{
  "abstract": "Background Primary liver cancer, predominantly hepatocellular carcinoma (HCC), has limited therapeutic options. While mutation-derived neoantigen vaccine holds promise, its success is hindered by low antigen availability. This study explores transcriptome-derived neoantigens (neoantigen-encoding tumor-specific transcripts, neoTSTs) in HCC, characterizing their features, generation mechanisms, and therapeutic potential.Methods We developed a computational pipeline integrating STAR/StringTie-based transcript assembly with multiexon/single-exon reference datasets (23,972 human control samples) for tumor-specific transcripts (TSTs) identification. A custom sliding-window algorithm compared TST-encoded peptides against UniProt, with neoTSTs predicted using netMHCPan. This framework was applied to 1,013 patients with liver cancer. NeoTSTs were validated through proteomics, immunopeptidomics, and HLA-transgenic models. Multiomics analyses characterized splicing patterns, transposable elements, and transcription factor regulation. Single-cell RNA-seq and Hep53.4 murine models assessed tumor coverage and immunotherapeutic efficacy.Results We analyzed RNA-seq data from 1,013 patients with liver cancer and constructed a multilayered reference dataset. Using a customized pipeline, we identified an average of 60 neoTSTs per patient, significantly surpassing mutation-derived neoantigens (neoMuts). NeoTSTs exhibited higher population frequencies, with 73.1% providing multiple epitopes, and were validated through mass spectrometry and HLA transgenic mouse models. Mechanistically, neoTSTs were generated via retained introns, transposable element activation, HNF4A-regulated alternative promoters, and de novo transmembrane domain generation. Single-cell analysis revealed neoTSTs cover >75% of tumor cells and identified antigen-presenting cancer-associated fibroblasts that enriched in immunotherapy responders and amplified CD4 + T-cell responses. In murine HCC models, neoTST vaccination outperformed neoMuts, inducing dual major histocompatibility complex-I/II activation and significant tumor growth inhibition.Conclusions NeoTSTs represent a superior neoantigen source in HCC, compensating for the limitations of mutation-derived targets. The remarkable abundance and patient-to-patient sharedness of neoTSTs underscore their dual potential: (1) as personalized immunotherapeutic targets, and (2) as broadly applicable antigens for low-TMB tumors. These findings provide a transformative framework for expanding treatment options in HCC immunotherapy.",
  "authors": [
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Peng Lin"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Yifan Wen"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Jingjing Zhao"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Feifei Zhang"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Yaoming Su"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Huiyi He"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Hongwu Yu"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Qiaojuan Li"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Chengye Liu"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Zhixiang Hu"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Yan Li"
    },
    {
      "affiliations": [
        "Department of Oncology and Vascular Interventional Therapy, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital (Fujian Branch of Fudan University Shanghai Cancer Center), Fuzhou, China"
      ],
      "name": "Zhuting Fang"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China"
      ],
      "name": "Linhui Liang"
    },
    {
      "affiliations": [
        "Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China",
        "Department of Oncology, Fudan University, Shanghai, China",
        "State Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai, Shanghai, China"
      ],
      "name": "Shenglin Huang"
    }
  ],
  "title": "Decoding neoantigen-encoding tumor-specific transcripts unveils a shared target reservoir for immunotherapy in hepatocellular carcinoma",
  "uid": "dc66a954-ea1b-5ecc-a4ad-7fb5f9ce0d8f"
}