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Zimmerlin L, Angarita A, Park TS, Evans-Moses R, Thomas J, Yan S, Uribe I, Vegas I, Kochendoerfer C, Buys W, Leung AKL, Zambidis ET. Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis. Cell Rep 2025; 44:115671. [PMID: 40338744 DOI: 10.1016/j.celrep.2025.115671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 02/17/2025] [Accepted: 04/16/2025] [Indexed: 05/10/2025] Open
Abstract
Here, we show that conventional human pluripotent stem cells cultured with non-specific tankyrase-PARP1-inhibited conditions underwent proteogenomic reprogramming to functional blastomere-like tankyrase/PARP inhibitor-regulated naive stem cells (TIRN-SC). TIRN-SCs concurrently expressed hundreds of pioneer factors in hybrid 2C-8C-morula-ICM programs that were augmented by induced expression of DUX4. Injection of TIRN-SCs into 8C-staged murine embryos equipotently differentiated human cells to the extra-embryonic and embryonic compartments of chimeric blastocysts and fetuses. Ectopic expression of murine-E-Cadherin in TIRN-SCs further enhanced interspecific chimeric tissue targeting. TIRN-SC-derived trophoblast stem cells efficiently generated placental chimeras. Proteome-ubiquitinome analyses revealed increased TNKS and reduced PARP1 levels and an ADP-ribosylation-deficient, hyper-ubiquitinated proteome that impacted expression of both tankyrase and PARP1 substrates. ChIP-seq of NANOG-SOX2-OCT4 and PARP1 (NSOP) revealed genome-wide NSOP co-binding at DUX4-accessible enhancers of embryonic lineage factors; suggesting a DUX4-NSOP axis regulated TIRN-SC lineage plasticity. TIRN-SCs may serve as valuable models for studying the proteogenomic regulation of pre-lineage human embryogenesis. VIDEO ABSTRACT.
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Affiliation(s)
- Ludovic Zimmerlin
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ariana Angarita
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tea Soon Park
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca Evans-Moses
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Justin Thomas
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sirui Yan
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Isabel Uribe
- Departments of Biochemistry and Molecular Biology, The Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Isabella Vegas
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Clara Kochendoerfer
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Willem Buys
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anthony K L Leung
- Departments of Biochemistry and Molecular Biology, The Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA.
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2
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Smith-Pillet ES, Billur R, Langelier MF, Talele TT, Pascal JM, Black BE. A PARP2 active site helix melts to permit DNA damage-induced enzymatic activation. Mol Cell 2025; 85:865-876.e4. [PMID: 39889708 PMCID: PMC11922190 DOI: 10.1016/j.molcel.2025.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 12/09/2024] [Accepted: 01/08/2025] [Indexed: 02/03/2025]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) and PARP2 recognize DNA breaks immediately upon their formation, generate a burst of local PARylation to signal their location, and are co-targeted by all current FDA-approved forms of PARP inhibitors (PARPi) used in the cancer clinic. Recent evidence indicates that the same PARPi molecules impact PARP2 differently from PARP1, raising the possibility that allosteric activation may also differ. We find that, unlike for PARP1, destabilization of the autoinhibitory domain of PARP2 is insufficient for DNA damage-induced catalytic activation. Rather, PARP2 activation requires further unfolding of an active site helix. In contrast, the corresponding helix in PARP1 only transiently forms, even prior to engaging DNA. Only one clinical PARPi, Olaparib, stabilizes the PARP2 active site helix, representing a structural feature with the potential to discriminate small molecule inhibitors. Collectively, our findings reveal unanticipated differences in local structure and changes in activation-coupled backbone dynamics between human PARP1 and PARP2.
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Affiliation(s)
- Emily S Smith-Pillet
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19140-6059, USA; Graduate Program in Biochemistry, Biophysics, Chemical Biology, University of Pennsylvania, Philadelphia, PA 19140-6059, USA
| | - Ramya Billur
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19140-6059, USA
| | - Marie-France Langelier
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - John M Pascal
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Ben E Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19140-6059, USA; Graduate Program in Biochemistry, Biophysics, Chemical Biology, University of Pennsylvania, Philadelphia, PA 19140-6059, USA.
