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Kim SY, Sim CK, Zhang Q, Tang H, Brunmeir R, Pan H, Karnani N, Han W, Zhang K, Xu F. An Alternative Strategy for Pan-acetyl-lysine Antibody Generation. PLoS One 2016; 11:e0162528. [PMID: 27606599 PMCID: PMC5015836 DOI: 10.1371/journal.pone.0162528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/24/2016] [Indexed: 01/01/2023] Open
Abstract
Lysine acetylation is an important post-translational modification in cell signaling. In acetylome studies, a high-quality pan-acetyl-lysine antibody is key to successful enrichment of acetylated peptides for subsequent mass spectrometry analysis. Here we show an alternative method to generate polyclonal pan-acetyl-lysine antibodies using a synthesized random library of acetylated peptides as the antigen. Our antibodies are tested to be specific for acetyl-lysine peptides/proteins via ELISA and dot blot. When pooled, five of our antibodies show broad reactivity to acetyl-lysine peptides, complementing a commercial antibody in terms of peptide coverage. The consensus sequence of peptides bound by our antibody cocktail differs slightly from that of the commercial antibody. Lastly, our antibodies are tested in a proof-of-concept to analyze the acetylome of HEK293 cells. In total we identified 1557 acetylated peptides from 416 proteins. We thus demonstrated that our antibodies are well-qualified for acetylome studies and can complement existing commercial antibodies.
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Affiliation(s)
- Sun-Yee Kim
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Choon Kiat Sim
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Qiongyi Zhang
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Hui Tang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Reinhard Brunmeir
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Hong Pan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Weiping Han
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail: (KZ); (FX)
| | - Feng Xu
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
- * E-mail: (KZ); (FX)
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Sandomenico A, Focà A, Sanguigno L, Caporale A, Focà G, Pignalosa A, Corvino G, Caragnano A, Beltrami AP, Antoniali G, Tell G, Leonardi A, Ruvo M. Monoclonal antibodies against pools of mono- and polyacetylated peptides selectively recognize acetylated lysines within the context of the original antigen. MAbs 2016; 8:1575-1589. [PMID: 27560983 DOI: 10.1080/19420862.2016.1225643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Post-translational modifications (PTMs) strongly influence the structure and function of proteins. Lysine side chain acetylation is one of the most widespread PTMs, and it plays a major role in several physiological and pathological mechanisms. Protein acetylation may be detected by mass spectrometry (MS), but the use of monoclonal antibodies (mAbs) is a useful and cheaper option. Here, we explored the feasibility of generating mAbs against single or multiple acetylations within the context of a specific sequence. As a model, we used the unstructured N-terminal domain of APE1, which is acetylated on Lys27, Lys31, Lys32 and Lys35. As immunogen, we used a peptide mixture containing all combinations of single or multi-acetylated variants encompassing the 24-39 protein region. Targeted screening of the resulting clones yielded mAbs that bind with high affinity to only the acetylated APE1 peptides and the acetylated protein. No binding was seen with the non-acetylated variant or unrelated acetylated peptides and proteins, suggesting a high specificity for the APE1 acetylated molecules. MAbs could not finely discriminate between the differently acetylated variants; however, they specifically bound the acetylated protein in mammalian cell extracts and in intact cells and tissue slices from both breast cancers and from a patient affected by idiopathic dilated cardiomyopathy. The data suggest that our approach is a rapid and cost-effective method to generate mAbs against specific proteins modified by multiple acetylations or other PTMs.
