| Literature DB >> 36128448 |
Haiyan Zhuo1, Jinhai Fan2, Bifeng Zhang3, Yixian Shi2, Liqing Zheng2, Yihong Chai2, Lvfeng Yao1.
Abstract
Genetic variation in UDP-glucuronosyltransferase 1A1 gene (UGT1A1) is a lithogenic risk factor for gallstone formation. This study aimed to assess genotype and allele frequencies of common UGT1A1 variants in patients with gallstone and hepatitis B virus (HBV)-related hepatic failure. This study enrolled 113 healthy individuals (CTRL), 54 patients with HBV infection (HBV), 134 patients with gallstone-free hepatic failure and HBV infection, and 34 patients with gallstone-related hepatic failure and HBV infection (GRHF). Peripheral venous blood samples were collected for genomic DNA isolation. Polymerase chain reaction amplification was carried out for UGT1A1, followed by direct sequencing. Analysis for genotype and allele frequencies of UGT1A1 variants (UGT1A1*6, UGT1A1*27, UGT1A1*28, and UGT1A1*60) was performed. The allele distributions of the four groups did not deviate from Hardy-Weinberg equilibrium. Allele (A) and genotype (CA) frequency distributions of UGT1A1*27 were significantly different between GRHF and CTRL, or between GRHF and HBV. GRHF and CTRL exhibited significant differences in allele (A) and genotype (CA) frequency distributions of UGT1A1*28. Linkage disequilibrium analysis suggested that haplotype G-G-[TA]7-T may be associated with gallstone in HBV-related hepatic failure. Our data reveal that UGT1A1*27 and UGT1A1*28 variants are significantly observed in patients with GRHF compared to healthy individuals.Entities:
Keywords: UGT1A1; gallstone; hepatitis B virus; liver failure; single-nucleotide polymorphism
Year: 2022 PMID: 36128448 PMCID: PMC9449690 DOI: 10.1515/med-2022-0549
Source DB: PubMed Journal: Open Med (Wars)
Sequence of primers for targeting genomic amplicon sequencing for UGT1A1
| Sites | ID | Primer sequences (5′−3′) | |
|---|---|---|---|
| Forward | Reverse | ||
| Enhancer | UGT1A10628-PBERM | AGGTGTAATGAGGATGTGTT | CTCTTACCCTCTAGCCATTC |
| TATA box | UGT1A10628-TATABOX | CCAGTTCAACTGTTGTTGCC | TCCTGCCAGAGGTTCGCCCT |
| Exon1a | 70316-UGT1A1-1a | TGAACTCCCTGCTACCTTTGT | CAGTGGGCAGAGACAGGTAC |
| Exon1b | 70316-UGT1A1-1b | TCTGCTATGCTTTTGTCTGGC | TGCCAAAGACAGACTCAAACC |
| Exon2 | 70316-UGT1A1-2 | CAAACACGCATGCCTTTAATCA | GGATTAATAGTTGGGAAGTGGCA |
| Exon3 | 70316-UGT1A1-3 | CCAGTCCTCAGAAGCCTTCA | GCAATGTAGGATATGTTGGCCA |
| Exon4 | 70316-UGT1A1-4 | TGGCCAACATATCCTACATTGC | AACAACGCTATTAAATGCTACGT |
| Exon5 | 70316-UGT1A1-5 | ACAGGGCAAGACTCTGTATCT | CCTGATCAAAGACACCAGAGG |
Figure 1Whole-exome seuqencing variants from UGT1A1. Electropherograms exhibit the variant positions, (a) UGT1A1*6 (rs4124874, c.-3279T>G, p.Gly71Arg), (b) UGT1A1*27 (c.686C>A, rs35350960, p.Pro229Glu), (c) UGT1A1*28 (rs3064744, [TA]6>[TA]7), and (d) UGT1A1*60 (rs4124874, c.-3279T>G) marked by red arrows.
