Abstract LB-113: Genome-wide mapping of TFE3-fusion target genes.

Abstract

Abstract Xp11.2 translocation renal cell carcinoma (RCC), also known as TFE3-fusion associated RCC, is a recently classified distinct subtype of RCC. It is defined by several different translocations involving chromosome Xp11.2, all resulting in gene fusions involving the Transcription Factor Binding to IGHM Enhancer 3 (TFE3) gene. However, the detailed function of TFE3-fusion proteins in TFE3-fusion associated RCC still remains unknown, and there is no effective treatment for patients with this RCC subtype. In this study we sought to investigate the detailed regulatory network of TFE3-fusion proteins by using doxycycline-inducible HA-tagged TFE3-fusion cell lines and chromatin immunoprecipitation (ChIP)-sequencing. Doxycycline-inducible cell lines that express HA-tagged TFE3-fusion (PRCC-TFE3, PSF-TFE3 and NONO-TFE3) and TFE3 wild-type proteins were established in the HK2 cell line. Genome-wide screening of the binding characteristics of TFE3-fusion proteins and TFE3 wild-type protein in doxycycline-induced cell lines was performed using a chromatin immunoprecipitation sequencing (ChIP-seq) assay. Hierarchical clustering was used to analyze the genes regulated by each type of TFE3-fusion protein compared with TFE3 wild-type protein. The total number of CHIP-seq reads in TFE3 wild-type cell line was 18552874 and enrichment of the promoter region was 1.2. In contrast, the total number of CHIP-seq reads in PRCC-TFE3, PSF-TFE3 and NONO-TFE3 cell lines were 15332969, 20426159 and 17639467, respectively. Enrichment of promoter region in each of the TFE3-fusion cell line was 1.5, 2.4 and 2.2, respectively. There were 80 motifs enriched (Z score >1.5) by expression of PRCC-TFE3 protein compared to TFE3-wild type protein, 104 motifs enriched by PSF-TFE3 protein and 39 motifs by NONO-TFE3 protein expression. Work is ongoing to identify the target genes that are co-regulated in TFE3-fusion cell lines relative to the TFE3 wild-type cell line. Our aim is to identify activated pathways in common among the different TFE3-fusion cell lines compared to the TFE3 wild-type cell line. We anticipate that this study will further our understanding of mechanisms that activate TFE3-fusion proteins facilitating the identification of therapeutic targets for effective treatment of TFE3-fusion associated RCC. Citation Format: Ying Huang, Masaya Baba, Hisashi Hasumi, Yukiko Hasumi, Laura Schmidt, Yoshi Wakabayashi, Jun Zhu, Wenjing Yang, Marston Linehan. Genome-wide mapping of TFE3-fusion target genes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-113. doi:10.1158/1538-7445.AM2013-LB-113