About

Roger A. Greenberg, MD, PhD, is the J. Samuel Staub Professor and Director of Basic Science at the Basser Research Center for BRCA, as well as a Program Leader for the Breast Cancer Program at the Abramson Cancer Center, all within the Perelman School of Medicine at the University of Pennsylvania. His research focuses on understanding the basic mechanisms of DNA repair and their impact on genome integrity, cancer etiology, and response to targeted therapies. Greenberg's laboratory investigates BRCA1- and BRCA2-dependent homologous recombination mechanisms in breast and ovarian cancer, telomere length maintenance mechanisms, and DNA damage-induced activation of immune responses to cancer. His work has contributed significantly to the understanding of how germline mutations in BRCA1 and BRCA2 predispose individuals to breast and ovarian cancers, revealing their roles in DNA damage checkpoint signaling and error-free repair processes. He has elucidated the molecular interactions of BRCA1 at DNA damage sites, identified new tumor suppressor networks, and developed insights into chromatin remodeling and telomere maintenance, including the ALT pathway. Greenberg's research also explores the activation of innate immune responses following DNA damage, with implications for combining DNA damaging therapies with immune checkpoint blockade. His contributions include identifying new drug targets such as ALC1, which is now in clinical trials to overcome resistance in homologous recombination-deficient cancers. He has developed methodologies for visualizing DNA repair processes in real time and has made key discoveries regarding chromatin dynamics, genome stability, and the relationship between chromatin structure and genome integrity. Greenberg's work has advanced the understanding of genome maintenance mechanisms and their relevance to cancer therapy, with ongoing projects aimed at defining the entire ALT process and exploring the complex interplay between DNA repair, chromatin, and immune responses.

Research topics

• Cell biology
• Cancer research
• Biology
• Genetics

Selected publications

• CHAMP1 complex promotes heterochromatin assembly and reduces replication stress

  Proceedings of the National Academy of Sciences · 2026-01-02

  articleOpen access

  Replication stress (RS) is a major driver of genomic instability and a hallmark of cancer cells. Although dynamic heterochromatin remodeling has been implicated in RS response, the precise mechanisms remain unclear. The CHAMP1 complex, composed of CHAMP1, POGZ, HP1α, and the H3K9 methyltransferase SETDB1, is known to regulate heterochromatin assembly at multiple genomic sites. Interestingly, upon RS, the CHAMP1 complex is transiently recruited to stalled replication forks, where it facilitates H3K9me3 deposition and establishes a repressive chromatin environment. The complex is required for stabilization of replication forks, and it shields forks from MRE11-mediated degradation. The complex also reduces RS at specific chromosomal sites, such as the heterochromatin-rich telomeric sites in tumor cells which use the ALT pathway of telomere maintenance. Loss of the CHAMP1 complex results in increased micronuclei formation and heightened sensitivity to RS. Loss of the complex also leads to a compensatory increase in other pathways which reduce RS, such as the FA pathway and the ATR/CHK1 pathway. Notably, CHAMP1 deficiency induces synthetic lethality with FANCM inhibition in ALT-positive tumor cells, and the CHAMP1 complex is essential for the survival of CCNE1-amplified ovarian cancers. These findings uncover a heterochromatin-based mechanism of replication fork stabilization and suggest that CHAMP1 may represent a candidate therapeutic vulnerability in cancers with elevated RS.

  PublisherOA PDFDOI

• Landscape of reversion alterations in homologous recombination genes reveals evolutionary constraints

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-21

  articleOpen access

  Reversion mutations (REVs) restore homologous recombination repair (HRR) and confer resistance to PARP inhibitors (PARPi) in HR-deficient cancers. Yet, their prevalence, mechanisms, and biological constraints remain undefined. We analyzed genomic profiling of 609,464 tissue and liquid biopsy samples across multiple cancer types to delineate the pan-cancer landscape of REVs. REVs were identified in eight HRR genes, most frequently BRCA2 and BRCA1 and notably never in ATM or CHEK2. REVs exclusively impacted truncating pathogenic variants, predominantly through large in-frame and exon-level deletions, associated with repetitive sequences. Conserved functional domains are relatively depleted of REVs. Structural modeling and functional studies support that exon-level deletions preserve critical domain architecture and confer PARPi resistance. The study establishes HRR reversion as a structurally permissive, yet evolutionarily constrained, resistance mechanism with implications on response, monitoring, and therapeutic strategy.

