Jacob Corn

The DNA damage response (DDR) is a sophisticated network of cellular pathways whose perturbation leads to genome instability and is a key hallmark of oncogenesis. Here, we present data from 32 genome-scale loss-of-function CRISPR interference chemical–genetic screens with inhibitors targeting core constituents of the DDR machinery (PARP, ATR, ATM, DNAPK and WEE1), as both single agents and in combination with poly(ADP-ribose) polymerase inhibitors. These experiments identify >1,000 genes whose perturbation modifies the DDR and provides a rich resource to the DDR community. In addition, this compendium of functional genomics data reveals key principles governing the DDR and highlights a strong chemical–genetic interaction between loss of activity of the peroxiredoxin PRDX1 and all tested DDR inhibitors through a mechanism involving iron availability mediated by an MRGBP–PAX7–IREB2 axis. Our data position PRDX1 as a key suppressor of DNA damage accumulation and potential druggable target in combination with DDR inhibitors. (Figure presented.)

DNA double-stranded breaks (DSBs) are toxic events that can be reversed without genetic information loss by homology-directed repair (HDR), wherein information is copied from an intact template molecule. Finding a correct template within millions to billions of other DNA bases is termed homology search and is mediated by the protein RAD51. To monitor transient search in cellulo, we develop RAD51 proximity identification sequencing (RaPID-seq), a highly sensitive method marking all DNA searched regardless of whether it is chosen as the final template. We find that HDR in human cells is hierarchical with DSB proximity constraining the search space from which sequence homology determines the chosen template. Exogenously introduced DNA templates, such as those used during genome editing, are unconstrained and efficiently searched by the DSB, thereby competing with endogenous template search. Our data reveal the invisible process of homology search and shed new light on fundamental mechanisms underlying genome editing.

Background: RNA-guided nucleases enable DNA editing and offer promise for treating genetic diseases, particularly when used for precise sequence replacement. However, many of the most effective enzymes, such as Streptococcus pyogenes Cas9, are too large for delivery using vectors like adeno-associated virus. This has prompted interest in smaller alternatives from the Cas12f and TnpB families. Yet, these nucleases often show low activity in mammalian cells, limiting their utility. Results: We use directed evolution in human cells to select variants with greatly improved activity. The resulting variants, Cas12f1Super and TnpBSuper, exhibit up to 11-fold increase in editing efficiency without increased off-target effects. When tested as a base editor, Cas12f1Super shows up to tenfold improvement relative to the previously engineered CasMINI, suggesting utility beyond nuclease-related activities. Conclusions: These compact and efficient genome editors expand the current toolkit and hold promise for both research and therapeutic use in mammalian systems.