1
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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. Mol Syst Biol 2025:10.1038/s44320-025-00107-3. [PMID: 40329044 DOI: 10.1038/s44320-025-00107-3] [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: 05/05/2024] [Revised: 03/31/2025] [Accepted: 04/10/2025] [Indexed: 05/08/2025] Open
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single-nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, and with Polycomb occupancy. We show that histone genes are expressed with allelic imbalance in mESCs, and are involved in haplotype-specific chromatin contacts marked by H3K27me3. Conditional knockouts of Polycomb enzymatic subunits, Ezh2 or Ring1, show that one-third of ASE genes, including histone genes, is regulated through Polycomb repression. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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Affiliation(s)
- Ibai Irastorza-Azcarate
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany.
| | - Alexander Kukalev
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
| | - Rieke Kempfer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
- Humboldt-Universität zu Berlin, Berlin, Germany
- Sophia Genetics SA, A-One Park, Rolle, 1180, Switzerland
| | - Christoph J Thieme
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
| | - Guido Mastrobuoni
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Proteomics and Metabolomic Platform, 10115, Berlin, Germany
| | - Julia Markowski
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
- Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Evolutionary and Cancer Genomics Group, 10115, Berlin, Germany
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gesa Loof
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
- Humboldt-Universität zu Berlin, Berlin, Germany
- Aix Marseille Univ, CNRS, IBDM (UMR 7288), Turing Centre for Living Systems, Marseille, France
| | - Thomas M Sparks
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
| | - Emily Brookes
- MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Kedar Nath Natarajan
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany
- MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stephan Sauer
- MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK
- Regeneron Ireland DAC, Dublin 2, D02 HH27, Ireland
| | - Amanda G Fisher
- MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli "Federico II", and INFN, Napoli, Italy
| | - Bing Ren
- Center for Epigenomics and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Roland F Schwarz
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Evolutionary and Cancer Genomics Group, 10115, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Cologne, Germany
- BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Stefan Kempa
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Proteomics and Metabolomic Platform, 10115, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany.
- Humboldt-Universität zu Berlin, Berlin, Germany.
- MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK.
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Offenhäuser C, Dave KA, Beckett KJ, Smith FM, Jayakody BA, Cooper LT, Agyei-Yeboah H, McCarron JK, Li Y, Bastick K, Al-Ejeh F, Cullen JK, Coulthard MG, Gorman JJ, Boyd AW, Day BW. EphA2 regulates vascular permeability and prostate cancer metastasis via modulation of cell junction protein phosphorylation. Oncogene 2025; 44:208-227. [PMID: 39511410 PMCID: PMC11753358 DOI: 10.1038/s41388-024-03206-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/09/2024] [Accepted: 10/22/2024] [Indexed: 11/15/2024]
Abstract
Prostate cancer morbidity and mortality demonstrate a need for more effective targeted therapies. One potential target is EphA2, although paradoxically, pro- and anti-oncogenic effects have been shown to be mediated by EphA2. We demonstrate that unique activating and blocking EphA2-targeting monoclonal antibodies display opposing tumor-suppressive and oncogenic properties in vivo. To further explore this complexity, we performed detailed phosphoproteomic analysis following ligand-induced EphA2 activation. Our analysis identified altered phosphorylation of 73 downstream proteins related to the PI3K/AKT/mTOR and ERK/MAPK pathways, with the majority implicated in cell junction and cytoskeletal organization, cell motility, and tumor metastasis. We demonstrate that the adapter protein SHB is an essential component in mediating the inhibition of the ERK/MAPK pathway in response to EphA2 receptor activation. Furthermore, we identify the adherence junction protein afadin as an EphA2-regulated phosphoprotein which is involved in prostate cancer migration and invasion.
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Affiliation(s)
- Carolin Offenhäuser
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
| | - Keyur A Dave
- Protein Discovery Center, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Kirrilee J Beckett
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Fiona M Smith
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Buddhika A Jayakody
- Protein Discovery Center, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Leanne T Cooper
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Helen Agyei-Yeboah
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Jennifer K McCarron
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Yuchen Li
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kate Bastick
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fares Al-Ejeh
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Jason K Cullen
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mark G Coulthard
- Mayne Academy of Paediatrics, Faculty of Medicine, The University of Queensland, Queensland Children's Hospital, Brisbane, QLD, 4101, Australia
- Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, QLD, 4101, Australia
| | - Jeffrey J Gorman
- Protein Discovery Center, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Andrew W Boyd
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Bryan W Day
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
- School of Medicine, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4059, Australia.
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3
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Jiang P, Hakim MA, Saffarian Delkhosh A, Ahmadi P, Li Y, Mechref Y. 4-plex quantitative glycoproteomics using glycan/protein-stable isotope labeling in cell culture. J Proteomics 2025; 310:105333. [PMID: 39426592 PMCID: PMC11834166 DOI: 10.1016/j.jprot.2024.105333] [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: 07/31/2024] [Revised: 09/20/2024] [Accepted: 10/13/2024] [Indexed: 10/21/2024]
Abstract
Alterations in glycoprotein abundance and glycan structures are closely linked to numerous diseases. The quantitative exploration of glycoproteomics is pivotal for biomarker discovery, but comprehensive analysis within biological samples remains challenging due to low abundance, complexity, and lack of universal technology. We developed a multiplex glycoproteomic approach using an LC-ESI-MS platform for direct comparison of glycoproteomic quantitation. Glycopeptides were isotopically labeled during cell culture, achieving high labeling efficiency (≥ 95 %) for both glycans and peptides. Quantitation was validated by mixing the same cell line in a 1:1:1:1 ratio, with mathematical correction applied to deconvolute the ratios. This method proved reliable and was applied to a comparative glycoproteomic study of three breast cancer cell lines (HTB22, MDA-MB-231, MDA-MB-231BR) and one brain cancer cell line (CRL-1620), quantifying glycopeptides from three replicates. The expression of glycopeptides was relatively quantified, and up/down-regulation between cell lines was investigated. This approach provided insights into glycosylation microheterogeneity, crucial for breast cancer brain metastasis research. Benefits include eliminating fluctuations from nano electrospray ionization and reducing analysis time, enabling up to 4-plex profiling in a single injection. Metabolic labeling introduced mass differences at the MS1 level, ensuring increased sensitivity and higher resolution for accurate quantitation. SIGNIFICANCE: Alternations in glycoprotein abundance, changes in glycosylation levels, and variations in glycan structures are closely linked to numerous diseases. The quantitative exploration of glycoproteomics has emerged as a popular area of research for biomarker discovery. However, conducting a comprehensive quantitative analysis of the glycoproteome within biological samples remains challenging due to low abundance, inherent complexities, and the absence of universal quantitative technology. Here, we developed a multiplex glycoproteomic approach using an LC-ESI-MS platform to facilitate direct comparison of glycoproteomic quantitation and enhance throughput. This approach offers benefits such as eliminating quantitative fluctuations arising from nano electrospray ionization (ESI) and reducing analysis time, enabling up to 4-plex glycoproteomic profiling in a single injection. Glycopeptides were stable isotopic labeled during cell culture procedure, attaching to monosaccharides, amino acids, or both. We achieved a high labeling efficiency (≥ 95 %) for both glycans and peptides. Quantitation validation was tested on glycopeptides by mixing the same cell line with 1:1:1:1 ratio. Due to the overlapped isotopes, a mathematical correction was applied to deconvolute the ratio of 4-plex glycopeptides. This method demonstrated quantitative reliability and was successfully applied to a comparative glycoproteomic study of three breast cancer cells (HTB22, MDA-MB-231, and MDA-MB-231BR) and one brain cancer cell (CRL-1620), identifying a total of 264 glycopeptides from three replicates. The expression of glycopeptides among these four cells was relatively quantified and up/down-regulation between two cell lines was investigated. The exploration of glycosylation microheterogeneity through glycopeptide quantification may offer valuable insights for further investigation into breast cancer brain metastasis. Conclusion: The primary advantage of our presented work lies in the multiplexing offered by combining two established labeling techniques, SILAC and IDAWG, both of which have been effectively used and widely cited in the scientific community. This combination enhances the applicability and accuracy of our method, as demonstrated by the extensive citations and successful use of these techniques independently. We believe that this multiplexing approach significantly advances the field, despite the method's current limitation to cell systems.
