{"lab": {"correspondence": [{"contact_email": "c2l5dWFuLndhbmdAeWFsZS5lZHU=", "@id": "/users/774c29b8-db1e-48bc-9669-a3e380f435c2/", "display_title": "Siyuan Wang"}], "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "status": "current", "title": "Siyuan Wang, YALE", "@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "display_title": "Siyuan Wang, YALE", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "name": "e72da879-82a1-4dab-b9f9-ba5f8dc92e0a", "award": {"description": "OFHHD: During the humoral immune response, somatic hypermutation (SHM) introduces point mutations in rearranged immunoglobulin (Ig) genes of activated germinal center (GC) B cells. SHM is essential for the fine-tuning of antibody affinity, the generation of B cells expressing high-affinity antibody, and the efficacy of many vaccines. Mistargeted SHM activities can lead to mutations and chromosomal translocations that contribute to the development of B cell lymphoma. Recent studies suggest that the three-dimensional (3D) organization of the genome regulates SHM targeting and mistargeting. However, it is largely unknown how the genome is spatially organized across multiple length scales in GC B cell development and lymphoma, and how 3D genome architecture mechanistically affects the targeting and mistargeting of SHM. Conventional approaches cannot address these questions in the primary GC tissue environment due to technical limitations. Here, we propose to apply a new method recently developed by our team, termed Multiplexed Imaging of Nucleome Architectures (MINA), to primary human tonsil tissue samples and malignant GC-derived human B cell lymphomas. We will investigate and test the association between SHM susceptibility and a variety of 3D nucleome architectures, including topologically associating domain (TAD) architecture, phase separation, and nuclear positioning of genomic regions relative to nuclear lamina, nucleoli, and nuclear pores. Through targeted genomic perturbations in human B cell lymphomas, we will test specific hypotheses linking SHM targeting elements to elevated chromatin looping interactions, TAD phase separation, nuclear pore proximity, and mutation vulnerability. Our study will significantly advance our understanding of the role of 3D genome architecture and nuclear organization in GC B cells undergoing SHM in both the developmental and tumorigenesis contexts. We expect this study to establish a new research paradigm and transform 3D nucleome investigations in immunobiology.", "center_title": "OFHHD - Schatz", "name": "1U01CA260701-01", "@type": ["Award", "Item"], "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "project": "4DN", "status": "current", "@id": "/awards/1U01CA260701-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Yale-Wang_lab_MINA_Nikon_Eclipse_Ti2-U_Hydra", "status": "released", "microscope": {"ID": "963c77e3-b00a-4010-a00d-8cdac9b27144", "Name": "Yale-Wang_lab_MINA_Nikon_Eclipse_Ti2-U_Hydra", "Tier": 3, "Schema_ID": "Instrument.json", "AppVersion": "1.7.28-b1", "components": [{"ID": "0191b84a-7117-4aaf-9c53-251a777d2818", "Name": "CELESTA Critical Epi-Illuminator (place holder)", "Tier": 2, "Model": "Epi-illuminator for CELESTA Light Engine for Nikon Ti/Ti2 microscope with double filter deck", "Width": 133.94584, "Domain": "MicroscopeHardwareSpecifications", "Height": 51.099999999999994, "OffsetX": 158.40000915527344, "OffsetY": 31.200000762939453, "Category": "OpticalAssembly", "Extension": "Basic", "LotNumber": ":unav", "PositionX": 801.7800064086914, "PositionY": 623.1700005340576, "PositionZ": 0, "Schema_ID": "BeamCollimator.json", "SpecsFile": "https://lumencor.com/resources/epi-illuminators-for-celesta-light-engines-in-super-resolution-imaging", "Description": "This is a place holder for a Epi-Illuminator for CELESTA Light Engines for Nikon Ti/Ti2 microscope with double filter deck.", "Manufacturer": "Lumencor", "ModelVersion": "2.01.1", "OccupiedSpot": null, "CatalogNumber": "82-10154"}, {"ID": "865fe900-f859-404f-9fed-6b3389e1c7d8", "Name": "storm-control software", "Tier": 1, "Width": 196.72982, "Domain": "MicroscopeSpecifications", "Height": 172.67928999999998, "OffsetX": 1632.6514892578125, "OffsetY": 0, "Version": "v2019.06.28", "Category": "Software", "Language": "Phython", "Developer": "Hazen Babcock and Xiaowei Zhuang\u2019s laboratory", "Extension": "Basic", "PositionX": 1521.3412199999998, "PositionY": 518.2828549999999, "PositionZ": 0, "Schema_ID": "AcquisitionSoftware.json", "OpenSource": true, "WebsiteURL": "https://github.com/ZhuangLab/ storm-control", "Description": " This software provides an intuitive GUI control system and Python wrappers to integrate and control many widely used optical components, including various motorized stages, piezo stages, AOTFs, laser systems and cameras. 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