Molecular Characterization of Multifocal Granular Cell Tumors

Abstract

Granular cell tumors (GrCT) were recently found to be driven by inactivating mutations in vacuolar H+-ATPase (V-ATPase) genes, most frequently ATP6AP1 and ATP6AP2. Multifocal presentation is present in ~10% of cases; however, the relationship between multifocal tumors in a given patient has not been elucidated. We hypothesized that benign-appearing multifocal GrCT are molecularly distinct whereas paired primary and metastatic malignant GrCT share identical mutations. To test this, we conducted targeted next-generation sequencing of the V-ATPase genes in multifocal GrCT and whole exome and Sanger sequencing in paired primary and metastatic malignant GrCT. Thirteen patients with≥2 GrCT were identified (total of 43 tumors). Forty-two tumors were successfully sequenced. Tumors showed somatic mutations in 3 of the 10 targeted genes in 32 of 42 samples (76%). Twenty tumors showed mutations in ATP6AP1 (48%), 10 tumors had mutations in ATP6AP2 (24%), and 2 tumors showed mutations in ATP6V0A4 (5%). Predicted loss-of-function mutations were found in ATP6AP1 in 17 tumors (40%), in ATP6AP2 in 10 tumors (24%), and in ATP6V0A4 in 1 tumor (2%). In 8 patients, mutually exclusive mutations were detected in at least 2 tumors per patient. Two patients were identified with malignant GrCT with material available from both primary and metastatic sites. Identical frameshift insertions were found in ATP6AP1 in 1 case and the second case showed identical nonsense mutations in ATP6AP1. In conclusion, multifocal GrCT within an individual patient are molecularly distinct, while paired primary and metastatic GrCT share identical mutations.

A Rare Case of Multifocal Asynchronous Benign Granular Cell Tumors with PIK3CA Subclonal Mutation Identified in One Tumor by Next-Generation Sequencing

“…Further, multifocal GCTs within a given patient were molecularly distinct, supporting interpretation as separate primaries. In contrast, paired primary and metastatic histologically malignant GCTs showed identical mutations, confirming the primary-metastatic relationship [ 17 ]. Wei et al [ 18 ] reported whole exome sequencing (WES) performed in a malignant GCT that exhibited low mutation burden and overall stable genome with local complex rearrangements.…”

Mesenchymal Tumors of the Breast: Fibroblastic/Myofibroblastic Lesions and Other Lesions

“…In 2018, Pareja et al performed whole exome sequencing of benign and malignant GCTs and identified inactivating mutations of ATP6AP1 and ATP6AP2 in 49-74% [92,[97][98][99]. In vitro inactivation impairs the V-ATPase gene complex in Schwann cells and leads to the formation of GCTs [97].…”

“…In vitro inactivation impairs the V-ATPase gene complex in Schwann cells and leads to the formation of GCTs [97]. Dehner et al demonstrated in 2022 that multifocal benign GCTs in the same patient are molecularly distinct, whereas multifocal malignant GCTs, which are much less common, harbor identical mutations [99].…”

Utility of sequencing for ATP6AP1 and ATP6AP2 to distinguish between atypical granular cell tumor with junctional component and melanoma

“…A multifocal benign variant also exists. 3 In addition there are reports of atypical and malignant GCTs with junctional components that raise a differential diagnosis of melanoma. 4 There are also reports of nevi and melanomas with granular cell cytoplasmic change.…”

“…Criteria have been proposed for distinguishing benign, atypical, and malignant GCTs 1,2 ; however, these are difficult to apply consistently and there are case reports of GCTs with benign histopathologic features going on to metastasize. A multifocal benign variant also exists 3 . In addition there are reports of atypical and malignant GCTs with junctional components that raise a differential diagnosis of melanoma 4 .…”