Machine Learning Analysis of Alzheimer’s Disease Single-Cell RNA-Sequencing Data across Cortex and Hippocampus Regions

• Published in: Current issues in molecular biology 2023-10, Vol.45 (11), p.8652-8669
• Main Authors: Krokidis, Marios G., Vrahatis, Aristidis G., Lazaros, Konstantinos, Skolariki, Konstantina, Exarchos, Themis P., Vlamos, Panagiotis
• Format: Article
• Language: English
• Subjects: Alzheimer’s disease; big data; brain; ensemble method; feature selection; machine learning
• ISSN: 1467-3045; 1467-3037; 1467-3045
• DOI: 10.3390/cimb45110544

Advancements in molecular biology have revolutionized our understanding of complex diseases, with Alzheimer’s disease being a prime example. Single-cell sequencing, currently the most suitable technology, facilitates profoundly detailed disease analysis at the cellular level. Prior research has established that the pathology of Alzheimer’s disease varies across different brain regions and cell types. In parallel, only machine learning has the capacity to address the myriad challenges presented by such studies, where the integration of large-scale data and numerous experiments is required to extract meaningful knowledge. Our methodology utilizes single-cell RNA sequencing data from healthy and Alzheimer’s disease (AD) samples, focused on the cortex and hippocampus regions in mice. We designed three distinct case studies and implemented an ensemble feature selection approach through machine learning, also performing an analysis of distinct age-related datasets to unravel age-specific effects, showing differential gene expression patterns within each condition. Important evidence was reported, such as enrichment in central nervous system development and regulation of oligodendrocyte differentiation between the hippocampus and cortex of 6-month-old AD mice as well as regulation of epinephrine secretion and dendritic spine morphogenesis in 15-month-old AD mice. Our outcomes from all three of our case studies illustrate the capacity of machine learning strategies when applied to single-cell data, revealing critical insights into Alzheimer’s disease.