Abstract Background: Mechanistic Target of Rapamycin (mTOR), a key component of the PI3K/Akt signaling pathway, coordinates various cellular processes such as metabolism, growth, cell proliferation and cell cycle progression. Dysregulations affecting mTOR frequently occur in cancer, and mTOR inhibitors/rapalogs are used as monotherapy or a part of combination therapy in breast or kidney metastatic cancer. Despite this, response rate is modest. Several mechanisms of resistance have been reported, but do not fully characterize insensitive tumor cells. Purpose: This study investigated new target genes of rapamycin/rapalogs. Methods: Expression levels of target genes were evaluated in a panel of cancer cell lines by transcriptomic analyses, real-time qPCR and western blot. Transcriptional regulation was investigated by in silico analyses of the promoter region, gene reporter assays using site-directed mutagenesis, and ChIP. Stably silenced cell lines were established by lentiviral transduction of shRNA sequences. Results: We identified one gene: TRIB3 (Tribbles Pseudokinase 3), whose expression is downregulated in the presence of rapamycin in a panel of cancer cell lines and in PBMCs isolated from cancer patients. This gene encodes for a pseudokinase involved in a glucose-induced insulin resistance in Type 2 Diabetes by inhibiting the activation of Akt1/2. We observed that silencing mTOR did not mimic rapamycin downregulation of TRIB3, suggesting an mTOR-independent effect of rapamycin. We identified a binding site for the transcriptional repressor GCF2/LRRFIP1 in the promoter region of TRIB3, and confirmed that the presence and the binding of GCF2 to TRIB3 promoter are required for TRIB3 downregulation by rapamycin. Finally, we identified FKBP3 (FK506-Binding Protein 3), a protein that can bind rapamycin with high affinity, as a GCF2 partner, confirming the direct effect of rapamycin on TRIB3 promoter. Conclusions: Taken together, our investigations identified a novel transcriptional target gene of rapamycin: TRIB3. We also characterized the molecular mechanism of regulation by rapamycin through a FKBP3/GCF2-dependent repression of TRIB3 promoter activity, and independently of mTOR signaling. Such variations in TRIB3 expression level in cancer cells could be linked to rapamycin sensitivity, and may represent a valuable therapeutic target. Citation Format: Bojana Stefanovska, Cécile Vicier, Véronique Scott, Guillaume Meurice, Fabrice André, Olivia Fromigué. A new mTOR-independent effect of rapamycin: Transcriptional regulation of TRIB3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2524.