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

• 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
• 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

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应答，或诱导能够 以高特异性破坏肿瘤细胞。然而，免疫疗法目前并不能使大多数患者受益。 患有胰腺导管腺癌（PDAC），这是最致命的癌症之一。像其他癌症一样， PDAC主要由体细胞突变驱动，其中一些突变会产生突变的肽。当呈现在 在肿瘤细胞表面，这些肽可以被细胞毒性T细胞识别。在免疫细胞识别的背景下， 突变的肽被称为新抗原，并且是抗肿瘤免疫应答的关键靶标。从历史上看，PDAC 被认为是一种“免疫冷”癌症，预计只含有稀缺的新抗原。但大多数 迄今为止的研究已经研究了来自错义突变的PDAC新抗原，很少关注其他潜在的PDAC新抗原。 来源，如移码突变。在肿瘤抑制基因（TSGs）的背景下，移码是常见的驱动因素 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。如果 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的新靶标。 目的：本研究将（1）预测和实验验证来自人胰腺癌的新抗原，（2）模型 在胰腺癌的鼠模型的情况下，评估移码衍生的新抗原的治疗性，和（3）评估移码衍生的新抗原的治疗性， 这些新抗原作为抗肿瘤细胞毒性T细胞的靶标的潜力。 目的1：确定从人PDAC预测的TSG衍生的移码新抗原的免疫原性。一 计算管道将使用胰腺癌的全外显子组测序预测移码衍生的新抗原 类器官将通过自体白细胞的体外刺激和ELISPOT测定来验证候选物。 目的2：建立一套小鼠模型新抗原，用于体内模拟新抗原驱动的抗肿瘤作用。 免疫反应将基于TSG的鼠直系同源物开发一组模型新抗原。一 生物信息学方法将建立一组候选模型，通过实验接种进行评估。 目的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细胞 细胞反应。已经建立了能够安装精确移码突变的基于CRISPR的小鼠模型。 胰腺类器官将来源于该模型，通过CRISPR编辑以生成模型新抗原，然后 原位移植到同基因小鼠中，随后纵向表征新抗原特异性T细胞。 奖学金培训计划和环境：本研究项目将在马萨诸塞州研究所进行， 技术的科赫综合癌症研究所，在泰勒杰克博士的实验室。研究 环境是高度协作的，研究培训将涉及博士后研究员的实践指导 和研究人员。研究培训将通过定期举办科学研讨会、研究 演讲，教学经验，并与杰克博士和其他学术顾问和教师经常会议。