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Zhou Y, Luo Q, Zeng F, Liu X, Han J, Gu L, Tian X, Zhang Y, Zhao Y, Wang F. Trichostatin A Promotes Cytotoxicity of Cisplatin, as Evidenced by Enhanced Apoptosis/Cell Death Markers. Molecules 2024; 29:2623. [PMID: 38893499 PMCID: PMC11173726 DOI: 10.3390/molecules29112623] [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: 03/26/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Trichostatin A (TSA), a histone deacetylase (HDAC) inhibitor, promotes the cytotoxicity of the genotoxic anticancer drug cisplatin, yet the underlying mechanism remains poorly understood. Herein, we revealed that TSA at a low concentration (1 μM) promoted the cisplatin-induced activation of caspase-3/6, which, in turn, increased the level of cleaved PARP1 and degraded lamin A&C, leading to more cisplatin-induced apoptosis and G2/M phase arrest of A549 cancer cells. Both ICP-MS and ToF-SIMS measurements demonstrated a significant increase in DNA-bound platinum in A549 cells in the presence of TSA, which was attributable to TSA-induced increase in the accessibility of genomic DNA to cisplatin attacking. The global quantitative proteomics results further showed that in the presence of TSA, cisplatin activated INF signaling to upregulate STAT1 and SAMHD1 to increase cisplatin sensitivity and downregulated ICAM1 and CD44 to reduce cell migration, synergistically promoting cisplatin cytotoxicity. Furthermore, in the presence of TSA, cisplatin downregulated TFAM and SLC3A2 to enhance cisplatin-induced ferroptosis, also contributing to the promotion of cisplatin cytotoxicity. Importantly, our posttranslational modification data indicated that acetylation at H4K8 played a dominant role in promoting cisplatin cytotoxicity. These findings provide novel insights into better understanding the principle of combining chemotherapy of genotoxic drugs and HDAC inhibitors for the treatment of cancers.
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Affiliation(s)
- Yang Zhou
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangang Zeng
- School of Environment of Natural Resources, Remin University of China, Beijing 100875, China;
| | - Xingkai Liu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
| | - Juanjuan Han
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- National Centre for Mass Spectrometry in Beijing, Beijing 100190, China
| | - Liangzhen Gu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Tian
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.Z.); (Q.L.); (J.H.); (L.G.); (X.T.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Centre for Mass Spectrometry in Beijing, Beijing 100190, China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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2
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Pan Q, Luo P, Shi C. PC4-mediated Ku complex PARylation facilitates NHEJ-dependent DNA damage repair. J Biol Chem 2023; 299:105032. [PMID: 37437887 PMCID: PMC10406618 DOI: 10.1016/j.jbc.2023.105032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Radiotherapy is one of the mainstay treatments for hepatocellular carcinoma (HCC). However, a substantial number of patients with HCC develop radioresistance and eventually suffer from tumor progression or relapse, which is a major impediment to the use of radiotherapy. Therefore, elucidating the mechanisms underlying radioresistance and identifying novel therapeutic targets to improve patient prognosis are important in HCC management. In this study, using in vitro and in vivo models, laser microirradiation and live cell imaging methods, and coimmunoprecipitation assays, we report that a DNA repair enhancer, human positive cofactor 4 (PC4), promotes nonhomologous end joining-based DNA repair and renders HCC cells resistant to radiation. Mechanistically, PC4 interacts with poly (ADP-ribose) polymerase 1 and directs Ku complex PARylation, resulting in the successful recruitment of the Ku complex to damaged chromatin and increasing the efficiency of nonhomologous end joining repair. Clinically, PC4 is highly expressed in tumor tissues and is correlated with poor prognosis in patients with HCC. Taken together, our data suggest that PC4 is a DNA repair driver that can be targeted to radiosensitize HCC cells.
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Affiliation(s)
- Qimei Pan
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Rocket Force Medicine, Third Military Medical University (Army Medical University), Chongqing, China
| | - Peng Luo
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Rocket Force Medicine, Third Military Medical University (Army Medical University), Chongqing, China
| | - Chunmeng Shi
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Rocket Force Medicine, Third Military Medical University (Army Medical University), Chongqing, China.
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3
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Zhu L, Liu H, Dou Y, Luo Q, Gu L, Liu X, Zhou Q, Han J, Wang F. A Photoactivated Ru (II) Polypyridine Complex Induced Oncotic Necrosis of A549 Cells by Activating Oxidative Phosphorylation and Inhibiting DNA Synthesis as Revealed by Quantitative Proteomics. Int J Mol Sci 2023; 24:ijms24097756. [PMID: 37175463 PMCID: PMC10178167 DOI: 10.3390/ijms24097756] [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: 02/14/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The ruthenium polypyridine complex [Ru(dppa)2(pytp)] (PF6)2 (termed as ZQX-1), where dppa = 4,7-diphenyl-1,10-phenanthroline and pytp = 4'-pyrene-2,2':6',2''-terpyridine, has been shown a high and selective cytotoxicity to hypoxic and cisplatin-resistant cancer cells either under irradiation with blue light or upon two-photon excitation. The IC50 values of ZQX-1 towards A549 cancer cells and HEK293 health cells are 0.16 ± 0.09 µM and >100 µM under irradiation at 420 nm, respectively. However, the mechanism of action of ZQX-1 remains unclear. In this work, using the quantitative proteomics method we identified 84 differentially expressed proteins (DEPs) with |fold-change| ≥ 1.2 in A549 cancer cells exposed to ZQX-1 under irradiation at 420 nm. Bioinformatics analysis of the DEPs revealed that photoactivated ZQX-1 generated reactive oxygen species (ROS) to activate oxidative phosphorylation signaling to overproduce ATP; it also released ROS and pyrene derivative to damage DNA and arrest A549 cells at S-phase, which synergistically led to oncotic necrosis and apoptosis of A549 cells to deplete excess ATP, evidenced by the elevated level of PRAP1 and cleaved capase-3. Moreover, the DNA damage inhibited the expression of DNA repair-related proteins, such as RBX1 and GPS1, enhancing photocytotoxicity of ZQX-1, which was reflected in the inhibition of integrin signaling and disruption of ribosome assembly. Importantly, the photoactivated ZQX-1 was shown to activate hypoxia-inducible factor 1A (HIF1A) survival signaling, implying that combining use of ZQX-1 with HIF1A signaling inhibitors may further promote the photocytotoxicity of the prodrug.
