Combining integrated genomics and functional genomics to dissect the biology of a cancer‐associated, aberrant transcription factor, the ASPSCR1–TFE3 fusion oncoprotein

Abstract

Oncogenic rearrangements of the TFE3 transcription factor gene are found in two distinct human cancers. These include ASPSCR1–TFE3 in all cases of alveolar soft part sarcoma (ASPS) and ASPSCR1–TFE3, PRCC-TFE3, SFPQ-TFE3 and others in a subset of paediatric and adult RCCs. Here we examined the functional properties of the ASPSCR1–TFE3 fusion oncoprotein, defined its target promoters on a genome-wide basis and performed a high-throughput RNA interference screen to identify which of its transcriptional targets contribute to cancer cell proliferation. We first confirmed that ASPSCR1–TFE3 has a predominantly nuclear localization and functions as a stronger transactivator than native TFE3. Genome-wide location analysis performed on the FU-UR-1 cell line, which expresses endogenous ASPSCR1–TFE3, identified 2193 genes bound by ASPSCR1–TFE3. Integration of these data with expression profiles of ASPS tumour samples and inducible cell lines expressing ASPSCR1–TFE3 defined a subset of 332 genes as putative up-regulated direct targets of ASPSCR1–TFE3, including MET (a previously known target gene) and 64 genes as down-regulated targets of ASPSCR1–TFE3. As validation of this approach to identify genuine ASPSCR1–TFE3 target genes, two up-regulated genes bound by ASPSCR1–TFE3, CYP17A1 and UPP1, were shown by multiple lines of evidence to be direct, endogenous targets of transactivation by ASPSCR1–TFE3. As the results indicated that ASPSCR1–TFE3 functions predominantly as a strong transcriptional activator, we hypothesized that a subset of its up-regulated direct targets mediate its oncogenic properties. We therefore chose 130 of these up-regulated direct target genes to study in high-throughput RNAi screens, using FU-UR-1 cells. In addition to MET, we provide evidence that 11 other ASPSCR1–TFE3 target genes contribute to the growth of ASPSCR1–TFE3-positive cells. Our data suggest new therapeutic possibilities for cancers driven by TFE3 fusions. More generally, this work establishes a combined integrated genomics/functional genomics strategy to dissect the biology of oncogenic, chimeric transcription factors.

Modeling Alveolar Soft Part Sarcomagenesis in the Mouse: A Role for Lactate in the Tumor Microenvironment

“…Exogenous lactate drove increases in proliferative index and vascular density (Fig.8D–F). As cross-validation of this effect, we cultured the only two described human cancer cell lines that express ASPSCR1-TFE3 , FU-UR-1 (Ishiguro et al, 2004; Kobos et al, 2013) and ASPS-1 (Kenney et al, 2011) in increasing concentrations of sodium lactate, identifying a proliferative response. We further confirmed that increased exogenous lactate concentration in normoxia drove higher HIF1α stabilization, evidenced by its increased nuclear presence.…”

“…Although many angiogenic genes are highly upregulated in the tumors (Lazar et al, 2007; Vistica et al, 2009), few were found to be direct transcriptional targets of the fusion protein by chromatin immunoprecipitation analyses (Kobos et al, 2013). This suggests that some other factor, possibly related to metabolism or microenvironment, enhances angiogenesis in ASPS.…”

Clinical heterogeneity of Xp11 translocation renal cell carcinoma: impact of fusion subtype, age, and stage

“…Moreover, the one patient who has survived with no evidence of disease despite hematogenous metastasis (M1 disease; ASPSCR1-TFE3 Case 33) responded to immune therapy including tumor vaccine and interleukin 2 treatments, whereas these treatments have been ineffective in other patients (such as case 12 of reference 38 and case 2 of reference 26). These reports highlight that a single effective treatment remains out of reach at the current time for these neoplasms, and underscore the importance of further genetic analysis 66,67 to identify potential targets such as MET (known to be induced by TFE3 gene fusions 66 ) for effective, nontoxic therapies for these patients.…”

Alveolar soft part sarcoma of the oral and maxillofacial region: clinical analysis in a series of 18 patients

“…A strong positive immunoreaction against TFE3 is characteristic for ASPS. 8,12,22 Treatment and outcomes Because of its rarity, unusual clinical course, and indolent disease progression, treatment for ASPS has been challenging for pathologists as well as surgeons. Radical surgical excision with 1.5-to 2.0-cm microscopically clear surgical margins of the primary tumoral tissue, as well as the recurrent tumor manifestation, seems to be essential for local control but is unable to prevent distant metastasis in case of early spreading.…”