Description of Research Expertise:
This laboratory is devoted to understanding how basic mechanisms of DNA repair impact cancer etiology and response to targeted therapies. As a focal point to interrogate these interrelationships, we are devoted to the elucidation of BRCA1- and BRCA2- dependent homologous recombination DNA repair mechanisms and their roles in breast and ovarian cancer susceptibility. We have more recently developed an additional focus on cancer associated telomere length maintenance mechanisms that rely on a specialized form of homologous recombination. Additionally, we have developed new insights into how DNA damage responses activate inflammatory cytokine signaling networks that influence immune responses to cancer. We utilize a myriad of approaches to investigate these areas, which include biochemistry, structural biology, cell biology, and genetically engineered mouse models.
Key words: BRCA1, BRCA2, ATM, Ubiquitin, DNA repair, Homologous Recombination, Telomeres, Chromatin, Epigenetics, Breast Cancer, Ovarian Cancer, cytokines, immune therapy.
Description of Research
Germline mutations to the Breast Cancer 1 (BRCA1) or Breast Cancer 2 (BRCA2) genes are the major cause of hereditary breast and ovarian cancer susceptibility. Clinical BRCA1 and BRCA2 mutations render cells deficient in DNA damage checkpoint signaling and error-free mechanisms of DNA repair known as homologous recombination, implicating these activities in tumor suppression.
The BRCA proteins interact with numerous other DNA repair factors in several distinct protein complexes to execute homologous recombination. Our work has revealed a partial molecular understanding for how BRCA1 recognizes DNA damage and competes with opposing DNA repair proteins to control genome integrity. We have demonstrated that an interaction between the BRCA1 BRCT domain and the RAP80 ubiquitin binding protein targets BRCA1 to K63-linked ubiquitin structures present at DNA damage sites. The RAP80 ubiquitin interaction motifs (UIMs) provide an ubiquitin recognition element to target the BRCA1 E3 ligase and a K63-ubiquitin specific deubiquitinating enzyme BRCC36 to DNA double strand breaks. Each of these activities is required for appropriate DNA damage checkpoint and repair responses (Sobhian et al. Science 2007; Shao et al. Genes&Dev 2009; Tang et al. Nat Struct & Mol Biol 2013; Jiang et al. Genes Dev 2015; Zeqiraj et al. Mol Cell 2015). Cancer causing BRCA1 BRCT mutants fail to interact with RAP80 and consequently demonstrate inefficient recruitment to DNA damage sites. Moreover, in collaboration with Dr. Robert Winqvist (University of Oulu, Finland), we have identified germline mutations in RAP80 and Abraxas as a cause of familial breast cancer (Nikkila et al. Oncogene 2009; Solyom et al Sci Transl Med 2012) and are causative for a new subtype of Fanconi Anemia known as Fanc-S (Sawyer et al Cancer Discov 2015). Thus, a series of ordered events involving ubiquitin recognition, breakdown and synthesis are required for BRCA1-dependent DNA damage responses and tumor suppression.
A second area of interest in the laboratory is the complex relationship between chromatin structure and DNA repair. We have developed several novel systems to investigate interrelationships between chromatin structure and DNA double strand break (DSB) repair (Shanbhag et al. Cell 2010; Cho et al. Cell 2014; Dilley et al. Nature 2016). This was instrumental to our finding that DSBs induce an ATM kinase dependent transcriptional silencing that spans multiple kilobases of chromatin in cis to the site of DNA damage. This process has significance towards understanding how the DNA damage response impacts the genesis of chromosome translocations, meiotic sex chromosome inactivation, and DNA damage dependent interferon responses that impact immune responses to cancers. We have also gained an understanding of how chromatin environment affects DNA repair mechanism choice (i.e. whether a break is repaired by homologous recombination or nonhomologous end-joining). These studies have implicated combinatorial histone modifications in mediating competition between BRCA1 and 53BP1, thus impacting cellular responses to DNA damage inducing targeted therapies such as PARP inhibitors (Tang et al. Nat Struct Mol Biol 2013). More recently, we have discovered a novel form of homology directed repair that is responsible for alternative telomere length maintenance mechanisms in approximately 15% of human cancers (Cho et al. Cell 2014; Dilley et al. Nature 2016). We will continue to use these systems to investigate how chromatin structure impacts DNA repair mechanisms and contributes to genome integrity, cancer etiology and response to therapy.
Rotation projects are open to students in each of the areas the lab focuses on. Please see Roger Greenberg to discuss potential rotation projects.
