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Naciff JM, Shan YK, Wang X, Daston GP. Article title: Transcriptional profiling efficacy to define biological activity similarity for cosmetic ingredients' safety assessment based on next-generation read-across. FRONTIERS IN TOXICOLOGY 2022; 4:1082222. [PMID: 36618549 PMCID: PMC9811170 DOI: 10.3389/ftox.2022.1082222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The objective of this work was to use transcriptional profiling to assess the biological activity of structurally related chemicals to define their biological similarity and with that, substantiate the validity of a read-across approach usable in risk assessment. Two case studies are presented, one with 4 short alkyl chain parabens: methyl (MP), ethyl (EP), butyl (BP), and propylparaben (PP), as well as their main metabolite, p-hydroxybenzoic acid (pHBA) with the assumption that propylparaben was the target chemical; and a second one with caffeine and its main metabolites theophylline, theobromine and paraxanthine where CA was the target chemical. The comprehensive transcriptional response of MCF7, HepG2, A549 and ICell cardiomyocytes was evaluated (TempO-Seq) after exposure to vehicle-control, each paraben or pHBA, CA or its metabolites, at 3 non-cytotoxic concentrations, for 6 h. Differentially expressed genes (FDR ≥0.05, and fold change ±1.2≥) were identified for each chemical, at each concentration, and used to determine similarities. Each of the chemicals is able to elicit changes in the expression of a number of genes, as compared to controls. Importantly, the transcriptional profile elicited by each of the parabens shares a high degree of similarity across the group. The highest number of genes commonly affected was between butylparaben and PP. The transcriptional profile of the parabens is similar to the one elicited by estrogen receptor agonists, with BP being the closest structural and biological analogue for PP. In the CA case, the transcriptional profile elicited of all four methylxanthines had a high degree of similarity across the cell types, with CA and theophylline being the most active. The most robust response was obtained in the cardiomyocytes with the highest transcriptional profile similarity between CA and TP. The transcriptional profile of the methylxanthines is similar to the one elicited by inhibitors of phosphatidylinositol 3-kinase as well as other kinase inhibitors. Overall, our results support the approach of incorporating transcriptional profiling in well-designed in vitro tests as one robust stream of data to support biological similarity driven read-across procedures and strengthening the traditional structure-based approaches useful in risk assessment.
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Rush CM, Blanchard Z, Polaski JT, Osborne KS, Osby K, Vahrenkamp JM, Yang CH, Lum DH, Hagan CR, Leslie KK, Pufall MA, Thiel KW, Gertz J. Characterization of HCI-EC-23 a novel estrogen- and progesterone-responsive endometrial cancer cell line. Sci Rep 2022; 12:19731. [PMID: 36396974 PMCID: PMC9672046 DOI: 10.1038/s41598-022-24211-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Most endometrial cancers express the hormone receptor estrogen receptor alpha (ER) and are driven by excess estrogen signaling. However, evaluation of the estrogen response in endometrial cancer cells has been limited by the availability of hormonally responsive in vitro models, with one cell line, Ishikawa, being used in most studies. Here, we describe a novel, adherent endometrioid endometrial cancer (EEC) cell line model, HCI-EC-23. We show that HCI-EC-23 retains ER expression and that ER functionally responds to estrogen induction over a range of passages. We also demonstrate that this cell line retains paradoxical activation of ER by tamoxifen, which is also observed in Ishikawa and is consistent with clinical data. The mutational landscape shows that HCI-EC-23 is mutated at many of the commonly altered genes in EEC, has relatively few copy-number alterations, and is microsatellite instable high (MSI-high). In vitro proliferation of HCI-EC-23 is strongly reduced upon combination estrogen and progesterone treatment. HCI-EC-23 exhibits strong estrogen dependence for tumor growth in vivo and tumor size is reduced by combination estrogen and progesterone treatment. Molecular characterization of estrogen induction in HCI-EC-23 revealed hundreds of estrogen-responsive genes that significantly overlapped with those regulated in Ishikawa. Analysis of ER genome binding identified similar patterns in HCI-EC-23 and Ishikawa, although ER exhibited more bound sites in Ishikawa. This study demonstrates that HCI-EC-23 is an estrogen- and progesterone-responsive cell line model that can be used to study the hormonal aspects of endometrial cancer.
