TA Repeat Polymorphism Research Articles

EP376: NGS detection of NUDT15 6-bp insertion and UGT1A1 (TA) repeat polymorphism on a preventative genomics assay

Application of Next-Generation Sequencing (NGS) for pharmacogenetic analysis provides cost-effective and high-throughput alternatives to other genotyping methodologies, making it a method of choice for pharmacogenetic testing. However, the nature of short-read sequencing technologies may carry challenges when it comes to the detection of specific complex structures/variants such as large insertion/deletions (indels), or repeat polymorphisms. These limitations can be overcome by the design of sequencing probes and optimized NGS library preparation process, as well as customized bioinformatic analysis pipelines. UGT1A1 is an important pharmacogene that impacts response to multiple drugs, including the HIV treatment, Atazanavir. The TA repeat polymorphism, rs3064744, is identified across various geographic, ethnic and racial populations and causes reduction in gene activity, resulting in toxicity and dosage effects. NUDT15 plays an important role in the metabolism of thiopurines. The rs746071566 microsatellite polymorphism, c.38GAGTCG[4] (p.13GV[4]), plays a critical role in thiopurine-induced adverse reactions and has been identified as a commonly observed variant in pan-ethnic populations. The current study evaluated the performance of a targeted NGS capture and bioinformatics platform to identify the promoter (TA)7 repeat polymorphism UDP glucuronosyl-transferase UGT1A1, as well as a 6 bp insertion NUDT15 variant. Both variants were analyzed as a part of a 455 gene panel utilized for a preventative genomics assay. The study consisted of 413 validation samples analyzed for UGT1A1 (rs3064744), and 186 analyzed for NUDT15 (rs746071566). The specimens were retrieved from various sources: DNA from Coriell Repository, and DNA isolated from whole blood and saliva by the Maxwell RSC Blood DNA Kit (Promega, Madison, Wisconsin) on the automated Maxwell RSC 48 Instrument (Promega). Sequencing was performed using custom-designed targeted capture and Fast Hybridization Target Enrichment workflow (Twist Bioscience, South San Francisco, CA). The samples were prepared using 50 ng of input DNA and the Twist EF Library Prep Kit 2.0 + UDIs and Fast Hyb reagents (Twist Bioscience), and run in a format of 12 samples per pool and 36 per single run on MiniSeq System (Illumina, San Diego, CA). Selected samples were confirmed using Sanger sequencing. The data was analyzed using the Edico Dragen server (Illumina), and in-house developed proprietary pipeline. For the purpose of this study, the reference ranges were defined for UGT1A1 as *1 AT[7], *28 AT[8], *36 AT[6] and *39 AT[9]. The genotypes frequency detected for UGT1A1 rs3064744 were as follow: AT[7]/AT[6] 0.97%, AT[7]/AT[7] 62%, AT[7]/AT[8] 24%, AT[7]/AT[9] 0.97%, AT[8]/AT[8] 11.8%, AT[9]/AT[9] 0.24%; and for NUDT15 rs746071566 GGAGTC[1]/GGAGTC[1] 99.5%, GGAGTC[1]/GGAGTC[2] 0.5% and GGAGTC[1]/GGAGTC[0] 0%. This data is comparable to the frequency published in the gnomAD database. Additionally, Sanger confirmation analysis performed for selected Coriell samples yielded 100% concordance between NGS and Sanger sequencing data. As previously reported, ∼14% of variants (eg, indels, small CNVs, and complex changes) identified during NGS analysis can impose technical difficulties resulting in decreased detection rates. Both of the variants investigated in this study (UGT1A1 rs3064744 and NUDT15 rs746071566) belong to this group of challenging variants, and thus require specific consideration during the analytical and bioinformatic design and validation. The NGS capture presented in this study was iteratively designed to optimize the ability to sequence across these regions. Performance data for these variants is dependent on wet laboratory procedure and bioinformatic variant assembly because standard VCF calling software packages do not account for repetitive elements. The in-house developed bioinformatic script accurately translated the output of the VCF pipeline into the genotype calls. The comparability of the obtained genotype frequencies with the published data in gnomAD further confirmed the accuracy of the assay performance. Analysis of the samples using Sanger sequencing further confirmed data received on NGS analysis.

