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Luo J, Meng Y, Zhai J, Zhu Y, Li Y, Wu Y. Screening of SLE-susceptible SNPs in One Chinese Family with Systemic Lupus Erythematosus. Curr Bioinform 2020. [DOI: 10.2174/1574893615666200120105153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Background:
Systemic lupus erythematosus (SLE) is a complex autoimmune disease,
which mainly affects childbearing-aged women. Although its pathogenesis is not fully clear yet,
studies have shown that genetic factors are vital in exploring SLE pathogenic mechanisms.
Objective:
The purpose of this study is to predict and screen potential pathogenic single nucleotide
polymorphisms (SNPs). By comparing the genomes of members of a family with SLE and
performing functional analysis on mutation loci, possible pathogenic polymorphisms are screened.
These analyses lay the foundation for further research mechanisms.
Method:
Genomic alignment, variant calling and functional annotation were performed and then
~92,778 original SNPs were obtained for each specimen. We found that the patient/healthyspecific
SNPs show different conservative score distribution. Many patient-specific SNPs were
detected in SLE-related pathways. We therefore investigated the patient-specific SNPs from four
diverse perspectives, including nonsynonymous variations in exon regions, expression quantitative
trait loci (eQTLs), RNA binding sites and RNA-binding protein (RBP) binding sites.
Results:
18 potential pathogenic SNPs were identified in SLE risk genes, which were associated
with functional loci. Systematic literature study was then performed to verify these potential
pathogenic SNPs.
Conclusion:
This study could help to better explain possible genetic mechanisms of SLE from the
perspective of variation. It could provide effective strategy for the accurate diagnosis and
personalized treatment of SLE patients.
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Affiliation(s)
- Juan Luo
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yanming Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jianzhao Zhai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Zhu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yongkang Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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Zhang J, Zhao Z, Bai H, Wang M, Jiao L, Peng W, Wu T, Liu T, Chen H, Song X, Wu L, Hu X, Wu Q, Zhou J, Song J, Lyv M, Ying B. Genetic polymorphisms in PXR and NF-κB1 influence susceptibility to anti-tuberculosis drug-induced liver injury. PLoS One 2019; 14:e0222033. [PMID: 31490979 PMCID: PMC6730870 DOI: 10.1371/journal.pone.0222033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/20/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Pregnane X receptor (PXR) regulates the expression of drug-metabolizing enzymes and transport enzymes. NF-κB not only plays a role in liver homeostasis and injury-healing processes by regulating inflammatory responses but may also regulate the transcription of PXR. Currently, genetic polymorphisms in PXR are associated with adverse drug effects. Because little is known about the association between NF-κB1 genetic polymorphisms and adverse drug reactions, we explored the association between PXR and NF-κB1 single nucleotide polymorphisms (SNPs) and susceptibility to anti-tuberculosis drug-induced liver injury (ATDILI). MATERIALS AND METHODS A total of 746 tuberculosis patients (118 with ATDILI and 628 without ATDILI) were prospectively enrolled at West China Hospital between December 2014 and April 2018. Nine selected SNPs (rs3814055, rs13059232, rs7643645 and rs3732360 in PXR and rs78872571, rs4647992, rs60371688, rs1598861 and rs3774959 in NF-κB1) were genotyped with a custom-designed 2x48-plex SNP Scan TM Kit. The frequencies of the alleles, genotypes and genetic models of the variants were compared between patients with or without ATDILI, while joint effect analysis of the SNP-SNP interactions was performed using multiplicative and additive models. The odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) were calculated. RESULTS The T allele of rs3814055 in PXR was associated with a decreased risk for ATDILI (OR 0.61; 95% CI: 0.42-0.89, p = 0.0098). The T alleles of rs78872571 and rs4647992 in NF-κB1 were significantly associated with an increased risk for ATDILI (OR 1.91; 95% CI: 1.06-3.43, p = 0.028 and OR 1.81; 1.06-3.10, p = 0.029, respectively). The allele, genotype and genetic model frequencies were similar in the two groups for the other six SNPs (all P>0.05). There were no multiplicative or additive interactions between the SNPs. CONCLUSION Our study is the first to reveal that rs3814055 variants in PXR and rs78872571 and rs4647992 variants in NF-κB1 are associated with susceptibility to ATDILI caused by first-line anti-tuberculosis combination treatment in the Han Chinese population.
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Affiliation(s)
- Jingwei Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Hao Bai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Wu Peng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Tao Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Hao Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Lijuan Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Qian Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiajia Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Lyv
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- * E-mail:
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