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Ge J, Ngo LP, Kaushal S, Tay IJ, Thadhani E, Kay JE, Mazzucato P, Chow D, Fessler J, Weingeist DM, Sobol RW, Samson LD, Floyd SR, Engelward BP. CometChip enables parallel analysis of multiple DNA repair activities [DNA repair 106 (2021) 103176-103202]. DNA Repair (Amst) 2024; 138:103677. [PMID: 38582050 DOI: 10.1016/j.dnarep.2024.103677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Ian J Tay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elina Thadhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jennifer E Kay
- Silent Spring, Institute, 320 Nevada Street, Newton, MA 02460, United States
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Danielle Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jessica Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, 02912, United States
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Scott R Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27514, United States
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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2
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Lin CH, Chin Y, Zhou M, Sobol RW, Hung MC, Tan M. Protein lipoylation: mitochondria, cuproptosis, and beyond. Trends Biochem Sci 2024:S0968-0004(24)00096-3. [PMID: 38714376 DOI: 10.1016/j.tibs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024]
Abstract
Protein lipoylation, a crucial post-translational modification (PTM), plays a pivotal role in mitochondrial function and emerges as a key player in cell death through cuproptosis. This novel copper-driven cell death pathway is activated by excessive copper ions binding to lipoylated mitochondrial proteins, disrupting energy production and causing lethal protein aggregation and cell death. The intricate relationship among protein lipoylation, cellular energy metabolism, and cuproptosis offers a promising avenue for regulating essential cellular functions. This review focuses on the mechanisms of lipoylation and its significant impact on cell metabolism and cuproptosis, emphasizing the key genes involved and their implications for human diseases. It offers valuable insights into targeting dysregulated cellular metabolism for therapeutic purposes.
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Affiliation(s)
- Cheng-Han Lin
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Yeh Chin
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School and Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Mien-Chie Hung
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.
| | - Ming Tan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.
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Inanc B, Fang Q, Andrews JF, Zeng X, Clark J, Li J, Dey NB, Ibrahim M, Sykora P, Yu Z, Braganza A, Verheij M, Jonkers J, Yates NA, Vens C, Sobol RW. TRIP12 governs DNA Polymerase β involvement in DNA damage response and repair. bioRxiv 2024:2024.04.08.588474. [PMID: 38645048 PMCID: PMC11030427 DOI: 10.1101/2024.04.08.588474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The multitude of DNA lesion types, and the nuclear dynamic context in which they occur, present a challenge for genome integrity maintenance as this requires the engagement of different DNA repair pathways. Specific 'repair controllers' that facilitate DNA repair pathway crosstalk between double strand break (DSB) repair and base excision repair (BER), and regulate BER protein trafficking at lesion sites, have yet to be identified. We find that DNA polymerase β (Polβ), crucial for BER, is ubiquitylated in a BER complex-dependent manner by TRIP12, an E3 ligase that partners with UBR5 and restrains DSB repair signaling. Here we find that, TRIP12, but not UBR5, controls cellular levels and chromatin loading of Polβ. Required for Polβ foci formation, TRIP12 regulates Polβ involvement after DNA damage. Notably, excessive TRIP12-mediated shuttling of Polβ affects DSB formation and radiation sensitivity, underscoring its precedence for BER. We conclude that the herein discovered trafficking function at the nexus of DNA repair signaling pathways, towards Polβ-directed BER, optimizes DNA repair pathway choice at complex lesion sites.
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Sobol RW. Mouse models to explore the biological and organismic role of DNA polymerase beta. Environ Mol Mutagen 2024; 65 Suppl 1:57-71. [PMID: 38619421 PMCID: PMC11027944 DOI: 10.1002/em.22593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Gene knock-out (KO) mouse models for DNA polymerase beta (Polβ) revealed that loss of Polβ leads to neonatal lethality, highlighting the critical organismic role for this DNA polymerase. While biochemical analysis and gene KO cell lines have confirmed its biochemical role in base excision repair and in TET-mediated demethylation, more long-lived mouse models continue to be developed to further define its organismic role. The Polb-KO mouse was the first of the Cre-mediated tissue-specific KO mouse models. This technology was exploited to investigate roles for Polβ in V(D)J recombination (variable-diversity-joining rearrangement), DNA demethylation, gene complementation, SPO11-induced DNA double-strand break repair, germ cell genome stability, as well as neuronal differentiation, susceptibility to genotoxin-induced DNA damage, and cancer onset. The revolution in knock-in (KI) mouse models was made possible by CRISPR/cas9-mediated gene editing directly in C57BL/6 zygotes. This technology has helped identify phenotypes associated with germline or somatic mutants of Polβ. Such KI mouse models have helped uncover the importance of key Polβ active site residues or specific Polβ enzyme activities, such as the PolbY265C mouse that develops lupus symptoms. More recently, we have used this KI technology to mutate the Polb gene with two codon changes, yielding the PolbL301R/V303R mouse. In this KI mouse model, the expressed Polβ protein cannot bind to its obligate heterodimer partner, Xrcc1. Although the expressed mutant Polβ protein is proteolytically unstable and defective in recruitment to sites of DNA damage, the homozygous PolbL301R/V303R mouse is viable and fertile, yet small in stature. We expect that this and additional targeted mouse models under development are poised to reveal new biological and organismic roles for Polβ.
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Affiliation(s)
- Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912
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Yan S, Gaddameedhi S, Sobol RW. Inspiring basic and applied research in genome integrity mechanisms: Dedication to Samuel H. Wilson. Environ Mol Mutagen 2024; 65 Suppl 1:4-8. [PMID: 38619433 DOI: 10.1002/em.22595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
This Special Issue (SI) of Environmental and Molecular Mutagenesis (EMM), entitled "Inspiring Basic and Applied Research in Genome Integrity Mechanisms," is to update the community on recent findings and advances on genome integrity mechanisms with emphasis on their importance for basic and environmental health sciences. This SI includes two research articles, one brief research communication, and four reviews that highlight cutting edge research findings and perspectives, from both established leaders and junior trainees, on DNA repair mechanisms. In particular, the authors provided an updated understanding on several distinct enzymes (e.g., DNA polymerase beta, DNA polymerase theta, DNA glycosylase NEIL2) and the associated molecular mechanisms in base excision repair, nucleotide excision repair, and microhomology-mediated end joining of double-strand breaks. In addition, genome-wide sequencing analysis or site-specific mutational signature analysis of DNA lesions from environmental mutagens (e.g., UV light and aflatoxin) provide further characterization and sequence context impact of DNA damage and mutations. This SI is dedicated to the legacy of Dr. Samuel H. Wilson from the U.S. National Institute of Environmental Health Sciences at the National Institutes of Health.
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Affiliation(s)
- Shan Yan
- Department of Biological Sciences and School of Data Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Shobhan Gaddameedhi
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Brown University, Providence, Rhode Island, USA
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Almohdar D, Gulkis M, Ortiz A, Tang Q, Sobol RW, Çağlayan M. Impact of polβ/XRCC1 Interaction Variants on the Efficiency of Nick Sealing by DNA Ligase IIIα in the Base Excision Repair Pathway. J Mol Biol 2024; 436:168410. [PMID: 38135179 PMCID: PMC11090158 DOI: 10.1016/j.jmb.2023.168410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
Base excision repair (BER) requires a coordination from gap filling by DNA polymerase (pol) β to subsequent nick sealing by DNA ligase (LIG) IIIα at downstream steps of the repair pathway. X-ray cross-complementing protein 1 (XRCC1), a non-enzymatic scaffolding protein, forms repair complexes with polβ and LIGIIIα. Yet, the impact of the polβ mutations that affect XRCC1 interaction and protein stability on the repair pathway coordination during nick sealing by LIGIIIα remains unknown. Our results show that the polβ colon cancer-associated variant T304 exhibits a reduced interaction with XRCC1 and the mutations in the interaction interface of V303 loop (L301R/V303R/V306R) and at the lysine residues (K206A/K244A) that prevent ubiquitin-mediated degradation of the protein exhibit a diminished repair protein complex formation with XRCC1. Furthermore, we demonstrate no significant effect on gap and nick DNA binding affinity of wild-type polβ by these mutations. Finally, our results reveal that XRCC1 leads to an efficient channeling of nick repair products after nucleotide incorporation by polβ variants to LIGIIIα, which is compromised by the L301R/V303R/V306R and K206A/K244A mutations. Overall, our findings provide insight into how the mutations in the polβ/XRCC1 interface and the regions affecting protein stability could dictate accurate BER pathway coordination at the downstream steps involving nick sealing by LIGIIIα.
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Affiliation(s)
- Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Abigail Ortiz
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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Al-Rahahleh RQ, Saville KM, Andrews JF, Wu Z, Koczor CA, Sobol RW. Overexpression of the WWE domain of RNF146 modulates poly-(ADP)-ribose dynamics at sites of DNA damage. bioRxiv 2023:2023.12.29.573650. [PMID: 38234836 PMCID: PMC10793466 DOI: 10.1101/2023.12.29.573650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Protein poly-ADP-ribosylation (PARylation) is a post-translational modification formed by transfer of successive units of ADP-ribose to target proteins to form poly-ADP-ribose (PAR) chains. PAR plays a critical role in the DNA damage response (DDR) by acting as a signaling platform to promote the recruitment of DNA repair factors to the sites of DNA damage that bind via their PAR-binding domains (PBDs). Several classes of PBD families have been recognized, which identify distinct parts of the PAR chain. Proteins encoding PBDs play an essential role in conveying the PAR-mediated signal through their interaction with PAR chains, which mediates many cellular functions, including the DDR. The WWE domain identifies the iso-ADP-ribose moiety of the PAR chain. We recently described the WWE domain of RNF146 as a robust genetically encoded probe, when fused to EGFP, for detection of PAR in live cells. Here, we evaluated other PBD candidates as molecular PAR probes in live cells, including several other WWE domains and an engineered macrodomain. In addition, we demonstrate unique PAR dynamics when tracked by different PAR binding domains, a finding that that can be exploited for modulation of the PAR-dependent DNA damage response.
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Affiliation(s)
- Rasha Q. Al-Rahahleh
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912
- Department of Pharmacology & Mitchell Cancer Institute, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Kate M. Saville
- Department of Pharmacology & Mitchell Cancer Institute, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Joel F. Andrews
- Department of Pharmacology & Mitchell Cancer Institute, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Zhijin Wu
- Department of Biostatistics, Brown University, Providence, RI 02912
| | - Christopher A. Koczor
- Department of Pharmacology & Mitchell Cancer Institute, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912
- Department of Pharmacology & Mitchell Cancer Institute, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
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Das D, Duncton MAJ, Georgiadis TM, Pellicena P, Clark J, Sobol RW, Georgiadis MM, King-Underwood J, Jobes DV, Chang C, Gao Y, Deacon AM, Wilson DM. A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1. Int J Mol Sci 2023; 24:16637. [PMID: 38068959 PMCID: PMC10706420 DOI: 10.3390/ijms242316637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM ("SAR by X-ray Poses Quickly") platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or "undruggable" targets, allows for (i) hit generation; (ii) the mapping of protein-ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.
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Affiliation(s)
- Debanu Das
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | | | | | | | - Jennifer Clark
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
- Department of Pathology & Laboratory Medicine, Warrant Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Millie M. Georgiadis
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - David V. Jobes
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Mid-Atlantic BioTherapeutics, Inc., Doylestown, PA 18902, USA
| | - Caleb Chang
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Yang Gao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashley M. Deacon
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | - David M. Wilson
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Biomedical Research Institute, Hasselt University, 3500 Diepenbeek, Belgium
- Belgium & Boost Scientific, 3550 Heusden-Zolder, Belgium
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Sobol RW. Editorial: DNA repair and nucleic acid therapeutics in cancer. NAR Cancer 2023; 5:zcad044. [PMID: 37645072 PMCID: PMC10461458 DOI: 10.1093/narcan/zcad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023] Open
Affiliation(s)
- Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst 2023; 14:447-463.e8. [PMID: 37220749 PMCID: PMC10330685 DOI: 10.1016/j.cels.2023.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into complexes, including constitutive interactions and those responding to genomic insult. Here, we use multi-conditional network analysis to systematically map DDR assemblies at multiple scales. Affinity purifications of 21 DDR proteins, with/without genotoxin exposure, are combined with multi-omics data to reveal a hierarchical organization of 605 proteins into 109 assemblies. The map captures canonical repair mechanisms and proposes new DDR-associated proteins extending to stress, transport, and chromatin functions. We find that protein assemblies closely align with genetic dependencies in processing specific genotoxins and that proteins in multiple assemblies typically act in multiple genotoxin responses. Follow-up by DDR functional readouts newly implicates 12 assembly members in double-strand-break repair. The DNA damage response assemblies map is available for interactive visualization and query (ccmi.org/ddram/).
