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Sialana F, Roumeliotis TI, Bouguenina H, Chan Wah Hak L, Wang H, Caldwell J, Collins I, Chopra R, Choudhary JS. SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics. J Proteome Res 2022; 21:1842-1856. [PMID: 35848491 PMCID: PMC9361352 DOI: 10.1021/acs.jproteome.2c00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation of pharmacological mechanisms of action. Although isobaric labeling has increased the throughput of proteomic analysis, the commonly used sample preparation workflows often require time-consuming steps and costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost-effective one-pot reaction workflow in a 96-well plate format (SimPLIT) that minimizes processing steps and demonstrates improved reproducibility compared to alternative approaches. The workflow is based on a sodium deoxycholate lysis buffer and a single detergent cleanup step after peptide labeling, followed by quick off-line fractionation and MS2 analysis. We showcase the applicability of the workflow in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we report frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of seven cereblon E3 ligase modulators (CRL4CRBN). Overall, SimPLIT is a robust method that can be easily implemented in any proteomics laboratory for medium-to-large scale TMT-based studies for deep profiling of cell lines.
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Affiliation(s)
- Fernando
J. Sialana
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Theodoros I. Roumeliotis
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
| | - Habib Bouguenina
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Laura Chan Wah Hak
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hannah Wang
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - John Caldwell
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Ian Collins
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rajesh Chopra
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
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Wohak LE, Monien B, Phillips DH, Arlt VM. Impact of p53 function on the sulfotransferase-mediated bioactivation of the alkylated polycyclic aromatic hydrocarbon 1-hydroxymethylpyrene in vitro. Environ Mol Mutagen 2019; 60:752-758. [PMID: 31102418 DOI: 10.1002/em.22299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/24/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
The tumor suppressor p53, encoded by TP53, is known as the "guardian of the genome." Sulfotransferases (SULTs) are involved in the metabolism of alkylated polycyclic aromatic hydrocarbons such as 1-hydroxymethylpyrene (1-HMP), which is a known substrate for SULT1A1. To investigate the impact of TP53 on the metabolic activation of 1-HMP, a panel of isogenic human colorectal HCT116 cells having TP53(+/+), TP53(+/-), or TP53(-/-) were treated with 10 μM 1-HMP for 24 hr. 1-HMP-DNA adduct formation was determined by ultraperformance liquid chromatography-tandem mass spectrometry analysis, which quantified two nucleoside adducts N2 -(1-methylpyrenyl)-2'-deoxyguanosine and N6 -(1-methylpyrenyl)-2'-deoxyadenosine. 1-HMP treatment resulted in significantly (~40-fold) higher DNA adduct levels in TP53(+/+) cells than in the other cell lines. Higher levels of 1-HMP-induced DNA adducts in TP53(+/+) cells correlated with higher basal expression of SULT1A1/3 in this cell line, but 1-HMP treatment showed no effect on the expression of this protein. These results indicate that the cellular TP53 status is linked to the SULT1A1/3-mediated bioactivation of 1-HMP, thereby broadening the spectrum of p53's targets. Environ. Mol. Mutagen., 60:752-758, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Laura E Wohak
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, United Kingdom
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Bernhard Monien
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, United Kingdom
- NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King's College London in partnership with Public Health England, London, United Kingdom
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, United Kingdom
- NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King's College London in partnership with Public Health England, London, United Kingdom
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Guan J, Tucker ER, Wan H, Chand D, Danielson LS, Ruuth K, El Wakil A, Witek B, Jamin Y, Umapathy G, Robinson SP, Johnson TW, Smeal T, Martinsson T, Chesler L, Palmer RH, Hallberg B. The ALK inhibitor PF-06463922 is effective as a single agent in neuroblastoma driven by expression of ALK and MYCN. Dis Model Mech 2016; 9:941-52. [PMID: 27483357 PMCID: PMC5047689 DOI: 10.1242/dmm.024448] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/04/2016] [Indexed: 12/24/2022] Open
Abstract
The first-in-class inhibitor of ALK, c-MET and ROS1, crizotinib (Xalkori), has shown remarkable clinical efficacy in treatment of ALK-positive non-small cell lung cancer. However, in neuroblastoma, activating mutations in the ALK kinase domain are typically refractory to crizotinib treatment, highlighting the need for more potent inhibitors. The next-generation ALK inhibitor PF-06463922 is predicted to exhibit increased affinity for ALK mutants prevalent in neuroblastoma. We examined PF-06463922 activity in ALK-driven neuroblastoma models in vitro and in vivo In vitro kinase assays and cell-based experiments examining ALK mutations of increasing potency show that PF-06463922 is an effective inhibitor of ALK with greater activity towards ALK neuroblastoma mutants. In contrast to crizotinib, single agent administration of PF-06463922 caused dramatic tumor inhibition in both subcutaneous and orthotopic xenografts as well as a mouse model of high-risk neuroblastoma driven by Th-ALK(F1174L)/MYCN Taken together, our results suggest PF-06463922 is a potent inhibitor of crizotinib-resistant ALK mutations, and highlights an important new treatment option for neuroblastoma patients.
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Affiliation(s)
- J Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - E R Tucker
- Division of Clinical Studies Cancer Therapeutics, The Institute of Cancer Research, London and Royal Marsden NHS Foundation Trust, Sutton SM2 5NG, UK
| | - H Wan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - D Chand
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - L S Danielson
- Division of Clinical Studies Cancer Therapeutics, The Institute of Cancer Research, London and Royal Marsden NHS Foundation Trust, Sutton SM2 5NG, UK
| | - K Ruuth
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden Department of Molecular Biology, Building 6L, Umeå University, Umeå 901 87, Sweden
| | - A El Wakil
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden Department of Molecular Biology, Building 6L, Umeå University, Umeå 901 87, Sweden
| | - B Witek
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden Department of Molecular Biology, Building 6L, Umeå University, Umeå 901 87, Sweden
| | - Y Jamin
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London and Royal Marsden NHS Foundation Trust, Sutton SM2 5NG, UK
| | - G Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - S P Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London and Royal Marsden NHS Foundation Trust, Sutton SM2 5NG, UK
| | - T W Johnson
- La Jolla Laboratories, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - T Smeal
- La Jolla Laboratories, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - T Martinsson
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - L Chesler
- Division of Clinical Studies Cancer Therapeutics, The Institute of Cancer Research, London and Royal Marsden NHS Foundation Trust, Sutton SM2 5NG, UK
| | - R H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - B Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-405 30, Sweden
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