Spatial transcriptomics at the interface of implanted electrodes in the brain

项目总结 通过电活动的“读出”和“写入”，大脑中植入的电极使新的 基础神经科学研究的发现和神经疾病治疗的突破 受伤。然而，人们普遍认为电极的生物反应会导致记录的变化 以及随时间推移的刺激效果。尽管进行了数十年的研究，但仍不清楚组织中的哪些成分 反应是性能决定的，因为传统的组织反应指标无法完全解释 信号质量、刺激阈值或设备寿命的变化。我们的目标是探索新的假说 并运用新的方法来解决这个长期存在的问题。在这项提案中，我们将把最先进的技术应用于 设备-组织界面的空间转录。这种方法将建立在我们最近报道的 描述了设备周围基因表达的时空变化 激光捕获显微镜和RNA测序的结合。数据显示有157个差异表达 (De)植入电极周围组织中的基因，并与未植入的对照组织进行比较。然而， 空间转录学通过条形码RNA检测组织中转录变化的空间分布 捕获安装在载玻片上的寡核苷酸。与以前的方法相比，该方法有几个优点： (1)卓越的空间分辨率，(2)出色的RNA质量，以及(3)评估基因转录变化的能力 与传统的免疫组织化学标记相结合，在同一组织切片内。最近，我们 空间转录技术成功应用于植入单一电极的大鼠运动皮质组织 数组，为期一周。初步数据显示转录变化的空间抽样更好。 以及新发现的DE基因。此R03应用程序的目的是收集更全面的 试点数据集，以探索跨多个动物和时间点(2小时至6周)的这些变化，同时 开发分析技术以揭示设备局部组织中表达的新基因模块。这项研究 包括两个目标：目标1将揭示植入周围转录变化的空间组织 在六周的时间过程中，大鼠运动皮质中的电极和目标2将进行网络分析 揭示设备诱导的基因模块和定位于植入界面的关键中枢基因的技术。我们 预计该项目将提供一个新的数据集，它将作为独立的努力对外地有用(所有数据和 代码将向公众开放)，同时为未来更大规模的后续研究提供基础 求婚。

PROJECT SUMMARY Through “read-out” and “write-in” of electrical activity, implanted electrodes in the brain have enabled new discoveries in basic neuroscience research and breakthroughs in the treatment of neurological diseases and injury. However, the biological response to electrodes is widely believed to contribute to variations in recording and stimulation efficacy over time. Despite decades of research, it remains unclear which elements of the tissue response are performance-determining, as traditional metrics of the tissue response have failed to fully explain changes in signal quality, stimulation thresholds, or device longevity. It is our objective to explore new hypotheses and apply new methods to this long-standing issue. In this proposal, we will apply state-of-the-art techniques in spatial transcriptomics to the device-tissue interface. This approach will build upon our recently reported publication, which described spatiotemporal changes in gene expression surrounding devices using a combination of laser capture microscopy and RNA-sequencing. The data revealed 157 differentially expressed (DE) genes in tissue surrounding implanted electrodes in comparison to unimplanted control tissue. However, spatial transcriptomics detects the spatial distribution of transcriptional changes in tissue via barcoded RNA- capture oligonucleotides mounted to slides. The method delivers several advantages over previous approaches: (1) superior spatial resolution, (2) excellent RNA quality, and (3) the ability to assess transcriptional changes in combination with traditional immunohistochemistry labeling within the same tissue slice. Recently, we successfully applied spatial transcriptomics to rat motor cortex tissue following implantation of a single electrode array for a period of one week. The preliminary data revealed superior spatial sampling of transcriptional changes as well as newly unmasked DE genes. The purpose of this R03 application is to collect a more comprehensive pilot data set to explore these changes across multiple animals and time points (2 hours to 6 weeks), while developing analysis techniques to reveal novel gene modules expressed in tissue local to devices. The study includes two aims: Aim 1 will reveal the spatial organization of transcriptional changes surrounding implanted electrodes in the motor cortex of rats across a six-week time course and Aim 2 will develop network analysis techniques to reveal device-induced gene modules and key hub genes localized to the implant interface. We expect the project to deliver a novel data set which will be useful to the field as a stand-alone effort (all data and codes will be publicly accessible), while providing a foundation for future follow-on studies in a larger-scale proposal.