Childhood Cancer Data Initiative

儿童癌症数据倡议

• 批准号: 10926698
• 负责人: Carol J Thiele
• 金额: $ 344.48万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10926698
• 关键词: 3-Dimensional; ATAC-seq; Address; Adrenocortical carcinoma; Adult; Age; American Association of Cancer Research; Animal Experiments; Antigens; Archives; Area; Atlases; Bar Codes; Benign; Biological Assay; Biopsy; Brain Neoplasms; CAR T cell therapy; CCR; CD3 Antigens; Cancer Therapy Evaluation Program; Cell Nucleus; Cells; Child; Childhood; Childhood Brain Neoplasm; Childhood Solid Neoplasm; Clinical; Clinical Trials; Clinical/Radiologic; Combined Modality Therapy; Complex; Computing Methodologies; Core Facility; Data; Data Analyses; Data Set; Development; Disease Outcome; Disease remission; Effector Cell; Evaluation; Exclusion; Freezing; Funding; Future; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Generations; Genetic; Genetic Transcription; Genomics; Heterogeneity; High-Risk Cancer; Histologic; Histology; Human; Image; Immune; Immune response; Immunology; Immunophenotyping; Immunotherapeutic agent; Immunotherapy; Individual; Infrastructure; Intramural Research Program; Link; Lymphocyte; Malignant - descriptor; Malignant Childhood Neoplasm; Malignant Neoplasms; Manuscripts; Mediating; Medical; Metabolism; Metastatic Osteosarcoma; Modeling; Molecular; Morphology; NF1 gene; Natural History; Neoplasm Metastasis; Nerve; Nerve Sheath Tumors; Neuroblastoma; Newly Diagnosed; Operative Surgical Procedures; Pathology; Pathway interactions; Patient Outcomes Assessments; Patient advocacy; Patients; Pediatric Neoplasm; Pediatric Oncology; Phase; Population; Pre-Clinical Model; Precision therapeutics; Preclinical Testing; Predisposition; Preparation; Primary Brain Neoplasms; Process; Proteomics; Protocols documentation; Public Domains; Publishing; Relapse; Research; Research Personnel; Residual Neoplasm; Resistance; Sampling; Solid Neoplasm; Specimen; Survival Rate; T cell infiltration; T-Lymphocyte; Testing; Therapeutic; Therapeutic Trials; Tissues; Translating; Translational Research; Validation; Visualization software; Work; cell free DNA; chimeric antigen receptor T cells; complex data; computerized tools; cytokine; data integration; data modeling; data tools; data visualization; effectiveness evaluation; epigenetic profiling; epigenomics; experience; experimental study; extracellular vesicles; feasibility testing; gut microbiome; high risk; immune activation; immunoregulation; immunotherapy trials; improved; insight; meetings; metabolomics; mouse model; multiple omics; nano-string; neoplastic; neoplastic cell; novel; osteosarcoma; patient derived xenograft model; patient engagement; pediatric patients; pre-clinical; precision medicine; precision medicine clinical trials; preclinical development; prediction algorithm; premalignant; programs; protocol development; rare cancer; recruit; resistance mechanism; response; single cell analysis; single nucleus RNA-sequencing; transcriptome; transcriptomics; translational study; tumor; tumor heterogeneity; tumor microenvironment; tumor-immune system interactions; whole body imaging; young adult

