Molecular confirmation of t(6;11)(p21;q12) renal cell carcinoma in archival paraffin-embedded material using a break-apart TFEB FISH assay expands its clinicopathologic spectrum.

The past decade has witnessed the characterization of a subset of renal cell carcinomas (RCCs) that have chromosomal translocations resulting in gene fusions involving members of the MiT subfamily of transcription factors. The best known members of this subset are the Xp11 translocation RCCs, which were recognized by the World Health Organization in 2004.1 These neoplasms comprise the majority of pediatric RCCs and a smaller percentage of adult RCCs and classically feature a papillary architecture lined by clear cells with extensive psammomatous calcification.2–8 Xp11 translocation RCCs are characterized by gene fusions involving the TFE3 transcription factor gene that maps to this locus; at least 5 different fusion partners for TFE3 have been identified to date.2,3,5,9,10 A less well-known member of the translocation RCC family is the subset of RCCs characterized by t(6;11)(p21;q12), which results in fusion of the untranslated Alpha (MALAT1) gene on 11q12 to the related TFEB gene on 6p21.11–14 Only 21 genetically confirmed cases of t(6;11) RCCs have been reported.5,11–23 This neoplasm typically demonstrates a distinctive biphasic morphology, comprising larger epithelioid cells and smaller cells clustered around basement membrane material; however, the full spectrum of its morphologic appearances is not known. The t(6;11) RCCs differ from most conventional RCCs in that they consistently express melanocytic immunohistochemical (IHC) markers such as HMB45, Melan A, and the cysteine protease cathepsin K24,25 but are either negative or only focally positive for epithelial markers such as cytokeratins.11,12 On the basis of clinical, pathologic, and genetic similarities between the t(6;11) RCCs and the Xp11 translocation RCCs, we have proposed that these 2 neoplasms be classified together under the broader category of “MiT family translocation RCC.”12 Molecular confirmation of a diagnosis of a translocation RCC is relatively simple if fresh tissue is available for either cytogenetics or reverse transcriptase polymerase chain reaction assay using primers from the genes known to be involved in the gene fusion. However, in many cases, only archival, formalin-fixed, paraffin-embedded material is available. For the Xp11 translocation RCCs and t(6;11) RCCs, IHC for TFE3 and TFEB, respectively, have proven to be useful for confirming the diagnosis in archival material.6,12 This is because both TFE3 fusion proteins and native TFEB are upregulated by promoter substitution by the gene fusions in these 2 RCCs relative to the level of expression of the respective native proteins. However, IHC is highly fixation dependent and has proven to be particularly difficult for TFE3 and TFEB for several reasons. These include the scarcity of genetically confirmed positive controls and the fact that the assays are optimally performed by overnight incubation, which is difficult to automate.26 Recently, break-apart fluorescence in situ hybridization (FISH) assays for TFE3 gene fusions were developed for archival material27–29 and have allowed the expansion of the morphologic spectrum of the Xp11 translocation RCCs.30 A validated FISH assay for molecular confirmation of t(6;11) RCC has not been reported previously. We report herein the development of a break-apart TFEB FISH assay for the diagnosis of t(6;11)(p21;q12) RCCs. We validated the assay on 4 genetically confirmed cases and 76 pertinent negative control cases, confirmed the presence of a TFEB gene rearrangement in a previously reported TFEB IHC-positive case from 46 years ago, and used the assay to report 8 new cases that expanded the clinicopathologic spectrum of t(6;11) RCCs.