Mutational signature analysis reveals widespread contribution of pyrrolizidine alkaloid exposure to human liver cancer

BACKGROUND AND AIMS: Mutational signature analyses are effective tool for identifying cancer etiology. Humans are frequently exposed to pyrrolizidine alkaloids (PAs), the most common carcinogenic phytotoxins widely distributed in herbal remedies and foods. However, due to the lack of human epidemiological data, PAs are classified as group II hepatocarcinogens by WHO. This study identified PA mutational signature as the biomarker to investigate the association of PA exposure with human liver cancer. APPROACH AND RESULTS: Pyrrole-protein adducts (PPA), the PA exposure biomarker, were measured and found in 32% of surgically resected specimens from 34 liver cancer patients in Hong Kong. Next, we delineated the mode of mutagenic and tumorigenic actions of retrorsine, a representative PA, in mice and human hepatocytes (HepaRG). Retrorsine induced DNA adduction, DNA damage, and activation of tumorigenic hepatic progenitor cells that initiated hepatocarcinogenesis. PA mutational signature, as the unique molecular fingerprint of PA-induced mutation, was derived from exome mutations in retrorsine-exposed mice and HepaRG cells. Notably, PA mutational signature was validated in genomes of PPA-positive liver cancer patients but not PPA-negative patients, confirming the specificity of this biomarker in revealing PA-associated liver cancers. Further, we examined the established PA mutational signature in 1,513 liver cancer genomes and found that PA-associated liver cancers were potentially prevalent in Asia: Mainland China (48%), Hong Kong (44%), Japan (22%), South Korea (6%), Southeast Asia (25%); but minor in Western countries: North America (3%), and Europe (5%). CONCLUSIONS: This study provides the first clinical indication of PA-associated liver cancer. We discover an unexpectedly extensive implication of PA exposure in liver cancer patients, laying the scientific basis for precautionary approaches and prevention of PA-associated human liver cancers.