  PublisherDOI

• Transactions on micronuclear DNA and implications for immune signaling

  Trends in Biochemical Sciences · 2025-11-21 · 2 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• CHAMP1 complex directs heterochromatin assembly and promotes homology-directed DNA repair

  Nature Communications · 2025-02-17 · 8 citations

  articleOpen access

  The CHAMP1 complex, a little-known but highly conserved protein complex consisting of CHAMP1, POGZ, and HP1α, is enriched in heterochromatin though its cellular function in these regions of the genome remain unknown. Here we show that the CHAMP complex promotes heterochromatin assembly at multiple chromosomal sites, including centromeres and telomeres, and promotes homology-directed repair (HDR) of DNA double strand breaks (DSBs) in these regions. The CHAMP1 complex is also required for heterochromatin assembly and DSB repair in highly-specialized chromosomal regions, such as the highly-compacted telomeres of ALT (Alternative Lengthening of Telomeres) positive tumor cells. Moreover, the CHAMP1 complex binds and recruits the writer methyltransferase SETDB1 to heterochromatin regions of the genome and is required for efficient DSB repair at these sites. Importantly, peripheral blood lymphocytes from individuals with CHAMP1 syndrome, an inherited neurologic disorder resulting from heterozygous mutations in CHAMP1, also exhibit defective heterochromatin clustering and defective repair of DSBs, suggesting that a defect in DNA repair underlies this syndrome. Taken together, the CHAMP1 complex has a specific role in heterochromatin assembly and the enhancement of HDR in heterochromatin. The CHAMP1 complex, consisting of CHAMP1, POGZ, and HP1α, is enriched in heterochromatin, but its role was unclear. Here, the authors demonstrate that the CHAMP1 complex promotes heterochromatin assembly and homology-directed repair, with its dysfunction linked to CHAMP1 syndrome.

  PublisherOA PDFDOI

• Molecular glues that inhibit deubiquitylase activity and inflammatory signaling

  Nature Structural & Molecular Biology · 2025-03-17 · 5 citations

  articleOpen access

  Abstract Deubiquitylases (DUBs) are crucial in cell signaling and are often regulated by interactions within protein complexes. The BRCC36 isopeptidase complex (BRISC) regulates inflammatory signaling by cleaving K63-linked polyubiquitin chains on type I interferon receptors (IFNAR1). As a Zn 2+ -dependent JAMM/MPN (JAB1, MOV34, MPR1, Pad1 N-terminal) DUB, BRCC36 is challenging to target with selective inhibitors. Here, we discover first-in-class inhibitors, termed BRISC molecular glues (BLUEs), which stabilize a 16-subunit human BRISC dimer in an autoinhibited conformation, blocking active sites and interactions with the targeting subunit, serine hydroxymethyltransferase 2. This unique mode of action results in selective inhibition of BRISC over related complexes with the same catalytic subunit, splice variants and other JAMM/MPN DUBs. BLUE treatment reduced interferon-stimulated gene expression in cells containing wild-type BRISC and this effect was abolished when using structure-guided, inhibitor-resistant BRISC mutants. Additionally, BLUEs increase IFNAR1 ubiquitylation and decrease IFNAR1 surface levels, offering a potential strategy to mitigate type I interferon-mediated diseases. Our approach also provides a template for designing selective inhibitors of large protein complexes by promoting rather than blocking protein–protein interactions.

