Bulk and single‐cell transcriptome reveal the immuno‐prognostic subtypes and tumour microenvironment heterogeneity in HCC

Abstract Background & Aims Accumulating evidences suggest tumour microenvironment (TME) profoundly influence clinical outcome in hepatocellular carcinoma (HCC). Existing immune subtypes are susceptible to batch effects, and integrative analysis of bulk and single‐cell transcriptome is helpful to recognize immune subtypes and TME in HCC. Methods Based on the relative expression ordering (REO) of 1259 immune‐related genes, an immuno‐prognostic signature was developed and validated in 907 HCC samples from five bulk transcriptomic cohorts, including 72 in‐house samples. The machine learning models based on subtype‐specific gene pairs with stable REOs were constructed to jointly predict immuno‐prognostic subtypes in single‐cell RNA‐seq data and validated in another single‐cell data. Then, cancer characteristics, immune landscape, underlying mechanism and therapeutic benefits between subtypes were analysed. Results An immune‐related signature with 29 gene pairs stratified HCC samples individually into two risk subgroups (C1 and C2), which was an independent prognostic factor for overall survival. The machine learning models verified the immune subtypes from five bulk cohorts to two single‐cell transcriptomic data. Integrative analysis revealed that C1 had poorer outcomes, higher CNV burden and malignant scores, higher sensitivity to sorafenib, and exhibited an immunosuppressive phenotype with more regulators, e.g., myeloid‐derived suppressor cells (MDSCs), Mø_SPP1, while C2 was characterized with better outcomes, higher metabolism, more benefit from immunotherapy, and displayed active immune with more effectors, e.g., tumour infiltrating lymphocyte and dendritic cell. Moreover, both two single‐cell data revealed the crosstalk of SPP1‐related L–R pairs between cancer and immune cells, especially SPP1‐CD44, might lead to immunosuppression in C1. Conclusions The REO‐based immuno‐prognostic subtypes were conducive to individualized prognosis prediction and treatment options for HCC. This study paved the way for understanding TME heterogeneity between immuno‐prognostic subtypes of HCC.