Understanding the tumor microenvironment of osteosarcoma

Abstract

Osteosarcoma is the most common primary malignant bone tumor affecting children, adolescents and young adults. Patients with localized disease are cured in 65% of patients, but no improvement in prognosis has been seen since the addition of chemotherapy 40 years ago. In order to better understand the biology of osteosarcoma and to develop novel immunotherapies, we propose to use the latest genomic technologies to study the microenvironment of osteosarcoma in high resolution. We will be using two highly innovative but very expensive techniques to make the initial discovery with a limited number of cases (20). Single cell transcriptomic (SCT) sequencing will be carried to determine the cell-type content of these tumors. We will then develop an antibody panel to be employed in imaging mass cytometry (IMC). Moreover, long read RNA sequencing (LRseq) will be carried out in a subset of TARGET cases that already have RNAseq, WES and WGS data available. Candidate isoform or fusion transcripts will be rigorously validated, and the annotation will include localization of the expressed proteins which would be useful in prioritizing further exploitation of these potential targets for immunotherapy. Monoclonal antibodies or CAR-T cells will be developed against cell surface proteins while tumor vaccines will be developed against intracellular neo-antigens. In this application, we propose to address a critical knowledge gap in pediatric osteosarcoma, by creating a detailed and comprehensive map of the tumor microenvironment as well as a comprehensive library of isoform and fusion proteins that could be targetable neoantigens for immunotherapy.