| Literature DB >> 21688148 |
Kamil K Hozyasz1, Adrianna Mostowska, Anna Szaflarska-Poplawska, Margarita Lianeri, Pawel P Jagodzinski.
Abstract
Celiac disease (CD) is a polygenic chronic enteropathy conferring an increased risk for various nutrient deficiency states. Hyperhomocysteinemia is a frequent finding in CD and may be related to the development of venous thrombosis, cardiovascular disease, and stroke in untreated CD patients. Recently, a possible excess in the frequency of the MTHFR c.677C>T (rs1801133) gene variant in CD patients was reported. The purpose of this study was to determine if there exist differences in the distribution of polymorphic variants of genes involved in homocysteine/methyl group metabolism between CD patients and the general population. A set of 10 gene polymorphisms (MTHFR rs1801133, MTR rs1805087, MTHFD1 rs2236225, MTRR rs1801394, CBS 844ins68, BHMT1 rs7356530 and rs3733890, BHMT2 rs526264 and rs625879, and TCN2 rs1801198) was tested in 134 patients with CD and 160 matched healthy controls. The frequency of the MTR rs1805087 GG genotype in CD patients was lower than in controls (0.01 and 0.06, respectively), although statistical significance was not achieved (P = 0.06). For the other analyzed polymorphisms, there was no evidence of difference in both allelic and genotypic distribution between cases and controls. The exhaustive Multifactor Dimensionality Reduction analysis revealed no combination of interactive polymorphisms predicting the incidence of CD. In contrast to the well-documented clinical observations of increased risks of vascular disease in patients with longstanding untreated CD, in our group of patients no significant association with CD was found for all tested polymorphic variants of genes involved in homocysteine metabolism. These findings should be replicated in studies with a larger sample size.Entities:
Mesh:
Substances:
Year: 2011 PMID: 21688148 PMCID: PMC3271217 DOI: 10.1007/s11033-011-1077-7
Source DB: PubMed Journal: Mol Biol Rep ISSN: 0301-4851 Impact factor: 2.316
Characteristics of the polymorphisms genotyped in the data set
| Gene symbol | Gene name | rs no. | SNP functiona | Protein effect | Locationb | Allelesc | MAFd |
|---|---|---|---|---|---|---|---|
|
| Betaine-homocysteine methyltransferase | rs7356530 | Intergenic | – | chr5:78400908 | A/g | 0.44 |
| rs3733890 | Missense | Gln239Arg | chr5:78421959 | a/G | 0.28 | ||
|
| Betaine-homocysteine methyltransferase 2 | rs526264 | Intron | – | chr5:78378410 | a/T | 0.43 |
| rs625879 | Intron | – | chr5:78381689 | G/t | 0.43 | ||
|
| Cystathionine-beta-synthase | 844ins68 | –e | – | chr21:44483195 | W/insf | 0.06 |
|
| Methylenetetrahydrofolate dehydrogenase 1 | rs2236225 | Missense | Arg653Gln | chr14:64908845 | C/t | 0.44 |
|
| 5,10-Methylenetetrahydrofolate reductase | rs1801133 | Missense | Ala222Val | chr1:11856378 | C/t | 0.32 |
|
| 5-Methyltetrahydrofolate-homocysteine methyltransferase | rs1805087 | Missense | Asp919Gly | chr1:237048500 | A/g | 0.25 |
|
| Methionine synthase reductase | rs1801394 | Missense | Met22Ile | chr5:7870973 | A/g | 0.45 |
|
| Transcobalamin II | rs1801198 | Missense | Arg259Pro | chr22:31011610 | C/g | 0.44 |
aAccording to the Single Nucleotide Polymorphism database (dbSNP)