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Affiliation(s)
- Anton Kratz
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Minkyu Kim
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA; University of Texas Health Science Center San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX 78229, USA
| | - Marcus R Kelly
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Fan Zheng
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Christopher A Koczor
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Jianfeng Li
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Keiichiro Ono
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Yue Qin
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Christopher Churas
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jing Chen
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Rudolf T Pillich
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jisoo Park
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Rachel Collier
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Kate Licon
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Dexter Pratt
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Robert W Sobol
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA; Brown University, Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Providence, RI 02903, USA.
| | - Nevan J Krogan
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
| | - Trey Ideker
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
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11
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Parker LL, Bonner CM, Sobol RW, Arrieta MI. Co-creation and engagement in a DNA integrity cohort study. J Clin Transl Sci 2023; 7:e122. [PMID: 37313377 PMCID: PMC10260344 DOI: 10.1017/cts.2023.556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Introduction The partnership between a research community engagement team (CE Team) and a community advisory board (CAB) formed the basis for bidirectional communication in developing resources for participant recruitment in a DNA integrity study. Engaging with a minoritized community, this partnership focused on respect, accessibility, and expanded engagement. Methods A ten-member CAB, working in two groups defined by meeting time convenience, provided insight and feedback to the CE Team in the creation of recruitment and consent materials, via an iterative design process in which one CAB group reviewed and enhanced materials, and the second group tested and refined them further. The continuous analysis of CE Team notes from CAB meetings captured information needed both for materials refinement and implementation of CAB-suggested activities. Results The partnership resulted in the co-creation of recruitment and consent materials that facilitated the enrollment of 191 individuals into the study. The CAB encouraged and assisted in expanded engagement inclusive of community leaders. This broader engagement provided information about the DNA integrity study to community decision-makers as well as responded to questions and concerns about the research. The bidirectional communication between the CAB and the CE Team encouraged the researchers to consider topics and research interests related to the current study but also responsive to community concerns. Conclusions The CAB helped the CE Team develop a better understanding of the language of partnership and respect. In this way, the partnership opened doors for expanded community engagement and effective communication with potential study participants.
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Affiliation(s)
- L. Lynette Parker
- Center for Healthy Communities, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Chantel M. Bonner
- Center for Healthy Communities, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI, USA
| | - Martha I. Arrieta
- Center for Healthy Communities, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
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12
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Koczor CA, Thompson MK, Sharma N, Prakash A, Sobol RW. Polβ/XRCC1 heterodimerization dictates DNA damage recognition and basal Polβ protein levels without interfering with mouse viability or fertility. DNA Repair (Amst) 2023; 123:103452. [PMID: 36702010 PMCID: PMC9992099 DOI: 10.1016/j.dnarep.2023.103452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/07/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
DNA Polymerase β (Polβ) performs two critical enzymatic steps during base excision repair (BER) - gap filling (nucleotidyl transferase activity) and gap tailoring (dRP lyase activity). X-ray repair cross complementing 1 (XRCC1) facilitates the recruitment of Polβ to sites of DNA damage through an evolutionarily conserved Polβ/XRCC1 interaction interface, the V303 loop. While previous work describes the importance of the Polβ/XRCC1 interaction for human Polβ protein stability and recruitment to sites of DNA damage, the impact of disrupting the Polβ/XRCC1 interface on animal viability, physiology, and fertility is unknown. Here, we characterized the effect of disrupting Polβ/XRCC1 heterodimerization in mice and mouse cells by complimentary approaches. First, we demonstrate, via laser micro-irradiation, that mouse Polβ amino acid residues L301 and V303 are critical to facilitating Polβ recruitment to sites of DNA damage. Next, we solved the crystal structures of mouse wild type Polβ and a mutant protein harboring alterations in residues L301 and V303 (L301R/V303R). Our structural analyses suggest that Polβ amino acid residue V303 plays a role in maintaining an interaction with the oxidized form of XRCC1. Finally, we created CRISPR/Cas9-modified Polb mice with homozygous L301R/V303R mutations (PolbL301R-V303R/L301R-V303R) that are fertile yet exhibit 15% reduced body weight at 17 weeks of age, as compared to heterozygous mice. Fibroblasts derived from PolbL301R-V303R/L301R-V303R mice demonstrate that mutation of mouse Polβ's XRCC1 interaction domain leads to an ∼85% decrease in Polβ protein levels. In all, these studies are consistent with a role for the oxidized form of XRCC1 in providing stability to the Polβ protein through Polβ/XRCC1 heterodimer formation.
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Affiliation(s)
- Christopher A Koczor
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Marlo K Thompson
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Nidhi Sharma
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA.
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13
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Koczor CA, Saville KM, Al-Rahahleh RQ, Andrews JF, Li J, Sobol RW. Quantitative Analysis of Nuclear Poly(ADP-Ribose) Dynamics in Response to Laser-Induced DNA Damage. Methods Mol Biol 2023; 2609:43-59. [PMID: 36515828 PMCID: PMC9920208 DOI: 10.1007/978-1-0716-2891-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Poly(ADP-ribose) (PAR), catalyzed by members of the poly(ADP-ribose) polymerase family of enzymes, is a posttranslational modification with a critical role in most mechanisms of DNA repair. Upon activation of poly(ADP-ribose) polymerase isoforms 1 and 2 (PARP-1 and PARP-2), the proteins of the base excision repair (BER) and single-strand break repair (SSBR) pathways form DNA lesion-dependent, transient complexes to facilitate repair. PAR is central to the temporal dynamics of BER/SSBR complex assembly and disassembly. To enhance cellular PAR analysis, we developed LivePAR, a fluorescently tagged PAR-binding fusion protein and genetically encoded imaging probe for live cell, quantitative analysis of PAR in mammalian cells. LivePAR has the advantage that it enables real-time imaging of PAR formation in cells and significantly overcomes limitations of immunocytochemistry for PAR analysis. This chapter describes the protocols needed to develop cells expressing LivePAR or EGFP-tagged BER proteins and to evaluate laser-induced formation of PAR and comparison to the assembly of the BER proteins XRCC1 and DNA polymerase-β.
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Affiliation(s)
- Christopher A Koczor
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kate M Saville
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Rasha Q Al-Rahahleh
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
- Department of Pathology and Laboratory Medicine & Legorreta Cancer Center, Brown University, Providence, RI, USA
| | - Joel F Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
- Department of Pathology and Laboratory Medicine & Legorreta Cancer Center, Brown University, Providence, RI, USA.
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14
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Chin Y, Gumilar KE, Li XG, Tjokroprawiro BA, Lu CH, Lu J, Zhou M, Sobol RW, Tan M. Targeting HSF1 for cancer treatment: mechanisms and inhibitor development. Theranostics 2023; 13:2281-2300. [PMID: 37153737 PMCID: PMC10157728 DOI: 10.7150/thno.82431] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/06/2023] [Indexed: 05/10/2023] Open
Abstract
Heat Shock Factor 1 (HSF1) is a master regulator of heat shock responsive signaling. In addition to playing critical roles in cellular heat shock response, emerging evidence suggests that HSF1 also regulates a non-heat shock responsive transcriptional network to handle metabolic, chemical, and genetic stress. The function of HSF1 in cellular transformation and cancer development has been extensively studied in recent years. Due to important roles for HSF1 for coping with various stressful cellular states, research on HSF1 has been very active. New functions and molecular mechanisms underlying these functions have been continuously discovered, providing new targets for novel cancer treatment strategies. In this article, we review the essential roles and mechanisms of HSF1 action in cancer cells, focusing more on recently discovered functions and their underlying mechanisms to reflect the new advances in cancer biology. In addition, we emphasize new advances with regard to HSF1 inhibitors for cancer drug development.
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Affiliation(s)
- Yeh Chin
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
| | - Khanisyah E Gumilar
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
- The Department of Obstetrics and Gynecology, Medical Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, China Medical University, Taichung, Taiwan, R.O.C
| | - Brahmana A. Tjokroprawiro
- The Department of Obstetrics and Gynecology, Medical Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Chien-Hsing Lu
- Department of Gynecology and Obstetrics, Taichung Veterans General Hospital, Taichung, Taiwan, R.O.C
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, USA
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, USA
| | - Ming Tan
- Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, China Medical University, Taichung, Taiwan, R.O.C
- ✉ Corresponding author: Ming Tan, Institute of Biochemistry and Molecular Biology, China Medical University (Taiwan), E-mail:
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15
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Yan S, Zhao J, Kemp M, Sobol RW. Editorial: Mechanistic studies of genome integrity, environmental health, and cancer etiology. Front Cell Dev Biol 2022; 10:1026326. [PMID: 36247007 PMCID: PMC9554606 DOI: 10.3389/fcell.2022.1026326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/07/2022] [Indexed: 01/31/2023] Open
Affiliation(s)
- Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
| | - Jianjun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
| | - Michael Kemp
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
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16
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Koczor CA, Haider AJ, Saville KM, Li J, Andrews JF, Beiser AV, Sobol RW. Live Cell Detection of Poly(ADP-Ribose) for Use in Genetic and Genotoxic Compound Screens. Cancers (Basel) 2022; 14:3676. [PMID: 35954352 PMCID: PMC9367489 DOI: 10.3390/cancers14153676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Poly(ADP-ribose) (PAR) is a molecular scaffold that aids in the formation of DNA repair protein complexes. Tools to sensitively quantify PAR in live cells have been lacking. We recently described the LivePAR probe (EGFP fused to the RNF146-encoded WWE PAR binding domain) to measure PAR formation at sites of laser micro-irradiation in live cells. Here, we present two methods that expand on the use of LivePAR and its WWE domain. First, LivePAR enriches in the nucleus of cells following genotoxic challenge. Image quantitation can identify single-cell PAR formation following genotoxic stress at concentrations lower than PAR ELISA or PAR immunoblot, with greater sensitivity to genotoxic stress than CometChip. In a second approach, we used the RNF146-encoded WWE domain to develop a split luciferase probe for analysis in a 96-well plate assay. We then applied these PAR analysis tools to demonstrate their broad applicability. First, we show that both approaches can identify genetic modifications that alter PARylation levels, such as hyper-PARylation in BRCA2-deficient cancer cells. Second, we demonstrate the utility of the WWE split luciferase assay to characterize the cellular response of genotoxins, PARP inhibitors, and PARG inhibitors, thereby providing a screening method to identify PAR modulating compounds.
