Integrated Molecular, Cellular and Spatial Analysis of the Mammalian Brain

The mammalian brain exhibits remarkable cellular diversity, but how different cell types are spatially organized in the human cortex and how this organization varies across species remain unclear. In this talk, I will first describe our spatially resolved single-cell profiling of 4,000 genes using multiplexed error-robust fluorescence in situ hybridization (MERFISH). Using this approach, we identified over 100 transcriptionally distinct cell populations and constructed a molecularly defined, spatially resolved cell atlas of the human middle and superior temporal gyrus. Additionally, we examined cell-cell interactions arising from soma contact or proximity in a cell type-specific manner. Comparing the human and mouse cortices, we observed conserved laminar organization of cells but notable species-specific differences in somatic interactions. Our data revealed human-specific patterns of cell-cell proximity and a significant increase in interactions between neurons and non-neuronal cells in the human cortex.
While MERFISH enables genome-scale imaging of RNAs in individual cells within intact tissues, so far, it has primarily been applied to thin tissue samples (~10 µm thickness). Many functional and anatomical studies, however, require volumetric analysis of thicker tissue blocks. In the second part of this talk, I will introduce a new method-3D MERFISH-that allows three-dimensional single-cell transcriptome imaging of thick tissue specimens. This method combines MERFISH with confocal microscopy for optical sectioning and deep learning to enhance imaging speed and quality. We successfully demonstrated 3D MERFISH on mouse brain tissue sections up to 200 µm thick, achieving high detection efficiency and accuracy. We anticipate that both the genome-scale and 3D MERFISH imaging will significantly expand the range of biological questions that can be addressed using spatial genomics.
Bio:
Rongxin is an incoming Assistant Professor at Stanford University in the Departments of Neurosurgery and Genetics (by courtesy) and a member of the Wu Tsai Neuroscience Institute.
Rongxin received his Ph.D. in Bioinformatics and Systems Biology in the Department of Bioengineering at UC San Diego, where he was advised by Bing Ren (2015-2019). During this time, he developed high-throughput genomic technologies and computational tools to map the structure and activity of the mammalian genome at a large scale with high resolution. He then applied these approaches to understand how cis-regulatory elements in the genome control gene expression and how this process can give rise to the distinct gene expression programs that underlie the cellular diversity in the mammalian brain.
As an HHMI-Damon Runyon Postdoctoral Fellow in the laboratory of Xiaowei Zhuang at Harvard University, he developed and applied genome-scale and volumetric MERFISH transcriptome imaging methods to map the molecular and cellular architecture of the human brain during evolution and aging.
He received multiple fellowships and awards, including the HHMI/Damon Runyon Postdoctoral Fellowship, Rising Star in Health and Engineering - Johns Hopkins and Columbia University, Next Generation Leader - Allen Institute, Damon Runyon-Dale F. Frey Award for Breakthrough Scientists. His work has been supported by HHMI, Damon Runyon Cancer Research Foundation, 4D Nucleome, ENCODE Project, Roadmap Epigenome Consortia, and BRAIN Initiative.