Abstract 3887: Clonal expansion in the bile duct associated with primary sclerosing cholangitis

Abstract [Introduction] Chronic inflammation has been implicated in cancer development in many tissues and has recently been shown to promote clonal expansion in non-cancer tissues. Primary sclerosing cholangitis (PSC) is a chronic progressive disease of unknown etiology that affects the bile ducts and has been associated with an increased risk of cholangiocarcinoma. However, clonal dynamics in the normal bile duct and PSC epithelium remain poorly understood due to the limited accessibility to normal/inflamed bile ducts. In this study, we investigated somatic clonal events in the chronically inflamed bile duct epithelium and identified clonal expansions with and without cancer-associated driver mutations. [Methods] Single cell-derived organoids were established from the bile and subjected to whole genome sequencing to estimate the mutation accumulation rate in the normal bile duct epithelium. Next to evaluate clonal expansion in the bile duct in PSC, we performed whole exome sequencing in bile duct-derived organoids and samples from the bile duct epithelium obtained from PSC patients using laser-capture microdissection (LCM) and detected somatic mutations and copy number alterations therein. [Results] In total, 14 single cell-derived organoids were established from 2 PSC patients and 3 control donors. Based on the whole genome sequencing of these organoids, the number of mutations found in non-PSC bile duct epithelium increases with age at an estimated mutation rate of 34.3 mutations per genome per year. The mutation rate did not significantly differ from the rate in the PSC epithelium, suggesting that the inflammatory process in PSC does not substantially affect the mutation rate in the biliary epithelium. We next investigated the effect of chronic inflammation on clonal expansion in the biliary epithelium, in which we analyzed 120 bulk organoid samples from 3 PSC patients and 304 LCM samples from histologically normal bile duct and biliary intraepithelial neoplasia (BilIN) from 7 PSC patients. Excluding a case with hypermutation, we detected the presence of clones in 20 (16.7%) and 105 (47.1%) of organoid and LCM samples, where a median of 13 [1-30] and 19 [5-41] somatic mutations per exome were detected in organoid and LCM samples, respectively. Most mutations were detected in a single sample, but some were shared between multiple samples. In total, 51 clones were detected across multiple samples. These clones were observed regardless of the presence or absence of BilIN lesions and found in the samples separated up to 40mm. Mutations in known cancer drivers, such as ARID1A and KRAS, and chromosomal instability were detected in 11 clones in 64 samples, suggesting their roles in the clonal expansion in PSC bile ducts. [Conclusions] Clonal expansion in the bile duct from PSC patients are common and accompanied by known cancer driver mutations, suggesting their role in biliary carcinogenesis associated with PSC. Citation Format: Hirona Maeda, Nobuyuki Kakiuchi, Takashi Ito, Eri Ogawa, Masahiro Shiokawa, Norimitsu Uza, Koichi Watanabe, Yasuhito Nannya, Yuzo Kodama, Tatsuki Kataoka, Hatano Etsuro, Seishi Ogawa. Clonal expansion in the bile duct associated with primary sclerosing cholangitis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3887.