TY - JOUR
T1 - A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain
AU - Del-Aguila, Jorge L.
AU - Li, Zeran
AU - Dube, Umber
AU - Mihindukulasuriya, Kathie A.
AU - Budde, John P.
AU - Fernandez, Maria Victoria
AU - Ibanez, Laura
AU - Bradley, Joseph
AU - Wang, Fengxian
AU - Bergmann, Kristy
AU - Davenport, Richard
AU - Morris, John C.
AU - Holtzman, David M.
AU - Perrin, Richard J.
AU - Benitez, Bruno A.
AU - Dougherty, Joseph
AU - Cruchaga, Carlos
AU - Harari, Oscar
N1 - Funding Information:
This work was supported by grants from the National Institutes of Health (R01AG057777, R01AG044546, P01AG003991, RF1AG053303, R01AG035083, and R01NS085419) and the Alzheimer Association (NIRG-11-200110, BAND-14-338165, and BFG-15-362540). We thank the McDonnell Center for Cellular and Molecular Neurobiology for the funds provided to generate the data we analyzed. BAB is supported by 2018 pilot funding from the Hope Center for Neurological Disorders and the Danforth Foundation Challenge at Washington University. The recruitment and clinical characterization of research participants at Washington University were supported by NIH P50 AG05681, P01 AG03991, and P01 AG026276. We would like to thank the operations staff at the Elizabeth H. and James S. McDonnell III Genome Institute at Washington University for their assistance in constructing the single-nuclei RNA-seq libraries and generating sequence data for our project. This work was also supported by access to the equipment made possible by the Hope Center for Neurological Disorders and the Departments of Neurology and Psychiatry at Washington University School of Medicine.
Publisher Copyright:
© 2019 The Author(s).
PY - 2019/8/9
Y1 - 2019/8/9
N2 - Background: Alzheimer's disease (AD) is the most common form of dementia. This neurodegenerative disorder is associated with neuronal death and gliosis heavily impacting the cerebral cortex. AD has a substantial but heterogeneous genetic component, presenting both Mendelian and complex genetic architectures. Using bulk RNA-seq from the parietal lobes and deconvolution methods, we previously reported that brains exhibiting different AD genetic architecture exhibit different cellular proportions. Here, we sought to directly investigate AD brain changes in cell proportion and gene expression using single-cell resolution. Methods: We generated unsorted single-nuclei RNA sequencing data from brain tissue. We leveraged the tissue donated from a carrier of a Mendelian genetic mutation, PSEN1 p.A79V, and two family members who suffer from sporadic AD, but do not carry any autosomal mutations. We evaluated alternative alignment approaches to maximize the titer of reads, genes, and cells with high quality. In addition, we employed distinct clustering strategies to determine the best approach to identify cell clusters that reveal neuronal and glial cell types and avoid artifacts such as sample and batch effects. We propose an approach to cluster cells that reduces biases and enable further analyses. Results: We identified distinct types of neurons, both excitatory and inhibitory, and glial cells, including astrocytes, oligodendrocytes, and microglia, among others. In particular, we identified a reduced proportion of excitatory neurons in the Mendelian mutation carrier, but a similar distribution of inhibitory neurons. Furthermore, we investigated whether single-nuclei RNA-seq from the human brains recapitulate the expression profile of disease-associated microglia (DAM) discovered in mouse models. We also determined that when analyzing human single-nuclei data, it is critical to control for biases introduced by donor-specific expression profiles. Conclusion: We propose a collection of best practices to generate a highly detailed molecular cell atlas of highly informative frozen tissue stored in brain banks. Importantly, we have developed a new web application to make this unique single-nuclei molecular atlas publicly available.
AB - Background: Alzheimer's disease (AD) is the most common form of dementia. This neurodegenerative disorder is associated with neuronal death and gliosis heavily impacting the cerebral cortex. AD has a substantial but heterogeneous genetic component, presenting both Mendelian and complex genetic architectures. Using bulk RNA-seq from the parietal lobes and deconvolution methods, we previously reported that brains exhibiting different AD genetic architecture exhibit different cellular proportions. Here, we sought to directly investigate AD brain changes in cell proportion and gene expression using single-cell resolution. Methods: We generated unsorted single-nuclei RNA sequencing data from brain tissue. We leveraged the tissue donated from a carrier of a Mendelian genetic mutation, PSEN1 p.A79V, and two family members who suffer from sporadic AD, but do not carry any autosomal mutations. We evaluated alternative alignment approaches to maximize the titer of reads, genes, and cells with high quality. In addition, we employed distinct clustering strategies to determine the best approach to identify cell clusters that reveal neuronal and glial cell types and avoid artifacts such as sample and batch effects. We propose an approach to cluster cells that reduces biases and enable further analyses. Results: We identified distinct types of neurons, both excitatory and inhibitory, and glial cells, including astrocytes, oligodendrocytes, and microglia, among others. In particular, we identified a reduced proportion of excitatory neurons in the Mendelian mutation carrier, but a similar distribution of inhibitory neurons. Furthermore, we investigated whether single-nuclei RNA-seq from the human brains recapitulate the expression profile of disease-associated microglia (DAM) discovered in mouse models. We also determined that when analyzing human single-nuclei data, it is critical to control for biases introduced by donor-specific expression profiles. Conclusion: We propose a collection of best practices to generate a highly detailed molecular cell atlas of highly informative frozen tissue stored in brain banks. Importantly, we have developed a new web application to make this unique single-nuclei molecular atlas publicly available.
KW - Alzheimer's disease
KW - PSEN1
KW - Single-nuclei RNA-seq
KW - Web-based brain molecular atlas
UR - http://www.scopus.com/inward/record.url?scp=85070617971&partnerID=8YFLogxK
U2 - 10.1186/s13195-019-0524-x
DO - 10.1186/s13195-019-0524-x
M3 - Article
C2 - 31399126
AN - SCOPUS:85070617971
SN - 1758-9193
VL - 11
JO - Alzheimer's Research and Therapy
JF - Alzheimer's Research and Therapy
IS - 1
M1 - 71
ER -