Phosphoproteomics adds value to treatment recommendations in molecular tumor boards

Precision oncology approaches employing genomics-guided targeted therapies for individual patients have provided significant survival benefits in several cancer types. However, varying response rates in solid malignancies, many patients without actionable genomic lesions, and increasing evidence that non-genomic mechanisms may play an important role in tumors indicate that genomics alone is often insufficient to inform and guide the clinical care of patients. Since most targeted anti-cancer drugs inhibit the activity of protein kinases, measuring the tumor phosphoproteome as a direct readout of kinase activity is poised to enhance molecular stratification. We established a clinical (phospho)proteomic workflow for integration into the molecular tumor board (MTB) workflow of the Germany-wide INFORM (for children with relapsed cancers) and MASTER (for young adults with refractory cancers and patients with rare tumors) registry studies and profiled > 1300 tumor tissue specimen from patients enrolled in the DKFZ/NCT/DKTK MASTER study or the INFORM registry trial. To assess the aberrant activity of druggable signaling pathways, we developed a new tumor pathway activity (TUPAC) scoring methodology using expression data of > 8,000 proteins and > 20,000 phospho-sites per patient in a heterogeneous pan-cancer cohort. TUPAC scores integrate protein expression and phosphopeptide abundance data at several levels to detect aberrant signaling pathway activities of several interdependent oncogenic signaling pathways within one tumor specimen. We show for the first time that comprehensive (phospho)proteome profiling is feasible and informative in a real-world prospective precision oncology setting. Discussion of (phospho)proteomic data of > 500 prospective patients in weekly MTB meetings revealed that adding a (phospho)proteomic layer can supply critical information for personalized therapies that is not discernable from genomic and transcriptomic data. In an independent value evaluation (329 target recommendations in 104 patients), the phosphoproteome layer was decisive in 22% of all recommended targets. Based on anecdotal cases with available clinical follow-up, we provide evidence that (phospho)proteome profiling carries important diagnostic value by detecting actionable tumor-driving kinase signaling in patients without actionable genomic lesions or by functionalizing genomic variants of unknown significance. Overall, our work demonstrates the utility of the additional phosphoproteome data layer to enhance therapeutic recommendations in molecular tumor boards.