Carri Ibel, Schwab Erika, Trivino Juan Carlos, von Euw Erika M, Nielsen Morten, Mordoh José, Barrio María Marcela
Centro de Investigaciones Oncológicas (FUCA), Fundación Cáncer, Ciudad Autónoma de Buenos Aires, Argentina.
Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
Front Immunol. 2025 Jan 7;15:1496204. doi: 10.3389/fimmu.2024.1496204. eCollection 2024.
VACCIMEL is a therapeutic cancer vaccine composed of four irradiated allogeneic human melanoma cell lines rationally selected to cover a wide range of melanoma tumor-associated antigens (TAA). We previously demonstrated that vaccination in the adjuvant setting prolonged the distant-metastasis-free survival of cutaneous melanoma patients and that T cells reactive to TAA and the patient's private neoantigens increased during treatment. However, immune responses directed to vaccine antigens that may arise from VACCIMEL's somatic mutations and human polymorphisms remain unexplored. To study these immunogens, we performed whole-exome sequencing of paired tumor and germinal samples from four vaccinated patients and the vaccine cells. VACCIMEL variants were called by comparing the vaccine and the patient's exomes, and non-synonymous coding variants were used to predict T cell epitopes. Candidates were ranked based on their mRNA expression in VACCIMEL, predicted peptide-HLA (pHLA) presentation, and pHLA stability. Then, the immune responses to prioritized epitope candidates were tested using IFNγ ELISpot assays on vaccinated patients' PBMC samples. The comparison of the vaccine with the patients' germinal exomes revealed on average 9481 coding non-synonymous variants, suggesting that VACCIMEL offers a high number of potential antigens. Between 0,05 and 0,2% of these variants were also found in the tumors of three vaccinated patients; however, one patient with a high tumor mutational burden (TMB) shared 19,5% somatic variants. The assessment of T cell responses showed that vaccinated patients mounted highly diverse responses against VACCIMEL peptides. Notably, effector T cells targeting the patient's tumor antigens, comprising neoantigens and TAA, were found in higher frequencies than T cells targeting VACCIMEL-exclusive antigens. On the other hand, we observed that the immunogenic epitopes are not conserved across patients, despite sharing HLA and that immune responses fluctuate over time. Finally, a positive correlation between VACCIMEL antigen expression and the intensity of the T cell responses was found. Our results demonstrate that the immune system simultaneously responds to a high number of antigens, either vaccinal or private, proving that immune responses against epitopes not expressed in the patient's tumors were not detrimental to the immune recognition of neoantigens and TAA.
VACCIMEL是一种治疗性癌症疫苗，由四种经过辐照的同种异体人类黑色素瘤细胞系组成，这些细胞系经过合理选择，以涵盖广泛的黑色素瘤肿瘤相关抗原（TAA）。我们之前证明，在辅助治疗中进行疫苗接种可延长皮肤黑色素瘤患者的无远处转移生存期，并且在治疗期间，对TAA和患者个体新抗原产生反应的T细胞数量会增加。然而，针对可能由VACCIMEL的体细胞突变和人类多态性产生的疫苗抗原的免疫反应仍未得到探索。为了研究这些免疫原，我们对四名接种疫苗患者以及疫苗细胞的配对肿瘤和生发样本进行了全外显子组测序。通过比较疫苗和患者的外显子组来识别VACCIMEL变体，并使用非同义编码变体来预测T细胞表位。根据它们在VACCIMEL中的mRNA表达、预测的肽-HLA（pHLA）呈递以及pHLA稳定性对候选物进行排名。然后，使用IFNγ ELISpot检测对接种疫苗患者的PBMC样本测试对优先表位候选物的免疫反应。将疫苗与患者的生发外显子组进行比较，平均发现9481个编码非同义变体，这表明VACCIMEL提供了大量潜在抗原。在三名接种疫苗患者的肿瘤中也发现了这些变体的0.05%至0.2%；然而，一名肿瘤突变负荷（TMB）较高的患者共享了19.5%的体细胞变体。T细胞反应评估表明，接种疫苗的患者对VACCIMEL肽产生了高度多样化的反应。值得注意的是，与靶向VACCIMEL特有的抗原的T细胞相比，靶向患者肿瘤抗原（包括新抗原和TAA）的效应T细胞的频率更高。另一方面，我们观察到，尽管共享HLA，但免疫原性表位在患者之间并不保守，并且免疫反应会随时间波动。最后，发现VACCIMEL抗原表达与T细胞反应强度之间存在正相关。我们的结果表明，免疫系统同时对大量抗原（无论是疫苗抗原还是个体抗原）产生反应，证明针对患者肿瘤中未表达的表位的免疫反应对新抗原和TAA的免疫识别没有不利影响。
