Abstract

Background

   The problem of prostate cancer progression to androgen independence has
   been extensively studied. Several studies systematically analyzed gene
   expression profiles in the context of biological networks and pathways,
   uncovering novel aspects of prostate cancer. Despite significant
   research efforts, the mechanisms underlying tumor progression are
   poorly understood. We applied a novel approach to reconstruct
   system-wide molecular events following stimulation of LNCaP prostate
   cancer cells with synthetic androgen and to identify potential
   mechanisms of androgen-independent progression of prostate cancer.

Methodology/Principal Findings

   We have performed concurrent measurements of gene expression and
   protein levels following the treatment using microarrays and iTRAQ
   proteomics. Sets of up-regulated genes and proteins were analyzed using
   our novel concept of “topological significance”. This method combines
   high-throughput molecular data with the global network of protein
   interactions to identify nodes which occupy significant network
   positions with respect to differentially expressed genes or proteins.
   Our analysis identified the network of growth factor regulation of cell
   cycle as the main response module for androgen treatment in LNCap
   cells. We show that the majority of signaling nodes in this network
   occupy significant positions with respect to the observed gene
   expression and proteomic profiles elicited by androgen stimulus. Our
   results further indicate that growth factor signaling probably
   represents a “second phase” response, not directly dependent on the
   initial androgen stimulus.

Conclusions/Significance

   We conclude that in prostate cancer cells the proliferative signals are
   likely to be transmitted from multiple growth factor receptors by a
   multitude of signaling pathways converging on several key regulators of
   cell proliferation such as c-Myc, Cyclin D and CREB1. Moreover, these
   pathways are not isolated but constitute an interconnected network
   module containing many alternative routes from inputs to outputs. If
   the whole network is involved, a precisely formulated combination
   therapy may be required to fight the tumor growth effectively.

Introduction

   Prostate cancer is one of the most commonly diagnosed cancers and the
   second leading cause of cancer-related death in North American men
   [37][1]. While androgen withdrawal therapy is often effective
   initially, most cases progress to the much more aggressive
   androgen-independent phenotype. Despite significant research efforts,
   the mechanisms underlying tumor progression are poorly understood.
   Roles for several signaling pathways have been established, but not a
   systemic picture. For example, IGF signaling has been implicated in the
   progression from androgen-dependent to androgen-independent states
   [38][2], but also has been shown to suppress AR trans-activation via
   FoxO1 and thus have inhibitory effects on the growth of prostate cancer
   cells [39][3], EGF was reported to mimic effects of androgen on the
   gene expression and independently stimulate growth of
   androgen-dependent prostate cancer cells [40][4]. Other studies have
   produced evidence of interplay between androgen signaling and TGF-beta
   [41][5],[42][6], FGF [43][7],[44][8] and VEGF [45][9].

   Most of the research cited above has been hypothesis-driven rather than
   data-driven. Hypothesis formulation is susceptible to bias due to
   investigators' preferences and current research trends about what is