Mapping cell-type-specific regulatory genomic variation in Alzheimer's disease pathology.
Lead Research Organisation:
UNIVERSITY OF EXETER
Department Name: Institute of Biomed & Clinical Science
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disorder affecting >26 million people worldwide, with no disease-modifying treatments available. Despite major advances in identifying genetic risk factors for AD, there remains uncertainty about the specific causal genes involved and how their function is dysregulated during the progression of neuropathology.
Sequencing the genome was only the first step in our quest to understand how genes are expressed and regulated. Increased understanding about the functional complexity of the genome has led to recognition about the role of regulatory variation in health and disease. Sitting above the DNA sequence is a second layer of information (the 'epigenome') that mediates the regulation of when and where genes are functionally transcribed. These mechanisms play a critical role in determining cell-type-specific patterns of gene transcription in the human brain.
Previous genomic analyses of AD brain have been limited by their use of 'bulk' tissue, comprising a mix of different neural cell-types. Because AD is characterised by changes in specific cell-types (for example it involves the extensive loss of neurons and the proliferation of glial cells) it is critical to consider cellular differences in gene regulation. Our study will, for the first time, systematically examine the role of regulatory genomic processes in specific cell types in AD pathology.
Our innovative proposal leverages the unprecedented brain-banking efforts currently taking place in the UK, specifically within the Brains for Dementia Research (BDR) cohort. We propose an integrative-genomics approach, profiling purified populations of cortical nuclei from donors with low and high levels of AD pathology. Our project has the following key aims
First, we will profile markers of epigenomic regulation in purified nuclei from three different cell types (neurons, oligodendrocytes and microglia) isolated from cortex tissue from donors with low and high levels of AD pathology.
Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets.
Third, we will examine how AD-associated genetic variation influences gene regulation in specific cortical cell-types.
Our team is uniquely placed to undertake this ambitious project given our pioneering work assessing epigenomic variation in AD brain and our role in developing novel methods for regulatory genomic profiling across distinct neural cell-types.
Finally, we are passionate advocates for Open Science, and we will make all data and methods freely available to the wider research community. In conjunction with the extensive clinical and neuropathological data being collected on each donor included in the study, we will generate an unrivalled data resource that will stimulate dementia research and enable a step-change in understanding of the mechanistic pathways involved in AD.
Sequencing the genome was only the first step in our quest to understand how genes are expressed and regulated. Increased understanding about the functional complexity of the genome has led to recognition about the role of regulatory variation in health and disease. Sitting above the DNA sequence is a second layer of information (the 'epigenome') that mediates the regulation of when and where genes are functionally transcribed. These mechanisms play a critical role in determining cell-type-specific patterns of gene transcription in the human brain.
Previous genomic analyses of AD brain have been limited by their use of 'bulk' tissue, comprising a mix of different neural cell-types. Because AD is characterised by changes in specific cell-types (for example it involves the extensive loss of neurons and the proliferation of glial cells) it is critical to consider cellular differences in gene regulation. Our study will, for the first time, systematically examine the role of regulatory genomic processes in specific cell types in AD pathology.
Our innovative proposal leverages the unprecedented brain-banking efforts currently taking place in the UK, specifically within the Brains for Dementia Research (BDR) cohort. We propose an integrative-genomics approach, profiling purified populations of cortical nuclei from donors with low and high levels of AD pathology. Our project has the following key aims
First, we will profile markers of epigenomic regulation in purified nuclei from three different cell types (neurons, oligodendrocytes and microglia) isolated from cortex tissue from donors with low and high levels of AD pathology.
Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets.
Third, we will examine how AD-associated genetic variation influences gene regulation in specific cortical cell-types.
Our team is uniquely placed to undertake this ambitious project given our pioneering work assessing epigenomic variation in AD brain and our role in developing novel methods for regulatory genomic profiling across distinct neural cell-types.
Finally, we are passionate advocates for Open Science, and we will make all data and methods freely available to the wider research community. In conjunction with the extensive clinical and neuropathological data being collected on each donor included in the study, we will generate an unrivalled data resource that will stimulate dementia research and enable a step-change in understanding of the mechanistic pathways involved in AD.
Technical Summary
We propose the most comprehensive analysis of regulatory genomic variation associated with Alzheimer's disease (AD). The project builds on our previous work assessing the role of epigenomic variation in AD and success in developing methods for regulatory genomic profiling across distinct neural cell-types.
First, we will profile multiple markers of genomic regulation (DNA methylation, DNA hydroxymethylation, lysine H3K27 acetylation (H3K27ac) and chromatin accessibility) in purified nuclei populations from the dorsolateral prefrontal cortex (DLPFC) from 200 donors with low and high AD neuropathology. We will use a fluorescence-activated nuclei sorting (FANS) protocol developed by our group to simultaneously purify nuclei from neurons, oligodendrocytes and microglia prior to genomic profiling.
Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets. We will use cell-type-specific epigenomic data to develop and validate cellular deconvolution algorithms, enabling us to leverage large existing AD genomic datasets generated by us and our collaborators for replication. We will also integrate our cell-type-specific epigenomic data with single nuclei transcriptomic data from the Multi-Omics Atlas Project (MAP) funded by the UK Dementia Research Institute (DRI). Finally, we will explore overlap with cortical genomic changes identified in our ongoing analyses of transgenic mouse models of tau and amyloid pathology.