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Affiliation(s)
- Li Zhu
- College of Applied Science and Technology, Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing 100101, China
| | - Hui Liu
- College of Applied Science and Technology, Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing 100101, China
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Dou
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhen Gu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xingkai Liu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qianxiong Zhou
- Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Juanjuan Han
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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Ma L, Gong Q, Liu G, Chen J, Wang Y, luo P, Shi C. Positive Cofactor 4 as a Potential Radiation Biodosimeter for Early Assessment. Dose Response 2022; 20:15593258221081317. [PMID: 35221823 PMCID: PMC8874181 DOI: 10.1177/15593258221081317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
During a major radiation event, a large number of people need to be rapidly assessed for radiation damage to ensure effective medical treatment and efficient use of medical resources. However, current techniques cannot meet the requirement of rapid detection of large quantities of samples in an emergency. It is essential to develop rapid and accurate radiation biodosimeters in peripheral blood. Here, we identified radiation sensitive genes in mice by RNA sequencing and evaluated their utility as radiation biodosimeters in human cell lines. Mice were subjected to gamma-irradiation with different doses (0–8 Gy, .85 Gy/min), and the tail venous blood was analyzed by RNA sequencing. We have identified 5 genes with significantly differential expression after radiation exposure. We found that positive cofactor 4(PC4) had well correlation with radiation dose in human lymphoblastoid cell line after irradiation. The relative expression of PC4 gene showed a good linear correlation with the radiation dose after 1–5 Gy irradiation (.85 Gy/min). PC4 gene can be rapidly recruited to the DNA damage sites faster than γ-H2AX after radiation in immunofluorescence detection. In conclusion, PC4 may be represented as new radiation biological dosimeter for early assessment.
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Affiliation(s)
- Le Ma
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qiang Gong
- Department of Hematology, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Gaoyu Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jieping Chen
- Department of Hematology, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Yu Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
| | - Peng luo
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
| | - Chunmeng Shi
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
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Hou Y, Liang Z, Qi L, Tang C, Liu X, Tang J, Zhao Y, Zhang Y, Fang T, Luo Q, Wang S, Wang F. Baicalin Targets HSP70/90 to Regulate PKR/PI3K/AKT/eNOS Signaling Pathways. Molecules 2022; 27:1432. [PMID: 35209223 PMCID: PMC8874410 DOI: 10.3390/molecules27041432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Baicalin is a major active ingredient of traditional Chinese medicine Scutellaria baicalensis, and has been shown to have antiviral, anti-inflammatory, and antitumor activities. However, the protein targets of baicalin have remained unclear. Herein, a chemical proteomics strategy was developed by combining baicalin-functionalized magnetic nanoparticles (BCL-N3@MNPs) and quantitative mass spectrometry to identify the target proteins of baicalin. Bioinformatics analysis with the use of Gene Ontology, STRING and Ingenuity Pathway Analysis, was performed to annotate the biological functions and the associated signaling pathways of the baicalin targeting proteins. Fourteen proteins in human embryonic kidney cells were identified to interact with baicalin with various binding affinities. Bioinformatics analysis revealed these proteins are mainly ATP-binding and/or ATPase activity proteins, such as CKB, HSP86, HSP70-1, HSP90, ATPSF1β and ACTG1, and highly associated with the regulation of the role of PKR in interferon induction and the antiviral response signaling pathway (P = 10-6), PI3K/AKT signaling pathway (P = 10-5) and eNOS signaling pathway (P = 10-4). The results show that baicalin exerts multiply pharmacological functions, such as antiviral, anti-inflammatory, antitumor, and antioxidant functions, through regulating the PKR and PI3K/AKT/eNOS signaling pathways by targeting ATP-binding and ATPase activity proteins. These findings provide a fundamental insight into further studies on the mechanism of action of baicalin.
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Affiliation(s)
- Yinzhu Hou
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuqing Liang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyu Qi
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Tang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
| | - Xingkai Liu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jilin Tang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
| | - Tiantian Fang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijun Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (Y.H.); (Z.L.); (L.Q.); (C.T.); (X.L.); (J.T.); (Y.Z.); (Y.Z.); (T.F.)
