基于双样本孟德尔随机化分析探索人肠道菌群与增生性瘢痕之间的因果关系

陈文涛; 王小祥; 郑文炼; 张伟强; 毛璐佳; 卓佳楠; 周思彤; 杨荣华

doi:10.3760/cma.j.cn501225-20231129-00215

基于双样本孟德尔随机化分析探索人肠道菌群与增生性瘢痕之间的因果关系

doi: 10.3760/cma.j.cn501225-20231129-00215

1.
广东医科大学第一临床医学院，湛江　　524023
2.
中山大学附属第一医院烧伤外科，广州　　510030
3.
韶关市第一人民医院烧伤整形外科，韶关　　512000
4.
广州市第一人民医院烧伤整形美容与创面修复科，广州　　510180
5.
佛山市第一人民医院皮肤科，佛山　　528000

基金项目:

国家自然科学基金面上项目 82272276

重庆市中医药创新团队项目 2023090006KJZX2022WJW008

详细信息

通讯作者:
杨荣华，Email：21720091@qq.com

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出版历程
- 收稿日期: 2023-11-29

Exploring the causality between intestinal flora and hyperplastic scars of human based on two-sample Mendelian randomization analysis

1.
The First Clinical College of Medicine, Guangdong Medical University, Zhanjiang 524023, China
2.
Department of Burn Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510030, China
3.
Department of Burn and Plastic Surgery, the First People's Hospital of Shaoguan, Shaoguan 512000, China
4.
Department of Burn Plastic Surgery and Wound Repair, Guangzhou First People's Hospital, Guangzhou 510180, China
5.
Dermatology Department, Foshan First People's Hospital, Foshan 528000, China

Funds:

General Program of National Natural Science Foundation of China 82272276

Chongqing Traditional Chinese Medicine Innovation Team Project 2023090006KJZX2022WJW008

