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

基本信息

批准号：
10371441
负责人：
Gay M Crooks
金额：
$ 25万
依托单位：
UNIVERSITY OF CALIFORNIA LOS ANGELES
依托单位国家：
美国
项目类别：
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/10371441
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

项目摘要

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项协作免疫治疗探索计划，该计划利用替代性MRNA 作为小细胞癌的T细胞受体（TCR）治疗的癌症特异性表位来源的剪接。前列腺和肺。小细胞癌来自许多不同的上皮组织，但通常是侵略性，没有治疗性治疗，并进行可怕的预后。小细胞肺癌（SCLC）是最大的常见的亚型。小细胞前列腺癌（SCPC）很少是一种原发性疾病，但越来越多通常，作为对马内剥夺疗法的后期表型过渡常见。新兴研究表明渴望其原产地组织，SCPC和SCLC在行为上高度相似，分子表型。这表明有效的有针对性疗法可以解决这两种恶性肿瘤。我们的策略是定义由小细胞中的替代前mRNA剪接产生的癌症特异性表位癌，然后使用这些靶标制定基于TCR的治疗。嵌合抗原受体T细胞（CAR-T）针对细胞表面蛋白的疗法已为某些血液学恶性肿瘤开发但是这种策略对上皮肿瘤没有成功。目标表位的癌症特异性有限在人类试验中导致了大量目标，非肿瘤的毒性。我们选择追求TCR来扩展电池表面以外的可用目标池。我们假设该利用额外的蛋白质组学通过对剪接外显子进行详细分析所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替代剪接计算生物学专家（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（同性恋骗子）。我们正在编译小细胞癌和正常组织的RNA-seq数据 SCPC和SCLC的公共数据集和新的人类细胞系模型由慢性病毒衍生而成转导。这个结合的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鉴定影响蛋白质组成的剪接的同工型。这些数据将进一步与免疫肽分析分析集成，定义呈现给免疫系统的辣椒池由目标癌细胞。源自表现高癌特异性的替代剪接事件的表位，蛋白质表达以及预测或观察到的发作表现将优先用于TCR发育。我们将使用这些表位从幼稚的人类T细胞种群中选择使用高度有机的TCR 骗子实验室开发的体外人造人造胸腺培养系统。