- College of Chemical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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Hou Y, Gan T, Fang T, Zhao Y, Luo Q, Liu X, Qi L, Zhang Y, Jia F, Han J, Li S, Wang S, Wang F. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3070-3082. [PMID: 35258624 PMCID: PMC8989551 DOI: 10.1093/nar/gkac151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 11/23/2022] Open
Abstract
Pyridostatin (PDS) is a well-known G-quadruplex (G4) inducer and stabilizer, yet its target genes have remained unclear. Herein, applying MS proteomics strategy, we revealed PDS significantly downregulated 22 proteins but upregulated 16 proteins in HeLa cancer cells, of which the genes both contain a number of G4 potential sequences, implying that PDS regulation on gene expression is far more complicated than inducing/stabilizing G4 structures. The PDS-downregulated proteins consequently upregulated 6 proteins to activate cyclin and cell cycle regulation, suggesting that PDS itself is not a potential anticancer agent, at least toward HeLa cancer cells. Importantly, SUB1, which encodes human positive cofactor and DNA lesion sensor PC4, was downregulated by 4.76-fold. Further studies demonstrated that the downregulation of PC4 dramatically promoted the cytotoxicity of trans-[PtCl2(NH3)(thiazole)] (trans-PtTz) toward HeLa cells to a similar level of cisplatin, contributable to retarding the repair of 1,3-trans-PtTz crosslinked DNA lesion mediated by PC4. These findings not only provide new insights into better understanding on the biological functions of PDS but also implicate a strategy for the rational design of novel multi-targeting platinum anticancer drugs via conjugation of PDS as a ligand to the coordination scaffold of transplatin for battling drug resistance to cisplatin.
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Affiliation(s)
- Yinzhu Hou
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Tieliang Gan
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Tiantian Fang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Yao Zhao
- Correspondence may also be addressed to Yao Zhao. Tel: +86 010 62529069;
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Xingkai Liu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Luyu Qi
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
- College of Chemical Science, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, 100049 Beijing, P.R. China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Juanjuan Han
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Shumu Li
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Analytical Chemistry for Living Biosystems; National Centre for Mass Spectrometry in Beijing, Institute of Chemistry, Chinese Academy of Sciences, No. 2 Zhongguancun North First Street, Haidian District, 100190 Beijing, P.R. China
| | - Shijun Wang
- Correspondence may also be addressed to Shijun Wang. Tel: +86 0531 89628750;
| | - Fuyi Wang
- To whom correspondence should be addressed. Tel: +86 010 62529069;
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He X, Wang P, Wang Y. Mitochondrial Transcription Factor A Binds to and Promotes Mutagenic Transcriptional Bypass of O4-Alkylthymidine Lesions. Anal Chem 2021; 93:1161-1169. [PMID: 33290046 PMCID: PMC7904241 DOI: 10.1021/acs.analchem.0c04224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
O2- and O4-alkylated thymidine lesions are known to be poorly repaired and persist in mammalian tissues. To understand how mammalian cells sense the presence and regulate the repair of these lesions, we employed a quantitative proteomic method to discover regioisomeric O2- and O4-n-butylthymidine (O2- and O4-nBudT)-binding proteins. We were able to identify 21 and 74 candidate DNA damage recognition proteins for O2-nBudT- and O4-nBudT-bearing DNA probes, respectively. Among these proteins, DDB1 and DDB2 selectively bind to O2-nBudT-containing DNA, whereas three high-mobility group (HMG) proteins (i.e., HMGB1, HMGB2, and mitochondrial transcription factor A (TFAM)) exhibit preferential binding to O4-nBudT-bearing DNA. We further demonstrated that TFAM binds directly and selectively with O4-alkyldT-harboring DNA, and the binding capacity depends mainly on the HMG box-A domain of TFAM. We also found that TFAM promotes transcriptional mutagenesis of O4-nBudT and O4-pyridyloxobutylthymidine, which is a DNA adduct induced by tobacco-specific N-nitrosamines, in vitro and in human cells. Together, we explored, for the first time, the interaction proteomes of O-alkyldT lesions, and our study expanded the functions of TFAM by revealing its capability in the recognition of O4-alkyldT-bearing DNA and uncovering its modulation of transcriptional mutagenesis of these lesions in human cells.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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10
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Jia F, Wang J, Zhao Y, Zhang Y, Luo Q, Qi L, Hou Y, Du J, Wang F. In Situ Visualization of Proteins in Single Cells by Time-of-Flight-Secondary Ion Mass Spectrometry Coupled with Genetically Encoded Chemical Tags. Anal Chem 2020; 92:15517-15525. [PMID: 33203209 DOI: 10.1021/acs.analchem.0c03448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In situ visualization of proteins of interest in single cells is attractive in cell biology, molecular biology, and biomedicine fields. Time-of-flight-secondary ion mass spectrometry (ToF-SIMS) is a powerful tool for imaging small organic molecules in single cells, yet difficult to image biomacromolecules such as proteins and DNA. Herein, a universal strategy is reported to image specific proteins in single cells by ToF-SIMS following genetic incorporation of fluorine-containing unnatural amino acids as a chemical tag into the proteins via a genetic code expansion technique. The method was developed and validated by imaging a green fluorescence protein (GFP) in Escherichia coli (E. coli) and human HeLa cancer cells and then utilized to visualize the characteristic polar distribution of chemotaxis protein CheA in E. coli cells and the interaction between high-mobility group box 1 protein and cisplatin-damaged DNA in HeLa cells. The present work highlights the power of ToF-SIMS imaging combined with genetically encoded chemical tags for in situ visualization of specific proteins as well as the interactions between proteins and drugs or drug-damaged DNA in single cells.
