Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool

Abstract

Aristolochic acid (AA), a natural product of Aristolochia plants found in herbal remedies and health supplements, is a group 1 carcinogen that can cause nephrotoxicity and upper urinary tract urothelial cell carcinoma (UTUC). Whole-genome and exome analysis of nine AA-associated UTUCs revealed a strikingly high somatic mutation rate (150 mutations/Mb), exceeding smoking-associated lung cancer (8 mutations/Mb) and ultraviolet radiation-associated melanoma (111 mutations/Mb). The AA-UTUC mutational signature was characterized by A:T to T:A transversions at the sequence motif A[C|T]AGG, located primarily on nontranscribed strands. AA-induced mutations were also significantly enriched at splice sites, suggesting a role for splice-site mutations in UTUC pathogenesis. RNA sequencing of AA-UTUC confirmed a general up-regulation of nonsense-mediated decay machinery components and aberrant splicing events associated with splice-site mutations. We observed a high frequency of somatic mutations in chromatin modifiers, particularly KDM6A, in AA-UTUC, demonstrated the sufficiency of AA to induce renal dysplasia in mice, and reproduced the AA mutational signature in experimentally treated human renal tubular cells. Finally, exploring other malignancies that were not known to be associated with AA, we screened 93 hepatocellular carcinoma genomes/exomes and identified AA-like mutational signatures in 11. Our study highlights an unusual genome-wide AA mutational signature and the potential use of mutation signatures as "molecular fingerprints" for interrogating high-throughput cancer genome data to infer previous carcinogen exposures.

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

“…The predominance of A4T transversion on the non-transcribed strand of DNA along with a preference for deoxyadenosine in the C/T[A:T]A/G motif supports exposure to AA as the underlying factor. Similar patterns have recently been observed in urothelial carcinoma of the upper urinary tract in patients 12,27 as well as in cultured primary cells 27,28 exposed to AA, with C/T[A:T]G being the preferential sequence context. Our WGS data show that a less marked increase in A4T transversions also occurs in other sequence contexts.…”

Mutational landscape of intrahepatic cholangiocarcinoma

“…The ICC-unique mutation spectrum (CTG4CAG and CAG4CTG) is tightly associated with liver inflammation, fibrosis and cirrhosis, suggesting that mutagens that have caused such mutations have also caused inflammation, fibrosis and cirrhosis. It is also likely that these ICC patients who harbour the ICC-unique mutation spectrum may have been exposed to aristolochic acid (AA), a nitrophenanthrene carboxylic acid found in all members of the genus Aristolochia plants that have been used in medicine for over 2,000 years 65,66 . Recent studies showed that humans exposed to AA causes A:T4T:A transversions 65,66 .…”

“…It is also likely that these ICC patients who harbour the ICC-unique mutation spectrum may have been exposed to aristolochic acid (AA), a nitrophenanthrene carboxylic acid found in all members of the genus Aristolochia plants that have been used in medicine for over 2,000 years 65,66 . Recent studies showed that humans exposed to AA causes A:T4T:A transversions 65,66 . AA has been demonstrated to be a causative carcinogen of urothelial carcinoma of the upper urinary tract (UTUC) 30,31 .…”

SomaticTP53Mutations in the Era of Genome Sequencing

“…Exposure of human bronchial cells to the diol epoxide of the PAH benzo[a]pyrene causes DNA damage at the same G:C pairs that are frequently mutated into T:A in lung cancers from smokers (Denissenko et al 1996;Tretyakova et al 2002). Recently, a mutational fingerprint of aristolochic acid has been reported in urothelial carcinomas of subjects with a history of exposure to herbal remedies and food products containing seeds of Aristolochia clematitis (Hollstein et al 2013;Poon et al 2013). Last, all cancer types harbor at least 20% of G:C.A:T mutations at hypermutable CpG dinucleotides, attributed to the normal cellular event of deamination of 5-methylcytosine to thymine.…”