFR enzyme activity, which can increase total plasma homocysteine (tHcy) levels and decrease plasma folate levels, contributes to stroke development16,17,18. Folate concentrations inversely correlate with tHcy levels19. The role of hyperhomocysteinemia in vascular and thromboembolic disease has been extensively studied. Previous studies reported significant vascular disease in patients with markedly elevated tHcy levels20,21,22. The tHcy is hypothesized to increase thrombotic risk by inducing endothelial injury in venous and arterial vasculatures21. Abnormal folate concentrations have also been implicated in the development of diseases, such as cardiovascular diseases, neural tube defects, cleft lip and palate, late pregnancy complications, and neurodegenerative and psychiatric disorders23,24. Recent studies have shown the clinical impacts of polymorphisms in the 3′-UTR of certain genes, which may potentially bind to specific microRNAs (miRNAs) in various diseases25,26,27. However, variants in the MTHFR 3′-UTR have not been extensively examined.

In the present study, we selected four single nucleotide polymorphisms (SNPs) in the MTHFR 3′-UTR region: MTHFR 2572 C > A (rs4846049), 4869 C > G (rs1537514), 5488 C > T (rs3737967), and 6685 T > C (rs4846048). We then determined their associations with ischemic stroke prevalence and prognosis. The minor allele frequencies of the studied polymorphisms are higher than 5% in the Asian population, and little is known about their genetic associations with ischemic stroke. Therefore, we investigated whether MTHFR 3′-UTR polymorphisms correlate with ischemic stroke susceptibility in Korean subjects.


Genetic susceptibility of single markers in ischemic stroke subtypes and control subjects

We investigated the MTHFR 2572 C > A, 4869 C > G, 5488 C > T, and 6685 T > C polymorphisms. Table 1 shows their genotype distributions in ischemic stroke patients and control subjects. The MTHFR 3′-UTR polymorphisms were not significantly correlated with ischemic stroke prevalence. To examine whether the effect of each polymorphism was confined to a specific subtype or related to generalized risks, we further separated the stroke group into three subgroups [large arterial disease (LAD), small-vessel disease (SVD), and, cardioembolism (CE)] according to the Trial of Org 10172 in Acute Stroke Treatment (TOAST) classification25. In subgroup analyses, LAD was significantly associated with the MTHFR 6685 T > C polymorphism [TT vs. TC: adjusted odds ratio (AOR), 0.517; 95% confidence interval (CI), 0.308–0.867; P = 0.012; TT vs. TC + CC: AOR, 0.543; 95% CI, 0.328–0.899; P = 0.018]. The MTHFR 2572 C > A polymorphism (CC vs. CA: AOR, 2.098; 95% CI, 1.160–3.793; P = 0.014; CC vs. CA + AA: AOR, 2.145; 95% CI, 1.203–3.827; P = 0.010) and 6685 T > C polymorphism (TT vs. CC: AOR, 10.146; 95% CI, 1.297–79.336; P = 0.027; TT + TC vs. CC: AOR, 10.504; 95% CI, 1.373–80.377; P = 0.024) were significantly associated with the CE type (Table 1). In addition, we analyzed the association with/without patients of undetermined subtypes for ischemic stroke susceptibilities (Supplemental Table 1).

Table 1 Comparison of genotype frequencies and AOR of MTHFR gene polymorphisms between the ischemic stroke, subtypes, and control subjects

Combined effects of MTHFR gene polymorphisms and clinical parameters on disease prevalence

To determine additional clinical significance, we evaluated the combined effects of the gene environment. The MTHFR gene polymorphism elevated stroke prevalence in several conditions, including hypertension, diabetes mellitus, hyperlipidemia, smoking, high density lipoprotein-cholesterol levels, triglyceride levels, folate levels ≤3.45 nmol/mL, and tHcy levels ≥11.22 μmol/L (Table 2). The MTHFR 2572 CA + AA genotype was shown to have synergic effects with ischemic stroke prevalence. In particular, low folate levels were the most predictive, with MTHFR 2572CA + AA and folate ≤3.45 nmol/L (AOR, 6.532; 95% CI, 2.592–16.46) shown to significantly increase ischemic stroke incidence. In addition, the MTHFR 4869CG + GG genotype had a combinatorial effect with hypertension (AOR, 3.217; 95% CI, 1.763–5.872) and smoking (AOR, 5.067; 95% CI, 1.788–14.360), whereas the MTHFR 5488CT + TT genotype was significant only in the smoking group (AOR, 2.740; 95% CI, 1.196–6.278). In addition, we performed stratified analyses for clinical factors including sex, age, hypertension, diabetes mellitus, hyperlipidemia, smoking status, folate levels, and homocysteine levels (Supplemental Table 2).