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Affiliation(s)
- Feifei Jia
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Jie Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,College of Chemistry and Materials Science, Key Laboratory of Functional Molecular Solids, the Ministry of Education, Anhui Laboratory of Molecular-Based Materials, Anhui Normal University, Wuhu, Anhui 241000, People's Republic of China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Luyu Qi
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yinzhu Hou
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jun Du
- College of Chemistry and Materials Science, Key Laboratory of Functional Molecular Solids, the Ministry of Education, Anhui Laboratory of Molecular-Based Materials, Anhui Normal University, Wuhu, Anhui 241000, People's Republic of China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Basic Medical College, Shandong University of Chinese Traditional Medicine, Jinan 250355, People's Republic of China
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11
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Yuan X, Zhang W, He Y, Yuan J, Song D, Chen H, Qin W, Qian X, Yu H, Guo Z. Proteomic analysis of cisplatin- and oxaliplatin-induced phosphorylation in proteins bound to Pt-DNA adducts. Metallomics 2020; 12:1834-1840. [PMID: 33151228 DOI: 10.1039/d0mt00194e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cisplatin and oxaliplatin are widely used anti-tumour chemotherapeutic agents with different spectra of activity. The therapeutic efficacy of such platinum-based drug is believed to, at least in part, result from formation of Pt-DNA adducts, followed by DNA damage response and ultimately apoptosis. However, it remains unclear whether these DNA lesions caused by cisplatin and oxaliplatin elicit distinct reactions in cellular signaling pathways. Here, a label-free comparative proteomic study was performed to profile the protein phosphorylation patterns using Pt-DNA probes with different ligand identities and geometries. Phosphorylated proteins recognizing different cisplatin- and oxaliplatin-DNA lesions were enriched and analyzed on LC-MS/MS. Proteomic analysis revealed that cisplatin mainly affected proteins involved in mRNA processing, while chromatin organization and rRNA processing are two major biological processes influenced by oxaliplatin. Changes to site-specific phosphorylation levels of two proteins YBX1 and UBF1 were also validated by Western blotting. In particular, platinum drug treatment in colon and liver cancer cell lines down-regulated S484 phosphorylation of UBF1, which is an essential transcription factor responsible for ribosomal DNA transcription activation, implying that inhibition of ribosome biogenesis might be involved in the cytotoxic mechanism of platinum drugs. Collectively, these results directly reflected distinct protein phosphorylation patterns triggered by cisplatin and oxaliplatin, and could also provide valuable resources for future mechanistic studies of platinum-based anti-tumour agents.
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Affiliation(s)
- Xin Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China.
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12
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A kinetic investigation of mononuclear trans-platinum(II) complexes with mixed amine ligands. TRANSIT METAL CHEM 2020. [DOI: 10.1007/s11243-020-00381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Liao F, Chen L, Luo P, Jiang Z, Chen Z, Wang Z, Zhang C, Wang Y, He J, Wang Q, Wang Y, Liu L, Huang Y, Wang H, Jiang Q, Luo M, Gan Y, Liu Y, Wang Y, Wu J, Xie W, Cheng Z, Dai Y, Li J, Liu Z, Yang F, Shi C. PC4 serves as a negative regulator of skin wound healing in mice. BURNS & TRAUMA 2020; 8:tkaa010. [PMID: 32373645 PMCID: PMC7198317 DOI: 10.1093/burnst/tkaa010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/29/2020] [Indexed: 01/13/2023]
Abstract
Background Human positive cofactor 4 (PC4) was initially characterized as a multifunctional transcriptional cofactor, but its role in skin wound healing is still unclear. The purpose of this study was to explore the role of PC4 in skin wound healing through PC4 knock-in mouse model. Methods A PC4 knock-in mouse model (PC4+/+) with a dorsal full-thickness wound was used to investigate the biological functions of PC4 in skin wound healing. Quantitative PCR, Western blot analysis and immunohistochemistry were performed to evaluate the expression of PC4; Sirius red staining and immunofluorescence were performed to explore the change of collagen deposition and angiogenesis. Proliferation and apoptosis were detected using Ki67 staining and TUNEL assay. Primary dermal fibroblasts were isolated from mouse skin to perform cell scratch experiments, cck-8 assay and colony formation assay. Results The PC4+/+ mice were fertile and did not display overt abnormalities but showed an obvious delay in cutaneous healing of dorsal skin. Histological staining showed insufficient re-epithelialization, decreased angiogenesis and collagen deposition, increased apoptosis and decreased cell proliferation in PC4+/+ skin. Our data also showed decreased migration rate and proliferation ability in cultured primary fibroblasts from PC4+/+ mice in vitro. Conclusions This study suggests that PC4 might serve as a negative regulator of skin wound healing in mice.