Figure 2Serum levels of (a) TBIL, (b) DBIL, and (c) IBIL increased in patients with HBV infection, GFHF and GRHF. Boxplots represted the median, 25th percentile, 75th percentile, and error bars. TBIL, total bilirubin; DBIL, direct bilirubin; IBIL, indirect bilirubin. HBV, hepatitis B virus. CTRL group, healthy individuals without HBV infection, gallstone, or hepatic failure; HBV group, patients with HBV infection; GFHF, patients with gallstone-free hepatic failure and HBV infection; GRHF, patients with gallstone-related hepatic failure and HBV infection. CTRL (n = 113), HBV (n = 54), GFHF (n = 134), and GRHF (n = 34). *p < 0.05, **p < 0.01, and ***p < 0.001 by one-way ANOVA corrected by Tukey test.
Odds ratio and 95% CI for gallbladder stone-related hepatic failure associated with UGT1A1 (NM_000463) variants
| Polymorphisms | ||||
|---|---|---|---|---|
|
|
|
|
| |
| Variant | c.211G>A | c.686C>A | [TA]6>[TA]7 | c.-3279T>G |
| Amino acid change | p.Gly71Arg | p.Pro229Glu | — | — |
| SNP ID | rs4148323 | rs35350960 | rs3064744 | rs4124874 |
| Location | Exon 1 | Exon 1 | Promoter | Promoter |
| Position | GRCh38.p13 | GRCh38.p13 | GRCh38.p13 | GRCh38.p13 |
| Type of variant | Missense | Missense | Upstream transcript | Upstream transcript |
| CTRL ( | 30, 26.5% | 0, 0.0% | 18, 15.9% | 67, 59.3% |
| HBV ( | 16, 29.6% | 0, 0.0% | 13, 24.1% | 29, 53.7% |
| GFHF ( | 46, 34.3% | 6, 4.5% | 35, 26.1% | 75, 56.0% |
| GRHF ( | 11, 32.4% | 3, 8.8%a | 12, 35.3%a | 18, 52.9% |
UGT1A1, UDP-glucuronosyltransferase 1A1; SNP, single-nucleotide polymorphism; HBV, hepatitis B virus. p-values were calculated using Fisher’s exact test or Pearson’s chi-square test (a p < 0.05 compared to CTRL group). CTRL group, healthy individuals without HBV infection, gallstone, or hepatic failure; HBV group, patients with HBV infection; GFHF, patients with gallstone-free hepatic failure and HBV infection; GRHF, patients with gallstone-related hepatic failure and HBV infection. CTRL (n = 113), HBV (n = 54), GFHF (n = 134), and GRHF (n = 34).
Hardy–Weinberg equilibrium analysis
| Polymorphisms | Fisher’s | |||
|---|---|---|---|---|
| CTRL | HBV | GFHF | GRHF | |
|
| 0.6559 | 0.7288 | 0.9341 | 0.4010 |
|
| 1.0000 | 1.0000 | 0.7909 | 0.7878 |
|
| 0.3577 | 0.9111 | 0.0821 | 0.7878 |
|
| 0.8330 | 0.8382 | 0.4033 | 0.7296 |
The p-values of Fisher’s exact test or or Pearson’s chi-square test more than 0.05 meet the Hardy–Weinberg equilibrium. UGT1A1, UDP-glucuronosyltransferase 1A1; HBV, hepatitis B virus. CTRL group, healthy individuals without HBV infection, gallstone, or hepatic failure; HBV group, patients with HBV infection; GFHF, patients with gallstone-free hepatic failure and HBV infection; GRHF, patients with gallstone-related hepatic failure and HBV infection. CTRL (n = 113), HBV (n = 54), GFHF (n = 134), and GRHF (n = 34).
Genotype distribution and allele frequencies of four SNPs in UGT1A1 gene with the development of hepatic failure associated with gallbladder stone
| Polymorphisms | Genotype ( | Allele ( | |||
|---|---|---|---|---|---|
|
| GG | GA | AA | G | A |
| CTRL ( | 83, 73.5% | 27, 23.9% | 3, 2.7% | 193, 85.4% | 33, 14.6% |
| HBV ( | 38, 70.4% | 15, 27.8% | 1, 1.9% | 91, 84.3% | 17, 15.7% |
| GFHF ( | 88, 65.7% | 41, 30.6% | 5, 3.7% | 217, 81.0% | 51, 19.0% |
| GRHF ( | 23, 67.6% | 9, 26.5% | 2, 5.9% | 55, 80.9% | 13, 19.1% |
p-values were calculated using Fisher’s exact test or or Pearson’s chi-square test (lowercase character “a” indicates p < 0.05 compared to the CTRL group, “b” indicating p < 0.05 compared to the HBV group). UGT1A1, UDP-glucuronosyltransferase 1A1; SNP, single-nucleotide polymorphism; HBV, hepatitis B virus. CTRL group, healthy individuals without HBV infection, gallstone, or hepatic failure; HBV group, patients with HBV infection; GFHF, patients with gallstone-free hepatic failure and HBV infection; GRHF, patients with gallstone-related hepatic failure and HBV infection. CTRL (n = 113), HBV (n = 54), GFHF (n = 134), and GRHF (n = 34).