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Affiliation(s)
- Annamaria Sandomenico
- a Istituto di Biostrutture e Bioimmagini , Consiglio Nazionale delle Ricerche (IBB-CNR) , Napoli , Italy
| | - Annalia Focà
- a Istituto di Biostrutture e Bioimmagini , Consiglio Nazionale delle Ricerche (IBB-CNR) , Napoli , Italy
| | | | - Andrea Caporale
- c Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPeB) , Napoli , Italy
| | - Giuseppina Focà
- a Istituto di Biostrutture e Bioimmagini , Consiglio Nazionale delle Ricerche (IBB-CNR) , Napoli , Italy
| | - Angelica Pignalosa
- a Istituto di Biostrutture e Bioimmagini , Consiglio Nazionale delle Ricerche (IBB-CNR) , Napoli , Italy
| | | | - Angela Caragnano
- d University of Udine , Department of Medical and Biological Sciences , Udine , Italy
| | | | - Giulia Antoniali
- d University of Udine , Department of Medical and Biological Sciences , Udine , Italy
| | - Gianluca Tell
- d University of Udine , Department of Medical and Biological Sciences , Udine , Italy
| | - Antonio Leonardi
- e University of Napoli "Federico II," Department of Molecular Medicine and Medical Biotechnology , Napoli , Italy
| | - Menotti Ruvo
- a Istituto di Biostrutture e Bioimmagini , Consiglio Nazionale delle Ricerche (IBB-CNR) , Napoli , Italy
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Ouidir T, Kentache T, Hardouin J. Protein lysine acetylation in bacteria: Current state of the art. Proteomics 2015; 16:301-9. [DOI: 10.1002/pmic.201500258] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/11/2015] [Accepted: 09/15/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
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Abstract
The posttranslational modification of proteins and their regulation by metabolites represent conserved mechanisms in biology. At the confluence of these two processes, we report that the primary glycolytic intermediate 1,3-bisphosphoglycerate (1,3-BPG) reacts with select lysine residues in proteins to form 3-phosphoglyceryl-lysine (pgK). This reaction, which does not require enzyme catalysis, but rather exploits the electrophilicity of 1,3-BPG, was found by proteomic profiling to be enriched on diverse classes of proteins and prominently in or around the active sites of glycolytic enzymes. pgK modifications inhibit glycolytic enzymes and, in cells exposed to high glucose, accumulate on these enzymes to create a potential feedback mechanism that contributes to the buildup and redirection of glycolytic intermediates to alternate biosynthetic pathways.
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Affiliation(s)
- Raymond E Moellering
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Abstract
Pan-specific anti-acetylated lysine antibody is a valuable tool to detect, validate, and quantify protein lysine acetylation. Compared to site-specific acetyllysine antibodies that are not readily available in most cases, polyclonal pan-specific acetyllysine antibodies can be generated with synthetic antigen of a carrier protein that has its lysine residues chemically acetylated. Here, we describe protocols of synthesizing acetylated ovalbumin (OVA), immunizing rabbits, and characterizing pan-specific polyclonal anti-acetylated lysine antibodies.
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Affiliation(s)
- Wei Xu
- State Key Lab of Genetic Engineering, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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Wang Y, Yao J, Yang P, Deng C, Fan H. Immobilization of Antibodies on Magnetic Carbonaceous Microspheres for Selective Enrichment of Lysine-acetylated Proteins and Peptides. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ning ZQ, Li ZB, Newman MJ, Shan S, Wang XH, Pan DS, Zhang J, Dong M, Du X, Lu XP. Chidamide (CS055/HBI-8000): a new histone deacetylase inhibitor of the benzamide class with antitumor activity and the ability to enhance immune cell-mediated tumor cell cytotoxicity. Cancer Chemother Pharmacol. 2012;69:901-909. [PMID: 22080169 DOI: 10.1007/s00280-011-1766-x] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 10/12/2011] [Indexed: 12/18/2022]
Abstract
PURPOSE Chidamide (CS055/HBI-8000) is a new histone deacetylase (HDAC) inhibitor of the benzamide class currently under clinical development in cancer indications. This study reports the in vitro and in vivo antitumor characteristics of the compound. METHODS Selectivity and potency of chidamide in inhibition of HDAC isotypes were analyzed by using a panel of human recombinant HDAC proteins. Tumor cell lines either in culture or inoculated in nude mice were used for the evaluation of the compound's antitumor activity. To investigate the immune cell-mediated antitumor effect, isolated peripheral blood mononuclear cells from healthy donors were treated with chidamide, and cytotoxicity and expression of relevant surface proteins were analyzed. Microarray gene expression studies were performed on peripheral white blood cells from two T-cell lymphoma patients treated with chidamide. RESULTS Chidamide was found to be a low nanomolar inhibitor of HDAC1, 2, 3, and 10, the HDAC isotypes well documented to be associated with the malignant phenotype. Significant and broad spectrum in vitro and in vivo antitumor activity, including a wide therapeutic index, was observed. Chidamide was also shown to enhance the cytotoxic effect of human peripheral mononuclear cells ex vivo on K562 target cells, accompanied by the upregulation of proteins involved in NK cell functions. Furthermore, the expression of a number of genes involved in immune cell-mediated antitumor activity was observed to be upregulated in peripheral white blood cells from two T-cell lymphoma patients who responded to chidamide administration. CONCLUSIONS The results presented in this study provide evidence that chidamide has potential applicability for the treatment of a variety of tumor types, either as a single agent or in combination therapies.