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3
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Lin X, Leung K, Wolfe K, Call N, Bhandari S, Huang X, Lee B, Tomkinson A, Zha S. XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites. Nucleic Acids Res 2025; 53:gkaf086. [PMID: 39970298 PMCID: PMC11838041 DOI: 10.1093/nar/gkaf086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 01/22/2025] [Accepted: 02/18/2025] [Indexed: 02/21/2025] Open
Abstract
Poly-ADP-ribose polymerases 1 and 2 (PARP1 and 2) are critical sensors of DNA-strand breaks and targets for cancer therapy. Upon DNA damage, PARP1 and 2 synthesize poly-ADP-ribose (PAR) chains on themselves and other substrates, facilitating DNA single-strand break repair by recruiting PAR-binding DNA repair factors, including X-ray repair cross-complementing group 1 (XRCC1) and aprataxin and polynucleotide kinase phosphatase-like factor (APLF). While diverse DNA lesions activate PARP1, PARP2 is selectively activated by 5' phosphorylated nicks. They function independently and compensate for each other. Previous studies suggest that PARP1 and its PAR chains act upstream to recruit PARP2 to DNA damage sites. Here, we report that the scaffold protein XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to damage sites. XRCC1-deficiency causes hyperactivation of PARP1 while attenuating micro-irradiation-induced PARP2 foci. Mechanistically, the BRCT1 domain of XRCC1 binds to PAR, while its BRCT2 domain interacts with the PARP2 catalytic domain independently of the PARP2 enzymatic activity and the LIG3 BRCT domain via residues D575 and Y576. This mode of PARP2 enrichment is important for the recruitment of certain PAR-binding proteins, such as APLF, but dispensable for others, such as the XRCC1-BRCT1 domain. These findings highlight the distinct role of PARP1 and PARP2 in PAR synthesis and uncover unexpected hierarchical roles of PARP1 and XRCC1 upstream of PARP2.
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Affiliation(s)
- Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | | | - Kaitlynn F Wolfe
- Columbia College, Columbia University, New York, NY 10027, United States
| | - Nicolas Call
- Department of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, United States
| | - Seema Khattri Bhandari
- Department of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, United States
| | - Xiaoyu Huang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | - Alan E Tomkinson
- Department of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, United States
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
- Division of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
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4
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Samarasekera G, Go NE, Choutka C, Xu J, Takemon Y, Chan J, Chan M, Perera S, Aparicio S, Morin GB, Marra MA, Chittaranjan S, Gorski SM. Caspase 3 and caspase 7 promote cytoprotective autophagy and the DNA damage response during non-lethal stress conditions in human breast cancer cells. PLoS Biol 2025; 23:e3003034. [PMID: 39982959 PMCID: PMC11882052 DOI: 10.1371/journal.pbio.3003034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/05/2025] [Accepted: 01/24/2025] [Indexed: 02/23/2025] Open
Abstract
Cell stress adaptation plays a key role in normal development and in various diseases including cancer. Caspases are activated in response to cell stress, and growing evidence supports their function in non-apoptotic cellular processes. A role for effector caspases in promoting stress-induced cytoprotective autophagy was demonstrated in Drosophila, but has not been explored in the context of human cells. We found a functionally conserved role for effector caspase 3 (CASP3) and caspase 7 (CASP7) in promoting starvation or proteasome inhibition-induced cytoprotective autophagy in human breast cancer cells. The loss of CASP3 and CASP7 resulted in an increase in PARP1 cleavage, reduction in LC3B and ATG7 transcript levels, and a reduction in H2AX phosphorylation, consistent with a block in autophagy and DNA damage-induced stress response pathways. Surprisingly, in non-lethal cell stress conditions, CASP7 underwent non-canonical processing at two calpain cleavage sites flanking a PARP1 exosite, resulting in stable CASP7-p29/p30 fragments. Expression of CASP7-p29/p30 fragment(s) could rescue H2AX phosphorylation in the CASP3 and CASP7 double knockout background. Strikingly, yet consistent with these phenotypes, the loss of CASP3 and CASP7 exhibited synthetic lethality with BRCA1 loss. These findings support a role for human caspases in stress adaptation through PARP1 modulation and reveal new therapeutic avenues for investigation.