Functional genetic variants of the IFN-λ3 (IL28B) gene and transcription factor interactions on its promoter

Interferon lambda 3 (IFN-λ3 or IFNL3, formerly IL28B), a type III interferon, modulates immune responses during infection/inflammation. Several human studies have reported an association of single nucleotide polymorphisms (SNP) in the IFNL3 locus with expression level of IFNL3. Previous genetic studies, in the context of hepatitis C virus infections, had predicted three regulatory SNPs: rs4803219, rs28416813 and rs4803217 that could have functional/causal roles. Subsequent studies confirmed this prediction for rs28416813 and rs4803217. A dinucleotide TA-repeat variant (rs72258881) has also been reported to be regulating the IFN-λ3 promoter. In this study, we tested all these genetic variants using a sensitive reporter assay. We show that the minor/ancestral alleles of both rs28416813 and rs4803217, together have a strong inhibitory effect on reporter gene expression. We also show an interaction between the two principal transcription factors regulating IFNL3 promoter: IRF7 and NF-kB RelA/p65. We show that IRF7 and p65 physically interact with each other. By using a transient ChIP assay, we show that presence of p65 increases the promoter occupancy of IRF7, thereby leading to synergistic activation of the IFNL3 promoter. We reason that, in contrast to p65, a unique nature of IRF7 binding to its specific DNA sequence makes it more sensitive to changes in DNA phasing. As a result, we see that IRF7, but not p65-mediated transcriptional activity is affected by the phase changes introduced by the TA-repeat polymorphism. Overall, we see that three genetic variants: rs28416813, rs4803217 and rs72258881 could have functional roles in controlling IFNL3 gene expression.

Pazopanib-Induced Liver Toxicity in Patients With Metastatic Renal Cell Carcinoma: Effect of UGT1A1 Polymorphism on Pazopanib Dose Reduction, Safety, and Patient Outcomes.

Pazopanib can induce liver toxicity in patients with metastatic renal cell carcinoma (mRCC). We assessed the effect of a TA repeat polymorphism in the UGT1A1 (uridine diphosphate glucuronosyltransferase 1A1) gene encoding uridine diphosphate glucuronosyltransferase 1A1 on liver toxicity, dose reductions, and patient outcomes. Patients with mRCC treated with first-line pazopanib developing liver toxicity underwent genotyping for the UGT1A1 polymorphism. Liver toxicity was assessed using the Common Terminology Criteria for Adverse Events, version 4.0. Progression-free survival and overall survival were assessed using the Kaplan-Meier and log-rank methods. Of 261 patients, 34 (13%) had developed liver toxicity after a median of 29 days (range, 5-155 days). Grade 4, 3, and 2 alanine aminotransferase or bilirubin had increased in 2 (6%), 17 (50%), and 8 (24%) patients, respectively. The UGT1A1 assessment demonstrated that 18 patients (53%) had TA6/TA7, 7 (21%) had TA7/TA7, and 9 (26%) had wild-type TA6/TA6. The UGT1A1 polymorphism was associated with improved median progression-free survival (TA6/TA6, 5.5 months; TA6/TA7, 34.2 months; TA7/TA7, 22.3 months; unknown UGT1A1 status, 9.2 months; UGT1A1 polymorphisms combined vs. unknown status, P= .021). UGT1A1 polymorphism was associated with improved median overall survival (TA6/TA6, 8.1 months, TA6/TA7 or TA7/TA7 not reached, unknown UGT1A1 status, 16.6 months; UGT1A1 polymorphisms combined vs. unknown status, P= .033). Patients with UGT1A1 polymorphism safely resumed pazopanib at ultra-low doses determined by the degree of liver toxicity and UGT1A1 polymorphism. UGT1A1 polymorphisms were associated with improved outcomes, despite pazopanib interruption and dose reductions. UGT1A1 assessment could improve the management of pazopanib-induced liver toxicity in patients with mRCC.

