JPND TRanslating Individual Alzheimer GEnetic risk into disease phenotypes
Lead Research Organisation:
CARDIFF UNIVERSITY
Department Name: School of Medicine
Abstract
By sequencing the genome of an individual, we can calculate a measure called a polygenic risk score (PRS). This is a single number that represents the risk that that individual has for developing a particular disease, such as Alzheimer's disease. We will be creating PRSs for two groups of individuals - one group from a memory clinic, and one group who have a high genetic risk for developing Alzheimer's disease. We will then take some cell samples from a subset of those individuals and turn them into pluripotent cells - cells which have the potential to become any other type of cell. We will differentiate these cells into microglia, which are a type of cell found between neurons in the brain. Microglia have recently been linked to the development of Alzheimer's disease. We can take these microglia and look at how they behave when transplanted into mice, and when interacting with simple brain models called organoids. From this we can learn how the PRSs we have calculated are linked to the way that microglia behave in the brain. This will teach us about how risk for developing Alzheimer's disease translates into the behavior of cells in the brain. This has the potential to point us towards new interventions and medicines for Alzheimer's patients, and will provide new information for researchers developing clinical trials.
Technical Summary
We here propose to develop a method to link the individual genetic risk of developing AD to functional information about the underlying disease process and manifestations with focus on the microglia. We will genotype 200 participants from a memory-clinic based cohort of individuals with biomarker-proven AD at different clinical stages (prodromal, early, mid and late dementia stage). We will also include 180 participants from a longitudinal observation cohort of older adults at high genetic risk of developing AD. We will calculate Polygenic Risk Scores and profile the immune system of all individuals, and integrate those data with clinical data to obtain a complete map linking genetic profiles and disease manifestations across the entire spectrum of AD.
From a selected subset of individuals across this map, we will generate induced pluripotent stem cells and differentiate them into microglia. We will then investigate microglia responses unbiasedly by single-cell RNA sequencing and functionally on synapse, amyloid and Tau effects, both in vivo in the context of a mature brain, after transplantation into mouse models for Abeta and/or Tau pathology, and in vitro in brain organoids. Both datasets will be benchmarked against ex-vivo human brain tissue. We will investigate how different PRS affect the response of microglia to amyloid plaques, neuronal tangles and their interaction with synapses. This work will establish how AD genetic risk translates into microglia behavior, and point to molecular and cellular pathways contributing to pathogenesis.
By maximally exploiting clinical and research data and linking them to an individual risk score, this project will establish a roadmap towards precision medicine for AD. Our results will reveal novel therapeutic targets in AD and lay the foundations of a pre-clinical drug testing platform for AD.
From a selected subset of individuals across this map, we will generate induced pluripotent stem cells and differentiate them into microglia. We will then investigate microglia responses unbiasedly by single-cell RNA sequencing and functionally on synapse, amyloid and Tau effects, both in vivo in the context of a mature brain, after transplantation into mouse models for Abeta and/or Tau pathology, and in vitro in brain organoids. Both datasets will be benchmarked against ex-vivo human brain tissue. We will investigate how different PRS affect the response of microglia to amyloid plaques, neuronal tangles and their interaction with synapses. This work will establish how AD genetic risk translates into microglia behavior, and point to molecular and cellular pathways contributing to pathogenesis.
By maximally exploiting clinical and research data and linking them to an individual risk score, this project will establish a roadmap towards precision medicine for AD. Our results will reveal novel therapeutic targets in AD and lay the foundations of a pre-clinical drug testing platform for AD.
Planned Impact
The most immediate impact of TRIAGE will be the ability to use PRS to refine inclusion criteria for clinical trials. Genetic stratification is already used today, for example in the Generation Program (a collaboration between Novartis, Amgen and the Banner Alzheimer's Institute), but it relies only on one gene polymorphism (APOE). The whole-genome and pathway-specific PRS defined in the present study will allow a much more precise stratification, supported by extensive knowledge of the associated microglia biology and clinical manifestations. Similarly, pathway-specific PRS will enable to determine the predisposition to disease and deliver timely and targeted prevention, for example by implementing specific diets (e.g. LipidiDiet study, http://www.lipididiet.eu/) for individuals having a high lipid-associated pathway PRS.
In the mid-term, we expect that our study will impact all aspects of personalised medicine and will impact the entire healthcare system by:
- exploiting innovative and human relevant pre-clinical models to gain a deeper understanding of the biological mechanisms that trigger and drive AD;
- developing effective therapeutic interventions based on these biological insights by using translatable models and performing clinical trials on carefully stratified populations;
- using whole-genome and pathway-specific PRS for early screening and to tailor the right therapeutic strategy for each individual at any given time, thus effectively improving care.
