The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Hum Reprod. 2020 Feb 29;35(2):377-393. doi: 10.1093/humrep/dez279.
Are genetic effects on endometrial gene expression tissue specific and/or associated with reproductive traits and diseases?
Analyses of RNA-sequence data and individual genotype data from the endometrium identified novel and disease associated, genetic mechanisms regulating gene expression in the endometrium and showed evidence that these mechanisms are shared across biologically similar tissues.
The endometrium is a complex tissue vital for female reproduction and is a hypothesized source of cells initiating endometriosis. Understanding genetic regulation specific to, and shared between, tissue types can aid the identification of genes involved in complex genetic diseases.
STUDY DESIGN, SIZE, DURATION: RNA-sequence and genotype data from 206 individuals was analysed and results were compared with large publicly available datasets.
PARTICIPANTS/MATERIALS, SETTING, METHODS: RNA-sequencing and genotype data from 206 endometrial samples was used to identify the influence of genetic variants on gene expression, via expression quantitative trait loci (eQTL) analysis and to compare these endometrial eQTLs with those in other tissues. To investigate the association between endometrial gene expression regulation and reproductive traits and diseases, we conducted a tissue enrichment analysis, transcriptome-wide association study (TWAS) and summary data-based Mendelian randomisation (SMR) analyses. Transcriptomic data was used to test differential gene expression between women with and without endometriosis.
A tissue enrichment analysis with endometriosis genome-wide association study summary statistics showed that genes surrounding endometriosis risk loci were significantly enriched in reproductive tissues. A total of 444 sentinel cis-eQTLs (P < 2.57 × 10-9) and 30 trans-eQTLs (P < 4.65 × 10-13) were detected, including 327 novel cis-eQTLs in endometrium. A large proportion (85%) of endometrial eQTLs are present in other tissues. Genetic effects on endometrial gene expression were highly correlated with the genetic effects on reproductive (e.g. uterus, ovary) and digestive tissues (e.g. salivary gland, stomach), supporting a shared genetic regulation of gene expression in biologically similar tissues. The TWAS analysis indicated that gene expression at 39 loci is associated with endometriosis, including five known endometriosis risk loci. SMR analyses identified potential target genes pleiotropically or causally associated with reproductive traits and diseases including endometriosis. However, without taking account of genetic variants, a direct comparison between women with and without endometriosis showed no significant difference in endometrial gene expression.
The eQTL dataset generated in this study is available at http://reproductivegenomics.com.au/shiny/endo_eqtl_rna/. Additional datasets supporting the conclusions of this article are included within the article and the supplementary information files, or are available on reasonable request.
LIMITATIONS, REASONS FOR CAUTION: Data are derived from fresh tissue samples and expression levels are an average of expression from different cell types within the endometrium. Subtle cell-specifc expression changes may not be detected and differences in cell composition between samples and across the menstrual cycle will contribute to sample variability. Power to detect tissue specific eQTLs and differences between women with and without endometriosis was limited by the sample size in this study. The statistical approaches used in this study identify the likely gene targets for specific genetic risk factors, but not the functional mechanism by which changes in gene expression may influence disease risk.
Our results identify novel genetic variants that regulate gene expression in endometrium and the majority of these are shared across tissues. This allows analysis with large publicly available datasets to identify targets for female reproductive traits and diseases. Much larger studies will be required to identify genetic regulation of gene expression that will be specific to endometrium.
STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the National Health and Medical Research Council (NHMRC) under project grants GNT1026033, GNT1049472, GNT1046880, GNT1050208, GNT1105321, GNT1083405 and GNT1107258. G.W.M is supported by a NHMRC Fellowship (GNT1078399). J.Y is supported by an ARC Fellowship (FT180100186). There are no competing interests.
基因对子宫内膜基因表达的影响是否具有组织特异性，并且/或者与生殖性状和疾病相关？
对来自子宫内膜的 RNA-seq 数据分析和个体基因型数据进行分析，确定了调控子宫内膜基因表达的新型和与疾病相关的遗传机制，并表明这些机制在生物学相似的组织中具有共享性。
子宫内膜是女性生殖所必需的复杂组织，被认为是子宫内膜异位症起始细胞的来源。了解特定于组织类型和组织之间共享的遗传调控机制有助于识别参与复杂遗传疾病的基因。
研究设计、规模、持续时间：分析了 206 个人的 RNA-seq 和基因型数据，并将结果与大型公开可用数据集进行了比较。
参与者/材料、设置、方法：使用来自 206 个子宫内膜样本的 RNA-seq 和基因型数据，通过表达数量性状基因座（eQTL）分析来确定遗传变异对基因表达的影响，并比较这些子宫内膜 eQTL 与其他组织中的 eQTL。为了研究子宫内膜基因表达调控与生殖性状和疾病之间的关联，我们进行了组织富集分析、全基因组关联研究（TWAS）和基于汇总数据的孟德尔随机化（SMR）分析。使用转录组数据来测试患有和不患有子宫内膜异位症的女性之间的基因表达差异。
对子宫内膜异位症全基因组关联研究汇总统计数据进行的组织富集分析表明，围绕子宫内膜异位症风险位点的基因在生殖组织中显著富集。总共检测到 444 个先发顺式-eQTL（P<2.57×10-9）和 30 个反式-eQTL（P<4.65×10-13），包括子宫内膜中 327 个新的顺式-eQTL。很大一部分（85%）的子宫内膜 eQTL 存在于其他组织中。子宫内膜基因表达的遗传效应与生殖（如子宫、卵巢）和消化组织（如唾液腺、胃）的遗传效应高度相关，支持在生物学相似的组织中存在共享的基因表达遗传调控。TWAS 分析表明，39 个基因座的基因表达与子宫内膜异位症相关，包括五个已知的子宫内膜异位症风险位点。SMR 分析确定了与生殖性状和疾病（包括子宫内膜异位症）多效或因果相关的潜在靶基因。然而，在不考虑遗传变异的情况下，对患有和不患有子宫内膜异位症的女性进行直接比较，并没有显示出子宫内膜基因表达存在显著差异。
本研究中生成的 eQTL 数据集可在 http://reproductivegenomics.com.au/shiny/endo_eqtl_rna/ 上获得。支持本文结论的其他数据集包含在文章和补充信息文件中，或可应合理要求提供。
局限性、谨慎的原因：数据来自新鲜组织样本，表达水平是子宫内膜中不同细胞类型表达的平均值。可能无法检测到微妙的细胞特异性表达变化，并且样本之间和月经周期内的细胞组成差异将导致样本变异性。本研究中样本量有限，限制了检测组织特异性 eQTL 和患有和不患有子宫内膜异位症的女性之间差异的能力。本研究中使用的统计方法识别了特定遗传风险因素的可能基因靶标，但没有识别出基因表达变化可能影响疾病风险的功能机制。
我们的研究结果确定了调控子宫内膜基因表达的新型遗传变异，其中大多数在组织中具有共享性。这允许使用大型公共可用数据集来识别女性生殖性状和疾病的靶标。需要更大的研究来确定将特定于子宫内膜的基因表达调控。
研究资金/利益冲突：这项工作得到了澳大利亚国家卫生和医学研究委员会（NHMRC）的支持，项目拨款包括 GNT1026033、GNT1049472、GNT1046880、GNT1105321、GNT1083405 和 GNT1107258。G.W.M 由 NHMRC 奖学金（GNT1078399）支持。J.Y 由澳大利亚研究委员会（ARC）奖学金（FT180100186）支持。没有利益冲突。
