SCAD-Brain: a public database of single cell RNA-seq data in human and mouse brains with Alzheimer's disease

Abstract

IntroductionAlzheimer's disease (AD), a severe neurodegenerative disorder, is the most common type of dementia, affecting 57.4 million patients worldwide in 2019 and will reach 152.8 million by 2050 (GBD 2019 Dementia Forecasting Collaborators, 2022).However, there is currently no effective treatment for AD (Gao et al., 2016).Part of the reason is the lacking understanding of the high cellular heterogeneity in AD brains, which is closely associated with the onset, progression, and pathological process of AD (Lau et al., 2020).Single-cell RNA sequencing (scRNA-seq) is extremely effective in interpreting the cellular heterogeneity of AD (Habib et al., 2020).Advances in scRNA-seq technologies in the past decade have generated a large amount of AD scRNA-seq data, but studies integrated these multi-source data are rare, which greatly limited non-bioinformatics users' access to such public data.Therefore, it is essential to establish a database that collects AD scRNA-seq data.Here, we collected 17 AD or mild cognitive impairment (MCI) scRNA-seq projects from the Gene Expression Omnibus (GEO) and the Synapse databases, covering 21 datasets with 359 samples, 10 brain regions, 16 major brain cell types, and 1,564,825 cells to explore cellular heterogeneity, cell communication, and cell trajectory in brain tissues with AD/MCI pathology.The results were integrated into a database named SCAD-Brain (scRNA-seq analysis for AD Brain, https://www.bioinform.cn/SCAD/).The users can access, reuse, and analyze the data by visiting the website, to perform cell marker analysis, gene expression analysis, pathway enrichment analysis, cell communication analysis, and cell trajectory analysis for multiple brain regions from patients with AD/MCI and AD mouse models.SCAD-Brain provides a user-friendly platform to explore and visualize scRNA-seq data of AD brain, assist in experiments design, verify hypotheses, and especially investigate the cellular heterogeneity of AD brain.. Methods . . Data collection and quality controlRaw data of AD brain scRNA-seq from the GEO database and Synapse database were collected in October 2021.For data collection through the GEO database, medical subject headings of AD and scRNA-seq were collected from the MeSH database to build Frontiers in Aging Neuroscience frontiersin.org

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