Table 2 Ischemic stroke incidence by interactions with hypertension, diabetes mellitus, hyperlipidemia, smoking, HDL-cholesterol, folate, and homocysteine.

Haplotype analysis with disease incidence

The linkage disequilibrium (LD) of MTHFR polymorphisms at loci 2572 (rs4846049)/4869, (rs1537514)/5488, (rs3737967)/6685 (rs4846048) in ischemic stroke patients and control subjects is shown in the Supplemental Figure 1. There was a strong LD between loci 4869/5488 (D’ = 0.944), 2572/5488 (D’ = 0.949), and 2572/4869 (D’ = 0.938). To evaluate the combined effects of the MTHFR 3′-UTR SNP loci on ischemic stroke incidence, logistic regression for the combined genotypes and haplotypes was performed. The 2572CC/4869CC/5488CC/6685TC (AOR, 0.095; 95% CI, 0.012–0.761; P = 0.027), 2572CA/4869CC/5488CC/6685TT (AOR, 2.922, 95% CI, 1.342–6.361; P = 0.007), 2572A-4869C-5488C-6685T (AOR, 0.062; 95% CI, 0.008–0.477; P = 0.001), and 2572A-4869C-5488C-6685T (AOR, 2.239, 95% CI, 1.178–4.257, P = 0.013) types contributed to ischemic stroke prevalence (Table 3). In the ischemic stroke subgroup, the MTHFR haplotypes were shown to have a significant association with CE subtype prevalence (Supplemental Table 3).

Table 3 Combined genotype and allele frequencies of the MTHFR 3′-UTR polymorphisms for ischemic stroke patients and control subjects.

Differences of blood coagulation factors according to MTHFR polymorphisms

Analyses of variance were used to show differences in blood coagulant factors (fibrinogen, antithrombin, platelet, activated partial thromboplastin time, and prothrombin time), folate, and tHcy levels according to genotype (Table 4). The tHcy levels in subjects with the MTHFR 2572AA polymorphism were elevated compared to the tHcy levels in subjects with the MTHFR 2572CC (P = 0.011). Additionally, the MTHFR 5488 and 6685 mutant genotypes had higher tHcy levels than that of the wild-type genotypes (MTHFR 5488, P = 0.020; MTHFR 6685, P = 0.005). Supplemental Table 4 shows the combination models with MTHFR 677 C > T, which measured the Hcy levels. The MTHFR 677-2572 combination group (677CC-2572AA: 12.14 ± 5.56; P = 0.010) and MTHFR 677-6685 combination group (677CC-6685CC: 14.61 ± 6.53; P < 0.0001) were significantly different compare to each wild type genotype.

Table 4 Altered plasma folate and homocysteine levels, and blood coagulation factors according to MTHFR genotypes.

Survival analysis of MTHFR polymorphisms and ischemic stroke mortality

During a mean follow-up period of 7 years, 98 patients (17.5%) died. We investigated whether the MTHFR 3′-UTR genotypes were associated with long-term overall survival (OS) after ischemic stroke using Kaplan-Meier analyses. However, we did not find significant associations with individual MTHFR 3′-UTR genotypes (Supplemental Figure 2).


Hcy is a well-known thrombotic factor in vascular diseases including coronary artery disease28, heart disease29, arteriosclerosis3,15, myocardial infarction30, venous thrombosis31, chronic kidney disease32, and ischemic stroke33,34,35. There is increasing evidence that Hcy may affect the coagulation system and the resistance of the endothelium to thrombosis36. Moreover, Hcy may interfere with the vasodilator and antithrombotic functions of nitric oxide37. Notably, vascular complications reported in patients with homocystinuria are related to thrombosis rather than atherosclerosis38, and a relationship between tHcy levels and the incidence of thrombotic events has recently been reported in patients with systemic lupus erythematosus30.

