Relationship between N-acetyltransferase 2 single-nucleotide polymorphisms and phenotype.
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ABSTRACT:
SUBMITTER: Hein DW
PROVIDER: S-EPMC2812573 | biostudies-literature | 2010 Feb
REPOSITORIES: biostudies-literature
Publications
Relationship between N-acetyltransferase 2 single-nucleotide polymorphisms and phenotype.
Hein David W DW Millner Lori M LM Leggett Carmine S CS Doll Mark A MA
Carcinogenesis 20091123 2
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Project description:ObjectivesThe purpose of this review was to evaluate the relationship between genetic polymorphisms and dental implant loss.Materials and methodsAll case-control studies examining single nucleotide polymorphisms (SNPs) and dental implant failure were considered. A Boolean search was conducted on PubMed and Scopus to find eligible studies.ResultsThe initial search produced 78 results. Twenty-one studies were considered for inclusion after review and 16 were included in the final review. Twenty-two different polymorphisms were analyzed and statistically significant correlation was found for IL-4, IL-1A, IL-1B, MMP-8, and MMP-1 polymorphisms for dental implant failure.DiscussionA limited number of comprehensive studies have been done in this field. Additional studies with larger sample sizes and different ethnic backgrounds need to be done to see if the results can be reproduced. Of the polymorphisms studied, the IL-4 (+33), MMP-8 (-799), MMP-1 (-519), and MMP-1 (-1607) polymorphisms show the greatest association with dental implant loss.
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Project description:Arylamine N-acetyltransferase 2 (NAT2) modifies drug efficacy/toxicity and cancer risk due to its role in bioactivation and detoxification of arylamine and hydrazine drugs and carcinogens. Human NAT2 alleles possess a combination of single nucleotide polymorphisms (SNPs) associated with slow acetylation phenotypes. Clinical and molecular epidemiology studies investigating associations of NAT2 genotype with drug efficacy/toxicity and/or cancer risk are compromised by incomplete and sometimes conflicting information regarding genotype/phenotype relationships. Studies in our laboratory and others have characterized the functional effects of SNPs alone, and in combinations present in alleles or haplotypes. We extrapolate this data generated following recombinant expression in yeast and COS-1 cells to assist in the interpretation of NAT2 structure. Whereas previous structural studies used homology models based on templates of N-acetyltransferase enzyme crystal structures from various prokaryotic species, alignment scores between bacterial and mammalian N-acetyltransferase protein sequences are low (approximately 30%) with important differences between the bacterial and mammalian protein structures. Recently, the crystal structure of human NAT2 was released from the Protein Data Bank under accession number 2PFR. We utilized the NAT2 crystal structure to evaluate the functional effects of SNPs resulting in the protein substitutions R64Q (G191A), R64W (C190T), I114T (T341C), D122N (G364A), L137F (A411T), Q145P (A434C), E167K (G499A), R197Q (C590A), K268R (A803G), K282T (A845C), and G286E (G857A) of NAT2. This analysis advances understanding of NAT2 structure-function relationships, important for interpreting the role of NAT2 genetic polymorphisms in bioactivation and detoxification of arylamine and hydrazine drugs and carcinogens.
| S-EPMC2507886 | biostudies-literature
Project description:Human N-acetyltransferase 1 (NAT1) alleles are characterized by one or more single nucleotide polymorphisms (SNPs) associated with rapid and slow acetylation phenotypes. NAT1 both activates and deactivates arylamine drugs and carcinogens, and NAT1 polymorphisms are associated with increased frequencies of many cancers and birth defects. The recently resolved human NAT1 crystal structure was used to evaluate SNPs resulting in the protein substitutions R64W, V149I, R187Q, M205V, S214A, D251V, E261K, and I263V. The analysis enhances knowledge of NAT1 structure-function relationships, important for understanding associations of NAT1 SNPs with genetic predisposition to cancer, birth defects, and other diseases.
