Construction of a Prognostic Model for Hepatocellular Carcinoma Based on Macrophage Polarization-Related Genes

Abstract

Background

The progression of hepatocellular carcinoma (HCC) is related to macrophage polarization (MP). Our aim was to identify genes associated with MP in HCC patients and develop a prognostic model based on these genes.

Results

We successfully developed a prognostic model consisting of six MP-related genes (SCN4A, EBF3, ADGRB2, HOXD9, CLEC1B, and MSC) to calculate the risk score for each patient. Patients were then classified into high- and low-risk groups based on their median risk score. The performance of the MP-related prognostic model was evaluated using Kaplan-Meier and ROC curves, which yielded favorable results. Additionally, the nomogram demonstrated good clinical effectiveness and displayed consistent survival predictions with actual observations. Gene Set Enrichment Analysis (GSEA) revealed enrichment of pathways related to KRAS signaling downregulation, the G2M checkpoint, and E2F targets in the high-risk group. Conversely, pathways associated with fatty acid metabolism, xenobiotic metabolism, bile acid metabolism, and adipogenesis were enriched in the low-risk group. The risk score positively correlated with the number of invasion-related genes. Immune checkpoint expression differed significantly between the two groups. Patients in the high-risk group exhibited increased sensitivity to mitomycin C, cisplatin, gemcitabine, rapamycin, and paclitaxel, while those in the low-risk group showed heightened sensitivity to doxorubicin. These findings suggest that the high-risk group may have more invasive HCC with greater susceptibility to specific drugs. IHC staining revealed higher expression levels of SCN4A in HCC tissues. Furthermore, experiments conducted on HepG2 cells demonstrated that supernatants from cells with reduced SCN4A expression promoted M2 macrophage polarization marker, CD163 in THP-1 cells. Reduced SCN4A expression induced HCC-related genes, while increased SCN4A expression reduced their expression in HepG2 cells.

Conclusion

The MP-related prognostic model comprising six MPRGs can effectively predict HCC prognosis, infer invasiveness, and guide drug therapy. SCN4A is identified as a suppressor gene in HCC.

Keywords:

• hepatocellular carcinoma
• macrophage polarization-related genes
• tumor microenvironment
• prognosis
• SCN4A

Abbreviation

ACTB, beta-actin; ADGRB2, adhesion G protein-coupled receptor B2; BAI2, brain angiogenesis inhibitor 2; bFGF, basic fibroblast growth factor; C7, complement C7; CD163, Cluster of Differentiation 163; CD34, CD34 molecule; CD5L, CD5 molecule like; cDNA, complementary DNA; CFP, complement factor properdin; CLEC1B, C-type lectin domain family 1 member B; CNDP1, carnosine dipeptidase 1; COL15A1, collagen type XV alpha 1 chain; COL9A1, collagen type IX alpha 1 chain; COLEC10, collectin subfamily member 10; COLEC10, collectin subfamily member 12; CRHBP, corticotropin releasing hormone binding protein; CTHRC1, collagen triple helix repeat containing 1; DEG, differentially expressed gene; DEMPRG, differentially expressed MP-related gene; DN, Down regulation; EBF3, early B cell factor 3; EMT, epithelial-mesenchymal transition; EGF, epidermal growth factor; EGFL6, EGF like domain multiple 6; FABP4, fatty acid binding protein 4; FAM163B, family with sequence similarity 163 member B; FCN3, ficolin 3; FOSB, FBJ osteosarcoma oncogene B; G2/M, G2 phase to mitotic phase; GDF10, growth differentiation factor 10; GO, Gene Ontology; GPR1, G protein-coupled receptor 1; GPR182, G protein-coupled receptor 182; GPM6A, glycoprotein M6A; GSEA, Gene Set Enrichment Analysis; GSVA, Gene Set Variation Analysis; HCC, hepatocellular carcinoma; HOXD8, homeobox D8; HOXD9, homeobox D9; HOXD10, homeobox D10; HME, human macrophage metalloelastase; ICGC, International Cancer Genome Consortium; IGFALS, insulin like growth factor binding protein acid labile subunit; IHC, Immunohistochemistry; IL-, Interleukin-; IL1RL1, interleukin 1 receptor like 1; INMT, indolethylamine N-methyltransferase; KCNH2, potassium voltage-gated channel subfamily H member 2; KCNQ3, potassium voltage-gated channel subfamily Q member 3; KDM8, lysine demethylase 8; KEGG, Kyoto Encyclopedia of Genes and Genomes; KRAS, Kirsten rat sarcoma; LY6H, lymphocyte antigen 6 family member H; MAPT, microtubule associated protein tau; MMP9, matrix metallopeptidase 9; MMP12, matrix metallopeptidase 12; MP, macrophage polarization; MSC, musculin; NR4A3, nuclear receptor subfamily 4 group A member 3; NTF3, neurotrophin 3; OLFML2B, olfactomedin like 2B; OS, overall survival; PBS, phosphate-buffered saline; PD-L1, Programmed death-ligand 1; PDGF, platelet-derived growth factor; PLVAP, plasmalemma vesicle associated protein; PLPP2, phospholipid phosphatase 2; PRDM9, PR/SET domain 9; ROC curves, receiver operating characteristic curve; RIPOR3, RIPOR family member 3; RFX8, regulatory factor X8; SCN4A, Sodium Voltage-Gated Channel Alpha Subunit 4; ST8SIA6, ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6; TAM, Tumor-associated macrophage; TCGA, The Cancer Genome Atlas; TME, tumor microenvironment; TNF-α, tumor necrosis factor α; TRPC6, transient receptor potential cation channel subfamily C member 6; UCHL1, ubiquitin C-terminal hydrolase L1; VEGFA, vascular endothelial growth factor A; WGCNA, Weighted Gene Co-expression Network Analysis.

Data Sharing Statement

Gene expression data described in this study were deposited in TCGA and GTE databases. Additional relevant data supporting the findings of this study are available from the corresponding authors upon request. The datasets used and materials in this study are available upon reasonable request.

Ethics Approval and Consent to Participate

Clinical Samples

The study was conducted in accordance with the guidelines of the Declaration of Helsinki and approved by the ethics committee of the West China Hospital of Sichuan University (No. 2016-91).

Consent for Publication

All the authors agreed to publish the article.

Acknowledgment

We thank Miss Mingming Zhang for preparing HCC specimens.

Author Contributions

All authors made a significant contribution to the work reported, whether in the conception, study design, execution, acquisition of data, analysis, and interpretation, or in all these areas, took part in drafting, revising, or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors declare no potential conflicts of interest regarding the research, authorship, or publication of this article.

Additional information

Funding

This study was supported by 1.3.5 project for disciplines of excellence, West China Hospital, Sichuan University (No.ZYGD23030).