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Bae H, Jeon H, Lee C. Genetic regulation of B cell receptor signaling pathway: Insights from expression quantitative trait locus analysis using a mixed model. Comput Biol Chem 2024; 113:108188. [PMID: 39236423 DOI: 10.1016/j.compbiolchem.2024.108188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/23/2024] [Accepted: 08/24/2024] [Indexed: 09/07/2024]
Abstract
The B cell receptor (BCR) signaling pathway regulates non-immune cellular response through various pathways like MAPK, NF-kB, and PI3K-Akt. This study aimed to identify expression quantitative trait loci (eQTL) and their regulatory functions on BCR signaling pathway genes. A mixed model was employed to analyze eQTL using RNA expression levels in lymphoblastoid from 376 Europeans in the GEUVADIS dataset. In total, 266 SNPs, including 115 cis-acting SNPs, were found for association with transcription of 13 genes (P < 5 × 10-8), revealing 19 independent signals for five genes through linkage disequilibrium analysis. Functional analysis, aligning them with DNase sensitive sites, transcription factor binding sites, histone modification, promoters/enhancers, CpG islands, and ChIA-PET, identified regulatory variants targeting SYK, VAV2, and PLCG2. Notably, rs2562397 was validated as a SYK promoter variant, and rs694505, rs636667, and rs4889409 were confirmed as enhancer variants for VAV2 and PLCG2. Their allelic differences in gene expression were also confirmed using ENCODE ChIP-seq and Sei neural network prediction. Persistent differential expression of these genes by alleles might impact the adaptive immune system, vascular development, and/or relevant diseases that have been previously associated with other variants of the genes. Comprehensive genetic architecture studies of the BCR signaling pathway, along with experiments demonstrating related mechanisms, will greatly contribute to understanding the underlying mechanisms of relevant disease development and implementing precision medicine.
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Affiliation(s)
- Hojin Bae
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea
| | - Hyowon Jeon
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea
| | - Chaeyoung Lee
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Republic of Korea.
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Lv D, Wang H, Leng Y, Chen S, Sun H, Meng X, Liu T, Xiong Z. Association between diabetes mellitus and primary biliary cholangitis: a two-sample Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1362584. [PMID: 38774228 PMCID: PMC11106416 DOI: 10.3389/fendo.2024.1362584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
Background Previous observational studies have demonstrated a link between diabetes mellitus(DM) and primary biliary cholangitis (PBC). Nevertheless, since these relationships might be confused, whether there is any causal connection or in which direction it exists is unclear. Our investigation aimed to identify the causal associations between DM and PBC. Methods We acquired genome-wide association study (GWAS) datasets for PBC, Type 1 diabetes(T1DM), and Type 2 diabetes(T2DM) from published GWASs. Inverse variance-weighted (IVW), MR-Egger, weighted median (WM), Simple mode, and weighted mode methods were used to determine the causal relationships between DM(T1DM or T2DM) and PBC. Sensitivity analyses were also carried out to ensure the results were robust. To determine the causal relationship between PBC and DM(T1DM or T2DM), we also used reverse MR analysis. Results T1DM was associated with a higher risk of PBC (OR 1.1525; 95% CI 1.0612-1.2517; p = 0.0007) in the IVW method, but no evidence of a causal effect T2DM on PBC was found (OR 0.9905; 95% CI 0.8446-1.1616; p = 0.9071) in IVW. Results of the reverse MR analysis suggested genetic susceptibility that PBC was associated with an increased risk of T1DM (IVW: OR 1.1991; 95% CI 1.12-1.2838; p = 1.81E-07), but no evidence of a causal effect PBC on T2DM was found (IVW: OR 1.0101; 95% CI 0.9892-1.0315; p = 0.3420). Conclusion The current study indicated that T1DM increased the risk of developing PBC and vice versa. There was no proof of a causal connection between PBC probability and T2DM. Our results require confirmation through additional replication in larger populations.
