Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer

H Alexander Ebhardt,Yansheng Liu,Alex Root,Chris Sander,Ruedi Aebersold,Nicholas Paul Gauthier

doi:10.1038/s41540-018-0064-1

Abstract

In the United States alone one in five newly diagnosed cancers in men are prostate carcinomas (PCa). Androgen receptor (AR) status and the PI3K-AKT-mTOR signal transduction pathway are critical in PCa. After initial response to single drugs targeting these pathways resistance often emerges, indicating the need for combination therapy. Here, we address the question of efficacy of drug combinations and development of resistance mechanisms to targeted therapy by a systems pharmacology approach. We combine targeted perturbation with detailed observation of the molecular response by mass spectrometry. We hypothesize that the molecular short-term (24 h) response reveals details of how PCa cells adapt to counter the anti-proliferative drug effect. With focus on six drugs currently used in PCa treatment or targeting the PI3K-AKT-mTOR signal transduction pathway, we perturbed the LNCaP clone FGC cell line by a total of 21 treatment conditions using single and paired drug combinations. The molecular response was analyzed by the mass spectrometric quantification of 52 proteins. Analysis of the data revealed a pattern of strong responders, i.e., proteins that were consistently downregulated or upregulated across many of the perturbation conditions. The downregulated proteins, HN1, PAK1, and SPAG5, are potential early indicators of drug efficacy and point to previously less well-characterized response pathways in PCa cells. Some of the upregulated proteins such as 14-3-3 proteins and KLK2 may be useful early markers of adaptive response and indicate potential resistance pathways targetable as part of combination therapy to overcome drug resistance. The potential of 14-3-3ζ (YWHAZ) as a target is underscored by the independent observation, based on cancer genomics of surgical specimens, that its DNA copy number and transcript levels tend to increase with PCa disease progression. The combination of systematic drug perturbation combined with detailed observation of short-term molecular response using mass spectrometry is a potentially powerful tool to discover response markers and anti-resistance targets.

Highlights

IntroductionProstate cancer (PCa) is classified into distinct stages: localized PCa (treated with surgery and/or radiation), metastatic PCa (treated with androgen deprivation therapy (ADT)), castration-resistant PCa (CRPC, treated with second-line therapy), and treatment refractory disease.[1] The stages largely indicate the course of PCa disease progression and define common clinical interventions during respective stages
Prostate cancer (PCa) is classified into distinct stages: localized PCa, metastatic PCa (treated with androgen deprivation therapy (ADT)), castration-resistant PCa (CRPC, treated with second-line therapy), and treatment refractory disease.[1]
(2) Is there a uniform protein response to pharmacological drug perturbation or does each drug and drug combination induce a different protein response in a metastatic PCa model? (3) Can we identify proteins outside the androgen receptor (AR) and PI3K-AKT-mTOR signal transduction pathways that are important for the cellular response to pharmacological treatment within the AR and PI3K-AKT-mTOR pathways? As PCa model we chose the hormone sensitive LNCaP clone FGC (ATCC® CRL-1740TM)

Summary

Introduction

Prostate cancer (PCa) is classified into distinct stages: localized PCa (treated with surgery and/or radiation), metastatic PCa (treated with androgen deprivation therapy (ADT)), castration-resistant PCa (CRPC, treated with second-line therapy), and treatment refractory disease.[1] The stages largely indicate the course of PCa disease progression and define common clinical interventions during respective stages. In PCa diagnosis and risk assessment pose particular challenges.[2] Approximately 99% of men who are diagnosed with PCa will not die from PCa but rather die from unrelated medical hazards.[3,4] with 30% of the male population diagnosed with PCa the challenge remains beyond localized PCa and to better understand disease progression. As genomic alterations are common in PCa large cohorts of patients across the entire spectrum of PCa were genotyped and recurrent genomic alterations were identified using the latest DNA sequencing and DNA copy number variation methodologies

Methods

Results

Conclusion