IRE1 is a protein that senses the presence of endoplasmic reticulum stress. It is constitutively active in several cancers, including triple-negative breast cancer (TNBC). Its RNase activity allows it to cleave CUGCAG sequences found inside stem loops. Among its well-known targets is XBP1 mRNA, which has two such sequences and whose cleavage leads to the formation of an active transcription factor called XBP1s. As XBP1s has the ability to facilitate the progression of TNBC, IRE1 presents itself and its downstream targets as promising candidates for therapeutic interventions. Additionally, IRE1 can cause the degradation of other RNA molecules (including mRNAs, miRNAs, lncRNAs) in a process known as Regulated IRE1-dependent decay (RIDD).

Omics datasets encompassing mRNA, miRNA, proteins, and metabolic products were generated from the TNBC cell line MDA-MB-231 following treatment with MKC8866, an IRE1 inhibitor, at multiple time points. These datasets were analyzed using MultiOmicsIntegrator, a Nextflow pipeline previously developed and published by the authors of this abstract (available at https://github.com/ASAGlab/MOI--An-integrated-solution-for-omics-analyses). The analysis included detailed isoform switching, RNA-seq, proteomics, and lipidomics investigations. Additionally, to further focus on IRE1 signaling, we predicted novel XBP1 and RIDD candidates, incorporating recent advancements in the field.

The results provide valuable insights into IRE1 signaling in the context of TNBC pathology. By integrating data across multiple omics layers, several novel candidates downstream of the XBP1 and RIDD axis were identified. These candidates play key roles in metabolism, migration, and survival of TNBC cells. Additionally, we examined their behavior in single-cell datasets to better understand their impact on tumor microenvironment formation. Experimental validation of these candidates is currently underway. The robustness of the signature was evaluated using BRCA cell lines, and its prognostic potential was assessed through survival analysis with TCGA samples.

We focused on identifying novel downstream targets of IRE1/XBP1 and IRE1/RIDD signaling pathways. We believe that our work will aid in deciphering the role of IRE1 in TNBC progression and characterization.