<p>Alzheimer’s Disease (AD) is a devastating neurodegenerative disease, strongly linked to cellular stress originating from the accumulation of the Amyloid-beta (Aβ) peptide and phosphorylated tau protein. Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) are reported as early events in the AD pathology. Mitochondria-Associated Membrane (MAM) is a proteinaceous tethering between the ER and mitochondria that plays a role in regulating ER stress and related responses. A high level of ER-mitochondria tethering, thereby mitochondrial Calcium (Ca²⁺) overload and cell death, has been reported in AD brain cells. Despite the independent recognition of these pathways, a precise mechanism that integrates MAM activity, ER stress response, and AD pathogenesis remains elusive. We used three transcriptomic datasets collected from the NCBI-Gene Expression Omnibus (GEO) database, which deal with AD, ER stress, and MAM, and processed them with a multi-layered bioinformatics approach combining differential gene expression analysis, Weighted Gene Co-expression Network Analysis (WGCNA), protein interaction network construction, and identification of hub genes using different cytoHubba topological algorithms. Four hub genes, namely Calreticulin (CALR), Calnexin (CANX), Heat Shock Protein 90 Beta Family Member 1 (HSP90B1), and Valosin-Containing Protein (VCP), were identified. CALR, CANX, and HSP90B1 are known chaperones that regulate proteostasis. VCP is an ER ATPase that induces autophagy. These genes are not only associated with MAM regulation and ER stress but also with AD pathology. The results suggest hub genes as a new set of biomarkers and the likely existence of a ‘three-component system’ among MAM, ER stress, and Neurodegeneration. The study highlights the potential of MAM-related genes as therapeutic targets of AD.</p> Graphical Abstract <p></p>