Project 3 Zha

查项目3

基本信息

批准号：
10614967
负责人：
Shan Zha
金额：
$ 35.23万
依托单位：
COLUMBIA UNIVERSITY HEALTH SCIENCES
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-04-08 至 2025-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10614967
关键词：
3-Dimensional ATAC-seq ATM deficient Address Affect Antigen Receptors B-Lymphocytes BRCA1 gene Beak Binding Cell Cycle Cell Proliferation Cells Chromatin Chromosomal Rearrangement Chromosomal translocation Collaborations Complex DNA DNA Damage DNA Double Strand Break Development Distant Double Strand Break Repair Etiology Excision Frequencies Funding G1 Arrest Genetic Recombination Genetic Transcription Genome Genomic Instability Genomics H2AFX gene Heterogeneity Human Human Genome Immunoglobulin Class Switching Immunoglobulin Switch Recombination Immunoglobulins Inbred Mouse Lesion Link Lymphocyte Lymphoma Lymphomagenesis Malignant Neoplasms Malignant neoplasm of ovary Measures Mediating Modification Molecular Monitor Nucleosomes Null Lymphocytes Oncogenic Organ Outcome Pathogenicity Pattern Phase Phosphorylation Physiological Proliferating Proto-Oncogenes RNA Receptor Gene Recurrence Regulation Risk Role Sequence Analysis T-Cell Lymphoma T-Cell Receptor Testing Tissues Tn5 transposase Transposase Tumor Suppressor Genes Tumor Suppressor Proteins V(D)J Recombination cancer type cell type density ds-DNA endonuclease experience gene product genome-wide genomic signature leukemia/lymphoma lymphoid neoplasm malignant breast neoplasm mouse model p53-binding protein 1 recruit repaired replication stress response

项目摘要

PROJECT SUMMARY/ABSTRACT (<31 LINES) Genomic instability is a hallmark of human cancers. Both ATM and BRCA1 (Project 1) are ubiquitously expressed tumor suppressor genes implicated in DNA double strand break (DSB) repair. Yet, their losses cause very different types of cancers – predominantly lymphomas in ATM-deficiency, and breast or ovarian cancers in BRCA1-deficiency (Project 1). The causes for such tissue-specific malignancy risk are not fully understood. Sequence analyses of human cancers identified a unique substitution and rearrangement signatures, some of which (e.g. substitution signature 3 and short tandem duplications) have been linked to BRCA1 deficiency. ATM- loss has not been linked to any signature, in part due to the low frequency (2-8%) ATM-inactivation in many cancer types. As such, the ATM-loss signatures is concealed by tissue-specific genomic signatures and the heterogeneity of human genomes. Here we use inbred mouse models (identical genome) to uncover ATM-loss associated substitution and rearrangement signatures in lymphocytes (uniform cell type) and use the High Throughput Genomic Translocation Sequencing (HTGTS) to examine lymphoma relevant translocations from antigen receptor genes. Using ATAC-seq, which measures chromosomal accessibility via Tn5 transposase insertion, we observed temporal changes of local accessibility around DSBs and, surprisingly, polarization of global accessibility in regions distant from the targeted breaks: increases accessibility of accessible regions and decrease the accessibility of non-accessible regions in a 53BP1-dependent manner. And the high accessibility regions are also at risk for additional breaks measured by End-Seq and chromosomal translocations measured by HTGTS. Since ATM phosphorylates histone H2AX and 53BP1 to promotes their recruitment to nucleosome occupied regions, we hypothesize that DNA damage response leads to redistribution of the chromatin bounded factors (e.g. 53BP1) based on nucleosome density and contribute to cell type specific genomic instability (breaks and translocations) and malignancies. To test this, we will 1) address the molecular mechanisms by which ATM mediated DNA damage response regulates the pattern and outcome of chromosomal translocations during the assembly and modification of antigen receptor gene products and during lymphomagenesis, 2) characterize the impact of cell cycle phases (G1, G2, proliferating) on translocation pattern, and 3) elucidate the translocation outcome of different type of breaks – clean breaks, RAG or AID initiated breaks and replication stress induced lesions. In collaboration with others in the P01, we will integrate the damage induced accessibility changes with substitution and rearrangement signatures (Project 1 & 2), cell cycle (Project 2 & 4) and 3D organization (Project 4). By comparing the signatures from ATM-deficient vs BRCA1- deficient (Project 1) cells, the results will shed lights on how loss of these two major tumor suppressors cause different genomic instability signatures and eventually lead to tissue/organ specific malignancies.

项目摘要/摘要（<31 行）基因组不稳定是人类癌症的一个标志。ATM 和 BRCA1（项目 1）普遍存在。表达与 DNA 双链断裂 (DSB) 修复有关的肿瘤抑制基因，但它们的丢失会导致。非常不同类型的癌症——主要是 ATM 缺乏的淋巴瘤，以及乳腺癌或卵巢癌 BRCA1 缺陷（项目 1）。这种组织特异性恶性肿瘤风险的原因尚不完全清楚。人类癌症的序列分析确定了独特的取代和重排特征，其中一些其中（例如替换签名 3 和短串联重复）与 BRCA1 缺陷有关。损失与任何签名无关，部分原因是许多地方 ATM 失活的频率较低（2-8%）因此，ATM 丢失特征被组织特异性基因组特征和在这里，我们使用近交小鼠模型（相同的基因组）来揭示 ATM 丢失。淋巴细胞（统一细胞类型）中相关的取代和重排特征，并使用高通量基因组易位测序 (HTGTS) 用于检查淋巴瘤相关易位使用 ATAC-seq，通过 Tn5 转座酶测量染色体可及性。插入后，我们观察到 DSB 周围局部可达性的时间变化，并且令人惊讶的是，远离目标休息区的全球可访问性：提高可访问区域的可访问性以53BP1依赖的方式降低不可访问性和高可访问性。这些区域也面临着通过 End-Seq 测量的额外断裂和染色体易位测量的风险由于 ATM 磷酸化组蛋白 H2AX 和 53BP1，以促进它们招募至核小体。占领区域，我们追求 DNA 损伤反应导致染色质重新分布基于核小体密度的结合因子（例如 53BP1）并有助于细胞类型特异性基因组为了测试这一点，我们将 1) 解决分子问题。 ATM 介导的 DNA 损伤反应调节模式和结果的机制抗原受体基因产物组装和修饰过程中的染色体易位淋巴瘤发生，2) 表征细胞周期阶段（G1、G2、增殖）对易位模式的影响， 3) 阐明不同类型断裂的易位结果——干净断裂、RAG 或 AID 启动与 P01 中的其他人合作，我们将整合断裂和复制应激引起的病变。通过替换和重排特征诱导可及性变化（项目 1 和 2）、细胞周期（项目 2 和 4）和 3D 组织（项目 4）通过比较 ATM 缺陷与 BRCA1 的签名。缺陷（项目 1）细胞，结果将揭示这两种主要肿瘤抑制因子的缺失如何导致不同的基因组不稳定性特征并最终导致组织/器官特异性恶性肿瘤。