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Affiliation(s)
- Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Arvin Saffarian Delkhosh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, TX 76204, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States.
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Sun Y, Li C, Deng X, Li W, Deng X, Ge W, Shi M, Guo Y, Yu YV, Zhou HB, Jin YN. Target protein identification in live cells and organisms with a non-diffusive proximity tagging system. eLife 2024; 13:RP102667. [PMID: 39728918 DOI: 10.7554/elife.102667] [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] [Indexed: 12/28/2024] Open
Abstract
Identifying target proteins for bioactive molecules is essential for understanding their mechanisms, developing improved derivatives, and minimizing off-target effects. Despite advances in target identification (target-ID) technologies, significant challenges remain, impeding drug development. Most target-ID methods use cell lysates, but maintaining an intact cellular context is vital for capturing specific drug-protein interactions, such as those with transient protein complexes and membrane-associated proteins. To address these limitations, we developed POST-IT (Pup-On-target for Small molecule Target Identification Technology), a non-diffusive proximity tagging system for live cells, orthogonal to the eukaryotic system. POST-IT utilizes an engineered fusion of proteasomal accessory factor A and HaloTag to transfer Pup to proximal proteins upon directly binding to the small molecule. After significant optimization to eliminate self-pupylation and polypupylation, minimize depupylation, and optimize chemical linkers, POST-IT successfully identified known targets and discovered a new binder, SEPHS2, for dasatinib, and VPS37C as a new target for hydroxychloroquine, enhancing our understanding these drugs' mechanisms of action. Furthermore, we demonstrated the application of POST-IT in live zebrafish embryos, highlighting its potential for broad biological research and drug development.
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Affiliation(s)
- Yingjie Sun
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Changheng Li
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiaofei Deng
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wenjie Li
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiaoyi Deng
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Weiqi Ge
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Miaoyuan Shi
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ying Guo
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yanxun V Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Hai-Bing Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Youngnam N Jin
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
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5
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Yang YY, Cao Z, Wang Y. Mass Spectrometry-Based Proteomics for Assessing Epitranscriptomic Regulations. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39422510 DOI: 10.1002/mas.21911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/26/2024] [Accepted: 09/28/2024] [Indexed: 10/19/2024]
Abstract
Epitranscriptomics is a rapidly evolving field that explores chemical modifications in RNA and how they contribute to dynamic and reversible regulations of gene expression. These modifications, for example, N6-methyladenosine (m6A), are crucial in various RNA metabolic processes, including splicing, stability, subcellular localization, and translation efficiency of mRNAs. Mass spectrometry-based proteomics has become an indispensable tool in unraveling the complexities of epitranscriptomics, offering high-throughput, precise protein identification, and accurate quantification of differential protein expression. Over the past two decades, advances in mass spectrometry, including the improvement of high-resolution mass spectrometers and innovative sample preparation methods, have allowed researchers to perform in-depth analyses of epitranscriptomic regulations. This review focuses on the applications of bottom-up proteomics in the field of epitranscriptomics, particularly in identifying and quantifying epitranscriptomic reader, writer, and eraser (RWE) proteins and in characterizing their functions, posttranslational modifications, and interactions with other proteins. Together, by leveraging modern proteomics, researchers can gain deep insights into the intricate regulatory networks of RNA modifications, advancing fundamental biology, and fostering potential therapeutic applications.
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Affiliation(s)
- Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, California, USA
| | - Zhongwen Cao
- Environmental Toxicology Graduate Program, University of California, Riverside, California, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California, USA
- Environmental Toxicology Graduate Program, University of California, Riverside, California, USA
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Oeljeklaus S, Sharma L, Bender J, Warscheid B. Mass spectrometry-based proteomics to study mutants and interactomes of mitochondrial translocation proteins. Methods Enzymol 2024; 707:101-152. [PMID: 39488372 DOI: 10.1016/bs.mie.2024.07.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2024]
Abstract
The multiple functions of mitochondria are governed by their proteome comprising 1000-1500 proteins depending on the organism. However, only few proteins are synthesized inside mitochondria, whereas most are "born" outside mitochondria. To reach their destined location, these mitochondrial proteins follow specific import routes established by a mitochondrial translocase network. A detailed understanding of the role and interplay of the different translocases is imperative to understand mitochondrial biology and how mitochondria are integrated into the cellular network. Mass spectrometry (MS) proved to be effective to study the translocase network regarding composition, functions, interplay, and cellular responses evoked by dysfunction. In this chapter, we provide protocols tailored to MS-enabled functional analysis of mutants and interactomes of mitochondrial translocation proteins. In the first part, we exemplify the MS-based proteomics analysis of translocation mutants for delineating the human mitochondrial importome following depletion of the central translocation protein TOMM40. The protocol comprises metabolic stable isotope labeling, TOMM40 knockdown, preparation of mitochondrial fractions, and sample preparation for liquid chromatography (LC)-MS. For deep MS analysis, prefractionation of peptide mixtures by high pH reversed-phase LC is described. In the second part, we outline an affinity purification MS approach to reveal the association of an orphaned protein with the translocase TIM23. The protocol covers FLAG-tag affinity purification of protein complexes from mitochondrial fractions and downstream sample preparation for interactome analysis. In the last unifying part, we describe methods for LC-MS, data processing, statistical analysis and visualization of quantitative MS data, and provide a Python code for effective, customizable analysis.
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Affiliation(s)
- Silke Oeljeklaus
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Lakshita Sharma
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Julian Bender
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Bettina Warscheid
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany.
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7
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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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8
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Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA. In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. CELL REPORTS METHODS 2024; 4:100713. [PMID: 38412836 PMCID: PMC10921036 DOI: 10.1016/j.crmeth.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
Protein translational control is critical for ensuring that the fetus develops correctly and that necessary organs and tissues are formed and functional. We developed an in utero method to quantify tissue-specific protein dynamics by monitoring amino acid incorporation into the proteome after pulse injection. Fetuses of pregnant mice were injected with isotopically labeled lysine and arginine via the vitelline vein at various embyonic days, and organs and tissues were harvested. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates were calculated between 3.81E-5 and 0.424 h-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver vs. brain); however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates, which correlated with known physiological changes during mouse development.
