Comprehensive modeling of tumor suppressor gene-derived neoantigens in pancreatic cancer

胰腺癌中抑癌基因衍生的新抗原的综合建模

基本信息

批准号：
10389366
负责人：
Zackery Ely
金额：
$ 3.01万
依托单位：
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-01 至 2022-11-12
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10389366
关键词：
Achievement Affinity Alleles Amino Acids Antigens Autologous Binding Bioinformatics Biological Assay CD8-Positive T-Lymphocytes CRISPR/Cas technology Cells Clonality Clustered Regularly Interspaced Short Palindromic Repeats Coculture Techniques Cytotoxic T-Lymphocytes Data Dendritic Cells Disease Educational process of instructing Environment Exhibits Faculty Fellowship Flow Cytometry Fluorescence-Activated Cell Sorting Frameshift Mutation Genes Growth Harvest Human Immune Immune response Immunologics Immunotherapy In Vitro Individual Institutes Investigation Laboratories Leukocytes Life MHC Class I Genes MHC binding peptide Malignant Neoplasms Malignant neoplasm of pancreas Massachusetts Mediating Mentorship Missense Mutation Modality Modeling Mus Mutate Mutation Oncology Organoids Orthologous Gene Pancreas Pancreatic Ductal Adenocarcinoma Patients Peptides Peripheral Blood Mononuclear Cell Postdoctoral Fellow Preparation Property Reading Frames Recurrence Reporting Research Research Project Grants Research Training Sampling Schedule Somatic Mutation Source Specificity Stains Surface Survival Rate T cell response T-Cell Activation T-Lymphocyte Technology Testing Therapeutic Training Transplantation Tumor Suppressor Genes Vaccination Validation anti-tumor immune response anticancer research antigen-specific T cells base cancer genomics cancer therapy cohort computational pipelines computer studies cytokine enzyme linked immunospot assay exome sequencing experience immunogenicity in vitro Assay in vivo in vivo Model meetings mouse model mutant neoantigens neoplastic cell novel novel therapeutics organoid transplantation pancreatic cancer model pancreatic cancer patients pancreatic neoplasm patient subsets pre-clinical prime editor response tumor tumor growth

项目摘要

PROJECT ABSTRACT Immunotherapies potentiate pre-existing immune responses, or induce de novo responses, that are capable of destroying tumor cells with high specificity. However, immunotherapies do not currently benefit the majority of patients suffering from pancreatic ductal adenocarcinoma (PDAC), one of the most lethal forms of cancer. Like other cancers, PDAC is primarily driven by somatic mutations, some of which give rise to mutated peptides. When presented on the surface of tumor cells, these peptides can be recognized by cytotoxic T cells. In this context of immune cell recognition, mutated peptides are called neoantigens and are critical targets of the anti-tumor immune response. Historically, PDAC has been considered an ‘immunologically cold’ cancer, predicted to contain only a scarcity of neoantigens. However, most research to date has studied PDAC neoantigens derived from missense mutations, with little focus on other potential sources, such as frameshift mutations. In the context of tumor suppressor genes (TSGs), frameshifts are frequent drivers of PDAC, and it is currently unknown if these mutations give rise to neoantigens shared by different patients. If confirmed, TSG-derived frameshift neoantigens could represent novel targets for immunotherapy with broad applicability. Objectives: This study will (1) predict and experimentally validate neoantigens from human pancreas cancer, (2) model frameshift-derived neoantigens in the context of a murine model of pancreas cancer, and (3) assess the therapeutic potential of these neoantigens as targets of anti-tumor cytotoxic T cells. Aim 1: Determine immunogenicity of TSG-derived frameshift neoantigens predicted from human PDAC. A computational pipeline will predict frameshift-derived neoantigens using whole-exome sequencing of pancreatic cancer organoids. Candidates will be validated through in vitro stimulation of autologous leukocytes and ELISPOT assays. Aim 2: Establish a suite of murine model neoantigens for in vivo modeling of the neoantigen-driven, anti-tumor immune response. A cohort of model neoantigens will be developed based on the murine orthologs of TSGs. A bioinformatics approach will establish a set of candidate models that will be evaluated via experimental vaccinations. Aim 3: Install TSG-derived neoantigens in an orthotopic mouse model and evaluate the antigen-specific cytotoxic T cell response. A CRISPR-based mouse model capable of installing precise frameshift mutations has been established. Pancreatic organoids will be derived from this model, edited via CRISPR to generate model neoantigens, and then orthotopically transplanted into syngeneic mice, followed by longitudinal characterization of neoantigen-specific T cells. Fellowship training plan and environment: This research project will be conducted at the Massachusetts Institute of Technology’s Koch Institute for Integrative Cancer Research, in the laboratory of Dr. Tyler Jacks. The research environment is highly collaborative, and research training will involve hands-on mentorship from postdoctoral fellows and research staff. Research training will be significantly enriched by a regular schedule of scientific seminars, research presentations, teaching experiences, and frequent meetings with Dr. Jacks and other academic advisors and faculty.

项目摘要免疫疗法增强预先存在的免疫反应，或诱导从头反应，这些反应能够高度特异性地破坏肿瘤细胞然而，免疫疗法目前并未使大多数患者受益。患有胰腺导管腺癌（PDAC），与其他癌症一样，这是最致命的癌症之一。 PDAC 主要由体细胞突变驱动，其中一些突变出现在肽上。在肿瘤细胞表面，这些肽可以被细胞毒性 T 细胞识别。突变肽被称为新抗原，是历史上 PDAC 抗肿瘤免疫反应的关键靶点。被认为是一种“免疫冷”癌症，预计仅含有稀缺的新抗原。迄今为止的研究已经研究了源自错义突变的 PDAC 新抗原，很少关注其他潜在的来源，例如移码突变在肿瘤抑制基因 (TSG) 的背景下，移码是常见的驱动因素。 PDAC 的突变，目前尚不清楚这些突变是否会产生不同患者共有的新抗原。经证实，TSG 衍生的移码新抗原可以代表具有广泛适用性的免疫治疗新靶标。目标：本研究将 (1) 预测并通过实验验证人类胰腺癌的新抗原，(2) 模型在小鼠胰腺癌模型中研究移码衍生的新抗原，以及（3）评估治疗效果这些新抗原作为抗肿瘤细胞毒性 T 细胞靶标的潜力。目标 1：确定从人 PDAC A 预测的 TSG 衍生移码新抗原的免疫原性。计算管道将使用胰腺癌的全外显子组测序来预测移码衍生的新抗原候选者将通过自体白细胞的体外刺激和 ELISPOT 检测进行验证。目标 2：建立一套小鼠模型新抗原，用于新抗原驱动的抗肿瘤的体内建模将基于 TSG A 的小鼠直系同源物开发一组模型新抗原。生物信息学方法将建立一组候选模型，并通过实验疫苗接种进行评估。目标 3：在原位小鼠模型中安装 TSG 衍生的新抗原并评估抗原特异性细胞毒性 T 已经建立了能够安装精确移码突变的基于 CRISPR 的小鼠模型。胰腺类器官将从该模型中衍生出来，通过 CRISPR 编辑以生成模型新抗原，然后原位移植到同系小鼠中，然后对新抗原特异性 T 细胞进行纵向表征。奖学金培训计划和环境：该研究项目将在麻省理工学院进行科技科赫综合癌症研究所，泰勒·杰克斯博士的实验室进行这项研究。环境高度协作，研究培训将涉及博士后研究员的实践指导定期举办的科学研讨会和研究将大大丰富研究人员的培训。演讲、教学经验以及与杰克斯博士和其他学术顾问和教师的频繁会面。