MSN and Alzheimer disease: Genes with the highest likelihood fit and a gradual increase in expression during the transition from M1 to M3-M2 included components of the response to unfolded proteins (HSP90AB1, DNAJA1, HSPA8, BAG3, ST13, HSP90AA1, HSPD1, HSPH1), genes linked to lipid response metabolism and transport (HSPA8, MSN, LCP1, SCARB2, ABHD3), and GPNMB. In contrast, a gradual decrease in homeostatic genes (GRID2, RASGEF1C, CX3CR1, SYNDIG1, FOXP2) was observed when transitioning from both CSF1R-RD and AD-associated clusters to the homeostatic microglia.