  PublisherOA PDFDOI

• Lnk deficiency enhances translesion synthesis to alleviate replication stress and promote hematopoietic stem cell fitness

  Journal of Clinical Investigation · 2025-10-30

  articleOpen access

  The adaptor protein LNK/SH2B3 negatively regulates hematopoietic stem cell (HSC) homeostasis. Lnk-deficient mice show marked expansion of HSCs without premature exhaustion. Lnk deficiency largely restores HSC function in Fanconi anemia (FA) mouse models and primary FA patient cells, albeit protective mechanisms remain enigmatic. Here, we uncover a role for LNK in regulating translesion synthesis (TLS) during HSC replication. Lnk deficiency reduced replication stress-associated DNA damage, particularly in the FA background. Lnk deficiency suppressed single-strand DNA breaks, while enhancing replication fork restart in FA-deficient HSCs. Diminished replication-associated damage in Lnk-deficient HSCs occurred commensurate with reduced ATR/p53 checkpoint activation that is linked to HSC attrition. Notably, Lnk deficiency ameliorated HSC attrition in FA mice without exacerbating carcinogenesis during aging. Moreover, we demonstrated that enhanced HSC fitness from Lnk deficiency was associated with increased TLS activity via REV1 and, to a lesser extent, TLS polymerase eta (η). TLS polymerases are specialized to execute DNA replication in the presence of lesions or natural replication fork barriers that stall replicative polymerases. Our findings implicate elevated use of these specialized DNA polymerases as critical to the enhanced HSC function imparted by Lnk deficiency, which has important ramifications for stem cell therapy and regenerative medicine in general.

  PublisherOA PDFDOI

• Abstract P2-02-02: CHEMOTHERAPEUTIC TOPOISOMERASE 2 POISONS GENERATE TREX1 RESISTANT DNA FRAGMENTS THAT INDUCE A POTENT cGAS/STING RESPONSE

  Clinical Cancer Research · 2025-06-13

  article

  Abstract Tumours with genomic instability display enhanced immunogenicity and potential for response to immune checkpoint blockade (ICB). Interestingly, chemotherapy mediated DNA damage can also stimulate the immune system through activation of the cGAS/STING innate immune pathway and therefore, improve clinical outcomes in combination with ICB. Here we set out to compare the ability of classically used chemotherapies to activate innate immunity, as well as characterise the mechanism(s) behind it. We identified topoisomerase 2 (TOP2) poisons, such as anthracyclines, as the most effective activators of cGAS/STING, leading to a potent type I interferon response. Mechanistically, we demonstrate that abortive TOP2cc repair intermediates (dsDNA fragments containing 5’-phosphotyrosyl residues) get encapsulated within micronuclei and activate cGAS, which can be blocked with antimitotic agents (e.g. taxanes). Crucially, we discovered that these 5’-phosphotyrosyl linked fragments are resistant to nuclease degradation by the cytoplasmic nuclease TREX1, which stabilises them, resulting in robust cGAS/STING mediated inflammation. Finally, using in vivo modelling, we confirmed that Top2 poisons enhance anti-tumour responses to ICB in comparison to taxanes. In line with this, using pre and on-treatment breast tumour biopsies, we have shown that anthracycline-based chemotherapy induces a robust type I interferon response in breast tumours, driving tumour lymphocytic infiltration. Moreover, following anthracycline treatment with taxane treatment results in supression of lymphocytic infiltration in these same tumours. Collectively, our findings reveal that TOP2 poison mediated DNA lesions enhance cGAS substrate availability by impairing cytoplasmic dsDNA degradation, highlighting their ability to drive anti-tumour immune responses and enhance the therapeutic efficacy of ICB. Citation Format: Kienan Savage, Eliana M. Barros, Richard D.A. Wilkinson, Guido Zagnoli-Viera, Stuart A. McIntosh, Katrina M. Lappin, Oliver Barker, Ieuan L. Morgan, Eileen E. Parkes, Marc A. Fuchs, Nuala McCabe, Roger A. Greenberg, Tim Harrison, Keith W. Caldecott, Richard D. Kennedy. CHEMOTHERAPEUTIC TOPOISOMERASE 2 POISONS GENERATE TREX1 RESISTANT DNA FRAGMENTS THAT INDUCE A POTENT cGAS/STING RESPONSE [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P2-02-02.