Association of estrogen, progesterone and follicle stimulating hormone receptor polymorphisms with in vitro fertilization outcomes

ABSTRACTDespite the advances in in vitro fertilization (IVF), the implantation success rate for infertile women remains approximately only 15%. In this study, we sought to determine whether implantation failure after repeated IVF treatments is influenced by the presence of common variants in estrogen α, progesterone and follicle stimulating hormone receptor genes. The study population included three groups of women: group 1 were 50 women who had the transfer of ≥3 high-quality embryos during the IVF procedure without ever having had a clinical pregnancy; group 2 were 50 women who achieved a clinical pregnancy after ≤3 high-quality embryos transfers and group 3 were 50 control subjects who achieved a clinical pregnancy without any fertility therapy that resulted in a one live-born infant. Genotype analysis was performed using polymerase chain reaction and Sanger sequencing for rs6165, rs6166, rs2234693, rs9340799. While progesterone receptor single nucleotide polymorphism (SNP) was genotyped based on the amplicon size, the repeats for the ESR1 TA-repeat polymorphism were calculated based on the fragment length. A higher frequency of the heterozygote AG genotype was observed in the infertile groups when compared to controls. Significantly, an allele combination of T of rs2234693, A of rs9340799; S of ESR1 (TA), A of rs6166, G of rs6165 and del of PROGINS had a higher frequency in women who had a successful IVF outcome compared to women who had an unsuccessful IVF outcome, indicating a possible protective combined genotype that could reduce a negative outcome during IVF. This study has demonstrated that combining several candidate genes is needed to assess which may play a role in fertility.Abbreviations: CI: confidence interval; COH: controlled ovarian hyperstimulation; DNA: deoxyribonucleic acid; ESR: estrogen receptors; FSH: follicle stimulating hormones; FSHR: FSH receptor; IVF: in vitro fertilization; PGR: progesterone receptors; SNP: single nucleotide polymorphism

Longer TA repeat but not V89L polymorphisms in the SRD5A2 gene may confer acne risk in the Chinese population.

IntroductionSeveral studies have reported that the V89L and TA repeat polymorphisms [(TA)n] of the SRD5A2 gene were associated with SRD5A2 activity. The activity of dihydrotestosterone, which is converted from testosterone by SRD5A2, is responsible for sebum secretion and the formation of acne. We hypothesized that abnormalities in SRD5A2 action could contribute to the formation of acne.AimTo study whether the structural change of the SRD5A2 gene may affect the risk of acne in patients with normal serum testosterone levels.Material and methodsGenotyping of rs523349 and (TA)n of SRD5A2 was performed in 49 Chinese acne patients with significant improvements with SRD5A2 inhibitor-finasteride but normal serum testosterone levels, and in 50 healthy Chinese age-matched controls without acne.ResultsThere was no significant difference between the two groups in the frequencies of V and L alleles and VV, VL, and LL genotypes of V89L (χ2 test, p > 0.5). (TA)n polymorphic repeat sites are 5 alleles (TA0, TA3, TA6, TA9, TA12) in our population. The differences in S and L allele frequencies between the two groups were statistically significant (p < 0.005). People with a longer (n ≥ 6) allele of the (TA)n repeat polymorphism had a higher risk of having acne than those with a shorter (n < 6) allele (OR = 3.52, 95% CI: 1.73–7.16).ConclusionsThis study suggests that SRD5A2 polymorphisms might be associated with acne risk. This is the first report focusing on the Chinese population according to our knowledge. Further large sample studies may be required to confirm the association and to assess any interactions with environmental factors.

Associations between the SRD5A2 gene V89L and TA repeat polymorphisms and breast cancer risk: a meta-analysis.

The 5α-reductase type 2 (SRD5A2) gene plays a significant role in the development of breast cancer. The V89L and TA repeat polymorphisms of the SRD5A2 gene have been considered as risk factors for breast cancer. However, the results have been inconsistent. To resolve this conflict, we performed a meta-analysis of studies with V89L (1144 patients and 808 controls) and with TA repeat genotyping (1952 cases and 1008 controls). The associations were evaluated by calculating odds ratios (ORs) and 95% confidence intervals (CIs). The result showed that there was no relationship between the V89L polymorphism of the SRD5A2 gene (V/V versus V/L + L/L genotypes) and breast cancer susceptibility (OR = 1.21; 95%CI = 0.99-1.47; P = 0.28). In addition, there was no difference between patients with breast cancer and healthy people in the distributions of the L allele (OR = 1.06; 95%CI = 0.75-1.49; P = 0.003). Similarly, no significant association between the SRDA5A2 TA repeat polymorphism and breast cancer risk was discovered. The comparison of (TA)0/(TA)0versus (TA)0/(TA)9 + (TA)9/(TA)9 genotypes found no difference in the risk of breast cancer (OR = 0.91; 95%CI = 0.66-1.25; P = 0.05). The OR for the (TA)0 versus (TA)9 allele was 0.89 (95%CI = 0.67-1.19). In conclusion, the V89L and TA repeat polymorphisms of SRD5A2 gene were found to have no significant associations with breast cancer risk.