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Affiliation(s)
- Josue Baeza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara E Coons
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - John Riley
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mariel Mendoza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William H Peranteau
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Benjamin A Garcia
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA.
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9
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Jiang P, Peng W, Zhao J, Goli M, Huang Y, Li Y, Mechref Y. Glycan/Protein-Stable Isotope Labeling in Cell Culture for Enabling Concurrent Quantitative Glycomics/Proteomics/Glycoproteomics. Anal Chem 2023; 95:16059-16069. [PMID: 37843510 DOI: 10.1021/acs.analchem.3c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The complexity and heterogeneity of protein glycosylation present an analytical challenge to the studies of characterization and quantitation. Various LC-MS-based quantitation strategies have emerged in recent decades. Metabolic stable isotope labeling has been developed to enhance the accurate LC/MS-based quantitation between different cell lines. Stable isotope labeling by amino acids in a cell culture (SILAC) is the most widely used metabolic labeling method in proteomic analysis. However, it can only label the peptide backbone and is thus limited in glycomic studies. Here, we present a metabolic isotope labeling strategy, named GlyProSILC (Glycan Protein Stable Isotope Labeling in Cell Culture), that can label both the glycan motif and peptide backbone from the same batch of cells. It was performed by feeding cells with a heavy medium containing amide-15N-glutamine, 13C6-arginine (Arg6), and 13C6-15N2-lysine (Lys8). No significant change of cell line metabolism after GlyProSILC labeling was observed based on transcriptomic, glycomic, and proteomic data. The labeling conditions, labeling efficiency, and quantitation accuracy were investigated. After quantitation correction, we simultaneously quantified 62 N-glycans, 574 proteins, and 344 glycopeptides using the same batch of mixed 231BR/231 cell lines. So far, GlyProSILC provides an accurate and effective quantitation approach for glycomics, proteomics, and glycoproteomics in a cell culture system.
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Affiliation(s)
- Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, Texas 76204, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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10
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Lefebvre C, Pellizzari S, Bhat V, Jurcic K, Litchfield DW, Allan AL. Involvement of the AKT Pathway in Resistance to Erlotinib and Cabozantinib in Triple-Negative Breast Cancer Cell Lines. Biomedicines 2023; 11:2406. [PMID: 37760847 PMCID: PMC10525382 DOI: 10.3390/biomedicines11092406] [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: 06/29/2023] [Revised: 08/14/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Resistance to protein tyrosine kinase inhibitors (TKIs) presents a significant challenge in therapeutic target development for cancers such as triple-negative breast cancer (TNBC), where conventional therapies are ineffective at combatting systemic disease. Due to increased expression, the receptor tyrosine kinases EGFR (epidermal growth factor receptor) and c-Met are potential targets for treatment. However, targeted anti-EGFR and anti-c-Met therapies have faced mixed results in clinical trials due to acquired resistance. We hypothesize that adaptive responses in regulatory kinase networks within the EGFR and c-Met signaling axes contribute to the development of acquired erlotinib and cabozantinib resistance. To test this, we developed two separate models for cabozantinib and erlotinib resistance using the MDA-MB-231 and MDA-MB-468 cell lines, respectively. We observed that erlotinib- or cabozantinib-resistant cell lines demonstrate enhanced cell proliferation, migration, invasion, and activation of EGFR or c-Met downstream signaling (respectively). Using a SILAC (Stable Isotope Labeling of Amino acids in Cell Culture)-labeled quantitative mass spectrometry proteomics approach, we assessed the effects of erlotinib or cabozantinib resistance on the phosphoproteome, proteome, and kinome. Using this integrated proteomics approach, we identified several potential kinase mediators of cabozantinib resistance and confirmed the contribution of AKT1 to erlotinib resistance in TNBC-resistant cell lines.
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Affiliation(s)
- Cory Lefebvre
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
| | - Sierra Pellizzari
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
| | - Vasudeva Bhat
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Western University, London, ON N6A 3K7, Canada; (K.J.); (D.W.L.)
| | - David W. Litchfield
- Department of Biochemistry, Western University, London, ON N6A 3K7, Canada; (K.J.); (D.W.L.)
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
| | - Alison L. Allan
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- Lawson Health Research Institute, London, ON N6A 5W9, Canada
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11
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Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA. In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541242. [PMID: 37293076 PMCID: PMC10245746 DOI: 10.1101/2023.05.18.541242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein translational control is highly regulated step in the gene expression program during mammalian development that is critical for ensuring that the fetus develops correctly and that all of the necessary organs and tissues are formed and functional. Defects in protein expression during fetal development can lead to severe developmental abnormalities or premature death. Currently, quantitative techniques to monitor protein synthesis rates in a developing fetus (in utero) are limited. Here, we developed a novel in utero stable isotope labeling approach to quantify tissue-specific protein dynamics of the nascent proteome during mouse fetal development. Fetuses of pregnant C57BL/6J mice were injected with isotopically labeled lysine (Lys8) and arginine (Arg10) via the vitelline vein at various gestational days. After treatment, fetal organs/tissues including brain, liver, lung, and heart were harvested for sample preparation and proteomic analysis. We show that the mean incorporation rate for injected amino acids into all organs was 17.50 ± 0.6%. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates (kobs) were calculated between 3.81E-5 and 0.424 hour-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver versus brain), however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates which correlated with known physiological changes during mouse development.
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Affiliation(s)
- Josue Baeza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
- Contributed equally to this work
| | - Barbara E. Coons
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Contributed equally to this work
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - John Riley
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Mariel Mendoza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - William H. Peranteau
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Benjamin A Garcia
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
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12
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Pavkova I, Kopeckova M, Link M, Vlcak E, Filimonenko V, Lecova L, Zakova J, Laskova P, Sheshko V, Machacek M, Stulik J. Francisella tularensis Glyceraldehyde-3-Phosphate Dehydrogenase Is Relocalized during Intracellular Infection and Reveals Effect on Cytokine Gene Expression and Signaling. Cells 2023; 12:cells12040607. [PMID: 36831274 PMCID: PMC9954481 DOI: 10.3390/cells12040607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known for its multifunctionality in several pathogenic bacteria. Our previously reported data suggest that the GAPDH homologue of Francisella tularensis, GapA, might also be involved in other processes beyond metabolism. In the present study, we explored GapA's potential implication in pathogenic processes at the host cell level. Using immunoelectron microscopy, we demonstrated the localization of this bacterial protein inside infected macrophages and its peripheral distribution in bacterial cells increasing with infection time. A quantitative proteomic approach based on stable isotope labeling of amino acids in cell culture (SILAC) combined with pull-down assay enabled the identification of several of GapA's potential interacting partners within the host cell proteome. Two of these partners were further confirmed by alternative methods. We also investigated the impact of gapA deletion on the transcription of selected cytokine genes and the activation of the main signaling pathways. Our results show that ∆gapA-induced transcription of genes encoding several cytokines whose expressions were not affected in cells infected with a fully virulent wild-type strain. That might be caused, at least in part, by the detected differences in ERK/MAPK signaling activation. The experimental observations together demonstrate that the F. tularensis GAPDH homologue is directly implicated in multiple host cellular processes and, thereby, that it participates in several molecular mechanisms of pathogenesis.