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Affiliation(s)
- Gayathri Samarasekera
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy E. Go
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Courtney Choutka
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jing Xu
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Yuka Takemon
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Chan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michelle Chan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Shivani Perera
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suganthi Chittaranjan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Sharon M. Gorski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
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5
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Drew Y, Zenke FT, Curtin NJ. DNA damage response inhibitors in cancer therapy: lessons from the past, current status and future implications. Nat Rev Drug Discov 2025; 24:19-39. [PMID: 39533099 DOI: 10.1038/s41573-024-01060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2024] [Indexed: 11/16/2024]
Abstract
The DNA damage response (DDR) is a network of proteins that coordinate DNA repair and cell-cycle checkpoints to prevent damage being transmitted to daughter cells. DDR defects lead to genomic instability, which enables tumour development, but they also create vulnerabilities that can be used for cancer therapy. Historically, this vulnerability has been taken advantage of using DNA-damaging cytotoxic drugs and radiotherapy, which are more toxic to tumour cells than to normal tissues. However, the discovery of the unique sensitivity of tumours defective in the homologous recombination DNA repair pathway to PARP inhibition led to the approval of six PARP inhibitors worldwide and to a focus on making use of DDR defects through the development of other DDR-targeting drugs. Here, we analyse the lessons learnt from PARP inhibitor development and how these may be applied to new targets to maximize success. We explore why, despite so much research, no other DDR inhibitor class has been approved, and only a handful have advanced to later-stage clinical trials. We discuss why more reliable predictive biomarkers are needed, explore study design from past and current trials, and suggest alternative models for monotherapy and combination studies. Targeting multiple DDR pathways simultaneously and potential combinations with anti-angiogenic agents or immune checkpoint inhibitors are also discussed.
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Affiliation(s)
- Yvette Drew
- BC Cancer Vancouver Centre and Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frank T Zenke
- Research Unit Oncology, EMD Serono, Billerica, MA, USA
| | - Nicola J Curtin
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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6
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Huang D, Su Z, Mei Y, Shao Z. The complex universe of inactive PARP1. Trends Genet 2024; 40:1074-1085. [PMID: 39306519 DOI: 10.1016/j.tig.2024.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 12/06/2024]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is a crucial member of the PARP family, which modifies targets through ADP-ribosylation and plays key roles in a variety of biological processes. PARP inhibitors (PARPis) hinder ADP-ribosylation and lead to the retention of PARP1 at the DNA lesion (also known as trapping), which underlies their toxicity. However, inhibitors and mutations that make PARP1 inactive do not necessarily correlate with trapping potency, challenging the current understanding of inactivation-caused trapping. Recent studies on mouse models indicate that both trapping and non-trapping inactivating mutations of PARP1 lead to embryonic lethality, suggesting the unexpected toxicity of the current inhibition strategy. The allosteric model, complicated automodification, and various biological functions of PARP1 all contribute to the complexity of PARP1 inactivation.
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Affiliation(s)
- Doudou Huang
- Department of Pathology and Pathophysiology, Institute of Colorectal Surgery and Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ziyi Su
- Department of Pathology and Pathophysiology, Institute of Colorectal Surgery and Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanxia Mei
- Department of Colorectal Surgery and Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengping Shao
- Department of Pathology and Pathophysiology, Institute of Colorectal Surgery and Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Zhejiang University Cancer Center, Hangzhou, China.
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7
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Paradkar S, Purcell J, Cui A, Friedman S, Noronha KJ, Murray MA, Sundaram RK, Bindra RS, Jensen RB. PARG inhibition induces nuclear aggregation of PARylated PARP1. Structure 2024; 32:2083-2093.e5. [PMID: 39406247 DOI: 10.1016/j.str.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 08/01/2024] [Accepted: 09/05/2024] [Indexed: 11/10/2024]
Abstract
Poly (ADP-ribose) glycohydrolase (PARG) inhibitors are currently under clinical development for the treatment of DNA repair-deficient cancers; however, their precise mechanism of action is still unclear. Here, we report that PARG inhibition leads to excessive PARylated poly (ADP-ribose) polymerase 1 (PARP1) reducing the ability of PARP1 to properly localize to sites of DNA damage. Strikingly, the mis-localized PARP1 accumulates as aggregates throughout the nucleus. Abrogation of the catalytic activity of PARP1 prevents aggregate formation, indicating that PAR chains play a key role in this process. Finally, we find that PARP1 nuclear aggregates were highly persistent and were associated with cleaved cytoplasmic PARP1, ultimately leading to cell death. Overall, our data uncover an unexpected mechanism of PARG inhibitor cytotoxicity, which will shed light on the use of these drugs as anti-cancer therapeutics.
