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Lopes M, Lund PJ, Garcia BA. An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.596744. [PMID: 38915586 PMCID: PMC11195131 DOI: 10.1101/2024.06.11.596744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The eukaryotic genome is packaged around histone proteins, which are subject to a myriad of post-translational modifications. By controlling DNA accessibility and the recruitment of protein complexes that mediate chromatin-related processes, these modifications constitute a key mechanism of epigenetic regulation. Since mass spectrometry can easily distinguish between these different modifications, it has become an essential technique in deciphering the histone code. Although robust LC-MS/MS methods are available to analyze modifications on the histone N-terminal tails, routine methods for characterizing ubiquitin marks on histone C-terminal regions, especially H2AK119ub, are less robust. Here we report the development of a simple workflow for the detection and improved quantification of the canonical histone ubiquitination marks H2AK119ub and H2BK120ub. The method entails a fully tryptic digestion of acid-extracted histones followed by derivatization with heavy or light propionic anhydride. A pooled sample is then spiked into oppositely labeled single samples as a reference channel for relative quantification, and data is acquired using PRM-based nanoLC-MS/MS. We validated our approach with synthetic peptides as well as treatments known to modulate the levels of H2AK119ub and H2BK120ub. This new method complements existing histone workflows, largely focused on the lysine-rich N-terminal regions, by extending modification analysis to other sequence contexts.
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Affiliation(s)
- Mariana Lopes
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peder J. Lund
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Benjamin A. Garcia
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Dept. of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110
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Kimura T, Okada K, Morohashi Y, Kato Y, Mori M, Kato H, Matsumoto T, Shimoyama S. Quantification of Unencapsulated Drug in Target Tissues Demonstrates Pharmacological Properties and Therapeutic Effects of Liposomal Topotecan (FF-10850). Pharm Res 2024; 41:795-806. [PMID: 38536615 PMCID: PMC11024016 DOI: 10.1007/s11095-023-03652-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/27/2023] [Indexed: 04/18/2024]
Abstract
PURPOSE Quantifying unencapsulated drug concentrations in tissues is crucial for understanding the mechanisms underlying the efficacy and safety of liposomal drugs; however, the methodology for this has not been fully established. Herein, we aimed to investigate the enhanced therapeutic potential of a pegylated liposomal formulation of topotecan (FF-10850) by analyzing the concentrations of the unencapsulated drug in target tissues, to guide the improvement of its dosing regimen. METHODS We developed a method for measuring unencapsulated topotecan concentrations in tumor and bone marrow interstitial fluid (BM-ISF) and applied this method to pharmacokinetic assessments. The ratios of the area under the concentration-time curves (AUCs) between tumor and BM-ISF were calculated for total and unencapsulated topotecan. DNA damage and antitumor effects of FF-10850 or non-liposomal topotecan (TPT) were evaluated in an ES-2 mice xenograft model. RESULTS FF-10850 exhibited a much larger AUC ratio between tumor and BM-ISF for unencapsulated topotecan (2.96), but not for total topotecan (0.752), than TPT (0.833). FF-10850 promoted milder DNA damage in the bone marrow than TPT; however, FF-10850 and TPT elicited comparable DNA damage in the tumor. These findings highlight the greater tumor exposure to unencapsulated topotecan and lower bone marrow exposure to FF-10850 than TPT. The dosing regimen was successfully improved based on the kinetics of unencapsulated topotecan and DNA damage. CONCLUSIONS Tissue pharmacokinetics of unencapsulated topotecan elucidated the favorable pharmacological properties of FF-10850. Evaluation of tissue exposure to an unencapsulated drug with appropriate pharmacodynamic markers can be valuable in optimizing liposomal drugs and dosing regimens.
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Affiliation(s)
- Toshifumi Kimura
- Bio Science & Engineering Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-Machi, Ashigarakami-Gun, Kanagawa, 258-8577, Japan.
