Epigenetic regulation of pancreatic cancer subtype identity and tumorigenesis by PHF2

PHF2 对胰腺癌亚型识别和肿瘤发生的表观遗传调控

基本信息

批准号：
10657989
负责人：
Andrew Liss
金额：
$ 37.89万
依托单位：
MASSACHUSETTS GENERAL HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-07 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10657989
关键词：
3-Dimensional Acinar Cell Acute Architecture Biological Biology CRISPR/Cas technology CSPG6 gene Cancer Etiology Cell Culture Techniques Cell Line Cells Cessation of life Chemoresistance Chromatin Chromatin Loop Chromosomes Co-Immunoprecipitations Collection DNA Data Development Disease Resistance Epigenetic Process Evolution Expression Profiling Gene Expression Genes Genetic Screening Genetic Transcription Genetically Engineered Mouse Growth and Development function Human Cell Line Investigation KRAS2 gene Maintenance Malignant Neoplasms Malignant neoplasm of pancreas Maps Mediating Mediator Mesenchymal Modeling Molecular Target Mutation Outcome Pancreas Pancreatic Ductal Adenocarcinoma Patient-Focused Outcomes Patients Proteins Publishing Regimen Research Resolution Role Specimen System Testing Therapeutic Therapeutic Intervention Tumor-infiltrating immune cells United States Work cancer invasiveness cancer subtypes cell type chemotherapy cohesin cohesion defined contribution digital epigenetic regulation experimental study histone demethylase human RNA sequencing in vivo innovation insight molecular subtypes mouse model nano-string novel novel therapeutic intervention novel therapeutics pancreas development pancreatic ductal adenocarcinoma cell pancreatic ductal adenocarcinoma model pancreatic neoplasm patient response patient subsets pre-clinical progenitor programs recruit response single-cell RNA sequencing therapeutic target transcriptome sequencing transcriptomics tumor tumor growth tumor initiation tumor microenvironment tumor xenograft tumor-immune system interactions tumorigenesis virtual

项目摘要

Molecular subtyping of pancreatic ductal adenocarcinoma (PDAC) has defined two major transcriptional subtypes, Classical and Basal-like, which are presently the most powerful predictors of patient outcomes. Thus, there is a critical need to determine the underlying mechanisms responsible for PDAC cell identity. Our preliminary experiments demonstrate that inactivation of PHF2, a histone demethylase, in low-passage patient-derived Classical PDAC cells results in a striking loss of the Classical gene program and virtually abolishes tumor growth. In addition, deletion of Phf2 suppresses pancreatic tumor initiation and prolongs survival in genetically engineered mouse models. Moreover, our CUT&RUN experiments reveal that PHF2 co-localizes on chromosomes with CTCF and SMC3, proteins that contribute to cell identity by regulating the three-dimensional architecture of chromatin. Based on these exciting preliminary results, our central hypothesis is that PHF2, controls the Classical gene program in PDAC by regulating three-dimensional architecture of chromatin. Experiments in this proposal will employ a unique collection of low-passage human cell lines, high resolution mapping of chromatin-associated proteins and chromatin architecture, and NanoString GeoMx spatial transcriptomic analysis of genetically engineered mouse models to define the role of PHF2 in PDAC. Three specific aims are proposed to test the central hypothesis: 1) Define the subsets of PDAC that are dependent on PHF2; 2) Identify the mechanisms by which PHF2 regulates gene expression in PDAC; and 3) Define the contribution of Phf2 to tumorigenesis in genetically engineered mice. In the first aim, orthotopic xenograft tumor models allowing for the temporal inactivation of PHF2 by CRISPR/Cas9 will be employed to determine the importance of PHF2 in the maintenance of PDAC tumors as well as their response to chemotherapy. In the second aim, CUT&RUN, HiChIP, and RNA-seq experiments will be employed to define the global localization of PHF2 on chromatin in PDAC cells and ascertain its role in recruiting CTCF and cohesion to DNA to mediate DNA loop formation. For the third aim, genetically engineered mouse models of PDAC lacking Phf2 will be used to elucidate its role in the KRAS-driven changes in cell identity required for pancreatic acinar cells to transform to invasive cancer . Spatial transcriptomic studies will be performed to ascertain how Phf2 deficiency alters the composition of the tumor microenvironment by the development of PDAC that is deficient in the Classical program. The research proposed in this application is innovative because it will define a novel function for PHF2 in regulating chromatin architecture, further elucidating the mechanisms that allow for cell type-specific chromatin architecture. The proposed research is significant because it will provide strong evidence for the role of epigenetic regulation of PDAC cell identity, ultimately providing new opportunities for the development of novel therapies for PDAC.

胰腺导管腺癌 (PDAC) 的分子分型定义了两个主要的转录亚型，经典型和基础型，目前是患者结果最有力的预测因子。因此，迫切需要确定负责 PDAC 细胞身份的潜在机制。我们的初步实验表明，PHF2（一种组蛋白去甲基化酶）在低传代中失活患者来源的经典 PDAC 细胞会导致经典基因程序的显着丧失，并且实际上消除肿瘤生长。此外，Phf2 的缺失可抑制胰腺肿瘤的发生并延长胰腺肿瘤的存活时间。基因工程小鼠模型中的存活率。此外，我们的 CUT&RUN 实验表明 PHF2 与 CTCF 和 SMC3 共定位在染色体上，这些蛋白质通过调节来促进细胞身份染色质的三维结构。基于这些令人兴奋的初步结果，我们的中央假设 PHF2 通过调节三维空间来控制 PDAC 中的经典基因程序染色质的结构。本提案中的实验将采用独特的低通道集合人类细胞系、染色质相关蛋白和染色质结构的高分辨率图谱，以及 NanoString GeoMx 对基因工程小鼠模型进行空间转录组分析，以定义 PHF2 在 PDAC 中的作用。提出了三个具体目标来检验中心假设：1）定义子集依赖于 PHF2 的 PDAC； 2) 确定PHF2调节基因表达的机制在 PDAC 中； 3) 确定 Phf2 对基因工程小鼠肿瘤发生的贡献。在第一个目的，允许通过 CRISPR/Cas9 暂时失活 PHF2 的原位异种移植肿瘤模型将用于确定 PHF2 在 PDAC 肿瘤及其维持中的重要性对化疗的反应。在第二个目标中，CUT&RUN、HiChIP 和 RNA-seq 实验将用于定义 PHF2 在 PDAC 细胞染色质上的全局定位并确定其在募集 CTCF 和 DNA 内聚力来介导 DNA 环的形成。对于第三个目标，从基因上来说缺乏 Phf2 的 PDAC 工程小鼠模型将用于阐明其在 KRAS 驱动的胰腺腺泡细胞转变为侵袭性癌症所需的细胞特性的变化。空间将进行转录组研究以确定 Phf2 缺乏如何改变肿瘤的组成通过开发 PDAC 来弥补经典程序中存在的缺陷。研究本申请中提出的方案具有创新性，因为它将定义 PHF2 在调节方面的新功能染色质结构，进一步阐明细胞类型特异性染色质的机制建筑学。拟议的研究意义重大，因为它将为证明其作用提供强有力的证据 PDAC细胞身份的表观遗传调控，最终为PDAC细胞的发展提供新的机遇 PDAC 的新疗法。