Tumor and immune determinants of effective anti-tumor immunity in renal cell carcinoma

项目摘要 靶向PD-1通路的免疫检查点抑制剂（ICI）已经改变了许多疾病的管理， 晚期癌症，包括肾细胞癌（RCC），但大多数患者不能从 这些治疗。尽管许多努力了解ICI反应和其他肿瘤类型的耐药性， 通常侧重于研究总突变负荷（以及随之而来的新抗原负荷）或总T细胞 由于RCC在肿瘤微环境中的浸润（即“热”肿瘤对“冷”肿瘤），RCC在生物学上不同于其他肿瘤。 免疫原性实体瘤。与其他实体瘤相比，总突变负荷与 对RCC中ICI的反应。此外，尽管其相对适度的肿瘤突变负荷，RCC脱颖而出，作为一个 基线时CD 8 + T细胞浸润最高的实体瘤，但CD 8 + T细胞浸润到 肿瘤免疫微环境（TME）与ICI反应无关。这些观察突出了 我们对体细胞改变和浸润性免疫细胞组成、表型状态和 在ICI的背景下介导针对RCC的有效免疫应答的细胞相互作用。因此， 迫切需要更好地了解对当前ICI的反应和抗性的疾病特异性机制- 这也可能揭示适度的突变负荷肿瘤的一般原理， 像肾细胞癌是免疫原性的。先前在RCC中的小规模分析确定了肿瘤内在的体细胞改变 影响RCC中ICI反应的免疫细胞，以及共同发生和相互作用的免疫群体（终末耗竭 CD 8 + T细胞和免疫抑制性巨噬细胞）在晚期疾病中富集。因此我们 假设体细胞改变和TME相互作用来解释RCC独特的免疫景观， 调节对ICI的反应。通过利用我们在免疫基因组学分析方面的专业知识和我们的密切合作， 与学术界和业界的伙伴合作，我们现在已准备好解决这一假设。在目标1中，我们寻求 系统地定义影响免疫浸润和治疗的复发性体细胞改变， 通过询问大规模基因组数据（全外显子组测序和批量RNA- 测序）从超过2，800个RCC肿瘤（包括超过1，500个用ICI治疗的RCC肿瘤）中获得。在目标2中，我们努力 揭示TME内的细胞组成和细胞相互作用，通过以下途径介导对ICI的反应： 对96例治疗前RCC肿瘤标本（包括75例肿瘤）进行大规模单细胞转录组学分析 随后用ICI处理）。我们的目标是使用先进的空间表型来验证推断的相互作用 方法和通过使用离体患者来源的肿瘤碎片模型的功能询问。总体而言， 这项工作将鉴定RCC中有效ICI介导的抗肿瘤免疫的遗传和免疫决定因素， 并将在TME中指定用于临床的特异性治疗靶向免疫抑制相互作用， 对于RCC患者（以及潜在的其他低和中等突变负荷肿瘤）的翻译。

PROJECT SUMMARY Immune checkpoint inhibitors (ICIs) targeting the PD-1 pathway have transformed the management of many advanced cancers, including renal cell carcinoma (RCC), but most patients do not receive durable benefit from these treatments. Whereas many efforts to understand ICI response and resistance in other tumor types have often focused on investigating the role of total mutation burden (and consequent neoantigen load) or total T cell infiltration in the tumor microenvironment (i.e. “hot” vs. “cold” tumors), RCC is biologically distinct from other immunogenic solid tumors. In contrast to other solid tumors, the total mutation burden does not correlate with response to ICI in RCC. Further, despite its relatively modest tumor mutational load, RCC stands out as one of the most highly CD8+ T cell-infiltrated solid tumors at baseline, but the degree of CD8+ T cell infiltration into the tumor-immune microenvironment (TME) does not associate with ICI response. These observations highlight the gaps in our knowledge of the somatic alterations and infiltrating immune cell composition, phenotypic states, and cellular interactions that mediate an effective immune response against RCC in the context of ICI. Thus, there is a critical need to better understand the disease-specific mechanisms of response and resistance to current ICI- based therapies in RCC, which may also uncover the general principles of how a modest mutation burden tumor like RCC can be immunogenic. Prior smaller-scale analyses in RCC identified tumor-intrinsic somatic alterations that impact ICI response in RCC, and co-occurring and interacting immune populations (terminally exhausted CD8+ T cells and immunosuppressive macrophages) that are enriched in advanced disease. We therefore hypothesize that somatic alterations and the TME interact to explain the unique immune landscape of RCC and modulate response to ICI. By leveraging our expertise in immunogenomic analysis and our close collaborations with academic and industry partners, we are now uniquely poised to address this hypothesis. In Aim 1, we seek to systematically define the recurrent somatic alterations that impact immune infiltration and therapeutic response through the interrogation of large-scale genomic data (whole exome sequencing and bulk RNA- sequencing) from over 2,800 RCC tumors (including over 1,500 RCC tumors treated with ICI). In Aim 2, we strive to uncover the cell composition and cellular interactions within the TME that mediate response to ICI through large-scale single-cell transcriptomic analysis of 96 pre-treatment RCC tumor specimens (including 75 tumors subsequently treated with ICI). We aim to validate inferred interactions using advanced spatial phenotyping methods and through functional interrogation using an ex vivo patient-derived tumor fragment model. Overall, this work will identify genetic and immune determinants of effective ICI-mediated anti-tumor immunity in RCC, and will nominate specific therapeutically targetable immune inhibitory interactions in the TME for clinical translation for patients with RCC (and potentially other low and intermediate mutation burden tumors).