Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway

Courtney A Lovejoy,Yaara Zwang,Neal F Lue,William C Hahn,Titia De Lange,Steven Reisenweber,Joseph Rosenbluh,Supawat Thongthip,Yuchen Jiao,Roger R Reddel,Alan K Meeker,Elena Ivanova,Maria Jasin,Wendi Li,Barbara A Weir,Joanne Bruno,Charlie Hatton,Bert Vogelstein,Megan Hanna,Nickolas Papadopoulos,Saurav De,Kenneth W Kinzler ,Laura E Macconaill ,John H.j Petrini ,Patricia Sung

doi:10.1371/journal.pgen.1002772

Abstract

The Alternative Lengthening of Telomeres (ALT) pathway is a telomerase-independent pathway for telomere maintenance that is active in a significant subset of human cancers and in vitro immortalized cell lines. ALT is thought to involve templated extension of telomeres through homologous recombination, but the genetic or epigenetic changes that unleash ALT are not known. Recently, mutations in the ATRX/DAXX chromatin remodeling complex and histone H3.3 were found to correlate with features of ALT in pancreatic neuroendocrine cancers, pediatric glioblastomas, and other tumors of the central nervous system, suggesting that these mutations might contribute to the activation of the ALT pathway in these cancers. We have taken a comprehensive approach to deciphering ALT by applying genomic, molecular biological, and cell biological approaches to a panel of 22 ALT cell lines, including cell lines derived in vitro. Here we show that loss of ATRX protein and mutations in the ATRX gene are hallmarks of ALT–immortalized cell lines. In addition, ALT is associated with extensive genome rearrangements, marked micronucleation, defects in the G2/M checkpoint, and altered double-strand break (DSB) repair. These attributes will facilitate the diagnosis and treatment of ALT positive human cancers.

Highlights

In the absence of telomerase activity, telomeres shorten with cell division, leading to senescence
We have examined a large panel of Alternative Lengthening of Telomeres (ALT) cell lines for their genetic and cell biological features and found that loss of ATRX is a common event in the genesis of ALT lines
We document that ALT cell lines frequently undergo chromosomal changes and are impaired in their ability to detect and repair damage in their DNA

Summary

Introduction

In the absence of telomerase activity, telomeres shorten with cell division, leading to senescence. Telomerase reactivation is the most common mechanism of telomeric repeat addition in cancers, a significant subset of human tumors employs a telomeraseindependent telomere maintenance pathway, referred to as ALT [1]. The emerging view is that ALT maintains telomeres through homology-directed recombination (HDR) [2]. Supporting this view, ALT cells show an elevated frequency of sequence exchanges between telomeres [2,3,4], contain extrachromosomal linear and circular telomeric DNA [5,6,7,8], and often exhibit heterogeneouslysized telomeres [1], features consistent with hyperactive HDR. Several proteins involved in recombination are known to be required for ALT, including the Mre complex, Mus, and the SMC5/6 sumoylation pathway [6,12,13,14,15]

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Discussion

Conclusion