The POB-CCDI supported 6 projects in FY23 Project 1. Single Cell Atlas of NF1 tumors from benign to malignant- PIs Shern, Widemann APIs Zhang Hypothesis- The malignant transformation of benign NF1-associated PN through precancerous AN to MPNST is demonstrated by the transcriptional diversity of the complex TME. Specific Aim: Characterize the intratumoral heterogeneity of NF1-associated nerve sheath tumors to elucidate the transcriptional diversity accompanying the malignant transformation. The objective of this aim is to characterize individual cell populations that comprise NF1 nerve tumors to identify different cellular states, transcriptional profiles, and relevant actionable targets using fresh surgical specimen. We aim to build a NF1 tumor single-cell atlas, which will be used to develop an algorithm for the prediction of NF1 tumor malignant transformation. Completed Work- scRNAseq and protocol development (Platform-10x Genomics single-cell gene expression) N = 51 captures from 24 fresh tumor specimens from NF1 patients on Widemann NF1 MyPART protocols Preliminary results were published in: Zhang, X., Gopalan, V., Syed, N., Hannenhalli, S., and Shern, J.F. (2023). STAR Protoc 4, 102297. Project 2. Comprehensive characterization of the Osteosarcoma tumor microenvironment (McEachron, Shern, Kaplan Osteosarcoma is a complex and heterogenous malignancy at both genomically and histologically. The 5-year survival rate for pediatric patients with metastatic osteosarcoma is 30% and this rate has not significantly improved since the early 1980's, justifying metastatic osteosarcoma as an unmet medical need. Molecular drivers of osteosarcoma show that osteosarcoma is a complex malignancy with profound inter-tumoral genomic heterogeneity and intra-tumoral transcriptional heterogeneity. Despite these studies, there is an overall lack of information pertaining to the microenvironment of metastatic osteosarcoma. Hypothesis: The interactions between tissue-specific resident stromal (immune and non-immune) cells and metastatic osteosarcoma cells creates distinguishable regional microenvironments with concordant spatially distinct immunoregulatory mechanisms. Specific Aims- Aim 1-Deconvolution of metastatic osteosarcoma specimens using single nuclei transcriptional and epigenetic profiling. The objective of this aim is to comprehensively characterize individual cell populations that comprise metastatic osteosarcoma to identify different cellular states, transcriptional profiles, and relevant actionable targets using archived fresh-frozen tissues. To the best of our knowledge, a single nuclei RNA-seq+ATAC-seq dataset pediatric metastatic osteosarcoma does not yet exist in the public domain. Completed Work: snRNAseq and snATACseq (Platform:10X Genomics snMulti-ome) N = 26 captures from frozen metastatic osteosarcoma specimens. Status- Data is currently under analysis Aim 2-Region-specific profiling of T-cells identify transcriptional programs associated with T-cell infiltration and/or exclusion in metastatic osteosarcoma specimens. The objective of this experiment is to determine the specific transcriptional programs that mediate T-cell in metastatic osteosarcoma and identify the underlying targetable pathways for downstream functional validation using syngeneic murine models. Targeting lymphocyte exclusion is an active area of research and this approach will provide a contextually relevant and dataset with