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Cong X, Held JM, DeGiacomo F, Bonner A, Chen JM, Schilling B, Czerwieniec GA, Gibson BW, Ellerby LM. Mass spectrometric identification of novel lysine acetylation sites in huntingtin. Mol Cell Proteomics 2011; 10:M111.009829. [PMID: 21685499 PMCID: PMC3205870 DOI: 10.1074/mcp.m111.009829] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/02/2011] [Indexed: 12/26/2022] Open
Abstract
Huntingtin (Htt) is a protein with a polyglutamine stretch in the N-terminus and expansion of the polyglutamine stretch causes Huntington's disease (HD). Htt is a multiple domain protein whose function has not been well characterized. Previous reports have shown, however, that post-translational modifications of Htt such as phosphorylation and acetylation modulate mutant Htt toxicity, localization, and vesicular trafficking. Lysine acetylation of Htt is of particular importance in HD as this modification regulates disease progression and toxicity. Treatment of mouse models with histone deacetylase inhibitors ameliorates HD-like symptoms and alterations in acetylation of Htt promotes clearance of the protein. Given the importance of acetylation in HD and other diseases, we focused on the systematic identification of lysine acetylation sites in Htt23Q (1-612) in a cell culture model using mass spectrometry. Myc-tagged Htt23Q (1-612) overexpressed in the HEK 293T cell line was immunoprecipitated, separated by SDS-PAGE, digested and subjected to high performance liquid chromatography tandem MS analysis. Five lysine acetylation sites were identified, including three novel sites Lys-178, Lys-236, Lys-345 and two previously described sites Lys-9 and Lys-444. Antibodies specific to three of the Htt acetylation sites were produced and confirmed the acetylation sites in Htt. A multiple reaction monitoring MS assay was developed to compare quantitatively the Lys-178 acetylation level between wild-type Htt23Q and mutant Htt148Q (1-612). This report represents the first comprehensive mapping of lysine acetylation sites in N-terminal region of Htt.
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Affiliation(s)
- Xin Cong
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | - Jason M. Held
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | | | - Akilah Bonner
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | - Jan Marie Chen
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | - Birgit Schilling
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | | | | | - Lisa M. Ellerby
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
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Mischerikow N, Heck AJR. Targeted large-scale analysis of protein acetylation. Proteomics 2011; 11:571-89. [DOI: 10.1002/pmic.201000397] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/10/2010] [Accepted: 09/27/2010] [Indexed: 11/06/2022]
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Guan KL, Yu W, Lin Y, Xiong Y, Zhao S. Generation of acetyllysine antibodies and affinity enrichment of acetylated peptides. Nat Protoc. 2010;5:1583-1595. [PMID: 21085124 DOI: 10.1038/nprot.2010.117] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Lysine acetylation has emerged as one of the major post-translational modifications, as indicated by its roles in chromatin remodeling, activation of transcription factors and, most recently, regulation of metabolic enzymes. Identification of acetylation sites in a protein is the first essential step for functional characterization of acetylation in physiological regulation. However, the study of the acetylome is hindered by the lack of suitable physical and biochemical properties of the acetyl group and existence of high-abundance acetylated histones in the cell, and needs a robust method to overcome these problems. Here we present protocols for (i) using chemically acetylated ovalbumin and synthetic acetylated peptide to generate a pan-acetyllysine antibody and a site-specific antibody to Lys288-acetylated argininosuccinate lyase, respectively; (ii) using subcellular fractionation to reduce highly abundant acetylated histones; and (iii) using acetyllysine antibody affinity purification and mass spectrometry to characterize acetylome of human liver tissue. The entire characterization procedure takes ∼2-3 d to complete.
