Identification of a novel PARP14‐TFE3 gene fusion from 10‐year‐old FFPE tissue by RNA‐seq

Abstract

Xp11 (TFE3) translocation renal cell carcinoma (RCC) is officially recognized as a distinct subtype of RCC in the 2004 WHO classification. This neoplasm is characterized by several chromosomal translocations between the TFE3-involving Xp11.2 breakpoint and various fusion partners. To date, five partner genes have been identified, that is, PRCC in 1q21, PSF in 1q34, ASPL in 17q25, CLTC in 17q23, and NONO in Xq12; and three additional translocations have been reported with no partner gene being defined: t(X;3)(p11;q23), t(X;10)(p11;q23), and t(X;19)(p11;q13). Here, we report the identification of a novel TFE3 fusion partner, PARP14 in chromosome band3q21. We used RNA-seq on a 10-year-old FFPE (formalin-fixed, paraffin-embedded) tissue sample, which carried t(X;3)(p11;q23) as detected in the original cytogenetic study. The fusion transcript connected the 5'-end of the first two exons of PARP14 to the 3'-end of five exons of TFE3, which was verified by reverse transcription PCR (RT-PCR) and Sanger sequencing. Similar to other TFE3 fusions previously reported, the predicted PARP14-TFE3 product retains the nuclear localization and DNA-binding domains of TFE3. This finding expands the list of TFE3 translocation partner genes and re-emphasizes the essential oncogenic role of TFE3 fusion proteins in this tumor. Our result also clearly demonstrated the feasibility of identifying chromosomal translocation by RNA-seq in clinical FFPE, which are easily accessible and associated with valuable clinical information. © 2015 Wiley Periodicals, Inc.

TFE3-Fusion Variant Analysis Defines Specific Clinicopathologic Associations Among Xp11 Translocation Cancers

“…To verify FISH results in 5 selected cases with available material, RNA-seq was performed as described previously (5). Briefly, total RNA was extracted after xylene deparaffinization, using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany).…”

“…Xp11 translocation RCC bear chromosome translocations that result in one of a variety of gene fusions that involve the TFE3 transcription factor gene, which maps to the Xp11.2 locus. Reported TFE3 fusion partners include ASPSCR1 (ASPL), PRCC, SFPQ1 (PSF), NONO, CLTC, PARP14, LUC7L3, and KHSRP (3,4,5,6). Xp11 translocation RCC comprise the majority of pediatric RCC and approximately 1–4% adult RCC (7–10).…”

Xp11 neoplasm with melanocytic differentiation of the prostate harbouring the novel NONO–TFE3 gene fusion: report of a unique case expanding the gene fusion spectrum

“…Advances in molecular genetic studies have shown that TFE3 gene fusions are present in two types of cancer, including alveolar soft part sarcoma (ASPS) and Xp11.2 translocation renal cell carcinomas (RCCs) . In these diseases, the TFE3 gene can be fused by translocation to one of several other genes, including ASPL , PRCC , NONO(p54 nrb ) , CLTC , PSF , LUC7L3 , KHSRP , PARP14 and unknown genes on chromosomes 10 …”

Advances in the Molecular Analysis of Soft Tissue Tumors and Clinical Implications

“…The quality of RNA from old FFPE tissue blocks may be suboptimal for some applications, but some technologies are specifically designed to extract information from substantially degraded RNA molecules utilizing very short reads; 38,39 in addition, extraction protocols continue to improve and there are good examples of successful RNA-seq application to archival material up to 10 years old. 40 Once the library is prepared and converted to cDNA, sequencing takes place by MPS as for genome-based approaches. The length of the reads (ultimately depending on the quality of the starting RNA) is a big determinant of the analytical sensitivity and the quality of the results.…”