Integrated proteogenomic characterization and immune response evaluation reveal an imbalanced hepatocellular carcinoma microenvironment induced by incomplete radiofrequency ablation

Abstract Background: Efforts to precisely assess tumor-specific T-cell immune responses capable of mediating imbalanced hepatocellular carcinoma (HCC) ecosystems after incomplete radiofrequency ablation (iRFA) still face major challenges. Here, we assessed the immune response and performed transcriptomic and proteomic analyses in patients with HCC following iRFA. Methods: Peripheral blood and tissue samples were collected from HCC patients who underwent RFA. Multiplex immunostaining and flow cytometry were used to assess the local and systemic immune response. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were explored via transcriptomic and proteogenomic analyses. The ability of proteinase-3 (PRTN3) to predict overall survival (OS) was assessed in HCC patients with early recurrence after RFA. Results: Multiplex immunostaining revealed no immediate significant change in local immune cell counts. Flow cytometry analysis showed that the levels of CD4+ T cells, CD4+CD8+ T cells, and CD4+CD25+CD127- Treg cells were significantly increased, while the levels of CD16+CD56+ natural killer cells were significantly decreased on day 5 after cRFA (P<0.05). Transcriptomics and proteomics allow the identification of hundreds of DEGs and DEPs. Pathways related to immunoinflammation response, cancer progression and metabolism were found to be dysregulated at the transcriptomic and proteomic levels. Proteinase 3 (PRTN3) was observed to be persistently upregulated at the gene and protein levels and closely associated with the OS of early recurrent HCC following RFA. Conclusion: This study provides a comprehensive overview of the immune response and transcriptomic and proteogenomic landscapes of HCC milieus, revealing the mechanisms involved in the iRFA-induced immune response and tumor progression. Trial registration: ChiCTR2200055606, http://www.chictr.org.cn/showproj.aspx?proj=32588.