In silico analysis of the structural and functional implications of SLC19A1 R27H polymorphism.

In view of the documented association of solute carrier family 19 member 1 (SLC19A1) G80A (R27H) polymorphism with the risk for different types of cancers and systemic lupus erythematosus (SLE), we have reanalysed the case-control study on breast cancer to ascertain the conditions in which this polymorphic variant exerts the risk of breast cancer. Association statistics have revealed that this polymorphism exerts the risk for breast cancer under the conditions of low folate intake, and in the absence of well-documented protective polymorphism in cytosolic serine hydroxymethyltransferase. To substantiate this observation, we have developed a homology model of SLC19A1 using glycerol-3-phosphate transporter (d1pw4a) as a template where 73% of the residues were modelled at 90% confidence while 162 residues were modelled ab initio. The wild and mutant proteins shared same topology in S3, S5, S6, S7, S11 and S12 transmembrane domains. The topology varied at S1 (28-43 residue vs 28-44 residue), S2 (66-87 residue vs 69-87 residue), S4 (117-140 residue vs 117-139 residue), S8 (305-325 residue vs 305-324 residue), S9 (336-356 residue vs 336-355residue), and S10 (361-386 residue vs 361-385 residue) transmembrane domains between wild versus mutant proteins. S2 domain is shortened by three amino acid residues in the mutant while in other domains the difference corresponds to one amino acid residue. The 3DLigandSite analysis revealed that the metallic-ligand-binding sites at 273Trp, 277Asn, 379Leu, 439Phe and 442Leu are although unaffected, there is a loss of active sites corresponding to nonmetallic ligand binding. Tetrahydrofolate and methotrexate have lesser affinity towards the mutant protein than the wild protein. To conclude, the R27H polymorphism affects the secondary and tertiary structures of SLC19A1 with the significant loss in ligand-binding sites.

Neuro-fuzzy model of homocysteine metabolism.

In view of well-documented association of hyperhomocysteinaemia with a wide spectrum of diseases and higher incidence of vitamin deficiencies in Indians, we proposed a mathematical model to forecast the role of demographic and genetic variables in influencing homocysteinemetabolism and investigated the influence of life style modulations in controlling homocysteine levels. Total plasma homocysteine levels were measured in fasting samples using reverse phase HPLC. Multiple linear regression (MLR) and neuro-fuzzy models were developed. The MLR model explained 64% variability in homocysteine, while the neurofuzzy model showed higher accuracy in predicting homocysteine with a mean absolute error of 0.00002 µmol/L. Methylene tetrahydrofolate reductase (MTHFR) C677T, 5-methyltetrahydrofolate homocysteine methyltransferase (MTR) A2756G and 5- methyltetrahydrofolate homocysteine methyltransferase reductase (MTRR) A66G were shown to be positively associatiated with homocysteine, while nonvegetarian diet, serine hydroxymethyltransferase 1 (SHMT1) C1420T and TYMS 5'-UTR 28 bp tandem repeat exhibited negative association with homocysteine. The protective role of SHMT1 C1420T was attributed to more H-bonding interactions in the mutant modelled compared to the wild type, as shown through in silico analysis. To conclude, polymorphisms in genes regulating remethylation of homocysteine strongly influence homocysteine levels. The restoration of one-carbon homeostasis by SHMT1 C1420T or increased flux of folate towards remethylation due to TYMS 5'-UTR 28 bp tandem repeat or nonvegetarian diet can lower homocysteine levels.

Genetic and environmental influences on total plasma homocysteine and coronary artery disease (CAD) risk among South Indians.

BACKGROUND: Hyperhomocysteinemia, a documented risk factor for CAD is highly prevalent in Indians. The rationale behind the current study is to explore the genetic and environmental causes for such high prevalence as there are limited studies in this context. METHODS: A total of 108 CAD cases and 108 controls were analyzed for tHcy and 4 folate pathway genetic polymorphisms [methylene tetrahydrofolate reductase (MTHFR) C677T, 5-methyltetrahydrofolate homocysteine methyl transferase (MTR) A2756G, methionine synthase reductase (MTRR) A66G and glutamate carboxypeptidase II (GCPII) C1561T] using reverse phase HPLC and PCR-RFLP methods respectively. RESULTS: MTHFR 677T, MTRR 66A, GCPII 1561T, male gender, alcohol intake, smoking, diabetes, creatinine and hypertension were found to influence tHcy. After controlling for confounding factors, Hyperhomocysteinemia and two of its genetic determinants i.e. MTHFR C677T [OR: 1.96, 95% CI: 1.06-3.61] and GCP II C1561T [OR: 2.09, 95% CI: 1.09-3.97] were found to be associated with risk for CAD. Significant epistatic interactions were observed between MTHFR 677T/MTR 2756G and GCP II 1561T/MTRR 66G. Alcohol intake in subjects with MTR 2756G allele was found to inflate the risk for CAD [OR: 4.15, 95% CI: 1.35-12.69]. CONCLUSION: Hyperhomocysteinemia, C677T MTHFR and C1561T GCPII are risk factors for CAD. Potential gene--gene and gene--environment interactions indicate the need for multi-variate analyses for risk prediction.

Relationship between methionine synthase, methionine synthase reductase genetic polymorphisms and deep vein thrombosis among South Indians.

BACKGROUND: The rationale behind this study was to examine the relationship between polymorphisms in genes that regulate remethylation of homocysteine to methionine, i.e., methionine synthase (MTR A2756G) and methionine synthase reductase (MTRR A66G), and risk of deep vein thrombosis (DVT) in a South Indian cohort (163 DVT cases and 163 controls), as elevated homocysteine has been documented as an independent risk factor for DVT in the same cohort. METHODS: Plasma homocysteine analysis was carried out by reverse phase HPLC. The MTR A2756G and MTRR A66G genetic polymorphisms were detected using PCR-restriction fragment length polymorphism method. For statistical analyses, Fisher's exact test was used for categorical variables and Student's t-test and analysis of variance were used for continuous variables. RESULTS: The MTRR 66GG genotype was associated with a 2.74-fold [95% confidence interval (CI): 1.73, 4.34] risk of DVT. The MTR A2756G polymorphism was not a risk factor. MTRR GG/MTR AG and MTRR GG/MTR GG genotypes cumulatively were found to increase the risk of DVT by 2.38-fold (95% CI: 1.43, 3.96). A positive association was observed between plasma homocysteine and the MTRR G allele, and the MTR G allele was shown to have an additive effect. The risk associated with the MTRR 66GG genotype was further increased in subjects compound heterozygous for methylene tetrahydrofolate reductase (MTHFR) [odds ratio (OR): 3.46, 95% CI: 1.38, 8.63]. CONCLUSIONS: The MTRR 66GG genotype is a risk factor for DVT among South Indians. This risk is increased further in the presence of the MTHFR 677CT/1298AC genotype.