In the mid-term, we expect that our study will impact all aspects of personalised medicine and will impact the entire healthcare system by:
- exploiting innovative and human relevant pre-clinical models to gain a deeper understanding of the biological mechanisms that trigger and drive AD;
- developing effective therapeutic interventions based on these biological insights by using translatable models and performing clinical trials on carefully stratified populations;
- using whole-genome and pathway-specific PRS for early screening and to tailor the right therapeutic strategy for each individual at any given time, thus effectively improving care.
Organisations
- CARDIFF UNIVERSITY (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- University of California, Irvine (Collaboration)
- Catalan Health Institute (ICS) (Collaboration)
- The Hong Kong University of Science and Technology (Collaboration)
- Stanford University (Collaboration)
- University of Liege (Collaboration)
- Syracuse University (Collaboration)
- University of Leuven (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
People |
ORCID iD |
Valentina Escott-Price (Principal Investigator) |
Publications
Akingbuwa W
(2020)
Genetic Associations Between Childhood Psychopathology and Adult Depression and Associated Traits in 42 998 Individuals A Meta-analysis
in JAMA Psychiatry
Amare AT
(2021)
Association of polygenic score for major depression with response to lithium in patients with bipolar disorder.
in Molecular psychiatry
Baker E
(2020)
Polygenic Risk Scores in Alzheimer's Disease: Current Applications and Future Directions
in Frontiers in Digital Health
Baker E
(2023)
What does heritability of Alzheimer's disease represent?
in PLOS ONE
Baldacci F
(2020)
Age and sex impact plasma NFL and t-Tau trajectories in individuals with subjective memory complaints: a 3-year follow-up study.
in Alzheimer's research & therapy
Bellenguez C
(2022)
New insights into the genetic etiology of Alzheimer's disease and related dementias.
in Nature genetics
Bellou E
(2020)
Age-dependent effect of APOE and polygenic component on Alzheimer's disease.
in Neurobiology of aging
Bellou E
(2020)
Polygenic risk and pleiotropy in neurodegenerative diseases.
in Neurobiology of disease
Bellou E
(2022)
Are Alzheimer's and coronary artery diseases genetically related to longevity?
in Frontiers in psychiatry
Bracher-Smith M
(2022)
Machine learning for prediction of schizophrenia using genetic and demographic factors in the UK biobank.
in Schizophrenia research
Bracher-Smith M
(2022)
Whole genome analysis in APOE4 homozygotes identifies the DAB1-RELN pathway in Alzheimer's disease pathogenesis.
in Neurobiology of aging
Bracher-Smith M
(2021)
Machine learning for genetic prediction of psychiatric disorders: a systematic review.
in Molecular psychiatry
Caseras X
(2021)
Effects of genomic copy number variants penetrant for schizophrenia on cortical thickness and surface area in healthy individuals: analysis of the UK Biobank.
in The British journal of psychiatry : the journal of mental science
Chambers T
(2022)
Genetic common variants associated with cerebellar volume and their overlap with mental disorders: a study on 33,265 individuals from the UK-Biobank.
in Molecular psychiatry
Coleman JRI
(2020)
Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank.
in Molecular psychiatry
Costa B
(2020)
C9orf72, age at onset, and ancestry help discriminate behavioral from language variants in FTLD cohorts.
in Neurology
Crawford K
(2023)
Golgi apparatus, endoplasmic reticulum and mitochondrial function implicated in Alzheimer's disease through polygenic risk and RNA sequencing.
in Molecular psychiatry
De Rojas I
(2021)
Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.
in Nature communications
Dennison CA
(2021)
Association of genetic liability for psychiatric disorders with accelerometer-assessed physical activity in the UK Biobank.
in PloS one
Di Florio A
(2021)
Post-partum psychosis and its association with bipolar disorder in the UK: a case-control study using polygenic risk scores.
in The lancet. Psychiatry
Donnelly N
(2023)
Identifying the neurodevelopmental and psychiatric signatures of genomic disorders associated with intellectual disability: a machine learning approach.
in Molecular autism
Escott-Price V
(2021)
Correction to: Probability of Alzheimer's disease based on common and rare genetic variants.
in Alzheimer's research & therapy
Escott-Price V
(2021)
Probability of the Alzheimer's disease based on common and rare genetic variants
Escott-Price V
(2020)
Challenges of Adjusting Single-Nucleotide Polymorphism Effect Sizes for Linkage Disequilibrium
in Human Heredity
Escott-Price V
(2023)
Pitfalls of predicting age-related traits by polygenic risk scores.
