Genome-wide association studies (GWAS) are large-scale research efforts that examine DNA sequences across entire populations to identify genetic variations linked to specific diseases. They have been invaluable for discovering genetic variants linked to increased risk for or resilience to Alzheimer’s disease (AD). In addition to being instrumental in furthering our understanding of the biology of AD, GWAS studies are also uncovering potential targets for future drug development.
While existing AD GWAS datasets, including the CureAlz Alzheimer’s Genome Project™, have undeniable value, they contain a significant genetic gap. Most studies have excluded or minimized analysis of the X and Y sex chromosomes due to technical challenges that make data from these chromosomes appear less statistically reliable than information from the other chromosomes.
This omission represents a missed opportunity. AD and Parkinson’s disease (PD) both demonstrate clear sex differences in how common they are, how they progress and how patients respond to treatments. Dr. Belloy believes that some of these sex-based differences may stem from genetic variations located on the X chromosome. Since males carry one X chromosome (paired with a Y) while females carry two X chromosomes, genetic variations on the X chromosome could affect men and women differently. This suggests that important Alzheimer’s-related genes on the X chromosome remain undiscovered and may explain why these diseases affect the sexes differently.
To overcome this knowledge gap, Dr. Belloy developed a computational data processing pipeline that resolves issues that previously led to the exclusion of X-chromosome data. Using this pipeline, his team performed the first large-scale X chromosome-wide association study (XWAS) for AD and PD risk. Excitingly, they identified several genetic variations on the X chromosome associated with increased risk of each disease. However, they still face obstacles in determining which of these genetic candidates are truly causal, and which genes would make appropriate drug targets.
When researchers and pharmaceutical companies identify potential genetic targets through GWAS, they typically evaluate these findings using two additional criteria before investing in clinical development: (1) whether the genetic variant actually affects how much of the corresponding gene or protein is produced in the body, and (2) whether the genetic variant is linked to the specific disease pathologies and clinical symptoms observed in patients.
For the first criterion, scientists use specialized analytical techniques. Expression quantitative trait locus (eQTL) analysis measures how genetic variants influence gene activity levels, while protein quantitative trait locus (pQTL) analysis measures how these variants affect the actual amount of proteins produced. However, the resources needed for these analyses are severely limited for X chromosome genes compared to the large datasets available for the other chromosomes. This creates a significant barrier to assessing whether XWAS hits will translate into viable therapeutic targets.
There is also a huge gap in the research that relates X chromosome genetic variation to AD-relevant pathologies, such as amyloid beta or tau, which affects the second criterion for drug development.
Dr. Belloy’s project addresses these research gaps as he plans to generate these missing analytical resources for X chromosome studies and integrate them with XWAS results. This approach will enable researchers to identify and prioritize X-linked genes that show the greatest promise for drug development.
Dr. Belloy’s team proposed three aims to address these goals. In the first aim, they are creating the missing resource that shows how X chromosome genetic variations impact protein expression (pQTL). They will utilize two large existing human genetic datasets: one from the brain (AMP-AD: Accelerating Medicines Partnership for AD) and one from CSF (NGI: Neurogenomics and Informatics center). In both datasets, levels of thousands of different proteins were measured using modern large-scale protein assays (proteomics). Dr. Belloy’s team will analyze these existing measurements to map the relationships between specific protein levels and genetic variations on the X chromosome in matched samples. An important advantage of these datasets is that they include samples from both healthy participants and those diagnosed with AD or PD. This diversity enables the second aim: conducting a protein-wide association study (PWAS) to identify which proteins produced by genes on the X chromosome are associated with increased AD and PD risk. In the third aim, a new XWAS will be done to identify X-linked gene variants associated with key AD- or PD-relevant brain pathologies as measured via brain scans (amyloid PET, tau PET, hippocampal atrophy, or Lewy body pathology for PD). This approach differs from previous AD GWAS analyses, which only looked for gene variations that impact the risk of a diagnosis. Across all aims, sex and APOE4 status will be accounted for. Finally, they plan to integrate their findings across various analyses to prioritize genes and proteins for future drug targeting.
In the first year of funding, Dr. Belloy’s team made strong progress across their aims. They identified several genetic variants on the X chromosome that may increase the risk for Alzheimer’s disease. They also investigated how these risks differ between men and women, as well as in individuals with different versions of the APOE gene. Several of these newly identified AD risk regions on the X chromosome seem to be more important in women. One particularly interesting gene, SLC9A7, may play a role in hormone levels and brain health. Numerous genes were linked to the brain’s structure and function as assessed by MRI. These findings help us better understand why women are more likely to develop AD and point to new ways we might treat or prevent the disease differently in men and women in the future.
