双样本双向孟德尔随机化法分析人免疫细胞与增生性瘢痕之间的因果关系

吴虹林; 陈咏菲; 李舒婷; 杨浩; 李晓卉; 唐冰; 朱家源; 胡志成

doi:10.3760/cma.j.cn501225-20240203-00046

双样本双向孟德尔随机化法分析人免疫细胞与增生性瘢痕之间的因果关系

doi: 10.3760/cma.j.cn501225-20240203-00046

1.
中山大学附属第一医院烧伤与创面修复科，广州　　510080
2.
中山大学附属第一医院整形外科，广州　　510080

基金项目:

国家自然科学基金面上项目 82172213

详细信息

通讯作者:
胡志成，Email：huzhch5@mail.sysu.edu.cn

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出版历程
- 收稿日期: 2024-02-03

Analysis of the causal relationship between human immune cells and hypertrophic scar using two-sample bidirectional Mendelian randomization method

1.
Department of Burn and Wound Repair Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
2.
Department of Plastic Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China

Funds:

General Program of National Natural Science Foundation of China 82172213

More Information

Corresponding author: Hu Zhicheng, Email: huzhch5@mail.sysu.edu.cn

摘要

摘要: 目的运用双样本双向孟德尔随机化法，探讨人免疫细胞与增生性瘢痕（HS）之间的因果关系。方法该研究基于双样本双向孟德尔随机化（MR）法，分别从全基因组关联分析catalog数据库和FinnGen数据库获取731种人免疫细胞与HS的数据集。设置显著阈值，筛选与免疫细胞及HS显著相关的单核苷酸多态性（SNP）并排除弱工具变量偏倚的影响。采用逆方差加权（IVW）法［同时采用错误发现率（FDR）中的Benjamini-Hochberg法校正其P值］初步检测免疫细胞与HS的因果关系并筛选与HS有显著因果关系的免疫细胞。进一步地，采用双样本MR分析的5种方法：IVW法、加权中位数法、简单模式法、加权模式法和MR-Egger法绘制散布图检测筛选出的免疫细胞与HS的因果关系。针对符合假设的免疫细胞SNP，进行Cochran Q检验评估异质性，进行MR-Egger回归和MR-PRESSO法排除水平多效性，进行留一法分析来评估显著结果是否由单个SNP决定。采用双样本MR分析中IVW法反向检测HS与免疫细胞之间的因果关系。结果 731种免疫细胞达到显著阈值的SNP数量从7个到1 786个不等，HS中达到显著阈值的SNP数量有119个，这些SNP的F值均>10，提示具有弱工具变量偏倚的可能性较小。IVW法分析显示，60种免疫细胞与HS具有潜在因果关系（P值均<0.05），经Benjamini-Hochberg法校正后，仅CD45RA和CD39双阳性调节性T细胞（Treg）与HS具有潜在因果关系（P_FDR<0.05）。IVW法（比值比为1.16，95%置信区间为1.08~1.24，P<0.05、P_FDR<0.05）、加权中位数法（比值比为1.16，95%置信区间为1.05~1.28，P<0.05）、加权模式法（比值比为1.14，95%置信区间为1.02~1.27，P<0.05）和MR-Egger 法（比值比为1.18，95%置信区间为1.07~1.30，P<0.05）的散布图均显示，CD45RA和CD39双阳性Treg的14个SNP与HS患病风险存在因果关系；仅简单模式法的散布图显示，CD45RA和CD39双阳性Treg的14个SNP与HS患病风险的因果关系不明显（P>0.05）。Cochran Q检验显示，CD45RA和CD39双阳性Treg与HS的因果关系不存在异质性（P>0.05）。MR-Egger回归、MR-PRESSO法分析显示，CD45RA和CD39双阳性Treg与HS的显著因果关系不存在水平多效性（P>0.05）。留一法分析显示，CD45RA和CD39双阳性Treg与HS的显著因果关系在逐个剔除SNP后结果稳定。双样本反向MR分析显示，HS与731种免疫细胞均无潜在因果关系（P>0.05）。结论从遗传学的角度揭示，免疫细胞CD45RA和CD39双阳性Treg可能会增加HS患病风险。
- 免疫，细胞 /
- 孟德尔随机化分析 /
- 因果律 /
- 增生性瘢痕
Abstract: Objective To explore the causal relationship between human immune cells and hypertrophic scar (HS) using two-sample bidirectional Mendelian randomization (MR) method. Methods This study was based on two-sample MR method, and the datasets of 731 immune cells and HS were obtained from the genome-wide association study (GWAS) catalog database and Finngen database, respectively. A significance threshold was established to discern single nucleotide polymorphism (SNP) significantly correlated with immune cells or HS, thereby eliminating the impact of weak instrumental variable bias. The inverse variance weighted (IVW) method (meanwhile, the Benjamini-Hochberg (BH) procedure of false discovery rate (FDR) to adjust P values) was used for preliminary detection of the causal relationship between immune cells and HS and screen the immune cells that had a significant causal relationship with HS. Further, the causal relationship between the selected immune cells and HS was detected through five two-sample MR methods: IVW method, weighted median method, simple mode method, weighted mode method, and MR-Egger method, and the scatter plot was drawn. SNPs conformed to the hypothesis were subjected to Cochran Q test for heterogeneity assessment, MR-Egger regression coupled with MR-PRESSO to eliminate horizontal pleiotropic effects, and a leave-one-out analysis was also conducted to determine if significant results were driven by individual SNP. Finally, the IVW method contained in the two-sample MR analysis was utilized to inversely examine the causal relationship between HS and immune cells. Results The number of SNPs in 731 immune cells reaching the significance threshold varied from 7 to 1 786, while in HS, 119 SNPs met the significance threshold, with the F values of all SNPs being greater than 10, suggesting a low likelihood of bias from weak instrumental variables. The IVW method revealed that 60 types of immune cells potentially had a causal relationship with HS (with all P values <0.05), and after adjustment using the BH method, only CD45RA and CD39 positive regulatory T cell (Treg) maintained a potentially strong causal relationship with HS (P_FDR<0.05). The IVW method (with odds ratio of 1.16 and 95% confidence interval of 1.08-1.24, P<0.05, P_FDR<0.05), weighted median method (with odds ratio of 1.16 and 95% confidence interval of 1.05-1.28, P<0.05), weighted mode method (with odds ratio of 1.14 and 95% confidence interval of 1.02-1.27, P<0.05), and MR-Egger method (with odds ratio of 1.18 and 95% confidence interval of 1.07-1.30, P<0.05) of scatter plot all suggested a causal relationship between the 14 SNPs of CD45RA and CD39 positive Treg and risk of HS, only simple mode method of scatter plot suggested a not obvious relationship between the 14 SNPs of CD45RA and CD39 positive Treg and risk of HS (P>0.05). Cochran Q test indicated no heterogeneity in the causal relationship between CD45RA on CD39 positive Treg and HS (P>0.05). MR-Egger regression and MR-PRESSO analyses showed that there was no horizontal pleiotropy in the significant causal relationship between CD45RA and CD39 positive Treg and HS (P>0.05). Leave-one-out analysis confirmed that the significant causal relationship between CD45RA and CD39 positive Treg and HS remained stable after sequentially removing individual SNP. Reverse two-sample MR analysis showed that HS had no potential causal relationship with any of the 731 types of immune cells (P>0.05). Conclusions From the perspective of genetics, it is revealed that immune cells CD45RA and CD39 positive Treg may increase the risk of HS.
- Immunity, cellular /
- Mendelian randomization analysis /
- Causality /
- Hypertrophic scar
吴虹林：研究设计、数据分析、文章的撰写及修改；陈咏菲、李舒婷：数据分析、图表绘制；杨浩、李晓卉：数据采集分析；唐冰、朱家源：研究指导与文章修改；胡志成：研究设计、研究指导、文章修改和经费支持

