A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain

Abstract

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. Electronic supplementary material The online version of this article (10.1186/s13195-019-0524-x) contains supplementary material, which is available to authorized users.

Neuroinflammation and protein pathology in Parkinson’s disease dementia

“…Therefore, future work in postmortem brain could make use of additional markers such as P2RY12 and TMEM119 (homeostatic microglia) [ 4 ], and TREM2 (DAM) to better understand the role of microglia in PD. Future work could also utilise comprehensive genome-wide expression analyses which have become possible through the use of protocols to isolate microglia from human brain tissue [ 58 ] or by singe-cell RNA sequencing using bulk tissue, as has recently been done in Alzheimer’s disease postmortem brain [ 14 ].…”

A meta-analysis of the effect of binge drinking on the oral microbiome and its relation to Alzheimer’s disease

“…The single cell level response due to the alteration of the oral microbiome in the presence of alcohol can provide insight into the continuous cellular response and mechanism that may lead to the permeability of BBB and eventually AD 59 . This technique has been used to study the effects of LPS in neuroinflammatory responses and also 2 different AD studies [60][61][62] . By using scRNA-seq, the distinct types of neurons, glial cells and microglia can be precisely identified by this change 61 .…”

“…This technique has been used to study the effects of LPS in neuroinflammatory responses and also 2 different AD studies [60][61][62] . By using scRNA-seq, the distinct types of neurons, glial cells and microglia can be precisely identified by this change 61 . This method can also be used to further profile the diversity of the oral cavity as seen in the study done on the effects of koumiss on the oral microbiome 63 .…”

Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases

“…Among them, long-read sequencing (e.g., Oxford Nanopore Technology) enables the detection of structural variants [ 116 ], short tandem repeats (STR) [ 117 ], and variable number of tandem repeats (VNTRs) [ 118 ]. High-throughput RNA sequencing (RNA-seq) transcriptomics (e.g., single-cell and single-nuclei RNA-seq) can identify expression signatures potentially associated with disease pathology, providing important insights into potential subpopulations of cells directly involved in disease [ 119 ]. A study showed that the brain of carriers of rare pathogenic APP , PSEN1 , or PSEN2 mutations presented with lower neuron and higher astrocyte relative proportions compared to sporadic AD patients [ 120 ].…”