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Affiliation(s)
- Fengying Liao
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Long Chen
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Peng Luo
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zhongyong Jiang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zelin Chen
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ziwen Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Chi Zhang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yu Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jintao He
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Qing Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Clinical Medicine, Southwest Medical University, 646000 Luzhou, China
| | - Yawei Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Lang Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Department of Toxicology, Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, 550025 Guiyang, China
| | - Yu Huang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Department of Toxicology, Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, 550025 Guiyang, China
| | - Huilan Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Clinical Medicine, Southwest Medical University, 646000 Luzhou, China
| | - Qingzhi Jiang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Clinical Medicine, Southwest Medical University, 646000 Luzhou, China
| | - Min Luo
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Department of Toxicology, Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, 550025 Guiyang, China
| | - Yibo Gan
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yunsheng Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yang Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jie Wu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Wentao Xie
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zhuo Cheng
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yali Dai
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jialun Li
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zujuan Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Fan Yang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Chunmeng Shi
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing 400038, China
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14
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Luo P, Tan X, Luo S, Wang Z, Long L, Wang Y, Liao F, Chen L, Zhang C, He J, Huang Y, Liu Z, Gan Y, Chen Z, Wang Y, Liu Y, Wang Y, Shi C. An NIR‐Fluorophore‐Based Inhibitor of SOD1 Induces Apoptosis by Targeting Transcription Cofactor PC4. ADVANCED THERAPEUTICS 2019. [DOI: 10.1002/adtp.201800148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Peng Luo
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Xu Tan
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Shenglin Luo
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Ziwen Wang
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Lei Long
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Yawei Wang
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Fengying Liao
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Long Chen
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Chi Zhang
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Jintao He
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Yinghui Huang
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Zujuan Liu
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Yibo Gan
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Zelin Chen
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Yang Wang
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Yunsheng Liu
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Yu Wang
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
| | - Chunmeng Shi
- Institute of Rocket Force MedicineState Key Laboratory of TraumaBurns and Combined InjuryThird Military Medical University Chongqing 400038 China
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15
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Zeng W, Du Z, Luo Q, Zhao Y, Wang Y, Wu K, Jia F, Zhang Y, Wang F. Proteomic Strategy for Identification of Proteins Responding to Cisplatin-Damaged DNA. Anal Chem 2019; 91:6035-6042. [PMID: 30990031 DOI: 10.1021/acs.analchem.9b00554] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new proteomic strategy combining functionalized magnetic nanoparticle affinity probes with mass spectrometry was developed to capture and identify proteins specifically responding to 1,2-d(GpG) intrastrand cisplatin-cross-linked DNA, the major DNA lesion caused by cisplatin and thought to induce apoptosis. A 16-mer oligodeoxynucleotide (ODN) duplex and its cisplatin-cross-linked adduct were immobilized on magnetic nanoparticles via click reaction, respectively, to fabricate negative and positive affinity probes which were very stable in cellular protein extracts due to the excellent bio-orthogonality of click chemistry and the inertness of covalent triazole linker. Quantitative mass spectrometry results unambiguously revealed the predominant binding of HMGB1 and HMGB2, the well-established specific binders of 1,2-cisplatin-cross-linked DNA, to the cisplatin-cross-linked ODN, thus validating the accuracy and reliability of our strategy. Furthermore, 5 RNA or single-stranded DNA binding proteins, namely, hnRNP A/B, RRP44, RL30, RL13, and NCL, were demonstrated to recognize specifically the cisplatinated ODN, indicating the significantly unwound ODN duplex by cisplatin cross-linking. In contrast, the binding of a transcription factor TFIIFa to DNA was retarded due to cisplatin damage, implying that the cisplatin lesion stalls DNA transcription. These findings promote understanding in the cellular responses to cisplatin-damaged DNA and inspire further precise elucidation of the action mechanism of cisplatin.
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Affiliation(s)
- Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhifeng Du
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Yuanyuan Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China.,Basic Medical College , Shandong University of Chinese Traditional Medicine , Jinan 250355 , P. R. China
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16
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Transcriptional positive cofactor 4 promotes breast cancer proliferation and metastasis through c-Myc mediated Warburg effect. Cell Commun Signal 2019; 17:36. [PMID: 30992017 PMCID: PMC6469038 DOI: 10.1186/s12964-019-0348-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/03/2019] [Indexed: 12/24/2022] Open
Abstract
Background The human positive cofactor 4 (PC4) is initially identified as a transcriptional cofactor and has an important role in embryonic development and malignant transformation. However, the clinical significance and the molecular mechanisms of PC4 in breast cancer development and progression are still unknown. Methods We investigated PC4 expression in 114 cases of primary breast cancer and matched normal breast tissue specimens, and studied the impact of PC4 expression as well as the molecular mechanisms of this altered expression on breast cancer growth and metastasis both in vitro and in vivo. Results PC4 was significantly upregulated in breast cancer and high PC4 expression was positively correlated with metastasis and poor prognosis of patients. Gene set enrichment analysis (GSEA) demonstrated that the gene sets of cell proliferation and Epithelial-Mesenchymal Transition (EMT) were positively correlated with elevated PC4 expression. Consistently, loss of PC4 markedly inhibited the growth and metastasis of breast cancer both in vitro and in vivo. Mechanistically, PC4 exerted its oncogenic functions by directly binding to c-Myc promoters and inducing Warburg effect. Conclusions Our study reveals for the first time that PC4 promotes breast cancer progression by directly regulating c-Myc transcription to promote Warburg effect, implying a novel therapeutic target for breast cancer. Electronic supplementary material The online version of this article (10.1186/s12964-019-0348-0) contains supplementary material, which is available to authorized users.
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17
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Kritchenkov AS, Stanishevskii YM, Skorik YA. Design and Antitumor Activity of Platinum Complexes. Pharm Chem J 2019. [DOI: 10.1007/s11094-019-01947-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Jia S, Wang R, Wu K, Jiang H, Du Z. Elucidation of the Mechanism of Action for Metal Based Anticancer Drugs by Mass Spectrometry-Based Quantitative Proteomics. Molecules 2019; 24:molecules24030581. [PMID: 30736320 PMCID: PMC6384660 DOI: 10.3390/molecules24030581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 02/06/2023] Open
Abstract
The discovery of the anticancer activity of cisplatin and its clinical application has opened a new field for studying metal-coordinated anticancer drugs. Metal-based anticancer drugs, such as cisplatin, can be transported to cells after entering into the human body and form metal–DNA or metal–protein adducts. Then, responding proteins will recognize adducts and form stable complexes. The proteins that were binding with metal-based anticancer drugs were relevant to their mechanism of action. Herein, investigation of the recognition between metal-based anticancer drugs and its binding partners will further our understanding about the pharmacology of cytotoxic anticancer drugs and help optimize the structure of anticancer drugs. The “soft” ionization mass spectrometric methods have many advantages such as high sensitivity and low sample consumption, which are suitable for the analyses of complex biological samples. Thus, MS has become a powerful tool for the identification of proteins binding or responding to metal-based anticancer drugs. In this review, we focused on the mass spectrometry-based quantitative strategy for the identification of proteins specifically responding or binding to metal-based anticancer drugs, ultimately elucidating their mechanism of action.
