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pmid:41619135
A novel signature of palmitoylation for predicting prognosis and therapeutic response of hepatocellular carcinoma.
Yun Li · Zhongquan Yi · Linhua Liu · Danping Huang
Discover oncology · 2026 doi:10.1007/s12672-026-04544-w
Paper
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Experiment
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Data
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Analysis
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Complete file
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Protein palmitoylation, a highly conserved and pivotal form of post-translational protein modification, is extensively implicated in cancer progression and exerts a regulatory role in immune responses. Nevertheless, the prognosis significance and therapeutic potential of palmitoylation-related genes (PRGs) in HCC remain incompletely explored. In the present study, we systematically analyzed multiple transcriptome cohort samples from the TCGA, ICGC and GEO databases, including the TCGA-LIHC, ICGC-LIRI, GSE16757, GSE54236, GSE14520, GSE45267 and GSE36376 cohorts. Subsequently, within the TCGA training cohort, a PRGsSig comprising three hub PRGs, namely HSP90AA1, CTHRC1, and PTDSS2, was constructed via machine learning algorithms. Then, the efficacy of this PRGsSig on prognosis prediction was assessed in the training and validation cohorts. Further analysis of immunotherapy response indicated that patients with low PRGsSig scores benefited more from treatment. Additionally, remarkable disparities were observed between patients in different signature score groups in terms of clinical characteristics, tumor mutation burden, tumor microenvironment, and potential drugs. Furthermore, among the three hub PRGs, PTDSS2 was significantly upregulated in HCC cells and its knockdown significantly inhibited the proliferation and metastasis of HCC cells. 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Lentivirus transfection was carried out on HepG2 and Huh7 cells by e", "t instructions provided. Following a 48-hour transfection, the subsequent analysis was carried out. To", "(Shanghai, China). The specific sequences of shRNA are as follows: sh-PTDSS2: CATAGCCAAGCGTACAG"], "order_basis": "paper_text_order:1447", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nt (Vazyme, China). Subsequently, ChamQ SYBR qPCR Master Mix supplied by Vazyme utilized for q", "ls and methods Cell culture and quantitative real-time PCR (qRT-PCR) The HepG2 and Huh7 HCC cell lines,"], "order_basis": "paper_text_order:1724", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["technology (Shanghai, China). The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibc", "and quantitative real-time PCR (qRT-PCR) The HepG2 and Huh7 HCC cell lines, along with the LO2", ". Lentivirus transfection was carried out on HepG2 and Huh7 cells by employing the Lipofectamin"], "order_basis": "paper_text_order:1752", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In the training cohort, leveraging the aforementioned 301 PRGs, the PRGsSig was established through univariate cox regression (p < 0.01), LASSO regression, and multiple stepwise cox regression analysis."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}