Spatial transcriptomics at the interface of implanted electrodes in the brain

大脑植入电极界面的空间转录组学

• 批准号: 10532895
• 负责人: Erin K Purcell
• 金额: $ 15.62万
• 依托单位: MICHIGAN STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10532895
• 关键词: Acute; Animals; Bar Codes; Basic Science; Benchmarking; Biological; Biological Markers; Blood - brain barrier anatomy; Brain; Chemicals; Chromosome Mapping; Chronic; Code; Data; Data Set; Devices; Distal; Electric Stimulation; Electrodes; Elements; Epilepsy; Foreign Bodies; Foundations; Future; Gene Cluster; Gene Combinations; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Gliosis; Goals; Gorilla gorilla; Hour; Immunofluorescence Immunologic; Immunohistochemistry; Implant; Implanted Electrodes; Individual; Injury; Interruption; Intractable Epilepsy; Knowledge; Label; Lasers; Longevity; Mental Depression; Methods; Microscopy; Motor Cortex; Nervous System Trauma; Neurons; Neurosciences Research; Obsessive-Compulsive Disorder; Oligonucleotides; Ontology; Parkinson Disease; Pathologic; Pathway Analysis; Patients; Performance; Phase; Principal Component Analysis; Process; Publications; RNA; Rattus; Reporting; Research; Research Personnel; Resolution; Sampling; Seizures; Signal Transduction; Silicon; Slice; Slide; Spatial Distribution; Stains; Synaptic Transmission; Techniques; Time; Tissues; Variant; Writing; astrogliosis; biomaterial compatibility; brain tissue; candidate marker; chronic pain management; clinical application; cohort; conditioning; differential expression; flexibility; implantable device; implantation; improved; insight; interest; nervous system disorder; neuronal excitability; neuroregulation; novel; novel marker; open source; response; response biomarker; spatiotemporal; tissue biomarkers; tool; transcriptome; transcriptome sequencing; transcriptomics

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.

项目摘要 通过“读出”和“写入”脑电活动，植入大脑的电极使新的 基础神经科学研究的发现和神经疾病治疗的突破， 损伤然而，对电极的生物反应被广泛认为是导致记录变化的原因。 和刺激功效。尽管进行了数十年的研究，但仍不清楚组织中的哪些成分 反应是性能决定因素，因为组织反应的传统指标未能完全解释 信号质量、刺激阈值或器械寿命的变化。我们的目标是探索新的假设 并将新方法应用于这个长期存在的问题。在本提案中，我们将采用最先进的技术， 将空间转录组学应用于装置-组织界面。这种方法将建立在我们最近报告的基础上， 该出版物描述了使用一种生物传感器的装置周围的基因表达的时空变化。 激光捕获显微镜和RNA测序的组合。数据显示157个差异表达的 (DE)与未植入的对照组织相比，植入电极周围组织中的基因。然而，在这方面， 空间转录组学通过条形码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。该方法与以前的方法相比具有几个优点： (1)上级空间分辨率，（2）优异的RNA质量，和（3）评估转录变化的能力， 与同一组织切片内的传统免疫组织化学标记相结合。最近我们 在植入单个电极后，成功地将空间转录组学应用于大鼠运动皮层组织 一个星期的数组。初步数据显示转录变化的上级空间采样 以及新发现的DE基因。此R 03应用程序的目的是收集更全面的 探索多只动物和多个时间点（2小时至6周）的这些变化的试验数据集， 开发分析技术，以揭示在器械局部组织中表达的新基因模块。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，Aim 2将开发大鼠运动皮层中的电极， 技术，以揭示设备诱导的基因模块和关键枢纽基因定位到植入界面。我们 预计该项目将提供一个新的数据集，这将是有用的外地作为一个独立的努力（所有数据和 代码将公开获取），同时为未来更大规模的后续研究奠定基础。 提议