Single sample scoring of hepatocellular carcinoma: A study based on data mining

Abstract

Hepatocellular carcinoma (HCC) is a high mortality malignancy and the second leading cause of cancer-related deaths. Because the immune system plays a dual role by assisting the host barrier and tumor progression, there are complex interactions with considerable prognostic significance. Herein, we performed single-sample gene set enrichment (ssGSEA) to explore the tumor microenvironment (TME) and quantify the tumor-infiltrating immune cell (TIIC) subgroups of immune responses based on the HCC cohort of The Cancer Genome Atlas (TCGA) database. We evaluate molecular subpopulations, survival, function, and expression differential associations, as well as reveal potential targets, and biomarkers for immunotherapy. We combined the TME score and the 29 immune cell types in the low, medium, and high immunity groups. The stromal score, immune score, and ESTIMATE score were positively correlated with immune activity but negatively correlated with the tumor purity. There were 23 human leukocyte antigen (HLA)-related genes that were significantly different. However, KIAA1429 was not significant among the different immunity groups. Besides, programmed death-ligand 1 (PD-L1) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) expression increased with the increase of immune activity. This may provide valuable information for HCC immunotherapy. We also found that there was no significant difference in naïve B cells, macrophages M1, activated mast cells, resting natural killer (NK) cells, and T cells gamma delta among the different immunity groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differential proteins were mainly enriched in alpha-linolenic acid (ALA) metabolism, cytokine-cytokine receptor interaction, glycosaminoglycan biosynthesis-heparan sulfate/heparin, glycosphingolipid biosynthesis-ganglio series and proteasome. Our findings provide a deeper understanding of the immune scene, uncovering remarkable immune infiltration patterns of various subtypes of HCC using ssGSEA. This study advances the understanding of immune response and provides a basis for research to enhance immunotherapy.

Identifying the tumor immune microenvironment-associated prognostic genes for prostate cancer

“…In addition, KEGG results indicated that the DEGs were related to the cytokine–cytokine receptor interaction pathway. Previous studies have found that this pathway always involved some immune-related genes that are involved in different cancers, such as renal cell carcinoma and hepatocellular carcinoma [ 35 , 36 ]. This pathway might be an important factor in the immunotherapy for PRAD.…”

Update on Glycosphingolipids Abundance in Hepatocellular Carcinoma

“…Another important parameter to consider is the immune response in HCC development. Zhu et al investigated immune responses based on the HCC cohort of The Cancer Genome Atlas (TCGA) database [62]. By assigning immune cell types to three different immunity groups (low, medium, and high) and following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the authors showed that the immunity groups differ in gene expression of ganglio series GSL producing proteins [62] (Figure 2B).…”

“…Zhu et al investigated immune responses based on the HCC cohort of The Cancer Genome Atlas (TCGA) database [62]. By assigning immune cell types to three different immunity groups (low, medium, and high) and following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the authors showed that the immunity groups differ in gene expression of ganglio series GSL producing proteins [62] (Figure 2B). This poses the question as to whether the immune response (immune cell infiltration of the tumor) can be influenced and therefore immunotherapy enhanced.…”