Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas

M Udugama,P P Das,L H Wong,H P J Voon,L Hii,J R Mann,F.-L Chan,B Vinod,A Garvie,M Cervini,P Collas

doi:10.1038/s41467-021-22543-z

Abstract

Alternative Lengthening of Telomeres (ALT) is a telomere maintenance pathway utilised in 15% of cancers. ALT cancers are strongly associated with inactivating mutations in ATRX; yet loss of ATRX alone is insufficient to trigger ALT, suggesting that additional cooperating factors are involved. We identify H3.3G34R and IDH1/2 mutations as two such factors in ATRX-mutated glioblastomas. Both mutations are capable of inactivating histone demethylases, and we identify KDM4B as the key demethylase inactivated in ALT. Mouse embryonic stem cells inactivated for ATRX, TP53, TERT and KDM4B (KDM4B knockout or H3.3G34R) show characteristic features of ALT. Conversely, KDM4B over-expression in ALT cancer cells abrogates ALT-associated features. In this work, we demonstrate that inactivation of KDM4B, through H3.3G34R or IDH1/2 mutations, acts in tandem with ATRX mutations to promote ALT in glioblastomas.

Highlights

Alternative Lengthening of Telomeres (ALT) is a telomere maintenance pathway utilised in 15% of cancers
ALT is common in glioblastoma multiforme (GBM) in younger patient cohorts where it is highly correlated with ATRX mutations[6,7,9,10,11,24,25,26]
We found that the majority of ATRX-mutated GBMs have additional mutations in the checkpoint regulator TP53, and either H3F3A (H3.3) or IDH1 (Isocitrate Dehydrogenase 1) (Fig. 1a, Supplementary Table S1)

Summary

Introduction

Alternative Lengthening of Telomeres (ALT) is a telomere maintenance pathway utilised in 15% of cancers. Telomeres are comprised of a tandemly repeated hexamer (TTAGGG) several kilobases long, which is recognised and bound by Shelterin[1,2], a multimeric protein complex that prevents the natural ends of chromosomes from being recognised as DNA breaks. One hallmark of cancers is the capacity for unlimited cell division This oncogenic process must be supported by a telomere maintenance programme, either through reactivation of telomerase or activation of the Alternative Lengthening of Telomeres (ALT) pathway[4,5]. Neither knockdown nor knockout of ATRX is sufficient to activate ALT9,23, suggesting that additional cooperating factors are necessary To identify these factors, we searched public cancer genome databases for mutations that segregated with ATRX inactivation in glioblastoma multiforme (GBM), where ALT is prevalent[6,10]. Our results demonstrate that H3.3G34R and IDH1/2 are parallel mutations that promote ALT by inhibiting KDM4B

Methods

Results

Conclusion