A therapeutic peptide vaccine for fibrolamellar hepatocellular carcinoma: A phase 1 trial

Therapeutic vaccination against a fusion oncogene underlying fibrolamellar HCC

Fibrolamellar hepatocellular carcinoma (FLC or FL-HCC) is a rare subtype of hepatocellular carcinoma (HCC) that typically manifests in adolescents and young adults in the absence of chronic liver disease. Radiologically, a calcified central scar is typically observed. Histologically, the tumor shows cells with eosinophilic cytoplasm and large nuclei, surrounded by lamellated fibrosis. FL-HCC arises due to DNAJB1-PRKACA gene fusion and DNAJB1-PRKCA FISH is becoming the gold standard for diagnosis of the condition. Surgery is the primary treatment in patients with resectable disease. In cases of unresectable FL-HCC, management is often performed in analogy to HCC guidelines, as sufficiently powered prospective trials specific to FL-HCC are lacking. 
A retrospective analysis by Chen at al. (DOI: 10.3390/cancers14215347) reported objective tumor responses to immune checkpoint inhibitor therapy (ICI) directed against PD-(L)1 and CTLA-4 in 15.8% (3/19) of FL-HCC patients, showing an overall limited response to checkpoint therapy. The presence of the oncogenic fusion protein in FL-HCC, however, may represent a targetable conserved neoantigen and provide an opportunity for an entity-specific personalized oncologic vaccination strategy. Indeed, individual case reports (Bauer et al., DOI: 10.1038/s41467-022-33746-3) highlight durable responses after peptide-based vaccination against the oncogenic fusion protein.
Baretti et al. reported the results from a phase 1 trial using a therapeutic peptide vaccine targeting the fusion protein (FLC-Vac) applied in combination with an ICI therapy regimen. The regimen included 8 doses of FLC-Vac, 4 doses of the anti-CTLA4 antibody ipilimumab, and 8 doses of the anti-PD-1 antibody nivolumab. Sixteen patients were enrolled in the trial, with a median age of 23.5 years. Four patients discontinued treatment early during the priming phase (< 10 weeks) before the planned immunological investigations. Among the remaining 12 patients, the disease control rate was 75% (9/12), including partial responses in 25% (3/12). The safety profile (any adverse event [AE] = 100%, CTCAE grade 3 AEs 37.5%) was consistent with the known incidence of immune-related AEs associated with an ipilimumab/nivolumab regimen. Baretti et al. performed a comprehensive assessment of T-cell responses, including functional and phenotypic analysis of T-cell responses using ELISPOT and CyTOF methodology, combined with scRNA sequencing and TCR sequencing. Only 1/12 patients had a detectable DNAJ-PKAc specific T-cell response at baseline. After vaccination and ICI therapy, however, these responses were present in 9/12 patients, including all patients that showed clinical responses. 
An expansion of tumor-antigen-related T-cell clones is expected after vaccination and expanded clones are associated with responses to ICI therapy in other entities. Indeed, a stronger expansion of closely related TCRs indicative of antigen-specific T-cell proliferation in the peripheral blood was associated with responder patients in this trial. Importantly, such expanding T-cell clones were also observed in infiltrating tumors, suggesting that they can engage tumor cells. In one responding patient, the authors further identified several induced T-cell clones that targeted the DNAJB1-PRKCA fusion protein. Interestingly, these were mainly CD4+ T-cell responses restricted by the MHC class II HLADRB3 molecule. Despite the de novo generated immune responses that could drive immune escape mechanisms in the targeted epitopes, in the follow-up analysis of patients that later developed cancer progression, the authors found no evidence for a loss of the targeted antigen or an altered antigen presentation. However, they observed increased T-cell exhaustion signatures and spatial T-cell exclusion in the tumor microenvironment. Several responding patients remained tumor free at the time of manuscript preparation. In sum, the study highlights a promising concept for a tumor vaccination strategy against an oncogenic neoantigen in FL-HCC. The “public” nature of the oncogenic fusion protein (i.e., shared across many patients) and its critical role for cancer cell biology limits immune escape mechanism available to the cancer cell and makes it a particularly suitable target for vaccine development. Patients with evidence of successful generation of tumor-specific responses experienced significant and durable anti-tumor responses. The FLC-Vac strategy therefore holds significant promise for patients with FL-HCC, a rare subtype of HCC. 
Nevertheless, several caveats warrant further consideration. First, while the observed responses are promising, the single-arm design and overall small patient cohort available for detailed immunological analysis prevents conclusions with respect to alternative treatment strategies. In particular, an ICI control arm without therapeutic vaccination would be of interest. While retrospective analysis of historical cohorts showed response rates in FL-HCC below those observed in this trial, it cannot be excluded that a significant part of the observed response is due to the effects of the ICI regime on immune responses independent of the vaccinated peptide. Second, vaccination may exert effects independent of antigen specificity, a notion supported by findings of better ICI therapy responses in patients who received mRNA vaccines during the pandemic (study by Grippin et al., DOI 10.1038/s41586-025-09655-y). Third, the role of the underlying immune architecture in the tumor microenvironment remains poorly understood. For example, it is unclear whether patients with a depleted or compartmentalized immunotype at baseline (when no significant T cell infiltration into the tumor parenchyma is observed) can respond to the therapeutic vaccination and ICI therapy, as the induced antigen-specific T cells might not reach the tumor: In conventional HCC, ICI-related responses are strongly associated with immune-enriched immunotypes (study by Salié et al., DOI: 10.1136/gutjnl-2024-332837). Fourth, antigen-specific immune responses were not observed in all patients. Strategies to increase vaccination efficacy could increase these rates. These strategies may entail different vaccine formulations, including mRNA-based regimes, or different dosing regimens. Despite these open questions, the data shed light on a promising novel therapeutic strategy for a rare subtype of HCC.