Two Major Types of Primary Liver Cancer Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) together account for most primary liver cancers worldwide. HCC arises from hepatocytes (the main liver cell type) and accounts for approximately 80-90% of primary liver cancers, while iCCA arises from cholangiocytes (bile duct epithelial cells) and accounts for most of the remainder. Understanding the cell of origin and molecular drivers of each is essential for developing rational treatments.
Why Cell of Origin Matters The cell from which a cancer originates determines much of its initial gene expression program, its growth dependencies, and its vulnerabilities. For liver cancer, the relevant question is not only 'mature hepatocyte vs. biliary cell' but also 'mature cell vs. liver progenitor cell' - the latter being immature cells that retain the ability to give rise to both hepatocytes and cholangiocytes.
Molecular Classification as Clinical Tool Beyond histological diagnosis, molecular classification divides liver cancers into subtypes with distinct biology and prognosis. This review synthesizes evidence for molecular subtypes of HCC and iCCA, their genetic drivers, and how molecular features could eventually guide treatment selection - moving toward precision oncology for liver cancer.
The Genomic Revolution Next-generation sequencing has characterized the genomic landscape of HCC and iCCA in large patient cohorts, identifying recurrently mutated genes, copy number alterations, fusion genes, and epigenetic changes. This genomic data forms the foundation for molecular classification and highlights potential therapeutic targets.
Mature Hepatocytes Can Form HCC Lineage-tracing experiments in mouse models have definitively shown that mature adult hepatocytes, when exposed to carcinogenic insults, can de-differentiate and give rise to HCC. This occurs through a process of epigenetic reprogramming that re-activates fetal/progenitor cell gene expression programs without requiring a pre-existing stem cell population.
Liver Progenitor Cells Also Contribute Conversely, liver progenitor cells (also called oval cells in rodents or hepatic progenitor cells in humans) can also give rise to HCC and iCCA. Progenitor cell-derived HCCs tend to be more aggressive, with poorer differentiation and higher expression of stem cell markers like EpCAM, CD44, and CD133. These progenitor-derived tumors may explain the subset of HCCs with combined hepatocellular-cholangiocarcinoma features.
Implications for Molecular Classification The cell of origin influences which molecular subtype a tumor belongs to: progenitor cell-derived HCCs generally fall into the 'proliferation' subclass with poor prognosis, while mature hepatocyte-derived tumors tend toward the 'non-proliferation' subclass with better differentiation and prognosis. This biological connection between cell of origin and molecular subtype may explain why specific mutations (like TERT promoter) are more common in well-differentiated tumors (hepatocyte-derived) while TP53 mutations predominate in poorly differentiated tumors.
iCCA Cell of Origin For intrahepatic cholangiocarcinoma, both cholangiocytes and hepatocytes can serve as cells of origin depending on the oncogenic stimulus. Experiments in mice show that hepatocytes can trans-differentiate into biliary-type cells when specific oncogenes (such as activated KRAS with p53 loss) are expressed, suggesting flexibility in the cell of origin for this cancer type.
Proliferation vs. Non-Proliferation Subtypes Gene expression profiling studies consistently identify two broad HCC subtypes: a 'proliferation' class characterized by high expression of cell cycle, stem cell, and oncogenic signaling genes (corresponding to poorly differentiated tumors with worse prognosis), and a 'non-proliferation' class with better differentiation, lower proliferation markers, and relatively better outcomes.
CTNNB1-Mutant Subtype Within the non-proliferation class, a distinct subtype defined by activating mutations in CTNNB1 (beta-catenin) can be identified. These tumors have high Wnt signaling activity, tend to be well-differentiated, occur in the absence of cirrhosis, and carry a distinctive gene expression signature including high expression of glutamine synthetase. Patients with CTNNB1-mutant HCC may respond differently to systemic therapies.
Mutation Landscape Large-scale sequencing studies identify TERT promoter mutations (60-70% of HCC) as the most common genetic alteration, followed by TP53 mutations (25-50%), CTNNB1 mutations (25-30%), AXIN1 mutations (15%), and alterations in chromatin remodeling genes (ARID1A, ARID2). TERT promoter mutations enable replicative immortality, while TP53 and CTNNB1 are mutually exclusive in most datasets.
Immune Class More recent transcriptomic analyses have identified an 'immune class' of HCC with high immune infiltration and expression of immune checkpoint molecules including PD-L1. This subtype may be most responsive to immune checkpoint inhibitor therapy, and biomarkers defining this class are being actively developed for clinical use.