A49T, R227Q and TA repeat polymorphism of steroid 5 alpha-reductase type II gene and Hypospadias risk in North Indian children

Background/AimsHypospadias is a common congenital error of genital development, the frequency of which is increasing. As androgens have a significant role in the development of the male urethra, we sought to investigate the association between functional polymorphisms of SRD5A2 gene in relation to hypospadias. MethodsWe examined DNA samples of 96 cases and 105 controls for SRD5A2-A49T, R227Q and TA repeat gene polymorphisms. ResultAbsence of 49T locus and 227Q locus was observed in the present study. At the (TA) n repeat site, TA (0) allele was observed to be the most common allele in both cases (91.7%) and controls (90%). TA (9/9) genotype exhibited an odds ratio of 3.03 (95% C.I.=0.18–50.14, p=0) with respect to only middle phenotypes. Analysis of the demographic data depicted the agricultural background aspect of the parents of the cases. 72.27% of the cases (affected with Hypospadias) have parents having agriculture as a primary occupation. ConclusionAs longer TA repeats are associated with lower enzymatic activity and lower DHT levels as reported among Caucasians, this polymorphism may have an effect (rather small) in predisposing the population of the present study to the risk of Hypospadias of lesser severity. Due to small sample size, the 3.03 O.R. is not significant and a larger sample is needed to validate the results.Large scale screening of Hypospadias and other 46 X,Y disorders of sexual development is needed especially in India, where the majority of the population is from agricultural background. The results of the present study are likely to assist the health planners to initiate screening of Hypospadias among the farmer community to combat the risk of Hypospadias.

Association of Benign Prostate Hyperplasia with Polymorphisms in VDR, CYP17, and SRD5A2 Genes among Lebanese Men

The aim of the study was to investigate any associations between benign prostate hyperplasia (BPH) and single nucleotide polymorphisms (SNPs) in the VDR gene (FokI, BsmI, ApaI and TaqαI loci) and the CYP17 gene (MspA1I locus), as well as TA repeat polymorphism in SRD5A2 gene among Lebanese men. DNA extracted from blood of 68 subjects with confirmed BPH and 79 age-matched controls was subjected to PCR/PCR-restriction fragment length polymorphism analysis. The odds ra=tio (OR) of having a genotype and the relative risk (RR) of developing BPH for having the genotype were calculated and the alleles were designated risk-bearing or protective. Our data indicated that the A and B alleles of the VDR ApaI and BsmI SNPs were highly associated with increased risk of BPH (p=0.0168 and 0.0002, respectively). Moreover, 63% of the controls compared to 43% of the subjects with BPH were homozygous for none of the risk-bearing alleles (p=0.0123) whereas 60% of the controls and 28% of the subjects with BPH were homozygous for two or more protective alleles (p<0.0001). For the first time, our study demonstrated that ApaI and BsmI of the VDR gene are associated with risk of BPH among Lebanese men. Our study also indicated that overall polymorphism profile of all the genes involved in prostate physiology could be a better predictor of BPH risk.

Lack of association between the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene polymorphism and the risk of benign prostatic hyperplasia in Caucasian men

Glucuronidation, mediated by the UDP-glucuronosyltransferase 1A1 (UGT1A1) enzyme, is an important metabolic process during which steroids are converted to more easily excreted compounds in steroid target tissues, such as the prostate. The aim of our study was to investigate the possible correlation between UGT1A1 promoter gene polymorphism and benign prostatic hyperplasia. 421 blood samples were obtained from 138 consecutive patients diagnosed with benign prostatic hypeplasia (BPH group) and 283 healthy volunteers (control group). A(TA)6TAA promoter polymorphism of UGT1A1 gene was studied using the Fragment Analysis Software of an automated DNA sequencer and three genotypes (homozygous 7/7, heterozygous 6/7 and normal homozygous 6/6) were identified. No significant differences were observed between the BPH group and controls regarding the genotyping distribution of the three UGT1A1 promoter genotypes (P=0.39). Also, no association was found between overall disease risk and the presence of the polymorphic homozygous genotype (TA(7)/TA)7) vs. TA(6)/TA(7)+TA(6)/TA(6)) (P=0.31). Our data suggest that the TA repeat polymorphism of UGT1A1 is not associated with increased BPH risk susceptibility in Caucasian men.