Linkage disequilibrium between different SNPs of UGT1A1 gene
| GRHF vs CTRL | HBV vs CTRL | GFHF vs HBV | GRHF vs HBV | GRHF vs GFHF | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| | | Site 2 | Site 3 | Site 4 | Site 2 | Site 3 | Site 4 | Site 2 | Site 3 | Site 4 | Site 2 | Site 3 | Site 4 | Site 2 | Site 3 | Site 4 |
| Site 1 | 0.024 | 0.998 | 0.999 | 0.000 | 1.000 | 0.999 | 0.183 | 0.998 | 1.000 | 0.036 | 0.997 | 0.999 | 0.325 | 0.997 | 1.000 |
| Site 2 | — | 0.255 | 0.487 | — | 0.000 | 0.000 | — | 1.000 | 0.998 | — | 0.213 | 0.507 | — | 0.704 | 0.790 |
| Site 3 | — | — | 0.782 | — | — | 0.859 | — | — | 0.923 | — | — | 0.790 | — | — | 0.883 |
SNP, single-nucleotide polymorphism; UGT1A1, UDP-glucuronosyltransferase 1A1; HBV, hepatitis B virus. |D′|, the normalizing coefficient linkage disequilibrium; r 2, the square of correlation coefficient between pairs of loci; |D′| and r 2 of 1 correspond to complete LD, while 0 presents no LD. CTRL group, healthy individuals without HBV infection, gallstone, or hepatic failure; HBV group, patients with HBV infection; GFHF, patients with gallstone-free hepatic failure and HBV infection; GRHF, patients with gallstone-related hepatic failure and HBV infection. CTRL (n = 113), HBV (n = 54), GFHF (n = 134), and GRHF (n = 34).
Haplotype distribution of UGT1A1 polymorphisms (UGT1A1*6, UGT1A1*27, UGT1A1*28, and UGT1A1*60) among different groups
| Haplotype | GRHF ( | CTRL ( |
| OR [95% CI] |
|---|---|---|---|---|
| G C [TA]6G | 10.39, 15.3% | 64.93, 28.7% | 0.0388 | 0.472 [0.229, 0.973] |
| G C [TA]7G | 9.60, 14.1% | 16.07, 7.1% | 0.0551 | 2.264 [0.965, 5.310] |
| A C [TA]6T | 11.99, 17.6% | 33.00, 14.6% | 0.4498 | 1.323 [0.639, 2.738] |
| G C [TA]6T | 30.6, 45.0% | 110.07, 48.7% | 0.8215 | 0.938 [0.540, 1.631] |
| G C [TA]7T | 2.39, 3.5% | 1.93, 0.9% | 0.0972 | 4.434 [0.652, 30.177] |
All those frequency <0.03 was ignored in analysis; P-values were calculated using Fisher’s exact test or Pearson’s chi-square test. UGT1A1, UDP-glucuronosyltransferase 1A1; OR, odds ratio; CI, confidence interval; SNP, single-nucleotide polymorphism; UGT1A1, UDP-glucuronosyltransferase 1A1; HBV, hepatitis B virus. CTRL group, healthy individuals without HBV infection, gallstone, or hepatic failure; HBV group, patients with HBV infection; GFHF, patients with gallstone-free hepatic failure and HBV infection; GRHF, patients with gallstone-related hepatic failure and HBV infection. CTRL (n = 113), HBV (n = 54), GFHF (n = 134), and GRHF (n = 34).