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Affiliation(s)
- Shuailong Jia
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Runjing Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Kui Wu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Hongliang Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zhifeng Du
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
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19
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Zhai G, Dong H, Guo Z, Feng W, Jin J, Zhang T, Chen C, Chen P, Tian S, Bai X, Shi L, Fan E, Zhang Y, Zhang K. An Efficient Approach for Selective Enrichment of Histone Modification Readers Using Self-Assembled Multivalent Photoaffinity Peptide Probes. Anal Chem 2018; 90:11385-11392. [PMID: 30188686 DOI: 10.1021/acs.analchem.8b02342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone post-translational modifications (HPTMs) provide signaling platforms to recruit proteins or protein complexes (e.g., transcription factors, the so-called "readers" of the histone code), changing DNA accessibility in the regulation of gene expression. Thus, it is an essential task to identify HPTM readers for understanding of epigenetic regulation. Herein we designed and prepared a novel HPTM probe based on self-assembled multivalent photo-cross-linking technique for selective enrichment and identification of HPTM readers. By use of trimethylation of histone H3 lysine 4, we showcased that the functionalized HPTM probe was able to capture its reader with high enrichment efficiency and remarkable specificity even in a complex environment. Notably, this approach was readily applicable for exploring crosstalk among multiple HPTMs. Combining the probes with a mass spectrometry-based proteomic approach, our approach reached a fairly high coverage of known H3K4me3 readers. We further demonstrated that the HPTM probes can enrich a new type of HPTM readers and uncovered several novel putative binders of crotonylation of histone H3 lysine 9, expanding the repertoire of readers for this epigenetic mark. More broadly, our work provides a general strategy for rapid and robust interrogating HPTM readers and will be of great importance to elucidate epigenetic mechanism in regulating gene activity.
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Affiliation(s)
- Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Hanyang Dong
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Zhenchang Guo
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Wei Feng
- School of Biomedical Engineering , Tianjin Medical University , Tianjin 300070 , China
| | - Jin Jin
- College of Pharmacy , Nankai University , Tianjin 300071 , China
| | - Tao Zhang
- School of Biomedical Engineering , Tianjin Medical University , Tianjin 300070 , China
| | - Cong Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Pu Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Lei Shi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie , Universität Freiburg , Stefan-Meier-Straße 17 , Freiburg 79104 , Germany
| | - Yukui Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
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20
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Wu C, Liang Y, Zhu X, Zhao Q, Fang F, Zhang X, Liang Z, Zhang L, Zhang Y. Macro-mesoporous organosilica monoliths with bridged-ethylene and terminal-vinyl: High-density click functionalization for chromatographic separation. Anal Chim Acta 2018; 1038:198-205. [PMID: 30278903 DOI: 10.1016/j.aca.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/20/2018] [Accepted: 07/02/2018] [Indexed: 11/24/2022]
Abstract
A novel kind of macro-mesoporous organosilica monolith, with not only bridged-ethylene groups incorporated into the skeleton but also terminal-vinyl groups protruded from the pore-wall, was prepared so that high-loaded double bonds were achieved. Via highly efficient "thiol-ene" click reaction of such high-loaded double bonds, the surface coverage of C18 groups on monolith could be 5.54 μmol m-2, significantly larger than that of the reported separation materials, beneficial to improvement of separation resolution, especially for peptide separation. The separation performance was evaluated using alkylbenzenes and standard peptides. Furthermore, the tryptic digests of complex sample was successfully analyzed. Because of high separation resolution of our prepared hybrid monolith, the peak capacity for 6-h gradient was achieved as 482. Coupling to LTQ Orbitrap Velos Mass Spectrometry, 22523 tryptic peptides from 4423 proteins were identified from the HeLa cells, more than that using the other long-gradient separation by the same system reported, showing great promising of such monolith for large-scale in-depth proteomic analysis.