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Affiliation(s)
- Christopher A. Koczor
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Aaron J. Haider
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Kate M. Saville
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Jianfeng Li
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Joel F. Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Alison V. Beiser
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Robert W. Sobol
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
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17
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Li J, Koczor CA, Saville KM, Hayat F, Beiser A, McClellan S, Migaud ME, Sobol RW. Overcoming Temozolomide Resistance in Glioblastoma via Enhanced NAD + Bioavailability and Inhibition of Poly-ADP-Ribose Glycohydrolase. Cancers (Basel) 2022; 14:3572. [PMID: 35892832 PMCID: PMC9331395 DOI: 10.3390/cancers14153572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Glioblastoma multiforme (GBM) is an incurable brain cancer with an average survival of approximately 15 months. Temozolomide (TMZ) is a DNA alkylating agent for the treatment of GBM. However, at least 50% of the patients treated with TMZ show poor response, primarily due to elevated expression of the repair protein O6-methylguanine-DNA methyltransferase (MGMT) or due to defects in the mismatch repair (MMR) pathway. These resistance mechanisms are either somatic or arise in response to treatment, highlighting the need to uncover treatments to overcome resistance. We found that administration of the NAD+ precursor dihydronicotinamide riboside (NRH) to raise cellular NAD+ levels combined with PARG inhibition (PARGi) triggers hyperaccumulation of poly(ADP-ribose) (PAR), resulting from both DNA damage-induced and replication-stress-induced PARP1 activation. Here, we show that the NRH/PARGi combination enhances the cytotoxicity of TMZ. Specifically, NRH rapidly increases NAD+ levels in both TMZ-sensitive and TMZ-resistant GBM-derived cells and enhances the accumulation of PAR following TMZ treatment. Furthermore, NRH promotes hyperaccumulation of PAR in the presence of TMZ and PARGi. This combination strongly suppresses the cell growth of GBM cells depleted of MSH6 or cells expressing MGMT, suggesting that this regimen may improve the efficacy of TMZ to overcome treatment resistance in GBM.
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Affiliation(s)
- Jianfeng Li
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Christopher A. Koczor
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Kate M. Saville
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Faisal Hayat
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Alison Beiser
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Steven McClellan
- Mitchell Cancer Institute Flow Cytometry SRL, University of South Alabama, Mobile, AL 36604, USA;
| | - Marie E. Migaud
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (J.L.); (C.A.K.); (K.M.S.); (F.H.); (A.B.); (M.E.M.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
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18
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Mancuso P, Tricarico R, Bhattacharjee V, Cosentino L, Kadariya Y, Jelinek J, Nicolas E, Einarson M, Beeharry N, Devarajan K, Katz RA, Dorjsuren DG, Sun H, Simeonov A, Giordano A, Testa JR, Davidson G, Davidson I, Larue L, Sobol RW, Yen TJ, Bellacosa A. Correction to: Thymine DNA glycosylase as a novel target for melanoma. Oncogene 2022; 41:3300-3301. [PMID: 35505094 DOI: 10.1038/s41388-022-02335-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pietro Mancuso
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.,Department of Medical Biotechnologies, Universita' degli Studi di Siena, Siena, Italy.,Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, 91405, Orsay, France
| | - Rossella Tricarico
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Vikram Bhattacharjee
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Laura Cosentino
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Yuwaraj Kadariya
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Emmanuelle Nicolas
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Margret Einarson
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Neil Beeharry
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Karthik Devarajan
- Department of Biostatistics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Richard A Katz
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Dorjbal G Dorjsuren
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Hongmao Sun
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Antonio Giordano
- Department of Medical Biotechnologies, Universita' degli Studi di Siena, Siena, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Joseph R Testa
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404, Illkirch, France.,Equipe Labellisée Ligue Contre le Cancer, Orsay, France
| | - Lionel Larue
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, 91405, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Orsay, France.,University Paris-Sud, University Paris-Saclay, CNRS UMR3347, Orsay, France
| | - Robert W Sobol
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Timothy J Yen
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
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19
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Fujii S, Sobol RW, Fuchs RP. Double-Strand Breaks: when DNA Repair Events Accidentally Meet. DNA Repair (Amst) 2022; 112:103303. [PMID: 35219626 PMCID: PMC8898275 DOI: 10.1016/j.dnarep.2022.103303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/23/2022] [Accepted: 02/17/2022] [Indexed: 01/26/2023]
Abstract
The cellular response to alkylation damage is complex, involving multiple DNA repair pathways and checkpoint proteins, depending on the DNA lesion, the cell type, and the cellular proliferation state. The repair of and response to O-alkylation damage, primarily O6-methylguaine DNA adducts (O6-mG), is the purview of O6-methylguanine-DNA methyltransferase (MGMT). Alternatively, this lesion, if left un-repaired, induces replication-dependent formation of the O6-mG:T mis-pair and recognition of this mis-pair by the post-replication mismatch DNA repair pathway (MMR). Two models have been suggested to account for MMR and O6-mG DNA lesion dependent formation of DNA double-strand breaks (DSBs) and the resulting cytotoxicity - futile cycling and direct DNA damage signaling. While there have been hints at crosstalk between the MMR and base excision repair (BER) pathways, clear mechanistic evidence for such pathway coordination in the formation of DSBs has remained elusive. However, using a novel protein capture approach, Fuchs and colleagues have demonstrated that DSBs result from an encounter between MMR-induced gaps initiated at alkylation induced O6-mG:C sites and BER-induced nicks at nearby N-alkylation adducts in the opposite strand. The accidental encounter between these two repair events is causal in the formation of DSBs and the resulting cellular response, documenting a third model to account for O6-mG induced cell death in non-replicating cells. This graphical review highlights the details of this Repair Accident model, as compared to current models, and we discuss potential strategies to improve clinical use of alkylating agents such as temozolomide, that can be inferred from the Repair Accident model.
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Affiliation(s)
- Shingo Fujii
- Marseille Medical Genetics, UMR1251 Marseille, France
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA; Dept of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
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20
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Li J, Garavaglia S, Ye Z, Moretti A, Belyaeva OV, Beiser A, Ibrahim M, Wilk A, McClellan S, Klyuyeva AV, Goggans KR, Kedishvili NY, Salter EA, Wierzbicki A, Migaud ME, Mullett SJ, Yates NA, Camacho CJ, Rizzi M, Sobol RW. A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells. Commun Biol 2021; 4:1420. [PMID: 34934174 PMCID: PMC8692581 DOI: 10.1038/s42003-021-02949-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 12/07/2021] [Indexed: 01/31/2023] Open
Abstract
Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH+ cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.
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Affiliation(s)
- Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Zhaofeng Ye
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Andrea Moretti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Alison Beiser
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Md Ibrahim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steve McClellan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - E Alan Salter
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steven J Mullett
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nathan A Yates
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA.
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21
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Snyder NW, O'Brien J, Singh B, Buchan G, Arroyo AD, Liu X, Bostwick A, Varner EL, Angajala A, Sobol RW, Blair IA, Mesaros C, Wendell SG. Primary saturation of α, β-unsaturated carbonyl containing fatty acids does not abolish electrophilicity. Chem Biol Interact 2021; 350:109689. [PMID: 34634267 PMCID: PMC8574066 DOI: 10.1016/j.cbi.2021.109689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022]
Abstract
Metabolism of polyunsaturated fatty acids results in the formation of hydroxylated fatty acids that can be further oxidized by dehydrogenases, often resulting in the formation of electrophilic, α,β-unsaturated ketone containing fatty acids. As electrophiles are associated with redox signaling, we sought to investigate the metabolism of the oxo-fatty acid products in relation to their double bond architecture. Using an untargeted liquid chromatography mass spectrometry approach, we identified mono- and di-saturated products of the arachidonic acid-derived 11-oxoeicosatetraenoic acid (11-oxoETE) and mono-saturated metabolites of 15-oxoETE and docosahexaenoic acid-derived 17-oxodocosahexaenoinc acid (17-oxoDHA) in both human A549 lung carcinoma and umbilical vein endothelial cells. Notably, mono-saturated oxo-fatty acids maintained their electrophilicity as determined by nucleophilic conjugation to glutathione while a second saturation of 11-oxoETE resulted in a loss of electrophilicity. These results would suggest that prostaglandin reductase 1 (PTGR1), known only for its reduction of the α,β-unsaturated double bond, was not responsible for the saturation of oxo-fatty acids at alternative double bonds. Surprisingly, knockdown of PTGR1 expression by shRNA confirmed its participation in the formation of 15-oxoETE and 17-oxoDHA mono-saturated metabolites. Furthermore, overexpression of PTGR1 in A549 cells increased the rate and total amount of oxo-fatty acid saturation. These findings will further facilitate the study of electrophilic fatty acid metabolism and signaling in the context of inflammatory diseases and cancer where they have been shown to have anti-inflammatory and anti-proliferative signaling properties.
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Affiliation(s)
- Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - James O'Brien
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Bhupinder Singh
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Gregory Buchan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Alejandro D Arroyo
- Department of Systems Pharmacology and Translational Therapeutics, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27695, USA
| | - Anna Bostwick
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Erika L Varner
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Anusha Angajala
- Department of Pharmacology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36688, USA
| | - Robert W Sobol
- Department of Pharmacology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36688, USA
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Clementina Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stacy G Wendell
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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22
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Li J, M. Saville K, Ibrahim M, Zeng X, McClellan S, Angajala A, Beiser A, Andrews JF, Sun M, Koczor CA, Clark J, Hayat F, Makarov MV, Wilk A, Yates NA, Migaud ME, Sobol RW. NAD + bioavailability mediates PARG inhibition-induced replication arrest, intra S-phase checkpoint and apoptosis in glioma stem cells. NAR Cancer 2021; 3:zcab044. [PMID: 34806016 PMCID: PMC8600031 DOI: 10.1093/narcan/zcab044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/20/2021] [Accepted: 11/10/2021] [Indexed: 01/31/2023] Open
Abstract
Elevated expression of the DNA damage response proteins PARP1 and poly(ADP-ribose) glycohydrolase (PARG) in glioma stem cells (GSCs) suggests that glioma may be a unique target for PARG inhibitors (PARGi). While PARGi-induced cell death is achieved when combined with ionizing radiation, as a single agent PARG inhibitors appear to be mostly cytostatic. Supplementation with the NAD+ precursor dihydronicotinamide riboside (NRH) rapidly increased NAD+ levels in GSCs and glioma cells, inducing PARP1 activation and mild suppression of replication fork progression. Administration of NRH+PARGi triggers hyperaccumulation of poly(ADP-ribose) (PAR), intra S-phase arrest and apoptosis in GSCs but minimal PAR induction or cytotoxicity in normal astrocytes. PAR accumulation is regulated by select PARP1- and PAR-interacting proteins. The involvement of XRCC1 highlights the base excision repair pathway in responding to replication stress while enhanced interaction of PARP1 with PCNA, RPA and ORC2 upon PAR accumulation implicates replication associated PARP1 activation and assembly with pre-replication complex proteins upon initiation of replication arrest, the intra S-phase checkpoint and the onset of apoptosis.
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Affiliation(s)
- Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Kate M. Saville
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Md Ibrahim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, PA 15213, USA
| | - Steve McClellan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Anusha Angajala
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Alison Beiser
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Joel F Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Mai Sun
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, PA 15213, USA
| | - Christopher A Koczor
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Jennifer Clark
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Faisal Hayat
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Mikhail V Makarov
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Nathan A Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, PA 15213, USA,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W Sobol
- To whom correspondence should be addressed. Tel: +1 251 445 9846;
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23
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Ge J, Ngo LP, Kaushal S, Tay IJ, Thadhani E, Kay JE, Mazzucato P, Chow DN, Fessler JL, Weingeist DM, Sobol RW, Samson LD, Floyd SR, Engelward BP. CometChip enables parallel analysis of multiple DNA repair activities. DNA Repair (Amst) 2021; 106:103176. [PMID: 34365116 PMCID: PMC8439179 DOI: 10.1016/j.dnarep.2021.103176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/28/2022]
Abstract
DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these applications of the CometChip platform, we expand the utility of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.
