Alternative Lengthening of Telomeres in Malignant Perivascular Epithelioid Cell Neoplasms: Correlation With Molecular Features Including ATRX Gene Mutation Status.

A subset of perivascular epithelioid cell neoplasms (PEComas) is histologically malignant and at high risk for metastasis, and there is limited literature available on the genetic features of these lesions. In addition to driver alterations in the tuberous sclerosis complex/mammalian target of rapamycin pathway or TFE3 fusions, recurrent ATRX mutations have been identified in malignant PEComas. ATRX mutations have been tightly associated with the alternative lengthening of telomeres (ALT) phenotype in a variety of other tumor types. Whether malignant PEComas-regardless of ATRX mutational status-harbor the ALT phenotype has not been characterized. We conducted immunohistochemistry (IHC), next-generation sequencing (NGS), and telomere-specific fluorescence in situ hybridization (FISH) on a cohort of 32 malignant PEComas to evaluate for the ALT phenotype and to correlate with underlying genomic features. TSC1/2/mTOR/RICTOR mutations or TFE3 translocations were detected in 16 of 31 (52%) cases by NGS. Recurrent ATRX alterations were identified in 10 (32%) cases. Sixteen cases underwent ALT FISH, 8 of which harbored ATRX alterations by NGS and/or ATRX loss based on IHC, and 8 cases without detectable ATRX alterations by NGS or loss based on IHC. Twelve (75%) of these 16 cases demonstrated the ALT phenotype by FISH. All 8 (100%) cases with ATRX mutations were ALT positive by FISH. In 8 (50%) cases without ATRX alterations based on NGS, 4 cases demonstrated ALT by FISH. Of these 4 ALT-positive cases lacking ATRX genomic alterations, IHC revealed ATRX protein loss in 1 case. Overall, ATRX alterations were identified in 75% of ALT-positive tumors. Our study provides the first correlation between ALT and genomic features of malignant PEComas, demonstrating that ATRX alterations invariably predict ALT, but that a subset of tumors without mutations in known ALT suppressor genes also activate ALT. These findings confirm that the association between ATRX alterations and ALT observed in other tumor types applies to PEComas and indicates that in a subset of cases, ALT may be activated by ATRX-independent mechanisms.