Integrative Approaches for Identifying Causal Gene-Cell Type Pairs of Complex Disease

项目摘要 识别疾病病因的致病基因和细胞类型是设计靶向的关键 诊断和治疗策略。全基因组关联研究、DNA测序和RNA- 测序研究已经在多种人类疾病中发现了潜在的致病基因。虽然这些方法 提供与疾病相关的“基因列表”，但由于缺乏细胞类型，它们存在重大缺陷。 信息。首先，每个组织由多种类型的细胞组成，这些细胞对疾病有不同的贡献 表型，因此单独使用大块组织数据的研究导致因果细胞群的模糊性。 其次，来自稀有细胞类型的因果基因信号可能在块状组织中被掩盖。最后，理解 在设计下游功能研究所需的细胞类型中，哪些基因受到干扰。至 确定导致人类疾病的基因-细胞对，系统地将患者队列数据与 迫切需要特定于细胞类型的数据。我的研究项目旨在识别致病基因和细胞类型 使用多组学方法推动人类疾病。我们的中心假设是失调的基因 映射到特定的细胞类型会导致疾病的发生。在此之前，我们开发了集成 识别常见和罕见的基因组变异、表观基因组、转录组和蛋白质组的大规模数据 影响特定细胞类型的组织中的因果基因，为 项目。此外，所提出的方法是由快速扩展的细胞特异性表观基因组和 使用分类细胞群体或单细胞图谱的转录组数据。在未来5年内，我们将 专门开发算法，将来自患者队列的基因组发现与特定于细胞的 转录数据，解决两个主要问题：(1)基因-细胞类型对对什么有贡献 疾病病因？(2)疾病相关基因的表达是如何在单个细胞中被调节的？ 级别？拟议的项目将通过发现与广泛的基因相关的基因-细胞对而对该领域产生重大影响。 用于下游调查的疾病范围。这一发展将提供整合纯化的新方法 和单细胞转录组数据，以扩展来自大规模患者基因组队列的发现。在漫长的岁月里 术语，成功识别的基因-细胞对可以被翻译成诊断标记或治疗靶点 人类疾病的威胁。

Project Summary Identifying causal genes and cell types underlying disease etiologies are essential for designing targeted diagnostic and treatment strategies. Genome-wide association study (GWAS), DNA-sequencing, and RNA- sequencing studies have identified potentially causal genes in multiple human diseases. While these methods provide disease-associated “gene lists”, they suffer from major shortcomings given the lack of cell-type information. First, each tissue is composed of multiple cell types with diverse contributions to disease phenotypes, and thus studies using bulk-tissue data alone result in the ambiguity of the causal cell populations. Secondly, causal gene signals from rare cell types may be masked in bulk tissues. Finally, understanding which genes are perturbed in which cell types is required for designing downstream functional studies. To identify the gene-cell pairs driving human disease, systematic approaches to integrate patient-cohort data with cell-type-specific data are urgently needed. My research program aims to identify causal genes and cell types driving human diseases using multi-omics approaches. Our central hypothesis is that dysregulated genes mapped to specific cell types drive disease etiologies. Previously, we developed algorithms that integrate large-scale data of common and rare genomic variants, epigenomes, transcriptomes, and proteomes to identify causal genes in tissue affecting specific cell types, providing strong biological and technical foundations for the project. Further, the proposed approaches are empowered by rapidly-expanding cell-specific epigenomic and transcriptomic data using sorted cell populations or single-cell profiling. In the next 5-year period, we will specifically develop algorithms that integrate genomic findings from patient cohorts with cell-specific transcriptomic data, addressing two major questions: (1) What are the gene-cell type pairs contributing to disease etiologies? (2) How are expressions of disease-associated genes regulated at a single-cell level? The proposed project will strongly impact the field by discovering gene-cell pairs associated with a wide range of diseases for downstream investigation. The development will afford new methods to integrate purified and single-cell transcriptome data to expand on findings from large-scale patient genomic cohorts. In the long term, the successfully identified gene-cell pairs can be translated into diagnostic markers or treatment targets of human disease.