Previous studies have identified the MTHFR gene as being associated with ischemic stroke prevalence33,34,35,36,37. Numerous studies reported that MTHFR 677 C > T was associated with increased stroke risk34,35, likely because the MTHFR 677 T allele decreased MTHFR gene activity35. Other studies reported that the methylation pattern of CpG island regions in the MTHFR gene had decreased MTHFR activity, causing an abnormality for tHcy and serum folate levels that were associated with ischemic stroke occurrence36,37. Moreover, we have shown an association with ischemic stroke risk based on computational epigenetic profiling of CpG islands in the MTHFR gene37. However, epigenetic regulation of the MTHFR gene could occur via another mechanism that included RNA interference with miRNA binding. In addition, a previous study showed differential mRNA expression levels of the MTHFR gene according to 3′-UTR polymorphisms38,39.

Therefore, understanding the genesis of ischemic events due to decreased MTHFR activity might explain why 3′-UTR polymorphisms could affect ischemic events, stroke occurrence, and patient prognosis. Polymorphisms in the 3′-UTR region could affect mRNA stability and translation, which may significantly impact gene expression by abolishing, weakening, or creating miRNA binding sites. Currently, there are not sufficient data to indicate that miRNA binding activity is modulated depending on MTHFR 3′-UTR polymorphisms. One study reported that miR-149 binding activity was affected by the MTHFR 2572 C > A polymorphism in coronary heart disease risk38. Therefore, we investigated MTHFR 3′-UTR polymorphisms that have potential miRNA binding sites. We found that these regions were capable of binding with miRNA. Despite the lack of data, these miRNAs may be important genetic factors for the prevalence and progression of ischemic stroke because their expression is altered in some genotypes38.

In conclusion, we investigated the relationship of the MTHFR 2572 C > A and 6685 T > C polymorphisms with ischemic stroke incidence and progression. The MTHFR 2572 C > A and 6685 T > C polymorphisms were shown to increase the risk of embolisms of cardiac origin and ischemic stroke occurrence, and the prevalence of large-artery-origin ischemic stroke had a decreased odds ratio (OR) for the MTHFR 6685 T > C polymorphism. Moreover, the combination of MTHFR 2572CA + AA genotypes and serum folate levels or tHcy levels were synergic for ischemic stroke susceptibility, whereas other MTHFR 3′-UTR polymorphisms were not associated with serum folate and tHcy for ischemic stroke risk. Therefore, we hypothesized that the MTHFR 3′-UTR regulates one-carbon metabolism through miRNA binding. We found that these genotypes and haplotypes positively correlated with the occurrence and unfavorable prognosis of stroke, according to vascular disease risk factors, including hypertension, diabetes mellitus, HDL-C levels, tHcy levels, and folate levels.

This study has several limitations. First, the mechanisms by which 3′-UTR polymorphisms in the MTHFR gene affect stroke development remain unclear. Second, the controls in our study were not completely healthy because some of them were seeking medical attention. However, the recruitment of only healthy participants for imaging and laboratory tests would markedly reduce the enrollment number, and enrollment of participants without imaging and laboratory tests may produce other biases in vascular risk factor assessment. Third, information regarding additional environmental risk factors in stroke patients remains to be investigated. Finally, the population of this study was restricted to patients of Korean ethnicity. Although the results from this study provide the first evidence for 3′-UTR variants in MTHFR as potential biomarkers of stroke prevention and prognosis, a prospective study using a larger cohort of patients is warranted to validate these findings.


Ethics statement

All study protocols of participants were reviewed and approved by The Institutional Review Board of CHA Bundang Medical Center and followed the recommendations of the Declaration of Helsinki. Study subjects were recruited from the South Korean provinces of Seoul and Gyeonggi-do between 2000 and 2008. The Institutional Review Board of CHA Bundang Medical Center approved this genetic study in June 2000 and informed consent was obtained from the study participants.

Study population

We included 511 consecutive patients with ischemic stroke referred from the Department of Neurology at CHA Bundang Medical Center, CHA University. Ischemic stroke was defined as a stroke (a clinical syndrome characterized by rapidly developing clinical symptoms and signs of focal or global loss of brain function) with evidence of cerebral infarction in clinically relevant areas of the brain according to brain imaging using magnetic resonance imaging (MRI). The date and cause of death were identified using death certificates from the Korean National Statistical Office. Patients who were alive on Dec 31, 2012 were censored at that point. The death statistics of the Korean National Statistical Office have been previously reported to be reliable40.

