Project 3 Zha

查项目3

• 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
• 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

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.

项目概要/摘要（<31行） 基因组不稳定性是人类癌症的一个标志。ATM和BRCA 1（项目1）都是无处不在的 表达与DNA双链断裂（DSB）修复有关的肿瘤抑制基因。然而，他们的损失导致 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， BRCA 1-缺陷（项目1）。这种组织特异性恶性肿瘤风险的原因尚未完全了解。 人类癌症的序列分析鉴定了一种独特的取代和重排特征， 其中（例如，取代标记3和短串联重复）与BRCA 1缺陷有关。ATM- 丢失与任何特征没有联系，部分原因是在许多情况下ATM失活频率低（2-8%）。 癌症类型。因此，ATM丢失签名被组织特异性基因组签名隐藏，并且ATM丢失签名被组织特异性基因组签名隐藏。 人类基因组的异质性。在这里，我们使用近交系小鼠模型（相同的基因组）来揭示ATM丢失 相关的替代和重排的签名淋巴细胞（统一的细胞类型），并使用高 基因组易位测序（HTGTS）检查淋巴瘤相关易位， 抗原受体基因使用ATAC-seq，通过Tn 5转座酶测量染色体可及性 插入时，我们观察到DSB周围局部可达性的时间变化，令人惊讶的是， 在远离目标休息区的地区实现全面无障碍：提高可进入地区的无障碍程度， 以53 BP 1依赖的方式降低不可接近区域的可接近性。和高可及性 区域也存在通过End-Seq测量的额外断裂和测量的染色体易位的风险 通过HTGTS。由于ATM磷酸化组蛋白H2 AX和53 BP 1以促进其向核小体的募集， 我们假设DNA损伤反应导致染色质的重新分布， 基于核小体密度的结合因子（例如53 BP 1），并有助于细胞类型特异性基因组 不稳定性（断裂和易位）和恶性肿瘤。为了验证这一点，我们将1）解决分子 ATM介导的DNA损伤反应调节细胞凋亡的模式和结果的机制 在抗原受体基因产物的组装和修饰过程中以及 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 断裂和复制应力引起的损伤。与P01中的其他人合作，我们将 损伤诱导的可及性变化与取代和重排签名（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缺陷和BRCA 1- 缺陷（项目1）细胞，结果将阐明这两个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。