Revealing the transcriptional and developmental mechanisms of interneuron identity

皮质GABA能中间神经元是神经回路的重要组成部分，其功能障碍已被 与神经发育疾病有关。尽管中间神经元的多样性没有争议，但无论是程度上 它们的异质性以及驱动这种异质性的基因调控机制仍不清楚。的最新进展 单细胞RNA测序技术为这一问题提供了新的线索，使预测新的 基于基因表达的中间神经元亚型。跨物种荟萃分析将提供对 神经元间多样性的保守机制。然而，交叉研究整合仍然是一个重大挑战。 我假设，神经元间的同一性是由跨物种的统一分子过程定义的。这个项目 旨在通过使用集成的、跨物种的方法来探索 控制神经元间多样性的转录、表观遗传和发育机制。首先，我有 显示小鼠中间神经元亚型可复制地表达与细胞间通讯相关的基因， 启用跨数据集元分析。目标1的目标是使用改进的计算和系统发生学 方法定义跨物种的同源中间神经元亚型，并确定强大的基因靶点。第二, 对单细胞甲基组测序数据的初步研究表明，它可以很容易地与 表达式数据。在目标2中，我将使用机器学习方法从表观基因组和 表达数据，并识别特定亚型的调控特征。第三，我已经证明了转录 根据成人的表达数据，可以对发育中神经元的图谱进行定量评估。目标3 将使用时态推理方法的元分析聚合来实现跨数据集比较和 定义保守的发育基因计划。这些研究将揭示一个多维的肖像 神经元间分子识别并使基因能够接触到这些细胞类型，这是大脑倡议的一个关键目标。 我还提出了一个广泛的培训计划，以支持我向独立的过渡。CSHL提供了一个 卓越的研究环境，拥有无与伦比的科学讨论机会，高级技能 培训和职业发展。我已经组建了一支出色的合作者和导师团队，他们将 帮助我实现我的目标。转录组元分析专家杰西·吉利斯博士和乔希·黄博士， GABA能中间神经元识别方面的专家，将是我的导师。任兵博士、亚当·西佩尔博士、郭平博士 冯、杰西卡·托尔库恩博士和迈克尔·格林伯格博士将是我咨询的合作者和成员 委员会，确保我的研究将是最高水平的。我的培训还将包括 多组学数据集成和比较基因组学，我将继续我的职业发展，通过 在国际会议上发表演讲，指导学生并参加CSHL的研讨会。团结在一起， 拟议的学习和专业培训将确保我成功地过渡到一个独立的职位 我将在主要大学领导一个实验室，以推进大脑倡议的目标。

Cortical GABAergic interneurons are critical components of neural circuitry, and their dysfunction has been linked to neurodevelopmental diseases. Although the diversity of interneurons is not disputed, both the extent of their heterogeneity and the gene regulatory mechanisms that drive it remain unclear. Recent advances in single cell RNA-sequencing technology have shed new light on this issue, enabling the prediction of novel interneuron subtypes based on gene expression. Cross-species meta-analysis would provide key insight into conserved mechanisms of interneuron diversity. However, cross-study integration remains a major challenge. I hypothesize that interneuron identity is defined by unifying molecular processes across species. This project is designed to reveal these processes by using an integrative, cross-species approach to explore the transcriptional, epigenetic, and developmental mechanisms that govern interneuron diversity. First, I have shown that mouse interneuron subtypes replicably express genes associated with cell-cell communication, enabling cross-dataset meta-analysis. The goal of Aim 1 is to use improved computational and phylogenetic methods to define homologous interneuron subtypes across species and identify robust gene targets. Second, preliminary investigation of single cell methylome-sequencing data indicates that it can be readily aligned with expression data. In Aim 2 I will use machine learning methods to generate networks from epigenomic and expression data and identify subtype-specific regulatory features. Third, I have shown that transcriptional profiles from developing neurons can be quantitatively assessed with respect to adult expression data. Aim 3 will use meta-analytic aggregation of temporal inference methods to enable cross-dataset comparisons and define conserved developmental gene programs. These studies will reveal a multidimensional portrait of interneuron molecular identity and enable genetic access to these cell types, a key aim of the BRAIN Initiative. I also propose an extensive training plan that will support my transition to independence. CSHL provides an outstanding research environment, with unequaled opportunities for scientific discussion, advanced skills training and career development. I have assembled an exceptional team of collaborators and mentors who will help me to achieve my goals. Dr. Jesse Gillis, expert in transcriptome meta-analysis, and Dr. Josh Huang, expert in GABAergic interneuron identity, will be my mentors. Dr. Bing Ren, Dr. Adam Siepel, Dr. Guoping Feng, Dr. Jessica Tollkuhn and Dr. Michael Greenberg will be collaborators and members of my advisory committee, ensuring that my research will be of the highest caliber. My training will also involve coursework in multiomics data integration and comparative genomics, and I will continue my professional development by presenting at international conferences, mentoring students and attending workshops at CSHL. Together, the proposed studies and professional training will ensure my successful transition to an independent position at a major university where I will lead a lab that will advance the goals of the BRAIN Initiative.