Analysis of the Coding Transcriptome in NSCLC Highlights Variant-Specific Gene Expression and Signaling in CD74-ROS1 Fusions

The CD74-ROS1 fusion protein is an aggressive oncogenic driver detected in non-small cell lung cancer (NSCLC) patients from stages I-IV. Despite the low occurrence, CD74-ROS1 has a notable clinical value serving as a therapeutic target when the primary treatment plan fails. Upon targeting the cancer cells with ROS1 tyrosine kinase inhibitors (TKIs), resistance occasionally emerges for reasons that are not well-understood. Therefore, analyzing the individual roles of CD74 and ROS1 in the CD74–ROS1 fusion may reveal mechanistic insights that would guide the scientific community to more effective therapies. Here, we describe the development and characterization of carefully engineered CD74-ROS1 variants that allow the analysis CD74 and ROS1 functional roles, at both the mRNA and protein levels. Differential gene expression analysis among the variants under study demonstrated unique gene profiles, which can be explained only by assigning specific functional contributions to each protein partner. In alignment with the mRNA findings, the phospho-kinase array results exposed variant-mediated signaling events that were not previously linked with the functionality of CD74-ROS1. Together, these findings provide a better understanding of CD74-ROS1 role in NSCLC and contribute a list of novel molecular targets for further mechanistic analysis and drug development.