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支持了23财年项目1的6个项目。从良性到恶性的NF1肿瘤的单细胞地图集，Widemann apis Zhang假设 - 通过预癌AN到MPNST的良性NF1相关PN的恶性转化，由MPNST证明了复杂Tme的转录型Tmme的转录。具体目的：表征NF1相关神经鞘肿瘤的肿瘤内异质性，以阐明伴随恶性转化的转录多样性。此目的的目的是表征包括NF1神经肿瘤的单个细胞群体，以鉴定使用新鲜手术标本的不同细胞状态，转录谱和相关可行的靶标。我们旨在建立NF1肿瘤单细胞地图集，该地图集将用于开发用于预测NF1肿瘤恶性转化的算法。完成的工作 - SCRNASEQ和方案开发（平台-10x基因组学单细胞基因表达）n = 51 nf1患者的24个新鲜肿瘤样品捕获了Widemann NF1 MyPart方案的初步结果，发表在：Zhang，X. Star Protoc 4，102297。项目2。骨肉瘤肿瘤微环境的全面表征（McEachron，Shern，Kaplan骨肉瘤是基因组和组织学上的复杂而异质的恶性肿瘤。将转移性骨肉瘤作为未满足的骨肉瘤的合理性组织特异性的驻留基质（免疫和非免疫）细胞与转移性骨肉瘤细胞之间的相互作用可与可与空间上不同的免疫调节机制相一致的区域微环境 - 瞄准单一效力。该目标的目的是全面表征各个细胞群，包括转移性骨肉瘤，以鉴定使用存档的新鲜液体组织，以鉴定不同的细胞状态，转录谱和相关可行的靶标。据我们所知，单个核RNA-seq+ATAC-SEQ数据集儿童转移性骨肉瘤尚未存在于公共领域中。完成的工作：SNRNASEQ和SNATACSEQ（平台：10x Genomics SNMulti-Ome）n = 26从冷冻转移性骨肉瘤标本中捕获。状态数据当前正在分析中，AIM 2区特定于T细胞的特定分析识别与T细胞浸润相关的转录程序和/或在转移性骨肉瘤标本中的排除。该实验的目的是确定在转移性骨肉瘤中介导T细胞的特定转录程序，并使用Syngeneic Murine模型确定下游功能验证的基本目标途径。靶向淋巴细胞排除是一个积极的研究领域，这种方法将提供具有转化意义的上下文相关和数据集。完成的工作 - 盖子整个转录组测定（平台：纳米弦GEOMX）n = 5转移性骨肉肉瘤FFPE样品o用于CD3+细胞的差分ROI屏蔽，并且数据正在与手稿进行分析。项目3。解决肿瘤异质性及其对神经母细胞瘤，PIS Thiele，Nguyen高危神经母细胞瘤（NB）的CAR T细胞耐药性的贡献。尽管大多数新诊断为高风险NB的患者在多模式治疗后达到了缓解，但超过50％的儿童经历了由最小残留疾病（MRD）引起的较晚复发，并屈服于其癌症。现在，正在为NB患者积极开发几种CAR T细胞疗法。该提案重点是解决NB中CAR T细胞耐药性的分子原因，以改善NB的CAR T细胞疗法。假设：神经母细胞瘤的肿瘤异质性可能有助于NB实体瘤的CAR T细胞耐药性。拟议的研究将是首次使用NB PDX的临床前模型来了解在CAR T疗法中克隆转移的研究，并在I/II期临床CAR T细胞试验中评估异质性。这将通过特定的目标1：确定在NB的患者衍生异种移植临床前模型中GPC2-CAR T细胞治疗后NB的克隆选择。具体目标2：在GPC2 CAR T细胞免疫疗法试验后评估NB患者活检，以评估肿瘤细胞异质性。成就；开发了一个条形码的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。已经进行了初步的动物实验，并从肿瘤中进行了肿瘤，然后进行了CAR T细胞疗法，并且数据正在分析中。项目4。通过空间转录组分析（Nellan，nguyen，Nguyen）在患有脑肿瘤儿童的CAR T细胞试验的早期结果中创建一个肿瘤和免疫细胞图，并没有表现出远距离放射线和临床的改善，但没有持久的好处，但没有持久的好处。患者对CAR T细胞疗法的反应有限主要是由于小儿脑肿瘤中存在的免疫抑制性肿瘤微环境（TME）和异质性抗原表达。假设：有人提出，原发性脑肿瘤的空间转录组将提供有关细胞亚群异质性以及TME中肿瘤和免疫种群相互作用的新颖见解。该表征将提供小儿脑肿瘤复杂TME的初步数据，并在持续的临床前发育中确定CAR T细胞疗法的潜在抗药性机制。研究目标：1。产生最高风险的儿童脑肿瘤的肿瘤 /免疫细胞地图集，以告知未来的临床前免疫疗法测试。 2。描述与表达抗原有关的肿瘤中免疫细胞的地形分布，以了解哪种效应细胞可能对治疗性免疫反应很重要。 3。了解抗原表达与克隆异质性之间的关系，以得出可以预测CAR T细胞疗法易感性的标记。迄今为止的成就：目前正在使用FFTE上的vistassist平台捕获18个捕获，目前正在分析数据。项目5，6-从罕见肿瘤和POB肿瘤的患者进行单细胞分析的开发90个样品。 （Kaplan，Widemann）。对来自患者年龄（9-66岁）的9个肾上腺皮质癌标本进行的SCRNASEQ分析已进行，并在2023年AACR Meeting Sikder等人Sikder等人的初步数据中进行了“相邻组织的表征和转移性微生物环境的表征，并揭示了肾上腺皮质瘤的疾病和细胞疾病的进程，并揭示了与肾上腺疾病的进程。