Periodic Reporting for period 1 - MAP-AD (A multimodal approach to accelerate drug discovery and development in Alzheimer’s disease)
Reporting period: 2021-02-01 to 2023-01-31
Alzheimer’s disease (AD) is a major societal challenge, impacting up to one-third of the population over 85 years old. The European Commission and various international bodies have repeatedly fostered research initiatives to prevent the development or stem the progression of the disease. Several recent phase 3 clinical trials have failed to show any efficacy in slowing disease progression, calling into question the current drug targets, notably the ones targeted at the so-called amyloid cascade. This project used genetic data to identify new AD-relevant molecular pathways and their associated drug targets. Apart from aging, the strongest contributing factor for late-onset AD is a specific allele of the Apolipoprotein E (APOE) gene, which has three common alleles ε2, ε3, and ε4. While ε3 is the most common and considered as the reference, ε2 is associated with decreased AD risk and ε4 is associated with increased AD risk. Notably, the prevalence of ε4 among AD patients is high with about 60% of these carrying at least one ε4 allele, while solely about 30% of Europeans carry one ε4 allele. In addition, in the current era of precision medicine, genetic studies suggest that each AD case may have different dysregulated pathways, due to various genetic variants, and each may thus need a specific cocktail/combination of drugs to re-balance their brain to closer to a homeostatic state. In this context, developing drugs that mitigate the effect of APOE ε4 has a high potential and should impact a large percentage of AD cases.
ε4, with AD, to gain some insights into the APOE isoform's functional properties which are protective or deleterious in the process of AD pathogenesis. This work led to the discovery of two novel rare missense variants located near and within APOE’s lipid binding domain. We demonstrated that these are associated with a two-to-three-fold decreased risk of developing AD. This result was obtained by testing the association of these variants in 400,000 European ancestry individuals, with about 1 every 1,000 carryings either of the two variants (V236E and R251G), and was published in JAMA Neurology (PMID: 35639372). In addition, another part of this project focused on APOE variants specific to African ancestry individuals. This is essential to guarantee an equitable precision medicine, albeit ensuring that AD genetic risk is assessed with the same quality in all populations and also enables us to gain additional insights on APOE by studying variants not present in European ancestry. This work led to the discovery of a missense variant within APOE’s receptor binding region (R145C) which was associated with a five-to-eight-fold increased AD risk when combined with ε4. This result, published in JAMA (PMID: 36809323) was obtained by testing the association of this variant in 32,000 African ancestry individuals, with about 4% carrying R145C and 1.5% carrying the combination of ε3[R145C]/ε4 and displaying a similar risk of developing AD as ε4/ε4 individuals with significantly earlier disease onset.
Additionally, this project also identified novel genetic variants associated with AD risk by developing new statistical methods and results were published in Alzheimer’s Research & Therapy (PMID: 33794991) and The American Journal of Human Genetics (PMID: 34767756). These results identified genetic associations in novel and known genetic pathways and will foster functional studies to identify the mechanism by which these genes modify AD risk. Given the increased risk of AD in women, this project is also investigating the association of X chromosome (females have two copies, while males have one) variants with AD, which has until now been excluded from AD genetic association. This X-chromosome-wide association analysis is ongoing.
Last, this project tackled the fine-mapping of the Human Leukocyte Antigen (HLA) locus in AD, which is one of the genetic loci (a region of the genome) identified in AD genome-wide association studies but for which the causal gene(s) remained undetermined. First, this project demonstrated that the protective association observed at the HLA locus is common to some other neurodegenerative diseases, notably Parkinson’s disease (PD) and Amyotrophic lateral sclerosis (ALS). Second, we gathered data from across the globe to perform HLA fine-mapping, which not only increases statistical power but also ensures to cover of a large diversity of HLA alleles. By studying over 120,000 AD cases and 400,000 cognitively healthy older controls, we determined that the protective association was supported by HLA-DRB1*04 allele subtypes, and similar associations were observed in PD by studying over 55,000 PD cases and 1,450,000 non-PD controls (preprint medxriv: doi.org/10.1101/2021.12.26.21268354). We then demonstrate that protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. This HLA-DRB1*04-mediated adaptive immune response, common to AD and PD, offers the possibility of new therapeutic avenues.
Additionally, this project also identified novel genetic variants associated with AD risk by developing new statistical methods and results were published in Alzheimer’s Research & Therapy (PMID: 33794991) and The American Journal of Human Genetics (PMID: 34767756). These results identified genetic associations in novel and known genetic pathways and will foster functional studies to identify the mechanism by which these genes modify AD risk. Given the increased risk of AD in women, this project is also investigating the association of X chromosome (females have two copies, while males have one) variants with AD, which has until now been excluded from AD genetic association. This X-chromosome-wide association analysis is ongoing.
Last, this project tackled the fine-mapping of the Human Leukocyte Antigen (HLA) locus in AD, which is one of the genetic loci (a region of the genome) identified in AD genome-wide association studies but for which the causal gene(s) remained undetermined. First, this project demonstrated that the protective association observed at the HLA locus is common to some other neurodegenerative diseases, notably Parkinson’s disease (PD) and Amyotrophic lateral sclerosis (ALS). Second, we gathered data from across the globe to perform HLA fine-mapping, which not only increases statistical power but also ensures to cover of a large diversity of HLA alleles. By studying over 120,000 AD cases and 400,000 cognitively healthy older controls, we determined that the protective association was supported by HLA-DRB1*04 allele subtypes, and similar associations were observed in PD by studying over 55,000 PD cases and 1,450,000 non-PD controls (preprint medxriv: doi.org/10.1101/2021.12.26.21268354). We then demonstrate that protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. This HLA-DRB1*04-mediated adaptive immune response, common to AD and PD, offers the possibility of new therapeutic avenues.
The two publications on APOE described above provide robust statistical association results to the AD research community and will serve as a beacon to guide future functional studies of APOE. Currently, most of these try to compare properties between ε2, ε3, and ε4 genotypes to infer which APOE’s function/property need to be modified/targeted by therapy. However, many properties differ between these isoforms, and several have been marshaled as necessary for AD, bringing additional isoforms with known associations will help disentangle the wheat from the chaff in these properties. In time these results will contribute to the development of APOE ε4 targeted therapies which are likely to have an impact on many individuals. These will help alleviate the AD burden on society, by hopefully enabling prolonged cognitively healthy aging for more individuals. Additionally, this project has identified X chromosome associations in AD, and the immediate next steps before publication include replicating these associations in external collaborators and linking these associations to functional mechanisms. To this date, no robust genetic association has been identified on the X chromosome in AD, identifying some may shed light on the difference in AD incidence between sex.