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Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, United States
| | - Ian J Tay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elina Thadhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jennifer E Kay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Danielle N Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jessica L Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, United States; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, United States
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Scott R Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27514, United States
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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24
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Kim JH, Jeong K, Li J, Murphy JM, Vukadin L, Stone JK, Richard A, Tran J, Gillespie GY, Flemington EK, Sobol RW, Lim STS, Ahn EYE. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun 2021; 12:5551. [PMID: 34548489 PMCID: PMC8455679 DOI: 10.1038/s41467-021-25892-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a master regulator that activates PTBP1-mediated oncogenic splicing while suppressing RBFOX2-mediated non-oncogenic neuronal splicing in glioblastoma multiforme (GBM). SON is overexpressed in GBM patients and SON knockdown causes failure in intron removal from the PTBP1 transcript, resulting in PTBP1 downregulation and inhibition of its downstream oncogenic splicing. Furthermore, SON forms a complex with hnRNP A2B1 and antagonizes RBFOX2, which leads to skipping of RBFOX2-targeted cassette exons, including the PTBP2 neuronal exon. SON knockdown inhibits proliferation and clonogenicity of GBM cells in vitro and significantly suppresses tumor growth in orthotopic xenografts in vivo. Collectively, our study reveals that SON-mediated RNA splicing is a GBM vulnerability, implicating SON as a potential therapeutic target in brain tumors.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kyuho Jeong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - James M Murphy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Johnny Tran
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Ssang-Teak Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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25
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Kratz A, Kim M, Zheng F, Koczor CA, Fong S, Li J, Sobol RW, Krogan N, Ideker T. Abstract 2078: A multiscale map of DNA damage response in human cells. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The DNA damage response (DDR) ensures error-free genome replication and transcription, but is often disrupted in cancer. We developed DDRAM, a multilayered map of DDR derived from our own high-throughput physical interaction screen as well as genome, transcriptome, and proteome datasets from published sources. DDRAM organizes 328 genes into 41 hierarchical pathways. We identify 55 (17%) novel DDR genes with functions distributed across various pathways, and novel and more specific roles for 153 (47%) of established DDR genes. We perform epistasis mapping to support novel pathway assignments of FOXK1 in nucleotide metabolism and XRCC3 in the Fanconi anemia pathway. Using quantitative imaging of a fluorescent probe, in some cases confirmed by epistasis mapping, we experimentally validate members of the Short Patch Base Excision Repair pathway over a time course, revealing a more complete model of poly(ADP-ribose)-dependent recruitment to sites of DNA damage.
Citation Format: Anton Kratz, Minkyu Kim, Fan Zheng, Christopher A. Koczor, Samson Fong, Jianfeng Li, Robert W. Sobol, Nevan Krogan, Trey Ideker. A multiscale map of DNA damage response in human cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2078.
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Affiliation(s)
- Anton Kratz
- 1University of California San Diego, San Diego, CA
| | - Minkyu Kim
- 2University of California San Francisco, San Francisco, CA
| | - Fan Zheng
- 1University of California San Diego, San Diego, CA
| | | | - Samson Fong
- 1University of California San Diego, San Diego, CA
| | | | | | - Nevan Krogan
- 2University of California San Francisco, San Francisco, CA
| | - Trey Ideker
- 1University of California San Diego, San Diego, CA
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26
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. Biology (Basel) 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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27
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Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol 2020; 27:1152-1164. [PMID: 33046907 PMCID: PMC7809635 DOI: 10.1038/s41594-020-0512-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Abstract
The synthesis of poly(ADP-ribose) (PAR) reconfigures the local chromatin environment and recruits DNA-repair complexes to damaged chromatin. PAR degradation by poly(ADP-ribose) glycohydrolase (PARG) is essential for progression and completion of DNA repair. Here, we show that inhibition of PARG disrupts homology-directed repair (HDR) mechanisms that underpin alternative lengthening of telomeres (ALT). Proteomic analyses uncover a new role for poly(ADP-ribosyl)ation (PARylation) in regulating the chromatin-assembly factor HIRA in ALT cancer cells. We show that HIRA is enriched at telomeres during the G2 phase and is required for histone H3.3 deposition and telomere DNA synthesis. Depletion of HIRA elicits systemic death of ALT cancer cells that is mitigated by re-expression of ATRX, a protein that is frequently inactivated in ALT tumors. We propose that PARylation enables HIRA to fulfill its essential role in the adaptive response to ATRX deficiency that pervades ALT cancers.
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Affiliation(s)
- Song My Hoang
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle L Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Callen T Wallace
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dominic I James
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Ian D Waddell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Donald Ogilvie
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Kate M Smith
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | | | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jianfeng Li
- Department of Pharmacology and the Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée, Ligue contre le Cancer, Paris, France
| | - Robert W Sobol
- Department of Pharmacology and the Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Genevieve Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée, Ligue contre le Cancer, Paris, France
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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28
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Fang Q, Andrews J, Sharma N, Wilk A, Clark J, Slyskova J, Koczor CA, Lans H, Prakash A, Sobol RW. Stability and sub-cellular localization of DNA polymerase β is regulated by interactions with NQO1 and XRCC1 in response to oxidative stress. Nucleic Acids Res 2020; 47:6269-6286. [PMID: 31287140 PMCID: PMC6614843 DOI: 10.1093/nar/gkz293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/24/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
Protein–protein interactions regulate many essential enzymatic processes in the cell. Somatic mutations outside of an enzyme active site can therefore impact cellular function by disruption of critical protein–protein interactions. In our investigation of the cellular impact of the T304I cancer mutation of DNA Polymerase β (Polβ), we find that mutation of this surface threonine residue impacts critical Polβ protein–protein interactions. We show that proteasome-mediated degradation of Polβ is regulated by both ubiquitin-dependent and ubiquitin-independent processes via unique protein–protein interactions. The ubiquitin-independent proteasome pathway regulates the stability of Polβ in the cytosol via interaction between Polβ and NAD(P)H quinone dehydrogenase 1 (NQO1) in an NADH-dependent manner. Conversely, the interaction of Polβ with the scaffold protein X-ray repair cross complementing 1 (XRCC1) plays a role in the localization of Polβ to the nuclear compartment and regulates the stability of Polβ via a ubiquitin-dependent pathway. Further, we find that oxidative stress promotes the dissociation of the Polβ/NQO1 complex, enhancing the interaction of Polβ with XRCC1. Our results reveal that somatic mutations such as T304I in Polβ impact critical protein–protein interactions, altering the stability and sub-cellular localization of Polβ and providing mechanistic insight into how key protein–protein interactions regulate cellular responses to stress.
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Affiliation(s)
- Qingming Fang
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Joel Andrews
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Nidhi Sharma
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Anna Wilk
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Jennifer Clark
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Christopher A Koczor
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Aishwarya Prakash
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Robert W Sobol
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
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Wilk A, Hayat F, Cunningham R, Li J, Garavaglia S, Zamani L, Ferraris DM, Sykora P, Andrews J, Clark J, Davis A, Chaloin L, Rizzi M, Migaud M, Sobol RW. Extracellular NAD + enhances PARP-dependent DNA repair capacity independently of CD73 activity. Sci Rep 2020; 10:651. [PMID: 31959836 PMCID: PMC6971268 DOI: 10.1038/s41598-020-57506-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/29/2019] [Indexed: 02/06/2023] Open
Abstract
Changes in nicotinamide adenine dinucleotide (NAD+) levels that compromise mitochondrial function trigger release of DNA damaging reactive oxygen species. NAD+ levels also affect DNA repair capacity as NAD+ is a substrate for PARP-enzymes (mono/poly-ADP-ribosylation) and sirtuins (deacetylation). The ecto-5′-nucleotidase CD73, an ectoenzyme highly expressed in cancer, is suggested to regulate intracellular NAD+ levels by processing NAD+ and its bio-precursor, nicotinamide mononucleotide (NMN), from tumor microenvironments, thereby enhancing tumor DNA repair capacity and chemotherapy resistance. We therefore investigated whether expression of CD73 impacts intracellular NAD+ content and NAD+-dependent DNA repair capacity. Reduced intracellular NAD+ levels suppressed recruitment of the DNA repair protein XRCC1 to sites of genomic DNA damage and impacted the amount of accumulated DNA damage. Further, decreased NAD+ reduced the capacity to repair DNA damage induced by DNA alkylating agents. Overall, reversal of these outcomes through NAD+ or NMN supplementation was independent of CD73. In opposition to its proposed role in extracellular NAD+ bioprocessing, we found that recombinant human CD73 only poorly processes NMN but not NAD+. A positive correlation between CD73 expression and intracellular NAD+ content could not be made as CD73 knockout human cells were efficient in generating intracellular NAD+ when supplemented with NAD+ or NMN.
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Affiliation(s)
- Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Faisal Hayat
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Richard Cunningham
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Leila Zamani
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Davide M Ferraris
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Peter Sykora
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Amelia Technologies, 14676 Rothgeb Drive, Rockville, MD, 20850, USA
| | - Joel Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Jennifer Clark
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Amanda Davis
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, 34293, Montpellier, France
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Marie Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA. .,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA.
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30
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Sannai M, Doneddu V, Giri V, Seeholzer S, Nicolas E, Yip SC, Bassi MR, Mancuso P, Cortellino S, Cigliano A, Lurie R, Ding H, Chernoff J, Sobol RW, Yen TJ, Bagella L, Bellacosa A. Modification of the base excision repair enzyme MBD4 by the small ubiquitin-like molecule SUMO1. DNA Repair (Amst) 2019; 82:102687. [PMID: 31476572 PMCID: PMC6785017 DOI: 10.1016/j.dnarep.2019.102687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/21/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
Abstract
The base excision repair DNA N-glycosylase MBD4 (also known as MED1), an interactor of the DNA mismatch repair protein MLH1, plays a central role in the maintenance of genomic stability of CpG sites by removing thymine and uracil from G:T and G:U mismatches, respectively. MBD4 is also involved in DNA damage response and transcriptional regulation. The interaction with other proteins is likely critical for understanding MBD4 functions. To identify novel proteins that interact with MBD4, we used tandem affinity purification (TAP) from HEK-293 cells. The MBD4-TAP fusion and its co-associated proteins were purified sequentially on IgG and calmodulin affinity columns; the final eluate was shown to contain MLH1 by western blotting, and MBD4-associated proteins were identified by mass spectrometry. Bands with molecular weight higher than that expected for MBD4 (˜66 kD) yielded peptides corresponding to MBD4 itself and the small ubiquitin-like molecule-1 (SUMO1), suggesting that MBD4 is sumoylated in vivo. MBD4 sumoylation was validated by co-immunoprecipitation in HEK-293 and MCF7 cells, and by an in vitrosumoylation assay. Sequence and mutation analysis identified three main sumoylation sites: MBD4 is sumoylated preferentially on K137, with additional sumoylation at K215 and K377. Patterns of MBD4 sumoylation were altered, in a DNA damage-specific way, by the anti-metabolite 5-fluorouracil, the alkylating agent N-Methyl-N-nitrosourea and the crosslinking agent cisplatin. MCF7 extract expressing sumoylated MBD4 displays higher thymine glycosylase activity than the unmodified species. Of the 67 MBD4 missense mutations reported in The Cancer Genome Atlas, 14 (20.9%) map near sumoylation sites. These results indicate that MBD4 is sumoylated in vivo in a DNA damage-specific manner, and suggest that sumoylation serves to regulate its repair activity and could be compromised in cancer. This study expands the role played by sumoylation in fine-tuning DNA damage response and repair.
