Research Spotlight: Unprocessed Genomic Uracil as a Targetable Vulnerability of Cancer Cells

Sneha Saxena, PhD, a postdoctoral research fellow in the Mass General Cancer Center, is lead author of a recently published article in Molecular Cell, Unprocessed Genomic Uracil as a Source of DNA Replication Stress in Cancer Cells. 

What Question Were You Investigating? 

As cancer cells divide and grow in number, they often have high levels of base alterations in their genome. This constitutes an important source of potential instability, which could provide researchers with an opportunity for targeted genome therapy.  

Targeting this area requires an in-depth understanding of the underlying mechanisms for genomic instability by different types of base lesions that occur. 

When cancer cells are replicating and multiplying, ATR kinase is a master regulator of the cellular response to replication stress (RS), and it is critical for cancer cells to cope with this stress and their potential genomic instability.  

Recently, researchers have successfully used ATR inhibitors (ATRi) to eliminate cancer cells under specific oncogene-induced RS.  

Therefore, we wanted to know, can cancer cells that are harboring high levels of base alterations be selectively targeted by ATR inhibitors?  

What Methods or Approach Did You Use? 

We used patient-derived lung cancer cell lines and mouse xenograft models, and we targeted the enzymes that recognize the base alterations and instability, and typically initiates the repair of it.  

We then inhibited this process, allowing for us to see if our hypothesis was correct.  

What Did You Find? 

We made an unexpected finding that uracil, a common type of base alteration in the genome, actually induces DNA replication stress (RS).  

In the absence of uracil DNA glycosylase (UNG2), genomic uracil will accumulate to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA.  

In other words, we found a way to force the creation of gaps in the DNA of cancer cells, threatening their genomic stability. 

By inhibiting ATR, we can prevent these gaps from being repaired, generating more DNA damage in cancer cells, eventually killing them.  

Interestingly, some cancers try to prevent uracil buildup through UNG2. These cancers with high UNG2 are especially vulnerable to a treatment that combines ATR inhibition with drugs that increase uracil levels. This discovery presents a promising new avenue for targeted cancer therapy.  

These results reveal unprocessed genomic uracil as an unexpected source of cell replication stress and a targetable vulnerability of cancer cells. 

What are the Implications? 

Our findings reveal that certain cancers are addicted to suppressors of genomic uracil, creating an opportunity to exploit uracil-induced replication stress (RS) by unsuppressing it.  

Both upregulation of base-excision repair and metabolic changes reducing the dUTP/dTTP ratio could be used by cancer cells to limit genomic uracil, making them reliable biomarkers for tumors harboring high uracil stress, as well as attractive targets for cancer therapy.  

What are the Next Steps? 

Our analysis serves as a hypothesis-generating investigation, suggesting alterations in the expression of DNA repair and metabolic enzymes as a mechanism used by cancer cells to cope with high uracil stress. Additional biomarkers and clinical assays need to be developed in future studies to identify these tumors. 

Paper cited: 

Saxena et al., Unprocessed genomic uracil as a source of DNA replication stress in cancer cells, Molecular Cell (2024), https://doi.org/10.1016/j.molcel.2024.04.004