About

Stephen J. Kron is a Professor of Molecular Genetics and Cell Biology at the University of Chicago, with appointments on several committees including Cancer Biology, Clinical Pharmacology and Pharmacogenomics, and Genetics, Genomics and Systems Biology. His research focuses on defining roles for chromatin dynamics and cell cycle regulation in DNA damage checkpoint response and cellular senescence, dissecting cross-talk between metabolism and DNA damage response, developing novel molecular assays to interrogate cell signaling in cancer, and implementing novel mass spectrometry approaches to enable quantitative proteomics. His laboratory is a diverse and collaborative group comprising cell biologists, geneticists, biochemists, chemists, and computer scientists, working on both basic and translational projects aimed at understanding and targeting DNA damage responses, with implications for cancer therapy and immunotherapy.

Research topics

• Genetics
• Biology
• Pharmacology
• Cell biology
• Medicine
• Cancer research
• Bioinformatics
• Internal medicine
• Computational biology

Selected publications

• Cancer metabolism in radiation sensitization – complementary roles of O-GlcNAc transferase and PARP1

  Journal of Cell Science · 2026-03-04 · 1 citations

  articleOpen accessSenior author

  For double-strand breaks (DSBs) formed by radiation, the onset of 5' to 3' end resection is a deciding factor in repair pathway choice, favoring homologous recombination (HR) over non-homologous end-joining (NHEJ). Studying HR-proficient MCF7 breast cancer cells, we confirmed a role for PARP1 in promoting DSB repair and limiting resection stress and identified the hexosamine biosynthetic pathway (HBP)-dependent post-translational modification O-GlcNAcylation as an independent regulator. Using pharmacological and genetic perturbations of O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and O-GlcNAcase (OGA), we showed that O-GlcNAcylation can limit end resection as measured by BrdU and RPA staining, recruitment of HR proteins BRCA1 and RAD51, and accumulation of cytosolic DNA in S/G2-phase cells. These effects were independent of PARP1 but required the histone methyltransferase EZH2. Loss of OGT or EZH2 phenocopied PARP inhibition, leading to hyper-resection after irradiation. The OGA inhibitor PUGNAc suppressed hyper-resection due to PARP1 knockout whereas treatment with the PARP inhibitor veliparib exacerbated defects in OGT- or EZH2-deficient cells. In each case, increased resection correlated with cytosolic DNA accumulation, suggesting a link to inflammatory signaling. These findings implicate the Warburg effect, via the HBP and O-GlcNAcylation, in favoring NHEJ over HR and suggest that disrupting EZH2 may sensitize HR-proficient tumor cells to radiation via resection-dependent mechanisms. Our results highlight the potential of targeting cancer-associated metabolic reprogramming to overwhelm HR repair and drive resection stress. Combining PARP inhibition with blockade of O-GlcNAcylation or EZH2 might offer a strategy to radiosensitize proliferating HR-proficient cancers while sparing non-cycling normal tissues.

  PublisherDOI

• Abstract 4098: PARP1 and EZH2 independently limit 5'-3' end resection to promote rapid DNA repair after radiation