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Affiliation(s)
- Mara Sannai
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Valentina Doneddu
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA; Department of Biomedical Sciences, University of Sassari, Sassari, 07100, Italy
| | - Veda Giri
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Steven Seeholzer
- Proteomics Core, The Children's Hospital of Philadelphia, Philadelphia PA, 19104, USA
| | - Emmanuelle Nicolas
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Shu-Chin Yip
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Maria Rosaria Bassi
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Pietro Mancuso
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Salvatore Cortellino
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Antonio Cigliano
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Rebecca Lurie
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Hua Ding
- Proteomics Core, The Children's Hospital of Philadelphia, Philadelphia PA, 19104, USA
| | - Jonathan Chernoff
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Robert W Sobol
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Timothy J Yen
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, 07100, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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31
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Rai P, Sobol RW. Mechanisms of MTH1 inhibition-induced DNA strand breaks: The slippery slope from the oxidized nucleotide pool to genotoxic damage. DNA Repair (Amst) 2019; 77:18-26. [PMID: 30852368 DOI: 10.1016/j.dnarep.2019.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022]
Abstract
Unlike normal tissues, tumor cells possess a propensity for genomic instability, resulting from elevated oxidant levels produced by oncogenic signaling and aberrant cellular metabolism. Thus, targeting mechanisms that protect cancer cells from the tumor-inhibitory consequences of their redox imbalance and spontaneous DNA-damaging events is expected to have broad-spectrum efficacy and a high therapeutic index. One critical mechanism for tumor cell protection from oxidant stress is the hydrolysis of oxidized nucleotides. Human MutT homolog 1 (MTH1), the mammalian nudix (nucleoside diphosphate X) pyrophosphatase (NUDT1), protects tumor cells from oxidative stress-induced genomic DNA damage by cleansing the nucleotide pool of oxidized purine nucleotides. Depletion or pharmacologic inhibition of MTH1 results in genomic DNA strand breaks in many cancer cells. However, the mechanisms underlying how oxidized nucleotides, thought mainly to be mutagenic rather than genotoxic, induce DNA strand breaks are largely unknown. Given the recent therapeutic interest in targeting MTH1, a better understanding of such mechanisms is crucial to its successful translation into the clinic and in identifying the molecular contexts under which its inhibition is likely to be beneficial. Here we provide a comprehensive perspective on MTH1 function and its importance in protecting genome integrity, in the context of tumor-associated oxidative stress and the mechanisms that likely lead to irreparable DNA strand breaks as a result of MTH1 inhibition.
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Affiliation(s)
- Priyamvada Rai
- Department of Medicine/Division of Medical Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, United States; Sylvester Comprehensive Cancer Center, Miami, FL, 33136, United States.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, United States.
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32
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Liu Z, Zhang W, Phillips JB, Arora R, McClellan S, Li J, Kim JH, Sobol RW, Tan M. Immunoregulatory protein B7-H3 regulates cancer stem cell enrichment and drug resistance through MVP-mediated MEK activation. Oncogene 2019; 38:88-102. [PMID: 30082909 PMCID: PMC6318029 DOI: 10.1038/s41388-018-0407-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/31/2018] [Accepted: 06/03/2018] [Indexed: 12/05/2022]
Abstract
B7-H3 is a tumor-promoting glycoprotein that is expressed at low levels in most normal tissues, but is overexpressed in various human cancers which is associated with disease progression and poor patient outcome. Although numerous publications have reported the correlation between B7-H3 and cancer progression in many types of cancers, mechanistic studies on how B7-H3 regulates cancer malignancy are rare, and the mechanisms underlying the role of B7-H3 in drug resistance are almost unknown. Here we report a novel finding that upregulation of B7-H3 increases the breast cancer stem cell population and promotes cancer development. Depletion of B7-H3 in breast cancer significantly inhibits the cancer stem cells. By immunoprecipitation and mass spectrometry, we found that B7-H3 is associated with the major vault protein (MVP) and activates MEK through MVP-enhancing B-RAF and MEK interaction. B7-H3 expression increases stem cell population by binding to MVP which regulates the activation of the MAPK kinase pathway. Depletion of MVP blocks the activation of MEK induced by B7-H3 and dramatically inhibits B7-H3 induced stem cells. This study reports novel functions of B7-H3 in regulating breast cancer stem cell enrichment. The novel mechanism for B7-H3-induced stem cell propagation by regulating MVP/MEK signaling axis independent of the classic Ras pathway may have important implications in the development of strategies for overcoming cancer cell resistance to chemotherapy.
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Affiliation(s)
- Zixing Liu
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Wenling Zhang
- Department of Medical Laboratory Science, Xiangya School of Medicine, Central South University, Changsha, China
| | - Joshua B Phillips
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Ritu Arora
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Steven McClellan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Jiangfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Jin-Hwan Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Ming Tan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Biochemistry and Molecular Biology, University of South Alabama, 307N. University Blvd, Mobile, AL, 36688, USA.
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33
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Li J, Svilar D, McClellan S, Kim JH, Ahn EYE, Vens C, Wilson DM, Sobol RW. DNA Repair Molecular Beacon assay: a platform for real-time functional analysis of cellular DNA repair capacity. Oncotarget 2018; 9:31719-31743. [PMID: 30167090 PMCID: PMC6114979 DOI: 10.18632/oncotarget.25859] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/12/2018] [Indexed: 12/15/2022] Open
Abstract
Numerous studies have shown that select DNA repair enzyme activities impact response and/or toxicity of genotoxins, suggesting a requirement for enzyme functional analyses to bolster precision medicine or prevention. To address this need, we developed a DNA Repair Molecular Beacon (DRMB) platform that rapidly measures DNA repair enzyme activity in real-time. The DRMB assay is applicable for discovery of DNA repair enzyme inhibitors, for the quantification of enzyme rates and is sufficiently sensitive to differentiate cellular enzymatic activity that stems from variation in expression or effects of amino acid substitutions. We show activity measures of several different base excision repair (BER) enzymes, including proteins with tumor-identified point mutations, revealing lesion-, lesion-context- and cell-type-specific repair dependence; suggesting application for DNA repair capacity analysis of tumors. DRMB measurements using lysates from isogenic control and APE1-deficient human cells suggests the major mechanism of base lesion removal by most DNA glycosylases may be mono-functional base hydrolysis. In addition, development of a microbead-conjugated DRMB assay amenable to flow cytometric analysis further advances its application. Our studies establish an analytical platform capable of evaluating the enzyme activity of select DNA repair proteins in an effort to design and guide inhibitor development and precision cancer therapy options.
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Affiliation(s)
- Jianfeng Li
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - David Svilar
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steven McClellan
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Jung-Hyun Kim
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | | | - Conchita Vens
- The Netherlands Cancer Institute, Division of Cell Biology, Amsterdam, The Netherlands
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, IRP, NIH Baltimore, MD, USA
| | - Robert W Sobol
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA
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34
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Tricarico R, Mancuso P, Bhattacharjee V, Cosentino L, Nicolas E, Einarson M, Beeharry N, Devarajan K, Katz R, Dorjsuren DG, Simeonov A, Kadariya Y, Davidson G, Testa JR, Davidson I, Larue L, Sobol RW, Yen T, Bellacosa A. Abstract 1940: Thymine DNA glycosylase (TDG) as a novel target for melanoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Melanoma is an aggressive neoplasm with increasing incidence that bears the infamous distinction of being a recalcitrant cancer, i.e. a cancer with poor prognosis, lacking progress in diagnosis and treatment. In addition to conventional therapy, melanoma treatment is currently based on targeting the BRAF/MEK/ERK signal transduction pathway and immune checkpoints; however, advanced therapeutic approaches based on novel targets are urgently needed. We reasoned that the base excision repair enzyme Thymine DNA Glycosylase (TDG) could be such a target for its dual role in safeguarding genome stability and in effecting active DNA demethylation downstream the Ten-Eleven Translocation (TET) dioxygenases. TDG knockdown in melanoma cell lines causes cell cycle arrest, senescence and death by mitotic alterations, and impairs xenograft formation. Importantly, untransformed melanocytes are not affected by TDG knockdown, and adult mice with conditional knockout of TDG are viable. Candidate TDG inhibitors, identified through a high-throughput screen, reduced viability and clonogenic capacity of melanoma cell lines. Candidate TDG inhibitors increased cellular levels of 5-carboxylcytosine, the last intermediate in DNA demethylation, which is specifically removed by TDG, indicating successful targeting. These findings suggest that TDG may provide critical functions in cancer cells, but not in normal cells, that make it a highly suitable anti-melanoma drug target. By potentially disrupting both DNA repair and the epigenetic state, targeting TDG may represent a completely new approach to melanoma therapy.
Citation Format: Rossella Tricarico, Pietro Mancuso, Vikram Bhattacharjee, Laura Cosentino, Emmanuelle Nicolas, Margret Einarson, Neil Beeharry, Karthik Devarajan, Rich Katz, Dorjbal G. Dorjsuren, Anton Simeonov, Yuwaraj Kadariya, Guillaume Davidson, Joseph R. Testa, Irwin Davidson, Lionel Larue, Robert W. Sobol, Timothy Yen, Alfonso Bellacosa. Thymine DNA glycosylase (TDG) as a novel target for melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1940.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rich Katz
- 1Fox Chase Cancer Ctr., Philadelphia, PA
| | | | - Anton Simeonov
- 2National Center for Advancing Translational Sciences, NIH, Rockville, MD
| | | | | | | | | | - Lionel Larue
- 4Institut Curie Centre de Recherche, Orsay, France
| | - Robert W. Sobol
- 5Mitchell Cancer Institute, University of South Alabama, Mobile, AL
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Kim JH, Stone JK, Li J, Richard A, Vukadin L, Gillespie GY, Sobol RW, Lim S, Ahn EYE. Abstract LB-204: SON controls the oncogenic alternative splicing program in glioblastoma by regulating PTBP1/2 switch and RBFOX2 activity. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Alternative RNA splicing is a critical regulatory step of gene expression that generates various spliced isoforms and controls RNA stability. While dysregulation of alternative splicing has been implicated in pathogenesis of several cancers, molecular mechanisms of aberrant RNA splicing in brain tumors remain largely uninvestigated. Here, we identified SON, a nuclear speckle protein containing both RNA and DNA binding domains, as a key regulator of the oncogenic alternative splicing program in glioblastoma. Analyses of brain tumor patient samples as well as publicly available databases demonstrated that SON is significantly upregulated in high grade gliomas and correlated with poor prognosis of the patients. SON depletion in glioblastoma cells resulted in inhibition of cell growth and colony formation, suggesting that SON play a pro-survival and oncogenic role in glioblastoma. Interestingly, we found that the SON level in glioblastoma patients has a strong positive correlation with the expression level of PTBP1, a well-known oncogenic RNA splicing factor, and furthermore exhibits an inverse correlation with PTBP2, a neuronal-specific PTBP1 paralog. RNA splicing analysis together with RNA-IP reveals that SON directly interacts with PTBP1 pre-mRNA, and SON knockdown leads to downregulation of PTBP1 through intron retention in PTBP1 pre-mRNA, resulting in inhibition of oncogenic RNA splicing of PTBP1 target genes. On the other hand, SON knockdown strongly induces PTBP2 cassette exon (exon 10) inclusion, resulting in generation of PTBP2 mRNA that does not bear a pre-mature stop codon and subsequent upregulation of PTBP2. To further identify the molecular mechanism of PTBP2 exon 10 inclusion upon SON knockdown, we searched for binding motifs of RNA splicing factors in the PTBP2 pre-mRNA and identified RBFOX2 binding motifs in intron sequences. Interestingly, RNA-IP experiments revealed that both SON and RBFOX2 are enriched in introns flanking the cassette exon and SON knockdown significantly increased RBFOX2-binding to PTBP2 RNA and subsequent cassette exon inclusion. Conversely, RBFOX2 knockdown facilitated SON-binding to PTBP2 RNA and induced skipping of the cassette exon. These results demonstrate that SON competes with RBFOX2 for RNA binding at PTBP2 introns to regulate exon exclusion, affecting PTBP2 expression. Finally, we verified that SON knockdown in human patient-derived glioblastoma stem cells (GSCs) indeed induces downregulation of PTBP1 and its downstream oncogenic splicing program while enhancing RBFOX2-mediated cassette exon inclusion that are found in healthy brains. Taken together, our study defines SON as a novel master splicing regulator that initiates “the oncogenic alternative splicing program” in glioblastoma by promoting PTBP1-mediated oncogenic splicing while suppressing non-oncogenic splicing mediated by RBFOX2 through its competitive binding to target RNAs. Therefore, our findings strongly implicate SON as a potential therapeutic target in malignant brain tumors.
Citation Format: Jung-Hyun Kim, Joshua K. Stone, Jianfeng Li, Alexander Richard, Lana Vukadin, G. Yancey Gillespie, Robert W. Sobol, Steve Lim, Eun-Young Erin Ahn. SON controls the oncogenic alternative splicing program in glioblastoma by regulating PTBP1/2 switch and RBFOX2 activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-204.