in Annals of human genetics
Escott-Price V
(2021)
Probability of Alzheimer's disease based on common and rare genetic variants
in Alzheimer's Research & Therapy
Escott-Price V
(2022)
Genome-wide association studies for Alzheimer's disease: bigger is not always better.
in Brain communications
Grama S
(2020)
Polygenic risk for schizophrenia and subcortical brain anatomy in the UK Biobank cohort.
in Translational psychiatry
Guelfi S
(2020)
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information.
in Nature communications
Hampel H
(2020)
ß-Secretase1 biological markers for Alzheimer's disease: state-of-art of validation and qualification.
in Alzheimer's research & therapy
Hardy J
(2022)
Diabetes and Alzheimer's disease: shared genetic susceptibility?
in The Lancet. Neurology
Harrison JR
(2023)
Pathway-specific polygenic scores for Alzheimer's disease are associated with changes in brain structure in younger and older adults.
in Brain communications
Harrison JR
(2020)
From Polygenic Scores to Precision Medicine in Alzheimer's Disease: A Systematic Review.
in Journal of Alzheimer's disease : JAD
Harwood JC
(2021)
Defining functional variants associated with Alzheimer's disease in the induced immune response.
in Brain communications
Hou J
(2022)
Polygenic resilience scores capture protective genetic effects for Alzheimer's disease.
in Translational psychiatry
Iwaki H
(2020)
Penetrance of Parkinson's Disease in LRRK2 p.G2019S Carriers Is Modified by a Polygenic Risk Score.
in Movement disorders : official journal of the Movement Disorder Society
Kamitaki N
(2020)
Complement genes contribute sex-biased vulnerability in diverse disorders.
in Nature
Karlsson IK
(2022)
Measuring heritable contributions to Alzheimer's disease: polygenic risk score analysis with twins.
in Brain communications
Katzourou I
(2021)
Cognitive Decline in Alzheimer's Disease Is Not Associated with APOE
in Journal of Alzheimer's Disease
Lancaster T
(2023)
Proof-of-concept recall-by-genotype study of extremely low and high Alzheimer's polygenic risk reveals autobiographical deficits and cingulate cortex correlates
in Alzheimer's Research & Therapy
Le Guen Y
(2023)
Multiancestry analysis of the HLA locus in Alzheimer's and Parkinson's diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes
in Proceedings of the National Academy of Sciences
Leonard H
(2020)
Genetic variability and potential effects on clinical trial outcomes: perspectives in Parkinson's disease.
in Journal of medical genetics
Leonenko G
(2021)
Identifying individuals with high risk of Alzheimer's disease using polygenic risk scores.
in Nature communications
Description | "UK DRI IPSC platform to model Alzheimer's disease risk (IPMAR) " |
Amount | £1,866,149 (GBP) |
Organisation | UK Dementia Research Institute |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 01/2021 |
End | 07/2023 |
Description | 3/3 Sequencing and Trans-Diagnostic Phenotyping of Severe Mental Illness in Diverse |
Amount | £413,336 (GBP) |
Organisation | National Institute of Mental Health |
Sector | Public |
Country | United States |
Start | 09/2022 |
End | 08/2027 |
Description | Bioinformatics and Functional Genomics |
Amount | £1,250,000 (GBP) |
Organisation | UK Dementia Research Institute |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2023 |
End | 03/2028 |
Description | Genetics collaboration with Prof Bart De Strooper UK DRI programme |
Amount | £50,000 (GBP) |
Organisation | UK Dementia Research Institute |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 05/2021 |
End | 04/2022 |
Description | Leveraging human genetics to identify target populations for dementia therapeutics (Eisai/DRI), project grant |
Amount | £200,000 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2020 |
End | 02/2023 |
Description | Polygenic risk scores for neurodegeneration and Alzheimer's pathophysiology |
Amount | £951 (GBP) |
Organisation | UK Dementia Research Institute |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 08/2020 |
End | 11/2021 |
Description | Cambridge Centre for Ageing and Neuroscience |
Organisation | University of Cambridge |
Department | Cambridge Neuroscience |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | My research team has received the permission and access to the genetic data of the CamCan cohort with the aim to analyse the genetic data and calculate dementia related PRS for this cohort. |
Collaborator Contribution | The partners have provided us with the data |
Impact | not yet |
Start Year | 2022 |
Description | DPUK-2 (2020 - 2023) |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Calculation of pathway specific PRS, relevant to the Neuroinflammation work package. |
Collaborator Contribution | Access to the DPUK cohorts |
Impact | data access to DPUK cohorts |
Start Year | 2020 |
Description | GR@CE |
Organisation | Catalan Health Institute (ICS) |
Country | Spain |
Sector | Public |
PI Contribution | we analyse the genome-wide data |
Collaborator Contribution | the collaborators provided the data to us |
Impact | it is a multidisciplinary collaboration, involve clinicians, biologists and bioinformaticians |
Start Year | 2020 |
Description | GWAIS |
Organisation | University of Liege |
Country | Belgium |