  Cancer Research · 2025-04-21

  articleSenior author

  Abstract Cellular metabolism and epigenetic regulation have overlapping roles in cancer cell responses to radiation, with dynamic, reversible post-translational modifications including poly-ADP-ribosylation, O-GlcNAcylation and methylation emerging as key targets. This study explored crosstalk between poly-ADP-ribose polymerase 1 (PARP1), O-GlcNAc transferase (OGT), and the PRC2 subunit and histone methyltransferase EZH2 in the context of DNA double-strand break (DSB) repair. We focused on 5'-3' end resection, which determines repair pathway choice during S and G2 via guiding DSB repair away from non-homologous end joining (NHEJ) and toward homologous recombination (HR). DSB repair was examined in the human breast cancer cell line MCF7 using neutral comet assay and immunofluorescent detection of γH2AX, 53BP1, and BRCA1 foci. 5'-3' end resection was followed by tracking BrdU, RPA and RAD51 foci. We used CRISPR RNP to form pools of PARP1 and EZH2 knockout (KO) cells. After irradiation, both PARP1 KO and PARP inhibitor veliparib-treated cells displayed persistent DSBs and increased ssDNA, each restricted to S/G2 cells. While increased 5'-3' end resection may result from NHEJ defects, deregulation of resection may divert DSBs away from NHEJ to saturate cellular capacity for HR. Indeed, PARP inhibition enhanced HR repair based on a repair pathway reporter. Increasing protein O-GlcNAcylation in PARP1 KO or veliparib-inhibited cells restored DSB repair and suppressed hyper-resection, suggesting an independent, OGT-regulated determinant of pathway choice. Prior studies had implicated EZH2 and resulting histone H3 K27 trimethylation in promoting NHEJ and as a mediator of O-GlcNAcylation effects. Much like PARP1 KO, irradiated EZH2 KO cells displayed an S/G2 DSB repair defect associated with increased ssDNA. Hyper-resection in EZH2 KO was enhanced by PARP inhibition but modulating O-GlcNAcylation had no effect. Interestingly, along with increased nuclear BrdU foci, irradiated PARP1 KO and EZH2 KO each displayed cytosolic ssDNA foci. We infer that limiting NHEJ repair and/or promoting 5'-3' end resection in S/G2 can overwhelm HR, leading to hyper-resection, cytosolic DNA, and inflammation. Toward overcoming resistance to PARP inhibitors, O-GlcNac metabolism, OGT activity and its downstream mediator EZH2 offer attractive targets for therapeutic intervention. Overall, strategies aimed at deregulating 5'-3' end resection may help focus effects of genotoxic stress on proliferating cells and potentiate combinations with immunotherapies. Citation Format: Elena Efimova, Yue Liu, Sera Averbek, Isabelle Lomeli, SeokGyeong Choi, Sojung Ha, Woo-Young Kim, Stephen J. Kron. PARP1 and EZH2 independently limit 5'-3' end resection to promote rapid DNA repair after radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4098.

  PublisherDOI

• Abstract 1970 Defining roles of telomerase reverse transcriptase in DNA damage response

  Journal of Biological Chemistry · 2025-05-01

  articleOpen accessSenior author

  Telomerase Reverse Transcriptase (TERT), the catalytic subunit of telomerase, is essential for telomere maintenance, elongating the G-strand of telomeric DNA using its associated RNA template (TR). Recruitment of TERT to telomeres is mediated by the shelterin component TPP1. While TERT is highly expressed in cancer cells, efforts to target its telomeric function have shown limited clinical efficacy. Recent studies have identified noncanonical roles for TERT, particularly in the DNA damage response (DDR), suggesting alternative therapeutic opportunities.

  PublisherOA PDFDOI

• N-Terminal deleted isoforms of E3 ligase RNF220 are ubiquitously expressed and required for mouse muscle differentiation

