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

项目总结 针对PD-1途径的免疫检查点抑制物(ICIS)已经改变了许多 晚期癌症，包括肾细胞癌(RCC)，但大多数患者不会从 这些治疗。尽管了解ICI在其他肿瘤类型中的反应和耐药性的许多努力 通常侧重于研究总突变负荷(以及由此产生的新抗原负荷)或总T细胞的作用 在肿瘤微环境(即“热”与“冷”的肿瘤)中，肾细胞癌在生物学上与其他肿瘤不同。 免疫原性实体瘤。与其他实体肿瘤相比，总的突变负担与 RCC对ICI的反应。此外，尽管肾细胞癌的肿瘤突变负荷相对较小，但它是 CD8+T细胞浸润率最高的实体瘤，但CD8+T细胞浸润度 肿瘤免疫微环境(TME)与ICI反应无关。这些观察结果突显了 我们对体细胞变化和渗入的免疫细胞成分、表型状态和 在ICI的背景下，细胞间的相互作用介导了对RCC的有效免疫反应。因此，有 迫切需要更好地了解对当前ICI的反应和耐药的疾病特异性机制- 肾癌的基础治疗，这也可能揭示适度突变如何加重肿瘤负担的一般原理 就像肾细胞癌一样具有免疫原性。先前在肾癌中进行的较小规模的分析确定了肿瘤固有的躯体改变 影响肾细胞癌的ICI反应，以及共生和相互作用的免疫群体(最终耗尽) CD8+T细胞和免疫抑制巨噬细胞)，在晚期疾病中富含。因此，我们 假设体细胞变化和TME相互作用来解释RCC和TME独特的免疫格局 调制对ICI的反应。通过利用我们在免疫基因组分析方面的专业知识和我们的密切合作 与学术界和业界的合作伙伴一起，我们现在正准备独一无二地解决这一假设。在目标1中，我们寻求 系统地定义影响免疫渗透和治疗的复发性躯体改变 通过询问大规模基因组数据(整个外显子组测序和批量RNA- 从2,800多个肾细胞癌肿瘤(包括1,500多个接受ICI治疗的肾细胞癌肿瘤)进行基因测序。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 96例肾癌治疗前标本(包括75例肿瘤)的大规模单细胞转录分析 随后用ICI治疗)。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 方法并通过使用体外患者来源的肿瘤碎片模型进行功能询问。总的来说， 这项工作将确定有效的ICI介导的肾癌抗肿瘤免疫的遗传和免疫决定因素， 并将提名TME中特定的治疗靶向免疫抑制相互作用用于临床 肾细胞癌(以及其他可能的低和中等突变负担的肿瘤)患者的翻译。

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).