translational significance. Completed Work-GeoMx Whole Transcriptome Assay (Platform: NanoString GeoMx) N = 5 metastatic osteosarcoma FFPE specimens o Differential ROI masking for CD3+ cells has been performed and data is under analysis with manuscript in preparation. Project 3. Resolving tumor heterogeneity and its contribution to CAR T cell resistance in Neuroblastoma, PIs Thiele, Nguyen High-risk neuroblastoma (NB) is a common pediatric cancer. Although most patients with newly diagnosed high-risk NB achieve remission after multi-modal therapy, more than 50% of these children experience late relapses caused by minimal residual disease (MRD) and succumb to their cancer. Several CAR T cell therapies are now being actively developed for patients with NB. This proposal focuses on resolving the molecular causes of CAR T cell resistance in NB to improve CAR T cell therapy for NB. Hypothesis: Tumor heterogeneity in neuroblastoma may contribute to CAR T cell resistance in NB solid tumors. The proposed research will be the first study to use preclinical models of NB PDX to understand clonal shifts in the context of CAR T therapy and evaluate heterogeneity in the context of a Phase I/II clinical CAR T cell trial. This will be accomplished by Specific Aim 1: Determine the clonal selection of NB after GPC2-CAR T cell therapy in Patient derived xenograft preclinical models of NB. Specific Aim 2: Evaluate NB patient biopsies after GPC2 CAR T cell immunotherapy trial, to assess tumor cell heterogeneity. Accomplishments; Developed a bar-coded NB PDX model and used scRNAseq to assess transcriptomes of NB tumor cells after GPC2 CAR T cell therapy. Preliminary animal experiment has been performed and scRNAseq from tumors before, during and after CAR T cell therapy has been performed and data are under analyses. Project 4. Creating a neoplastic and immune cell atlas of pediatric brain tumors through spatial transcriptomic analysis ( Nellan, Nguyen) Early results from CAR T cell trials in children with brain tumors demonstrate immune activation and transient radiologic and clinical improvement, but no lasting benefit.Thus, there is an immediate need for basic and translational studies to characterize and address potential resistance mechanisms. The limited response to CAR T cell therapy in patients is largely due to the immunosuppressive tumor microenvironment (TME) and heterogeneous antigen expression that exist in pediatric brain tumors. Hypothesis: It is proposed that the spatial transcriptomics of primary brain tumors will provide novel insights into the heterogeneity of cellular subpopulations and the interaction of neoplastic and immune populations within the TME. This characterization will provide preliminary data of the complex TME of pediatric brain tumors and identify potential resistance mechanisms of CAR T cell therapy under ongoing pre-clinical development. Study Objectives: 1. Generate a tumor / immune cell atlas of the highest-risk brain tumors of childhood to inform future preclinical immunotherapy testing. 2. Delineate the topographic distribution of immune cells in the tumor in relation to expressed antigens to understand which effector cells may be important for a therapeutic immune response. 