Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies.

Felix Oppel,Hui Shi,Mark W Zimmerman,A Thomas Look,Kenneth N Ross,Guangxiang Tong,Ting Tao,Jon C Aster,Shuning He,Richard Mark White

doi:10.1371/journal.pgen.1008039

Abstract

The SWI/SNF-family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas, gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells, while it also affects Polycomb repressive complex 2 (PRC2) silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis, we knocked out atrx in our previously reported p53/nf1-deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. Complete inactivation of atrx using CRISPR/Cas9 was lethal in developing fish and resulted in an alpha-thalassemia-like phenotype including reduced alpha-globin expression. In p53/nf1-deficient zebrafish neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/- fish, but these fish developed various tumors that were not observed in their atrx+/+ siblings, including epithelioid sarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma and rare types of carcinoma. These cancer types are included in the AACR Genie database of human tumors associated with mutant ATRX, indicating that our zebrafish model reliably mimics a role for ATRX-loss in the early pathogenesis of these human cancer types. RNA-seq of p53/nf1- and p53/nf1/atrx-deficient tumors revealed that down-regulation of telomerase accompanied ALT-mediated lengthening of the telomeres in atrx-mutant samples. Moreover, inactivating mutations in atrx disturbed PRC2-target gene silencing, indicating a connection between ATRX loss and PRC2 dysfunction in cancer development.

Highlights

The alpha thalassemia/mental retardation syndrome X-linked (ATRX) protein is involved in the epigenetic regulation of gene expression
Somatic mutations in genes coding for epigenetic regulators such as ATRX are found across a diverse group of cancer types, suggesting their broad relevance in tumor induction and progression
Further analysis revealed downregulation of telomerase during the lengthening of the telomeres through the alternative lengthening of telomeres (ALT) pathway, and disturbed function of the polycomb repressive complex 2 as key mechanistic components underlying atrx-linked tumorigenesis. These results demonstrate how a p53/nf1 compromised genetic background combined with ATRX haploinsufficiency leads to a broad spectrum of sarcomas and carcinomas associated with loss of this chromatin modulator

Summary

Introduction

The alpha thalassemia/mental retardation syndrome X-linked (ATRX) protein is involved in the epigenetic regulation of gene expression. It is classified as a SWI/SNF-family chromatin remodeling factor due to its ATP-dependent helicase domain. Germline loss of ATRX function causes mental retardation and alpha thalassemia that is associated with reduced alpha globin expression levels, lower blood-oxygen levels and hypochromia, anisocytosis, and poikilocytosis of red blood cells [1,2,3,4,5]. Loss of ATRX leads to reduced levels of histone 3.3 (H3.3) incorporation, telomere destabilization and increased homologous recombination facilitating the development of ALT. The ATRX/DAXXmediated deposition of H3.3 maintains the condensed heterochromatic state [7,8]

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