Spatial genomics and cell atlas of the human brain

The human brain is composed of an exceptionally high diversity of cells and brain function is orchestrated by complex interactions of these different types of cells. The enormous cellular diversity and complex organization of the brain have so far hindered our understanding of the molecular and cellular mechanisms underlying brain function. To date, it is still unclear how many different types of cells are present in the human brain and how they are organized. We have previously developed a spatially resolved single-cell genomics method, Multiplexed Error Robust Fluorescent In Situ Hybridization (MERFISH), which allows in situ gene- expression profiling of individual cells and hence in situ identification and spatial mapping of transcriptionally distinct cell types in complex tissue, including the brain. However, the technical limitations of MERFISH still prohibit a comprehensive spatial analysis of cell types and states across the entire human brain. In this project, we will extend MERFISH to enable higher imaging speed/throughput, 3D volumetric imaging, and epigenomic-transcriptomic multimodal imaging, and we will use these approaches to identify cell types and cell states, map their spatial organization, and predict cell-type-specific cell-cell interactions in the human brain, including the aging brain. In Aim 1, we will develop methods to drastically increase MERFISH imaging speed/throughput (by 10-fold or more) and to enable 3D volumetric MERFISH imaging of thick tissue samples, which will further increase the imaging throughput and greatly improve our ability to capture and map cell-cell interactions. We will also extend MERFISH to allow spatially resolved single-cell profiling of not only histone modifications but also DNA modifications, and combine transcriptomic and epigenomic MERFISH to enable spatial multi-omics. In Aim 2, we will use the above-described approaches to generate spatially resolved cell atlases and cell-cell interaction maps of several human brain regions, including several cortical regions (prefrontal cortex, primary motor cortex, primary visual cortex, and middle temporal gyrus), several regions in the basal ganglia (caudoputamen, globus pallidus, substantia nigra, and subthalamic nucleus), and the preoptic region of the hypothalamus. In Aim 3, we will use the MERFISH technology, including the newly developed capabilities described above, to study the human prefrontal cortex from donors of different ages, including advanced ages, to characterize how the composition, cell state, spatial organization, and cell-cell interactions of molecularly defined cell types in the prefrontal cortex change during aging. Our proposed studies will provide fundamental insights into the molecular and cellular architecture of the human brain and how it changes during aging.