Ribosomal DNA Copy Loss and Repeat Instability in ATRX-mutated Cancers.

Significance We demonstrate that ATRX maintains ribosomal DNA (rDNA) heterochromatin formation and stability. ATRX-depleted cells suffer extensive rDNA copy loss, resulting in a reduced ribosomal RNA transcription output and an increased sensitivity to RNA polymerase I (Pol I) inhibition. Supporting these data, we have also detected reduced rDNA copy in ATRX mutated ALT-positive human primary tumor samples and increased sensitivity of human ALT cancer cell lines to RNA Pol I transcription inhibitor. Our study highlights the therapeutic potential of Pol I transcription inhibitors for the treatment of ATRX-mutated cancers. ATRX (alpha thalassemia/mental retardation X-linked) complexes with DAXX to deposit histone variant H3.3 into repetitive heterochromatin. Recent genome sequencing studies in cancers have revealed mutations in ATRX and their association with ALT (alternative lengthening of telomeres) activation. Here we report depletion of ATRX in mouse ES cells leads to selective loss in ribosomal RNA gene (rDNA) copy number. Supporting this, ATRX-mutated human ALT-positive tumors also show a substantially lower rDNA copy than ALT-negative tumors. Further investigation shows that the rDNA copy loss and repeat instability are caused by a disruption in H3.3 deposition and thus a failure in heterochromatin formation at rDNA repeats in the absence of ATRX. We also find that ATRX-depleted cells are reduced in ribosomal RNA transcription output and show increased sensitivity to RNA polymerase I (Pol I) transcription inhibitor CX5461. In addition, human ALT-positive cancer cell lines are also more sensitive to CX5461 treatment. Our study provides insights into the contribution of ATRX loss of function to tumorigenesis through the loss of rDNA stability and suggests the therapeutic potential of targeting Pol I transcription in ALT cancers.