Not individual genes but the “mutational signatures” of many genes hold the key to better cancer therapies
Cancer therapy increasingly relies on a personalised approach, where genetic changes in an individual tumour can be used to determine the best therapeutic strategy. In many cases thus far, these genetic changes included a so-called “driver mutation” that would predict response to a drug. For instance, mutations in the BRAF gene in melanoma predict response to BRAF inhibitor drugs, and amplifications in the HER2 (ERBB2) gene in breast cancer predict response to anti-HER2 therapeutic antibodies.
However, these examples of successful drug markers are still quite rare. For many mutated driver genes, specific drugs to target them are not available. Moreover, tumours of different patients show high variability in response to drugs and such variability is often not linked to driver gene mutations.
Our study has found that so-called “mutational signatures” can accurately predict the activity of various drugs applied to cancer cells originating from many types of tumours. These mutational signatures do not originate from driver genes; instead, they reflect a collection of mutations found across the entire genome of a tumour. Such mutational signatures can reflect, for example, that the tumour has difficulties in copying or repairing DNA, which may make it more amenable to therapy.
We have performed statistical analysis using machine-learning methods, considering jointly cancer cell line genomes, their response to various drug treatments, and their response to CRISPR gene editing experiments. Surprisingly, our statistical analyses revealed that the 'classical' genetic markers such as driver gene mutations or copy-number changes are often less powerful than the mutational signature genetic markers in predicting drug response.
Interestingly, the cancer cells that bear genomic “scars” (mutational signatures) of previous exposure to mutagenic chemicals tended to be resistant to diverse chemotherapeutic drugs. One possible explanation for this is that cancer cells can switch off some DNA repair systems to better adapt to a treatment by a mutagenic drug, which could permanently covert them into hardy, hypermutating cells resistant to a range of future treatments.