Multimodal mechanistic control of autophagy by the CtBP1/KAISO/TRIM28 Complex in breast cancer cells

Autophagy plays a context-dependent role in breast cancer progression, alternately promoting or suppressing tumor survival. However, the transcriptional and metabolic mechanisms for autophagy remain poorly understood. Here, we identify a CtBP1/Kaiso/Trim28 transcriptional regulatory complex as a key metabolic sensor that coordinates both transcriptional control of autophagy genes in the nucleus and structural regulation of autophagic machinery in the cytoplasm. We demonstrate that this CtBP1/Kaiso/Trim28 complex mediates multimodal control of autophagy in response to glucose availability. Genome-wide chromatin occupancy (CNR-seq) and transcriptomic profiling (RNA-seq) across luminal (MCF7) and triple-negative (MDA-MB-231) breast cancer cells reveal that CtBP1 directs complex assembly at promoters of key autophagy-related genes, including ULK1 , MTOR , VPS34 , and TFEB . Loss of CtBP1 or Kaiso leads to de-regulation of these targets, underscoring their cooperative role in maintaining autophagic balance. Proximity ligation assays detect CtBP1/Kaiso/Trim28 complexes in both nucleus and cytoplasm, highlighting their “moonlighting” function together with autophagic components such as LC3 in regulating autophagosome formation and stability. Several of these complexes display glucose-dependent dynamics, directly linking metabolic flux to autophagic regulation. Together, these findings uncover a previously unrecognized CtBP1-linked multimodal mechanism that integrates metabolic signals with both transcriptional and structural control of autophagy. The defined coordination between CtBP1, Kaiso, and Trim28 establishes a critical metabolic-autophagy axis in breast cancer and suggests new therapeutic strategies targeting CtBP1-mediated metabolic adaptation in therapy-resistant tumors.