Roger A. Greenberg, MD, PhD

faculty photo
J. Samuel Staub, M.D. Professor
Department: Cancer Biology

Contact information
Department of Cancer Biology
The Perelman School of Medicine at the University of Pennsylvania
421 Curie Boulevard
Philadelphia, PA 19104-6160
Office: 215-746-2738
Fax: 215-573-2486
Lab: 215-746-7799
BA (Chemistry)
Haverford College, 1991.
Ph.D. (Microbiology and Immunology)
Albert Einstein College of Medicine, 2000.
Albert Einstein College of Medicine, 2000.
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Description of Research Expertise

Research Interests
This laboratory is devoted to understanding basic mechanisms of DNA repair and their impact on genome integrity, cancer etiology and response to targeted therapies. To investigate these interrelationships, we are devoted to elucidating BRCA1- and BRCA2- dependent homologous recombination mechanisms in breast and ovarian cancer, telomere length maintenance mechanisms that rely on a specialized form of homologous recombination, and DNA damage induced activation of 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, DNA repair, Homologous Recombination, Telomeres, Epigenetics, Breast Cancer, Ovarian Cancer, cytokines, immune therapy.

Description of Research

Germline mutation of either the Breast Cancer 1 (BRCA1) or Breast Cancer 2 (BRCA2) genes greatly predisposes individuals to breast and ovarian epithelial cancers. Clinical BRCA1 and BRCA2 mutations render cells deficient in DNA damage checkpoint signaling and error-free mechanisms of DNA repair known as homologous recombination, strongly supporting a role for these activities in tumor suppression. Our research has contributed to the concept of a BRCA-centered breast and ovarian tumor suppressor network. BRCA1 forms several distinct DNA damage inducible 'supercomplexes, each dedicated to specific checkpoint and repair activities following genotoxic stress. This work revealed a molecular understanding for how BRCA1 recognizes DNA damage sites. 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 (Sobhian et al. Science 2007; Jiang et al. Genes Dev 2015; Zeqiraj et al. Mol Cell 2015; Jiang et a. JCB 2022). Cancer causing BRCA1 mutants fail to interact with RAP80 and consequently demonstrate inefficient recruitment to DNA damage sites. Our subsequent studies identified biallelic mutations in BRCA1 as a cause of a new Fanconi Anemia subtype, and received HUGO approval to designate BRCA1 as FANCS (Sawyer et al. Cancer Discov 2015; Domchek et al. Cancer Discov 2013). This syndrome is characterized by developmental abnormalities consistent with Fanconi Anemia along with extremely early onset breast and ovarian cancer. We demonstrated that histone H4 acetylation promotes BRCA1 displacement of 53BP1 on damaged chromatin (Tang et al. Nat Struct Mol Biol 2013) to enable homologous recombination. This work was the first to show that transcriptionally active chromatin regions preferentially use homologous recombination over nonhomologous end-joining repair mechanisms. Recently, we revealed the importance of PARylation dependent chromatin remodeling to viability of BRCA mutant cancer cells. This work showed the PAR binding SNF2 ATPase, ALC1 is essential for base damage repair (Verma Nat Cell Biol 2021). Importantly, loss of ALC1 creates profound PARP inhibitor sensitivity in homologous recombination deficient cells and overcomes known resistance mechanisms, defining ALC1 as an exciting new drug target.

Telomere length maintenance is a requisite feature of cellular immortalization and a hallmark of cancer. Approximately 85% of cancers rely on the re-expression of telomerase reverse transcriptase, while nearly 15% utilize a recombination-based mechanism known as alternative lengthening of telomeres (ALT). We developed a methodology for real-time visualization of each major step of homology-directed DNA repair during ALT (Cho et al. Cell 2014; Dilley et al. Nature 2016, Verma et al. Genes Dev 2019; Jiang et al. Mol Cell 2024). Telomere damage initiated rapid directional ALT telomere movement, culminating in synapsis and homologous recombination dependent long tract telomere synthesis. These findings have implications for understanding large-scale chromatin dynamics, fundamental mechanisms of homology searches, and potential targets to selectively inhibit telomere maintenance in ALT positive cancers. We are actively pursuing these areas with the aspirational goal of defining the entire ALT process.

Our investigations in the DNA damage response have expanded to the question of how DNA damage activates innate immune responses. This revealed the importance of progression through mitosis and pattern recognition within micronuclei to DNA damage as critical steps in eliciting anti-tumor immune responses (Harding et al. Nature 2017; Chen et al. Cell Reports 2020; Lippert and Greenberg JCI 2021). We also described parallel ubiquitin-dependent signaling mechanisms between DNA damage and immune responses (Zheng et al. Cell Rep 2013; Zeqiraj et al. Mol Cell 2015; Walden et al. Nature 2019). Collectively, our research in this area provides new avenues for combining DNA damaging therapies with immune checkpoint blockade and insights into indications such as cancer and autoimmunity. We are pursuing these areas with the recent development of homologous recombination deficient ovarian cancer models that reveal new aspects of innate immune signaling that influences tumor progression and response top immune therapy.