| S-EPMC2265210 | biostudies-literature
Project description:BackgroundSeveral single-nucleotide polymorphisms (SNPs) associated with breast cancer risk have been identified through genome-wide association studies (GWAS). We investigated whether eight risk SNPs identified in GWAS were associated with breast cancer disease-free survival (DFS) and overall survival (OS) rates.Patients and methodsA cohort of 739 white women with early-stage breast cancer was genotyped for eight GWAS-identified SNPs (rs2981582, rs1219648 [FGFR2], rs3803662, rs12443621, rs8051542 [TOX3], rs999737 [RAD51L1], rs6504950 [17q23], and rs4973768 [3p24]). Relationships between SNPs and breast cancer outcomes were evaluated using Cox proportional hazard regression models. The cumulative effects of SNPs on breast cancer outcomes were assessed by computing the number of at-risk genotypes.ResultsAt a median follow-up of 121 months (range: 188-231 months) for survivors, 237 deaths (32%) and 186 breast cancer events (25%) were identified among the 739 patients. After adjusting for age, clinical stage, and treatment, rs12443621 (16q12; p = .03) and rs6504950 (17q23; p = .008) were prognostic for OS but not DFS. A higher risk for death was also found in the multivariable analysis of patients harboring three or four at-risk genotypes of the GWAS SNPs compared to patients carrying two or less at-risk genotypes (hazard ratio: 1.60, 95% confidence interval: 1.23-2.24; p = .0008).ConclusionThe study results suggest that previously identified breast cancer risk susceptibility loci, rs12443621 (16q12) and rs6504950 (17q23), may influence breast cancer prognosis or comorbid conditions associated with overall survival. The precise molecular mechanisms through which these risk SNPs, as well as others that were not included in the analysis, influence clinical outcomes remain to be determined.
| S-EPMC3662839 | biostudies-literature
Project description:ObjectiveTo investigate the relationship between therapeutic efficacy in children with asthma and interleukin-13 (IL-13) rs20541 polymorphisms.MethodsFifty children with moderate-to-severe asthma were assigned to the GG, GA, and AA groups according to the IL-13 gene locus rs20541 polymorphism. The patients received budesonide inhalation suspension 1 mg twice daily combined with fluticasone propionate 80 µg/inhalation. The improvement of clinical symptoms (gasping, coughing, and wheezing), improvement of lung function, and adverse reactions were observed.ResultsLung function did not significantly differ among three groups before treatment. After treatment, the time to symptom relief was significantly shorter in the GG group than that in the other two groups. The forced expiratory volume in one second and percent predicted peak expiratory flow were also significantly better in the GG group than in the other two groups.ConclusionBudesonide inhalation suspension combined with fluticasone propionate is an effective treatment regimen for moderate-to-severe asthma. Polymorphism of the IL-13 rs20541 locus may be correlated with therapeutic efficacy. Patients carrying the GG allele were more responsive than their counterparts with the GA or AA allele.
| S-EPMC7325458 | biostudies-literature
Project description:MicroRNAs (miRNAs) play an important role in the pathogenesis of sepsis, but the association of miRNAs single nucleotide polymorphisms (SNPs) and sepsis risk is not clear. We analyzed plasma levels of miR-187, miR-21, and miR-145 in 180 patients with sepsis and 180 healthy controls were analyzed, and the SNPs: rs12605436, rs13137, and rs353291 were detected by sequencing. Plasma levels of tumor necrosis factor (TNF)-α and interleukin (IL)-6 were measured in all subjects by enzyme-linked immunosorbent assay (ELISA). The results showed that the levels of TNF-α and IL-6 in the plasma of patients with sepsis were significantly higher than those in patients of the control group (P < .0001). Plasma levels of miR-187 in patients with sepsis were significantly lower than those in the control group, while those of miR-21 and miR-145 were significantly higher than those in the control group (P < .0001). Plasma levels of miR-187 in sepsis patients were inversely correlated with those of TNF-α and IL-6 (r = -0.2841, -0.2163), and plasma levels of miR-21 and miR-145 were positively correlated with those of TNF-α and IL-6 (r = 0.615, 0.3057, 0.4465, 0.2734). The T allele of the miR-187 SNP rs12605436 was found to be a risk factor for sepsis (OR = 1.403, 95% CI = 1.205-1.612, P < .001). The T allele of the miR-21 SNP rs13137 and the T allele of the miR-145 SNP rs353291 (OR = 0.685, 95% CI = 0.566-0.820, P < .001) were found to be a protective factor for sepsis (OR = 0.755, 95% CI = 0.632-0.896, P < .001). From our results, we can see that the plasma levels of miRNAs containing the SNPs rs12605436, rs13137, and rs353291 are associated with the occurrence of sepsis.
| S-EPMC6831168 | biostudies-literature
Project description:Recent literature has reported a higher occurrence of cognitive impairment among individuals with Age-related Macular Degeneration (AMD) compared to older adults with normal vision. This pilot study explored potential links between single nucleotide polymorphisms (SNPs) in AMD and cognitive status. Individuals with AMD (N = 21) and controls (N = 18) were genotyped for the SNPs CFHY402H, ARMS2A69S and FADS1 rs174547. Cognitive status was evaluated using the Montreal Cognitive Assessment. The two groups differed significantly on which subscales were most difficult. The control group had difficulty with delayed recall while those with AMD had difficulty on delayed recall in addition to abstraction and orientation. Homozygous carriers of the FADS1 rs174547 SNP had significantly lower scores than heterozygotes or non-carriers on the MoCA. The results suggest that the FADS1 SNP may play a role in visual impairment/cognitive impairment comorbidity as reflected in the poorer cognitive scores among homozygotes with AMD compared to those carrying only one, or no copies of the SNP.