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Affiliation(s)
- Jung-Hyun Kim
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - Joshua K. Stone
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - Jianfeng Li
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | | | - Lana Vukadin
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - G. Yancey Gillespie
- 2Division of Neurosurgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL
| | - Robert W. Sobol
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - Steve Lim
- 3Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL
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Sonavane M, Sykora P, Andrews JF, Sobol RW, Gassman NR. Camptothecin Efficacy to Poison Top1 Is Altered by Bisphenol A in Mouse Embryonic Fibroblasts. Chem Res Toxicol 2018; 31:510-519. [PMID: 29799191 DOI: 10.1021/acs.chemrestox.8b00050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bisphenol A (BPA) is used heavily in the production of polycarbonate plastics, thermal receipt paper, and epoxies. Ubiquitous exposure to BPA has been linked to obesity, diabetes, and breast and reproductive system cancers. Resistance to chemotherapeutic agents has also been shown in cancer cell models. Here, we investigated BPA's ability to confer resistance to camptothecin (CPT) in mouse embryonic fibroblasts (MEFs). MEFs are sensitive to CPT; however, co-exposure of BPA with CPT improved cell survival. Co-exposure significantly reduced Top1-DNA adducts, decreasing chromosomal aberrations and DNA strand break formation. This decrease occurs despite BPA treatment increasing the protein levels of Top1. By examining chromatin structure after BPA exposure, we determined that widespread compaction and loss of nuclear volume occurs. Therefore, BPA reduced CPT activity by reducing the accessibility of DNA to Top1, inhibiting DNA adduct formation, the generation of toxic DNA strand breaks, and improving cell survival.
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Affiliation(s)
- Manoj Sonavane
- Department of Oncologic Sciences , University of South Alabama Mitchell Cancer Institute , 1660 Spring Hill Avenue , Mobile , Alabama 36604 , United States
| | - Peter Sykora
- Department of Oncologic Sciences , University of South Alabama Mitchell Cancer Institute , 1660 Spring Hill Avenue , Mobile , Alabama 36604 , United States
| | - Joel F Andrews
- Department of Oncologic Sciences , University of South Alabama Mitchell Cancer Institute , 1660 Spring Hill Avenue , Mobile , Alabama 36604 , United States
| | - Robert W Sobol
- Department of Oncologic Sciences , University of South Alabama Mitchell Cancer Institute , 1660 Spring Hill Avenue , Mobile , Alabama 36604 , United States
| | - Natalie R Gassman
- Department of Oncologic Sciences , University of South Alabama Mitchell Cancer Institute , 1660 Spring Hill Avenue , Mobile , Alabama 36604 , United States
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Sykora P, Witt KL, Revanna P, Smith-Roe SL, Dismukes J, Lloyd DG, Engelward BP, Sobol RW. Next generation high throughput DNA damage detection platform for genotoxic compound screening. Sci Rep 2018; 8:2771. [PMID: 29426857 PMCID: PMC5807538 DOI: 10.1038/s41598-018-20995-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/29/2018] [Indexed: 11/23/2022] Open
Abstract
Methods for quantifying DNA damage, as well as repair of that damage, in a high-throughput format are lacking. Single cell gel electrophoresis (SCGE; comet assay) is a widely-used method due to its technical simplicity and sensitivity, but the standard comet assay has limitations in reproducibility and throughput. We have advanced the SCGE assay by creating a 96-well hardware platform coupled with dedicated data processing software (CometChip Platform). Based on the original cometchip approach, the CometChip Platform increases capacity ~200 times over the traditional slide-based SCGE protocol, with excellent reproducibility. We tested this platform in several applications, demonstrating a broad range of potential uses including the routine identification of DNA damaging agents, using a 74-compound library provided by the National Toxicology Program. Additionally, we demonstrated how this tool can be used to evaluate human populations by analysis of peripheral blood mononuclear cells to characterize susceptibility to genotoxic exposures, with implications for epidemiological studies. In summary, we demonstrated a high level of reproducibility and quantitative capacity for the CometChip Platform, making it suitable for high-throughput screening to identify and characterize genotoxic agents in large compound libraries, as well as for human epidemiological studies of genetic diversity relating to DNA damage and repair.
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Affiliation(s)
- Peter Sykora
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | - Kristine L Witt
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Pooja Revanna
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | - Stephanie L Smith-Roe
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Jonathan Dismukes
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | | | - Bevin P Engelward
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
| | - Robert W Sobol
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA.
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Ding L, Dean-Ben XL, Burton NC, Sobol RW, Ntziachristos V, Razansky D. Constrained Inversion and Spectral Unmixing in Multispectral Optoacoustic Tomography. IEEE Trans Med Imaging 2017; 36:1676-1685. [PMID: 28333622 PMCID: PMC5585740 DOI: 10.1109/tmi.2017.2686006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Accurate extraction of physical and biochemical parameters from optoacoustic images is often impeded due to the use of unrigorous inversion schemes, incomplete tomographic detection coverage, or other experimental factors that cannot be readily accounted for during the image acquisition and reconstruction process. For instance, inaccurate assumptions in the physical forward model may lead to negative optical absorption values in the reconstructed images. Any artifacts present in the single wavelength optoacoustic images can be significantly aggravated when performing a two-step reconstruction consisting in acoustic inversion and spectral unmixing aimed at rendering the distributions of spectrally distinct absorbers. We investigate a number of algorithmic strategies with non-negativity constraints imposed at the different phases of the reconstruction process. Performance is evaluated in cross-sectional multispectral optoacoustic tomography recordings from tissue-mimicking phantoms and in vivo mice embedded with varying concentrations of contrast agents. Additional in vivo validation is subsequently performed with molecular imaging data involving subcutaneous tumors labeled with genetically expressed iRFP proteins and organ perfusion by optical contrast agents. It is shown that constrained reconstruction is essential for reducing the critical image artifacts associated with inaccurate modeling assumptions. Furthermore, imposing the non-negativity constraint directly on the unmixed distribution of the probe of interest was found to maintain the most robust and accurate reconstruction performance in all experiments.
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Sawant A, Floyd AM, Dangeti M, Lei W, Sobol RW, Patrick SM. Differential role of base excision repair proteins in mediating cisplatin cytotoxicity. DNA Repair (Amst) 2017; 51:46-59. [PMID: 28110804 DOI: 10.1016/j.dnarep.2017.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 02/04/2023]
Abstract
Interstrand crosslinks (ICLs) are covalent lesions formed by cisplatin. The mechanism for the processing and removal of ICLs by DNA repair proteins involves nucleotide excision repair (NER), homologous recombination (HR) and fanconi anemia (FA) pathways. In this report, we monitored the processing of a flanking uracil adjacent to a cisplatin ICL by the proteins involved in the base excision repair (BER) pathway. Using a combination of extracts, purified proteins, inhibitors, functional assays and cell culture studies, we determined the specific BER proteins required for processing a DNA substrate with a uracil adjacent to a cisplatin ICL. Uracil DNA glycosylase (UNG) is the primary glycosylase responsible for the removal of uracils adjacent to cisplatin ICLs, whereas other uracil glycosylases can process uracils in the context of undamaged DNA. Repair of the uracil adjacent to cisplatin ICLs proceeds through the classical BER pathway, highlighting the importance of specific proteins in this redundant pathway. Removal of uracil is followed by the generation of an abasic site and subsequent cleavage by AP endonuclease 1 (APE1). Inhibition of either the repair or redox domain of APE1 gives rise to cisplatin resistance. Inhibition of the lyase domain of Polymerase β (Polβ) does not influence cisplatin cytotoxicity. In addition, lack of XRCC1 leads to increased DNA damage and results in increased cisplatin cytotoxicity. Our results indicate that BER activation at cisplatin ICLs influences crosslink repair and modulates cisplatin cytotoxicity via specific UNG, APE1 and Polβ polymerase functions.
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Affiliation(s)
- Akshada Sawant
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Ashley M Floyd
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Mohan Dangeti
- Department of Biochemistry and Cancer Biology, University of Toledo - Health Science Campus, Toledo, OH 43614, United States
| | - Wen Lei
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Robert W Sobol
- Department of Oncologic Sciences, Molecular & Metabolic Oncology Program, Mitchell Cancer Institute, University of South Alabama,1660 Springhill Avenue, Mobile, AL 36604, United States
| | - Steve M Patrick
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States.
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Braganza A, Li J, Zeng X, Yates NA, Dey NB, Andrews J, Clark J, Zamani L, Wang XH, St Croix C, O'Sullivan R, Garcia-Exposito L, Brodsky JL, Sobol RW. UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase. J Biol Chem 2016; 292:2470-2484. [PMID: 28003368 DOI: 10.1074/jbc.m116.766824] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
Recent genome-wide studies found that patients with hypotonia, developmental delay, intellectual disability, congenital anomalies, characteristic facial dysmorphic features, and low cholesterol levels suffer from Kaufman oculocerebrofacial syndrome (KOS, also reported as blepharophimosis-ptosis-intellectual disability syndrome). The primary cause of KOS is autosomal recessive mutations in the gene UBE3B However, to date, there are no studies that have determined the cellular or enzymatic function of UBE3B. Here, we report that UBE3B is a mitochondrion-associated protein with homologous to the E6-AP Cterminus (HECT) E3 ubiquitin ligase activity. Mutating the catalytic cysteine (C1036A) or deleting the entire HECT domain (amino acids 758-1068) results in loss of UBE3B's ubiquitylation activity. Knockdown of UBE3B in human cells induces changes in mitochondrial morphology and physiology, a decrease in mitochondrial volume, and a severe suppression of cellular proliferation. We also discovered that UBE3B interacts with calmodulin via its N-terminal isoleucine-glutamine (IQ) motif. Deletion of the IQ motif (amino acids 29-58) results in loss of calmodulin binding and a significant increase in the in vitro ubiquitylation activity of UBE3B. In addition, we found that changes in calcium levels in vitro disrupt the calmodulin-UBE3B interaction. These studies demonstrate that UBE3B is an E3 ubiquitin ligase and reveal that the enzyme is regulated by calmodulin. Furthermore, the modulation of UBE3B via calmodulin and calcium implicates a role for calcium signaling in mitochondrial protein ubiquitylation, protein turnover, and disease.
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Affiliation(s)
- Andrea Braganza
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Jianfeng Li
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, School of the Health Sciences, and
| | - Nathan A Yates
- the Hillman Cancer Center, University of Pittsburgh Cancer Institute.,Biomedical Mass Spectrometry Center, School of the Health Sciences, and.,the Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and
| | - Nupur B Dey
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Joel Andrews
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Jennifer Clark
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Leila Zamani
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Xiao-Hong Wang
- the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Claudette St Croix
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Roderick O'Sullivan
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Laura Garcia-Exposito
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Jeffrey L Brodsky
- the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Robert W Sobol
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, .,the Hillman Cancer Center, University of Pittsburgh Cancer Institute.,the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
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Bigarella CL, Li J, Rimmelé P, Liang R, Sobol RW, Ghaffari S. FOXO3 Transcription Factor Is Essential for Protecting Hematopoietic Stem and Progenitor Cells from Oxidative DNA Damage. J Biol Chem 2016; 292:3005-3015. [PMID: 27994057 DOI: 10.1074/jbc.m116.769455] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/16/2016] [Indexed: 12/29/2022] Open
Abstract
Accumulation of damaged DNA in hematopoietic stem cells (HSC) is associated with chromosomal abnormalities, genomic instability, and HSC aging and might promote hematological malignancies with age. Despite this, the regulatory pathways implicated in the HSC DNA damage response have not been fully elucidated. One of the sources of DNA damage is reactive oxygen species (ROS) generated by both exogenous and endogenous insults. Balancing ROS levels in HSC requires FOXO3, which is an essential transcription factor for HSC maintenance implicated in HSC aging. Elevated ROS levels result in defective Foxo3-/- HSC cycling, among many other deficiencies. Here, we show that loss of FOXO3 leads to the accumulation of DNA damage in primitive hematopoietic stem and progenitor cells (HSPC), associated specifically with reduced expression of genes implicated in the repair of oxidative DNA damage. We provide further evidence that Foxo3-/- HSPC are defective in DNA damage repair. Specifically, we show that the base excision repair pathway, the main pathway utilized for the repair of oxidative DNA damage, is compromised in Foxo3-/- primitive hematopoietic cells. Treating mice in vivo with N-acetylcysteine reduces ROS levels, rescues HSC cycling defects, and partially mitigates HSPC DNA damage. These results indicate that DNA damage accrued as a result of elevated ROS in Foxo3-/- mutant HSPC is at least partially reversible. Collectively, our findings suggest that FOXO3 serves as a protector of HSC genomic stability and health.