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Affiliation(s)
- Sateja Paradkar
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06510-8034, USA.
| | - Julia Purcell
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA
| | - Annie Cui
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA
| | - Sam Friedman
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA
| | - Katelyn J Noronha
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA
| | - Matthew A Murray
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06510-8034, USA
| | - Ranjini K Sundaram
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06510-8034, USA.
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510-8034, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06510-8034, USA.
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8
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Lin X, Gupta D, Vaitsiankova A, Bhandari SK, Leung KSK, Menolfi D, Lee BJ, Russell HR, Gershik S, Huang X, Gu W, McKinnon PJ, Dantzer F, Rothenberg E, Tomkinson AE, Zha S. Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts. Mol Cell 2024; 84:3916-3931.e7. [PMID: 39383878 PMCID: PMC11615737 DOI: 10.1016/j.molcel.2024.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/22/2024] [Accepted: 09/16/2024] [Indexed: 10/11/2024]
Abstract
Poly (ADP-ribose) polymerase (PARP) 1 and 2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1 and 2 at DNA lesions. Here we report that, unlike Parp2-/- mice, which develop normally, mice expressing catalytically inactive Parp2 (E534A and Parp2EA/EA) succumb to Tp53- and Chk2-dependent erythropoietic failure in utero, mirroring Lig1-/- mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5'-phosphorylated nicks (5'p-nicks), including those between Okazaki fragments, resolved by ligase 1 (Lig1) and Lig3. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, which is detrimental to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5'p-nicks explains the detrimental effects of PARP2 inactivation on erythropoiesis, shedding light on PARPi-induced anemia and the selection for TP53/CHK2 loss.
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Affiliation(s)
- Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Dipika Gupta
- New York University School of Medicine, New York, NY 10016, USA
| | - Alina Vaitsiankova
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Seema Khattri Bhandari
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Demis Menolfi
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Helen R Russell
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gershik
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Xiaoyu Huang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Wei Gu
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology & Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Françoise Dantzer
- Poly(ADP-ribosyl)ation and Genome Integrity, Strasbourg drug discovery and development Institute (IMS), UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, CS10413, 67412 Illkirch, France
| | - Eli Rothenberg
- New York University School of Medicine, New York, NY 10016, USA
| | - Alan E Tomkinson
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology & Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Department of Immunology & Microbiology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA.
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9
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Karpova Y, Tulin AV. Adaptive genetic mechanisms in mammalian Parp1 locus. G3 (BETHESDA, MD.) 2024; 14:jkae165. [PMID: 39056235 PMCID: PMC11373653 DOI: 10.1093/g3journal/jkae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 05/30/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is a highly conserved nuclear protein in multicellular organisms that by modulating chromatin opening facilitates gene expression during development. All reported Parp1 null knockout mouse strains are viable with no developmental anomalies. It was believed that functional redundancy with other PARP family members, mainly PARP2, explains such a controversy. However, while PARP2 has similar catalytic domain to PARP1, it lacks other domains, making the absence of developmental problems in Parp1 mice knockouts unlikely. Contrary to prior assumptions, in our analysis of the best-investigated Parp1 knockout mouse strain, we identified persistent mRNA expression, albeit at reduced levels. Transcript analysis revealed an alternatively spliced Parp1 variant lacking exon 2. Subsequent protein analysis confirmed the existence of a truncated PARP1 protein in knockout mice. The decreased level of poly(ADP-ribose) (pADPr) was detected in Parp1 knockout embryonic stem (ES) cells with western blotting analysis, but immunofluorescence staining did not detect any difference in distribution or level of pADPr in nuclei of knockout ES cells. pADPr level in double Parp1 Parg mutant ES cells greatly exceeded its amount in normal and even in hypomorph Parg mutant ES cells, suggesting the presence of functionally active PARP1. Therefore, our findings challenge the conventional understanding of PARP1 depletion effects.