More Information

Corresponding author: Yang Ronghua, Email: 21720091@qq.com

摘要

摘要: 目的探究人肠道菌群与增生性瘢痕（HS）之间的因果关系。方法该研究为基于双样本孟德尔随机化（TSMR）分析的研究。从全基因组关联分析数据库获得人肠道菌群（18 473个样本）和HS（208 248个样本）的数据。提取已知肠道菌群门、纲、目、科和属5个水平的遗传变异基因，即单核苷酸多态性（SNP）作为工具变量，并进行连锁不平衡（LD）分析。使用PhenoScanner V2数据库进行人类基因型-表型关联分析，排除与HS不相关的肠道菌群SNP并分析获得的SNP是否为弱工具变量。采用TSMR分析的4种方法，即逆方差加权（IVW）、MR-Egger回归、加权中位数和加权模式，对肠道菌群SNP与HS之间的因果关系进行分析。绘制前述4种分析方法得出重要结果的散布图，分析肠道菌群SNP与HS的相关性。采用IVW检验和MR-Egger回归检验评估肠道菌群SNP的异质性，采用MR-Egger回归检验和MR-PRESSO离群值检验评估肠道菌群SNP的水平多效性，采用留一敏感性分析确定HS是否由肠道菌群中的单个SNP引起。对HS SNP与肠杆菌属或HS SNP与瘤胃球菌2属分别进行逆向TSMR分析，检测它们之间是否存在反向因果关系。结果共获得196个已知肠道菌群，属于9门、16纲、20目、32科、119属，从每个菌群中均获得多个SNP作为工具变量。LD分析显示，除rs1000888、rs12566247、rs994794外，其余肠道菌群SNP均符合遗传变异与暴露因素密切相关的假设。人类基因型-表型关联分析显示，经LD分析后获得的SNP均未被排除且均不是弱工具变量。IVW、MR-Egger回归、加权中位数和加权模式的TSMR分析显示，肠杆菌属及瘤胃球菌2属均与HS存在因果关系。其中，IVW和MR-Egger回归的森林图分析还显示，肠杆菌属的16个SNP（该菌属SNP个数下同）和瘤胃球菌2属的15个SNP（该菌属SNP个数下同）均为HS的保护因素。进一步地，IVW分析显示肠杆菌属SNP（比值比为0.62，95%置信区间为0.41~0.93， P<0.05）和瘤胃球菌2属SNP（比值比为0.62，95%置信区间为0.40~0.97， P<0.05）均与HS发生风险呈负相关。散布图显示，肠杆菌属和瘤胃球菌2属的SNP均是HS的保护因素。IVW检验和MR-Egger回归检验均显示，肠杆菌属SNP（ Q值分别为5.73、5.76， P>0.05）和瘤胃球菌2属SNP（ Q值分别为13.67、15.61， P>0.05）均无异质性。MR-Egger回归检验显示，肠杆菌属和瘤胃球菌2属的SNP均无水平多效性（截距分别为0.01、0.06， P>0.05）；MR-PRESSO离群值检验显示，肠杆菌属和瘤胃球菌2属的SNP均无水平多效性（ P>0.05）。留一敏感性分析显示，无单个肠道菌群SNP驱动HS的发生。逆向TSMR分析显示，HS SNP与肠杆菌属之间、HS SNP与瘤胃球菌2属之间均不存在任何反向因果关系（比值比分别为1.01、0.99，95%置信区间分别为0.97~1.06、0.96~1.04， P>0.05）。结论人肠道菌群与HS之间存在一定因果关系，肠杆菌属及瘤胃球菌2属对抑制HS有一定作用。
- 孟德尔随机化分析 /
- 数据库，遗传学 /
- 因果律 /
- 胃肠道微生物组 /
- 增生性瘢痕
Abstract: Objective To investigate the causality between intestinal flora and hypertrophic scars (HS) of human. Methods This study was a study based on two-sample Mendelian randomization (TSMR) analysis. The data on intestinal flora ( n=18 473) and HS ( n=208 248) of human were obtained from the genome-wide association study database. Genetically variable genes at five levels (phylum, class, order, family, and genus) of known intestinal flora, i.e., single nucleotide polymorphisms (SNPs), were extracted as instrumental variables for linkage disequilibrium (LD) analysis. Human genotype-phenotype association analysis was performed using PhenoScanner V2 database to exclude SNPs unrelated to HS in intestinal flora and analyze whether the selected SNPs were weak instrumental variables. The causal relationship between intestinal flora SNPs and HS was analyzed through four methods of TSMR analysis, namely inverse variance weighted (IVW), MR-Egger regression, weighted median, and weighted mode. Scatter plots of significant results from the four aforementioned analysis methods were plotted to analyze the correlation between intestinal flora SNPs and HS. Both IVW test and MR-Egger regression test were used to assess the heterogeneity of intestinal flora SNPs, MR-Egger regression test and MR-PRESSO outlier test were used to assess the horizontal multiplicity of intestinal flora SNPs, and leave-one-out sensitivity analysis was used to determine whether HS was caused by a single SNP in the intestinal flora. Reverse TSMR analyses were performed for HS SNPs and genus Intestinimonas or genus Ruminococcus2, respectively, to detect whether there was reverse causality between them. Results A total of 196 known intestinal flora, belonging to 9 phyla, 16 classes, 20 orders, 32 families, and 119 genera, were obtained, and multiple SNPs were obtained from each flora as instrumental variables. LD analysis showed that the SNPs of the intestinal flora were consistent with the hypothesis that genetic variation was strongly associated with exposure factors, except for rs1000888, rs12566247, and rs994794. Human genotype-phenotype association analysis showed that none of the selected SNPs after LD analysis was excluded and there were no weak instrumental variables. IVW, MR-Egger regression, weighted median, and weighted mode of TSMR analysis showed that both genus Intestinimonas and genus Ruminococcus2 were causally associated with HS. Among them, forest plots of IVW and MR-Egger regression analyses also showed that 16 SNPs (the same SNPs number of this genus below) of genus Intestinimonas and 15 SNPs (the same SNPs number of this genus below) of genus Ruminococcus2 were protective factors for HS. Further, IVW analysis showed that genus Intestinimonas SNPs (with odds ratio of 0.62, 95% confidence interval of 0.41-0.93, P<0.05) and genus Ruminococcus2 SNPs (with odds ratio of 0.62, 95% confidence interval of 0.40-0.97, P<0.05) were negatively correlated with the risk of HS. Scatter plots showed that SNPs of genus Intestinimonas and genus Ruminococcus2 were protective factors of HS. Both IVW test and MR-Egger regression test showed that SNPs of genus Intestinimonas (with Q values of 5.73 and 5.76, respectively, P>0.05) and genus Ruminococcus2 (with Q values of 13.67 and 15.61, respectively, P>0.05) were not heterogeneous. MR-Egger regression test showed that the SNPs of genus Intestinimonas and genus Ruminococcus2 had no horizontal multiplicity (with intercepts of 0.01 and 0.06, respectively, P>0.05); MR-PRESSO outlier test showed that the SNPs of genus Intestinimonas and genus Ruminococcus2 had no horizontal multiplicity ( P>0.05). Leave-one-out sensitivity analysis showed that no single intestinal flora SNP drove the occurrence of HS. Reverse TSMR analysis showed no reverse causality between HS SNPs and genus Intestinimonas or genus Ruminococcus2 (with odds ratios of 1.01 and 0.99, respectively, 95% confidence intervals of 0.97-1.06 and 0.96-1.04, respectively, P>0.05). Conclusions There is a causal relationship between intestinal flora and HS of human, in which genus Intestinimonas and genus Ruminococcus2 have a certain effect on inhibiting HS.
- Mendelian randomization analysis /
- Databases, genetic /
- Causality /
- Gastrointestinal microbiome /
- Hyperplastic scar
陈文涛：研究设计、数据分析、文章的撰写及修改；王小祥：数据分析、图表绘制、文章修改；郑文炼、张伟强、毛璐佳、卓佳楠：数据采集与数据分析；周思彤：研究指导与数据采集；杨荣华：研究设计、研究指导、文章修改和经费支持