  Molecules and Cells · 2025-07-02 · 2 citations

  articleOpen accessCorresponding

  Four isoform peptides of the novel E3 ligase ring finger protein 220 (RNF220) have been identified in humans. However, all of the previous studies have predominantly focused on isoform 1 (the full-length form), which consists of 566 amino acids. Here, we show that a shorter isoform, which is 308 amino acids lacking most of the N-terminus (human isoform 4; mouse isoform 3; ΔN-RNF220), is the predominant and ubiquitously expressed variant that warrants functional investigation. Both isoform 1 and ΔN-RNF220 are expressed in the brain; however, ΔN-RNF220 is the major isoform expressed in all other tissues in mice. Consistently, H3K4me3 ChIP-seq data from ENCODE reveal that the transcription start site for ΔN-RNF220 demonstrates broader and stronger activity across human tissues than that of isoform 1. ΔN-RNF220 produces 2 peptides (4a and 4b) through alternative translation initiation, with isoform 4b displaying distinct subcellular localization, subnuclear structures and interaction with a nuclear protein WDR5. Notably, during embryonic stem cell differentiation into neural stem cells, isoform 1 expression increases, whereas ΔN-RNF220 expression decreases. In murine myoblasts, ΔN-RNF220 is the sole expressed isoform and is required for MyoD and myogenin expression, as well as for muscle differentiation. Our findings highlight ΔN-RNF220 as the ubiquitously and highly expressed variant, likely playing a fundamental role across tissues while exhibiting functional differences from isoform 1. These results emphasize the critical importance of ΔN-RNF220 in future studies investigating the biological functions of RNF220.

  PublisherDOI

• N-Terminal Deleted Isoforms of E3 Ligase RNF220 (Isoform 4) Are Ubiquitously Expressed and Required for Mouse Muscle Differentiation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-09

  preprintOpen access

  Abstract Four isoform peptides of the novel E3 ligase RNF220 have been identified in humans. However, all of previous studies have predominantly focused on isoform 1, which consists of 566 amino acids (aa). Here, we show that a shorter isoform, isoform 4 (308 aa), lacking most of the N-terminus, is the predominant and ubiquitously expressed variant that warrants functional investigation. Both isoform 1 and isoform 4 are expressed in the brain; however, isoform 4 is the major isoform expressed in all other tissues in mice. Consistently, H3K4me3 ChIP-seq data from ENCODE reveal that the transcription start site for isoform 4 demonstrates broader and stronger activity across human tissues than that of isoform 1. Isoform 4 produces two peptides (4a and 4b) through alternative translation initiation, with isoform 4b displaying distinct subcellular localization and subnuclear structures. Notably, during embryonic stem cell differentiation into neural stem cells, isoform 1 expression increases, whereas isoform 4 expression decreases. In murine myoblasts, isoform 4 is the sole expressed isoform and is required for MyoD and myogenin expression, as well as for muscle differentiation. Our findings highlight isoform 4 as the ubiquitously and highly expressed variant, likely playing a fundamental role across tissues while exhibiting functional differences from isoform 1. These results emphasize the critical importance of isoform 4 in future studies investigating the biological functions of RNF220.

  PublisherOA PDFDOI

• Abstract 639: Targeting TET3 potentiates an effective anti-tumor immune response after irradiation

  Cancer Research · 2025-04-21 · 1 citations

  articleSenior author

  Abstract The benefits of radiotherapy (RT) have long been appreciated as limited by formation and repair of DNA double-strand breaks (DSBs) in tumor cells, but recent understanding has identified a key role for RT and DNA damage in promoting inflammation that drives anti-tumor immune response. While chromosomal DSBs indeed directly limit cancer cell survival and proliferation, RT-induced damage leads to cytosolic DNA that activates cGAS/STING/IRF3 signaling and drives IFNα/β expression, recruiting cytotoxic T and NK cells to shrink tumors. In turn, along with DSB repair, another determinant of RT resistance is rebound immunosuppression. Here, IFNγ released by the infiltrating lymphocytes activates JAK/STAT to induce interferon-stimulated genes (ISGs) including PD-L1 that can reduce tumor inflammation and restore growth. Though combining PD-1/PD-L1 blockade with RT is sufficient to block this adaptive response in mice, the lack of benefit to patients suggests the need to more broadly target immunosuppressive ISG expression. Targeting IFNγ signaling by blocking JAK/STAT may limit immunosuppressive ISG expression but will impair T and NK cytotoxicity. Looking downstream, blocking JAK/STAT-dependent ISG promoter CpG demethylation by Ten Eleven Translocation (TET) dioxygenase enzymes may prevent PD-L1 expression without affecting cytotoxicity. In this study, we disrupted TET activity with small-molecule inhibitors and CRISPR RNP knockouts (KO) to evaluate effects on radiation response in vitro and in tumors. As predicted, TET inhibitors blocked PD-L1 induction in irradiated CT26 murine colon carcinoma cells. Assaying TET1, 2 and/or 3 KO CT26 cells for PD-L1 induction identified TET3 as the critical mediator. TET3 KO cells also exhibited slower DSB repair after irradiation, associated with markedly increased ssDNA resection and cytosolic DNA. The irradiated TET3 KO cells also displayed enhanced IFNα/β expression, suggesting intact cGAS/STING/IRF3 signaling. While TET3 KO CT26 cells formed tumors in syngeneic BALB/c mice much like CT26 controls, RT produced greater NK cell infiltrates by one week and increased tumor elimination by two weeks. TET3 KO 4T1 mammary carcinoma cells formed orthotopic tumors in BALB/c mice but produced fewer lung metastases compared to controls. In conclusion, TET3 may offer an attractive, druggable target for radiosensitization by slowing DSB repair, enhancing tumor inflammation, and blocking immunosuppressive ISG expression. Citation Format: Sera Averbek, Stephen J. Kron. Targeting TET3 potentiates an effective anti-tumor immune response after irradiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 639.