Simple and precise detection of UGT1A1 polymorphisms with a modified loop-hybrid mobility shift assay using Cy5-labeled loop probes

BackgroundIrinotecan, an inhibitor of topoisomerase I, has been widely used as an important anti-cancer therapeutic drug. Deleterious effects of the drug in hypersensitive patients are known to be associated with genetic polymorphisms of the UGT1A1 gene, namely the polymorphic variants, ⁎28 and ⁎6. MethodsA modified form of loop-hybrid mobility shift assay using a Cy5-tagged loop-hybrid probe was proposed as a precise and easy method of determining TA repeat polymorphisms at the ⁎28 locus. ResultsIn this modified method, only loop-hybrid bands were detected by a Cy5-fluorescent signal, despite several irregular electrophoretic bands due to TA repeats in the PCR product. ConclusionsWhen a loop-hybrid using a Cy5-tagged probe for the ⁎28 locus and ⁎6 locus were combined and used for mobility shift assay, simultaneous typing of the ⁎28 and ⁎6 variants was achieved in a single lane.

Serum Bilirubin Links UGT1A1*28 Polymorphism and Predicts Long-Term Cardiovascular Events and Mortality in Chronic Hemodialysis Patients

Bilirubin is a protective factor with antioxidant and anti-inflammatory properties, but its association with clinical outcomes of hemodialysis patients is unknown. Bilirubin degradation is mainly determined by the activity of hepatic bilirubin uridine diphosphate-glucuronosyltransferase (UGT1A1), which is significantly influenced by a TA-repeat polymorphism in the gene's promoter, an allele designated UGT1A1*28. The study aimed to clarify the association between serum bilirubin and UGT1A1*28 polymorphism and their respective effect on outcomes of chronic hemodialysis patients. The cohort study comprised 661 chronic hemodialysis patients who were prospectively followed for 12 years. The endpoints were cardiovascular events (CVEs) and all-cause mortality. After adjustment for traditional and dialysis-related risk factors, individuals with bilirubin in the upper tertile had an adjusted hazard ratio of 0.32 for CVEs and 0.48 for all-cause mortality compared with those in the lower tertile. Individuals homozygous for UGT1A1*28 (genotype 7/7) had significantly higher bilirubin levels than those with 6/6 and 7/6 genotypes. In the same multivariable-adjusted model, individuals with 7/7 had approximately one tenth the risk for CVEs and one fourth the risk for all-cause mortality as compared with carriers of the 6 allele. A graded, reverse association was noted between serum bilirubin and adverse outcomes among chronic hemodialysis patients. Moreover, the UGT1A1*28 polymorphism had strong effects on bilirubin levels and the 7/7 genotype might have an important effect on reducing CVEs and death.

Meta-analysis of three polymorphisms in the steroid-5-alpha-reductase, alpha polypeptide 2 gene (SRD5A2) and risk of prostate cancer

The steroid-5-alpha-reductase, alpha polypeptide 2 (SRD5A2) gene plays a crucial role in androgen metabolism pathway in human prostate. It encodes SRD5A2 enzyme, which catalyses testosterone to dihydrotestosterone (DHT). DHT is the main active structure binding with androgen receptor (AR). After the activation of AR, it further regulates a series of target genes in androgen metabolism pathway. However, no clear consensus has been reached on the association between the SRD5A2 V89L, A49T and TA repeat polymorphisms and prostate cancer (PCa) risk. Thus, we performed a meta-analysis of 31 association studies with 14,726 PCa cases and 15,802 controls. We found no association between PCa and 89L compared with 89V allele [odds ratio (OR) = 1.02, 95% confidence interval (CI) 0.98-1.06, P(heterogeneity) = 0.44]. The 49T allele showed a significantly elevated effect on the high stage (Stages III-IV) of PCa risk both under the dominant genetic model (OR = 2.13, 95% CI 1.44-3.15, P(heterogeneity) = 0.65) and in the contrast T versus A allele (OR = 2.06, 95% CI 1.41-3.02, P(heterogeneity) = 0.69). There was a significantly decreased association between PCa and long TA repeat as compared versus short TA repeat (OR = 0.86, 95% CI 0.74-1.00, P(heterogeneity) = 0.79). No significant between-study heterogeneity was found in all subjects under four genetic models (dominant model, recessive model, allele comparison and homozygosity comparison) for these three polymorphisms, respectively, so the fixed effects model was used to pool the result. Our result indicated that carriers of 49T might improve the risk of PCa in higher stages (Stages III-IV), carriers of long TA repeat might decrease the risk of PCa and 89L may not be an important risk factor for PCa. However, due to the limited sample sizes, this meta-analysis did not achieve sufficiently conclusive results. Still more well-designed studies should be performed to clarify the role of these three polymorphisms in the development of PCa.

Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism

Background:Pazopanib has shown clinical activity against multiple tumour types and is generally well tolerated. However, isolated elevations in transaminases and bilirubin have been observed. This study examined polymorphisms in molecules involved in pharmacokinetic and pharmacodynamic pathways of pazopanib and their association with hepatic dysfunction.Methods:Twenty-eight polymorphisms in 11 genes were evaluated in pazopanib-treated renal cell carcinoma patients. An exploratory analysis was conducted in 116 patients from a phase II study; a replication study was conducted in 130 patients from a phase III study.Results:No polymorphisms were associated with alanine aminotransferase elevation. The Gilbert's uridine-diphosphoglucuronate glucuronosyltransferase 1A1 (UGT1A1) TA-repeat polymorphism was significantly associated with pazopanib-induced hyperbilirubinemia in the phase II study. This association was replicated in the phase III study (P<0.01). Patients with TA6/TA6, TA6/TA7, and TA7/TA7 genotypes experienced median bilirubin increases of 0.31, 0.37, and 0.71 × upper limit of the normal range (ULN), respectively. Of the 38 patients with hyperbilirubinemia (⩾1.5 × ULN), 32 (84%) were either TA7 homozygotes (n=18) or TA7 heterozygotes (n=14). For TA7 homozygotes, the odds ratio (95% CI) for developing hyperbilirubinemia was 13.1 (5.3–32.2) compared with other genotypes.Conclusions:The UGT1A1 polymorphism is frequently associated with pazopanib-induced hyperbilirubinemia. These data suggest that some instances of isolated hyperbilirubinemia in pazopanib-treated patients are benign manifestations of Gilbert's syndrome, thus supporting continuation of pazopanib monotherapy in this setting.

Genetic polymorphisms in the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene and prostate cancer risk in Caucasian men

Background: Catechol-estrogen metabolites can induce carcinogenesis by acting as endogenous tumor initiators. Glucuronidation, mediated by the UDP-glucuronosyltransferase 1A1 (UGT1A1) enzyme, is a main metabolic pathway of estrogen detoxification in steroid target tissues, such as the prostate. The aim of our study was to investigate the possible correlation between UGT1A1 promoter gene polymorphisms and prostate cancer risk. Patients and methods: 129 patients with prostate cancer and 260 healthy controls were included in our study. A(TA)TAA promoter polymorphism of UGT1A1 gene was studied using the Fragment Analysis Software of an automated DNA sequencer and three genotypes (homozygous 7/7, heterozygous 6/7 and normal homozygous 6/6) were identified. Results: No significant differences were observed between the cancer group and controls regarding the genotyping distribution of the three UGT1A1 promoter genotypes ( P > 0.05). Also, no association was found between overall disease risk and the presence of the polymorphic homozygous genotype (TA(7)/TA(7) vs TA(6)/TA(7) + TA(6)/TA(6)) ( P = 0.18). In addition, no association was revealed between UGT1A1 genotype distribution and Gleason score ( P = 0.55). Conclusion: Our data suggest that the TA repeat polymorphism of UGT1A1 gene does not seem to alter prostate cancer risk susceptibility in Caucasian men.

The association between TA-repeat polymorphism in the promoter region of UGT1A1 and breast cancer risk: a meta-analysis

Uridine diphospho-glucuronosyltransferase 1A1 (UGT1A1) plays an important role in breast cancer development. To date, many publications have evaluated the correlation between UGT1A1 TA-repeat polymorphism and breast cancer risk. However, the results remain inconclusive. In order to resolve this conflict, a meta-analysis was performed by searching Medline, PubMed, and ISI Web of Knowledge databases. Seven studies including 5,746 cases and 8,365 controls were collected for UGT1A1 TA-repeat polymorphism. The strength of association between UGT1A1 TA-repeat polymorphism and breast cancer risk was assessed by calculating crude ORs with 95% CIs. Overall, no significant associations between UGT1A1 TA-repeat polymorphism and breast cancer susceptibility were found. In the stratified analysis by ethnicity and source of controls, significant associations were only observed for 6/6 versus 7/7 (OR = 0.88; 95% CI: 0.77-0.99; P = 0.425 for heterogeneity) in Caucasians, but no in other genetic models. In conclusion, this meta-analysis suggests that UGT1A1 A(TA)(7)TAA allele is a potential risk factor for breast cancer in Caucasians.

