Spatially Resolved Gene Expression Analysis of Primary and Metastatic Fibrolamellar Hepatocellular Carcinoma (FLC)

Fibrolamellar carcinoma (FLC) is a rare and aggressive malignancy of the liver that predominantly affects adolescents and young adults. These tumors are distinct from conventional hepatocellular carcinomas and are characterized histologically by thick fibrous collagen bands. The transcriptome of FLC is characterized by a recurrent oncogenic fusion between DNAJB1 and PRKACA. Liver resection is a potentially curative treatment option for early-stage FLC, but there are no standard systemic therapies available for advanced FLC. Most patients present with unresectable disease or relapse after surgery; for these individuals, outcomes are dismal with a median survival of only 12 months. This highlights the urgent need to understand the natural evolution of FLC, which in turn will support the development of effective targeted therapies. To investigate the evolution of FLC, we leveraged FLC tissue samples from n=5 patients with paired primary and distant metastatic surgical biopsies. Among these patients, 4/5 received systemic therapy including immunotherapy in the interval between primary resection and resection of the distant metastatic lesions. A histological view of the cases revealed notable morphological differences between the primary and metastatic tumors. Primary tumors showed the characteristic oncocytic tumor cells separated by thick cords of collagen fibrosis. However, the metastatic lesions exhibited reduced fibrosis or lacked it entirely, suggesting malignant progression of the tumor and loss of a key histological hallmark of FLC over time. To date, most transcriptomic analysis of FLC has been performed on bulk tissue which neglects the heterogeneity of the tumor. To capture the complexity of the lesion, we performed spatial transcriptomic analysis of our paired samples (n = 10, primary and metastatic lesions) using the VisiumHD platform by 10x Genomics. Furthermore, we succeeded in labeling the neoplastic cells using a custom-designed probe against the DNAJB1-PRKACA chimeric transcript which we included in the standard probe library. Spatially resolved gene expression analysis and neighborhood analysis using the Seurat workflow revealed marked differences in transcriptional networks coinciding with the progression of the tumor. Here we present a spatially and temporally resolved transcriptome atlas of FLC. This rich and valuable resource will be critical for understanding FLC biology and ultimately developing novel therapeutics. Waqar Arif, Luciane Kagohara, Robert A. Anders, Kiyoko Oshima, Mark Yarchoan. Spatially resolved gene expression analysis of primary and metastatic fibrolamellar hepatocellular carcinoma (FLC) [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 5071.