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.

项目摘要/摘要（<31行） 基因组不稳定性是人类癌症的标志。 ATM和BRCA1（项目1）都普遍存在 在DNA双链断裂（DSB）修复中实施的表达肿瘤抑制基因。然而，他们的损失导致 非常不同类型的癌症 - 主要是ATM缺乏症中的淋巴瘤，以及乳腺癌或卵巢癌 BRCA1缺陷（项目1）。这种组织特异性恶性风险的原因尚不完全了解。 人类癌症的序列分析确定了独特的替代和重排特征，其中一些 这（例如，替换签名3和简短的串联重复）与BRCA1缺陷有关。 ATM- 损失尚未与任何签名有关，部分原因是许多人在许多签名 癌症类型。因此，ATM损耗的特征特异性基因组特征和 人基因组的异质性。在这里，我们使用近交小鼠模型（相同的基因组）来发现ATM损失 淋巴细胞（均匀细胞类型）的相关替代和重排特征，并使用高 吞吐量基因组易位测序（HTGTS）检查淋巴瘤相关的易位 抗原受体基因。使用ATAC-SEQ，它通过TN5转座酶测量染色体可及性 插入，我们观察到DSB周围局部可访问性的暂时变化以及令人惊讶的极化 远离目标休息的地区的全球可访问性：增加可访问区域的可访问性 以53bp1依赖性方式降低不可接近区域的可访问性。以及高可访问性 区域还有可能通过测量的末端季节和染色体易位测量的额外休息时间 由htgts。由于ATM磷酸化组蛋白H2AX和53BP1以促进其募集到核小体 占领区域，我们假设DNA损伤响应导致染色质的重新分布 有界因子（例如53BP1）基于核病密度，并有助于细胞类型特异性基因组 不稳定（断裂和易位）和恶性肿瘤。要测试这一点，我们将1）解决分子 ATM介导的DNA损伤反应调节模式和结果的机制 抗原受体基因产物的组装和修饰期间的染色体易位以及 淋巴作用，2）表征细胞周期阶段（G1，G2，增殖）对易位模式的影响， 3）阐明不同类型的断裂的易位结果 - 干净的休息，抹布或援助开始 断裂和复制应力诱导的病变。与P01中的其他人合作，我们将集成 损坏引起的可访问性随着替代和重排特征（项目1和2）的变化，细胞周期 （项目2和4）和3D组织（项目4）。通过比较来自ATM缺陷与BRCA1-的签名 缺乏（项目1）细胞，结果将使这两种主要肿瘤补充的损失如何导致灯 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。