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1 人肠道菌群与增生性瘢痕的双样本孟德尔随机化分析假设图

注：图中“×”指违反假设2（独立性）和假设3（限定准则）；假设1指关联性

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2 人的196个肠道菌群单核苷酸多态性与增生性瘢痕因果关系的双样本孟德尔随机化分析

注：从外到内的圆圈依次代表肠道菌群的逆方差加权的比值比和P值、MR-Egger回归的比值比和P值、加权中位数的比值比和P值、加权模式的比值比和P值，同一个圆心的不同扇环块均代表一种肠道细菌，外圈中蓝色箭头指示肠杆菌属、红色箭头指示瘤胃球菌2属

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3 逆方差加权和MR-Egger回归分析人肠杆菌属16个SNP和瘤胃球菌2属15个SNP分别与增生性瘢痕因果关系的森林图。3A.肠杆菌属；3B.瘤胃球菌2属

注：线段中的圆点为比值比，该值>0为危险因素、<0为保护因素；SNP为单核苷酸多态性

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4 双样本孟德尔随机化分析人肠杆菌属16个SNP和瘤胃球菌2属15个SNP分别与增生性瘢痕之间因果关系的散布图。4A.肠杆菌属；4B.瘤胃球菌2属

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，斜率为负值表明肠道菌群SNP可降低增生性瘢痕发生风险

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5 留一敏感性分析人肠杆菌属16个SNP和瘤胃球菌2属15个SNP分别与增生性瘢痕的因果关系。5A.肠杆菌属；5B.瘤胃球菌2属

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

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