RIKEN HCC Genomics (lihc_riken)

Overview

The lihc_riken entry represents genomic studies of hepatocellular carcinoma (HCC) associated with RIKEN, synthesizing findings from multiple HBV-related HCC genomic surveys including deep WGS of 494 HCCs (Chen et al., Nature 2024). The primary paper in this corpus (PMID:22634756) is a narrative review synthesizing HBV integration patterns, copy-number alterations, and transcriptomic data from cell line and animal models alongside large WGS cohorts.

Composition

• Cancer type: HCC
• Primary focus: HBV-related HCC; WGS, RNA-seq, and spatial transcriptomics applied across referenced cohorts
• Up to 494 HCCs with deep WGS in referenced studies
• Key referenced methods: WGS, RNA-seq, spatial transcriptomics, droplet digital PCR (ddPCR)

Assays / panels (linked)

• Whole-genome sequencing
• RNA sequencing
• Spatial transcriptomics

Papers using this cohort

• PMID:22634756

Notable findings derived from this cohort

• HBV DNA integration occurs in ~90% of HBV-related HCCs; recurrent hotspots include TERT promoter (23.7%), KMT2D (11.8%), and CCNE1 (5%) PMID:22634756
• HBV-TERT integration can cyclize into extrachromosomal circular DNA (ecDNA) found in 27.3% of liver cancer samples, harboring 76 oncogenes including MYC PMID:22634756
• TERT promoter mutations, CTNNB1, and TP53 are top recurrent somatic alterations in HCC with Wnt and mTOR as key therapeutic pathways PMID:22634756
• Nucleos(t)ide analogues reduced HBV DNA integration frequency from median 1.01x10^9 to 4.84x10^7 after 10 years (n=28) PMID:22634756

Sources

• PMID:22634756

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