Childhood Cancer Data Initiative

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

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.".