(<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.
Our proposed study 1) addresses the molecular mechanisms by which DNA damage responses affect the substitution and translocation signatures during lymphomagenesis, 2) identifies the impact of cell cycle phases on the DNA damage induced accessibility changes and the translocation patterns, and 3) elucidates the translocation outcomes of different type of breaks ? clean breaks, RAG or AID initiated physiological break in antigen receptor genes, and Top1-cc like lesions.
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