Malignant Cell Engagement in Immune Circuits of Human Microsatellite-stable and Microsatellite-instable Colorectal Cancer

恶性细胞参与人类微卫星稳定和微卫星不稳定结直肠癌的免疫回路

基本信息

批准号：
10490347
负责人：
Karin Pelka
金额：
$ 24.9万
依托单位：
J. DAVID GLADSTONE INSTITUTES
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-04-08 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10490347
关键词：
Acute Address Aftercare Antitumor Response Automobile Driving BRAF gene Beds Biological Markers Biological Models CXCL13 gene Cancer Etiology Cancer Patient Cell Communication Cell Death Cell Line Cells Cessation of life Chronic Clinic Coculture Techniques Colorectal Cancer Communication Complex Conflict (Psychology)Data Development Environment Epigenetic Process Failure Foundations Gene Expression Genes Genetic Transcription Human Immune Immune Targeting Immune response Immune system Immunologics Immunotherapeutic agent Immunotherapy Impairment Interferons Knock-out Knowledge Malignant - descriptor Maps Measures Mediating Microsatellite Repeats Mission Modeling Myelogenous Myeloid Cells Neoplasm Transplantation Organoids Outcome Patients Pattern recognition receptor Peptides Phase Proteomics Public Health Research Resistance Rest Solid Neoplasm Specimen Stains Stimulus Stromal Cells T cell response T-Cell Proliferation T-Lymphocyte Technology Testing Therapeutic Time Tumor Immunity United States Work anti-PD-1 antigen-specific T cells base cancer cell career cell killing cohort colon cancer patients design epigenetic memory epigenetic therapy epigenomics exposed human population flexibility gene induction genetic signature in vitro testing in vivo inhibitor insight metastatic colorectal mutant nano-string neoplastic cell novel novel therapeutic intervention overexpression patient subsets pressure programs response single-cell RNA sequencing spatiotemporal targeted treatment therapy resistant transcriptome transcriptomics treatment response tumor tumor immunology

项目摘要

Project Summary An important question in cancer immunology is how malignant cells and T cells communicate and impact the efficacy of anti-tumor immunity. To generate hypotheses for how these cells interact, we have applied single cell RNA sequencing to profile the transcriptomes of >700,000 malignant, immune, and stromal cells in 2 cohorts: (1) 65 patients with two types of primary untreated CRC (31 MSS and 34 MSI tumors) which are characterized by vastly different immunotherapy response rates; (2) pre- and post-treatment specimens from 20 BRAF-mutant metastatic CRC patients treated with BRAFi/MEKi/anti-PD1. These data led us to formulate the central hypothesis for this proposal: malignant cells that express interferon-stimulated genes (ISGs) acutely promote anti-tumor immunity, while chronic interferon responses in malignant cells impair anti-tumor immunity and therapeutic responses. The proposed work is anticipated to reveal fundamental insights into human tumor immunology and provide a novel perspective for the design of robust biomarkers and new therapeutic strategies. We will address three major questions. First, is the MSI/responder-associated ISG program in malignant cells part of an intra-tumoral feed-forward loop that is driving anti-tumor immunity? This will be answered by spatially mapping the intratumoral cellular interaction network between ISG+ malignant cells and T cells in untreated primary CRC specimens, and in post-treatment specimens of patients treated with BRAFi/MEKi/anti-PD-1, which will reveal association of this spatial network with tumor regression. Second, what are the drivers of malignant ISGs in human CRC, and can interferons impact immune responses and responses to targeted therapy by epigenetically reprogramming human CRC cells? To address this, we will use interferons and innate immune stimuli to induce ISGs in CRC organoids, map the transcriptional and epigenetic signatures to the signatures found in freshly isolated CRC cells, and nominate ISG-inducing upstream regulators. IFN-stimulated and subsequently rested organoids will be assessed for epigenetic memory and for modulated secondary immune and drug responses. Third, how do pre-existing ISG signatures in malignant cells impact CTL-mediated anti-tumor responses? Using peptide-cognate T cell lines, we will test the in vitro killing of ISG+ and ISG- peptide-loaded CRC organoids. We will furthermore test how ISGs modulate in vivo tumor killing by temporally controlling malignant ISG expression in transplantable tumor models. In summary, we use scRNAseq to predict malignant cell – T cell interactions, and then test these hypotheses with cutting-edge technologies such as spatial profiling, single cell epigenomics, and human organoid T cell co-cultures. The results should elucidate how malignant cells that respond to interferons impact anti-tumor immunity and resistance, generate foundational results and model systems for an R01 proposal, and prepare the candidate for an independent career to study the cellular networks that drive human tumor immunity.

项目概要癌症免疫学中的一个重要问题是恶性细胞和 T 细胞如何沟通并影响为了产生这些细胞如何相互作用的假设，我们应用了单一的方法。细胞 RNA 测序可分析 2 年内超过 700,000 个恶性细胞、免疫细胞和基质细胞的转录组队列：(1) 65 名患有两种类型原发性未经治疗的 CRC 患者（31 例 MSS 和 34 例 MSI 肿瘤），其中其特点是免疫治疗反应率差异很大；（2）治疗前和治疗后的样本 20 名 BRAF 突变的转移性 CRC 患者接受了 BRAFi/MEKi/抗 PD1 治疗。这些数据使我们制定了以下方案。该提案的中心假设：急性表达干扰素刺激基因（ISG）的恶性细胞促进抗肿瘤免疫，而恶性细胞中的慢性干扰素反应会损害抗肿瘤免疫和治疗反应预计将揭示对人类肿瘤的基本见解。免疫学，为强大的生物标志物和新疗法的设计提供了新的视角我们将解决三个主要问题，即 MSI/响应者相关的 ISG 计划。恶性细胞是驱动抗肿瘤免疫的肿瘤内前馈循环的一部分？通过空间映射 ISG+ 恶性细胞和未经治疗的原发性 CRC 标本以及接受过治疗的患者的治疗后标本中的 T 细胞 BRAFi/MEKi/抗 PD-1，这将揭示该空间网络与肿瘤消退的关联。人类结直肠癌中恶性 ISG 的驱动因素是什么？干扰素是否会影响免疫反应和通过表观遗传重编程人类结直肠癌细胞对靶向治疗有何反应？为了解决这个问题，我们将使用干扰素和先天免疫刺激在 CRC 类器官中诱导 ISG，绘制转录和表观遗传特征与新鲜分离的 CRC 细胞中发现的特征相一致，并指定 ISG 诱导将评估 IFN 刺激和随后休息的类器官的表观遗传。第三，预先存在的 ISG 特征如何发挥作用。我们将使用肽同源 T 细胞系来测试恶性细胞中 CTL 介导的抗肿瘤反应的影响？我们将进一步测试 ISG 如何体外杀死负载 ISG+ 和 ISG- 肽的 CRC 类器官。通过暂时控制可移植肿瘤中的恶性 ISG 表达来调节体内肿瘤杀伤总之，我们使用 scRNAseq 来预测恶性细胞 - T 细胞相互作用，然后测试这些模型。利用空间分析、单细胞表观基因组学和人类等尖端技术提出假设类器官 T 细胞共培养的结果应能阐明对干扰素作出反应的恶性细胞如何影响。抗肿瘤免疫和耐药性，为 R01 提案生成基础结果和模型系统，并为候选人做好独立职业的准备，研究驱动人类肿瘤的细胞网络免疫。