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Affiliation(s)
- Ivona Pavkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
- Correspondence: ; Tel.: +420-973-255-201
| | - Monika Kopeckova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Erik Vlcak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Electron Microscopy Core Facility, Videnska 1083, 142 20 Prague, Czech Republic
| | - Vlada Filimonenko
- Institute of Molecular Genetics of the Czech Academy of Sciences, Electron Microscopy Core Facility, Videnska 1083, 142 20 Prague, Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences, Department of Biology of the Cell Nucleus, Videnska 1083, 142 20 Prague, Czech Republic
| | - Lenka Lecova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Jitka Zakova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Pavlina Laskova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Valeria Sheshko
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Miloslav Machacek
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Akademika Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
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13
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Ji Z, Moore J, Devarie-Baez NO, Lewis J, Wu H, Shukla K, Lopez EIS, Vitvitsky V, Key CCC, Porosnicu M, Kemp ML, Banerjee R, Parks JS, Tsang AW, Zhou X, Furdui CM. Redox integration of signaling and metabolism in a head and neck cancer model of radiation resistance using COSM RO. Front Oncol 2023; 12:946320. [PMID: 36686772 PMCID: PMC9846845 DOI: 10.3389/fonc.2022.946320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Redox metabolism is increasingly investigated in cancer as driving regulator of tumor progression, response to therapies and long-term patients' quality of life. Well-established cancer therapies, such as radiotherapy, either directly impact redox metabolism or have redox-dependent mechanisms of action defining their clinical efficacy. However, the ability to integrate redox information across signaling and metabolic networks to facilitate discovery and broader investigation of redox-regulated pathways in cancer remains a key unmet need limiting the advancement of new cancer therapies. To overcome this challenge, we developed a new constraint-based computational method (COSMro) and applied it to a Head and Neck Squamous Cell Cancer (HNSCC) model of radiation resistance. This novel integrative approach identified enhanced capacity for H2S production in radiation resistant cells and extracted a key relationship between intracellular redox state and cholesterol metabolism; experimental validation of this relationship highlights the importance of redox state in cellular metabolism and response to radiation.
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Affiliation(s)
- Zhiwei Ji
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Jade Moore
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Nelmi O. Devarie-Baez
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Joshua Lewis
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States
- Department of Internal Medicine, Section on Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Kirtikar Shukla
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Elsa I. Silva Lopez
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Victor Vitvitsky
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory School of Medicine, Atlanta, GA, United States
| | - Chia-Chi Chuang Key
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Mercedes Porosnicu
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Melissa L. Kemp
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States
- Department of Internal Medicine, Section on Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Ruma Banerjee
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory School of Medicine, Atlanta, GA, United States
| | - John S. Parks
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Allen W. Tsang
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Xiaobo Zhou
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
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14
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Gyenis L, Menyhart D, Cruise ES, Jurcic K, Roffey SE, Chai DB, Trifoi F, Fess SR, Desormeaux PJ, Núñez de Villavicencio Díaz T, Rabalski AJ, Zukowski SA, Turowec JP, Pittock P, Lajoie G, Litchfield DW. Chemical Genetic Validation of CSNK2 Substrates Using an Inhibitor-Resistant Mutant in Combination with Triple SILAC Quantitative Phosphoproteomics. Front Mol Biosci 2022; 9:909711. [PMID: 35755813 PMCID: PMC9225150 DOI: 10.3389/fmolb.2022.909711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Casein Kinase 2 (CSNK2) is an extremely pleiotropic, ubiquitously expressed protein kinase involved in the regulation of numerous key biological processes. Mapping the CSNK2-dependent phosphoproteome is necessary for better characterization of its fundamental role in cellular signalling. While ATP-competitive inhibitors have enabled the identification of many putative kinase substrates, compounds targeting the highly conserved ATP-binding pocket often exhibit off-target effects limiting their utility for definitive kinase-substrate assignment. To overcome this limitation, we devised a strategy combining chemical genetics and quantitative phosphoproteomics to identify and validate CSNK2 substrates. We engineered U2OS cells expressing exogenous wild type CSNK2A1 (WT) or a triple mutant (TM, V66A/H160D/I174A) with substitutions at residues important for inhibitor binding. These cells were treated with CX-4945, a clinical-stage inhibitor of CSNK2, and analyzed using large-scale triple SILAC (Stable Isotope Labelling of Amino Acids in Cell Culture) quantitative phosphoproteomics. In contrast to wild-type CSNK2A1, CSNK2A1-TM retained activity in the presence of CX-4945 enabling identification and validation of several CSNK2 substrates on the basis of their increased phosphorylation in cells expressing CSNK2A1-TM. Based on high conservation within the kinase family, we expect that this strategy can be broadly adapted for identification of other kinase-substrate relationships.
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Affiliation(s)
- Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Daniel Menyhart
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Edward S Cruise
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Scott E Roffey
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Darren B Chai
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Flaviu Trifoi
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Sam R Fess
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paul J Desormeaux
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | | | - Adam J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Stephanie A Zukowski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Jacob P Turowec
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paula Pittock
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
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15
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Kori Y, Lund PJ, Trovato M, Sidoli S, Yuan ZF, Noh KM, Garcia BA. Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation. Mol Omics 2022; 18:296-314. [PMID: 35044400 PMCID: PMC9098674 DOI: 10.1039/d1mo00352f] [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] [Indexed: 11/21/2022]
Abstract
Histone variants, such as histone H3.3, replace canonical histones within the nucleosome to alter chromatin accessibility and gene expression. Although the biological roles of selected histone post-translational modifications (PTMs) have been extensively characterized, the potential differences in the function of a given PTM on different histone variants is almost always elusive. By applying proteomics and genomics techniques, we investigate the role of lysine 27 tri-methylation specifically on the histone variant H3.3 (H3.3K27me3) in the context of mouse embryonic stem cell pluripotency and differentiation as a model system for development. We demonstrate that while the steady state overall levels of methylation on both H3K27 and H3.3K27 decrease during differentiation, methylation dynamics studies indicate that methylation on H3.3K27 is maintained more than on H3K27. Using a custom-made antibody, we identify a unique enrichment of H3.3K27me3 at lineage-specific genes, such as olfactory receptor genes, and at binding motifs for the transcription factors FOXJ2/3. REST, a predicted FOXJ2/3 target that acts as a transcriptional repressor of terminal neuronal genes, was identified with H3.3K27me3 at its promoter region. H3.3K27A mutant cells confirmed an upregulation of FOXJ2/3 targets upon the loss of methylation at H3.3K27. Thus, while canonical H3K27me3 has been characterized to regulate the expression of transcription factors that play a general role in differentiation, our work suggests H3.3K27me3 is essential for regulating distinct terminal differentiation genes. This work highlights the importance of understanding the effects of PTMs not only on canonical histones but also on specific histone variants, as they may exhibit distinct roles.
