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3-D spatial approach to discover genomic effectors of immunosuppression during malignant transformation

3-D 空间方法发现恶性转化过程中免疫抑制的基因组效应器

基本信息

批准号：
10651651
负责人：
Joseph F Costello
金额：
$ 56.02万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-07-01 至 2025-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10651651
关键词：
3-Dimensional Address Adrenal Cortex Hormones Affect Alleles Amino Acid Sequence Anatomy Biological Assay Brain Neoplasms CD8-Positive T-Lymphocytes Cells Cellular immunotherapy Cessation of life Clinical Clonality Clone Cells Collaborations Combination immunotherapy Cytometry Cytotoxic T-Lymphocytes DNA Sequence Alteration Data Elements Environment Event Evolution Expression Profiling Failure Gene Expression Genetic Genomics Glioma Goals Immune Immune system Immunogenomics Immunohistochemistry Immunologic Factors Immunologics Immunosuppression Immunotherapy Individual Knowledge Location Loss of Heterozygosity Malignant - descriptor Maps Mediating Mutation Newly Diagnosed Other Genetics Patients Production Publishing Recurrence Recurrent tumor Role Route STAT1 gene Sampling Source Specificity T cell infiltration T cell therapy T-Cell Receptor T-Lymphocyte Testing Therapeutic Time Validation alpha-beta T-Cell Receptor antigen-specific T cells cancer genome cell type chemokine clinically significant cohort design exome sequencing experimental study fitness genetic effector immune cell infiltrate immunosuppressed improved mutant neoantigens neoplastic cell novel personalized medicine prevent synergism targeted agent targeted treatment transcriptome sequencing tumor tumor heterogeneity tumor-immune system interactions

项目摘要

PROJECT SUMMARY/ABSTRACT Malignant transformation (MT) of IDH-mutant low grade glioma (LGG) to aggressive high grade tumors is an event of major clinical significance, eventually leading to death in the majority of LGG patients. We discovered that mutations in IDH promote an immunosuppressed microenvironment characterized by decreased production of STAT1-regulated chemokines and low CD8+ T cell infiltration in LGG. In malignantly transformed tumors, we identified the unexpected deletion of the IDH1 mutant allele that may drive counteracting changes to the immunosuppressed microenvironment specifically during MT. LGG that undergo treatment-induced hypermutation (HM), another route to MT, produce more high quality neoantigens. Overall in malignantly transformed tumors relative to patient-matched LGG, we found increasing numbers of T cell clones and increasing expression of genes involved in cytotoxic T cell attraction and effector function. Based on these data, we hypothesize that immunosuppression in IDH mutant LGG is reduced upon MT, driven by genetic alterations that are acquired primarily during malignant transformation. To address this hypothesis, we will quantify spatial and temporal changes in mutant IDH1-driven immunosuppression during MT (Aim 1). We have devised a novel 3-dimensional (3-D), tumor-wide approach in which we will acquire 10 spatially mapped samples per tumor representing maximal anatomy of the tumor. The full cohort will include 30 malignantly tranformed and 30 non-malignantly transformed recurrences from patients for which we have banked samples of the matching initial IDH1-mutant LGG. We will use a high-sensitivity T cell repertoire assay, cytometry by Time of Flight (CyTOF), RNAseq based deconvolution, and multiplex immunohistochemistry to map the immunologic landscape in 3-D, and determine the extent to which mutant IDH1-mediated immunosuppression is reduced during MT. In Aim 2, we will determine how genetic alterations acquired during MT affect mutant IDH1-mediated immunosuppression. We will perform deep whole exome sequencing on samples collected in Aim 1 to map the intratumoral genomic landscape in 3-D during MT. We will test for the local influence of MT- associated genetic alterations, including high quality neoantigens in hypermutated tumors, deletion of the mutant IDH1 allele, or other genetic events on immunosuppression. Understanding which genetic events contribute to changes in immunosuppression is critical for selecting targeted therapies that could synergize with immunotherapies to prevent or delay MT. To begin to develop T cell based therapies, we will capture neoepitope-specific T cells, prioritizing those that are present tumor-wide, and determine the neoepitopes/HLAs they target and the amino acid sequences for corresponding T Cell Receptor (TCR) α- and β-chains. We will then test the cloned TCR for relative target specificity and activity against neoantigen- positive patient-specific tumor cells. The 3-D immuno-genomic landscapes across wide swaths of the tumor will be essential to the design of personalized therapies that have activity against the whole tumor.

项目概要/摘要 IDH 突变的低级别胶质瘤 (LGG) 向侵袭性高级别肿瘤的恶性转化 (MT) 是一种具有重大临床意义的事件，最终导致大多数 LGG 患者死亡。我们发现 IDH 突变会促进免疫抑制的微环境，其特征是免疫抑制减少 LGG 中 STAT1 调节的趋化因子的产生和低 CD8+ T 细胞浸润。恶变中在肿瘤中，我们发现了 IDH1 突变等位基因的意外删除，这可能会导致抵消变化尤其是在 MT 期间的免疫抑制微环境。 LGG 接受治疗诱导超突变 (HM) 是 MT 的另一种途径，可产生更多高质量的新抗原。总体呈恶性相对于患者匹配的 LGG，转化的肿瘤，我们发现 T 细胞克隆数量不断增加，并且增加参与细胞毒性 T 细胞吸引和效应功能的基因表达。基于这些根据数据，我们假设 IDH 突变体 LGG 的免疫抑制在 MT 后减少，这是由遗传驱动的主要在恶性转化过程中获得的改变。为了解决这个假设，我们将量化 MT 期间突变 IDH1 驱动的免疫抑制的空间和时间变化（目标 1）。我们有设计了一种新颖的 3 维（3-D）肿瘤范围方法，我们将获得 10 个空间映射每个肿瘤的样本代表肿瘤的最大解剖结构。整个队列将包括 30 名恶性来自我们已储存样本的患者的转化和 30 例非恶性转化复发匹配的初始 IDH1 突变体 LGG。我们将使用高灵敏度 T 细胞谱分析、细胞计数法飞行时间 (CyTOF)、基于 RNAseq 的解卷积和多重免疫组织化学来绘制 3-D 免疫学景观，并确定突变 IDH1 介导的免疫抑制的程度 MT 期间减少。在目标 2 中，我们将确定 MT 期间获得的遗传改变如何影响突变体 IDH1 介导的免疫抑制。我们将对收集的样本进行深度全外显子组测序目标 1 在 MT 期间绘制 3D 肿瘤内基因组图谱。我们将测试MT的本地影响力- 相关的遗传改变，包括超突变肿瘤中的高质量新抗原、缺失 IDH1 等位基因突变，或其他影响免疫抑制的遗传事件。了解哪些遗传事件促进免疫抑制的变化对于选择可以协同作用的靶向疗法至关重要使用免疫疗法来预防或延迟 MT。为了开始开发基于 T 细胞的疗法，我们将捕获新表位特异性 T 细胞，优先考虑肿瘤范围内存在的 T 细胞，并确定它们针对的新表位/HLA 以及相应 T 细胞受体 (TCR) α- 和的氨基酸序列 β-链。然后，我们将测试克隆的 TCR 的相对靶标特异性和针对新抗原的活性。阳性患者特异性肿瘤细胞。肿瘤大范围的 3D 免疫基因组景观对于设计针对整个肿瘤具有活性的个性化疗法至关重要。