EWS-FLI1 triggered opportunistic de novo enhancer assembly activates potential cellular therapy targets in Ewing Sarcoma

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Irfan Asangani, PhD,  University of Pennsylvania
Recipient of the: $50,000 STL Cure Sarcoma Research Award

Ewings sarcoma is a rare type of cancerous tumor that grows in bones or the soft tissue around the bones, such as cartilage or the nerves. It usually affects children and young adults between the ages of 10 to 19. Ewings sarcoma affects about 250 children and young adults every year in the United States and shows up slightly more often in males. The incidence of Ewing sarcoma has remained unchanged for 30 years. The incidence for all ages is one case per 1 million people in the United States. In patients aged 10 to 19 years, the incidence is between nine and ten cases per 1 million people. Further, the incidence of Ewing sarcoma in the United States is nine times greater in whites than in African Americans, with an intermediate incidence in Asians. While effective surgical, radiation, chemotherapy exists for clinically localized Ewing sarcoma tumors, progression to metastatic cancer remains essentially incurable. Ewing sarcoma is caused due to the genetic exchange between chromosomes. Majority cases of Ewing’s sarcoma (85%) are the result of a translocation between chromosomes 11 and 22, which fuses the EWS gene to the FLI1 gene.

Therapeutic targeting of EWS/FLI1 protein has not been successful. Given the dearth of druggable oncogenic molecules, the identification of novel Ewing-specific gene products and a more efficient alternative to existing therapies are urgently required. Immunotherapy has shown most promising results in treating and curing many cancers in recent years. For example, clinical trials in patients with synovial sarcoma and metastatic melanoma have demonstrated the ability of engineered T cells to mediate durable complete cancer regression. However, a major impediment to the development of effective immune-based therapies for Ewing sarcoma is in identifying tumor-specific molecules with a limited expression on normal tissues. Through analysis of thousands of sequencing data, we have identified LOXHD1 gene expressed exclusively in Ewing sarcoma and our preliminary analysis suggests it to be an oncogene. This proposal aims to study in detail the role of LOXHD1 in Ewing sarcoma growth and metastasis, and test if this gene product can be used to engineer immune cells to treat this deadly cancer. This proposal will utilize cutting-edge molecular biology and next generation sequencing (NGS) technologies based genetic and epigenetic assays to study the role of LOXHD1 in Ewing sarcoma through the following three aims, Aim 1: To elucidate the role of LOXHD1 in transcription and oncogenesis. Aim 2: To investigate the role of LOXHD1 in Ewing sarcoma growth and metastasis. Aim 3: To identify LOXHD1 derived peptide presented by MHC class I molecules for cytotoxic T cell engineering.

Our comprehensive experimental approach is designed to uncover the role of the LOXHD1 in regulating EWS-FLI1 mediated transcription and identify HLA-bound LOXHD1 peptides as targets for new T cell-based immunotherapy approaches in Ewing sarcoma.