The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma

The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma, a lethal disease lacking specific therapies. This study reports on the identification, characterization, and immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in fibrolamellar hepatocellular carcinoma. DNAJB1-PRKACA-derived HLA class I and HLA class II ligands induce multifunctional cytotoxic CD8+ and T-helper 1 CD4+ T cells, and their cellular processing and presentation in DNAJB1-PRKACA expressing tumor cells is demonstrated by mass spectrometry-based immunopeptidome analysis. Single-cell RNA sequencing further identifies multiple T cell receptors from DNAJB1-PRKACA-specific T cells. Vaccination of a fibrolamellar hepatocellular carcinoma patient, suffering from recurrent short interval disease relapses, with DNAJB1-PRKACA-derived peptides under continued Poly (ADP-ribose) polymerase inhibitor therapy induces multifunctional CD4+ T cells, with an activated T-helper 1 phenotype and high T cell receptor clonality. Vaccine-induced DNAJB1-PRKACA-specific T cell responses persist over time and, in contrast to various previous treatments, are accompanied by durable relapse free survival of the patient for more than 21 months post vaccination. Our preclinical and clinical findings identify the DNAJB1-PRKACA protein as source for immunogenic neoepitopes and corresponding T cell receptors and provide efficacy in a single-patient study of T cell-based immunotherapy specifically targeting this oncogenic fusion.

DNAJB1-PRKACA融合转录本（DNAJB1-PRKACA fusion transcript）是纤维板层型肝细胞癌的致癌驱动因子，这类致命疾病目前尚无特异性治疗手段。本研究报道了针对纤维板层型肝细胞癌中DNAJB1-PRKACA融合转录本的HLA（人类白细胞抗原，Human Leukocyte Antigen）呈递新抗原的鉴定、表征及免疫治疗应用。DNAJB1-PRKACA衍生的HLA I类及HLA II类配体可诱导多功能细胞毒性CD8+ T细胞与T辅助1型（T-helper 1，Th1）CD4+ T细胞，基于质谱的免疫肽组分析证实了表达DNAJB1-PRKACA的肿瘤细胞对这类配体的细胞加工与呈递过程。单细胞RNA测序进一步从DNAJB1-PRKACA特异性T细胞中鉴定出多种T细胞受体（T cell receptor，TCR）。一名频繁出现短期疾病复发的纤维板层型肝细胞癌患者，在持续接受聚ADP核糖聚合酶（Poly (ADP-ribose) polymerase，PARP）抑制剂治疗的同时，接种DNAJB1-PRKACA衍生肽疫苗后，诱导出了具有活化T辅助1型表型与高T细胞受体克隆性的多功能CD4+ T细胞。疫苗诱导的DNAJB1-PRKACA特异性T细胞应答可长期持续；与既往多种治疗方案不同的是，该患者在接种疫苗后实现了超过21个月的持久无复发生存。本研究的临床前与临床结果证实，DNAJB1-PRKACA蛋白可作为免疫原性新表位及对应T细胞受体的来源，并在一项针对该致癌融合蛋白的特异性T细胞免疫治疗单病例研究中展现出疗效。