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Affiliation(s)
- Yekaterina Kori
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peder J Lund
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
| | - Matteo Trovato
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kyung-Min Noh
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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16
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Abstract
Ascorbate peroxidase (APEX)-catalyzed proximity labeling has been recently established as a robust approach to uncover localized protein environments and transient protein-protein interactions occurring across mammalian cells. This molecular tool enables improved identification of individual proteins localized to and involved in specific cellular and subcellular pathways and functions. Engineering of an APEX2 fusion protein into the endogenous loci of proteins of interest enables directed biotinylation of neighboring polypeptides and mRNAs. This results in identification of subcellular and context-dependent proteomes or transcriptomes via quantitative mass spectrometry or RNA sequencing, respectively. Here, we describe the utility of APEX-mediated proximity labeling to recover components of stress granules (SGs) by endogenous tagging of well-established SG-associated proteins.
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Affiliation(s)
- Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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17
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Morgenstern M, Peikert CD, Lübbert P, Suppanz I, Klemm C, Alka O, Steiert C, Naumenko N, Schendzielorz A, Melchionda L, Mühlhäuser WWD, Knapp B, Busch JD, Stiller SB, Dannenmaier S, Lindau C, Licheva M, Eickhorst C, Galbusera R, Zerbes RM, Ryan MT, Kraft C, Kozjak-Pavlovic V, Drepper F, Dennerlein S, Oeljeklaus S, Pfanner N, Wiedemann N, Warscheid B. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Cell Metab 2021; 33:2464-2483.e18. [PMID: 34800366 PMCID: PMC8664129 DOI: 10.1016/j.cmet.2021.11.001] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/01/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022]
Abstract
Mitochondria are key organelles for cellular energetics, metabolism, signaling, and quality control and have been linked to various diseases. Different views exist on the composition of the human mitochondrial proteome. We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP). We identified interactors of translocases, respiratory chain, and ATP synthase assembly factors. The abundance of MitoCoP proteins covers six orders of magnitude and amounts to 7% of the cellular proteome with the chaperones HSP60-HSP10 being the most abundant mitochondrial proteins. MitoCoP dynamics spans three orders of magnitudes, with half-lives from hours to months, and suggests a rapid regulation of biosynthesis and assembly processes. 460 MitoCoP genes are linked to human diseases with a strong prevalence for the central nervous system and metabolism. MitoCoP will provide a high-confidence resource for placing dynamics, functions, and dysfunctions of mitochondria into the cellular context.
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Affiliation(s)
- Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christian D Peikert
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Lübbert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ida Suppanz
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Cinzia Klemm
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Alka
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Conny Steiert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Alexander Schendzielorz
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Laura Melchionda
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Wignand W D Mühlhäuser
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Knapp
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Stefan Dannenmaier
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Eickhorst
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Riccardo Galbusera
- Neurologic Clinic and Policlinic, Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Ralf M Zerbes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, VIC, Australia
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Friedel Drepper
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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18
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Application of SILAC Labeling in Phosphoproteomics Analysis. Methods Mol Biol 2021. [PMID: 33950491 DOI: 10.1007/978-1-0716-1024-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The analysis of disease-related changes in the phosphorylation status of cellular signal transduction networks is of major interest to biomedical researchers. Mass spectrometry-based proteomics allows the analysis of phosphorylation in a global manner. However, several technical challenges need to be addressed when the phosphorylation of proteins is analyzed. Low-abundant phosphopeptides need to be enriched before analysis, thereby introducing additional steps in sample preparation. Consequently, the applied quantification strategies should be robust towards elaborate sampling handling, rendering label-based quantification strategies the methods of choice in many experiments. Here, we present a protocol for SILAC labeling and the subsequent isolation of phosphopeptides using TiO2 affinity chromatography. We outline the corresponding LC-MS/MS analysis and the essential steps of data processing.
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19
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Conde-Rubio MDC, Mylonas R, Widmann C. The proteolytic landscape of cells exposed to non-lethal stresses is shaped by executioner caspases. Cell Death Discov 2021; 7:164. [PMID: 34226511 PMCID: PMC8257705 DOI: 10.1038/s41420-021-00539-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/26/2021] [Accepted: 05/29/2021] [Indexed: 02/06/2023] Open
Abstract
Cells are in constant adaptation to environmental changes to insure their proper functioning. When exposed to stresses, cells activate specific pathways to elicit adaptive modifications. Those changes can be mediated by selective modulation of gene and protein expression as well as by post-translational modifications, such as phosphorylation and proteolytic processing. Protein cleavage, as a controlled and limited post-translational modification, is involved in diverse physiological processes such as the maintenance of protein homeostasis, activation of repair pathways, apoptosis and the regulation of proliferation. Here we assessed by quantitative proteomics the proteolytic landscape in two cell lines subjected to low cisplatin concentrations used as a mild non-lethal stress paradigm. This landscape was compared to the one obtained in the same cells stimulated with cisplatin concentrations inducing apoptosis. These analyses were performed in wild-type cells and in cells lacking the two main executioner caspases: caspase-3 and caspase-7. Ninety-two proteins were found to be cleaved at one or a few sites (discrete cleavage) in low stress conditions compared to four hundred and fifty-three in apoptotic cells. Many of the cleaved proteins in stressed cells were also found to be cleaved in apoptotic conditions. As expected, ~90% of the cleavage events were dependent on caspase-3/caspase-7 in apoptotic cells. Strikingly, upon exposure to non-lethal stresses, no discrete cleavage was detected in cells lacking caspase-3 and caspase-7. This indicates that the proteolytic landscape in stressed viable cells fully depends on the activity of executioner caspases. These results suggest that the so-called executioner caspases fulfill important stress adaptive responses distinct from their role in apoptosis. Mass spectrometry data are available via ProteomeXchange with identifier PXD023488.
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Affiliation(s)
| | - Roman Mylonas
- Protein Analysis Facility, University of Lausanne, Génopode, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Amphipole, Lausanne, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, University of Lausanne, Bugnon 7, Lausanne, Switzerland.
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20
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Dieters-Castator D, Dantonio PM, Piaseczny M, Zhang G, Liu J, Kuljanin M, Sherman S, Jewer M, Quesnel K, Kang EY, Köbel M, Siegers GM, Leask A, Hess D, Lajoie G, Postovit LM. Embryonic protein NODAL regulates the breast tumor microenvironment by reprogramming cancer-derived secretomes. Neoplasia 2021; 23:375-390. [PMID: 33784590 PMCID: PMC8041663 DOI: 10.1016/j.neo.2021.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The tumor microenvironment (TME) is an important mediator of breast cancer progression. Cancer-associated fibroblasts constitute a major component of the TME and may originate from tissue-associated fibroblasts or infiltrating mesenchymal stromal cells (MSCs). The mechanisms by which cancer cells activate fibroblasts and recruit MSCs to the TME are largely unknown, but likely include deposition of a pro-tumorigenic secretome. The secreted embryonic protein NODAL is clinically associated with breast cancer stage and promotes tumor growth, metastasis, and vascularization. Herein, we show that NODAL expression correlates with the presence of activated fibroblasts in human triple-negative breast cancers and that it directly induces Cancer-associated fibroblasts phenotypes. We further show that NODAL reprograms cancer cell secretomes by simultaneously altering levels of chemokines (e.g., CXCL1), cytokines (e.g., IL-6) and growth factors (e.g., PDGFRA), leading to alterations in MSC chemotaxis. We therefore demonstrate a hitherto unappreciated mechanism underlying the dynamic regulation of the TME.
