Project 2

项目2总结 免疫检查点抑制物(ICI)辅助治疗-包括ipilimumab(IPI；靶向细胞毒性T淋巴细胞- 抗原4)和nivolumab(Nivo；靶标程序死亡蛋白1)-增加患者的无复发生存率(RFS) 黑色素瘤患者。尽管如此，35-40%的患者在完成ICI后24个月内复发 治疗，没有生物标志物--无论是单独的还是共同的--可以预测ICI治疗后的RFS，并有可能确定 更有效的辅助治疗的新靶点。识别ICI疗效的生物标记物的努力集中在 主要取决于转移环境中的肿瘤微环境，留下佐剂ICI的假定生物标记物 治疗方法在很大程度上是未经探索的。由于抗肿瘤T细胞免疫是ICI的首要目标，因此焦点 以肿瘤T细胞浸润为主。在这里，我们提出了一种新的假设，即 影响宿主免疫的遗传因素影响佐剂ICI后的RFS。事实证明， T细胞亚群，包括CD8+T细胞的表型变异可归因于生殖系遗传变异。在……里面 最近的一项研究表明，这种遗传成分映射到非编码的调控基因组，影响 T细胞分化和功能的转录调控。基于这些数据，我们假设生殖系 T细胞特异性非编码调控基因组(Regulome)的遗传变异控制着循环中的CD4+和 CD8+T细胞(Nivo和Nivo+IPI ICI的主要靶点)，这种遗传变异与 ICI治疗后RFS。我们建议发现CD4+和CD8+T细胞调节体的遗传特征 可以预测ICI复发和RFS。使用600名接受辅助临床试验治疗的黑色素瘤患者的样本 与Nivo+IPI相比，我们将进行全基因组(WGS)和全转录组测序 ICI治疗前外周血中CD_4~+和CD_8~+T细胞分析 预测佐剂ICI后RFS的转录组特征(目标1)。我们还将全面评估开放 相同600例患者治疗前CD4+和CD8+T细胞染色质状态以确定表观遗传学 受遗传遗传变异控制的特征，并预测佐剂ICI后的RFs(目标2)，并整合 这些数据与项目1(目标3)中的微生物组、免疫表型和血清组学特征有关。我们的预赛 数据显示，非编码调节组中的新基因组印记可以预测ICI的反应，具有很高的临床意义 准确性，从而在很大程度上支持我们的假设和研究设计。我们将第一次阐明 遗传抗肿瘤宿主免疫对佐剂环境下ICI结果的影响。除了具有适用性外， 对于ICI收益的个性化预测，来自该项目所有三个目标的基因组信息的集成 有望揭示潜在影响ICI抵抗的新的T细胞特异性转录网络，并可能 作为黑色素瘤和其他癌症改进的ICI辅助疗法的靶点。

PROJECT 2 SUMMARY Immune checkpoint inhibitor (ICI) adjuvant therapies—including ipilimumab (IPI; targets cytotoxic T lymphocyte- antigen 4) and nivolumab (NIVO; targets programmed death protein 1)—increase relapse-free survival (RFS) in melanoma patients. Nonetheless, 35–40% of these patients relapse within 24 months after completing ICI therapy, and no biomarkers—either alone or together—can predict RFS after ICI therapy and potentially identify novel targets for more effective adjuvant treatments. Efforts to identify biomarkers of ICI efficacy have centered mainly on the tumor microenvironment in the metastatic setting, leaving putative biomarkers of adjuvant ICI treatments largely unexplored. Because anti-tumor T-cell immunity is the primary target of ICI, the focus has been predominantly on tumor T-cell infiltration. Here we propose the novel hypothesis that underlying inherited factors that influence host immunity impact RFS after adjuvant ICI. It has been demonstrated that phenotypic variation in T-cell subsets, including CD8+ T cells, can be attributed to germline genetic variation. In a recent study, we showed that this inherited component maps to the non-coding regulatory genome, impacting transcriptional regulation of T-cell differentiation and function. Based on these data, we hypothesize that germline genetic variation in the T-cell-specific non-coding regulatory genome (regulome) controls circulating CD4+ and CD8+ T cells (the primary targets of NIVO and NIVO+IPI ICI), and that this genetic variability is associated with RFS after ICI treatment. We propose to discover inherited signatures of the CD4+- and CD8+- T-cell regulome that predict ICI relapse and RFS. Using samples from 600 melanoma patients treated in an adjuvant clinical trial of NIVO compared to NIVO+IPI, we will perform whole-genome (WGS) and whole-transcriptome sequence analyses of CD4+ and CD8+ T cells from peripheral blood collected before ICI treatment to identify non-coding transcriptome signatures that predict RFS after adjuvant ICI (Aim 1). We will also comprehensively assess open chromatin states in pre-treatment CD4+ and CD8+ T cells from the same 600 patients to identify epigenetic signatures controlled by inherited genetic variation, and predict RFS after adjuvant ICI (Aim 2), and integrate these data with microbiome, immuno-phenotyping, and seromics profiles from Project 1 (Aim 3). Our preliminary data have revealed novel genomic imprints in the non-coding regulome that predict ICI response with high clinical accuracy, thus substantially supporting our hypotheses and study design. For the first time, we will elucidate the effect of inherited anti-tumor host immunity on ICI outcomes in the adjuvant setting. Besides having applicability to personalized prediction of ICI benefit, the integration of genomic information from all three aims of this project promises to reveal novel T-cell-specific transcriptional networks that potentially affect ICI resistance and might serve as targets for improved adjuvant ICI therapies in melanoma and other cancers.