Comprehensive analysis of lipid metabolism pathways and marker genes in brain cell types using single- cell RNA sequencing

Abstract

Lipid metabolism is a critical component of brain physiology, encompassing the synthesis, degradation, and regulation of lipids necessary for cellular homeostasis and signaling. Dysregulation in lipid metabolism pathways has been implicated in various neurological disorders, including Alzheimer’s Disease (AD), Parkinson’s Disease, and Multiple Sclerosis. This study focuses on analyzing single-cell RNA sequencing (scRNA-seq) datasets to identify marker genes, dysregulated lipid metabolism pathways, and transcription factors (TFs) involved in the regulation of these pathways in brain cells under diseased conditions. The pipeline integrates essential steps such as quality control, normalization, batch effect correction, differential gene expression analysis, pathway enrichment, and transcription factor binding site analysis. We utilized tools like Seurat, scran, and pathway databases (KEGG, Reactome, and LIPID MAPS) to uncover insights into cellular mechanisms. Visualization techniques including PCA, UMAP, dot plots, and bubble plots were employed to effectively interpret and present findings. This research provides significant insights into the molecular basis of lipid dysregulation in the brain and its contribution to disease pathogenesis.