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Affiliation(s)
- Yaroslava Karpova
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Grand Forks, ND 58202, USA
| | - Alexei V Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Grand Forks, ND 58202, USA
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Jessop M, Broadway BJ, Miller K, Guettler S. Regulation of PARP1/2 and the tankyrases: emerging parallels. Biochem J 2024; 481:1097-1123. [PMID: 39178157 DOI: 10.1042/bcj20230230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/25/2024]
Abstract
ADP-ribosylation is a prominent and versatile post-translational modification, which regulates a diverse set of cellular processes. Poly-ADP-ribose (PAR) is synthesised by the poly-ADP-ribosyltransferases PARP1, PARP2, tankyrase (TNKS), and tankyrase 2 (TNKS2), all of which are linked to human disease. PARP1/2 inhibitors have entered the clinic to target cancers with deficiencies in DNA damage repair. Conversely, tankyrase inhibitors have continued to face obstacles on their way to clinical use, largely owing to our limited knowledge of their molecular impacts on tankyrase and effector pathways, and linked concerns around their tolerability. Whilst detailed structure-function studies have revealed a comprehensive picture of PARP1/2 regulation, our mechanistic understanding of the tankyrases lags behind, and thereby our appreciation of the molecular consequences of tankyrase inhibition. Despite large differences in their architecture and cellular contexts, recent structure-function work has revealed striking parallels in the regulatory principles that govern these enzymes. This includes low basal activity, activation by intra- or inter-molecular assembly, negative feedback regulation by auto-PARylation, and allosteric communication. Here we compare these poly-ADP-ribosyltransferases and point towards emerging parallels and open questions, whose pursuit will inform future drug development efforts.
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Affiliation(s)
- Matthew Jessop
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, U.K
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, U.K
| | - Benjamin J Broadway
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, U.K
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, U.K
| | - Katy Miller
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, U.K
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, U.K
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, U.K
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, U.K
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Özdemir C, Purkey LR, Sanchez A, Miller KM. PARticular MARks: Histone ADP-ribosylation and the DNA damage response. DNA Repair (Amst) 2024; 140:103711. [PMID: 38924925 PMCID: PMC11877395 DOI: 10.1016/j.dnarep.2024.103711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Cellular and molecular responses to DNA damage are highly orchestrated and dynamic, acting to preserve the maintenance and integrity of the genome. Histone proteins bind DNA and organize the genome into chromatin. Post-translational modifications of histones have been shown to play an essential role in orchestrating the chromatin response to DNA damage by regulating the DNA damage response pathway. Among the histone modifications that contribute to this intricate network, histone ADP-ribosylation (ADPr) is emerging as a pivotal component of chromatin-based DNA damage response (DDR) pathways. In this review, we survey how histone ADPr is regulated to promote the DDR and how it impacts chromatin and other histone marks. Recent advancements have revealed histone ADPr effects on chromatin structure and the regulation of DNA repair factor recruitment to DNA lesions. Additionally, we highlight advancements in technology that have enabled the identification and functional validation of histone ADPr in cells and in response to DNA damage. Given the involvement of DNA damage and epigenetic regulation in human diseases including cancer, these findings have clinical implications for histone ADPr, which are also discussed. Overall, this review covers the involvement of histone ADPr in the DDR and highlights potential future investigations aimed at identifying mechanisms governed by histone ADPr that participate in the DDR, human diseases, and their treatments.
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Affiliation(s)
- Cem Özdemir
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laura R Purkey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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Previtali V, Bagnolini G, Ciamarone A, Ferrandi G, Rinaldi F, Myers SH, Roberti M, Cavalli A. New Horizons of Synthetic Lethality in Cancer: Current Development and Future Perspectives. J Med Chem 2024; 67:11488-11521. [PMID: 38955347 DOI: 10.1021/acs.jmedchem.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
In recent years, synthetic lethality has been recognized as a solid paradigm for anticancer therapies. The discovery of a growing number of synthetic lethal targets has led to a significant expansion in the use of synthetic lethality, far beyond poly(ADP-ribose) polymerase inhibitors used to treat BRCA1/2-defective tumors. In particular, molecular targets within DNA damage response have provided a source of inhibitors that have rapidly reached clinical trials. This Perspective focuses on the most recent progress in synthetic lethal targets and their inhibitors, within and beyond the DNA damage response, describing their design and associated therapeutic strategies. We will conclude by discussing the current challenges and new opportunities for this promising field of research, to stimulate discussion in the medicinal chemistry community, allowing the investigation of synthetic lethality to reach its full potential.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Ciamarone
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Ferrandi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel Harry Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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Smith-Pillet ES, Billur R, Langelier MF, Talele TT, Pascal JM, Black BE. A PARP2-specific active site α-helix melts to permit DNA damage-induced enzymatic activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.594972. [PMID: 38826291 PMCID: PMC11142140 DOI: 10.1101/2024.05.20.594972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
PARP1 and PARP2 recognize DNA breaks immediately upon their formation, generate a burst of local PARylation to signal their location, and are co-targeted by all current FDA-approved forms of PARP inhibitors (PARPi) used in the cancer clinic. Recent evidence indicates that the same PARPi molecules impact PARP2 differently from PARP1, raising the possibility that allosteric activation may also differ. We find that unlike for PARP1, destabilization of the autoinhibitory domain of PARP2 is insufficient for DNA damage-induced catalytic activation. Rather, PARP2 activation requires further unfolding of an active site α-helix absent in PARP1. Only one clinical PARPi, Olaparib, stabilizes the PARP2 active site α-helix, representing a structural feature with the potential to discriminate small molecule inhibitors. Collectively, our findings reveal unanticipated differences in local structure and changes in activation-coupled backbone dynamics between PARP1 and PARP2.
