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The cancer-specific biomarker TRIM63 was highly expressed in all classes of microphthalmia-associated transcription factor family aberration–associated renal cell carcinoma compared with other subtypes of RCC, where TRIM63 expression was low or absent.
The cancer-specific biomarker TRIM63 was highly expressed in all classes ofmicrophthalmia-associated transcription factor family aberration–associated renal cell carcinoma (MiTF-RCC) compared with other subtypes of RCC, where TRIM63 expression was low or absent, according to findings from an RNA-sequencing (RNAseq) analysis published in Modern Pathology.
Moreover, TRIM63 RNA-in situ hybridization (ISH) was strongly positive in TFE3 fluorescence ISH (FISH) false-negative cases with RBM10-TFE3 inversion, despite TRIM63 RNA-ISH and TFE3/TFEB FISH results yielding largely concordant results.
The results indicate that TRIM63 is a diagnostic marker that can be used to distinguish MiTF-RCC from other RCC subtypes that have overlapping morphology.
“Our results suggest this new biomarker, in combination with standard assays, can help improve the accuracy and efficiency in diagnosing this challenging kidney cancer subtype,” said Rohit Mehra, MBBS, principal investigator of the study, clinical professor, director of MLabs’ GU Service Line, and co-director of the University of Michigan Rapid Autopsy Discovery Program at Michigan Medicine, in a statement to OncLive®.
“It’s important to distinguish MiTF from other subtypes of kidney cancers—clear cell, papillary and chromophobe—because these tumors may not respond well to standard, frontline treatments and may respond better to other approaches,” Mehra added.
MiTF-RCC comprises approximately 40% of pediatric RCC and 5% of adult RCC. Notably, the higher absolute prevalence of RCC among adult patients means that MiTF-RCC affects a larger number of adult vs pediatric patients.
MiTF-RCC is characterized by the Xp11 translocation RCC harboring TFE3 gene fusions with multiple partners, t(6;11) translocation RCC harboring mainly MALATI-TFEB fusions, and RCC with TFEB amplifications. Notably, MiTF-RCC has demonstrated a wide morphologic spectrum that differs based on the 3 subtypes.
Regarding treatment, patients with MiTF-RCC may have variable responses to standard first-line therapies used for patients with clear cell RCC (ccRCC).
The study investigators aimed to further characterize MiTF-RCC molecularly, while identifying specific tumor biomarkers.
The evaluable cohort comprised 31 cytogenetically confirmed cases of MiTF-RCC and 70 cases of clinically and morphologically suspected MiTF-RCC with confirmed TFE3/TFEB expression with FISH.
Patients with cytogenetically confirmed MiTF-RCC were a median age of 57 years (range, 3-78), whereas those with suspected MiTF-RCC were a median age of 56.5 years (range, 15-88).
In addition, patients with ccRCC (primary, n = 10; metastatic n = 5), papillary RCC (pRCC; type 1, n = 9; type 2, n = 3), chromophobe RCC (chRCC; classic, n = 15; eosinophilic, n = 6; metastatic, n = 4), clear cell papillary RCC (ccpRCC; n = 5), oncocytoma (n = 6), mucinous tubular and spindle cell carcinoma (MTSCC; n = 5), hereditary leiomyomatosis and RCC (HLRCC)–associated RCC (n = 3), succinate dehydrogenase B (SDHB)–deficient RCC (n = 1), hybrid oncocytic/chromophobe tumor (HOCT; n = 2), eosinophilic solid and cystic (ESC) RCC (n = 2), and angiomyolipoma (AML; epithelioid, n = 3; classic, n = 5).
Results from RNAseq data demonstrated 734 up-regulated genes and 355 downregulated genes in the patients with MiTF-RCC compared with patients with other RCC subtypes and benign kidney tissues (fold-change > 2, Benjamini-Hochberg adjusted P < .05).
Additionally, up-regulated genes—notably TRIM63, NMRK2, and HHATL—were highly specific to the MiTF-RCC subtype. TRIM63 demonstrated the highest specificity among these up-regulated genes. Although these 3 genes were found to be enriched in normal human and benign muscle tissue, they were absent in benign kidney tissue.
Based on maximal enrichment of TRIM63 in a pilot cohort (n = 55) of patients with MiTF-RCC, TRIM63 expression by RNA-ISH was evaluated in an expanded cohort (n = 185) that represented common and rare RCC subtypes.
High-level TRIM63 signals were observed in 89% of cytogenetically confirmed MiTF-RCC cases, including TFE3-translocation RCC (n = 15), TFEB translocation RCC (n = 7), and TFEB amplification RCC (n = 3).
No TRIM63 signals were detected in 90% of primary ccRCC, 91% of pRCC, 100% of ccpRCC, 100% of chRCC, 100% of oncocytoma, 100% of MTSCC, 100% of HLRCC-associated RCC, 100% of SDHB deficient RCC, or 50% of HOCT, 100% of metastatic ccRCC, and 75% of metastatic chRCC cases evaluated.
Very low TRIM63 expression was observed in ccRCC (n = 1), pRCC type 1 (n = 1), and HOCT (n = 1). One muscle metastasis of chRCC demonstrated focal TRIM63 signals. One case of ESC-RCC had low TRIM63 expression, whereas another ESC-RCC case had moderate expression. Varying expression of TRIM63 was observed among acute myeloid leukemia (AML) cases; moderate-to-strong signals were identified in 2 of 3 epithelioid AML cases and 5 of 5 classic AML cases.
Notably, during characterization of FISH-negative/TRIM63-positive MiTF-RCC, sequencing revealed 1 case with low-level copy number gain (n = 3) on the short arm of chromosome 6 (6p), which is known to house TFEB and VEGFA genes. Another case had a rearrangement between chromosome X and 19 (t(X:19)(p11.23;q13.32)) resulting in a ZC3H4-TFE3 gene fusion. The novel fusion involved TFE3 and had not been previously reported in the literature.
“TRIM63 is specifically overexpressed in the majority of MiTF-RCC. Future functional studies will further explore the role of TRIM63 in MiTF-RCC tumorigenesis and tumor progression and determine if TRIM63 is a direct transcriptional target of [the] MiT family of transcription factors,” concluded lead study author Xiao-Ming (Mindy) Wang, a research investigator at the Michigan Center for Translational Pathology at the University of Michigan, and co-authors in the study publication.