Heterogeneous immunogenomic features and distinct escape mechanisms in multifocal hepatocellular carcinoma.

Abstract

BACKGROUND AIMS\nMultifocal tumors, developed either from intrahepatic metastasis (IM) or multicentric occurrence (MO), is a distinct feature of hepatocellular carcinoma (HCC). Immunogenomic characterization of multifocal HCC is important for understanding immune escape in different lesions and developing immunotherapy.\n\n\nMETHODS\nWe combined whole exome/transcriptome sequencing, multiplex immunostaining, immunopeptidomes, T-cell receptor (TCR) sequencing and bioinformatic analyses of 47 tumors from 15 HCC patients with multifocal lesions.\n\n\nRESULTS\nIM and MO demonstrated distinct clonal architecture, mutational spectrum and genetic susceptibility. The immune microenvironment also displayed spatiotemporal heterogeneity, such as less T cell and more M2 macrophage infiltration in IM and higher expression of inhibitory immune checkpoints in MO. Similar to mutational profiles, shared neoantigens and TCR repertoires among tumors from the same patients were abundant in IM but scarce in MO. Combining neoantigen prediction and immunopeptidomes identified T-cell specific neoepitopes and achieved a high verification rate in vitro. Immunoediting mainly occurred in MO but not IM, due to the relatively low immune infiltration. HLA LOH, identified in 17% of multifocal HCC, hampered the ability of MHC to present neoantigens, especially in IM. An integrated analysis of Immunoscore, Immunoediting, TCR clonality and HLA LOH of each tumor could stratify patients into two groups with high or low risk of recurrence (P=0.038).\n\n\nCONCLUSION\nOur study comprehensively characterized the genetic structure, neoepitope landscape, T cell profile and immunoediting status that collectively shape tumor evolution, which may optimize personalized immunotherapies for multifocal HCC.