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Affiliation(s)
- Ci Wu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Inspection and Quarantine Technical Center of Dalian Entry-Exit Inspection and Quarantine Bureau, Dalian, 116100, China
| | - Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xudong Zhu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Qun Zhao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fei Fang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaodan Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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21
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Wang Y, Du Z, Zheng W, Wu K, Xu D, Luo Q, Zhao Y, Han J, Liu Y, Wang F. Deciphering of interactions between platinated DNA and HMGB1 by hydrogen/deuterium exchange mass spectrometry. Dalton Trans 2018; 46:6187-6195. [PMID: 28426082 DOI: 10.1039/c7dt00275k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A high mobility group box 1 (HMGB1) protein has been reported to recognize both 1,2-intrastrand crosslinked DNA by cisplatin (1,2-cis-Pt-DNA) and monofunctional platinated DNA using trans-[PtCl2(NH3)(thiazole)] (1-trans-PtTz-DNA). However, the molecular basis of recognition between the trans-PtTz-DNA and HMGB1 remains unclear. In the present work, we described a hydrogen/deuterium exchange mass spectrometry (HDX-MS) method in combination with docking simulation to decipher the interactions of platinated DNA with domain A of HMGB1. The global deuterium uptake results indicated that 1-trans-PtTz-DNA bound to HMGB1a slightly tighter than the 1,2-cis-Pt-DNA. The local deuterium uptake at the peptide level revealed that the helices I and II, and loop 1 of HMGB1a were involved in the interactions with both platinated DNA adducts. However, docking simulation disclosed different H-bonding networks and distinct DNA-backbone orientations in the two Pt-DNA-HMGB1a complexes. Moreover, the Phe37 residue of HMGB1a was shown to play a key role in the recognition between HMGB1a and the platinated DNAs. In the cis-Pt-DNA-HMGB1a complex, the phenyl ring of Phe37 intercalates into a hydrophobic notch created by the two platinated guanines, while in the trans-PtTz-DNA-HMGB1a complex the phenyl ring appears to intercalate into a hydrophobic crevice formed by the platinated guanine and the opposite adenine in the complementary strand, forming a penta-layer π-π stacking associated with the adjacent thymine and the thiazole ligand. This work demonstrates that HDX-MS associated with docking simulation is a powerful tool to elucidate the interactions between platinated DNAs and proteins.
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Affiliation(s)
- Yuanyuan Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.
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22
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Williams P, Li L, Dong X, Wang Y. Identification of SLIRP as a G Quadruplex-Binding Protein. J Am Chem Soc 2017; 139:12426-12429. [PMID: 28859475 DOI: 10.1021/jacs.7b07563] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The guanine quadruplex (G4) structure in DNA is a secondary structure motif that plays important roles in DNA replication, transcriptional regulation, and maintenance of genomic stability. Here, we employed a quantitative mass spectrometry-based approach to profile the interaction proteomes of three well-defined G4 structures derived from the human telomere and the promoters of cMYC and cKIT genes. We identified SLIRP as a novel G4-interacting protein. We also demonstrated that the protein could bind directly with G4 DNA with Kd values in the low nanomolar range and revealed that the robust binding of the protein toward G4 DNA requires its RRM domain. We further assessed, by using CRISPR-Cas9-introduced affinity tag and ChIP-Seq analysis, the genome-wide occupancy of SLIRP, and showed that the protein binds preferentially to G-rich DNA sequences that can fold into G4 structures. Together, our results uncovered a novel cellular protein that can interact directly with G4 DNA, which underscored the complex regulatory networks involved in G4 biology.
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Affiliation(s)
- Preston Williams
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Xiaoli Dong
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
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23
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Jin Y, Xie Y, Wu K, Huang Y, Wang F, Zhao R. Probing the Dynamic Interaction between Damaged DNA and a Cellular Responsive Protein Using a Piezoelectric Mass Biosensor. ACS APPLIED MATERIALS & INTERFACES 2017; 9:8490-8497. [PMID: 28218519 DOI: 10.1021/acsami.6b15077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The binding events between damaged DNA and recognition biomolecules are of great interest for understanding the activity of DNA-damaging drugs and the related DNA repair networks. Herein, a simple and sensitive sensor system was tailored for real-time probing of the dynamic molecular recognition between cisplatin-damaged-DNA (cisPt-DNA) and a cellular responsive protein, high-mobility-group box 1 (HMGB1). By integration of flow injection analysis (FIA) with quartz crystal microbalance (QCM), the interaction time-course of cisPt-DNA and HMGB1 domain A (HMGB1a) was investigated. The highly specific sensing interface was carefully designed and fabricated using cisPt-DNA as recognition element. A hybrid self-assembled monolayer consisting of cysteamine and mercaptohexanol was introduced to resist nonspecific adsorption. The calculated kinetic parameters (kass and kdiss) and the dissociation constant (KD) demonstrated the rapid recognition and tight binding of HMGB1a toward cisPt-DNA. Molecular docking was employed to simulate the complex formed by cisPt-DNA and HMGB1a. The tight binding of such a DNA-damage responsive complex is appealing for the downstream molecular recognition event related to the resistance to DNA repair. This continuous-flow QCM biosensor is an ideal tool for studying specific interactions between drug-damaged-DNAs and their recognition proteins in a physiological-relevant environment, and will provide a potential sensor platform for rapid screening and evaluating metal anticancer drugs.
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Affiliation(s)
- Yulong Jin
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yunfeng Xie
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yanyan Huang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Rui Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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24
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Boteanu RM, Suica VI, Uyy E, Ivan L, Dima SO, Popescu I, Simionescu M, Antohe F. Alarmins in chronic noncommunicable diseases: Atherosclerosis, diabetes and cancer. J Proteomics 2017; 153:21-29. [DOI: 10.1016/j.jprot.2016.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 10/18/2016] [Accepted: 11/09/2016] [Indexed: 12/30/2022]
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25
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Huang Y, Huang W, Chan L, Zhou B, Chen T. A multifunctional DNA origami as carrier of metal complexes to achieve enhanced tumoral delivery and nullified systemic toxicity. Biomaterials 2016; 103:183-196. [PMID: 27388944 DOI: 10.1016/j.biomaterials.2016.06.053] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/20/2022]
Abstract
The use of metal complexes in cancer treatment is hampered by the insufficient accumulation in tumor regions and observable systemic toxicity due to their nonspecificity in vivo. Herein we present a cancer-targeted DNA origami as biocompatible nanocarrier of metal complexes to achieve advanced antitumor effect. The formation of unique tetrahedral nanostructure of DNA cages effectively enhances the interaction between ruthenium polypyridyl complexes (RuPOP) and the cages, thus increasing the drug loading efficacy. Conjugation of biotin to the DNA-based nanosystem (Bio-cage@Ru) enhances its specific cellular uptake, drug retention and cytotoxicity against HepG2 cells. Different from free RuPOP and the cage itself, Bio-cage@Ru translocates to cell nucleus after internalization, where it undergoes self-immolative cleavage in response to DNases, leading to triggered drug release and induction of ROS-mediated cell apoptosis. Moreover, in the nude mice model, the nanosystem specifically accumulates in tumor sites, thus exhibits satisfactory in vivo antitumor efficacy, and alleviates the damage of liver, kidney, lung and heart function of nude mice induced by RuPOP and tumor xenografts. Collectively, this study demonstrates a strategy for construction of biocompatible and cancer-targeted DNA origami with enhanced anticancer efficacy and reduced toxicity for next-generation cancer therapy.