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Affiliation(s)
- Craig M Rush
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Zannel Blanchard
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jacob T Polaski
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kyle S Osborne
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Krystle Osby
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Chieh-Hsiang Yang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - David H Lum
- Preclinical Research Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Christy R Hagan
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kimberly K Leslie
- Division of Molecular Medicine, Departments of Internal Medicine and Obstetrics and Gynecology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Miles A Pufall
- Department of Biochemistry and Molecular Biology, Holden Comprehensive Cancer Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kristina W Thiel
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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Newborn infant skin gene expression: Remarkable differences versus adults. PLoS One 2021; 16:e0258554. [PMID: 34665817 PMCID: PMC8525758 DOI: 10.1371/journal.pone.0258554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 01/03/2023] Open
Abstract
At birth, human infants are poised to survive in harsh, hostile conditions. An understanding of the state of newborn skin development and maturation is key to the maintenance of health, optimum response to injury, healing and disease. The observational study collected full-thickness newborn skin samples from 27 infants at surgery and compared them to skin samples from 43 adult sites protected from ultraviolet radiation exposure, as the standard for stable, mature skin. Transcriptomics profiling and gene set enrichment analysis were performed. Statistical analysis established over 25,000 differentially regulated probe sets, representing 10,647 distinct genes, in infant skin compared to adult skin. Gene set enrichment analysis showed a significant increase in 143 biological processes (adjusted p < 0.01) in infant skin, versus adult skin samples, including extracellular matrix (ECM) organization, cell adhesion, collagen fibril organization and fatty acid metabolic process. ECM organization and ECM structure organization were the biological processes in infant skin with the lowest adjusted P-value. Genes involving epidermal development, immune function, cell differentiation, and hair cycle were overexpressed in adults, representing 101 significantly enriched biological processes (adjusted p < 0.01). The processes with the highest significant difference were skin and epidermal development, e.g., keratinocyte differentiation, keratinization and cornification intermediate filament cytoskeleton organization and hair cycle. Enriched Gene Ontology (GO) biological processes also involved immune function, including antigen processing and presentation. When compared to ultraviolet radiation-protected adult skin, our results provide essential insight into infant skin and its ability to support the newborn's preparedness to survive and flourish, despite the infant's new environment laden with microbes, high oxygen tension and potential irritants. This fundamental knowledge is expected to guide strategies to protect and preserve the features of unperturbed, young skin.
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Monticolo F, Chiusano ML. Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods. Cancers (Basel) 2021; 13:4207. [PMID: 34439361 PMCID: PMC8393935 DOI: 10.3390/cancers13164207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 01/22/2023] Open
Abstract
It is today widely accepted that a healthy diet is very useful to prevent the risk for cancer or its deleterious effects. Nutrigenomics studies are therefore taking place with the aim to test the effects of nutrients at molecular level and contribute to the search for anti-cancer treatments. These efforts are expanding the precious source of information necessary for the selection of natural compounds useful for the design of novel drugs or functional foods. Here we present a computational study to select new candidate compounds that could play a role in cancer prevention and care. Starting from a dataset of genes that are co-expressed in programmed cell death experiments, we investigated on nutrigenomics treatments inducing apoptosis, and searched for compounds that determine the same expression pattern. Subsequently, we selected cancer types where the genes showed an opposite expression pattern and we confirmed that the apoptotic/nutrigenomics expression trend had a significant positive survival in cancer-affected patients. Furthermore, we considered the functional interactors of the genes as defined by public protein-protein interaction data, and inferred on their involvement in cancers and/or in programmed cell death. We identified 7 genes and, from available nutrigenomics experiments, 6 compounds effective on their expression. These 6 compounds were exploited to identify, by ligand-based virtual screening, additional molecules with similar structure. We checked for ADME criteria and selected 23 natural compounds representing suitable candidates for further testing their efficacy in apoptosis induction. Due to their presence in natural resources, novel drugs and/or the design of functional foods are conceivable from the presented results.