Our interests in BRCA and telomere maintenance has inspired our investigations into the complex relationship between chromatin structure and genome integrity. We recently reported a protein complex that we named 55LCC that unfolds DNA replication factors to prevent replication stress and severe chromosome instability due to mitotic errors (Krishnamoorthy et al. Cell 2024). All four members of the 55LCC complex are mutated in a human neurodevelopment syndrome EHLMRS (Epilepsy, Hearing Loss, Mental Retardation Syndrome). This reveals a new aspect of genome integrity that we will continue to investigate. We have also developed the first systems to visualize DSB responses and nascent transcription in real time in human cells. This enabled our discovery of ATM dependent transcriptional silencing that extends kilobases from the site of DNA damage (Shanbhag et al. Cell 2010; Harding et al. Cell Reports 2015), which relates to myriad aspects of biology, including suppression of chromosome translocations, intrinsic responses to viruses, ane meiotic sex chromosome inactivation.

Rotation Projects
Rotation projects are open to students in each of the areas the lab focuses on. We are particularly proud of the seven students that have successfully completed PhD studies in our lab. Three Greenberg lab students have received the Saul Winegrad Award for best thesis and almost all graduating students have continued in research as postdocs in outstanding laboratories.

Greenberg Lab Website
Learn more about the lab's research here.

Penn Center for Genome Integrity Website

Lab personnel:
Weihua Li - Research Specialist, Lab Manager
Adel Atari - Graduate Student
Taku Harada - Graduate Student
Arindam Datta - Postdoctoral Researcher
Reona Kato - Postdoctoral Researcher
Stefano Misino - Postdoctoral Researcher
Jie Chen - Postdoctoral Researcher
Haoyang Jiang - Postdoctoral Researcher
Tim Lippert - Postdoctoral Researcher
Sangin Kim - Postdoctoral Researcher
Tao Shi - Postdoctoral Researcher
Tianpeng Zhang - Postdoctoral Researcher
Uzair Bilal - Undergraduate Researcher
Holly Qiu - Undergraduate Student
Aravind Krishan - Undergraduate Student

Administrative Coordinator:
Laura Murillo

Selected Publications

Krishnamoorthy V#, Foglizzo M#, Dilley RL#*, Wu A, Datta A, Dutta P, Campbell LJ, Degtjarik O, Musgrove LJ, Calabrese AN, Zeqiraj E*, and Greenberg RA*.: The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity. Cell 187(9): 2250-2268, April 2024 Notes: *co-corresponding authorship #co-first authorship.

Jiang H*, Zhang T*, Kaur H, Shi T, Krishnan A, Kwon Y, Sung P, and Greenberg RA: BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response. Molecular Cell 84(9): 1684-1698, April 2024 Notes: online ahead of print *co-first authors.

Tianpeng Zhang, Yashpal Rawal, Haoyang Jiang, Youngho Kwon, Patrick Sung & Roger A. Greenberg: Break-induced replication orchestrates resection-dependent template switching. Nature 619(7968): 201-208, June 14 2023 Notes: https://doi.org/10.1038/s41586-023-06177-3

Jiang Q, Foglizzo M, Morozov YI, Yang X, Datta A, Tian L, Thada V, Li W, Zeqiraj E and Greenberg RA.: Autologous K63-deubiquitylation within the BRCA1-A complex licenses DNA damage recognition. J. Cell Biol. 221(9): e202111050, September 2022.

Verma P, Zhou Y, Cao Z, Deraska PV, Deb M, Arai E, Li W, Shao Y, Li Y, Puentes L, Patankar S, Mach RH, Faryabi RB, Shi Y*, and Greenberg RA*: ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination deficient cells. Nature Cell Biology January 2021 Notes: *co-corresponding authors doi: 10.1038/s41556-020-00624-3

Walden M*, Tian L*, Ross R, Sykora UM, Byrne DP, Hesketh EL, Masandi SK, Cassel J, Geirge R, Ault JR, Oualid FE, Pawlowski K, Salvino JM, Eyers PA, Ranson NA, Del Galdo F, Greenberg RA#, Zeqiraj E#: Metabolic control of BRISC-SHMT2 assembly regulates immune signaling. Nature 10.1038/s41586-019-1232-1, May 2019 Notes: * Co-first authors # co-corresponding authors.

Harding SM, Benci JL, Irianto J, Discher DE, Minn AJ, Greenberg RA: Mitotic progression following DNA damage enables pattern recognition within micronuclei. Nature 548: 466-470, August 2017.

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 Notes: Comment in Nature: Telomere-lengthening mechanism revealed. Roake CM, Artandi SE. Nature. 2016 Oct 19. doi: 10.1038/nature19483.

Cho NW, Dilley RL, Lampson MA, Greenberg RA: Interchromosomal Homology Searches Drive Directional ALT Telomere Movement and Synapsis. Cell 159(1): 108-21, 2014.

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 Notes: *co-corresponding authors.

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.

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.

Cho NW, Greenberg RA: Familiar ends with alternative endings. Nature 518(7538), 2015.

Greenberg RA: Assembling a protective shield. Nature Cell Biology 8: 862-863, July 2018.

Chen J, Harding SM, Natesan R, Tian L, Benci JL, Li W, Minn AJ, Asangani I, and Greenberg RA. : Cell cycle checkpoints cooperate to suppress DNA and RNA associated molecular pattern recognition and anti-tumor immune responses. Cell Reports 32(1): 1-15, September 2020.

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Last updated: 07/10/2024
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