Finally, we will integrate cell-type-specific genomic annotations with AD genetic data, exploring the extent to which AD-associated variants are enriched for regulatory quantitative trait loci (QTLs). We will extend our use of co-localization approaches and Summary data-based Mendelian Randomization (SMR) analyses to identify variants that are pleiotropically associated with both AD and regulatory variation in specific cortical cell-types.
First, we will profile multiple markers of genomic regulation (DNA methylation, DNA hydroxymethylation, lysine H3K27 acetylation (H3K27ac) and chromatin accessibility) in purified nuclei populations from the dorsolateral prefrontal cortex (DLPFC) from 200 donors with low and high AD neuropathology. We will use a fluorescence-activated nuclei sorting (FANS) protocol developed by our group to simultaneously purify nuclei from neurons, oligodendrocytes and microglia prior to genomic profiling.
Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets. We will use cell-type-specific epigenomic data to develop and validate cellular deconvolution algorithms, enabling us to leverage large existing AD genomic datasets generated by us and our collaborators for replication. We will also integrate our cell-type-specific epigenomic data with single nuclei transcriptomic data from the Multi-Omics Atlas Project (MAP) funded by the UK Dementia Research Institute (DRI). Finally, we will explore overlap with cortical genomic changes identified in our ongoing analyses of transgenic mouse models of tau and amyloid pathology.
Finally, we will integrate cell-type-specific genomic annotations with AD genetic data, exploring the extent to which AD-associated variants are enriched for regulatory quantitative trait loci (QTLs). We will extend our use of co-localization approaches and Summary data-based Mendelian Randomization (SMR) analyses to identify variants that are pleiotropically associated with both AD and regulatory variation in specific cortical cell-types.
Publications
Nabais MF
(2023)
An overview of DNA methylation-derived trait score methods and applications.
in Genome biology
Pihlstrøm L
(2022)
Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology.
in Nature communications
Seiler Vellame D
(2022)
Uncertainty quantification of reference based cellular deconvolution algorithms
Shireby G
(2022)
DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types.
in Nature communications
Wang Y
(2024)
Insights into ageing rates comparison across tissues from recalibrating cerebellum DNA methylation clock.
in GeroScience
Description | Defining Best Practises for Data Science Education across Disciplines |
Amount | £16,191 (GBP) |
Organisation | Alan Turing Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2023 |
End | 01/2024 |
Description | Exeter Brain Network |
Amount | £10,000 (GBP) |
Organisation | University of Exeter |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2023 |
End | 01/2024 |
Description | Collaboration with Cambridge Epigenetix |
Organisation | Cambridge Epigenetix |
Country | United Kingdom |
Sector | Private |
PI Contribution | Our lab is beta testing a new chemistry for profiling DNA methylation and DNA hydroxymethylation. |
Collaborator Contribution | We were provided with early access to a new kit, free of charge. |
Impact | Experiments ongoing. |
Start Year | 2023 |
Description | Collaboration with John Hardy and group, UCL |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are working with John Hardy and his team on a collaboration to use long-read sequencing to map isoform diversity in Alzheimer's disease. |
Collaborator Contribution | We are sharing protocols, analysis pipelines and data. |
Impact | We aim to submit a new research grant in the next year. |
Start Year | 2023 |
Description | Collaboration with Twist Bioscience |
Organisation | Twist Bioscience |
Country | United States |
Sector | Private |
PI Contribution | We are collaborating with them on new applications for their DNA methylation profiling methods -- Exploring the utility of EM-Seq with a targeted methylation system for cfDNA biomarker discovery |
Collaborator Contribution | They are providing reagents for us to use. |
Impact | We are currently optimising the method and will be applying to clinical samples soon. |
Start Year | 2022 |
Title | Scripts for our RNA-seq analysis of tau and amyloid pathology |
Description | Scripts for our RNA-seq analysis of tau and amyloid pathology |
Type Of Technology | Software |
Year Produced | 2023 |
Impact | Other researchers have used these methods to process their own long-read sequencing data. |
Description | - London Calling, Oxford Nanopore Technologies Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Invited platform presentation at flagship ONT meeting in London. Title - Long read transcriptome sequencing reveals isoform diversity across human neurodevelopment and aging. |
Year(s) Of Engagement Activity | 2022 |
URL | https://londoncallingconf.co.uk/lc23 |
Description | Neurogenomics Seminar - Imperial College London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Members of the team were invited to present our work at the online [international reach] Imperial College London neuogenomics seminar. Several hundred attendees joined the meeting and many questions were asked. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.youtube.com/watch?v=32_R9P_T0sQ |
Description | Presentations at the World Congress of Psychiatric Genetics, Florence, Italy. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We gave multiple presentations at the 2022 WCPG meeting in Florence, showcasing the results of our research projects. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.emedevents.com/c/medical-conferences-2022/world-congress-of-psychiatric-genetics-wcpg-20... |