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

• 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
• 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

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）的分子亚型定义了两个主要的转录因子， 亚型，经典和基底样，这是目前最有力的预测患者的结果。 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，在低传代细胞中，组蛋白去甲基化酶PHF 2的失活 患者来源的经典PDAC细胞导致经典基因程序的显著丢失， 消除肿瘤生长。此外，Phf 2的缺失抑制胰腺肿瘤的发生和转移。 在基因工程小鼠模型中存活。此外，我们的CUT&RUN实验表明，PHF 2 与CTCF和SMC 3共定位在染色体上，CTCF和SMC 3是通过调节细胞内的 染色质的三维结构。基于这些令人兴奋的初步结果，我们的中心 假设PHF 2通过调节PDAC中三维结构来控制经典基因编程， 染色质的结构在这个提议中的实验将采用一个独特的低通道收集， 人细胞系，染色质相关蛋白和染色质结构的高分辨率作图，以及 基因工程小鼠模型的NanoString GeoMx空间转录组学分析，以确定 PHF 2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 2）确定PHF 2调节基因表达的机制 在PDAC中;和3）确定Phf 2对基因工程小鼠中肿瘤发生的贡献。上 目的是，允许通过CRISPR/Cas9暂时灭活PHF 2的原位异种移植肿瘤模型将 可用于确定PHF 2在PDAC肿瘤维持中的重要性以及它们的 对化疗的反应。在第二个目标中，将进行CUT&RUN，HiChIP和RNA-seq实验。 用于确定PHF 2在PDAC细胞染色质上的整体定位，并确定其在PDAC细胞中的作用。 募集CTCF并与DNA结合以介导DNA环的形成。第三个目标，基因 缺乏Phf 2的PDAC的工程小鼠模型将用于阐明其在KRAS驱动的 胰腺腺泡细胞转化为侵袭性癌症所需的细胞特性变化。空间 将进行转录组学研究以确定Phf 2缺陷如何改变肿瘤的组成 通过开发PDAC来改善微环境，这是经典程序中的不足。研究 在本申请中提出的是创新的，因为它将定义PHF 2在调节中的新功能。 染色质结构，进一步阐明了允许细胞类型特异性染色质 架构这项拟议中的研究意义重大，因为它将为以下方面的作用提供有力证据： PDAC细胞身份的表观遗传调控，最终为PDAC的发展提供了新的机会。 PDAC的新疗法。