Next-Generation Sequencing of Translocation Renal Cell Carcinoma Reveals Novel RNA Splicing Partners and Frequent Mutations of Chromatin-Remodeling Genes

Abstract

Purpose MITF/TFE translocation renal cell carcinoma (TRCC) is a rare subtype of kidney cancer. Its incidence and the genome-wide characterization of its genetic origin have not been fully elucidated. Experimental design We performed RNA and exome sequencing on an exploratory set of TRCC (n=7), and validated our findings using The Cancer Genome Atlas (TCGA) clear-cell RCC (ccRCC) dataset (n=460). Results Using the TCGA dataset, we identified 7 TRCC (1.5%) cases and determined their genomic profile. We discovered three novel partners of MITF/TFE (LUC7L3, KHSRP and KHDRBS2), which are involved in RNA splicing. TRCC displayed a unique gene expression signature as compared to other RCC types, and showed activation of MITF, the transforming growth factor β1 and the PI3K complex targets. Genes differentially spliced between TRCC and other RCC types were enriched for MITF and ID2 targets. Exome sequencing of TRCC revealed a distinct mutational spectrum as compared to ccRCC, with frequent mutations in chromatin remodeling genes (six of eight cases, three of which from the TCGA). In two cases, we identified mutations in INO80D, an ATP-dependent chromatin remodeling gene, previously shown to control the amplitude of the S phase. Knockdown of INO80D decreased cell proliferation in a novel cell line bearing LUC7L3-TFE3 translocation. Conclusions This genome-wide study defines the incidence of TRCC within a ccRCC-directed project and expands the genomic spectrum of TRCC by identifying novel MITF/TFE partners involved in RNA splicing and frequent mutations in chromatin remodeling genes.

Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes

“…We analyzed our RNA-seq data to evaluate its usefulness for the discovery of new and known fusions in tRCC ( Supplementary Table 13 ). Of the samples classified as tRCC on the basis of morphology and TFE3 immunohistochemistry, we found evidence for the previously reported ASPSCR1-TFE3 fusion 25,70,71 and PRCC-TFE3 fusion 71 . We confirmed this result further using FISH analyses ( Supplementary Fig.…”

RBM10–TFE3 renal cell carcinoma characterised by paracentric inversion with consistent closely split signals in break‐apart fluorescence in‐situ hybridisation: study of 10 cases and a literature review

“…Cumulative studies have identified several gene fusion partners of TFE3 , including UBX domain containing tether for SLC2A4 ( ASPSCR1 ), proline‐rich mitotic checkpoint control factor ( PRCC ), and splicing factor proline and glutamine rich ( SFPQ ) . Less frequent fusion partners such as mediator complex subunit 15 ( MED15 ) and dishevelled segment polarity protein 2 ( DVL2 ) have also been identified . The histological diagnosis of Xp11 translocation RCCs is based on a characteristic morphology, such as papillary architecture composed of clear epithelioid cells with psammoma bodies, and strong nuclear immunostaining of TFE3.…”

MicroRNA expression profiling of Xp11 renal cell carcinoma

“…Expression profiling studies had demonstrated that the MET receptor tyrosine kinase is induced by TFE3 gene fusions, and MET protein expression has been verified by immunohistochemistry; however, results of a clinical trial targeting MET in Xp11 translocation neoplasms have been disappointing [8]. Whole genome and RNA sequencing studies have demonstrated frequent mutations in chromatin remolding genes such as INOEBD in Xp11 translocation RCC, though this mutation cannot be targeted at the current time [9]. Clearly, further studies to identify novel targets in Xp11 translocation RCC are sorely needed.…”