bBased on UCSC Human Genome Browser, February 2009 human reference sequence (GRCh37)
cUppercase denotes the more frequent allele in the control samples
dMAF, minor allele frequency calculated from the control samples
e844ins68 is a 68 bp insertion in exon 8 of CBS
fW, wild allele; ins, allele with insertion
Conditions for the identification of methyl group metabolism gene polymorphisms
| Gene symbol | rs no. | Primers for PCR amplification (5′–3′) | Annealing temperature (°C) | PCR product length (bp) | Restriction enzyme | Allelesa | Restriction fragment length (bp) | |
|---|---|---|---|---|---|---|---|---|
| Genotype [1][1]b | Genotype [2][2]b | |||||||
|
| rs7356530 | F: GCTTACCACAAGTGAAATGACG R: GGAACTACGCAAATAGCCATC | 64.5 | 549 |
| A/g | 316, 233 | 316, 121, 112 |
| rs3733890 | F: GTTTCTGGTGCATCCCTAAGT R: TTGCAGTCAGGAGTGTGGTA | 64 | 190 | –c | a/G | –c | –c | |
|
| rs526264 | F: TGGCAAAGACAGGGAGTAGC R: CAGCTTCTTCAACGTGCTCA | 66 | 576 |
| a/T | 576 | 329, 247 |
| rs625879 | F: TTCTCCCTTTGTCCAGCAAC R: TTGAATCTGAGGAGGCCAGA | 66 | 136 | –c | G/t | –c | –c | |
|
| 844ins68 | F: GGGTTTCTCATCCTGCCTCT R: TCGTCCCCCAGTCTACTTTG | 64.2 | 470 | – | W/insd | 470 | 538 |
|
| rs2236225 | F: TTCTTCTCATTCTTCCTCACACC R: TCTGCTCCAAATCCTGCTTC | 66 | 416 |
| C/t | 255, 161 | 416 |
|
| rs1801133 | F: AGGCTGTGCTGTGCTGTTG R: CGCTGTGCAAGTTCTGGAC | 67 | 477 |
| C/t | 425, 52 | 260, 165, 52 |
|
| rs1805087 | F: GTTGGTGAAGGGAGAAGAAATG R: CTGAAGAATGGGGGTCTGTG | 60 | 583 |
| A/g | 583 | 381, 202 |
|
| rs1801394 | F: CCCCATTTTTCAGTTTCACTGT R: CACTTCCCAACCAAAATTCTTC | 53 | 228 | –c | A/g | –c | –c |
|
| rs1801198 | F: GCATTACAGGTGGGAAAGAGAC R: CCAGGGATCTCCATTTACTGTC | 67.2 | 525 |
| C/g | 363, 118, 24, 17, 3 | 481, 24, 17, 3 |
aUppercase denotes the more frequent allele in the control samples
b[1], allele 1; [2], allele 2
cGenotyping with the use of high resolution melting curve analysis (HRM)
dW, wild allele; ins, allele with insertion
Associations of homocysteine metabolism gene SNPs and risk of CD incidence
| Gene | rs no. | Genotype | CD cases (frequency) | Controls (frequency) | Odds ratio (95% CI) |
| Power (%)b | Sample size for 80% powerb |
|---|---|---|---|---|---|---|---|---|
|
| rs7356530 | AA | 49 (0.37) | 48 (0.30) | Referent | – | – | – |
| AG | 64 (0.48) | 84 (0.52) | 0.7464 (0.446–1.248) | 0.2641 | 23 | 674 | ||
| GG | 20 (0.15) | 28 (0.18) | 0.6997 (0.348–1.407) | 0.3154 | 18 | 888 | ||
| AG + GG | 84 (0.63) | 112 (0.70) | 0.7347 (0.451–1.197) | 0.2153 | 24 | 681 | ||
| MAF | 0.39 | 0.44 | – | – | – | – | ||
|
| rs3733890 | GG | 73 (0.55) | 84 (0.53) | Referent | – | – | – |
| AG | 50 (0.38) | 64 (0.40) | 0.8990 (0.553–1.460) | 0.6669 | 7 | 5330 | ||
| AA | 9 (0.07) | 12 (0.07) | 0.8630 (0.344–2.165) | 0.7533 | 6 | 10164 | ||
| AG + AA | 59 (0.45) | 76 (0.47) | 0.8933 (0.562–1.419) | 0.6326 | 8 | 4531 | ||
| MAF | 0.26 | 0.28 | – | – | – | – | ||
|
| rs526264 | TT | 49 (0.37) | 49 (0.31) | Referent | – | – | – |
| AT | 62 (0.47) | 83 (0.52) | 0.7470 (0.446–1.250) | 0.2663 | 23 | 676 | ||
| AA | 21 (0.16) | 28 (0.17) | 0.7500 (0.376–1.496) | 0.4137 | 14 | 1329 | ||
| AT + AA | 83 (0.63) | 111 (0.69) | 0.7477 (0.459–1.218) | 0.2420 | 22 | 758 | ||
| MAF | 0.39 | 0.43 | – | – | – | – | ||
|
