Methodology

The Epigenomics and Mechanisms Branch (EGM) and collaborating partners are exploiting the characteristic aristolochic acid mutational signature (COSMIC SBS22) to devise a sensitive method for detection of exposure to aristolochic acid in the form of mutational signature(s), based on low-coverage whole-exome sequencing (LC-WES), optimized for analysis of tumour-specific DNA of limited quantity and integrity extracted from archived tissues. EGM is studying urothelial tumour samples originating from residents of the endemic nephropathy regions in southern Europe; to date, endemic nephropathy is the only recognized environmental form of aristolochic acid nephropathy (AAN).

LC-WES elucidates the impact of the aristolochic acid mutation spectra on key cancer driver genes, including oncogenes, tumour suppressor genes, and epigenetic regulators, and reveals the genetic relationship between the first, second, and third cancers developing in the affected patients. A study based on LC-WES has established that not only upper urinary tract urothelial carcinomas (UTUCs) but also clear cell and chromophobe renal cell carcinomas of patients with AAN harbour the mutational signature of aristolochic acid. The LC-WES technique is now being collaboratively implemented to identify the extent of exposure to aristolochic acid in Malaysia, where the use of herbal medicines that contain aristolochic acid is widespread.

Using integrated multi‐omics analysis, EGM recently reported molecular programmes of the UTUCs in patients in southern Europe with past exposure to carcinogenic aristolochic acid. Profiling analyses revealed complex tumour-specific molecular interaction networks among microRNAs (miRNAs), messenger RNAs (mRNAs), and key cellular proteins. EGM also established that aristolochic acid‐specific deleterious mutations in tumours are present at both the gene and mRNA transcript levels. Furthermore, EGM’s findings suggest that the presence and recurrence of tumours in the urinary tract can be monitored by a urine-specific miRNA signature (Figure 2).

Figure 2 Aristolochic acid-associated cancer programmes in upper tract urothelial carcinomas (UTUCs) from the endemic nephropathy regions. (A) Predicted protein interaction networks derived from transcriptomic profiling of UTUCs. (B) The highlighted 5-miRNA UTUC-specific signature extracted from the urine supernatants of patients with urothelial cancers (red dots = typical tumour location) can serve as a biomarker of tumour presence in the urinary tract. Pre-op/Post-op = pre- and post-operation. Adapted from Karanović et al. (2022), © 2021 IARC. Int J Cancer, published by John Wiley & Sons Ltd on behalf of UICC.