Using Reverse Phase Protein Array (RPPA) to Identify and Target Adaptive Resistance

Abstract

Tumor cells and the tumor ecosystem rapidly evolve in response to therapy. This tumor evolution results in the rapid emergence of drug resistance that limits the magnitude and duration of response to therapy including chemotherapy, targeted therapy, and immunotherapy. Thus, there is an urgent need to understand and interdict tumor evolution to improve patient benefit to therapy. Reverse phase protein array (RPPA) provides a powerful tool to evaluate and develop approaches to target the processes underlying one form of tumor evolution: adaptive evolution. Tumor cells and the tumor microenvironment rapidly evolve through rewiring of protein networks to bypass the effects of therapy. In this review, we present the concepts underlying adaptive resistance and use of RPPA in understanding resistance mechanisms and identification of effective drug combinations. We further demonstrate that this novel information is resulting in biomarker-driven trials aimed at targeting adaptive resistance and improving patient outcomes.

Keywords: Adaptive resistance; Combination therapy; Reverse phase protein array; Targeted therapy; Tumor evolution.

Figure 1A. Adaptive responses to PARP inhibitors predict rational combinations Individual patients have different adaptive responses Interlesional proteomic heterogeneity is markedly decreased following therapy

1A Adaptive responses across 3 separate lesions in 3 ovarian cancer patients treated with monotherapy PARPi in a window of opportunity trial (design is at the top). Samples were assessed by RPPA with 300 antibodies to key proteins of interest. Data is presented as the ratio of treated to untreated biopsy to remove patient specific effects and to allow focus on adaptive responses. Antibodies are plotted on the x axis organized from high (red) to low (green) based on the average of all samples and samples are plotted on the y axis.

Figure 1B.. Pathway analysis provides patient specific targets

1B Pathway analysis and a novel therapeutic opportunity (PDGFR)Responses are remarkably consistent across lesions in each patient with therapeutic opportunities being different between patients.