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Affiliation(s)
| | - Paola M Dantonio
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Matt Piaseczny
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada
| | - Guihua Zhang
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Jiahui Liu
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Miljan Kuljanin
- Robarts Research Institute, London, ON, Canada; Department of Biochemistry, Western University, London, ON, Canada
| | - Stephen Sherman
- Robarts Research Institute, London, ON, Canada; Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Michael Jewer
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada; Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Katherine Quesnel
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Eun Young Kang
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Andrew Leask
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - David Hess
- Robarts Research Institute, London, ON, Canada; Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada; Department of Oncology, University of Alberta, Edmonton, AB, Canada.
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21
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Ondrej M, Cechakova L, Fabrik I, Klimentova J, Tichy A. Lys05 - A Promising Autophagy Inhibitor in the Radiosensitization Battle: Phosphoproteomic Perspective. Cancer Genomics Proteomics 2021; 17:369-382. [PMID: 32576582 DOI: 10.21873/cgp.20196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Autophagy is a crucial factor contributing to radioresistance during radiotherapy. Although Lys05 has proven its ability to improve the results of radiotherapy through the inhibition of autophagy, molecular mechanisms of this inhibition remain elusive. We aimed to describe the molecular mechanisms involved in Lys05-induced inhibition of autophagy. MATERIALS AND METHODS Radioresistant human non-small cell lung carcinoma cells (H1299, p53-negative) and methods of quantitative phosphoproteomics were employed to define the molecular mechanisms involved in Lys05-induced inhibition of autophagy. RESULTS We confirmed that at an early stage after irradiation, autophagy was induced, whereas at a later stage after irradiation, it was inhibited. The early-stage induction of autophagy was characterized mainly by the activation of biosynthetic and metabolic processes through up- or down-regulation of the critical autophagic regulatory proteins Sequestosome-1 (SQSTM1) and proline-rich AKT1 substrate 1 (AKT1S1). The late-stage inhibition of autophagy was attributed mainly to down-regulation of Unc-51 like autophagy-activating kinase 1 (ULK1) through phosphorylation at Ser638. CONCLUSION This work contributes to emerging phosphoproteomic insights into autophagy-mediated global signaling in lung cancer cells, which might consequently facilitate the development of precision medicine therapeutics.
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Affiliation(s)
- Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Lucie Cechakova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Ivo Fabrik
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Jana Klimentova
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Ales Tichy
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
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22
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Michielin F, Giobbe GG, Luni C, Hu Q, Maroni I, Orford MR, Manfredi A, Di Filippo L, David AL, Cacchiarelli D, De Coppi P, Eaton S, Elvassore N. The Microfluidic Environment Reveals a Hidden Role of Self-Organizing Extracellular Matrix in Hepatic Commitment and Organoid Formation of hiPSCs. Cell Rep 2020; 33:108453. [PMID: 33264615 PMCID: PMC8237389 DOI: 10.1016/j.celrep.2020.108453] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/26/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022] Open
Abstract
The specification of the hepatic identity during human liver development is strictly controlled by extrinsic signals, yet it is still not clear how cells respond to these exogenous signals by activating secretory cascades, which are extremely relevant, especially in 3D self-organizing systems. Here, we investigate how the proteins secreted by human pluripotent stem cells (hPSCs) in response to developmental exogenous signals affect the progression from endoderm to the hepatic lineage, including their competence to generate nascent hepatic organoids. By using microfluidic confined environment and stable isotope labeling with amino acids in cell culture-coupled mass spectrometry (SILAC-MS) quantitative proteomic analysis, we find high abundancy of extracellular matrix (ECM)-associated proteins. Hepatic progenitor cells either derived in microfluidics or exposed to exogenous ECM stimuli show a significantly higher potential of forming hepatic organoids that can be rapidly expanded for several passages and further differentiated into functional hepatocytes. These results prove an additional control over the efficiency of hepatic organoid formation and differentiation for downstream applications.
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Affiliation(s)
- Federica Michielin
- Great Ormond Street Institute of Child Health, University College London, WC1N1EH London, UK
| | - Giovanni G Giobbe
- Great Ormond Street Institute of Child Health, University College London, WC1N1EH London, UK
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 201210 Shanghai, China
| | - Qianjiang Hu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 201210 Shanghai, China
| | - Ida Maroni
- Department of Industrial Engineering, University of Padova, 35131 Padova, Italy; Venetian Institute of Molecular Medicine (VIMM), 35129 Padova, Italy
| | - Michael R Orford
- Great Ormond Street Institute of Child Health, University College London, WC1N1EH London, UK
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, 80078 Pozzuoli, Italy
| | | | - Anna L David
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, WC1E 6AU London, UK
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, 80078 Pozzuoli, Italy; Department of Translational Medicine, University of Naples "Federico II," 80131 Naples, Italy
| | - Paolo De Coppi
- Great Ormond Street Institute of Child Health, University College London, WC1N1EH London, UK; Specialist Neonatal and Paediatric Surgery, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Simon Eaton
- Great Ormond Street Institute of Child Health, University College London, WC1N1EH London, UK
| | - Nicola Elvassore
- Great Ormond Street Institute of Child Health, University College London, WC1N1EH London, UK; Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 201210 Shanghai, China; Department of Industrial Engineering, University of Padova, 35131 Padova, Italy; Venetian Institute of Molecular Medicine (VIMM), 35129 Padova, Italy.
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23
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Shiny Matilda C, Madhusudan I, Gaurav Isola R, Shanthi C. Potential of proteomics to probe microbes. J Basic Microbiol 2020; 60:471-483. [PMID: 32212201 DOI: 10.1002/jobm.201900628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 01/05/2023]
Abstract
An organism exposed to a plethora of environmental perturbations undergoes proteomic changes which enable the characterization of total proteins in it. Much of the proteomic information is obtained from genomic data. Additional information on the proteome such as posttranslational modifications, protein-protein interactions, protein localization, metabolic pathways, and so on are deduced using proteomic tools which genomics and transcriptomics fail to offer. The proteomic analysis allows identification of precise changes in proteins, which in turn solve the complexity of microbial population providing insights into the microbial metabolism, cellular pathways, and behavior of microorganisms in new environments. Furthermore, they provide clues for the exploitation of their special features for biotechnological applications. Numerous techniques for the analysis of microbial proteome such as electrophoretic, chromatographic, mass spectrometric-based methods as well as quantitative proteomics are available which facilitate protein separation, expression, identification, and quantification of proteins. An understanding of the potential of each of the proteomic tools has created a significant impact on diverse microbiological aspects and the same has been discussed in this review.
