Cancer is a genetic disease caused by mutations in DNA. Most mutations are substitutions of single nucleotides, the basic building blocks of DNA. Mutations occur over time due to natural processes like faulty DNA repair or from external sources like ultraviolet light. Researchers have discovered that these so-called mutational processes tend to mutate DNA in particular ways, preferring some nucleotides over others [1]. These preferences are known as mutational signatures and allow us to study which exposures or defects have altered the DNA in specific cancer samples. 

 

If we think of the genome as an instruction manual for assembling the proteins essential for keeping our cells running like a well-oiled machine, genes would correspond to sentences that outline the sequence of amino acids making up each protein. Similarly to actual manuals, genes end with punctuation marks, known as stop codons, that tell the cell when to stop making a protein from a given sequence of genetic code.  

 

DNA mutations can affect cells in many ways. Some mutations substitute individual letters in protein instructions, causing changes in protein structures. The most damaging type of protein mutations are 'stop-gain' or 'nonsense' mutations. These insert a stop signal in the middle of a gene, causing the cell to stop making the protein too soon. This results in an incomplete protein that the cell usually discards. 

 

In our study [2], we asked whether stop-gain mutations in cancer genomes were preferentially generated by some mutational processes. Using statistics and data science tools, we analysed genomic data from over 12,000 tumour samples from 18 major cancer types. We found that some processes cause stop-gain mutations more often than expected by chance. Tobacco smoking was the most significant cause, especially in lung and liver cancers. Second was the activity of APOBEC proteins in breast cancer, which are a major source of cancer mutations and also act in our natural antiviral defences. Third was reactive oxygen species (ROS) in colorectal cancer. ROS are harmful by-products of cellular metabolism such as free radicals and have been linked to poor diet and excessive alcohol consumption. By examining the genetic code of amino acids along with the mutational signatures, we can explain how these three processes cause stop-gain mutations by targeting certain nucleotide patterns in DNA. 

 

Our findings are supported by molecular and lifestyle associations. We analysed the smoking history of lung cancer patients and found that current smokers and recently-reformed smokers had the highest number of stop-gain mutations while patients who quit smoking over 15 years ago and patients who were always non-smokers had significantly fewer stop-gain mutations. Therefore, smoking habits can directly impact gene function in cells. Similarly, we linked the levels APOBEC enzymes to stop-gain mutations. Breast cancer patients with higher levels of APOBEC enzymes had significantly more stop-gain mutations than those with lower levels of APOBEC enzymes. Lastly, using data from earlier wet-lab experiments [3], we found that experimentally reducing APOBEC activity in cancer cells led to fewer stop-gain mutations, indeed showing that the APOBEC enzymes indeed contribute to the creation of these harmful mutations. APOBEC enzymes are studied intensively due to their many roles in cancer and potential for therapy development. 

 

Some genes, known as tumour suppressor genes, protect us from cancer. When these genes are shut off, cells are allowed to proliferate in an unrestricted manner. We found that stop-gain mutations introduced by tobacco smoking and APOBEC activity frequently occurred in key tumour suppressor genes such as TP53, FAT1 and STK11 in multiple types of cancer. Therefore, these mutational processes can disable our protective mechanisms and contribute to the development and complexity of cancer. 

 

These mutational processes appear to create damaging stop-gain mutations across the genome. Therefore, each individual tumor may have a distinct set of genes disabled by these harmful mutations, increasing the complexity of cancer. Since anti-cancer drugs are often tailored to specific genes, these stop-gain mutations can make tumours more difficult to treat, because drugs that are effective for one person might not be effective for another. 

 

Taken together, our study shows how specific mutational processes can directly disable genes through harmful mutations. Since tobacco smoking and diet are lifestyle choices, these results allow us to better understand preventable causes of cancer with molecular insights. Healthier lifestyle choices can therefore reduce the risks of harmful mutations in cells. 

 

1.         Alexandrov, L.B., et al., Signatures of mutational processes in human cancer. Nature, 2013. 500(7463): p. 415-21. 

2.         Adler, N., et al., Mutational processes of tobacco smoking and APOBEC activity generate protein-truncating mutations in cancer genomes. Sci Adv, 2023. 9(44): p. eadh3083. 

3.         Petljak, M., et al., Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature, 2022. 607(7920): p. 799-807.