Targeting alternative splicing for TCR discovery in small cell carcinomas

针对小细胞癌 TCR 发现的选择性剪接

• 批准号: 10246939
• 负责人: Gay M Crooks
• 金额: $ 78万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-21 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10246939
• 关键词: Address; Affect; Affinity; Alternative Splicing; Antigen Presentation; Antigen-Presenting Cells; Antigens; Benign; Biological Assay; CAR T cell therapy; CD34 gene; Cancer Model; Cancer cell line; Carcinoma; Cell Line; Cell Surface Proteins; Cell surface; Cells; Cellular biology; Computational Biology; Data; Data Set; Development; Disease; Epithelial; Epitopes; Event; Exons; Foundations; Gays; Generations; Genes; Genomic approach; Genotype-Tissue Expression Project; HLA Antigens; Hematologic Neoplasms; Hematopoietic; Hematopoietic stem cells; Histocompatibility; Hormones; Human; Human Cell Line; Human Engineering; Immune system; Immunology; Immunotherapeutic agent; Immunotherapy; In Vitro; Label; Laboratories; Major Histocompatibility Complex; Malignant Neoplasms; Malignant neoplasm of prostate; Mass Spectrum Analysis; Measurement; Modeling; Normal tissue morphology; Oligopeptides; Oncogenes; Organoids; Patients; Peptides; Phenotype; Population; Population Heterogeneity; Pre-Clinical Model; Principal Investigator; Process; Prognosis; Prostate; Prostate Small Cell Carcinoma; Protein Isoforms; Proteins; Proteome; Proteomics; RNA Splicing; Research; Shotguns; Small Cell Carcinoma; Software Tools; Source; Specificity; Structure of parenchyma of lung; System; T cell therapy; T-Cell Development; T-Cell Receptor; T-Lymphocyte; T-Lymphocyte Epitopes; Therapeutic; Thymus Gland; Tissues; Toxic effect; Work; Xenograft Model; base; behavioral phenotyping; cancer cell; cancer genomics; cancer therapy; cancer type; cellular engineering; curative treatments; deprivation; effective therapy; human tissue; in silico; in vitro Assay; interest; lung Carcinoma; lung small cell carcinoma; mRNA Expression; mRNA Precursor; mRNA sequencing; molecular phenotype; new therapeutic target; novel; pre-clinical; programs; protein expression; proteogenomics; receptor expression; response; screening; stem cells; targeted treatment; tissue stem cells; transcriptome sequencing; transcriptomics; tumor

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.

抽象的 我们提出了一个协作免疫治疗发现计划，该计划利用替代的前 mRNA 剪接作为癌症特异性表位的来源，用于小细胞癌的 T 细胞受体 (TCR) 治疗 前列腺和肺。小细胞癌起源于许多不同的上皮组织，但通常是 侵袭性强，没有治愈方法，预后很差。小细胞肺癌（SCLC）是最常见的 常见亚型。小细胞前列腺癌 (SCPC) 作为一种原发性疾病很少见，但其发病率越来越高 常见于激素剥夺治疗的晚期表型转变。新兴研究 表明尽管 SCPC 和 SCLC 的组织来源不同，但其行为和行为高度相似 分子表型。这表明有效的靶向治疗可以治疗这两种恶性肿瘤。 我们的策略是定义小细胞中通过选择性前 mRNA 剪接创建的癌症特异性表位 癌症，然后使用这些靶点来开发基于 TCR 的疗法。嵌合抗原受体T细胞 针对细胞表面蛋白的（CAR-T）疗法已被开发用于治疗某些血液恶性肿瘤， 但这种策略对于上皮性肿瘤并不成功。目标表位的有限癌症特异性 在人体试验中导致了显着的靶向、非肿瘤毒性。我们选择追求 TCR 来扩大规模 细胞表面以外的可用靶标池。我们假设利用额外的蛋白质组 通过对可变剪接外显子的详细分析揭示的多样性将提供更好的目标。 我们的主要研究人员团队包括选择性剪接计算生物学方面的专家 （Yi Xing），癌细胞生物学和免疫学（Owen Witte），以及造血细胞发育和 免疫学（盖伊·克鲁克斯）。我们正在编译小细胞癌和正常组织的 RNA 测序数据 通过慢病毒从良性细胞衍生的 SCPC 和 SCLC 公共数据集和新人类细胞系模型 转导。这个组合数据集是我们发现工作的基础。我们计划将其与 总蛋白质组学分析，以确定影响蛋白质组成的剪接亚型。该数据将进一步 与免疫肽组学分析相结合，定义呈递给免疫系统的肽库 由目标癌细胞。来自选择性剪接事件的表位显示出高癌症特异性， TCR 开发将优先考虑蛋白质表达以及预测或观察到的表位呈现。 我们将使用这些表位，利用高度器官型的方法从初始人类 T 细胞群中选择 TCR。 Crooks实验室开发的体外人工胸腺培养系统。