| | - Ken Okada
- Bio Science & Engineering Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-Machi, Ashigarakami-Gun, Kanagawa, 258-8577, Japan
| | - Yasushi Morohashi
- Bio Science & Engineering Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-Machi, Ashigarakami-Gun, Kanagawa, 258-8577, Japan
| | - Yukio Kato
- Faculty of Pharmacy, Kanazawa University, Kakuma-Machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Mikinaga Mori
- Bio Science & Engineering Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-Machi, Ashigarakami-Gun, Kanagawa, 258-8577, Japan
| | - Hiroshi Kato
- Bio Science & Engineering Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-Machi, Ashigarakami-Gun, Kanagawa, 258-8577, Japan
| | - Takeshi Matsumoto
- Bio Science & Engineering Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-Machi, Ashigarakami-Gun, Kanagawa, 258-8577, Japan
| | - Susumu Shimoyama
- FUJIFILM Pharmaceuticals U.S.A., Inc, One Broadway, Cambridge, MA, 02142, USA
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Matsuda S, Ikura T, Matsuda T. Absolute quantification of DNA damage response proteins. Genes Environ 2023; 45:37. [PMID: 38111058 PMCID: PMC10726557 DOI: 10.1186/s41021-023-00295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND DNA damage response (DDR) and repair are vital for safeguarding genetic information and ensuring the survival and accurate transmission of genetic material. DNA damage, such as DNA double-strand breaks (DSBs), triggers a response where sensor proteins recognize DSBs. Information is transmitted to kinases, initiating a sequence resulting in the activation of the DNA damage response and recruitment of other DDR and repair proteins to the DSB site in a highly orderly sequence. Research has traditionally focused on individual protein functions and their order, with limited quantitative analysis, prompting this study's attempt at absolute quantification of DNA damage response and repair proteins and capturing changes in protein chromatin affinity after DNA damage through biochemical fractionation methods. RESULTS To assess the intracellular levels of proteins involved in DDR and repair, multiple proteins associated with different functions were quantified in EPC2-hTERT cells. H2AX had the highest intracellular abundance (1.93 × 106 molecules/cell). The components of the MRN complex were present at the comparable levels: 6.89 × 104 (MRE11), 2.17 × 104 (RAD50), and 2.35 × 104 (NBS1) molecules/cell. MDC1 was present at 1.27 × 104 molecules/cell. The intracellular levels of ATM and ATR kinases were relatively low: 555 and 4860 molecules/cell, respectively. The levels of cellular proteins involved in NHEJ (53BP1: 3.03 × 104; XRCC5: 2.62 × 104; XRCC6: 5.05 × 105 molecules/cell) were more than an order of magnitude higher than that involved in HR (RAD51: 2500 molecules/cell). Furthermore, we analyzed the dynamics of MDC1 and γH2AX proteins in response to DNA damage induced by the unstable agent neocarzinostatin (NCS). Using cell biochemical fractionation, cells were collected and analyzed at different time points after NCS exposure. Results showed that γH2AX in chromatin fraction peaked at 1 h post-exposure and gradually decreased, while MDC1 translocated from the isotonic to the hypertonic fraction, peaking at 1 hour as well. The study suggests increased MDC1 affinity for chromatin through binding to γH2AX induced by DNA damage. The γH2AX-bound MDC1 (in the hypertonic fraction) to γH2AX ratio at 1 h post-exposure was 1:56.4, with lower MDC1 levels which may attributed to competition with other proteins. CONCLUSIONS The approach provided quantitative insights into protein dynamics in DNA damage response.
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Affiliation(s)
- Shun Matsuda
- Research Center for Environmental Quality Management, Kyoto University, 1-2, Yumihama, Otsu, Shiga, 5200811, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Yoshidakonoecho, Kyoto Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, 1-2, Yumihama, Otsu, Shiga, 5200811, Japan.
- Laboratories for Environmental Health, Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto, 615-8530, Japan.
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Qu M, Xu H, Chen J, Zhang Y, Xu B, Guo L, Xie J. Distinct Orchestration and Dynamic Processes on γ-H2AX and p-H3 for Two Major Types of Genotoxic Chemicals Revealed by Mass Spectrometry Analysis. Chem Res Toxicol 2020; 33:2108-2119. [PMID: 32482060 DOI: 10.1021/acs.chemrestox.0c00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Genotoxic chemicals act by causing DNA damage, which, if left unrepaired, can have deleterious consequences for cell survival. DNA damage response (DDR) gets activated to repair or mitigate the effects of DNA damage. Histone H2AX and H3 phosphorylation biomarkers (γ-H2AX and p-H3) have attracted great attention as they play pivotal roles in the DDR. Simultaneous quantitation of γ-H2AX and p-H3 in exposed cells may monitor the toxicity of genotoxic chemicals and to some extent reflect the subsequent DDR process. Reported here is the first comprehensive characterization of distinct orchestration and dynamic processes on cellular γ-H2AX and p-H3 for two major types of genotoxic chemicals, clastogens and aneugens, by stable isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS). We find that clastogens significantly induce an increase in γ-H2AX and a decrease in p-H3; aneugens have no obvious effect on γ-H2AX, whereas induce either an increase or a decrease in p-H3. In addition, the specific profiles of clastogens and aneugens affecting DNA damage may be dynamically observed, which in turn provides insights into the processes involving DNA damage repair as well as transcription. Taken together, these results suggest that robust LC-MS/MS analysis of γ-H2AX and p-H3 can not only quantitatively differentiate mechanistic information on clastogens and aneugens but also dynamically present the detail profiles of DNA damage and repair processes.