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Affiliation(s)
- Carolina L Bigarella
- From the Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Jianfeng Li
- the Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama 36604
| | - Pauline Rimmelé
- From the Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Raymond Liang
- From the Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029.,the Developmental and Stem Cell Biology Multidisciplinary Training Area
| | - Robert W Sobol
- the Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama 36604
| | - Saghi Ghaffari
- From the Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, .,the Developmental and Stem Cell Biology Multidisciplinary Training Area.,Department of Medicine, Division of Hematology and, Oncology.,Black Family Stem Cell Institute, and.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
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Fouquerel E, Lormand J, Bose A, Lee HT, Kim GS, Li J, Sobol RW, Freudenthal BD, Myong S, Opresko PL. Oxidative guanine base damage regulates human telomerase activity. Nat Struct Mol Biol 2016; 23:1092-1100. [PMID: 27820808 PMCID: PMC5140714 DOI: 10.1038/nsmb.3319] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/11/2016] [Indexed: 12/19/2022]
Abstract
Changes in telomere length are associated with degenerative diseases and cancer. Oxidative stress and DNA damage have been linked to both positive and negative alterations in telomere length and integrity. Here we examined how the common oxidative lesion 8-oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG) regulates telomere elongation by telomerase. When present in the deoxynucleoside triphosphate pool as 8-oxodGTP, telomerase utilization of the oxidized nucleotide during telomere extension is mutagenic and terminates further elongation. Depletion of the enzyme that removes oxidized dNTPs, MTH1, increases telomere dysfunction and cell death in telomerase positive cancer cells harboring shortened telomeres. In contrast, a pre-existing 8-oxoG within the telomeric DNA sequence promotes telomerase activity by destabilizing G-quadruplex structure in the DNA. We show that the mechanism by which 8-oxoG arises in the telomere, either by insertion of oxidized nucleotides or by direct reaction with free radicals, dictates whether telomerase is inhibited or stimulated and thereby, mediates the biological outcome.
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Affiliation(s)
- Elise Fouquerel
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Justin Lormand
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Hui-Ting Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Grace S Kim
- Department of Bioengineering, University of Illinois, Urbana, IL, USA
| | - Jianfeng Li
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Robert W Sobol
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Department of Bioengineering, University of Illinois, Urbana, IL, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.,Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, USA
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Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol Cell 2016; 63:514-25. [PMID: 27453043 DOI: 10.1016/j.molcel.2016.06.022] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/03/2016] [Accepted: 06/15/2016] [Indexed: 01/06/2023]
Abstract
An emerging therapeutic strategy for cancer is to induce selective lethality in a tumor by exploiting interactions between its driving mutations and specific drug targets. Here we use a multi-species approach to develop a resource of synthetic lethal interactions relevant to cancer therapy. First, we screen in yeast ∼169,000 potential interactions among orthologs of human tumor suppressor genes (TSG) and genes encoding drug targets across multiple genotoxic environments. Guided by the strongest signal, we evaluate thousands of TSG-drug combinations in HeLa cells, resulting in networks of conserved synthetic lethal interactions. Analysis of these networks reveals that interaction stability across environments and shared gene function increase the likelihood of observing an interaction in human cancer cells. Using these rules, we prioritize ∼10(5) human TSG-drug combinations for future follow-up. We validate interactions based on cell and/or patient survival, including topoisomerases with RAD17 and checkpoint kinases with BLM.
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Affiliation(s)
- Rohith Srivas
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; The Cancer Cell Map Initiative
| | - John Paul Shen
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Cancer Cell Map Initiative
| | - Chih Cheng Yang
- Functional Genomics Core, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Su Ming Sun
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Jianfeng Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Andrew M Gross
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - James Jensen
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ana Bojorquez-Gomez
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kristin Klepper
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Huang
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel Pekin
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jia L Xu
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Huwate Yeerna
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Vignesh Sivaganesh
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Leonie Kollenstart
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Pedro Aza-Blanc
- Functional Genomics Core, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Robert W Sobol
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Cancer Cell Map Initiative.
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Wilk AM, Fouquerel E, Johnston B, Trammell SA, Schambeau L, Andrews JF, Pannell L, Cooper SJ, Brenner C, Sobol RW. Abstract 4: Hyper activation of poly(ADP-ribose) polymerase 1 initiates large-scale metabolic changes in a cellular model of glioblastoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
PARP1 is a key enzyme of the Base Excision Repair (BER) pathway, facilitating the repair of base damage and single-strand DNA breaks. Activated PARP1 synthesizes poly (ADP-ribose) (PAR), triggering chromatin de-condensation to facilitate recruitment of BER proteins to complete repair. PARP1 activation is attenuated upon successful repair of the DNA lesion. However, unrepaired DNA breaks lead to continuous PARP1 activation and cell death. The molecular mechanism underlying PARP1 activation induced cell death was recently revealed as independent from NAD+ depletion. We have shown that PARP1 activation and PAR synthesis affect glycolysis by directly inhibiting the glycolytic enzyme, hexokinase 1 (HK1). Following on these discoveries, we decided to investigate global metabolic changes triggered by hyperactivation of PARP1. For this study, we used gas chromatography mass spectrometry (GC-MS) to quantify over 150 cellular metabolites and Multiple-Reaction Monitoring Liquid Chromatography Mass Spectrometry (MRM LC-MS) to measure NAD+ metabolites. As a model, we tested glioblastoma cells overexpressing methylpurine DNA glycosylase (MPG) to enhance the PARP1-activation response to DNA damage induced by the alkylating agent MNNG. Simultaneously, to monitor independence from the DNA damaging effect of NAD+ depletion, we utilized an inhibitor of NAD+ biosynthesis, FK866. We found that PARP1 activation leads to a strong accumulation of glucose, likely as a secondary effect of HK1 inhibition. In addition, we observed a significant change in the level of other metabolites including an increase in inosine, inosine monophosphate (IMP), cytidine and uridine levels upon PARP1 activation, suggesting an indirect effect of PARP1 activation on purine and pyrimidine metabolism. Ongoing studies will use these global approaches to unravel the complete metabolic response of cancer cells to genotoxic treatment.
Citation Format: Anna M. Wilk, Elise Fouquerel, Bobbie Johnston, Samuel A.J. Trammell, Lindsay Schambeau, Joel F. Andrews, Lewis Pannell, Sara J. Cooper, Charles Brenner, Robert W. Sobol. Hyper activation of poly(ADP-ribose) polymerase 1 initiates large-scale metabolic changes in a cellular model of glioblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4.
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Affiliation(s)
- Anna M. Wilk
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - Elise Fouquerel
- 2Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Samuel A.J. Trammell
- 4Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | | | - Joel F. Andrews
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - Lewis Pannell
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
| | - Sara J. Cooper
- 3HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Charles Brenner
- 4Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Robert W. Sobol
- 1Mitchell Cancer Institute, University of South Alabama, Mobile, AL
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Simonelli V, Leuzzi G, Basile G, D'Errico M, Fortini P, Franchitto A, Viti V, Brown AR, Parlanti E, Pascucci B, Palli D, Giuliani A, Palombo F, Sobol RW, Dogliotti E. Crosstalk between mismatch repair and base excision repair in human gastric cancer. Oncotarget 2016; 8:84827-84840. [PMID: 29156686 PMCID: PMC5689576 DOI: 10.18632/oncotarget.10185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 05/23/2016] [Indexed: 12/05/2022] Open
Abstract
DNA repair gene expression in a set of gastric cancers suggested an inverse association between the expression of the mismatch repair (MMR) gene MLH1 and that of the base excision repair (BER) gene DNA polymerase β (Polβ). To gain insight into possible crosstalk of these two repair pathways in cancer, we analysed human gastric adenocarcinoma AGS cells over-expressing Polβ or Polβ active site mutants, alone or in combination with MLH1 silencing. Next, we investigated the cellular response to the alkylating agent methyl methanesulfonate (MMS) and the purine analogue 6-thioguanine (6-TG), agents that induce lesions that are substrates for BER and/or MMR. AGS cells over-expressing Polβ were resistant to 6-TG to a similar extent as when MLH1 was inactivated while inhibition of O6-methylguanine-DNA methyltransferase (MGMT) was required to detect resistance to MMS. Upon either treatment, the association with MLH1 down-regulation further amplified the resistant phenotype. Moreover, AGS cells mutated in Polβ were hypersensitive to both 6-TG and MMS killing and their sensitivity was partially rescued by MLH1 silencing. We provide evidence that the critical lethal lesions in this new pathway are double strand breaks that are exacerbated when Polβ is defective and relieved when MLH1 is silenced. In conclusion, we provide evidence of crosstalk between MLH1 and Polβ that modulates the response to alkylation damage. These studies suggest that the Polβ/MLH1 status should be taken into consideration when designing chemotherapeutic approaches for gastric cancer.
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Affiliation(s)
- Valeria Simonelli
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Leuzzi
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Giorgia Basile
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Mariarosaria D'Errico
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Fortini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Annapaola Franchitto
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Valentina Viti
- Istituto di Ricerche Biologia Molecolare P. Angeletti (IRBM), Pomezia (Rome), Italy
| | - Ashley R Brown
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Eleonora Parlanti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Barbara Pascucci
- Institute of Cristallography, Consiglio Nazionale delle Ricerche, Monterotondo Stazione, Rome, Italy
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, CSPO, Scientific Institute of Tuscany, Florence, Italy
| | - Alessandro Giuliani
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | | | - Robert W Sobol
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Eugenia Dogliotti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
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Godin SK, Zhang Z, Herken BW, Westmoreland JW, Lee AG, Mihalevic MJ, Yu Z, Sobol RW, Resnick MA, Bernstein KA. The Shu complex promotes error-free tolerance of alkylation-induced base excision repair products. Nucleic Acids Res 2016; 44:8199-215. [PMID: 27298254 PMCID: PMC5041462 DOI: 10.1093/nar/gkw535] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/02/2016] [Indexed: 12/24/2022] Open
Abstract
Here, we investigate the role of the budding yeast Shu complex in promoting homologous recombination (HR) upon replication fork damage. We recently found that the Shu complex stimulates Rad51 filament formation during HR through its physical interactions with Rad55-Rad57. Unlike other HR factors, Shu complex mutants are primarily sensitive to replicative stress caused by MMS and not to more direct DNA breaks. Here, we uncover a novel role for the Shu complex in the repair of specific MMS-induced DNA lesions and elucidate the interplay between HR and translesion DNA synthesis. We find that the Shu complex promotes high-fidelity bypass of MMS-induced alkylation damage, such as N3-methyladenine, as well as bypassing the abasic sites generated after Mag1 removes N3-methyladenine lesions. Furthermore, we find that the Shu complex responds to ssDNA breaks generated in cells lacking the abasic site endonucleases. At each lesion, the Shu complex promotes Rad51-dependent HR as the primary repair/tolerance mechanism over error-prone translesion DNA polymerases. Together, our work demonstrates that the Shu complex's promotion of Rad51 pre-synaptic filaments is critical for high-fidelity bypass of multiple replication-blocking lesion.