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Affiliation(s)
- Emily S. Smith-Pillet
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute
- Graduate Program in Biochemistry, Biophysics, Chemical Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19140-6059 USA
| | - Ramya Billur
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute
| | - Marie-France Langelier
- Département de Biochimie et Médecine Moléculaire, Université de Montréal Montréal, (Québec), H3C 3J7 Canada
| | - Tanaji T. Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439 USA
| | - John M. Pascal
- Département de Biochimie et Médecine Moléculaire, Université de Montréal Montréal, (Québec), H3C 3J7 Canada
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute
- Graduate Program in Biochemistry, Biophysics, Chemical Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19140-6059 USA
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Lin X, Leung KSK, Wolfe KF, Lee BJ, Zha S. XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594230. [PMID: 38798615 PMCID: PMC11118530 DOI: 10.1101/2024.05.14.594230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Poly-ADP-ribose polymerases 1 and 2 (PARP1 and PARP2) are crucial sensors of DNA-strand breaks and emerging cancer therapy targets. Once activated by DNA breaks, PARP1 and PARP2 generate poly-ADP-ribose (PAR) chains on themselves and other substrates to promote DNA single-strand break repair (SSBR). PARP1 can be activated by diverse DNA lesions, whereas PARP2 specifically recognizes 5' phosphorylated nicks. They can be activated independently and provide mutual backup in the absence of the other. However, whether PARP1 and PARP2 have synergistic functions in DNA damage response remains elusive. Here, we show that PARP1 and the PAR chains generated by PARP1 recruit PARP2 to the vicinity of DNA damage sites through the scaffold protein XRCC1. Using quantitative live-cell imaging, we found that loss of XRCC1 markedly reduces irradiation-induced PARP2 foci in PARP1-proficient cells. The central BRCT domain (BRCT1) of XRCC1 binds to the PAR chain, while the C-terminal BRCT domain (BRCT2) of XRCC1 interacts with the catalytic domain of PARP2, facilitating its localization near the breaks. Together, these findings unveil a new function of XRCC1 in augmenting PARP2 recruitment in response to PARP1 activation and explain why PARP1, but not PARP2, is aggregated and hyperactivated in XRCC1-deficient cells.
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Lin X, Gupta D, Vaitsiankova A, Bhandari SK, Leung KSK, Menolfi D, Lee BJ, Russell HR, Gershik S, Gu W, McKinnon PJ, Dantzer F, Rothenberg E, Tomkinson AE, Zha S. Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584665. [PMID: 38559022 PMCID: PMC10980059 DOI: 10.1101/2024.03.12.584665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PARP1&2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1&2 at DNA lesions. Here, we report that unlike Parp2 -/- mice, which develop normally, mice expressing catalytically-inactive Parp2 (E534A, Parp2 EA/EA ) succumb to Tp53- and Chk2 -dependent erythropoietic failure in utero , mirroring Lig1 -/- mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5'-phosphorylated nicks (5'p-nicks) between Okazaki fragments, typically resolved by Lig1. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, particularly harmful to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5'p-nicks explains the detrimental effects of PARP2 inhibition on erythropoiesis, revealing the mechanism behind the PARPi-induced anemia and leukemia, especially those with TP53/CHK2 loss. Significance This work shows that the hematological toxicities associated with PARP inhibitors stem not from impaired PARP1 or PARP2 enzymatic activity but rather from the presence of inactive PARP2 protein. Mechanistically, these toxicities reflect a unique role of PARP2 at 5'-phosphorylated DNA nicks during DNA replication in erythroblasts.
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