Project 2

项目2概要 免疫检查点抑制剂（ICI）辅助治疗-包括伊匹单抗（IPI;靶向细胞毒性T淋巴细胞- 抗原4）和纳武单抗（NIVO;目标程序性死亡蛋白1）-增加无复发生存期（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 没有生物标志物-单独或一起-可以预测ICI治疗后的RFS，并可能识别 更有效的辅助治疗的新靶点。确定ICI疗效生物标志物的努力集中在 主要是转移性环境中的肿瘤微环境，留下辅助ICI的推定生物标志物 治疗方法基本上未被探索。由于抗肿瘤T细胞免疫是ICI的主要靶点，因此重点是 主要是肿瘤T细胞浸润。在这里，我们提出了一个新的假设， 影响宿主免疫力的遗传因素影响佐剂ICI后的RFS。已经证明 T细胞亚群（包括CD 8 + T细胞）的表型变异可归因于种系遗传变异。在 在最近的一项研究中，我们发现这种遗传成分映射到非编码调控基因组， T细胞分化和功能的转录调节。基于这些数据，我们假设生殖细胞 T细胞特异性非编码调节基因组（调节基因组）中的遗传变异控制循环CD 4+， CD 8 + T细胞（NIVO和NIVO+IPI ICI的主要靶点），并且这种遗传变异性与 ICI治疗后RFS。我们建议发现CD 4+和CD 8 + T细胞调节组的遗传特征 预测ICI复发和RFS。使用来自600名在辅助临床试验中接受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， 分析ICI治疗前收集的外周血中的CD 4+和CD 8 + T细胞，以鉴定非编码 转录组特征预测佐剂ICI后RFS（Aim 1）。我们还将全面评估开放 来自相同600名患者的治疗前CD 4+和CD 8 + T细胞的染色质状态，以确定表观遗传 由遗传变异控制的特征，并预测佐剂ICI后的RFS（目标2），并整合 这些数据与来自项目1（Aim 3）的微生物组、免疫表型和血清组学图谱相结合。我们的初步 数据揭示了非编码调节组中的新基因组印记，其预测具有高临床意义的ICI反应。 准确性，从而充分支持我们的假设和研究设计。我们将首次阐明 在佐剂环境中，遗传性抗肿瘤宿主免疫对ICI结果的影响。除了具有适用性 个性化预测ICI的好处，整合基因组信息，从所有三个目标的这个项目 有望揭示新的T细胞特异性转录网络，可能影响ICI抗性， 作为改善黑色素瘤和其他癌症辅助ICI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.