FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines.

Joshua I Warrick,David J Degraff,Vasty Osei Amponsa,Eunah Chung,Lauren Shuman,Wilson Chan,Vonn Walter,Hironobu Yamashita,Tejaswi Iyyanki,Jay D Raman,Yuka I Kawasawa,Matthew Kaag,Feng Yue,Zongyu Zheng,Wansong Guo,Joo-Seop Park,Tiffany L Whitcomb

doi:10.1038/srep38531

Abstract

Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA). This identified a panel of bladder cancer cell lines which exhibit genetic alterations and gene expression patterns consistent with luminal and basal molecular subtypes of human disease. A subset of bladder cancer cell lines exhibit in vivo histomorphologic patterns consistent with luminal and basal subtypes, including papillary architecture and squamous differentiation. Using the molecular subtype assignments, and our own RNA-seq analysis, we found overexpression of GATA3 and FOXA1 cooperate with PPARɣ activation to drive transdifferentiation of a basal bladder cancer cells to a luminial phenotype. In summary, our analysis identified a set of human cell lines suitable for the study of molecular subtypes in bladder cancer, and furthermore indicates a cooperative regulatory network consisting of GATA3, FOXA1, and PPARɣ drive luminal cell fate.

Highlights

Downregulated in the basal subtype of bladder cancer[2,3,4,5,9,10,11,12,13,14,15,16,17,18,19,20]
In order to evaluate the suitability of commonly used bladder cancer cell lines for the study of molecular subtypes of disease, as well as to identify specific mechanistic drivers of molecular subtype, we undertook a detailed analysis of gene expression, copy number alteration (CNA), and mutational data on 27 UC cell lines available through the CCLE22
Mutations and CNAs associated with UC cell lines classified as luminal and basal mirrored those seen in the The Cancer Genome Atlas (TCGA) data (Fig. 1B)

Summary

Introduction

Downregulated in the basal subtype of bladder cancer[2,3,4,5,9,10,11,12,13,14,15,16,17,18,19,20]. An incomplete understanding of the suitability of available models to test the direct contribution of specific factors to the establishment of a given molecular subtype in UC is a significant hurdle to experimental design. Our research group undertook a detailed analysis of publically available gene expression, copy number alteration, and mutational data for 27 bladder UC cell lines available through the Cancer Cell Line Encyclopedia (CCLE22), and applied analyses similar to those performed in The Cancer Genome Atlas (TCGA4) study. This approach identified a subset of cell lines as suitable models for the study of molecular subtypes of bladder cancer. As previous research indicates transcriptional regulation is associated with molecular subtype in bladder cancer[12], we used our approach to directly test the ability of the transcription factors GATA3 and FOXA1, which are consistently associated with the luminal molecular subtype of UC, to cooperate with activation of PPARγto drive the luminal molecular subtype

Methods

Results

Conclusion