  PublisherDOI

• CHAMP1 Complex Promotes Heterochromatin Assembly and Reduces Replication Stress

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-05

  preprintOpen access

  Replication stress is a major driver of genomic instability and a hallmark of cancer cells. Although dynamic heterochromatin remodeling has been implicated in replication stress response, the precise mechanisms remain unclear. Here, we identify the CHAMP1 complex, composed of CHAMP1, POGZ, HP1α, and the H3K9 methyltransferase SETDB1, as a critical regulator of heterochromatin assembly at stalled replication forks. Upon replication stress, the CHAMP1 complex is recruited to stalled forks where it facilitates H3K9me3 deposition, creating a repressive chromatin environment that shields replication forks from MRE11-mediated degradation. The complex promotes the recruitment of the origin recognition complex (ORC) to sites of replication stress, such as the telomeric heterochromatin in alternative lengthening of telomeres (ALT)-positive tumor cells, thereby supporting efficient telomeric DNA replication. Loss of CHAMP1 disrupts ORC2 recruitment and impairs fork restart, leading to increased micronuclei formation and heightened sensitivity to replication stress. Notably, CHAMP1 deficiency induces synthetic lethality with FANCM inhibition in ALT-positive tumor cells, and the CHAMP1 complex is essential for the survival of CCNE1-amplified ovarian cancers. These findings uncover a chromatin-based mechanism of replication fork stabilization and suggest that CHAMP1 may represent a candidate therapeutic vulnerability in cancers with elevated replication stress.

  PublisherOA PDFDOI

• Mechanisms and genomic implications of break-induced replication

  Nature Structural & Molecular Biology · 2025-08-22 · 6 citations

  reviewOpen accessSenior author
  PublisherOA PDFDOI

• 53BP1 condensates function as bioreactors for NHEJ directed DNA repair and insulators to determine pathway choice

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-23 · 1 citations

  articleOpen access

  Genomic integrity requires efficient resolution of DNA damage. Non-homologous end joining (NHEJ) is the primary mechanism of DNA double strand break (DSB) repair in mammalian cells and is mediated by 53BP1, a tumor suppressor involved in preventing DSB end-resection and homologous recombination. NHEJ repair foci form following DSB formation, however how mesoscale assembly occurs and whether 53BP1 is the driver of this process are unknown. Also, despite knowledge of the identify of key pathway molecules, the specific functions of mesoscale repair condensates in DNA repair and pathway selectivity are unknown. To address these gaps, we determined the minimal domain of 53BP1 sufficient for phase separation in vitro and identified the key residues that governing its condensation. Utilizing a separation-of-function mutant, we demonstrate that 53BP1and its protein condensation is the core driver of NHEJ foci formation. 53BP1 condensates function as bioreactor compartments, increasing the effective concentration of substrates near double strand breaks and are essential for efficient DNA damage resolution. Additionally, we show that 53BP1 condensates function as insulators around DSB sites to prevent end-resection and direct repair pathway selectivity. Collectively our work reveals a specialized compartment for DNA repair through the spatial clustering of 53BP1 molecules into repair foci essential to maintain genome integrity.

  PublisherOA PDFDOI

Recent grants

• NIH Grant K08CA106597

  NIH · $779k · 2011

• NIH Grant R21CA194973

  NIH · $383k · 2017

• DNA double-strand break chromatin alterations and genome integrity

  NIH · $4.0M · 2013–2026

• The BRCA1-A complex function in DNA repair

  NIH · $5.2M · 2009–2031

• Roles of Chromatin Modification in BRCA1 Dependent DNA Repair

  NIH · $4.8M · 2013–2029

Frequent coauthors

• Katherine L. Nathanson

  University of Pennsylvania

  136 shared

• Susan M. Domchek

  University of Pennsylvania

  128 shared

• Fergus J. Couch

  Mayo Clinic in Arizona

  123 shared

• Dana R. Lilli

  105 shared

• Troy E. Messick

  The Wistar Institute

  95 shared

• Dennis E. Discher

  University of Pennsylvania

  89 shared

• Jiang-bo Tang

  Hiroshima University

  87 shared

• Shane M. Harding

  University of Toronto

  84 shared

Labs

• Greenberg LabPI

Awards & honors

• Saul Winegrad Award for best thesis