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MESH Headings
- Humans
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/complications
- Diabetes Mellitus, Type 1/epidemiology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/epidemiology
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Liver Cirrhosis, Biliary/genetics
- Liver Cirrhosis, Biliary/epidemiology
- Liver Cirrhosis, Biliary/complications
- Mendelian Randomization Analysis
- Polymorphism, Single Nucleotide
- Risk Factors
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Affiliation(s)
- Dan Lv
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Han Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- Department of Hepatology, First Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Yan Leng
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- Department of Hepatology, First Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Sitong Chen
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Haitao Sun
- College of Integrative Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Xiangyue Meng
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Tiejun Liu
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- Department of Hepatology, First Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Zhuang Xiong
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
- Department of Hepatology, First Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
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Zhao Y, Li D, Shi H, Liu W, Qiao J, Wang S, Geng Y, Liu R, Han F, Li J, Li W, Wu F. Associations between type 2 diabetes mellitus and chronic liver diseases: evidence from a Mendelian randomization study in Europeans and East Asians. Front Endocrinol (Lausanne) 2024; 15:1338465. [PMID: 38495785 PMCID: PMC10941029 DOI: 10.3389/fendo.2024.1338465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Abstract
Objective Multiple observational studies have demonstrated an association between type 2 diabetes mellitus (T2DM) and chronic liver diseases (CLDs). However, the causality of T2DM on CLDs remained unknown in various ethnic groups. Methods We obtained instrumental variables for T2DM and conducted a two-sample mendelian randomization (MR) study to examine the causal effect on nonalcoholic fatty liver disease (NAFLD), hepatocellular carcinoma (HCC), viral hepatitis, hepatitis B virus (HBV) infection, and hepatitis C virus (HCV) infection risk in Europeans and East Asians. The primary analysis utilized the inverse variance weighting (IVW) technique to evaluate the causal relationship between T2DM and CLDs. In addition, we conducted a series of rigorous analyses to bolster the reliability of our MR results. Results In Europeans, we found that genetic liability to T2DM has been linked with increased risk of NAFLD (IVW : OR =1.3654, 95% confidence interval [CI], 1.2250-1.5219, p=1.85e-8), viral hepatitis (IVW : OR =1.1173, 95%CI, 1.0271-1.2154, p=0.0098), and a suggestive positive association between T2DM and HCC (IVW : OR=1.2671, 95%CI, 1.0471-1.5333, p=0.0150), HBV (IVW : OR=1.1908, 95% CI, 1.0368-1.3677, p=0.0134). No causal association between T2DM and HCV was discovered. Among East Asians, however, there was a significant inverse association between T2DM and the proxies of NAFLD (ALT: IVW OR=0.9752, 95%CI 0.9597-0.9909, p=0.0021; AST: IVW OR=0.9673, 95%CI, 0.9528-0.9821, p=1.67e-5), and HCV (IVW: OR=0.9289, 95%CI, 0.8852-0.9747, p=0.0027). Notably, no causal association was found between T2DM and HCC, viral hepatitis, or HBV. Conclusion Our MR analysis revealed varying causal associations between T2DM and CLDs in East Asians and Europeans. Further research is required to investigate the potential mechanisms in various ethnic groups, which could yield new insights into early screening and prevention strategies for CLDs in T2DM patients.
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Affiliation(s)
- Yue Zhao
- Department of Surgery, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Di Li
- Department of Internal Medicine, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Hanyu Shi
- Department of Internal Medicine, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Wei Liu
- Department of General Surgery, Shandong Corps Hospital of Chinese People’s Armed Police Force, Jinan, China
| | - Jiaojiao Qiao
- Department of Nursing, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Shanfu Wang
- Department of Surgery, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Yiwei Geng
- School of Statistic and Data Science, Jiangxi University of Finance and Economics, Nanchang, Jiangxi, China
| | - Ruiying Liu
- Department of Nursing, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Feng Han
- Department of Surgery, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Jia Li
- Department of Health and Epidemic Prevention, Hospital of the First Mobile Corps of the Chinese People’s Armed Police Force, Dingzhou, Hebei, China
| | - Wei Li
- Department of General Surgery, The 980Hospital of the Chinese People's Liberation Army (PLA) Joint Logistics Support Force (Primary Bethune International Peace Hospital of Chinese People's Liberation Army (PLA), Shijiazhuang, Hebei, China
| | - Fengyun Wu
- Department of General Surgery, Characteristic Medical Center of the Chinese People’s Armed Police Force, Tianjin, China
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Dong J, Liu C, Lu J, Wang L, Xie S, Ji L, Lu B. The relationship between sex hormone-binding protein and non-alcoholic fatty liver disease using Mendelian randomisation. Eur J Clin Invest 2024; 54:e14082. [PMID: 37605959 DOI: 10.1111/eci.14082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND The incidence of non-alcohol fatty liver disease (NAFLD) has been increasing annually with the improvement of living standards. Numerous epidemiological observations have linked sex hormone-binding protein (SHBG) levels to NAFLD. However, evidence of the causal role of SHBG in the development and progression of NAFLD is still absent. Therefore, a systematic assessment of the causal relationship is needed. METHOD A two-sample Mendelian randomisation (MR) analysis was conducted. Genome-wide association study (GWAS) data for SHBG were obtained online from the IEU database (ebi-a-GCST90012111) as exposure. GWAS data from the NAFLD of the Finngen consortium were used for preliminary analysis, while NAFLD data from another GWAS involving 8434 participants were used for replication and meta-analyses. Causal effects were investigated with inverse variance weighted (IVW), weighted median and MR-Egger regression. Sensitivity analyses including Cochran's Q test, leave-one-out analysis and MR-Egger intercept analysis were simultaneously conducted to assess heterogeneity and pleiotropy. RESULTS After rigorous selection, 179 single-nucleotide polymorphisms (SNPs) were identified as strongly correlated instrumental variables. Preliminary analysis suggested a significant causal relationship between genetically determined serum SHBG levels and NAFLD [odds ratio (OR) IVW = .54, 95% confidence interval (CI) = .30-.98, p = .043], supported by the results of the replication analysis (ORIVW = .61, 95% CI = .46-.81, p = .0006) and further meta-analysis (OR = .59, 95% CI = .46-.77, p < .0001). CONCLUSION The genetic tendency to high levels of SHBG was causally correlated with a reduced risk of NAFLD, indicating that circulating high levels of SHBG was a protective factor for NAFLD.
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Affiliation(s)
- Jiaming Dong
- School of Medicine, Shaoxing University, Shaoxing, China
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Chenming Liu
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Jialiang Lu
- School of Medicine, Shaoxing University, Shaoxing, China
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Luna Wang
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Shisheng Xie
- School of Medicine, Shaoxing University, Shaoxing, China
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Lichao Ji
- School of Medicine, Shaoxing University, Shaoxing, China
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Baochun Lu
- Department of Hepatobiliary Surgery, Shaoxing People's Hospital, Shaoxing, China
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