Genetic correlates of malignancy in TFE3-rearranged PEComa: a series of 14 cases

Perivascular epithelioid cell tumours (PEComas) show variable smooth muscle and melanocytic differentiation and mostly harbour mTOR pathway activation via TSC2 inactivation. Five-10% of sporadic PEComas instead harbour fusions involving TFE3, an vmTOR pathway target. Malignancy in TSC2/1-inactivated PEComa correlates with TP53, RB1 or ATRX inactivation. Here, we investigated genetic correlates of malignancy in TFE3-rearranged PEComa.

Fourteen TFE3-rearranged PEComas, confirmed by FISH and/or sequencing, occurred in 11 females (79%) and 3 males aged 9-64 years (median: 31.5 yr). Body sites were uterus (3 tumours), extremities (3), colon (2), nasal cavity (2), neck (1), retroperitoneum (1), bladder (1) and ovary (1). Nine tumours (64%) lacking cytologic atypia were diagnosed prospectively as benign, and five cytologically atypical tumours were diagnosed prospectively as malignant. By immunohistochemistry, tumours expressed SMA (6/13; 46%), HMB-45 (5/13; 38%), desmin (3/13; 23%) and melan-A (2/13; 15%), and not MITF (10 tumours), S-100 (7), SOX10 (4), pan-K (5) or EMA (3). By DNA sequencing, all nine benign tumours lacked complex copy number alterations (CNAs) or inactivation of TP53, ATRX or RB1. In contrast, three of four (75%) assessable malignant tumours showed complex CNAs, and only one of five malignant PEComas (20%) harboured TP53 inactivation. Among eight patients with follow-up (57%), all four benign PEComas neither recurred nor metastasized (median: 5.0 yr; range: 3.3-8.1 yr), while all four malignant tumours metastasized.

We conclude that malignant TFE3-rearranged PEComas frequently harbour complex CNAs, which could be of diagnostic utility. Malignant TFE3-rearranged PEComas lacked highly recurrent alterations in TP53, RB1 or ATRX.