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Affiliation(s)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Via Università 100, 80055 Portici, Italy;
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Vergaro P, Tiscornia G, Zambelli F, Rodríguez A, Santaló J, Vassena R. Trophoblast attachment to the endometrial epithelium elicits compartment-specific transcriptional waves in an in-vitro model. Reprod Biomed Online 2020; 42:26-38. [PMID: 33051136 DOI: 10.1016/j.rbmo.2020.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 01/02/2023]
Abstract
RESEARCH QUESTION Which are the early compartment-specific transcriptional responses of the trophoblast and the endometrial epithelium throughout early attachment during implantation? DESIGN An endometrial epithelium proxy (cell line Ishikawa) was co-cultured with spheroids of a green fluorescent protein (GFP) expressing trophoblast cell line (JEG-3). After 0, 8 and 24 h of co-culture, the compartments were sorted by fluorescence-activated cell sorting; GFP+ (trophoblast), GFP- (epithelium) and non-co-cultured control populations were analysed (in triplicate) by RNA-seq and gene set enrichment analysis (GSEA). RESULTS Trophoblast challenge induced a wave of transcriptional changes in the epithelium that resulted in 295 differentially regulated genes involving epithelial to mesenchymal transition (EMT), cell movement, apoptosis, hypoxia, inflammation, allograft rejection, myogenesis and cell signalling at 8 h. Interestingly, many of the enriched pathways were subsequently de-enriched by 24 h (i.e. EMT, cell movement, allograft rejection, myogenesis and cell signalling). In the trophoblast, the co-culture induced more transcriptional changes and regulation of a variety of pathways. A total of 1247 and 481 genes were differentially expressed after 8 h and from 8 to 24 h, respectively. Angiogenesis and hypoxia were over-represented at both stages, while EMT and cell signalling only were at 8 h; from 8 to 24 h, inflammation and oestrogen response were enriched, while proliferation was under-represented. CONCLUSIONS Successful attachment produced a series of dynamic changes in gene expression, characterized by an overall early and transient transcriptional up-regulation in the receptive epithelium, in contrast to a more dynamic transcriptional response in the trophoblast.
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Affiliation(s)
- Paula Vergaro
- Clínica EUGIN Barcelona, Spain; Facultat de Biociències, Unitat de Biologia Cel•lular, Universitat Autònoma de Barcelona, Spain
| | - Gustavo Tiscornia
- Clínica EUGIN Barcelona, Spain; Centro de Investigação em Biomedicina (CBMR), Universidade do Algarve, Portugal
| | | | | | - Josep Santaló
- Facultat de Biociències, Unitat de Biologia Cel•lular, Universitat Autònoma de Barcelona, Spain
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VanderMolen KM, Naciff JM, Kennedy K, Otto-Bruc A, Shan Y, Wang X, Daston GP, Mahony C. Incorporation of in vitro techniques for botanicals dietary supplement safety assessment - Towards evaluation of developmental and reproductive toxicity (DART). Food Chem Toxicol 2020; 144:111539. [PMID: 32645467 DOI: 10.1016/j.fct.2020.111539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022]
Abstract
As complex mixtures, botanicals present unique challenges when assessing safe use, particularly when endpoint gaps exist that cannot be fully resolved by existing toxicological literature. Here we explore in vitro gene expression as well receptor binding and enzyme activity as alternative assays to inform on developmental and reproductive toxicity (DART) relevant modes of action, since DART data gaps are common for botanicals. Specifically, botanicals suspected to have DART effects, in addition to those with a significant history of use, were tested in these assays. Gene expression changes in a number of different cell types were analysed using the connectivity mapping approach (CMap) to identify modes of action through a functional read across approach. Taken together with ligand affinity data obtained using a set of molecular targets customised towards known DART relevant modes of action, it was possible to inform DART risk using functional analogues, potency comparisons and a margin of internal exposure approach.
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Affiliation(s)
- Karen M VanderMolen
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Jorge M Naciff
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Kevin Kennedy
- Eurofins Discovery, Bioanalytical, St Charles, MO, USA
| | | | - Yuqing Shan
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Xiaohong Wang
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - George P Daston
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Catherine Mahony
- Procter & Gamble Technical Centre, Whitehall Lane, Egham, Surrey, TW20 9AW, UK.
