Deciphering the cellular phase of AD using Single Cell Genomics

Lead Research Organisation: University College London

Abstract

Lay abstract
(around 200 words – max. 1,500 characters including spaces) We aim to understand the mechanisms that lead to Alzheimer’s disease, and the mechanisms that preserve brain function in healthy elderly people. Alzheimer’s disease is the main cause of dementia, currently affecting over 850,000 people in the UK and 50 million people worldwide. Alzheimer’s disease is thought to be initiated by the constant build-up over time of protein aggregates which eventually impair proper brain function. We do not know yet how these aggregates affect the brain and how they lead to dementia. Remarkably, some elderly people do have similar aggregates in their brains, but are not affected by dementia, suggesting that they have developed resistance mechanisms. Our goal is to identify the molecular mechanism that impart such resistance, and to develop strategies to activate the same protective mechanisms in patients to delay or cure dementia. We will analyse brain tissue donated by patients who died with dementia, and by people who were not affected. We will use recently developed methods to identify the genes which confer resistance to the development of dementia, and the genes which are responsible for the disease progression. Further, since the symptoms of Alzheimer’s disease are not the same for all patients, we will identify the genes responsible for different symptoms, so that we will be able to develop treatments tailored for each specific patient.

Technical Summary

The UK Dementia Research Institute (UK DRI) is an initiative funded by the Medical Research Council, Alzheimer's Society and Alzheimer's Research UK.

Scientific abstract
(around 400 words – max. 3,500 characters including spaces) The theme of the laboratory is to identify and characterize the cellular and molecular mechanisms which differentiate healthy brain ageing from dementia. In first instance, we are looking for the cellular alterations which, once initiated by the formation and deposition of protein aggregates (e.g. amyloid-beta and tau in Alzheimer’s disease), determine the clinical outcome of dementia. At the same time, our aim is to identify the cellular and molecular mechanisms that enable the preservation of intact brain functions in individuals which are clinically devoid of dementia while displaying signs of biochemical neuropathology. Indeed, cognitively intact elderly people may still display extensive amyloid-beta deposition.
Neurodegenerative diseases are characterized by the appearance of biochemically defined toxic insults which lead to stereotypical clinical presentations. As it appears increasingly evident, our current therapeutic approaches targeting the biochemical units causing disease are ill-timed, as by the time we can detect clinical signs of dementia, the biochemical mechanisms have already ignited self-sustaining cellular mechanisms which support pathology. Therefore, it is paramount to identify the cellular mechanisms leading to clinic manifestations of dementia, and we should do this by focusing not just on a single cell type, but on the whole set of cells making up the human brain, and on their interactions. Our approach is to use single cell genomics techniques, which allow to break down tissue heterogeneity and to identify changes in transcriptomic, epigenomic and proteomic makeup of individual cells. Aggregation of data collected across thousands of cells for each single brain tissue sample allows then to recapitulate the tissue-wide genomic and proteomic organization, while maintaining vital information about rare cell populations (e.g. activated microglia, perivascular macrophages,…) which cannot be captured using a classical “bulk tissue” approach.
We collaborate extensively with the Queen Square Brain Bank, to access neuropathologically well-characterized tissue samples coming from people for which extensive clinical records are available. We will compare the transcriptome and epigenome of tissue samples from dementia-affected patients and from cognitively intact subjects, either displaying signs of protein aggregation or free from them. Thus, we will identify the mechanisms underlying resistance to pathology, and the cellular events leading to Alzheimer’s disease. The next step will be to identify ways through which we can activate the resistance pathways in affected patients, to delay or cure dementia. Of importance, our approach will highlight not just the genes responsible, but the actual cellular populations to target, making the design of a therapy more targeted, and hence more effective.
 
Description UK DRI Pilot Study programme
Amount £44,000 (GBP)
Organisation UK Dementia Research Institute 
Sector Charity/Non Profit
Country United Kingdom
Start  
 
Description UK DRI Pilot Study programme
Amount £49,940 (GBP)
Organisation UK Dementia Research Institute 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2021 
End 04/2022
 
Title single cell RNA seq of mouse microglia 
Description We have performed single cell RNA-seq (scRNAseq) of single, live, microglia cells isolated from a mouse model of Alzheimer's disease (APP NL-G-F) and from control C57BL/6 mice. We have analysed microglia isolated from either cortex and hippocampus, from male and female mice, at four time points during amyloid pathology progression (3, 6, 12 and 21 months of age). In total, we have analysed over 10,000 single microglia transcriptomes across 32 experimental conditions. We have analysed the data and identified multiple microglia sub-populations, demonstrating age-, sex-, tissue- and genotype- effects. The results of our data analysis have been published (Sala Frigerio C. et al., 2019 Cell Reports). 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact The paper describing the dataset has received excellent attention (36 citations in less than a year) and the data have been used by at least another publication (Mancuso R et al., 2019 Nature Neuroscience). 
URL https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127893
 
Description Characterisation of a rat microglia cell platform 
Organisation Alzheimer's Research UK
Department UCL Drug Discovery Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The goal of the collaboration is to characterise a rat microglia cell platform for drug testing. We will characterise the heterogeneity of the cellular cultures in naive and stimulated/treated conditions using single cell RNA sequencing. We will optimise conditions for the preparation of sequencing libraries by adopting a CITE-seq approach: we will label each sample with a unique antibody-oligonucleotide barcode conjugate so that multiple samples can be pooled prior to library preparation, sequencing reads can then be retrieved and assigned to each respective sample. This approach has the advantage of reducing costs of library preparation and sequencing. My lab has proposed and planned the experimental strategy, prepared single cell RNA-sequencing libraries and analysed data.
Collaborator Contribution Partner has developed the rat microglia platform, including cell isolation and culturing. Partner has optimised antibody staining of microglia for CITE-seq. Partner will further analyse data, under my team's supervision.
Impact No output yet.
Start Year 2019
 
Description Characterisation of neuroinflammation in Alzheimer's disease associated with Down syndrome 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Preparation and analysis of single nucleus RNA seq libraries from brain tissue samples of individuals with Down syndrome.
Collaborator Contribution Procuration of well characterised tissue samples, validation experiments, development of cellular models.
Impact No output yet - together with the collaborator we have received a grant from the Rosetree trust in 2020 to fund this project.
Start Year 2020
 
Description Molecular neuropathology of dementia 
Organisation University College London
Department Queen Square Brain Bank
Country United Kingdom 
Sector Hospitals 
PI Contribution We have initiated a collaboration with Queen Square Brain Bank (QSBB) to integrate the neuropathological analysis of brain tissue (performed by QSBB) with transcriptomic and genomic analysis of the tissue (performed by us).
Collaborator Contribution QSBB has identified the tissue samples most relevant for our scientific question, and has provided the tissue responding to our technical needs. QSBB will review the data that we provide, in light of the clinical and neuropathological assessment of the donor.
Impact No output yet.
Start Year 2018
 
Description Selective neuronal vulnerability in C9orf72 models 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Single nucleus RNA seq analysis (optimisation of sample preparation, preparation of libraries, data analysis) of models of C9orf72 toxicity.
Collaborator Contribution Developement and characterisation of Drosophila melanogaster and mouse models of C9orf72 toxicity.
Impact No output yet - the collaborator (Teresa Niccoli) received an MRC grant in 2020 to fund this project.
Start Year 2020