3. Understand the relationship between antigen expression and clonal heterogeneity to derive markers that could predict susceptibility to CAR T cell therapy. Accomplishments to date: 18 captures using the Visium CytAssist Platform on FFTE and data is currently under analysis. Project 5, 6- Development of single cell analyses from patients on Rare tumor and POB tumors 90 samples have been processed. (Kaplan, Widemann). ScRNAseq analysis was performed on 9 Adrenocortical carcinoma specimens from patients ages(9-66yrs) has been performed and preliminary data presented at 2023 AACR meeting Sikder et al "Characterization of the adjacent tissues and metastatic microenvironment of adrenocortical carcinoma reveals profound molecular and cellular reprogramming with metastatic progression and disease outcome.".

POB-CCDI 在 FY23 项目中支持了 6 个项目 1. NF1 肿瘤从良性到恶性的单细胞图谱 - PIs Shern、Widemann APIs 张 假设 - 良性 NF1 相关 PN 通过癌前 AN 到 MPNST 的恶性转化是通过转录证明的复杂 TME 的多样性。具体目标：表征 NF1 相关神经鞘瘤的瘤内异质性，以阐明伴随恶性转化的转录多样性。该目标的目的是表征构成 NF1 神经肿瘤的单个细胞群，以使用新鲜的手术标本识别不同的细胞状态、转录谱和相关的可操作靶点。我们的目标是建立一个 NF1 肿瘤单细胞图谱，用于开发预测 NF1 肿瘤恶性转化的算法。已完成的工作 - scRNAseq 和方案开发（Platform-10x Genomics 单细胞基因表达） 根据 Widemann NF1 MyPART 方案从 NF1 患者的 24 个新鲜肿瘤标本中捕获 N = 51 初步结果发表于：Zhang, X.、Gopalan, V. ，Syed, N.、Hannenhalli, S. 和 Shern, J.F. (2023)。 STAR Protoc 4, 102297。项目 2. 骨肉瘤肿瘤微环境的综合表征（McEachron、Shern、Kaplan 骨肉瘤在基因组学和组织学上都是一种复杂且异质的恶性肿瘤。转移性骨肉瘤儿科患者的 5 年生存率为 30%自 20 世纪 80 年代初以来，这一比率并没有显着改善，这证明了转移性的合理性骨肉瘤作为未满足的医疗需求的分子驱动因素表明，骨肉瘤是一种复杂的恶性肿瘤，具有深刻的肿瘤间基因组异质性和肿瘤内转录异质性，尽管有这些研究，但总体上缺乏有关转移性骨肉瘤微环境的信息。假设：组织特异性驻留基质（免疫和非免疫）细胞和转移性骨肉瘤细胞之间的相互作用产生了可区分的特征。具有一致的空间上不同的免疫调节机制的区域微环境 - 目标 1 - 使用单核转录和表观遗传分析对转移性骨肉瘤标本进行解卷积。该目标的目的是全面表征包含转移性骨肉瘤的单个细胞群，以使用存档的新鲜冷冻组织识别不同的细胞状态、转录谱和相关的可操作靶标。据我们所知，公共领域尚不存在单核 RNA-seq+ATAC-seq 儿童转移性骨肉瘤数据集。已完成的工作：snRNAseq 和 snATACseq（平台：10X Genomics snMulti-ome）N = 26 个来自冷冻转移性骨肉瘤标本的捕获。状态 - 数据目前正在分析中 目标 2 - T 细胞的区域特异性分析可识别与转移性骨肉瘤标本中 T 细胞浸润和/或排除相关的转录程序。本实验的目的是确定介导转移性骨肉瘤中 T 细胞的特定转录程序，并确定使用同基因小鼠模型进行下游功能验证的潜在可靶向途径。靶向淋巴细胞排除是一个活跃的研究领域，这种方法将提供上下文相关且具有转化意义的数据集。已完成工作-GeoMx 全转录组测定（平台：NanoString GeoMx） N = 5 个转移性骨肉瘤 FFPE 标本 o 已对 CD3+ 细胞进行差异 ROI 掩蔽，数据正在与准备中的手稿一起分析。项目 3. 解决神经母细胞瘤中的肿瘤异质性及其对 CAR T 细胞耐药性的贡献，PIs Thiele, Nguyen 高危神经母细胞瘤 (NB) 是一种常见的儿科癌症。尽管大多数新诊断的高危 NB 患者在多模式治疗后获得缓解，但其中超过 50% 的儿童会因微小残留病 (MRD) 导致晚期复发并死于癌症。目前正在积极开发针对 NB 患者的几种 CAR T 细胞疗法。该提案重点解决NB中CAR T细胞耐药的分子原因，以改善NB的CAR T细胞治疗。假设：神经母细胞瘤中的肿瘤异质性可能导致 NB 实体瘤中的 CAR T 细胞耐药。拟议的研究将是第一项使用 NB PDX 临床前模型来了解 CAR T 治疗背景下的克隆转变并评估 I/II 期临床 CAR T 细胞试验背景下的异质性的研究。这将通过具体目标 1 来实现：在患者衍生的 NB 异种移植临床前模型中确定 GPC2-CAR T 细胞治疗后 NB 的克隆选择。具体目标 2：在 GPC2 CAR T 细胞免疫治疗试验后评估 NB 患者活检，以评估肿瘤细胞异质性。成就；开发了条形码 NB PDX 模型，并使用 scRNAseq 评估 GPC2 CAR T 细胞治疗后 NB 肿瘤细胞的转录组。已经进行了初步动物实验，并对 CAR T 细胞治疗之前、期间和之后的肿瘤进行了 scRNAseq，并且正在分析数据。项目 4. 通过空间转录组分析创建儿科脑肿瘤的肿瘤和免疫细胞图谱 (Nellan, Nguyen) 脑肿瘤儿童 CAR T 细胞试验的早期结果表明免疫激活和短暂的放射学和临床改善，但没有持久的益处。因此，迫切需要进行基础和转化研究来表征和解决潜在的耐药机制。患者对 CAR T 细胞疗法的有限反应很大程度上是由于儿童脑肿瘤中存在免疫抑制性肿瘤微环境 (TME) 和异质抗原表达。假设：原发性脑肿瘤的空间转录组学将为了解 TME 内细胞亚群的异质性以及肿瘤和免疫群体的相互作用提供新的见解。这一表征将提供儿科脑肿瘤复杂 TME 的初步数据，并确定正在进行的临床前开发中 CAR T 细胞疗法的潜在耐药机制。研究目标： 1. 生成儿童期最高风险脑肿瘤的肿瘤/免疫细胞图谱，为未来的临床前免疫治疗测试提供信息。 2. 描绘肿瘤中免疫细胞相对于表达抗原的拓扑分布，以了解哪些效应细胞对于治疗性免疫反应可能很重要。 3. 了解抗原表达和克隆异质性之间的关系，以得出可以预测对 CAR T 细胞疗法敏感性的标记物。迄今为止取得的成就：使用 Visium CytAssist 平台在 FFTE 上捕获了 18 次数据，目前正在分析数据。项目 5、6 - 对罕见肿瘤和 POB 肿瘤患者进行单细胞分析，已处理 90 个样本。 （卡普兰、维德曼）。对来自患者年龄（9-66 岁）的 9 份肾上腺皮质癌标本进行了 ScRNAseq 分析，并在 2023 年 AACR 会议上提交了初步数据 Sikder 等人“肾上腺皮质癌邻近组织和转移微环境的表征揭示了深刻的分子和细胞重编程转移进展和疾病结果。”。