  PublisherDOI

• Abstract 6877: Oxidative stress induced lipid peroxidation as a mechanism of topoisomerase II alpha poisoning by chemotherapeutic agents

  Cancer Research · 2025-04-21

  articleSenior author

  Abstract Topoisomerase II alpha (TOP2A) is an ATPase essential for maintaining optimal genomic DNA topology in cells. By relaxing DNA supercoils and entanglements, TOP2A relieves torsional stress to facilitate transcription, replication, and mitosis. In cancer cells, TOP2A is often overexpressed, enabling abnormally rapid genomic replication, in turn facilitating cellular hyperproliferation and driving tumor progression. Thus, TOP2A is a key target of several chemotherapeutic drugs, including etoposide and doxorubicin. While etoposide has long been proposed to stabilize the TOP2A-DNA cleavage complex (TOP2Acc) via interfacial inhibition, we have elucidated a complementary oxidative stress mediated pathway involving lipid peroxidation (LPO) and subsequent generation of reactive lipid electrophiles (LDEs). The LDE 4-hydroxynonenal (HNE) covalently modifies TOP2A at cysteine residues in its ATPase domain, in a DNA-dependent manner. HNE modification inhibits TOP2A catalytic activity and traps TOP2Acc, leading to accumulation of lethal DNA double strand breaks (DSBs). Induction of reactive oxygen species (ROS) by etoposide and doxorubicin were shown by flow cytometry assays, and LPO and HNE-protein adducts were imaged using fluorescence microscopy. Several chemotherapeutic TOP2A poisons significantly depleted reduced glutathione, a key antioxidant. In vitro, HNE inhibited DNA decatenation and relaxation activities of purified human TOP2A in kDNA and plasmid DNA assays. Mass spectrometry revealed sites of covalent HNE modification, including Cys216 within the ATPase domain. Malachite green ATPase assays demonstrated that HNE reduced ATP hydrolysis, consistent with disruption of ATP binding. In cell-based studies, HNE directly induced TOP2Acc and DSBs, as detected by trapped in agarose DNA immunostaining (TARDIS) assays and neutral comet assays, respectively. TOP2Acc and DSBs induced by etoposide or doxorubicin were mitigated by a lipid antioxidant, implicating LPO as a mediator of TOP2A targeted drug poisoning. An etoposide resistant cancer cell line exhibited cross resistance to HNE-induced toxicity, further supporting a shared mechanism involving redox metabolism. Proteasome inhibitors including bortezomib exacerbated the persistence of HNE-induced DSBs, indicating that repair of HNE-induced TOP2Acc primarily depends on the proteasome for degradation. Conclusion: Taken together, our data suggest an underappreciated role for TOP2A as a redox sensor in tumor cells, connecting oxidative stress to DNA damage signaling and creating a target for redox active drugs. This work suggests novel opportunities for improving chemotherapeutic strategies, by leveraging proteasome inhibitors or designing covalent inhibitors targeting Cys216 to optimize therapeutic outcomes and minimize off target toxicities. Citation Format: Amy C. Flor, Don Wolfgeher, Stephen J. Kron. Oxidative stress induced lipid peroxidation as a mechanism of topoisomerase II alpha poisoning by chemotherapeutic agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6877.