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Affiliation(s)
- Chellaiah Shiny Matilda
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Iyengar Madhusudan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Ravi Gaurav Isola
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Chittibabu Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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24
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Stepath M, Zülch B, Maghnouj A, Schork K, Turewicz M, Eisenacher M, Hahn S, Sitek B, Bracht T. Systematic Comparison of Label-Free, SILAC, and TMT Techniques to Study Early Adaption toward Inhibition of EGFR Signaling in the Colorectal Cancer Cell Line DiFi. J Proteome Res 2019; 19:926-937. [DOI: 10.1021/acs.jproteome.9b00701] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Birgit Zülch
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum, Bochum 44892, Germany
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25
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Karl M, Sommer C, Gabriel CH, Hecklau K, Venzke M, Hennig AF, Radbruch A, Selbach M, Baumgrass R. Recruitment of Histone Methyltransferase Ehmt1 to Foxp3 TSDR Counteracts Differentiation of Induced Regulatory T Cells. J Mol Biol 2019; 431:3606-3625. [PMID: 31362003 DOI: 10.1016/j.jmb.2019.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022]
Abstract
Differentiation toward CD4+ regulatory T (Treg) cells is essentially dependent on an epigenetic program at Treg signature genes, which involves remodeling of the Treg-specific demethylated regions (TSDRs). In particular, the epigenetic status of the conserved non-coding sequence 2 of Foxp3 (Foxp3 TSDR) determines expression stability of the master transcription factor and thus Treg lineage identity. However, the molecular mechanisms controlling the epigenetic remodeling at TSDRs in Treg and conventional T cells are largely unknown. Using a combined approach of DNA pull-down and mass spectrometric analysis, we report a novel regulatory mechanism in which transcription factor Wiz recruits the histone methyltransferase Ehmt1 to Foxp3 TSDR. We show that both Wiz and Ehmt1 are crucial for shaping the region with the repressive histone modification H3K9me2 in conventional T cells. Consistently, knocking out either Ehmt1 or Wiz by CRISPR/Cas resulted in the loss of H3K9me2 and enhanced Foxp3 expression during iTreg differentiation. Moreover, the essential role of the Wiz-Ehmt1 interaction as observed at several TSDRs indicates a global function of Ehmt1 in the Treg differentiation program.
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Affiliation(s)
- Martin Karl
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Sommer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christian H Gabriel
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Katharina Hecklau
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Melanie Venzke
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Anna Floriane Hennig
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Andreas Radbruch
- Cell Biology, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany; Charité-University Medicine, Charitéplatz 1, 10117 Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Ria Baumgrass
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany.
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26
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Zhao Y, Xiao K. Proteomic Analysis of the β-Arrestin Interactomes. Methods Mol Biol 2019; 1957:217-232. [PMID: 30919357 DOI: 10.1007/978-1-4939-9158-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interaction is crucial to protein function and cellular signaling. A number of approaches were developed and applied to characterize protein-protein interactions in the past decades. In recent years, mass spectrometry (MS)-based proteomic methods have emerged as powerful tools to identify protein binding partners in a global and high-throughput manner. In this chapter, we describe the proteomic methods used to characterize the whole sets of proteins associated with β-arrestins (β-arrestin interactomes). The method starts with co-immunoprecipitation (co-IP) of β-arrestin signaling complexes from cells followed by protease digestion and LC/MS/MS analysis (liquid chromatography/tandem mass spectrometry) of proteins in the β-arrestin signaling complexes. To investigate changes in the amounts of binding partners under different conditions, we also describe a SILAC (stable isotope labeling by amino acids in cell culture) method to obtain quantitative information for β-arrestin interactomes.
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Affiliation(s)
- Yang Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kunhong Xiao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA. .,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA. .,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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27
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Kurokawa N, Kishimoto T, Tanaka K, Kondo J, Takahashi N, Miura Y. New approach to evaluating the effects of a drug on protein complexes with quantitative proteomics, using the SILAC method and bioinformatic approach. Biosci Biotechnol Biochem 2019; 83:2034-2048. [PMID: 31282289 DOI: 10.1080/09168451.2019.1637244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Protein-protein interactions (PPIs) lead the formation of protein complexes that perform biochemical reactions that maintain the living state of the living cell. Although therapeutic drugs should influence the formation of protein complexes in addition to PPI network, the methodology analyzing such influences remain to be developed. Here, we demonstrate that a new approach combining HPLC (high performance liquid chromatography) for separating protein complexes, and the SILAC (stable isotope labeling using amino acids in cell culture) method for relative protein quantification, enable us to identify the protein complexes influenced by a drug. We applied this approach to the analysis of thalidomide action on HepG2 cells, assessed the identified proteins by clustering data analyses, and assigned 135 novel protein complexes affected by the drug. We propose that this approach is applicable to elucidating the mechanisms of actions of other therapeutic drugs on the PPI network, and the formation of protein complexes.
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Affiliation(s)
- Natsuki Kurokawa
- Graduate School of Agriculture, Tokyo University of Agriculture & Technology , Fuchu-shi, Tokyo , Japan.,Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Taro Kishimoto
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Kohei Tanaka
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Jun Kondo
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Nobuhiro Takahashi
- Graduate School of Agriculture, Tokyo University of Agriculture & Technology , Fuchu-shi, Tokyo , Japan
| | - Yutaka Miura
- Graduate School of Agriculture, Tokyo University of Agriculture & Technology , Fuchu-shi, Tokyo , Japan
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28
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Venturini G, Malagrino PA, Padilha K, Tanaka LY, Laurindo FR, Dariolli R, Carvalho VM, Cardozo KHM, Krieger JE, Pereira ADC. Integrated proteomics and metabolomics analysis reveals differential lipid metabolism in human umbilical vein endothelial cells under high and low shear stress. Am J Physiol Cell Physiol 2019; 317:C326-C338. [PMID: 31067084 DOI: 10.1152/ajpcell.00128.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atherosclerotic plaque development is closely associated with the hemodynamic forces applied to endothelial cells (ECs). Among these, shear stress (SS) plays a key role in disease development since changes in flow intensity and direction could stimulate an atheroprone or atheroprotective phenotype. ECs under low or oscillatory SS (LSS) show upregulation of inflammatory, adhesion, and cellular permeability molecules. On the contrary, cells under high or laminar SS (HSS) increase their expression of protective and anti-inflammatory factors. The mechanism behind SS regulation of an atheroprotective phenotype is not completely elucidated. Here we used proteomics and metabolomics to better understand the changes in endothelial cells (human umbilical vein endothelial cells) under in vitro LSS and HSS that promote an atheroprone or atheroprotective profile and how these modifications can be connected to atherosclerosis development. Our data showed that lipid metabolism, in special cholesterol metabolism, was downregulated in cells under LSS. The low-density lipoprotein receptor (LDLR) showed significant alterations both at the quantitative expression level as well as regarding posttranslational modifications. Under LSS, LDLR was seen at lower concentrations and with a different glycosylation profile. Finally, modulating LDLR with atorvastatin led to the recapitulation of a HSS metabolic phenotype in EC under LSS. Altogether, our data suggest that there is significant modulation of lipid metabolism in endothelial cells under different SS intensities and that this could contribute to the atheroprone phenotype of LSS. Statin treatment was able to partially recover the protective profile of these cells.