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Affiliation(s)
- Minmin Qu
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Hua Xu
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Jia Chen
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Yajiao Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China
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Matsuda S, Wanibuchi S, Kasahara T. Quantitative analysis of γH2AX reveals distinct responses in multiple mouse organs after administration of mitomycin C or ethyl methanesulfonate. Mutagenesis 2018; 33:371-378. [DOI: 10.1093/mutage/gey040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/25/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Shun Matsuda
- Safety Evaluation Center, Ecology and Quality Management Division, CSR Division, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa, Japan
| | - Sayaka Wanibuchi
- Safety Evaluation Center, Ecology and Quality Management Division, CSR Division, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa, Japan
| | - Toshihiko Kasahara
- Safety Evaluation Center, Ecology and Quality Management Division, CSR Division, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa, Japan
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Fan P, Chen W, Yu P, Bao L, Xu L, Qin C. Comparative Analysis of Serum Proteins from Patients with Severe and Mild EV-A71-induced HFMD using iTRAQ-Coupled LC-MS/MS Screening. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201700027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 09/01/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Peihu Fan
- Key Laboratory of Human Disease Comparative Medicine Ministry of Health; Institute of Laboratory Animal Sciences; Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center; Peking Union Medical College (PUMC); Beijing China
| | - Wei Chen
- Key Laboratory of Human Disease Comparative Medicine Ministry of Health; Institute of Laboratory Animal Sciences; Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center; Peking Union Medical College (PUMC); Beijing China
| | - Pin Yu
- Key Laboratory of Human Disease Comparative Medicine Ministry of Health; Institute of Laboratory Animal Sciences; Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center; Peking Union Medical College (PUMC); Beijing China
| | - Linlin Bao
- Key Laboratory of Human Disease Comparative Medicine Ministry of Health; Institute of Laboratory Animal Sciences; Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center; Peking Union Medical College (PUMC); Beijing China
| | - Lili Xu
- Key Laboratory of Human Disease Comparative Medicine Ministry of Health; Institute of Laboratory Animal Sciences; Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center; Peking Union Medical College (PUMC); Beijing China
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine Ministry of Health; Institute of Laboratory Animal Sciences; Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center; Peking Union Medical College (PUMC); Beijing China
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Casado P, Hijazi M, Britton D, Cutillas PR. Impact of phosphoproteomics in the translation of kinase-targeted therapies. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600235] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/29/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Pedro Casado
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - Maruan Hijazi
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - David Britton
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - Pedro R. Cutillas
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
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Progress on Molecular Mechanism of Phosphorylation/Dephosphorylation and Detection Technology of γH2AX. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60952-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Matsuda S, Matsuda Y, Yanagisawa SY, Ikura M, Ikura T, Matsuda T. Disruption of DNA Damage-Response by Propyl Gallate and 9-Aminoacridine. Toxicol Sci 2016; 151:224-35. [PMID: 26928355 DOI: 10.1093/toxsci/kfw039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The DNA-damage response (DDR) protects the genome from various types of endogenous and exogenous DNA damage, and can itself be a target of certain chemicals that give rise to chromosomal aberrations. Here, we developed a screening method to detect inhibition of Mediator of DNA damage Checkpoint 1 (MDC1) foci formation (the Enhanced Green Fluorescent Protein (EGFP)-MDC1 foci formation-inhibition assay) using EGFP-MDC1-expressing human cells. The assay identified propyl gallate (PG) and 9-aminoacridine (9-AA) as inhibitors of camptothecin (CPT)-induced MDC1 foci formation. We demonstrated that the inhibition of CPT-induced MDC1 foci formation by PG was caused by the direct suppression of histone H2AX phosphorylation at Ser139 (γH2AX), which is required for MDC1 foci formation, by quantifying γH2AX in cells and in vitro 9-AA also directly suppressed H2AX Ser139-phosphorylation in vitro but the concentration was much higher than that required to suppress CPT-induced MDC1 foci formation in cells. Consistent with these findings, PG and 9-AA both suppressed CPT-induced G2/M cell-cycle arrest and increased the number of abnormal nuclei. Our results suggest that early DDR-inhibitory effects of PG and 9-AA contribute to their chromosome-damaging potential, and that the EGFP-MDC1 foci formation-inhibition assay is useful for detection of and screening for H2AX Ser139-phosphorylation-inhibitory effects of chemicals.
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Affiliation(s)
- Shun Matsuda
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
| | - Yoko Matsuda
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
| | - Shin-Ya Yanagisawa
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
| | - Masae Ikura
- Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Tsuyoshi Ikura
- Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Tomonari Matsuda
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
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