Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC

Drug resistance is a major obstacle to targeted cancer therapies. Here we have used in-depth molecular response profiling and drug screening to investigate early adaptive responses after EGFR-inhibition and to identify new combination therapy targets. Response profiling at both mRNA and protein level revealed increased signaling in multiple pathways with the potential to blunt efficacy and cause drug resistance. Inhibition of several of these pathways resulted in synergistic effects together with EGFR-inhibitors, suggesting potential new combination therapy strategies. [Display omitted] Highlights •EGFR-TKI molecular response profiling covering 10138 proteins and 13486 mRNAs.•EGFR-TKI combination therapy screen using a library of 528 compounds.•Several new candidate EGFR-TKI escape mechanisms and combination therapy targets.•Combined targeting of the oncogene BCL6 and EGFR results in synergy in NSCLC cells. Drug resistance is a major obstacle to curative cancer therapies, and increased understanding of the molecular events contributing to resistance would enable better prediction of therapy response, as well as contribute to new targets for combination therapy. Here we have analyzed the early molecular response to epidermal growth factor receptor (EGFR) inhibition using RNA sequencing data covering 13,486 genes and mass spectrometry data covering 10,138 proteins. This analysis revealed a massive response to EGFR inhibition already within the first 24 h, including significant regulation of hundreds of genes known to control downstream signaling, such as transcription factors, kinases, phosphatases and ubiquitin E3-ligases. Importantly, this response included upregulation of key genes in multiple oncogenic signaling pathways that promote proliferation and survival, such as ERBB3, FGFR2, JAK3, and BCL6, indicating an early adaptive response to EGFR inhibition. Using a library of more than 500 approved and experimental compounds in a combination therapy screen, we could show that several kinase inhibitors with targets including JAK3 and FGFR2 increased the response to EGFR inhibitors. Further, we investigated the functional impact of BCL6 upregulation in response to EGFR inhibition using siRNA-based silencing of BCL6. Proteomics profiling revealed that BCL6 inhibited transcription of multiple target genes including p53, resulting in reduced apoptosis which implicates BCL6 upregulation as a new EGFR inhibitor treatment escape mechanism. Finally, we demonstrate