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Single‐nuclei RNA‐seq of brains carriers of high‐risk variants and Mendelian mutations
Author(s) -
DelAguila Jorge L.,
Brase Logan,
Benitez Bruno A.,
Karch Celeste M.,
Cruchaga Carlos,
Harari Oscar
Publication year - 2020
Publication title -
alzheimer's and dementia
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.713
H-Index - 118
eISSN - 1552-5279
pISSN - 1552-5260
DOI - 10.1002/alz.043125
Subject(s) - microglia , psen1 , biology , trem2 , computational biology , cell type , mendelian inheritance , pseudogene , genetics , cell , gene , alzheimer's disease , genome , medicine , disease , pathology , amyloid precursor protein , myeloid cells , immunology , inflammation
Background AD has a substantial but heterogeneous genetic component, presenting both Mendelian and complex genetic architectures. We sought to investigate the glial and neuronal pathways affected by AD at the cell specific resolution. To do so, we generated unsorted brain single‐nuclei RNA‐sequence from carrier of a Mendelian mutation and high‐risk variants associated with AD from the Knight‐ADRC and DIAN brain banks. Methods We sequenced 74 parietal lobe from carriers of APP , PSEN1 and PSEN2 mutations (N = 19), and high‐risk variants, including APOE e4 (N = 26) and TREM2 ( N = 21), non‐carrier AD (N = 15) and neuropath‐free controls (N = 9). We employed the 10X Chromium 3’ chemistry V3, to sequence 10,000 nuclei and 40,000 reads per nuclei. In total. We generated data for more than 1,2 million nuclei. We applied stringent quality control and data cleaning procedures, including alternative methods to detect empty droplets and doublets, and used alternative clustering methods to a very large number of nuclei. We have assembled and curated a reference panel that we employ in different supervised and unsupervised methods to annotate the cell‐type of the different clusters. Results We have identified the expression profile of Neurons, Oligodendrocytes, astrocytes, OPC and other cell‐types in the brain (Figure 1). Our dataset includes more than 17,500 nuclei from microglia cells (minimum 100 and mean 285 nuclei per donor) that present alternative transcriptional profiles that resemble that of the Disease Associated Microglia and Human Alzheimer Microglia. Conclusion Single‐nuclei transcriptomic data from human brains provides a detailed molecular atlas to study the pathways dysregulated in AD. We have developed a unique resource to investigate amyloid‐beta protein clearance and degradation pathways, endolysosomal pathways, cholesterol metabolism and immune system contribution to AD etiology and pathogenesis.