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吴虹林：研究设计、数据分析、文章的撰写及修改；陈咏菲、李舒婷：数据分析、图表绘制；杨浩、李晓卉：数据采集分析；唐冰、朱家源：研究指导与文章修改；胡志成：研究设计、研究指导、文章修改和经费支持

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1 人免疫细胞与增生性瘢痕的双样本双向孟德尔随机化分析假设图

注：图中虚线表示2个因子之间不产生作用、实线表示2个因子之间可以产生作用；图中免疫细胞目前已知有731种

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2 逆方差加权法分析人免疫细胞与增生性瘢痕之间的因果关系

注：FDR指错误发现率；P值为单纯逆方差加权法的所得值，P_FDR值为经Benjamini-Hochberg法校正后的逆方差加权法所得值；红色箭头指CD45RA和CD39双阳性调节性T细胞；每个条柱对应一种免疫细胞

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3 双样本孟德尔随机化法分析人免疫细胞CD45RA和CD39双阳性调节性T细胞的14个 SNP与增生性瘢痕因果关系的散布图

注：SNP为单核苷酸多态性；直线的斜率表示每种方法的因果关联，斜率为正值表明该免疫细胞可增加增生性瘢痕的发生风险

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4 留一法分析人免疫细胞CD45RA和CD39双阳性调节性T细胞的14个SNP与增生性瘢痕之间的因果关系

注：SNP为单核苷酸多态性；线段中的圆点为比值比，误差线均在0的右侧，提示结果可靠

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