Based on clinical manifestations and neuroimaging data, two neurologists classified all ischemic strokes into four causative subtypes using the TOAST criteria as follows: (1) large-artery disease (LAD), significant (≥50%) stenosis of a relevant cerebral artery confirmed by cerebral angiography; (2) small-vessel disease (SVD), an infarction lesion <15 mm in diameter, and classic lacunar syndrome without evidence of a cerebral cortical dysfunction or potentially detectable cardiac sources for embolism; (3) cardioembolism (CE), presumably due to an embolus arising in the heart, as detected by cardiac evaluation; and (4) undetermined pathogenesis, in which the cause of stroke could not be determined or patients with two or more potential causes41. The frequencies of the stroke subtypes were 40% LAD (n = 205), 29% SVD (n = 149), 11% CE (n = 55), and 20% undetermined pathogenesis (n = 102). These proportions are similar to previously reported values for the Korean population42.

We selected 411 sex- and age-matched (±5 years) control subjects from patients presenting at our hospitals during the same period for health examinations, including biochemical testing, electrocardiogram analyses, and brain MRI. Control subjects did not have a recent history of cerebrovascular disease or myocardial infarction. Exclusion criteria were the same as those used in the patient group. The demographic and laboratory data of patients with ischemic stroke, subtype patients [LAD, SVD, and CE] and control subjects are summarized in Table 5. In our sample, 43.1% and 42.1% of stroke patients and control subjects were male, respectively. The mean ages of stroke patients and the control population were 62.96 ± 10.90 years and 62.82 ± 10.61 years, respectively. There were few significant differences between the two groups. Ischemic stroke patients were significantly more likely to have metabolic syndrome, as well as DM, hypertension, fibrinogen, increased tHcy levels, and decreased folate levels (P < 0.05).

Table 5 Baseline characteristics of control and stroke patients

Estimation of tHcy and folate levels

Within 48 hours of stroke onset, we collected plasma samples to measure tHcy and folate levels. Twelve hours after the patient’s previous meal, we collected whole blood in a tube containing anticoagulant. Tubes were centrifuged for 15 minutes at 1000 × g to separate the plasma. The tHcy concentrations were measured using a fluorescent polarizing immunoassay with the IMx system (Abbott Laboratories, Chicago, IL, USA), and folate concentrations were measured using a radioimmunoassay kit (ACS 180; Bayer, Tarrytown, NY, USA).


DNA was extracted using the G-DEX blood extraction kit (iNtRON Biotechnology, Inc., Seongnam, Republic of Korea). The four best-studied SNPs in the MTHFR gene were determined by a documentary search, which included four 3′-UTR SNPs (2572 C > A, rs4846049; 4869 C > G, rs1537514; 5488 C > T, rs3737967; and 6685 T > C rs4846048). All SNP sequences were obtained from the HapMap database ( The MTHFR 2572 C > A and 4869 C > G polymorphisms were analyzed by the polymerase chain reaction-restriction fragment length polymorphism method. Real-time polymerase chain reaction (PCR) was used to analyze the MTHFR 5488 C > T and 6685 T > C polymorphisms. For each polymorphism, 30% of the PCR assay samples were randomly selected and repeated, and followed by DNA sequencing, to validate the RFLP findings. Sequencing was performed using an ABI 3730xl DNA Analyzer (Applied Biosystems, Foster City, CA, USA). The concordance of quality control samples was 100%.

Statistical analyses

To analyze baseline characteristics, we used chi-square tests for categorical data and Student’s t-tests or analyses of variance were used for continuous data. We estimated associations of MTHFR gene polymorphisms with ischemic stroke incidence using adjusted ratios (AORs) and 95% confidence intervals (CIs) from multivariate logistic regression analyses. Adjustments were performed for sex, age, HTN, DM, hyperlipidemia, and smoking, because they are well-established risk factors for ischemic stroke. To evaluate the impact of MTHFR gene polymorphisms on all-cause mortality, we conducted hazard ratios (HRs), and 95% CIs from Kaplan-Meier survival analyses. Analyses were performed using GraphPad Prism 4.0 (GraphPad Software Inc., San Diego, CA, USA) and Medcalc version (Medcalc Software, Mariakerke, Belgium). Haplotypes for multiple loci were estimated using the expectation-maximization algorithm with SNPAlyze (Version 5.1; DYNACOM Co. Ltd., Yokohama, Japan).