Prognostic and Immune Landscape Analysis of Ubiquitination-related Genes in Hepatocellular Carcinoma: Based on Bulk and Single-cell RNA Sequencing Data

Zibo Yuan; Qingwei Zhu; Qingsong Wu; Zhe Zhang; Junwei Guo; Gongqiang Wu; Cuiping Zheng; Qiuran Xu; Dongsheng Huang; Di Cui

doi:10.7150/jca.93425

Prognostic and Immune Landscape Analysis of Ubiquitination-related Genes in Hepatocellular Carcinoma: Based on Bulk and Single-cell RNA Sequencing Data

J Cancer. 2024 Mar 11;15(9):2580-2600. doi: 10.7150/jca.93425. eCollection 2024.

Authors

Zibo Yuan^{1

2}, Qingwei Zhu^{1

2}, Qingsong Wu³, Zhe Zhang³, Junwei Guo³, Gongqiang Wu⁴, Cuiping Zheng⁵, Qiuran Xu², Dongsheng Huang², Di Cui^{2

6}

Affiliations

¹ Qingdao Medical College, Qingdao University, Qingdao, 266000, China.
² The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, China.
³ The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, 310000, China.
⁴ Department of Hematology, Dongyang People's Hospital of Zhejiang Provincial, Dongyang, 322100, China.
⁵ Department of Hematology and Chemotherapy, Wenzhou Central Hospital, Wenzhou, 325000, China.
⁶ General Surgery, Cancer Center, Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, China.

Abstract

Background: Despite significant advances in tumor immunotherapy, hepatocellular carcinoma (HCC) remains a malignancy with a challenging prognosis. The increasing research emphasizes the crucial role of ubiquitination in tumor immunotherapy. However, the establishment of prognostic signatures based on ubiquitination-related genes (UbRGs) and their role in immunotherapy are still lacking in HCC. Methods: We employed datasets from TCGA and GEO for transcriptome differential expression analysis and single-cell RNA sequencing analysis. Applying weighted gene co-expression network analysis, cox regression, lasso, selection and visualization of the most relevant features, and gradient boosting machine, we identified hub UbRGs as a gene signature to develop a prognostic model. We evaluated the predictive utility concerning clinical characteristics as well as its role in the immune landscape and immunotherapy potential. Additionally, western blotting, reverse transcription-quantitative PCR, and immunofluorescence were employed to detect the expression and sub-localization of hub genes. Results: Three hub UbRGs (BOP1, CDC20, and UBE2S) were identified as a gene signature. In particular, the high-risk group exhibited notable characteristics, including higher tumor mutation burden, enrichment in immune-related pathways, up-regulation immune checkpoint, and higher immunity scores. Treatment response to immunotherapy varied based on the expression of PD-1 and CTLA-4. Furthermore, single-cell data analysis revealed heterogeneous expression of hub UbRGs across different cell subtypes, while cytological experiments provided additional confirmation of the high expression of hub UbRGs in HCC. Conclusion: Our study provides valuable insights into the identification of novel ubiquitination-related biomarkers with potential applications for prognosis, immunotherapy prediction, and drug sensitivity in HCC.

Keywords: drug sensitivity; hepatocellular carcinoma; immune checkpoints; risk model; tumor immune microenvironment; ubiquitination.