Identifying the joint signature of brain atrophy and gene variant scores in Alzheimer’s Disease

Abstract

The joint modeling of genetic data and brain imaging information allows for determining the pathophysiological pathways of neurodegenerative diseases such as Alzheimer’s disease (AD). This task has typically been approached using mass-univariate methods that rely on a complete set of Single Nucleotide Polymorphisms (SNPs) to assess their association with selected image-derived phenotypes (IDPs). However, such methods are prone to multiple comparisons bias and, most importantly, fail to account for potential cross-feature interactions, resulting in insufficient detection of significant associations. Ways to overcome these limitations while reducing the number of traits aim at conveying genetic information at the gene level and capturing the integrated genetic effects of a set of genetic variants, rather than looking at each SNP individually. Their associations with brain IDPs are still largely unexplored in the current literature, though they can uncover new potential genetic determinants for brain modulations in the AD continuum. In this work, we explored an explainable multivariate model to analyze the genetic basis of the grey matter modulations, relying on the AD Neuroimaging Initiative (ADNI) phase 3 dataset. Cortical thicknesses and subcortical volumes derived from T1-weighted Magnetic Resonance were considered to describe the imaging phenotypes. At the same time the genetic counterpart was represented by gene variant scores extracted by the Sequence Kernel Association Test (SKAT) filtering model. Moreover, transcriptomic analysis was carried on to assess the expression of the resulting genes in the main brain structures as a form of validation. Results highlighted meaningful genotype–phenotype interactionsas defined by three latent components showing a significant difference in the projection scores between patients and controls. Among the significant associations, the model highlighted EPHX1 and BCAS1 gene variant scores involved in neurodegenerative and myelination processes, hence relevant for AD. In particular, the first was associated with decreased subcortical volumes and the second with decreasedtemporal lobe thickness. Noteworthy, BCAS1 is particularly expressed in the dentate gyrus. Overall, the proposed approach allowed capturing genotype–phenotype interactions in a restricted study cohort that was confirmed by transcriptomic analysis, offering insights into the underlying mechanisms of neurodegeneration in AD in line with previous findings and suggesting new potential disease biomarkers.