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Construction and validation of a prognostic signature based on necroptosis-related genes in hepatocellular carcinoma

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  • Yue-ling Peng
  • Ling-xiao Wang
  • Mu-ye Li
  • Li-ping Liu
  • Rong-shan Li

Abstract

Background: Necroptosis is a necrotic programmed cell death with potent immunogenicity. Due to the dual effects of necroptosis on tumor growth, metastasis and immunosuppression, we evaluated the prognostic value of necroptosis-related genes (NRGs) in hepatocellular carcinoma (HCC). Methods: We first analyzed RNA sequencing and clinical HCC patient data obtained to develop an NRG prognostic signature based on the TCGA dataset. Differentially expressed NRGs were further evaluated by GO and KEGG pathway analyses. Next, we conducted univariate and multivariate Cox regression analyses to build a prognostic model. We also used the dataset obtained from the International Cancer Genome Consortium (ICGC) database to verify the signature. The Tumor Immune Dysfunction and Exclusion (TIDE) algorithm was used to investigate the immunotherapy response. Furthermore, we investigated the relationship between the prediction signature and chemotherapy treatment response in HCC. Results: We first identified 36 differentially expressed genes out of 159 NRGs in hepatocellular carcinoma. Enrichment analysis showed that they were mainly enriched in the necroptosis pathway. Four NRGs were screened by Cox regression analysis to establish a prognostic model. The survival analysis revealed that the overall survival of patients with high-risk scores was significantly shorter than that of patients with low-risk scores. The nomogram demonstrated satisfactory discrimination and calibration. The calibration curves validated a fine concordance between the nomogram prediction and actual observation. The efficacy of the necroptosis-related signature was also validated by an independent dataset and immunohistochemistry experiments. TIDE analysis revealed that patients in the high-risk group were possibly more susceptible to immunotherapy. Furthermore, high-risk patients were found to be more sensitive to conventional chemotherapeutic medicines such as bleomycin, bortezomib, and imatinib. Conclusion: We identified 4 necroptosis-related genes and established a prognostic risk model that could potentially predict prognosis and response to chemotherapy and immunotherapy in HCC patients in the future.

Suggested Citation

  • Yue-ling Peng & Ling-xiao Wang & Mu-ye Li & Li-ping Liu & Rong-shan Li, 2023. "Construction and validation of a prognostic signature based on necroptosis-related genes in hepatocellular carcinoma," PLOS ONE, Public Library of Science, vol. 18(2), pages 1-17, February.
    • Handle: RePEc:plo:pone00:0279744
    DOI: 10.1371/journal.pone.0279744
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    References listed on IDEAS

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    1. Marco Seehawer & Florian Heinzmann & Luana D’Artista & Jule Harbig & Pierre-François Roux & Lisa Hoenicke & Hien Dang & Sabrina Klotz & Lucas Robinson & Grégory Doré & Nir Rozenblum & Tae-Won Kang & R, 2018. "Necroptosis microenvironment directs lineage commitment in liver cancer," Nature, Nature, vol. 562(7725), pages 69-75, October.
    2. Marco Seehawer & Florian Heinzmann & Luana D’Artista & Jule Harbig & Pierre-François Roux & Lisa Hoenicke & Hien Dang & Sabrina Klotz & Lucas Robinson & Grégory Doré & Nir Rozenblum & Tae-Won Kang & R, 2018. "Author Correction: Necroptosis microenvironment directs lineage commitment in liver cancer," Nature, Nature, vol. 564(7735), pages 9-9, December.
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