Robert Dilley - Graduate Student
Melina Gyparaki - Graduate Student
Qinqin Jiang - Graduate Student
Mischa Li - Graduate Student
Jie Chen - Postdoctoral Researcher
Shane Harding - Postdoctoral Researcher
Lei Tian - Postdoctoral Researcher
Priyanka Verma - Postdoctoral Researcher
Xuejiao Yang - Postdoctoral Researcher
Karl Zahn - Postdoctoral Researcher
Sonali Patankar - Clinical Fellow
Weihua Li - Research Specialist, Lab Manager
Anne Wondisford – Undergraduate Student
Katherine Novak – Undergraduate Student
Dilley RL, Verma P, Cho NW, Winters HD, Wondisford AR, and Greenberg RA: Break-Induced Telomere Synthesis Underlies Homology-Directed Telomere Maintenance Nature 539 (7627): 54-58,2016.
Verma P, Greenberg RA: Noncanonical Views of Homology Directed DNA Repair Genes & Development 30 (10): 1138-54,2016.
Harding SM, Boiarsky J, and Greenberg RA: ATM dependent Silencing Links Nucleolar Chromatin Reorganization to DNA Damage Recognition Cell Reports 13 (2): 251-9,2015.
Zeqiraj E, Tian L, Piggott CA, Pillon MC, Duffy NM, Ceccarelli DF, Keszei AF, Lorenzen K, Kurinov I, Orlicky S, Gish G, Heck AJR, Guarné A, Greenberg RA* and Sicheri F*: Higher order assembly of BRCC36–KIAA0157 is required for DUB activity and biological function Molecular Cell 59 (6): 970-83,2015 .
Jiang Q, Paramasivam M, Aressy B, Wu J, Bellani M, Tong W, Seidman MM, Greenberg RA: MERIT40 cooperates with BRCA2 to resolve DNA inter-strand crosslinks Genes & Development 29 (18): 1955-68,2015.
Cho NW, Dilley RL, Lampson MA, Greenberg RA: Interchromosomal Homology Searches Drive Directional ALT Telomere Movement and Synapsis Cell 159 (1): 108-21,2014.
Cho NW, Greenberg RA: Familiar ends with alternative endings Nature 518 (7538): 2015.
Tang J, Cho NW, Cui G, Manion EM, Shanbhag NM, Botuyan MV, Mer G,
Greenberg RA: Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination Nature Structural & Molecular Biology 20 (3): 317-25,2013.
Sawyer SL, Tian L, Kahkonen M, Schwartzentruber J, Kircher M, Majewski J, Dyment DA, Innes AM, Boycott KM, Moreau LA, Moilanen JS, Greenberg RA: Biallelic Mutations in BRCA1 Cause a New Fanconi Anemia Subtype Cancer Discovery 5 (2): 135-42,2015.
Zheng H#, Gupta V#, Patterson-Fortin J#, Bhattacharya S#, Katlinski K, Wu J, Varghese B, Carbone CJ, Aressy B, Fuchs SY*, Greenberg RA*.: A BRISC-SHMT Complex Deubiquitinates IFNAR1 and Regulates Interferon Responses Cell Reports 5 (1): 180-93,2013.
Solyom S, Aressy B, Pylkäs K, Patterson-Fortin J, Hartikainen JM, Kallioniemi A, Kauppila S, Nikkilä J, Kosma VM, Mannermaa A, Greenberg RA*, Winqvist R*: Breast cancer-associated Abraxas mutation disrupts nuclear localization and DNA damage response functions Science Translational Medicine 4 (122): 122ra-23,2012.
Greenberg RA: BRCA1, everything but the RING? Science 334 (6055): 459-60,2012 .
Shanbhag NM, Rafalska-Metcalf IU, Balane-Bolivar C, Janicki SM, and Greenberg RA: ATM dependent chromatin changes silence transcription in cis to DNA Double Strand Breaks Cell 141 : 970-81,2010.
Sobhian B, Shao G, Lilli DR, Culhane AC, Moreau LA, Xia B, Livingston DM*, Greenberg RA*: RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites Science 316 (5828): 1198-202,2007.
Shao G, Patterson-Fortin J, Messick TE, Feng D, Shanbhag N, Wang Y, Greenberg RA: MERIT40 controls BRCA1-Rap80 complex integrity and recruitment to DNA double-strand breaks Genes & Development 23 (6): 740-54,2009.