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Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y. Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics 2008; 8:215-25. [PMID: 18723842 DOI: 10.1074/mcp.m800187-mcp200] [Citation(s) in RCA: 378] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine acetylation and its regulatory enzymes are known to have pivotal roles in mammalian cellular physiology. However, the extent and function of this modification in prokaryotic cells remain largely unexplored, thereby presenting a hurdle to further functional study of this modification in prokaryotic systems. Here we report the first global screening of lysine acetylation, identifying 138 modification sites in 91 proteins from Escherichia coli. None of the proteins has been previously associated with this modification. Among the identified proteins are transcriptional regulators, as well as others with diverse functions. Interestingly, more than 70% of the acetylated proteins are metabolic enzymes and translation regulators, suggesting an intimate link of this modification to energy metabolism. The new dataset suggests that lysine acetylation could be abundant in prokaryotic cells. In addition, these results also imply that functions of lysine acetylation beyond regulation of gene expression are evolutionarily conserved from bacteria to mammals. Furthermore, we demonstrate that bacterial lysine acetylation is regulated in response to stress stimuli.
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Affiliation(s)
- Junmei Zhang
- Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Liang Z, Wong RP, Li LH, Jiang H, Xiao H, Li G. Development of pan-specific antibody against trimethyllysine for protein research. Proteome Sci 2008; 6:2. [PMID: 18208619 PMCID: PMC2267453 DOI: 10.1186/1477-5956-6-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 01/22/2008] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Trimethylation of the Nepsilon-lysine residues in a protein is one of the most important events of posttranslational modifications. Simple methods for rapid detection and isolation of the Nepsilon-trimethylated protein species are needed. This report introduces a novel method to prepare the affinity purified antibody specific for the Nepsilon-trimethylated lysine (tMeK). The applications of the purified antibody are also reported in this paper. METHODS We generated the methylated keyhole limpet heomocyanin (KLH) under controlled chemical methylation reaction using CH3I and used it as an immunogen to raise anti-methylated lysine antibodies. The tMeK specific antibody was selectively isolated using a two-step affinity chromatography in which the mMeK/dMeK specific antibodies were removed and the tMeK specific antibody was captured. Finally, the eluted anti-tMeK antibody was characterized. RESULTS The ELISA results indicated that the antibody reacted only to tMeK but not to mono- and dimethyllysine. Western-blot results showed that the Nepsilon-trimethylated proteins were detected in both animal tissue and cultured cells and that the antibody signal could be competitively inhibited with free tMeK. CONCLUSION The specific tMeK antibody we developed is useful for one-step isolation of proteins with Nepsilon-trimethyllysine residues and also for the detection, identification and localization of proteins with trimethyllysine residues in the cells.
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Affiliation(s)
- Ziqian Liang
- Rehabilitation Center of Burns and Plastic Surgery and Medical Research Center, Guangxi Medical University, Nanning, China
| | - Ronald Pc Wong
- Department of Dermatology and Skin Science, Jack Bell Research Centre, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lin Hong Li
- Rehabilitation Center of Burns and Plastic Surgery and Medical Research Center, Guangxi Medical University, Nanning, China
| | - Hesheng Jiang
- Rehabilitation Center of Burns and Plastic Surgery and Medical Research Center, Guangxi Medical University, Nanning, China
| | - Hao Xiao
- Rehabilitation Center of Burns and Plastic Surgery and Medical Research Center, Guangxi Medical University, Nanning, China
| | - Gang Li
- Department of Dermatology and Skin Science, Jack Bell Research Centre, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Abstract
Histone deacetylases (HDACs) are considered to be among the most promising targets in drug development for cancer therapy, and first-generation histone deacetylase inhibitors (HDACi) are currently being tested in phase I/II clinical trials. A wide-ranging knowledge of the role of HDACs in tumorigenesis, and of the action of HDACi, has been achieved. However, several basic aspects are not yet fully understood. Investigating these aspects in the context of what we now understand about HDACi action both in vitro and in vivo will further improve the design of optimized clinical protocols.
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Affiliation(s)
- Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Via Ripamanti 435, 20141, Milan, Italy.
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