Visium_SPG_AD
Overview
Welcome to the Visium_SPG_AD project! This project
involves several interactive websites, which are publicly accessible for
you to browse and download.
We spatially resolved transcriptomics of the inferior temporal cortex (ITC) from postmortem human brain tissue to study local gene expression profiles of brain microenvironments associated with Alzheimer’s disease (AD) related neuropathology bearing abnormal protein aggregation of amyloid beta (Abeta; Ab) and phosphorylated Tau (pTau). Using a total of 10 tissue samples from 3 donors with late-stage Alzheimer’s disease (AD) and 1 age-matched control (Br3874), we generated proteomic-based, spatially-resolved transcriptome-scale (SRT) maps of the human ITC in which the immunofluorescence staining of Ab and pTau was integrated into the complementary SRT data of the identical tissue sections. With Visium Spatial Proteogenomics (Visium-SPG), we utilized a within-subjects design to study gene expression changes associated with spatially localized brain neuropathology across the 3 donors with AD (Br3854, Br3873, and Br3880). Here, using BayesSpace to identify the gray-matter associated spots in a data-driven manner, we discovered statistically significant differentially expressed genes in the core (Ab spots) and peripheral (next_Ab spots) compartments of Ab-associated microenvironment in the gray matter of ITC. For more detailed information about study design and experimental results, please refer to our manuscript. This work was performed by the Keri Martinowich, Kristen Maynard, and Leonardo Collado-Torres teams at the Lieber Institute for Brain Development as well as Stephanie Hicks’s group from JHBSPH’s Biostatistics Department. This project was done in collaboration with 10x Genomics.
This project involves the LieberInstitute/Visium_SPG_AD GitHub repository.
If you tweet about this website, the data or the R package please use
the #Visium_SPG_AD hashtag. You can find previous tweets
that way as shown
here.
Thank you for your interest in our work!