| rs625879 | GG | 50 (0.38) | 51 (0.32) | Referent | – | – | – |
| GT | 62 (0.47) | 81 (0.51) | 0.7807 (0.468–1.302) | 0.3425 | 18 | 939 | ||
| TT | 20 (0.15) | 28 (0.17) | 0.7286 (0.364–1.458) | 0.3703 | 16 | 1109 | ||
| GT + TT | 82 (0.62) | 109 (0.68) | 0.7673 (0.473–1.245) | 0.2831 | 19 | 900 | ||
| MAF | 0.39 | 0.43 | – | – | – | – | ||
|
| 844ins68 | WWb | 123 (0.92) | 140 (0.88) | Referent | – | – | – |
| Wins | 11 (0.08) | 20 (0.12) | 0.6260 (0.288–1.359) | 0.2328 | 22 | 731 | ||
| insins | 0 (0.00) | 0 (0.00) | – | – | – | – | ||
| Wins + insins | 11 (0.08) | 20 (0.12) | 0.6260 (0.288–1.359) | 0.2328 | 22 | 731 | ||
| MAF | 0.04 | 0.06 | – | – | – | – | ||
|
| rs2236225 | CC | 30 (0.23) | 50 (0.31) | Referent | – | – | – |
| CT | 75 (0.56) | 79 (0.49) | 1.582 (0.911–2.748) | 0.1022 | 49 | 278 | ||
| TT | 28 (0.21) | 31 (0.20) | 1.505 (0.760–2.980) | 0.2393 | 31 | 489 | ||
| CT + TT | 103 (0.77) | 110 (0.69) | 1.561 (0.922–2.642) | 0.0963 | 38 | 374 | ||
| MAF | 0.49 | 0.44 | – | – | – | – | ||
|
| rs1801133 | CC | 53 (0.40) | 73 (0.46) | Referent | – | – | – |
| CT | 70 (0.52) | 72 (0.45) | 1.339 (0.826–2.171) | 0.2357 | 24 | 679 | ||
| TT | 11 (0.08) | 15 (0.09) | 1.010 (0.430–2.375) | 0.9817 | 5 | 1703634 | ||
| CT + TT | 81 (0.60) | 87 (0.54) | 1.282 (0.805–2.043) | 0.2947 | 18 | 958 | ||
| MAF | 0.34 | 0.32 | – | – | – | – | ||
|
| rs1805087 | AA | 87 (0.65) | 88 (0.55) | Referent | – | – | – |
| AG | 45 (0.34) | 63 (0.39) | 0.7225 (0.445–1.172) | 0.1874 | 26 | 598 | ||
| GG | 2 (0.01) | 9 (0.06) | 0.2248 (0.047–1.071) | 0.0603c | 50 | 267 | ||
| AG + GG | 47 (0.35) | 72 (0.45) | 0.6603 (0.412–1.059) | 0.0842 | 41 | 351 | ||
| MAF | 0.18 | 0.25 | – | – | – | – | ||
|
| rs1801394 | AA | 44 (0.33) | 47 (0.29) | Referent | – | – | – |
| AG | 65 (0.49) | 83 (0.52) | 0.8365 (0.495–1.413) | 0.5041 | 12 | 1799 | ||
| GG | 23 (0.17) | 30 (0.19) | 0.8189 (0.414–1.619) | 0.5653 | 10 | 2526 | ||
| AG + GG | 88 (0.67) | 113 (0.71) | 0.8319 (0.506–1.367) | 0.4673 | 11 | 1965 | ||
| MAF | 0.42 | 0.45 | – | – | – | – | ||
|
| rs1801198 | CC | 33 (0.25) | 50 (0.31) | Referent | – | – | – |
| CG | 69 (0.52) | 80 (0.50) | 1.307 (0.758–2.254) | 0.3353 | 20 | 805 | ||
| GG | 30 (0.23) | 30 (0.19) | 1.515 (0.775–2.962) | 0.2235 | 31 | 483 | ||
| CG + GG | 99 (0.75) | 110 (0.69) | 1.364 (0.813–2.286) | 0.2386 | 22 | 740 | ||
| MAF | 0.49 | 0.44 | – | – | – | – | ||
aChi-square analysis
bStatistical power and sample size were calculated using the Power and Sample Size Calculation program v. 2.1.30 based on uncorrected chi-square test procedure (program parameters: α = 0.05, n = number of case patients)
cFisher exact test
Results of gene–gene interactions analyzed by MDR method
| Genes and rs numbers | Testing balanced accuracya | Cross validation consistencyb |
|
|---|---|---|---|
|
| 0.4442 | 4/10 | 0.9980 |
|
| 0.5181 | 5/10 | 0.7260 |
|
| 0.4852 | 7/10 | 0.9480 |
|
| 0.5074 | 5/10 | 0.8130 |
aTesting balanced accuracy of classification of cases and controls in the testing dataset calculated as (Sensitivity + Specificity)/2
bCross validation consistency is the number of times the model was selected as the best model after tenfold cross validation runs
cSignificance of accuracy, empirical P value based on 1,000 permutations