Dissecting mTOR-dependent gene and protein networks in normal and neurodegenerative states

The mechanistic Target of Rapamycin (mTOR) is a well-studied protein kinase that coordinates nutrient signalling within the cell, inhibition of this kinase has been associated with an extension in healthspan. The kinase regulates cellular physiology by balancing catabolic and anabolic responses in accordance with nutrient availability. Its widespread impact on various cellular functions is well- documented, with recent studies into the mTOR kinase focusing on the role it plays in transcription. The role of the kinase within neuronal cells is of great interest due to their post-mitotic nature and susceptibility to age-related changes. This study compared the effects of the mTORC1-specific inhibitor Rapalink-1 and pan-TOR inhibitor Torin 1 on transcriptional profiles. Rapalink-1 treated cells contrasted Torin 1 with an upregulation of several mitochondrial genes, including components on NADH dehydrogenase (MT-ND1, MT-ND2, and MT-ND4), ATP Synthase (MT-ATP6), and Cytochrome B (MT-CYB). Torin 1, however, had a greater number of differentially expressed genes, plus an upregulation in several genes involved in developmental pathways, including SIX3, RAG2 and TBX6. Both inhibitors downregulated genes involved in the Endoplasmic Reticulum stress response, such as SESN2, ATF3, CEBPB, and CHAC1. Notable differences emerged, with Rapalink-1 uniquely downregulating genes related to IL-6 Biosynthesis and Torin 1 demonstrating a strong downregulation of genes associated with calcium signalling. A disease-dependent transcriptome and the role of mTOR within this was also analysed to further understand the transcriptional control of the kinase in the context of neurodegeneration. Alzheimer’s is a neurodegenerative disease associated with the deposition and build-up of amyloid-beta plaques. In this context, Rapalink-1 induced the expression of genes associated with neuronal differentiation, such as CHGB and ECEL1. Contrasting this, Torin 1 exhibited an increase in the expression of long non-coding RNAs, including SNHG1 and SNHG7, along with a decrease in ER stress genes, such as ATF3. These findings underscore and contrast the complexity of mTOR inhibition with both Rapalink-1 and Torin 1 providing valuable insights into potential neuroprotective pathways associated with mTOR inhibition.