Targeting alternative isoform variation for TCR discovery in platinum-resistant ovarian cancer

PROJECT SUMMARY We present an interdisciplinary target discovery and T-cell receptor (TCR) therapy development program focused on platinum-resistant high-grade serous ovarian carcinoma (HGSOC), a highly lethal disease with no effective long-term treatments or targeted therapies. Nearly all patients diagnosed with HGSOC will relapse after

initial treatment. Disease recurrence within 6 months of platinum treatment is categorized as platinum-resistant HGSOC, which is highly fatal. Our strategy to develop TCR-based therapies for platinum-resistant ovarian cancer relies on unmasking the hidden diversity of cancer proteomes produced by RNA dysregulation and mRNA

isoform variation. RNA dysregulation in cancer cells can produce new epitopes through the generation of novel mRNA and protein isoforms with increased cancer specificity. To identify sufficiently cancer-specific peptide targets for immunotherapy development, our proposed strategy expands beyond target discovery from somatic

mutations alone. In particular, long-read RNA sequencing (RNA-seq) is a powerful approach for isoform analysis and tumor antigen discovery. We propose to exploit mRNA isoform variation as a source of shared tumor antigens for platinum-resistant ovarian cancer. We will first define the landscape of full-length mRNA isoforms in

platinum-resistant ovarian cancer by generating and analyzing long-read nanopore RNA-seq datasets across a broad cohort of patients with this disease. We will couple this analysis with a big data examination of long- and short-read transcriptome profiles in a large panel of tumor and normal tissues to assess cancer specificity.

Second, we will directly assay the peptides presented to the immune system by immunopeptidomics, and examine antigen heterogeneity by single-cell long-read nanopore RNA-seq. Integrating these multiple forms of - omics analyses with state-of-the-art computational epitope predictions, we will create a highly privileged set of

potential TCR targets. Finally, we will utilize a novel in vitro human artificial thymic organoid (ATO) culture-based TCR discovery platform to rapidly create and select reactive TCRs from T cells generated through directed differentiation of pluripotent stem cells. Antigen-specific TCRs will be preclinically evaluated as therapeutically

relevant reagents in vitro and by adoptive TCR-T cell therapy in patient-derived xenograft (PDX) models of platinum-resistant ovarian cancer. We have assembled a multi-disciplinary team of experts at UCLA and the Children’s Hospital of Philadelphia, with expertise in ovarian cancer biology and treatment (Memarzadeh), RNA

genomics and computational immuno-oncology (Xing), tumor biology and immunology (Memarzadeh, Seet, Witte), and T-cell developmental biology (Seet). Our research seeks to discover a new class of antigens and their cognate TCRs for platinum-resistant ovarian cancer and establish their initial efficacy in preclinical models.