Mapping gene-by-environment interactions using multiplexed single cell RNA-sequencing

摘要 虽然已知常见变异体对基因表达变异有相加作用，但已经存在有限的 人类基因与环境相互作用（GxE）的统计学证据。这是因为即使是最大的 表达数量性状基因座（eQTL）研究几乎没有统计能力来检测GxE相互作用， 大量的分离位点和环境暴露的广泛变异性。我们假设 多重扰动和单细胞RNA测序的整合是定位GxE的有效策略 在大型人群中的互动。然而，目前的方法不能扩展到测序107个细胞 在104个样本（即103个供体，10种条件）中， 人类队列在这项提案中，我们将首先开发一种成本效益高的单细胞RNA测序方法，称为 DIT-seq将测序成本降低到0.06美元/细胞（目标1）。然后，我们将制定编码策略， 环境扰动使用样品复用映射和表征GxE相互作用在人类 免疫应答（目标2）。最后，我们将开发一个新的统计模型和计算管道， 使用数千万个细胞进行有效的假设检验（目标3）。实验和计算 提出的技术有可能创造研究基因型-表型的基本新方法 关系和获得的生物学见解可以揭示基因表达的遗传结构 并有助于从大规模基因组和外显子组测序研究中解释疾病相关性。

ABSTRACT While common variants are known to additively contribute to gene expression variation, there has been limited statistical evidence of gene-by-environment interactions (GxE) in humans. This is because even the largest expression quantitative trait loci (eQTL) studies have little statistical power to detect GxE interactions given the large number of segregating loci and extensive variability in environmental exposure. We hypothesize that the integration of multiplexed perturbations and single-cell RNA-sequencing is an efficient strategy for mapping GxE interactions in large population cohorts. However, current approaches are not scalable to sequencing 107 cells across 104 samples (i.e. 103 donors by 10 conditions) needed for sufficiently powered perturbation screens in human cohorts. In this proposal, we will first develop a cost-effective single-cell RNA-sequencing approach called DIT-seq that reduces the cost of sequencing to $0.06/cell (Aim 1). We will then develop strategies for encoding environmental perturbations using sample multiplexing to map and characterize GxE interactions in the human immune response (Aim 2). Finally, we will develop a new statistical model and a computational pipeline for efficient hypothesis testing using tens of millions of cells (Aim 3). The experimental and computational technologies proposed have the potential to create fundamental new ways to study genotype-phenotype relationships and the biological insights gained could shed light on the genetic architecture of gene expression and facilitate the interpretation of disease-associations from large-scale genome and exome sequencing studies.