| S-EPMC7596199 | biostudies-literature
Project description:Wolfram syndrome (WS) is a rare, progressive, neurodegenerative disorder that has an autosomal recessive pattern of inheritance. The gene for WS, wolfram syndrome 1 gene (WFS1), is located on human chromosome 4p16.1 and encodes a transmembrane protein. To date, approximately 230 mutations in WFS1 have been confirmed, in which nonsynonymous single nucleotide polymorphisms (nsSNPs) are the most common forms of genetic variation. Nonetheless, there is poor knowledge on the relationship between SNP genotype and phenotype in other nsSNPs of the WFS1 gene. Here, we analysed 395 nsSNPs associated with the WFS1 gene using different computational methods and identified 20 nsSNPs to be potentially pathogenic. Furthermore, to identify the amino acid distributions and significances of pathogenic nsSNPs in the protein of WFS1, its transmembrane domain was constructed by the TMHMM server, which suggested that mutations outside of the TMhelix could have more effects on protein function. The predicted pathogenic mutations for the nsSNPs of the WFS1 gene provide an excellent guide for screening pathogenic mutations.
| S-EPMC4592972 | biostudies-literature
Project description:BackgroundThe tripartite motif containing (TRIM)-22 participates in innate immune responses and exhibits antiviral activities. The present study aimed to assess of the relationship between TRIM22 single-nucleotide polymorphisms and clinical parameters with the coronavirus disease 2019 (COVID-19) infection severity.MethodsTRIM22 polymorphisms (rs7113258, rs7935564, and rs1063303) were genotyped using TaqMan polymerase chain reaction (PCR) assay in 495 dead and 497 improved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive patients.ResultsIn this study, the frequencies of TRIM22 rs1063303 GG, rs7935564 GG, and rs7113258 TT were significantly higher in dead patients than in improved patients, and higher viral load with low PCR Ct value was noticed in dead patients. The multivariate logistic regression analysis revealed that the lower levels of low-density lipoprotein (LDL), cholesterol, PCR Ct value, and lower 25-hydroxyvitamin D, and also higher levels of erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and TRIM22 rs1063303 GG, rs7113258 TT, and rs3824949 GG genotypes were related to the COVID-19 infection severity.ConclusionOur finding proved the probable relationship between the COVID-19 infection severity with the genotypes of TRIM22 SNPs and clinical parameters. More research is required worldwide to show the association between the COVID-19 infection severity and host genetic factors.
| S-EPMC9412778 | biostudies-literature
Project description:BackgroundSingle nucleotide polymorphisms (SNPs) interfere with the function of certain genes and thus may influence the probability of skin cancer. The correlation between SNPs and skin cancer (SC) lacks statistical power, however. Therefore, the purpose of this study was to identify the gene polymorphisms involved in skin cancer susceptibility using network meta-analysis and to determine the relationship between SNPs and SC risk.MethodsPubMed, Embase, and Web of Science were searched for articles including "SNP" and different types of SC as keywords between January 2005 and May 2022. The Newcastle-Ottawa Scale was used to assess bias judgments. The odds ratio (ORs) and their 95% confidence intervals (CIs) were determined to estimate heterogeneity within and between studies. Meta-analysis and network meta-analysis were carried out to identify the SNPs associated with SC. The P-score of each SNP was compared to obtain the rank of probability. Subgroup analyses were performed by cancer type.ResultsA total of 275 SNPs from 59 studies were included in the study. Two subgroup SNP networks using the allele model and dominant model were analyzed. The alternative alleles of rs2228570 (FokI) and rs13181 (ERCC2) were the first-ranking SNPs in both subgroups one and two of the allele model, respectively. The homozygous dominant genotype and heterozygous genotype of rs475007 in subgroup one and the homozygous recessive genotype of rs238406 in subgroup two were most likely to be associated with skin cancer based on the dominant model.ConclusionsAccording to the allele model, SNPs FokI rs2228570 and ERCC2 rs13181 and, according to the dominant model, SNPs MMP1 rs475007 and ERCC2 rs238406 are closely linked to SC risk.
| S-EPMC9975575 | biostudies-literature