Identification of Two Molecular Subtypes of Hepatocellular Carcinoma Based on Dysregulated Immune LncRNAs

Hongsheng Lin; Yangyi Xie; Yinzhi Kong; Li Yang; Mingfen Li

doi:10.3389/fmolb.2021.625858

Identification of Two Molecular Subtypes of Hepatocellular Carcinoma Based on Dysregulated Immune LncRNAs

Front Mol Biosci. 2021 Nov 23:8:625858. doi: 10.3389/fmolb.2021.625858. eCollection 2021.

Authors

Hongsheng Lin^{1

2

3

4}, Yangyi Xie^{1

5}, Yinzhi Kong^{1

5}, Li Yang^{1

2}, Mingfen Li^{1

2}

Affiliations

¹ Guangxi University of Chinese Medicine, Nanning, China.
² Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China.
³ Guangxi Medical University, Nanning, China.
⁴ Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China.
⁵ The First Clinical Faculty of Guangxi University of Chinese Medicine, Nanning, China.

Abstract

Long non-coding RNAs (lncRNAs) as important regulators of gene expression also have critical functions in immune regulation. This study identified lncRNA modulators of immune-related pathways as biomarkers for hepatocellular carcinoma (HCC). The profile of lncRNA regulation in immune pathways in HCC was comprehensively mapped. To determine lncRNAs with immunomodulatory functions specific to HCC, the enrichment of lncRNAs in a collection of 17 immune functions was calculated applying gene set enrichment analysis (GSEA). Unsupervised clustering of samples were performed in the R package ConsensusClusterPlus to analyze subtype survival and immunological characteristics. The enrichment of 3,134 lncRNA-immune pathway pairs in both diseased and normal samples showed a total of 1,984 immunoregulatory functional lncRNAs specific to HCC only. In addition, 18 immune-related lncRNAs were disordered in HCC and were significantly associated with immune cell infiltration. Functional enrichment analysis indicated that the 18 dysregulated immune lncRNAs were enriched in cytokines, cytokine receptors, TGFb family members, TNF family members, and TNF family member receptor pathways. Two molecular subtypes of hepatocellular carcinoma were identified based on 18 dysregulated immune lncRNAs. Immunological profiling showed that subtype 1 samples with higher levels of cytokine response had a better survival, but subtype 2 samples with higher levels of tumor proliferation had poorer survival. This study identified 18 HCC-specific dysregulated immune lncRNAs and two HCC molecular subtypes with significant prognostic differences and immune characteristics. The current findings help understand the function of lncRNAs and promote the identification of immunotherapy targets.

Keywords: bioinformatics; hepatocellular carcinoma; immune; long non-coding RNA (lncRNA); molecular subtypes.