FGFR2 Fusions One of the most actionable discoveries in iCCA is the identification of FGFR2 (fibroblast growth factor receptor 2) fusion genes in approximately 10-25% of patients. These fusions, most commonly involving BICC1 or other partner genes, produce constitutively active FGFR2 kinase that drives tumor growth. FGFR2 fusion-positive iCCAs respond to FGFR inhibitors (pemigatinib, infigratinib), which are now FDA-approved for this indication.
IDH1/IDH2 Mutations Hotspot mutations in isocitrate dehydrogenase genes IDH1 and IDH2 occur in approximately 10-20% of iCCAs, producing the oncometabolite 2-hydroxyglutarate (2HG). 2HG inhibits alpha-ketoglutarate-dependent dioxygenases including histone and DNA demethylases, leading to a hypermethylated epigenome. IDH inhibitors are being tested in clinical trials for IDH-mutant iCCA.
Chromatin Remodeling Mutations Mutations in chromatin remodeling genes including BAP1, ARID1A, and PBRM1 are found in 20-30% of iCCAs. These loss-of-function mutations impair the cell's ability to properly regulate gene expression through chromatin modification. While not yet directly targetable, they may sensitize tumors to other interventions.
KRAS and Other Mutations KRAS mutations (15-30% of iCCA) activate the RAS/MAPK signaling pathway. TP53 mutations (20-25%) impair DNA damage response. Unlike pancreatic cancer where KRAS is nearly universal, iCCA has a more heterogeneous mutational landscape with multiple targetable alterations, making comprehensive genomic profiling particularly important for iCCA patients.
TERT Promoter and Surveillance TERT promoter mutations represent the earliest genomic event in HCC development, detectable even in pre-malignant nodules in cirrhotic livers. Liquid biopsy detection of TERT promoter mutations in cell-free DNA may enable earlier HCC detection than current alpha-fetoprotein (AFP) and ultrasound surveillance strategies.
Molecular Testing for iCCA Unlike HCC where molecular subtype has not yet changed first-line treatment decisions, iCCA has reached the point where molecular profiling directly guides therapy: FGFR2 fusion testing is now recommended for all patients with advanced iCCA, and IDH1 mutation testing is recommended to identify candidates for enasidenib/ivosidenib treatment.
Challenges of Intratumoral Heterogeneity Liver cancers show significant intratumoral heterogeneity - different parts of the same tumor may have different mutation profiles. This heterogeneity means that a single biopsy may not capture the full molecular landscape, potentially missing targetable alterations present in unsampled tumor regions. Liquid biopsy approaches that sample shed DNA from the whole tumor could help address this challenge.
Predictive vs. Prognostic Biomarkers A key distinction emphasized in the review is between prognostic biomarkers (predicting outcomes regardless of treatment) and predictive biomarkers (predicting response to a specific treatment). While many molecular features are prognostic, identifying truly predictive biomarkers for HCC treatment remains challenging, particularly for systemic therapies like sorafenib and immunotherapy.
Expanding Targeted Therapy in HCC Unlike iCCA with multiple targeted therapy approvals, HCC has very limited targeted options beyond sorafenib and lenvatinib (VEGFR/multi-kinase inhibitors). Developing molecularly targeted therapies for HCC subtypes - such as Wnt/beta-catenin inhibitors for CTNNB1-mutant tumors or MDM2 antagonists for MDM2-amplified, TP53-wild-type tumors - is a major research priority.
Immune Microenvironment Integration Future molecular classification schemes should integrate information about the tumor immune microenvironment alongside genomic alterations, since the immune context strongly influences treatment response to checkpoint inhibitors. Combined genomic-immune classification may better predict which patients benefit from immunotherapy.
Prevention and Surveillance Innovation Understanding the molecular evolution from pre-malignant lesions to HCC enables development of chemoprevention strategies. Identifying high-risk pre-malignant nodules using molecular biomarkers (TERT promoter mutations, epigenetic signatures) could enable more precise surveillance of at-risk cirrhotic patients and earlier intervention.
Functional Genomics and Drug Sensitivity Large-scale functional genomic screens (CRISPR essentiality screens, drug sensitivity profiling in patient-derived organoids) are needed to identify which genomic alterations are true synthetic lethal or drug sensitization targets versus passenger events. These functional studies will be necessary to translate the genomic landscape into actionable treatment choices.