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Affiliation(s)
- Yanyu Huang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Wei Huang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Leung Chan
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Binwei Zhou
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, China.
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26
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He Y, Yuan J, Qiao Y, Wang D, Chen W, Liu X, Chen H, Guo Z. The role of carrier ligands of platinum(II) anticancer complexes in the protein recognition of Pt-DNA adducts. Chem Commun (Camb) 2016; 51:14064-7. [PMID: 26248639 DOI: 10.1039/c5cc05257b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to systematically investigate the influence of carrier ligands on the interaction of Pt-DNA adducts with damage recognition proteins, a series of DNA probes containing 1,2-GG platinum compound crosslinks using cisplatin, oxaliplatin, (S,S-DACH)PtCl2 and (cis-1,4-DACH)PtCl2 (kiteplatin) has been constructed. These complexes share similar DNA binding properties although they exhibit quite different cytotoxicity. It is revealed that HMGB1 (high-mobility group protein B1) was the most commonly found protein that recognizes all Pt(II)-DNA probes and prefers cisplatin-DNA probes more than the others. Interestingly, an important component of the replication protein A complex, RPA2, was found to bind to kiteplatin much more tightly than other proteins. These results may be important for the interpretation of the roles of carrier ligands in platinum(II)-based anticancer complexes.
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Affiliation(s)
- Yafeng He
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Centre of Chemistry for Life Sciences, Nanjing University, 22 Hankou Road, Nanjing, 210093, P. R. China.
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27
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Wang X, Xu J, Liu C, Chen Y. Specific interaction of platinated DNA and proteins by surface plasmon resonance imaging. RSC Adv 2016. [DOI: 10.1039/c5ra27719a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A surface plasmon resonance imaging method to differentiate the interaction between the protein human high mobility group box 1 or human nuclear protein positive cofactor 4 (PC4) and DNAs has been developed.
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Affiliation(s)
- Xiao Wang
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Jiying Xu
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Chanjuan Liu
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Yi Chen
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
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28
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Hu S, Cui X, He W, Chen X, Gu Z, Zhao J, Zeng G, Shi Z, Zhu L, Nie H. Synthesis, Structural Characterization and Preliminary Biological Studies of Several Heterocyclic Transition Metal Carbonyl Complexes. Z Anorg Allg Chem 2015. [DOI: 10.1002/zaac.201500592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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29
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He Y, Ding Y, Wang D, Zhang W, Chen W, Liu X, Qin W, Qian X, Chen H, Guo Z. HMGB1 bound to cisplatin-DNA adducts undergoes extensive acetylation and phosphorylation in vivo. Chem Sci 2015; 6:2074-2078. [PMID: 29449921 PMCID: PMC5810237 DOI: 10.1039/c4sc03650f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/13/2014] [Indexed: 11/21/2022] Open
Abstract
Cisplatin, one of the most effective anticancer drugs, is a DNA-damaging agent that induces cell death primarily by apoptosis. For many years, HMGB1 has been known to be a recognition protein for cisplatin-DNA lesions. Here, an application of a biomolecular probe based on a peptide-oligonucleotide conjugate is presented as a novel method for investigating this recognition process in vivo. Proteins known to be involved in the recognition of cisplatin-damaged DNA were pulled down and identified, including members of the HMGB family and a number of other proteins. Interestingly, at least 4 subforms of HMGB1 bind to cisplatin-DNA adducts. These proteins were further identified as post-translationally acetylated or phosphorylated forms of HMGB1. These results provide a rich pool of protein candidates whose roles in the mechanism of action of platinum drugs should be explored. These newly discovered molecular components of the DNA damage signalling cascade could serve as novel links between the initial cell responses to DNA damage and the downstream apoptotic or DNA repair pathways.
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Affiliation(s)
- Yafeng He
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
| | - Yin Ding
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
| | - Dan Wang
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Institute of Radiation Medicine , 33 Life Science Park Road, Changping District , Beijing , 102206 P. R. China
| | - Weizhong Chen
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
| | - Xichun Liu
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
| | - Weijie Qin
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Institute of Radiation Medicine , 33 Life Science Park Road, Changping District , Beijing , 102206 P. R. China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Institute of Radiation Medicine , 33 Life Science Park Road, Changping District , Beijing , 102206 P. R. China
| | - Hao Chen
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry , State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , No. 22 Hankou Road , Nanjing , 210093 P. R. China . ;
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30
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Identification of a (H 2 O) 8 cluster in a supramolecular host of a charge transfer platinum(II) complex. J CHEM SCI 2014. [DOI: 10.1007/s12039-014-0656-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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