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Zhang Y, Zhou LP, Li XL, Zhao YJ, Ho MX, Qiu ZC, Zhao DF, Mok DKW, Shi Q, Wang YJ, Wong MS. 8-Prenylgenistein, a prenylated genistein derivative, exerted tissue selective osteoprotective effects in ovariectomized mice. Oncotarget 2018; 9:24221-24236. [PMID: 29849935 PMCID: PMC5966244 DOI: 10.18632/oncotarget.24823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/23/2017] [Indexed: 02/07/2023] Open
Abstract
Our previous study reported that the in vitro osteogenic effects of 8-prenylgenistein (8PG) were more potent than its parent compound genistein. This study aimed to evaluate the osteoprotective effects of 8PG in ovariectomized (OVX) mice as well as to characterize its estrogenic effects in uterus. Mature OVX mice were treated with phytoestrogen-free diet containing 8PG or genistein. Trabecular bone mass and most of the micro-structural parameters were ameliorated at the distal femoral metaphysis in OVX mice upon treatment with genistein and both doses of 8PG. The beneficial effects of 8PG on trabecular bone were confirmed by safranin O and ABHO staining. 8PG markedly inhibited the ovariectomy-induced mRNA expressions of RANKL/OPG, ALP, COL, OCN, cathepsin K and ER-α in bone. In contrast, genistein further increased the ovariectomy-induced ER-α expression in bone. The uterus index was increased in genistein-treated group. Genistein up-regulated the expression of ER-α and PR, while 8PG significantly down-regulated the ER-α and C3 expression in uterus of OVX mice. Moreover, genistein, but not 8PG, increased expressions of ER-α, PCNA and C3 in Ishikawa cell. This study suggested that 8PG improved trabecular bone properties in OVX mice without exerting uterotrophic effects and its estrogenic actions were distinct from those of genistein.
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Affiliation(s)
- Yan Zhang
- Spine Research Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PRC
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PRC
- Key Laboratory of Theory and Therapy of Muscles and Bones of Ministry of Education, Shanghai, PRC
| | - Li-Ping Zhou
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, PRC
| | - Xiao-Li Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PRC
| | - Yong-Jian Zhao
- Spine Research Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PRC
- Key Laboratory of Theory and Therapy of Muscles and Bones of Ministry of Education, Shanghai, PRC
| | - Ming-Xian Ho
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, PRC
| | - Zuo-Cheng Qiu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, PRC
| | - Dong-Feng Zhao
- Spine Research Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PRC
- Key Laboratory of Theory and Therapy of Muscles and Bones of Ministry of Education, Shanghai, PRC
| | - Daniel Kam-Wah Mok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, PRC
| | - Qi Shi
- Spine Research Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PRC
- Key Laboratory of Theory and Therapy of Muscles and Bones of Ministry of Education, Shanghai, PRC
| | - Yong-Jun Wang
- Spine Research Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PRC
- Key Laboratory of Theory and Therapy of Muscles and Bones of Ministry of Education, Shanghai, PRC
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, PRC
| | - Man-Sau Wong
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PRC
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, PRC
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Yang S, Rui KH, Tang XY, Xu Q, Shi M. Rhodium/Silver Synergistic Catalysis in Highly Enantioselective Cycloisomerization/Cross Coupling of Keto-Vinylidenecyclopropanes with Terminal Alkynes. J Am Chem Soc 2017; 139:5957-5964. [PMID: 28387514 DOI: 10.1021/jacs.7b02027] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A rhodium/silver synergistic catalysis has been established, enabling cycloisomerization/cross coupling of keto-vinylidenecyclopropanes (VDCPs) with terminal alkynes toward the regio- and enantioselective formation of diversified tetrahydropyridin-3-ol tethered 1,4-enynes in good yields and high ee values. In this synergistic catalysis, Rh(I) and Ag(I) catalysts selectively activate keto-VDCP substrates and terminal alkynes to generate the π-allyl Rh(III) complex of oxa-rhodacyclic intermediate and Ag alkynyl intermediate, respectively. The rapid transmetalation of alkynyl groups from Ag to Rh is proposed to play a key role in realizing the regioselective cleavage of the distal bond of the three-membered ring in this transformation.
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Affiliation(s)
- Song Yang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology , 130 Mei-Long Road, Shanghai 200237, China
| | - Kang-Hua Rui
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology , 130 Mei-Long Road, Shanghai 200237, China
| | - Xiang-Ying Tang
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Science, Chinese Academy of Sciences , 354 Fenglin Road, Shanghai 200032, China
| | - Qin Xu
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology , 130 Mei-Long Road, Shanghai 200237, China
| | - Min Shi
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology , 130 Mei-Long Road, Shanghai 200237, China.,State Key Laboratory and Institute of Element-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China.,State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Science, Chinese Academy of Sciences , 354 Fenglin Road, Shanghai 200032, China
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