Abstract 4475: Delineating translocation renal cell carcinoma oncogenesis in cells harboring TFE3 fusion with spliceosome machinery associated genes
Authors: Damayanti Nur P. , Chintala Sreenivasulu , Orillion Ashley , Adelaiye-Ogala Remi , Elbanna May F. , Hollenhorst Pete , Pili Roberto 
Published: July 2017

Background: Translocation Renal Cell Carcinoma (tRCC) represents an aggressive subtype of kidney cancer associated with various gene fusions involving translocation of one of two members of micropthalmia transcription factor (MiT) family, TFE3 or TFEB. Despite identification of multiple TFE3 gene fusions in tRCC, heterogeneous phenotype and various dysregulated signaling pathway resulting from variety of gene fusion partners pose a challenge to establish effective treatments for these patients. In this work, we sought to study the biology underlying oncogenesis in tRCC involving TFE3 fusion with genes associated with pre-mRNA splicing factor machinery; NONO, SFPQ and PRCC.

Methods: To investigate the biology of different TFE3 fusion proteins, oncogenic phenotypes and oncogenic signaling were compared among cells with distinct endogenous expression of TFE3 fusions such as SFPQ-TFE3, NONO-TFE3, PRCC-TFE3. Endogenous SFPQ-TFE3 expressing cells, RP-RO7, were generated from patient derived xenograft. UOK-109 and UOK-146 (kindly provided by Dr. Marston Lenehan, NCI) were used as endogenous NONO-TFE3 and PRCC-TFE3 expressing cells, respectively. TFE3 fusion transcripts were identified with RT-PCR. TFE3 fusion preferential DNA binding was assessed with ChIP-sequencing. Oncogenic phenotype assessment was done in 2D culture and two different 3D models; 1) Solid tumor model, in which cancer cell interaction with extracellular matrix and stromal cells, were represented in multiculture-spheroid system, 2) Invasion model, in which cell ability to invade basement membrane barrier was modeled with matrix restricted spheroid.

Results: Dissimilar oncogenic phenotypes were seen among RP-R07, UOK-109 and UOK-146 in 2D and 3D culture. The presence of nuclear E-Cadherin was observed in all three cells model, with increasing level of nuclear expression in fusion partner dependent manner (P&lt;0.05). Distinctive profiles of global phosphotyrosine and global phosphoserine were observed in cells model harboring different TFE3 fusions, despite common nuclear signal of TFE3. Nuclear expression of selected kinases and phosphokinases such as AKT, FAK, mTOR, VGEFR-2 were identified among TFE3 fusion cells with different level of expression (P&lt;0.05). These results suggest distinct alteration of kinases nucleocytoplasmic shuttling regulation in tRCC cells (P&lt;0.05), as compared to non TFE3 fusion cells. TFE3 ChIP-seq data in RP-R07 indicate novel DNA target involving metabolism and TGF-β signaling related genes.

Conclusions: Our results indicate a distinct biology underlying tRCC oncogenesis in different TFE3 fusion models involving kinase reprograming and nucleocytoplasmic shuttling regulation. These differences also suggest the possibility of generating personalized treatments targeting specific TFE3 fusion genes associated with the spliceosome machinery.

Citation Format: Nur P. Damayanti, Sreenivasulu Chintala, Ashley Orillion, Remi Adelaiye-Ogala, May F. Elbanna, Pete Hollenhorst, Roberto Pili. Delineating translocation renal cell carcinoma oncogenesis in cells harboring TFE3 fusion with spliceosome machinery associated genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4475. doi:10.1158/1538-7445.AM2017-4475