Renal cell carcinoma with biphasic morphology: A cohort showing similar morphology but distinct clinicopathological and molecular features.

Biphasic morphology, characterized by small cells clustered around basement membrane material, is a distinctive feature of TFEB-rearranged renal cell carcinoma (RCC). However, other RCC subtypes may exhibit similar histological characteristics. Clinicopathological data from 12 cases of RCC with biphasic morphology-including four cases of TFEB-rearranged RCC, four cases of TFE3-rearranged RCC, and four cases of chromophobe RCC (ChRCC)-were collected. Most of the 12 patients survived without complications, except for one patient with ChRCC who died accidentally 25 months after surgery. Microscopically, all 12 tumors showed varying proportions of biphasic morphology, comprising clear or eosinophilic large cells arranged in nests, glandular, or papillary structures, and clustered small cells forming pseudorosette structures around basement membrane-like deposits. Large pale cells with clear to foamy cytoplasm were observed in the four ChRCC tumors. IHC revealed consistent nuclear and cytoplasmic expression of TFEB in all four cases of TFEB-rearranged RCC and diffuse nuclear positivity of TFE3 in TFE3-rearranged RCC. Cathepsin K and GPNMB were expressed in most TFEB- and TFE3-rearranged RCCs, whereas the melanocytic markers Melan A and HMB45 were expressed to varying degrees. Additionally, PD-L1 (22C3) was expressed with a high CPS of approximately 90 in two cases of TFEB-rearranged RCC. CK7, CD117, and Ksp-cad were expressed in both large and small cells in the four cases of ChRCC. FISH identified TFEB rearrangement in all four cases of TFEB-rearranged RCC and TFE3 rearrangement in all four cases of TFE3-rearranged RCC. RNA sequencing and whole-exome sequencing revealed TFEB-MALAT1 fusion in all four cases of TFEB-rearranged RCC. TFE3-SFPQ fusion was detected in two cases, and TFE3-MED15 fusion in the other two TFE3-rearranged RCC cases. PD-L1 (22C3) expression was detected in three cases of TFE3-rearranged RCC, two TFE3-MED15 fusion subtype showed a CPS of approximately 30 and 20, whereas one TFE3-SFPQ fusion subtype showed a CPS of approximately 5. Additionally, in the four ChRCC cases, multiple segments of chromosomes 1, 2, 6, 8, 9, 10, and 17 were either lost or amplified. The biphasic structure with small cell components in RCC is observed in TFEB-rearranged RCC and in TFE3-rearranged RCC and ChRCC, which may be prone to misdiagnosis based solely on morphology. Patients with TFEB- and TFE3-rearranged RCCs exhibiting small cell components tend to be younger and have more favorable prognoses. The TFE3-MED15 gene fusion in RCC with a biphasic structure containing small cell components has been reported here for the first time. Genetic alterations in ChRCC with small cell components are similar to those in classical ChRCC, indicating that small cell components represent merely a histological variant without prognostic implication. A proportion of TFEB-rearranged RCC may exhibit high PD-L1 expression level and a favorable response to immunotherapy. In TFE3-rearranged RCC, the fusion gene might influence morphology or PD-L1 expression, thereby be likely to affect the efficacy of immunotherapy. Assessment of a combination of histological morphology, immunophenotype, and genetic alterations can facilitate precise pathological diagnosis of RCC, supporting personalized targeted therapy and prognosis assessment.