Targeting alternative splicing for TCR discovery in small cell carcinomas

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ABSTRACT We present a collaborative immunotherapeutics discovery program that exploits alternative pre-mRNA splicing as a source of cancer-specific epitopes for T-cell receptor (TCR) therapy of small cell carcinomas of the prostate and lung. Small cell carcinomas arise from many different epithelial tissues but are generally aggressive, have no curative treatment, and carry a dire prognosis. Small cell lung cancer (SCLC) is the most common subtype. Small cell prostate cancer (SCPC) is rare as a primary disease but is becoming increasingly common as a late-stage phenotypic transition in response to hormone-deprivation therapy. Emerging research indicates that despite their disparate tissues of origin, SCPC and SCLC are highly similar in behavior and molecular phenotype. This suggests effective targeted therapies could address both malignancies. Our strategy is to define cancer-specific epitopes created by alternative pre-mRNA splicing in small cell carcinomas and then use these targets to develop TCR-based therapeutics. Chimeric antigen receptor T-cell (CAR-T) therapies targeting cell surface proteins have been developed for some hematological malignancies, but this strategy has been unsuccessful for epithelial tumors. The limited cancer specificity of the target epitope has led to significant on-target, off-tumor toxicities in human trials. We have chosen to pursue TCRs to expand the pool of available targets beyond the cell surface. We hypothesize that tapping into the additional proteomic diversity revealed by a detailed analysis of alternatively spliced exons will provide better targets. Our team of principal investigators includes experts in the computational biology of alternative splicing (Yi Xing), cancer cell biology and immunology (Owen Witte), and hematopoietic cell development and immunology (Gay Crooks). We are compiling RNA-Seq data on small cell cancers and normal tissues from public datasets and new human cell line models of SCPC & SCLC derived from benign cells by lentiviral transduction. This combined dataset serves as the foundation for our discovery effort. We plan to pair this with total proteomics analysis to identify spliced isoforms that affect protein composition. This data will be further integrated with immunopeptidomics assays that define the pool of peptides presented to the immune system by the target cancer cells. Epitopes derived from alternative splicing events that show high cancer specificity, protein expression, and predicted or observed epitope presentation will be prioritized for TCR development. We will use these epitopes to select TCRs from naïve human T-cell populations using a highly organotypic in vitro artificial human thymic culture system developed in the Crooks laboratory.