Single cell RNA-seq and TCR-seq of T cell responses against DNAJB1-PRKACA. Single cell RNA-seq and TCR-seq of T cell responses against DNAJB1-PRKACA

The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma (FL-HCC), a lethal disease lacking specific therapies. Here, we report on the identification, characterization and first immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in FL-HCC. To characterize the T cell response against DNAJB1-PRKACA-derived HLA class I and HLA class II ligands, single cell RNA sequencing (scRNA-seq) and single cell TCR profiling from CD4+ and CD8+ T cells were performed using 10x Genomics single cell immune profiling. Overall design: In this study, we analyzed the expressional profile and T cell receptor (TCR) repertoire of CD4+ T cells from a patient with FL-HCC after vaccination with a personalized DNAJB1-PRKACA-derived peptide vaccine. Furthermore we analyzed flow cytometry-sorted PA*24-specific CD8+ T cells from two healthy volunteers (P3 and P4) after in vitro aAPC priming. Single cell RNA sequencing (scRNA-seq) and single cell TCR profiling were performed using 10x Genomics single cell immune profiling.

DNAJB1-PRKACA融合转录本是纤维板层型肝细胞癌（fibrolamellar hepatocellular carcinoma, FL-HCC）的致癌驱动因子，该致死性疾病目前尚无特异性治疗手段。本研究报道了FL-HCC中特异性靶向DNAJB1-PRKACA融合转录本的HLA呈递新抗原的鉴定、表征及首次免疫治疗应用。为表征针对DNAJB1-PRKACA衍生的HLA I类与HLA II类配体的T细胞应答，我们采用10x Genomics单细胞免疫分型技术，对CD4+及CD8+ T细胞开展了单细胞RNA测序（single cell RNA sequencing, scRNA-seq）与单细胞T细胞受体（T cell receptor, TCR）谱分析。实验设计：本研究分析了一名FL-HCC患者接受个性化DNAJB1-PRKACA衍生肽疫苗接种后，其CD4+ T细胞的表达谱与T细胞受体库。此外，我们还对两名健康志愿者（P3与P4）经体外人工抗原呈递细胞（artificial antigen-presenting cell, aAPC）致敏后、经流式细胞术分选得到的PA*24特异性CD8+ T细胞进行了分析。本研究同样采用10x Genomics单细胞免疫分型技术，完成了单细胞RNA测序（scRNA-seq）与单细胞T细胞受体谱分析。