Mutational signatures efficiently identify different mutational processes underlying cancers with similar somatic mutation spectra

• Mutational signatures of bladder urothelial cancer (BLCA) and squamous cell carcinoma (CESC) were studied.
• BLCA and CESC mutational signatures identify different mutational processes between the two cancers.
• Compared to mutational spectra, mutational signatures are more powerful in identifying specific cancer mutation processes.

Compared to analyzing mutations with conventional spectra, deciphering mutational signatures provides much greater resolution of biological processes that generate somatic mutations during cancer development. Previous studies of bladder urothelial cancer (BLCA) and cervical squamous cell carcinoma (CESC) mutational signatures failed to uncover different mutational processes underlying the two cancers, which diminishes the capability of mutational signature to differentiate between the two cancers. In this study, we deciphered and compared the mutational signatures of BLCA and CESC. Four BLCA mutational signatures were deciphered from 37,098 somatic mutations of 130 exomes. Five CESC mutational signatures were deciphered from 44,206 somatic mutations of 194 exomes. Three BLCA mutational signatures were very similar to the three CESC signatures. These mutational signatures exhibited common endogenous mutational processes during BLCA and CESC development. The respective BLCA and CESC mutational signature 4 revealed the role of viral infection in both cancers. Noticeably, CESC mutational signature 4 is a novel one that has not been described in other studies. In summary, we have demonstrated the similarities and differences between BLCA and CESC by deciphering mutational signatures. This study will shed light on the use of mutational signatures to clarify the mechanisms of endogenous and exogenous carcinogens that cause somatic mutations in human cancers.