July 28, 2022
The UW ADRC is excited about the official launch of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) web product (SEA-AD.org) and the first public release of the project’s data. This release is an important new resource for the Alzheimer’s community. The SEA-AD is a NIA-funded collaboration between the Allen Brain Institute, UW Medicine, and Kaiser Permanente Health Research Institute to create a higher resolution atlas of Alzheimer’s disease at the cellular level, in order to understand the early pathogenesis of AD, disease initiation, and cognitive decline.
SEA-AD is led by Ed Lein of the Allen Institute and UW ADRC. Investigators from the UW ADRC include C. Dirk Keene, Eric B. Larson, Thomas Grabowski, Paul Crane, Joey Mukherjee, Caitlin Latimer, Suman Jayadev, and Martin Darvas. Investigators from the Allen Institute include Kyle Travaglini, Michael Hawrylycz, Rebecca Hodge, Jeremy Miller, Jennie Close, Mariano Gabitto, Boaz Levi, and Michael Wang; and Erin Bowles of Kaiser Permanente WA.
The publicly available dataset—the first big public achievement of SEA-AD—features large-scale cellular and molecular information obtained from more than 1.2 million neurons and other cells from 84 research participants (UW ADRC and ACT subjects) postmortem, as well as detailed microscopy images of amyloid and other pathological proteins in their brain tissue from the middle temporal gyrus (MTG). The study data were generated from the UW BRaIN laboratory, which is supported by the UW ADRC and the ACT Study. The researchers used single-cell RNA sequencing and conducted highly quantitative neuropathology of the MTG to understand the spatial make-up of AD-related proteins and types of cells.
The data release is ready for ADRC researchers and everyone to explore —with elegant, user-friendly data visualizations and interactive data explorers. As announced on the Allen Institute website, the release includes for your perusal:
- A transcriptomics comparative viewer, which captures side-by-side changes in gene activity in single cells between healthy, reference brains and brains from cohorts of 84 donors across spectrum of AD. The viewer can filter by cell type, donor characteristics including age at death, sex, dementia status, and years of education.
- A transcriptomics explorer that shows the reference set of middle temporal gyrus (MTG) brain cell types from the healthy donors. This data visualization shows the relationships between all the cell types in this region, as well as expression levels for any genes of interest.
- A donor index and neuropathology image viewer which captures demographic, clinical, and cognitive and pathological information from the 84 brain donors and detailed pathological images and quantifications from each brain region. The UW Medicine ADRC pathology items developed machine learning techniques to precisely quantify levels of disease related proteins in these images.
- A link to the SEA-AD transcriptomics data in the Chan Zuckerberg CELL by GENE, and interactive data explorer for single-cell datasets.
- A link to the SEA-AD chromatin accessibility data in the UC Santa Cruz’s Genome Browser.
-The findings from the data release will be presented Tues, Aug. 2 at the Alzheimer’s Association International Conference in San Diego.
-The findings revealed certain types of neurons that are selectively vulnerable to disease and others that increase in abundance. Read more about the differences found in the Alzheimer’s patients’ cells in this Allen Institute article, Cell by cell, scientists are building a high-resolution map of brain changes in Alzheimer’s disease.
-This research was supported by the NIA awards U19AG060909, P30AG066509, and U19AG066567
-Stay tuned for future releases from the SEA-AD project that tackle new brain regions, new analyses, and include new data modalities.