Characterization and functional analysis of cancer-antigen specific tumour immune infiltrates from patients with head and neck squamous cell carcinoma

1)表征头颈部鳞状细胞癌不同腔室中CD8+和CD4+ t细胞的表型和功能能力。为此，将从原发肿瘤组织样本、引流淋巴结和外周血中分离出免疫细胞。研究的重点将放在组织驻留记忆细胞的分析上，这些细胞可能具有癌症抗原特异性。II)了解t细胞对突变和共享目标抗原的识别、免疫浸润的密度和组成以及癌症抗原特异性免疫的存在之间的联系。肿瘤活检中潜在靶抗原的曲目将通过外显子组DNA和总RNA的全肿瘤测序来表征。我们将使用在南安普顿建立的生物信息学管道来预测突变的新抗原，并量化共同的癌症抗原（病毒抗原，癌睾丸抗原）的表达。肿瘤浸润免疫细胞从各自的病人将扩大和测试对选定的目标抗原的反应性。III)确定抗pd -1抗体新辅助治疗对肿瘤浸润性免疫细胞的影响。在诊断前治疗活检和新辅助PD-1抗体治疗后的样本中，从手术切除时开始进行类比实验。

I) To characterize the phenotype and functional capability of CD8+ and CD4+ T-cells in different compartments of head and neck squamous cell carcinoma. To this end, immune cells from tissue samples of primary tumours, draining lymph nodes and the peripheral blood will be isolated. The primary focus will lie in the analysis of tissue resident memory cells, which are likely enriched for cancer antigen specificity. II) To understand the link between the T-cell recognition of mutated and shared target antigens, the density and composition of immune infiltrates and the presence of cancer-antigen specific immunity. The repertoire of potential target antigens in tumour biopsies will be characterized by whole tumour sequencing of exome DNA and total RNA. We will use bioinformatics pipelines established in Southampton to predict mutated neoantigens and to quantify the expression of shared cancer antigens (viral antigens, cancer-testis antigens). Tumour infiltrating immune cells from the respective patients will be expanded and tested for reactivity to selected target antigens. III) To determine the effect of neoadjuvant treatment with anti-PD-1 antibodies on tumour infiltrating immune cells. Experiments will be carried out in analogy to aim 2 in diagnostic pre-treatment biopsies and samples after neoadjuvant PD-1 antibody treatment from the time of surgical resection.