AI reveals insights into link between CD33 and cognitive impairment in Alzheimer’s Disease

Modeling biological mechanisms is a key for disease understanding and drug-target identification. However, formulating quantitative models in the field of Alzheimer’s Disease is challenged by a lack of detailed knowledge of relevant biochemical processes. Additionally, fitting differential equation systems usually requires time resolved data and the possibility to perform intervention experiments, which is difficult in neurological disorders. This work addresses these challenges by employing the recently published Variational Autoencoder Modular Bayesian Networks (VAMBN) method, which we here trained on combined clinical and patient level gene expression data while incorporating a disease focused knowledge graph. Our approach, called iVAMBN, resulted in a quantitative model that allowed us to simulate a down-expression of the putative drug target CD33, including potential impact on cognitive impairment and brain pathophysiology. Experimental validation demonstrated a high overlap of molecular mechanism predicted to be altered by CD33 perturbation with cell line data. Altogether, our modeling approach may help to select promising drug targets.Author summary: For the last 20 years, the field of Alzheimer’s Disease (AD) is marked by a series of continuous failures to deliver demonstrably effective medications to patients. One of the reasons for the continuous failure of trials in AD is the lack of understanding of how targeting a certain molecule would affect cognitive impairment in humans. One way to address this issue is the development of quantitative system level models connecting the molecular level with the phenotype. In this paper we propose a novel hybrid Artificial Intelligence (AI) approach, named Integrative Variational Autoencoder Modular Bayesian Networks (iVAMBN), combining clinical and patient level gene expression data while incorporating a disease focused knowledge graph. The model showed connections between various biological mechanisms playing a role in AD and allowed us to simulate a down-expression of the putative drug target CD33. Results showed a significantly increased cognition and predicted perturbation of several biological mechanisms. We experimentally validated these predictions using gene expression data from a knock-out THP-1 monocyte cell line, which confirmed our model predictions up to a very high extent. To our knowledge, we thus developed the first experimentally validated, quantitative, multi-scale model connecting molecular mechanisms with clinical outcomes in the AD field.