Liu X, Li J, Wang Q, Bai L, Xing J, Hu X, Li S, Li Q. Analysis on heterogeneity of hepatocellular carcinoma immune cells and a molecular risk model by integration of scRNA-seq and bulk RNA-seq.
Front Immunol 2022;
13:1012303. [PMID:
36311759 PMCID:
PMC9606610 DOI:
10.3389/fimmu.2022.1012303]
[Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
Background
Studies have shown that hepatocellular carcinoma (HCC) heterogeneity is a main cause leading to failure of treatment. Technology of single-cell sequencing (scRNA) could more accurately reveal the essential characteristics of tumor genetics.
Methods
From the Gene Expression Omnibus (GEO) database, HCC scRNA-seq data were extracted. The FindCluster function was applied to analyze cell clusters. Autophagy-related genes were acquired from the MSigDB database. The ConsensusClusterPlus package was used to identify molecular subtypes. A prognostic risk model was built with the Least Absolute Shrinkage and Selection Operator (LASSO)–Cox algorithm. A nomogram including a prognostic risk model and multiple clinicopathological factors was constructed.
Results
Eleven cell clusters labeled as various cell types by immune cell markers were obtained from the combined scRNA-seq GSE149614 dataset. ssGSEA revealed that autophagy-related pathways were more enriched in malignant tumors. Two autophagy-related clusters (C1 and C2) were identified, in which C1 predicted a better survival, enhanced immune infiltration, and a higher immunotherapy response. LASSO–Cox regression established an eight-gene signature. Next, the HCCDB18, GSA14520, and GSE76427 datasets confirmed a strong risk prediction ability of the signature. Moreover, the low-risk group had enhanced immune infiltration and higher immunotherapy response. A nomogram which consisted of RiskScore and clinical features had better prediction ability.
Conclusion
To precisely assess the prognostic risk, an eight-gene prognostic stratification signature was developed based on the heterogeneity of HCC immune cells.
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