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子

基本信息

批准号：
10066668
负责人：
Joseph F Costello
金额：
$ 46.64万
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/10066668
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 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 Infiltration Knowledge Location Loss of Heterozygosity Malignant - descriptor Maps Mediating Mutation Newly Diagnosed Non-Malignant Other Genetics Patients Production Publishing Recurrence Recurrent tumor Role Route STAT1 gene Sampling Source Specificity T cell therapy T-Cell Receptor T-Lymphocyte Testing Therapeutic Time Tumor-infiltrating immune cells Validation antigen-specific T cells base cancer genome cell type chemokine clinically significant cohort design exome sequencing experimental study fitness genetic effector immunosuppressed improved mutant neoantigens neoplastic cell novel personalized medicine prevent 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.

项目摘要/摘要 IDH-突变剂低级神经胶质瘤（LGG）对侵略性高级肿瘤的恶性转化（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。我们发现了 IDH中的突变促进了以改进为特征的免疫抑制的微环境 LGG中STAT1调节的趋化因子和低CD8+ T细胞浸润的产生。在恶性转变中肿瘤，我们确定了IDH1突变等位基因的意外删除，可能会驱动抵抗变化在MT期间专门针对免疫抑制的微环境。接受治疗引起的LGG MT的另一条途径超代（HM）产生更多高质量的新抗原。总体上是恶性的相对于患者匹配的LGG进行了转化的肿瘤，我们发现T细胞克隆数量越来越多增加了参与细胞毒性T细胞吸引和效应子功能的基因表达。基于这些数据，我们假设IDH突变体LGG中的免疫抑制在MT时降低，遗传驱动在恶性转化期间获得的主要变化。为了解决这一假设，我们将量化MT期间突变体IDH1驱动的免疫抑制的空间和临时变化（AIM 1）。我们有设计了一种新型的三维（3-D），肿瘤范围的方法，我们将在空间上获取10个每个肿瘤的样品代表肿瘤的最大解剖结构。完整的队列将包括30个恶性转化的和30个非政治转换的回报，我们已经为此提供了样本的患者匹配的初始IDH1突变lgg。我们将使用高敏性T细胞库分析，细胞仪飞行时间（cytof），基于RNASEQ的反卷积和多重免疫组织化学来绘制 3-D中的免疫学景观，并确定突变体IDH1介导的免疫抑制的程度在MT期间减少。在AIM 2中，我们将确定在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。我们将对收集的样品进行深度整个外显子组测序目标1在MT期间绘制3-D中的肿瘤内基因组景观。我们将测试MT-的局部影响相关的遗传改变，包括高质量肿瘤中的高质量新抗原，缺失突变的IDH1等位基因，或其他有关免疫抑制的遗传事件。了解哪些遗传事件有助于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采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 NeoEpitope特异性T细胞，优先考虑肿瘤范围内的T细胞，并确定它们靶向的Neoeppitopes/HLA和相应的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的相对目标特异性和针对新抗原的活性患者特异性肿瘤细胞阳性。在肿瘤的宽壁板上的3-D免疫基因组景观对于针对整个肿瘤活动的个性化疗法的设计至关重要。