HLA B44 motif neoepitopes in NSCLC: Evaluating their effects on the TME and adding them to established markers in a model to predict durable benefit from PD- 1 inhibition with and without chemotherapy

项目总结 肺癌是美国和世界上与癌症相关的死亡的主要原因。我们最近 证实了程序性细胞死亡1(PD-1)抑制剂，它能在少数患者中产生持久反应 非小细胞肺癌(NSCLC)患者，带电结合HLA-B的患者疗效更好 那些肿瘤含有突变的口袋(S)导致了我们指定的基序新表位。主题 新表位的第二位氨基酸被取代，产生电荷变化。 来自野生型多肽，生成的氨基酸具有与人类白细胞抗原-B结合口袋相反的电荷。 到目前为止，基序新表位诱导的免疫学变化还没有被探索过。我们提出了一个 以人类白细胞抗原B44超型等位基因患者为研究对象，对其潜在机制进行综合评价 由于人类白细胞抗原-B44的流行(约占总人口的40%)及其在各种族和地区的分布 种族群体。我们将评估癌症基因组图谱(TCGA)中的人类白细胞抗原-B44样本，以探索在 基因检测对有无Motif新表位患者肿瘤微环境的影响 通过幻灯片回顾和基于基因表达谱的算法来研究基因表达和细胞组成。我们会 评估具有或不具有HLA-B44基序新表位的治疗初治患者的手术标本 通过多重免疫荧光(MIF)评价TME的空间特征。我们将评估多个部分 从每个样本中确定与基序新表位最相关的生物标记物。我们将进一步 通过单细胞RNA-SEQ分析检测与基序新表位相关的TME的免疫环境。 探讨Motif新表位在早期和晚期非小细胞肺癌患者中的预测价值 评估相关的临床问题，我们将在三个不同的临床情景下对患者进行分析。AS 我们的NSCLC患者现在常规获得完整外显子组测序(WES)和转录组数据，如 作为患者临床护理的一部分，我们将分析含有Motif新表位的基因的存在和表达。 我们将评估75名早期患者的基线肿瘤活组织检查，这些患者带有HL A-B44等位基因 新辅助化疗加PD-1抑制，新表位与病理完全性的相关性 回应。在接受单一药物PD-1治疗的75名携带HLA-B44等位基因的晚期患者中 抑制和另外75名接受化疗加PD-1抑制的患者，我们将关联Motif 治疗开始后6个月内疾病进展的新表位。 总之，这些研究将提供对TME和其他免疫学变化的更好理解 与基序新表位的存在有关。此外，结果可以使我们识别患者的身份 对这一新抗原呈递标志物的评估可用于临床筛选患者 使用PD-1抑制剂治疗的三种不同临床方案的相关益处。作为推论，结果 还可以确定应该考虑其他治疗策略的患者群体。

PROJECT SUMMARY Lung cancer is the leading cause of cancer related deaths in the United States and the World. We recently demonstrated that programmed cell death 1 (PD-1) inhibitors, which lead to durable responses in a minority of non-small cell lung cancer (NSCLC) patients, have greater efficacy in patients with charged HLA-B binding pockets whose tumors harbor mutation(s) leading to what we have designated as motif neoepitopes. Motif neoepitopes have an amino acid substitution in the second position of a nonamer generating a change in charge from the wild type peptide with the resultant amino acid having a charge opposite from the HLA-B binding pocket. To date, the immunological changes induced by motif neoepitopes have not been explored. We propose a comprehensive evaluation of the underlying mechanism, focusing on patients with HLA-B44 supertype alleles because of the prevalence (approximately 40% of the population) and distribution of HLA-B44 across racial and ethnic groups. We will evaluate HLA-B44 samples in the cancer genome atlas (TCGA) to explore differences in the tumor microenvironment (TME) among patients with or without motif neoepitopes by examining gene expression and cellular composition by slide review and algorithms based on gene expression profiles. We will evaluate surgical specimens from treatment naïve patients with or without HLA-B44 motif neoepitopes and evaluate spatial signatures of the TME by multiplex immunofluorescence (MIF). We will assess multiple sections from each specimen to identify biomarkers most significantly associated with motif neoepitopes. We will further examine immune contextures of the TME associated with motif neoepitopes by single cell RNA-seq analysis. To elucidate the predictive value of motif neoepitopes in early and advanced stage NSCLC patients and to assess relevant clinical questions, we will perform analyses of patients in three separate clinical scenarios. As whole exome sequencing (WES) and transcriptomic data is now routinely obtained in our NSCLC patients as part of patients’ clinical care, we will analyze the presence and expression of genes harboring motif neoepitopes. We will evaluate baseline tumor biopsies from 75 early stage patients with an HLA-B44 allele who receive neoadjuvant chemotherapy plus PD-1 inhibition, correlating motif neoepitopes with pathologic complete response. Among 75 advanced stage patients with an HLA-B44 allele who are receiving single agent PD-1 inhibition and 75 additional patients being treated with chemotherapy plus PD-1 inhibition, we will correlate motif neoepitopes with progression of disease within 6 months of initiation of therapy. Together, these studies will provide a better understanding of the TME and other immunologic changes associated with the presence of motif neoepitopes. In addition, results could enable us to identify patients in whom evaluation of this marker of neoantigen presentation could be utilized to select patients with clinically relevant benefit in three separate clinical scenarios utilizing PD-1 inhibitor-based therapy. As a corollary, results could also identify populations of patients in whom other treatment strategies should be considered.