  PublisherDOI

• Telomerase reverse transcriptase degradation via a rationally designed covalent proteolysis targeting chimera

  Bioorganic & Medicinal Chemistry Letters · 2025-05-22

  articleCorresponding
  PublisherDOI

• Noncanonical inhibition of topoisomerase II alpha by oxidative stress metabolites

  Redox Biology · 2025-01-23

  articleOpen accessSenior author

  During its catalytic cycle, the homodimeric ATPase topoisomerase II alpha (TOP2A) cleaves double stranded DNA and remains covalently bound to 5' ends via tyrosine phosphodiester bonds. After passing a second, intact duplex through, TOP2A rejoins the break and releases from the DNA. Thereby, TOP2A can relieve strain accumulated during transcription, replication and chromatin remodeling and disentangle sister chromatids for mitosis. Chemotherapy agents such as etoposide are poisons that trap TOP2A mid-cycle, covalently bound to cleaved DNA, leaving behind DNA double strand breaks and activating DNA damage response. While etoposide has been proposed to stabilize the TOP2A-DNA cleavage complex (TOP2Acc) via interfacial inhibition, we have elucidated a complementary mechanism mediated by the ability of etoposide and other TOP2A poisons to induce oxidative stress. Consequently, lipid peroxidation and accumulation of lipid-derived electrophiles such as 4-hydroxynonenal (HNE) results in covalent modification of TOP2A, both blocking ATPase activity and trapping TOP2Acc. HNE modifies multiple sites on human TOP2A in vitro, including alkylating Cys216 in the ATPase domain in a DNA-dependent fashion. Taken together, our data suggest an underappreciated role for TOP2A as a redox sensor in tumor cells, connecting oxidative stress to DNA damage signaling and thereby creating a target for redox-active drugs.

  PublisherDOI

• Telomerase Reverse Transcriptase Degradation Via a Rationally Designed Covalent Proteolysis Targeting Chimera

  SSRN Electronic Journal · 2025-01-01

  preprintOpen accessSenior author
  PublisherDOI

Recent grants

• NIH Grant R01HG003864

  NIH · $2.3M · 2010

• NIH Grant R21CA126764

  NIH · $381k · 2011

• Tag-ChIP-MS for analysis of chromatin-level regulation of DNA repair

  NIH · $640k · 2017–2021

• NIH Grant R21CA138365

  NIH · $678k · 2013

• NIH Grant R21CA103235

  NIH · $153k · 2004

Frequent coauthors

• Ralph R. Weichselbaum

  University of Chicago

  77 shared

• Elena V. Efimova

  65 shared

• Donald J. Wolfgeher

  University of Chicago

  53 shared

• Vytautas P. Bindokas

  48 shared

• Amy C. Flor

  43 shared

• Seung Young Lee

  University of Illinois Chicago

  39 shared

• Edwardine Labay

  36 shared

• Yue Liu

  Tsinghua University

  34 shared

Labs

• Kron LabPI

Education

• B.A., Biochemistry

  University of Pennsylvania

  1982

• M.S., Bioengineering

  University of Pennsylvania

  1983

• M.D., Medicine

  Stanford University

  1990

• Ph.D., Cell Biology

  Stanford University

  1990

• Other, Genetics

  Whitehead Institute

  1995