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Affiliation(s)
- Stephen K Godin
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Zhuying Zhang
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 5117 Centre Avenue, Pittsburgh, PA 15213, USA Tsinghua University School of Medicine, Tsinghua University, Haidian District, Beijing 100084, China
| | - Benjamin W Herken
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - James W Westmoreland
- Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Alison G Lee
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Michael J Mihalevic
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Zhongxun Yu
- Tsinghua University School of Medicine, Tsinghua University, Haidian District, Beijing 100084, China Department of Pharmacology & Chemical Biology, Pittsburgh, PA 15217, USA
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, Pittsburgh, PA 15217, USA University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Michael A Resnick
- Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Kara A Bernstein
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
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Li H, Gu L, Zhong Y, Chen Y, Zhang L, Zhang AR, Sobol RW, Chen T, Li J. Administration of polysaccharide from Panax notoginseng prolonged the survival of H22 tumor-bearing mice. Onco Targets Ther 2016; 9:3433-41. [PMID: 27354815 PMCID: PMC4907734 DOI: 10.2147/ott.s79427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Polysaccharides from various sources are being considered potential sources for the treatment of liver cancer. The aim of this study was to investigate the impact of polysaccharide isolated from Panax notoginseng (PPN) on the proliferation of H22 liver cancer cells and the survival of the tumor-bearing mice transplanted with H22 cells. MATERIALS AND METHODS Polysaccharide from PPN was added to the culture medium of mouse hepatoma H22 cells at different doses. Cell proliferation was assayed with a standard MTT assay. Survival rates of tumor-bearing mice were recorded. Peripheral blood lymphocytes were assayed by flow cytometry. Serum interleukin-2 levels in peripheral blood were measured by enzyme-linked immunosorbent assay. RESULTS Polysaccharide from PPN inhibited the growth of H22 cells and significantly prolonged the survival of tumor-bearing mice. The increase in activated CD4(+) T-cells and the elevation of serum interleukin-2 may contribute to the antitumor activity of PPN. CONCLUSION PPN has potential antitumor activity for the treatment of liver cancer.
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Affiliation(s)
- Huaiyu Li
- Yunnan Key Laboratory of Pharmacology for Natural Products, School of Pharmaceutical Sciences, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Longlong Gu
- Yunnan Key Laboratory of Pharmacology for Natural Products, School of Pharmaceutical Sciences, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Haiyuan College, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Yuanyuan Zhong
- Yunnan Key Laboratory of Pharmacology for Natural Products, School of Pharmaceutical Sciences, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Yajuan Chen
- Yunnan Key Laboratory of Pharmacology for Natural Products, School of Pharmaceutical Sciences, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Lei Zhang
- Yunnan Key Laboratory of Pharmacology for Natural Products, School of Pharmaceutical Sciences, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Annie R Zhang
- Graduate School of Applied and Professional Psychology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Robert W Sobol
- Department of Oncologic Sciences, University of South Alabama, Mobile, AL, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Tong Chen
- Yunnan Key Laboratory of Pharmacology for Natural Products, School of Pharmaceutical Sciences, Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Yunnan Panax notoginseng (Burk) F.H. Chen Biotechnology and Pharmaceutical Engineering Research Center, Kunming, Yunnan, People’s Republic of China
| | - Jianfeng Li
- Department of Oncologic Sciences, University of South Alabama, Mobile, AL, USA
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
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Sawant A, Kothandapani A, Zhitkovich A, Sobol RW, Patrick SM. Role of mismatch repair proteins in the processing of cisplatin interstrand cross-links. DNA Repair (Amst) 2015; 35:126-36. [PMID: 26519826 DOI: 10.1016/j.dnarep.2015.10.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 12/13/2022]
Abstract
Mismatch repair (MMR) deficiency gives rise to cisplatin resistance and can lead to poor prognosis in cancers. Various models have been proposed to explain this low level of resistance caused due to loss of MMR proteins. We have shown that MMR proteins are required to maintain cisplatin interstrand cross-links (ICLs) on the DNA leading to increased cellular sensitivity. In our previous studies, we have shown that BER processing of the cisplatin ICLs is mutagenic. Polymerase β (Polβ) can generate mismatches which leads to the activation and the recruitment of mismatch repair proteins. In this paper, we distinguished between the requirement of different downstream MMR proteins for maintaining cisplatin sensitivity. We show that the MutSα (MSH2-MSH6) heterocomplex is required to maintain cisplatin sensitivity, whereas the Mutsβ complex has no effect. These results can be correlated with the increased repair of cisplatin ICLs and ICL induced DNA double strand breaks (DSBs) in the resistant cells. Moreover, we show that MLH1 proficient cells displayed a cisplatin sensitive phenotype when compared with the MLH1 deficient cells and the ATPase activity of MLH1 is essential to mediate this effect. Based on these results, we propose that MutSα as well as the downstream MMR pathway proteins are essential to maintain a cisplatin sensitive phenotype as a consequence of processing Polβ induced mismatches at sites flanking cisplatin ICLs.
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Affiliation(s)
- Akshada Sawant
- Department of Biochemistry and Cancer Biology, University of Toledo-Health Science Campus, Toledo, OH 43614, USA
| | - Anbarasi Kothandapani
- Department of Biochemistry and Cancer Biology, University of Toledo-Health Science Campus, Toledo, OH 43614, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15213, USA; Department of Oncologic Sciences, Molecular & Metabolic Oncology Program, University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Steve M Patrick
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA.
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Chandran UR, Luthra S, Santana-Santos L, Mao P, Kim SH, Minata M, Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW. Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells. Genom Data 2015; 5:333-336. [PMID: 26251826 PMCID: PMC4523279 DOI: 10.1016/j.gdata.2015.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Tumor heterogeneity of high-grade glioma (HGG) is recognized by four clinically relevant subtypes based on core gene signatures. However, molecular signaling in glioma stem cells (GSCs) in individual HGG subtypes is poorly characterized. Previously we identified and characterized two mutually exclusive GSC subtypes with distinct activated signaling pathways and biological phenotypes. One GSC subtype presented with a gene signature resembling Proneural (PN) HGG, whereas the other was similar to mesenchymal (Mes) HGG. Classical HGG-derived GSCs were sub-classified as either one of these two subtypes. Differential mRNA expression analysis of PN and Mes GSCs identified 5796 differentially expressed genes, revealing a pronounced correlation with the corresponding PN or Mes HGGs. Mes GSCs displayed more aggressive phenotypes in vitro and as intracranial xenografts in mice. Further, Mes GSCs were markedly resistant to radiation compared with PN GSCs. Expression of ALDH1A3 — one of the most up-regulated Mes representative genes and a universal cancer stem cell marker in non-brain cancers — was associated with self-renewal and a multi-potent stem cell population in Mes but not PN samples. Moreover, inhibition of ALDH1A3 attenuated the growth of Mes but not PN GSCs in vitro. Lastly, radiation treatment of PN GSCs up-regulated Mes-associated markers and down-regulated PN-associated markers, whereas inhibition of ALDH1A3 attenuated an irradiation-induced gain of Mes identity in PN GSCs in vitro. Taken together, our data suggest that two subtypes of GSCs, harboring distinct metabolic signaling pathways, represent intertumoral glioma heterogeneity and highlight previously unidentified roles of ALDH1A3-associated signaling that promotes aberrant proliferation of Mes HGGs and GSCs. Inhibition of ALDH1A3-mediated pathways therefore might provide a promising therapeutic approach for a subset of HGGs with the Mes signature. Here, we describe the gene expression analysis, including pre-processing methods for the data published by Mao and colleagues in PNAS [1], integration of microarray data from this study with The Cancer Genome Atlas (TCGA) glioblastoma data and also with another published study. The raw CEL files and processed data were submitted to Gene Expression Omnibus (GEO) under the accession GSE67089.
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Affiliation(s)
- Uma R Chandran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Soumya Luthra
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Lucas Santana-Santos
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA ; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ping Mao
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA ; Department of Neurosurgery, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Sung-Hak Kim
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA
| | - Mutsuko Minata
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA
| | - Jianfeng Li
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15216, USA ; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213-1863, USA ; University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Panayiotis V Benos
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA ; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mao DeWang
- Department of Neurosurgery, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Bo Hu
- Department of Neurology & Northwestern Brain Tumor Institute, Center for Genetic Medicine, Robert Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shi-Yuan Cheng
- Department of Neurology & Northwestern Brain Tumor Institute, Center for Genetic Medicine, Robert Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ichiro Nakano
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA ; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15216, USA ; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213-1863, USA ; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15216, USA ; University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA
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50
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Tricarico R, Mancuso P, Bhattacharjee V, Beeharry N, Nicolas E, Einarson M, Cosentino L, Davidson I, Larue L, Sobol RW, Yen TJ, Bellacosa A. Abstract LB-249: TDG, a dual genomic and epigenomic regulator, as a novel antimelanoma target. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Melanoma is an aggressive cancer resistant to treatment, whose incidence has increased over the past two decades. Although the majority of melanoma cases are cured after surgical excision of the primary tumor, metastases occur frequently, and the metastatic form of the disease has a poor prognosis and is highly resistant to all current forms of therapy. Thus, new prognostic factors and advanced therapeutic strategies are urgently needed.
We recently reported that the base excision repair protein Thymine DNA Glycosylase (TDG) has dual roles in safeguarding the genome and the epigenome (Cell 146:67, 2011). TDG not only protects CpG sites from spontaneous deamination of 5-methylcytosine and cytosine (genomic stability), but importantly, at the epigenomic level, acts in a DNA demethylation pathway that converts 5-methylcytosine to cytosine (epigenomic stability). Specifically TDG removes the novel bases 5-formylcytosine and 5-carboxylcytosine, demethylation intermediates produced by the upstream TET dioxygenases. TET alterations have been recently found in melanoma and correlate with poor prognosis. Moreover, TDG sequence variants in melanoma are reported in the TCGA database.
For these reasons, we began studying the functional significance of TDG in melanoma. We reasoned that the two non-redundant (genomic and epigenomic) functions of TDG may represent a vulnerability of tumor cells and be exploited as novel drug targets for cancer treatment, because targeting TDG would achieve the dual effect of impairing DNA repair and disrupting the epigenetic state of the cancer cell. We found that reduced TDG levels correlate with tumorigenic melanomas and therefore TDG inhibition might further promote aggressiveness. Unexpectedly, however, TDG knockdown in melanoma lines caused cell cycle arrest, senescence and ultimately cell death. Senescence and cell death induced by TDG knockdown occurred without apparent activation of the DNA damage response, based on absence of H2AX phosphorylation. These in vitro findings were confirmed in vivo, as TDG knockdown in melanoma lines blocked tumor formation in xenografts.
Given its potential as a novel therapeutic target, we conducted a pilot high-throughput screen and identified first-generation TDG chemical inhibitors. Two compounds were confirmed to inhibit TDG repair activity in vitro by radioactive-based glycosylase assay. Importantly, both inhibitors also blocked TDG demethylase function in cells, as evidenced by increased staining intensity of 5-carboxylcytosine. Both compounds inhibited proliferation (by clonogenic, MTT and Xcelligence assays) of melanoma cell lines in the micromolar range and could synergize with alkylating agents and other anti-melanoma drugs.
Thus, while reduced TDG levels may be part of the tumorigenesis process, limited levels of TDG are essential for melanoma viability. Therefore, TDG inhibition may represent a novel approach for melanoma treatment.
Citation Format: Rossella Tricarico, Pietro Mancuso, Vikram Bhattacharjee, Neil Beeharry, Emmanuelle Nicolas, Margret Einarson, Laura Cosentino, Irwin Davidson, Lionel Larue, Robert W. Sobol, Timothy J. Yen, Alfonso Bellacosa. TDG, a dual genomic and epigenomic regulator, as a novel antimelanoma target. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-249. doi:10.1158/1538-7445.AM2015-LB-249
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Affiliation(s)
| | - Pietro Mancuso
- 2Fox Chase Cancer Center, Philadelphia, PA and University of Siena, Siena, Italy
| | | | | | | | | | | | - Irwin Davidson
- 3Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | | | - Robert W. Sobol
- 5Mitchell Cancer Institute, University of South Alabama, Mobile, AL
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