Technology Development Initiative – Seminar Series

Talk Summary

This talk will focus on ongoing projects, which aim to generate data and develop methods for integrating single-nucleus and spatial transcriptomics data in the human brain in the context of complex brain disorders. While single cell sequencing approaches have rapidly advanced generation of molecular profiles for various cell types in the brain, a major disadvantage of these techniques is that spatial context is lost. Here, I will first describe how we used a combination of single-nucleus and spatial transcriptomic approaches to identify layer-enriched gene expression, spatially register single nucleus RNA-seq data and assess laminar enrichment of disease associated genes in the dorsal lateral prefrontal cortex of the human brain. I will follow with a description of how we have extended these studies to other areas of the brain that are implicated in complex brain disorders, including the locus coeruleus, where the cell types and patterns of spatial gene expression are less well-understood than the cortex. Finally, I will discuss how we are incorporating proteomics with spatial transcriptomics in the human brain of donors with neurodegenerative disorders to identify the impact of tau and amyloid neuropathology on local gene expression.
Title: “Cell-type and spatially-resolved multi-omic approaches for understanding human brain disorders”

Description of the highlighted technologies by Dr. Keri Martinowich

Single Cell Sequencing

Single nucleus RNA-sequencing: I will be discussing generation and analysis of single cell gene expression. Specifically, I will discuss single-nucleus RNA sequencing and downstream analysis platforms, including integration with spatial transcriptomics data from postmortem human tissue in various brain regions. The data I will be discussing was generating with the 10X Genomics Chromium Single Cell Gene Expression platform.

Spatial Transcriptomics

Visium: I will discuss the use of the 10X Genomics Visium Spatial Gene Expression platform in postmortem human tissue in a variety of brain regions. The Visium platform allows for profiling spatial gene expression. Visium assays were performed by placing fresh-frozen tissue sections onto each of four capture areas per Visium slide, where each capture area contains approximately 5,000 expression spots (spatial locations where transcripts are captured) laid out in a regular grid, and the tissue is histologically stained with hematoxylin and eosin (H&E). Spatial barcodes unique to each spot are incorporated during reverse transcription, followed by sequencing, thus allowing the spatial coordinates of the gene expression measurements to be identified.

Visium-Immunofluorescence: The Visium-immunofluorescence platform works similarly to the parent platform, but instead of capturing high resolution H&E images that can mark the neuroanatomical boundaries, multiplexed fluorescence images are captured following antibody staining for detection of proteins of interest. Hence, the Visium-IF platforms allows for multi-omic incorporation of gene expression and protein detection to allow mapping of local gene expression in the context of protein localization. These experiments were also conducted in various regions of the human brain in postmortem human tissue, localizing proteins that are linked to neurodegeneration and other complex brain disorders.