Hyperbilirubinemia in Lapatinib Treated Patients Is Associated with Gilbert's Syndrome UGT1A1 Polymorphism.

Abstract Background: Lapatinib, an oral EGFR/HER2 tyrosine kinase inhibitor, is approved in combination with capecitabine for the treatment of patients with advanced or metastatic HER2-positive breast cancer who have been treated previously with an anthracycline, taxane and trastuzumab. Treatment associated elevations in transaminases and bilirubin have been observed in lapatinib clinical trials. A common TA repeat polymorphism in the promoter region of uridine diphosphoglucuronyl transferase (UGT1A1*28, TA7 allele) reduces UGT1A1 enzyme levels and has been associated with hyperbilirubinemia for a range of drugs. We sought to determine the effect of the UGT1A1*28 variant on bilirubin elevation in lapatinib treated patients.Patients and Methods: Association between the UGT1A1 TA repeat polymorphism and total bilirubin levels (TBL) was examined in lapatinib treated patients using data pooled from 12 trials in advanced and metastatic breast cancer. A total of 899 lapatinib treated (as monotherapy or combined with chemotherapy) patients provided a germline DNA sample and were available for this analysis. UGT1A1 TA repeat genotype was determined by PCR amplification and sequencing. For case-control analysis, patients were defined as having normal TBL at baseline, with on-treatment TBL ≥1.5 and ≤1 times upper limit of normal for cases and controls, respectively, and at least 13 weeks of treatment for controls.Results: The UGT1A1 TA repeat polymorphism strongly correlated with lapatinib associated hyperbilirubinemia. A significant association (P=1.03x10-5, 60 cases and 396 controls) was observed. For hyperbilirubinemia cases, 21/60 (35%) were carriers of two TA7 alleles and 28/60 (47%) were carriers of one TA7 allele. Overall, when compared with other genotypes, the odds ratio (95% confidence interval) of the TA7/TA7 genotype for developing hyperbilirubinemia was 10.7 (5.3-21.6).Conclusion: These data suggest that UGT1A1*28 accounts for the major proportion of total bilirubin elevation observed during lapatinib treatment. This is consistent with an underlying predisposition to Gilbert's syndrome. Given the life-threatening nature of advanced and metastatic breast cancer and the benign clinical course of Gilbert's syndrome, these data support treatment continuation with lapatinib for patients with mild to moderate, isolated, indirect bilirubin elevation, when accompanied by appropriate ongoing safety evaluation (eg, bilirubin fractionation, ALT evaluation) to exclude liver injury risk in these patients. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1112.

Uridine diphosphate glucuronosyl transferase 1A1 promoter polymorphism is associated with choledocholithiasis in Taiwanese patients

The gene product of the uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1) is crucial to bilirubin metabolism. Mutations in this gene subsequently result in disease presented with unconjugated hyperbilirubinemia. A previous study showed that a TA-repeat polymorphism in the promoter region of this gene might play a role in the metabolism of bilirubin. Whether this polymorphism might predispose choledocholithiasis is unclear. We recruited 32 patients who were diagnosed with pigment choledocholithiasis (common bile duct stones) by endoscopic retrograde cholangiopancreatography (ERCP) morphology and 107 population controls. The TA-repeat in the UGT1A1 promoter was genotyped. We found that among the 32 patients, 15 (46.9%) were wild type (A[TA](6)TAA homozygous); 15 (46.9%) were a heterozygous variation (A[TA[(6)TAA/A[TA](7)TAA) and 2 (6.2%) were a homozygous variation (A[TA](7)TAA). Among the controls, 81 (75.7%) were wild type, 23 (21.5%) were a heterozygous variation and 3 (2.8%) were a homozygous variation. The genotype distribution was significantly different between patients and controls. The results suggest that the UGT1A1 promoter TA-repeat polymorphism is associated with choledocholithiasis in Taiwanese patients.