Sector | Academic/University |
PI Contribution | We bring our expertise in AI and ML |
Collaborator Contribution | Collaborators bring their expertise in genetic interaction analyses. |
Impact | It is a multidisciplinary collaboration involving mathematicians, software developers and bioinformaticians |
Start Year | 2021 |
Description | Harvard University |
Organisation | Harvard University |
Department | Harvard Medical School |
Country | United States |
Sector | Academic/University |
PI Contribution | generation of polygenic risk scores |
Collaborator Contribution | provision of tissue samples and genotyped data |
Impact | none yet |
Start Year | 2019 |
Description | Hong Kong University of Science and Technology |
Organisation | The Hong Kong University of Science and Technology |
Country | Hong Kong |
Sector | Academic/University |
PI Contribution | Then HKUST will provide the summary statistics from the previous publication work (DOI: 10.1073/pnas.1715554115) to Cardiff to test if models derived from the Chinese population data can be used for disease classification in the European-descent population. |
Collaborator Contribution | The Cardiff will provide the models derived from the European population, and HKUST will help to examine if those models can classify AD in the Chinese population. |
Impact | NA |
Start Year | 2022 |
Description | Leuven University |
Organisation | University of Leuven |
Country | Belgium |
Sector | Academic/University |
PI Contribution | generation of polygenic risk scores |
Collaborator Contribution | sharing genotyped data and PRS |
Impact | none yet |
Start Year | 2018 |
Description | Lothian birth cohorts |
Organisation | University of Edinburgh |
Department | Edinburgh Neuroscience |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | My research team will analyse the genetic and phenotypic data from the Lothian birth cohorts with the primary aim to investigate genetic of cognitive rate of decline in healthy ageing cohort. |
Collaborator Contribution | Provided the data. |
Impact | not yet |
Start Year | 2022 |
Description | Stanford University |
Organisation | Stanford University |
Country | United States |
Sector | Academic/University |
PI Contribution | generation of polygenic risk scores |
Collaborator Contribution | sharing genotyped data and PRS |
Impact | none yet |
Start Year | 2019 |
Description | Syracuse University |
Organisation | Syracuse University |
Country | United States |
Sector | Academic/University |
PI Contribution | still under negotiation |
Collaborator Contribution | data analysis consultancy |
Impact | none yet |
Start Year | 2019 |
Description | UC Irvine |
Organisation | University of California, Irvine |
Country | United States |
Sector | Academic/University |
PI Contribution | generation of polygenic risk scores |
Collaborator Contribution | sharing genotyped data and PRS |
Impact | none yet |
Start Year | 2019 |
Description | ARUK Oxford Drug Discovery Institute |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presenter at the ARUK Oxford Drug Discovery Institute (ODDI) Collaborators meeting |
Year(s) Of Engagement Activity | 2020 |
Description | Artificial Intelligence for Precision Dementia Medicine Summit at the Royal Society |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited to the round table discussion at the Artificial Intelligence for Precision Dementia Medicine Summit at the Royal Society |
Year(s) Of Engagement Activity | 2022 |
Description | Brains for Dementia Research |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A public engagement event for brain donors, their carriers and the researches who will access the data. |
Year(s) Of Engagement Activity | 2022 |
Description | Company Visit (Boston) |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | ~50 industrial partners attended my talk about blood biomarkers in neurodegeneration |
Year(s) Of Engagement Activity | 2022 |
Description | Eisai Ltd webinar |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Invited presenter at Eisai Ltd webinar |
Year(s) Of Engagement Activity | 2020 |
Description | Festival of Genomics and Biodata |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presented at he Festival of Genomics and Biodata |
Year(s) Of Engagement Activity | 2022 |
Description | Interview for UKDRI news and events |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Spotlight on Prof Valentina Escott-Price |
Year(s) Of Engagement Activity | 2020 |
URL | https://ukdri.ac.uk/news-and-events/spotlight-on-prof-valentina-escott-price |
Description | UK Biobank Winter Scientific Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Dementia session at the UK Biobank Winter Scientific Conference |
Year(s) Of Engagement Activity | 2022 |
Description | Video presentation on Youtube |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presented a video abstract of a recently published paper |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.youtube.com/channel/UClJJHH2xKQk8uZTC7-mJICg |
Description | the UK Pharmacogenetics and Stratified Medicine Network |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presenter at the UK Pharmacogenetics and Stratified Medicine Network Workshop |
Year(s) Of Engagement Activity | 2021 |