TFE3 and TFEB break-apart fluorescent in situ hybridization (FISH) assays are the gold standard for diagnostic confirmation of MiTF family altered renal cell carcinoma (MiTF RCC), which includes TFE3 rearranged RCC, and TFEB altered RCC. However, FISH assays for multiple reasons may lead to equivocal or false-negative results, especially in cryptic fusions resulting from intrachromosomal inversions involving 5' partner genes such as NONO, GRIPAP1, RBMX, and RBM10. When FISH results are negative in cases with strong morphologic suspicion of the listed tumor entities, pathologists may recommend targeted RT-PCR or panel-based RNA fusion sequencing for diagnostic confirmation. Our recent RNA in situ hybridization (RNA ISH) based study demonstrated RNA expression of the tripartite motif containing 63 (TRIM63) to be highly enriched in TFE3 rearranged RCC and TFEB altered RCC, including two FISH false-negative RCC cases harboring RBM10::TFE3 fusion. Based on these observations, we hypothesized that TRIM63 positivity could aid in diagnosing cases that are negative by conventional FISH assay but remain morphologically suspicious, representing an unmet clinical need in this area. We collected 20 RCC cases with morphological suspicion (equivocal/indeterminate immunohistochemistry panel) of MiTF RCC, which were TRIM63 positive, negative/equivocal for TFE3/TFEB gene rearrangement by FISH and underwent next generation sequencing (NGS). On NGS correlation, 14 of 20 (70%) FISH negative TRIM63 positive tumors harbored a MiTF gene rearrangement. In the remaining 6 cases, we were unable to fully ascertain the MITF rearrangement status due to the inherent limitation of the NGS panel utilized. The cases with MiTF gene rearrangement include TFE3 rearrangement in 60% (12/20), and TFEB low-level copy gains (with an additional missense mutation in one case) in 10% (2/20) of samples. RBM10:TFE3 fusion was seen in 67% (8/12) of TFE3 rearranged RCC in this cohort. TRIM63 RNA ISH assay could aid in identifying cases that harbor TFE3 or TFEB rearrangement associated with false-negative or equivocal TFE3/TFEB FISH results, especially those involving gene fusions with a paracentric Xp11 inversion. Overall, employment of TRIM63 RNA ISH coupled with TFE3/TFEB FISH assays and follow-up genomic interrogation enhanced diagnostic accuracy for patients with MiTF RCC.
Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc. 2025 Aug 25 [Epub ahead of print]
Rahul Mannan, Ying-Bei Chen, Xiaoming Wang, Yuping Zhang, Noshad Hosseini, Ankur R Sangoi, Andres Acosta, Sean R Williamson, Somnath Mahapatra, Anya K Chinnaiyan, Jing Hu, Ulka Vaishampayan, Lina Shao, Bryan L Betz, Annette S Kim, Xuhong Cao, Fengyun Su, Rui Wang, Pedram Argani, Noah Brown, Satish K Tickoo, Arul M Chinnaiyan, Victor E Reuter, Saravana M Dhanasekaran, Rohit Mehra
Department of Pathology, University of Michigan Medical School, Ann Arbor, MI-48109, USA; Michigan Center for Translational Pathology, Ann Arbor, MI-48109, USA., Department of Pathology, Memorial Sloan Kettering, New York, NY-10065, US48109, USA., Department of Pathology, University of Michigan Medical School, Ann Arbor, MI-48109, USA., Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA., Department of Pathology, School of Medicine, Stanford Medicine, CA-94305, USA., Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA., Department of Pathology, Cleveland Clinic, Cleaveland, OH 44195, USA., Michigan Center for Translational Pathology, Ann Arbor, MI-48109, USA., Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI-48109, USA., Michigan Center for Translational Pathology, Ann Arbor, MI-48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI., Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA., Department of Pathology, University of Michigan Medical School, Ann Arbor, MI-48109, USA; Michigan Center for Translational Pathology, Ann Arbor, MI-48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI; Department of Urology, University of Michigan Medical School, Ann Arbor, MI-48109, USA; Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI-48109, USA., Department of Pathology, University of Michigan Medical School, Ann Arbor, MI-48109, USA; Michigan Center for Translational Pathology, Ann Arbor, MI-48109, USA; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. Electronic address: .