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

• 批准号: 10183206
• 负责人: Joseph F Costello
• 金额: $ 57.16万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 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/10183206
• 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

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 我们发现，这一事件具有重大临床意义，最终导致大多数 LGG 患者死亡。 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。 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 免疫抑制的微环境，特别是在接受治疗引起的 LGG 期间。 超突变（HM）是 MT 的另一种途径，总体上在恶性细胞中产生更多高质量的新抗原。 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 在此基础上增加参与细胞毒性 T 细胞吸引和效应功能的基因表达。 根据数据，我们发现 IDH 突变体 LGG 的免疫抑制在 MT 后减少，这是由遗传驱动的 主要是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）。 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 个恶性肿瘤。 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 我们将使用高灵敏度 T 细胞谱分析、细胞计数法来检测匹配的初始 IDH1 突变体 LGG。 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 在目标 2 中，我们将确定 MT 期间获得的基因改变如何影响突变体。 我们将对 IDH1 介导的免疫抑制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 的局部影响。 相关的遗传改变，包括超突变肿瘤中的高质量新抗原、缺失 突变 IDH1 等位基因或其他遗传事件对免疫抑制的影响。 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 然后我们将测试克隆的 TCR 的相对靶点特异性和针对新抗原的活性。 肿瘤大范围内的阳性患者特异性肿瘤细胞的 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。