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

Abstract

A subset of renal cell carcinomas (RCCs) is characterized by t(6;11)(p21;q12), which results in fusion of the untranslated Alpha (MALAT1) gene to the TFEB gene. Only 21 genetically confirmed cases of t(6;11) RCCs have been reported. 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 and Melan A and the cysteine protease cathepsin K but are often negative for epithelial markers such as cytokeratins. TFEB IHC has been proven to be useful to confirm the diagnosis of t(6;11) RCCs in archival material, because native TFEB is upregulated through promoter substitution by the gene fusion. However, IHC is highly fixation dependent and has been proven to be particularly difficult for TFEB. A validated fluorescence in situ hybridization (FISH) assay for molecular confirmation of the t(6;11) RCC in archival formalin-fixed, paraffin-embedded material has not been previously reported. 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 relevant expected negative control cases and used the assay to report 8 new cases that expand the clinicopathologic spectrum of t(6;11) RCCs. An additional previously reported TFEB IHC-positive case was confirmed by TFEB FISH in 46-year-old archival material. In conclusion, TFEB FISH is a robust, clinically validated assay that can confirm the diagnosis of t(6;11) RCC in archival material and should allow a more comprehensive clinicopathologic delineation of this recently recognized neoplastic entity.

FIGURE 1

Selected TFEB FISH images from 2 positive test cases. Both of these neoplasms demonstrated split telomeric and centromeric TFEB FISH signals (isolated red and green dots) indicative of a TFEB gene rearrangement, in addition to the expected red-green fusion signal, which indicates an intact TFEB gene.

FIGURE 2

Case 2: this neoplasm was extensively hyalinized (A), with only small clusters of neoplastic epithelium, which mimicked clear cell RCC (B). The neoplasm demonstrated diffuse nuclear labeling for PAX8 (C) and cytoplasmic labeling for Melan A (D). The neoplasm demonstrated nuclear and cytoplasmic labeling for TFEB (E) and was diffuse positive for cathepsin K (F). This case was proven to harbor a TFEB gene rearrangement by FISH.

FIGURE 3

Case 6: this neoplasm demonstrated a predominant papillary oncocytic growth pattern, with only rare clusters of small cells on hematoxylin and eosin stains (A and B). The neoplastic cells demonstrated nuclear labeling for PAX8 (C) and diffuse immunoreactivity for Melan A (D) and patchy immunoreactivity for cathepsin K (E). This neoplasm was almost completely immunonegative for TFEB (F) but was proven by FISH to harbor a TFEB gene rearrangement.

FIGURE 4

Case 4: this neoplasm demonstrated variable morphology, including areas resembling oncocytoma (A, right; B; C, top) and other areas that resembled clear cell RCC (A, left; C, bottom). Both areas demonstrated diffuse nuclear labeling for PAX8 (D), demonstrated cytoplasmic labeling for Melan A (E), and showed focal labeling for cathepsin K (F). A minority of the neoplasm (< 5%) demonstrated a more conventional morphology for t(6;11) RCCs, featuring larger clear cells and smaller cells (G). The neoplasm demonstrated focal moderate immunolabeling for TFEB at its periphery (H), where it intermingled with native renal tubules. This case was proven to harbor a TFEB gene rearrangement by FISH.

FIGURE 5

Case 5: this neoplasm demonstrated a solid nested growth pattern, with clusters of somewhat smaller cells located centrally and larger polygonal cells located at the periphery of the nests (A). The neoplasm demonstrated diffuse cytoplasmic labeling for both Melan A (B) and cathepsin K (C) and also labeled for PAX8 (not shown). This neoplasm demonstrated a gradient of TFEB immunoreactivity, which was most prominent at the periphery of the lesion. (D, top of the figure). The central portion of the neoplasm did not show TFEB labeling (E), but the peripheral portion demonstrated moderate nuclear labeling for TFEB (F). This neoplasm demonstrated TFEB gene rearrangement by FISH.