KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells

Reviewer #1 (Public review):

Summary:

In this manuscript, Lau et al reported that KDM5 inhibition in luminal breast cancer cells results in R-loop-mediated DNA damage, reduced cell fitness and an increase in ISG and AP signatures as well as cell surface Major Histocompatibility Complex (MHC) class I, mediated by RNA:DNA hybrid activation of the CGAS/STING pathway.

Strengths:

More importantly, they have shown that KDM5 inhibition does not result in DNA damage or activation of the CGAS/STING pathway in normal breast epithelial cells. This suggests that KDM5 inhibitors may enable a wide therapeutic window in this setting, as compared to STING agonists or Type I Interferons. Their findings provide new insights into the interplay between epigenetic regulation of genomic repeats, R-loop formation, innate immunity, and cell fitness in the context of cancer evolution and therapeutic vulnerability.

Weaknesses:

More thorough analyses would be appreciated.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors investigated how the type-I interferon response (ISG) and antigen presentation (AP) pathways are repressed in luminal breast cancer cells and how this repression can be overcome. They found that a STING agonist can reactivate these pathways in breast cancer cells, but it also does so in normal cells, suggesting that this is not a good way to create a therapeutic window. Depletion of ADAR and inhibition of KDM5 also activate ISG and AP genes. The activation of ISG and AP genes is dependent on cGAS/STING and the JAK kinase. Interestingly, although both ADAR depletion and KDM5 inhibition activate ISG and AP genes, their effects on cell fitness are different. Furthermore, KDM5 inhibitor selectively activates ISG and AP genes in tumor cells but not normal cells, arguing that it may create a larger therapeutic window than the STING agonist. These results also suggest that KDM5 inhibition may activate ISG and AP genes in a way different from ADAR loss, and this process may affect tumor cell fitness independently of the activation of ISG and AP genes.

The authors further showed that KDM5 inhibition increases R-loops and DNA damage in tumor cells, and XPF, a nuclease that cuts R-loops, is required for the activation of ISG and AP genes. Using H3K4me3 CUT&RUN, they found that KMD5 inhibition results in increased H3K4me3 not only at genes, but also at repetitive elements including SINE, LINE, LTR, telomeres, and centromeres. Using S9.6 CUT&TAG, they confirmed that R-loops are increased at SINE, LINE, and LTR repeated with increased H3K4me3. Together, the results of this study suggest that KMD5 inhibition leads to H3K4me3 and R-loop accumulation in repetitive elements, which induces DNA damage and cGAS/STING activation and subsequently activates AP genes. This provides an exciting approach to stimulate the anti-tumor immunity against breast tumors.

KDM5 inhibition activates interferon and antigen presentation genes through R-loops.

Strengths:

Overall, this study was carefully designed and executed. This is a new approach to make breast tumors "hot" for anti-tumor immunity.

Weaknesses:

Future in vivo studies are needed to show the effects of KDM5 inhibitors on the immunotherapy responses of breast tumors.