Walking the tightrope between DNA damage repair and genomic integrity

Both normal and neoplastic cells are poised to handle genetic insults by employing a variety of DNA lesion-specific response pathways to mark and then repair the damaged DNA. This is especially true for DNA double-strand breaks, which are the most deleterious form of damaged DNA as they have the potential to lead to gross chromosomal rearrangements and/or cell death if not properly repaired. Radiotherapy, used clinically for brain and other tumors, generates double-strand breaks and hence is leveraged to increase tumor cell kill. Although many of the key proteins involved in these processes have been identified, the DNA damage field has more recently begun to appreciate that chromosome breaks can be mobilized and clustered to facilitate repair.¹ However, the full mechanistic underpinning of this clustering process during repair and any potential negative impacts that aggregating broken DNA ends may have on overall genomic integrity have remained unclear.

In an effort to fill this gap, Arnould et al² utilized a controlled system to induce double-strand breaks at known locations in an engineered human cell line along with state-of-the-art methodologies to evaluate 3D genome organization and protein localization. These efforts elucidated a new chromatin subcompartment induced by double-strand breaks, coined the D compartment by the authors. Formation of the D compartment was dependent on a key, apical kinase in the response to double-strand breaks, ATM, and was cell cycle-dependent with a prevalence in the G1 phase of the cell cycle. This compartment contained topology-associated domains that contained 2 other major components of the DNA damage response, 53BP1 and ƳH2AX. A surprising finding was that resident to the D compartment was also undamaged DNA, more specifically, genes crucial to the DNA damage response. These genes were not only localized to the D compartment, but optimal transcription was dependent on this localization. Hence, the authors have provided a refined view of the cellular response to double-strand breaks whereby the breaks themselves and the activation of the components required for repair are purposefully clustered in a chromosome environment that is permissive for both repair and transcription. Thus, the D compartment may serve as a rheostat, tuning cellular response to the extent of DNA damage.

However, also identified was a cost associated with this clustering. Namely, translocations, the errant rearrangement of broken chromosomes, were elevated and were specifically increased in the genes mobilized to the D compartment. Here, the authors extend beyond the experimental double-strand break cellular system and confirm overlap of genes targeted to the D compartment with the breakpoints of interchromosomal translocations across 18 different cancer types, including lower-grade gliomas.³ Given this finding, the authors propose that the integrity of tumor suppressor genes may be inadvertently at stake upon their recruitment to the D compartment.

Although further studies are needed to confirm the author’s model, a similar association of DNA damage clustering and translocation was recently reported.⁴ In light of these findings, it will be important to understand how the mechanism of D compartmentation may contribute to tumor evolution and fit into current models that address the loss of tumor suppressors. Seminal studies in adult glioma, and other tumor types, have highlighted that loss of the tumor suppressor p53 in disease progression is driven by the need to overcome oncogene-driven DNA damage.^5–7 This begs the question, does clustering in D compartments increase with increasing tumor grade and hence the probability of disrupting key tumor suppressors like p53? Furthermore, molecular diagnostics of certain brain tumors are associated with specific translocation events and future studies will need to address if these genes are mobilized to D compartments, even if they are not classified as canonical DNA damage response or repair genes. Along these lines, it is interesting that genes recruited to the D compartment display R-loops, which are DNA:RNA hybrids implicated in numerous cellular processes including the DNA damage response. It will thus be interesting to determine whether conditions, such as EGFRvIII expression in glioblastoma that promote R-loop formation, may induce the recruitment of certain genes to the D compartment and enhance the potential for translocations in cancer.⁸

Taken together, this study brings to light a previously unknown and important aspect of the cellular efforts to maintain genome stability. While the benefits of the D compartment in facilitating DNA repair must outweigh the costs identified by this work, these findings also clearly highlight the precarious balancing act the human genome is ever dealing with. Relevant to treatments such as radiotherapy and DNA damaging agents, which are part of clinical care for multiple brain tumors, it will be critical to understand how cancer cells may employ D compartments to increase translocations and clonal evolution associated with treatment resistance. This may be especially relevant in the context of treatment-resistant glioblastoma cancer stem cells which exhibit a heightened expression of DNA damage response factors and harbor a radioresistant phenotype contributory to recurrence.⁹ Future extensions of this work such as those noted, and beyond, will improve our understanding of the cellular cost:benefit analysis, how cancer cells may alter this balance to their advantage, and the potential for exploiting this clinically.