Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors

Fresia Pareja,Raymond S Lim,Edaise M Da Silva,Juan Palazzo,Dan Fan,Rahul Kumar,Travis J Hollmann ,Anqi Li,Brian P Rubin,John R Lozada,Emad A Rakha,Britta Weigelt,Rui Gardner,Ian O Ellis,Leona Cohen‐Gould ,Felipe C Geyer,Maria Isabel Albano Edelweiss ,Pedro Blecua,Alissa H Brandes,Rui Bi,Arnaud Da Cruz Paula,Rodrigo Gularte‐Mérida ,Achim A Jungbluth,Larry Norton,Ino De Bruijn,Bárbara Alemar ,David Brown ,Thais Basili,Pier Selenica,Marcia Edelweiss,Sho Fujisawa,Elvin Feng,Jorge S Reis‐Filho

doi:10.1038/s41467-018-05886-y

Abstract

Granular cell tumors (GCTs) are rare tumors that can arise in multiple anatomical locations, and are characterized by abundant intracytoplasmic granules. The genetic drivers of GCTs are currently unknown. Here, we apply whole-exome sequencing and targeted sequencing analysis to reveal mutually exclusive, clonal, inactivating somatic mutations in the endosomal pH regulators ATP6AP1 or ATP6AP2 in 72% of GCTs. Silencing of these genes in vitro results in impaired vesicle acidification, redistribution of endosomal compartments, and accumulation of intracytoplasmic granules, recapitulating the cardinal phenotypic characteristics of GCTs and providing a novel genotypic–phenotypic correlation. In addition, depletion of ATP6AP1 or ATP6AP2 results in the acquisition of oncogenic properties. Our results demonstrate that inactivating mutations of ATP6AP1 and ATP6AP2 are likely oncogenic drivers of GCTs and underpin the genesis of the intracytoplasmic granules that characterize them, providing a genetic link between endosomal pH regulation and tumorigenesis.

Highlights

Granular cell tumors (GCTs) are rare tumors that can arise in multiple anatomical locations, and are characterized by abundant intracytoplasmic granules
82 cases were classified as GCTs, which originated in different anatomic locations, including skin (n = 40), soft tissue (n = 15), gastrointestinal tract (n = 13), breast (n = 6), tongue (n = 5), and other locations (n = 3; Supplementary Table 1)
To determine whether ATP6AP1 and ATP6AP2 loss-offunction mutations are pathognomonic for GCTs, we investigated their presence in 6285 non-hypermutated cancers across 14 common cancer types from The Cancer Genome Atlas (TCGA) studies retrieved from the cBioPortal[6]

Summary

Introduction

Granular cell tumors (GCTs) are rare tumors that can arise in multiple anatomical locations, and are characterized by abundant intracytoplasmic granules. A subset of rare tumors not uncommonly have simple genomes, with a paucity of copy number alterations (CNAs) and somatic mutations, and are characterized by highly recurrent, specific, or even pathognomonic, somatic mutations, or fusion genes[4] These tumors have distinctive phenotypes and often arise in diverse anatomic locations. Through a whole-exome sequencing (WES) and targeted sequencing analysis of GCTs, we uncovered highly recurrent and mutually exclusive inactivating mutations targeting the endosomal pH regulators ATP6AP1 and ATP6AP2 in GCTs. In vitro silencing of ATP6AP1 and ATP6AP2 in human Schwann cells and epithelial cells resulted in the accumulation of intracytoplasmic granules that are ultra-structurally and phenotypically similar to those of human GCTs, altered endosomal acidification and oncogenic properties, thereby establishing a novel genotypic–phenotypic correlation. No differences in histologic features (Supplementary Table 5) or anatomical site (Fig. 2c) of GCTs according to the ATP6AP1/ATP6AP2 mutational status were observed

Methods

Results

Conclusion