Conditional linkage and genome-wide association studies identify UGT1A1 as a major gene for anti-atherogenic serum bilirubin levels—The Framingham Heart Study

Objective and methodsLow bilirubin levels are significantly associated with cardiovascular diseases (CVD). In previous genome-wide linkage studies we identified a major locus on chromosome 2q harboring the candidate gene UDP-glucuronosyltransferase (UGT1A1). The activity of this enzyme is significantly influenced by a TA-repeat polymorphism in the promoter of the gene. In a prospective study individuals with genotype (TA)7/(TA)7 had significantly higher bilirubin levels and approximately one-third the risk of CVD as carriers of the wildtype (TA)6 allele. In the present study we performed a conditional linkage study to investigate whether this polymorphism explains the observed linkage peak and extended our analysis by a genome-wide association study on bilirubin levels in 1345 individuals. ResultsAfter adjustment for the bilirubin variance explained by this polymorphism, the LOD score on chromosome 2q dropped from 3.8 to 0.4, demonstrating that this polymorphism explains the previous linkage result. For the genome-wide association study, the closest marker to UGT1A1 was in the top ranking SNPs. The association became even stronger when we considered the TA-repeat polymorphism in the analysis (p=2.68×10−53). Five other SNPs in other regions reached genome-wide significance without obvious connection to bilirubin metabolism. ConclusionsOur studies suggest that UGT1A1 may be the major gene with strong effects on bilirubin levels and the TA-repeat polymorphism might be the key polymorphism within the gene controlling bilirubin levels. Since this polymorphism has a high frequency and a substantial impact on the development of CVD, the gene might be an important drug target.

Association between the UGT1A1 TA-Repeat Polymorphism and Bilirubin Concentration in Patients with Intermittent Claudication: Results from the CAVASIC Study

Bilirubin has antioxidative and cytoprotective properties. Low plasma concentrations of bilirubin are reportedly associated with the development of coronary and cerebrovascular disease, and bilirubin concentrations are strongly correlated with the enzyme activity of the hepatic uridine diphosphate glucuronosyltransferase (UGT1A1). The activity of UGT1A1 is influenced by a TA-repeat polymorphism in the promoter of the UGT1A1 gene (UDP glucuronosyltransferase 1 family, polypeptide A1). In a case-control study, we investigated the association between the UGT1A1 polymorphism, bilirubin concentration, and intermittent claudication. We included 255 consecutive male patients presenting with intermittent claudication in the investigation and matched the patients by age and diabetes mellitus with 255 control individuals. Plasma bilirubin concentrations were significantly lower in patients than in controls [mean (SD), 12.5 (5.3) micromol/L vs 15.4 (7.9) micromol/L; P < 0.001]. We found a clear association between the number of TA repeats and plasma bilirubin concentration. Considering the 6/6 TA-repeat genotype as the wild type, we observed a slight increase in bilirubin concentration individuals with the heterozygous 6/7 genotype and pronounced increases for those with the homozygous 7/7 genotype. This association occurred in both controls and patients; however, patients and controls were not significantly different with respect to UGT1A1 TA-repeat genotype frequencies. Our study of a well-phenotyped group of patients with intermittent claudication and control individuals revealed a clear association between low bilirubin concentrations and peripheral arterial disease but no association between the UGT1A1 polymorphism and the disease.

Prostate Cancer Risk and ESR1 TA, ESR2 CA Repeat Polymorphisms

Experimental evidence has suggested that estrogen receptor alpha (coded by the gene ESR1) might increase prostate cancer risk, whereas estrogen receptor beta (coded by the gene ESR2) might reduce prostate cancer risk. We investigated the relationship with prostate cancer risk of both a TA repeat polymorphism in the ESR1 5' region, ESR1 (TA)(n), and with a CA repeat polymorphism in intron 5 of ESR2, ESR2 (CA)(n), in a case-control study (545 cases and 674 controls) nested in the Physicians' Health Study. Prostate cancer risk was highest for carriers of ESR1 (TA)(24) and ESR1 (TA)(25). Replacing one modal ESR1 (TA)(14) allele with one ESR1 (TA)(24) allele yielded an odds ratio of 1.42 (95% confidence interval, 1.00-2.00; P=0.05). Replacing one ESR1 (TA)(14) allele with one ESR1 (TA)(25) allele yielded an odds ratio of 2.10 (95% confidence interval, 1.15-3.84; P=0.02). ESR2 (CA)(n) showed no effects on prostate cancer risk. The ESR1 (TA)(n) polymorphism might play a role in prostate cancer risk.