Over half of hepatocellular carcinoma (HCC) cases diagnosed worldwide are in China. However, whole-genome analysis of hepatitis B virus (HBV)-associated HCC in Chinese individuals is limited, with current analyses of HCC mainly from non-HBV-enriched populations.

　　On February 14, 2024, Nature published a research article entitled "Deep whole-genome analysis of 494 hepatocellular carcinomas" from Prof. Fan Bai's research group (BIOPIC/ICG, Peking University), in collaboration with Prof. Hongyang Wang and Prof. Chen Lei's team (Naval Medical University), Prof. Steven G. Rozen's team (Duke-NUS Medical School), as well as Dr. Wu Lin's team (Berry Genomics). This study initiated the Chinese Liver Cancer Atlas (CLCA) project and depicts a detailed genomic landscape and evolutionary history of HCC in Chinese individuals, providing important clinical implications.

　　The CLCA-HCC cohort exhibits distinct epidemiological and clinical pathological characteristics compared with other cohorts (PCAWG and TCGA). By deep whole-genome sequencing (average depth, 120×) of 494 HCC tumors[MOU1]  from different regions in China, this study extensively analyzed features such as driver genes and mutations in coding and non-coding regions, mutational signatures, copy number variations, clustered alteration events (chromothripsis, chromoplexy, and kataegis), HBV integration, extrachromosomal circular DNA (ecDNA), as well as the evolutionary history. (Figure 1).

　　This study identified novel potential driver events in liver cancer, including six coding driver genes (FGA, HNF1A, PRDM11, CDKN1B, BMP5, and ECHS1) and 28 non-coding driver genes. 62.5% of non-coding driver events are enriched in subclonal status, suggesting that they played important roles in the late stage of hepatocarcinogenesis. Several variant events are closely associated with liver metabolic pathways.

　　Figure 1: Candidate driver landscape. a, The research strategy. b, The candidate driver landscape of the CLCA.

　　Five novel mutation signatures were identified in this study, including two doublet-base substitutions (DBS_H1, DBS_H2), two insertion-and-deletions (ID_H3, ID_H8), and one single-base substitution signature (SBS_H8). It is worth noting that ID_H8 is associated with aflatoxin exposure, while DBS_H2 and ID_H3 are related to aristolochic acid (AA) exposure. Compared to the PCAWG-HCC cohort (0.31%), SBS_H8 shows a high enrichment in the CLCA-HCC cohort (57.1%) and is closely associated with mutations in the Wnt/β-catenin signaling pathway and poor prognosis. Subclonal enrichment analysis also reveals significant enrichment of SBS_H8 in clonal mutations, indicating its crucial role in early progression of Chinese HCC. These new mutation signatures are important complements to the substitution signatures.

　　While HBV integration events have been reported in liver cancer before, how they integrate into the genome remains unclear. This study discovered that HBV can form ecDNA with host genomes. Compared to linear DNA integration forms, this HBV-oncogene-ecDNA structure significantly increases copy numbers and expression levels of oncogenes, suggesting that amplification of ecDNA may play an important role in HBV-related liver cancer. Clustered events such as Chromothripsis, chromoplexy, and kataegis are typically believed to occur early during the evolution history in tumors. However, this study found these clustered genomic catastrophic events also occur at later stages during tumor progression.

　　Finally, the researchers selected three newly identified potential driver genes (PPP1R12B, KCNJ12, FGA) for detailed functional validation. Through a combination of CRISPR point mutations and knockdown/knockout experiments in multiple cell lines, it was found that mutations in these genes were sufficient to cause significant changes in gene expression levels and contribute to the regulation of various malignant phenotypes in liver cancer. Further exploration into their underlying mechanisms revealed that the potential driver gene FGA (encoding fibrinogen alpha chain) regulates the TYK2-STAT3-IL6 signaling pathway to influence malignant phenotypes in various liver cancer cells. These results suggest that FGA and its related signaling pathways may serve as promising intervention and therapeutic targets for hepatocellular carcinoma (Figure 2).

　　Figure 2: A proposed model illustrating the role of the FGA/TYK2/STAT3 axis during HCC tumorigenesis.

　　In summary, the CLCA study is a valuable resource that provides important biological insights into HCC carcinogenesis and clinical implications to HCC diagnosis and treatment.

　　Prof. Fan Bai, Prof. Hongyang Wang, Prof. Lei Chen, Prof. Steven G. Rozen and Dr. Lin Wu are the co-corresponding authors of the paper. Prof. Lei Chen, Dr. Chong Zhang, Dr. Ruidong Xue, Dr. Mo Liu, Dr. Jian Bai, PhD candidate Jinxia Bao and Dr. Yin Wang are co-first authors of this paper.

　　This project was funded by the National Natural Science Foundation of China (NSFC), Key Research and Development Program of Ministry of Science and Technology (MOST), Shanghai Municipal Commission of Science and Technology Fund (SMCSTF), Scientific Exploration Award. [MOU2] 

　　Link: https://www.nature.com/articles/s41586-024-07054-3