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Alzheimers Disease Apolipoprotein Pathology for Treatment Elucidation and Development - Sofia ref.: 115975

Periodic Reporting for period 1 - ADAPTED (Alzheimers Disease Apolipoprotein Pathology for Treatment Elucidation and Development)

Reporting period: 2016-10-01 to 2017-09-30

ADAPTED has a focussed set of objectives aimed at;
1. Clarifying the role of APOE as a risk factor in the development of AD
2. Identifying promising entry points (targets) for the treatment of AD
3. Generate and validate selected high value APOE-related model systems
4. Uncover the basic scientific evidence required to progress the development of a stratified approach

The principles used to achieve this include;
+ Generation and characterization of novel high-quality gene-edited and patient derived iPSC-derived models as well as the use of available patient-derived tissue to identify APOE genotype and disease pathways and processes in an unbiased manner as well as directed approaches beyond APOE’s interaction with Aβ e.g. synaptic and mitochondrial function and neuroinflammation.
+ Elucidate the time course of APOE-ɛ4 effects on neurodegeneration and thus identify promising points of intervention for novel treatment strategies by studying cholesterol influx/efflux impairment in macrophages with different APOE genotypes and from large available Mild Cognitive Impairment (MCI) datasets evaluate the role of factors identified in MCI to AD phenoconversion.
+ Advance understanding of both cell-autonomous and non cell-autonomous phenotypes by differentiating iPSC to astrocytes, neurons, microglia and macrophages, and studying them in a physiological context in multi-well based solutions as well as using the Organ-on-a-Chip platform.
+ Resolve existing ‘toxic gain of function’ vs. ‘loss of function’ hypotheses and generate new, mechanistic hypotheses for APOE-ɛ4’s role in the development of AD.
+ Generate new knowledge of how APOE-ɛ4 interacts with other AD risk and genetic factors, including protective effects of APOE-ε2, influencing development of AD by integrating genomic, transcriptomic, metabolomics, proteomic and lipidomic data.
+ Identify early biomarkers of cognitive decline and MCI conversion to AD and prospective new targets for therapeutic interventions by integrative analysis of ADAPTED and publicly available data.
+ Provide evidence for biochemical markers in APOE-ɛ4 carriers that will convert to AD, or will develop a more aggressive phenotype, to inform decisions of when and how to intervene with treatments based on a systematic specificity analysis.
• iPSCs have been generated from one AD donor. Gene editing to generate four independent sets of iPSCs with APOE2/2, APOE3/3, APOE3/4, APOE4/4 and APOE KO is far advanced, from two male, two female donors (one HC and one AD per sex). Neuronal differentiation is standardized throughout the consortium, whereas astrocyte differentiation protocols are standardized, optimized and characterized throughout the consortium.
• Using existing multi-omics data of EMC, UKK and Janssen, 12 metabolites circulating in blood (11 HDL sub-fractions and the fatty acid DHA) were found to be associated with improved cognitive function and 3 circulating metabolites (glycoprotein acetyls, glutamine and ornithine) with cognitive impairment. Stratified by APOE, we found that in those carrying the APOE*3 and the APOE*4 genotype, the metabolites determine conversion to AD. Findings were validated by external partners.
• Existing CSF and blood samples from MCI subjects have been made available to the consortium, and also new samples have been collected. CSF samples have been measured using state-of-the-art analytical techniques, focusing on metabolites involved in oxidative and nitrosative stress, as well as inflammation.
• Harmonization protocols to define mild cognitive impairments across cohorts have been explored in longitudinal cohorts. This analysis concluded that best strategy for validation analysis in ADAPTED is that using the MCI definition given locally by each cohort.
• Using known AD susceptibility genes, different cognitive composites have been tested to define the best way to operationalize cognitive decline across longitudinal MCI cohorts. This analysis showed that when analysing several heterogeneous cohorts of MCI as in ADAPTED, MMSE has to be considered the most efficient neuropsychological discriminant factor for progression to dementia and rate of cognitive decline. Importantly, this analysis also revealed that a composite assessing memory and executive function detects the effect of ApoE4 more powerfully than the MMSE which assesses additional cognitive domains. This finding suggests that genetic risk factors for AD may exert their effect on specific neuronal networks underlying particular cognitive functions.
• Metabolite analysis revealed that AD patients carrying at least one APOE-ε4 allele showed a dysregulation in omega-3 and omega-6 fatty acid pathways. This dysregulation is not observed in healthy controls stratified similarly to AD patients. Additional experiments are now ongoing in iPSCs to understand potential pathways related to fatty acids metabolism in brain cells. Furthermore, these findings together with proteomic analysis of brain tissue of APOE transgenic mice showed that APOE effects might not be strong enough to be detected under normal conditions, requiring therefore stress conditions in experiments to uncover APOE-specific effects.
• Data from many publicly available datasets have been curated and integrated into the ADAPTED TranSMART database and is available for APOE stratified questioning. Initial analysis (pending the inclusion of additional datasets) point towards APOE genotype dependent roles of neuroinflammation, but not peripheral inflammation, endosomal and mitochondrial pathways in AD pathophysiology
• The extensive QC of the iPSC lines is providing us new insights into required standards for gene-editing of iPSCs. More genetic variations are identified that would have been with state of the art technology at the start of the project. The proposal to have four independently gene-edited iPSC sets comprising 5 genotypes each appeared conservative at the start of the project. The data which will be generated in the coming years with the generated cells will shed more light on robustness of phenotypes.
• We have successfully identified and validated metabolites in the circulation that are associated with AD.
• The preferential APOE4 allele link to neuroinflammatory pathways may drive stratification of these specific therapeutic approaches to APOE4 carriers in particular.
• Findings from analysis of fatty acids together with proteomic analysis in brain tissue of APOE transgenic mice showed that APOE effects might not be strong enough to be detected under normal conditions. Consequently, experimental procedures to uncover APOE-specific effect might require stress conditions.
• Analysis of omega-3 and omega-6 dysregulation in an APOE genotype dependent manner led to the development of experimental approaches in iPSCs to test these pathways in different APOE genotypes.