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Affiliation(s)
- Gabriela Venturini
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Pamella Araujo Malagrino
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Kallyandra Padilha
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leonardo Yuji Tanaka
- Vascular Biology Laboratory, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Francisco Rafael Laurindo
- Vascular Biology Laboratory, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Rafael Dariolli
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | - Jose Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Alexandre da Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
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29
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Borgo C, Franchin C, Cesaro L, Zaramella S, Arrigoni G, Salvi M, Pinna LA. A proteomics analysis of CK2β
(−/−)
C2C12 cells provides novel insights into the biological functions of the non‐catalytic β subunit. FEBS J 2019; 286:1561-1575. [DOI: 10.1111/febs.14799] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/02/2018] [Accepted: 02/28/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Christian Borgo
- Department of Biomedical Sciences University of Padova Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences University of Padova Italy
- Proteomics Center University of Padova and Azienda Ospedaliera di Padova Italy
| | - Luca Cesaro
- Proteomics Center University of Padova and Azienda Ospedaliera di Padova Italy
| | - Silvia Zaramella
- Department of Biomedical Sciences University of Padova Italy
- Proteomics Center University of Padova and Azienda Ospedaliera di Padova Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences University of Padova Italy
- Proteomics Center University of Padova and Azienda Ospedaliera di Padova Italy
| | - Mauro Salvi
- Department of Biomedical Sciences University of Padova Italy
| | - Lorenzo A. Pinna
- Department of Biomedical Sciences University of Padova Italy
- CNR Institute of Neurosciences Padova Italy
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Kubiniok P, Finicle BT, Piffaretti F, McCracken AN, Perryman M, Hanessian S, Edinger AL, Thibault P. Dynamic Phosphoproteomics Uncovers Signaling Pathways Modulated by Anti-oncogenic Sphingolipid Analogs. Mol Cell Proteomics 2019; 18:408-422. [PMID: 30482847 PMCID: PMC6398214 DOI: 10.1074/mcp.ra118.001053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/23/2018] [Indexed: 12/31/2022] Open
Abstract
The anti-neoplastic sphingolipid analog SH-BC-893 starves cancer cells to death by down-regulating cell surface nutrient transporters and blocking lysosomal trafficking events. These effects are mediated by the activation of protein phosphatase 2A (PP2A). To identify putative PP2A substrates, we used quantitative phosphoproteomics to profile the temporal changes in protein phosphorylation in FL5.12 cells following incubation with SH-BC-893 or the specific PP2A inhibitor LB-100. These analyses enabled the profiling of more than 15,000 phosphorylation sites, of which 958 sites on 644 proteins were dynamically regulated. We identified 114 putative PP2A substrates including several nutrient transporter proteins, GTPase regulators (e.g. Agap2, Git1), and proteins associated with actin cytoskeletal remodeling (e.g. Vim, Pxn). To identify SH-BC-893-induced cell signaling events that disrupt lysosomal trafficking, we compared phosphorylation profiles in cells treated with SH-BC-893 or C2-ceramide, a non-vacuolating sphingolipid that does not impair lysosomal fusion. These analyses combined with functional assays uncovered the differential regulation of Akt and Gsk3b by SH-BC-893 (vacuolating) and C2-ceramide (non-vacuolating). Dynamic phosphoproteomics of cells treated with compounds affecting PP2A activity thus enabled the correlation of cell signaling with phenotypes to rationalize their mode of action.
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Affiliation(s)
- Peter Kubiniok
- From the ‡Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
| | - Brendan T Finicle
- ¶Department of Developmental and Cell Biology, University of California Irvine, Irvine CA 92697
| | - Fanny Piffaretti
- From the ‡Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Alison N McCracken
- ¶Department of Developmental and Cell Biology, University of California Irvine, Irvine CA 92697
| | - Michael Perryman
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
| | - Stephen Hanessian
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
| | - Aimee L Edinger
- ¶Department of Developmental and Cell Biology, University of California Irvine, Irvine CA 92697;
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada;
- §Department of Chemistry, Université de Montréal, Quebec, H3C 3J7, Canada
- ‖Department of Biochemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
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Abstract
Selective autophagy enables degradation of specific cargo such as protein aggregates or organelles and thus plays an essential role in the regulation of cellular homeostasis. Cargo specificity is achieved on the level of autophagy receptors that concurrently bind the cargo and the autophagosomal membrane. Recent studies have demonstrated that selective autophagy is tightly regulated by posttranslational modifications of autophagy receptors, in particular protein phosphorylation. Phosphorylation of autophagy receptors by different kinases, including Tank-binding kinase (TBK1), can increase their affinity toward the cargo or autophagosomes and thereby regulate the specificity and activity of selective autophagy depending on the cellular condition.Here, we report an approach for quantitative analysis of phosphorylation sites on autophagy receptors using mass spectrometry-based proteomics. In this protocol, GFP-tagged autophagy receptors are purified based on the high-affinity binding between GFP and GFP-Trap agarose. Interaction partners and background binders are subsequently removed by washes under denaturing conditions to obtain a pure fraction of the bait protein, thereby reducing the complexity of the analyzed sample. The bait protein is then digested on-bead, and peptides are analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The described approach permits systematic identification and quantification of phosphorylation sites on autophagy receptors and other autophagic components. In addition to phosphorylation, this protocol is suitable for investigating other posttranslational modifications, including protein ubiquitylation.
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Adolf F, Rhiel M, Hessling B, Gao Q, Hellwig A, Béthune J, Wieland FT. Proteomic Profiling of Mammalian COPII and COPI Vesicles. Cell Rep 2019; 26:250-265.e5. [DOI: 10.1016/j.celrep.2018.12.041] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/08/2018] [Accepted: 12/10/2018] [Indexed: 12/26/2022] Open
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Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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35
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Dannenmaier S, Stiller SB, Morgenstern M, Lübbert P, Oeljeklaus S, Wiedemann N, Warscheid B. Complete Native Stable Isotope Labeling by Amino Acids of Saccharomyces cerevisiae for Global Proteomic Analysis. Anal Chem 2018; 90:10501-10509. [PMID: 30102515 PMCID: PMC6300314 DOI: 10.1021/acs.analchem.8b02557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Knowledge about the functions of individual proteins on a system-wide level is crucial to fully understand molecular mechanisms underlying cellular processes. A considerable part of the proteome across all organisms is still poorly characterized. Mass spectrometry is an efficient technology for the global study of proteins. One of the most prominent methods for accurate proteome-wide comparative quantification is stable isotope labeling by amino acids in cell culture (SILAC). However, application of SILAC to prototrophic organisms such as Saccharomyces cerevisiae, also known as baker's yeast, is compromised since they are able to synthesize all amino acids on their own. Here, we describe an advanced strategy, termed 2nSILAC, that allows for in vivo labeling of prototrophic baker's yeast using heavy arginine and lysine under fermentable and respiratory growth conditions, making it a suitable tool for the global study of protein functions. This generic 2nSILAC strategy allows for directly using and systematically screening yeast mutant strain collections available to the scientific community. We exemplarily demonstrate its high potential by analyzing the effects of mitochondrial gene deletions in mitochondrial fractions using quantitative mass spectrometry revealing the role of Coi1 for the assembly of cytochrome c oxidase (respiratory chain complex IV).
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36
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Sandoval GJ, Pulice JL, Pakula H, Schenone M, Takeda DY, Pop M, Boulay G, Williamson KE, McBride MJ, Pan J, St Pierre R, Hartman E, Garraway LA, Carr SA, Rivera MN, Li Z, Ronco L, Hahn WC, Kadoch C. Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. Mol Cell 2018; 71:554-566.e7. [PMID: 30078722 PMCID: PMC6140332 DOI: 10.1016/j.molcel.2018.06.040] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/04/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022]
Abstract
Chromosomal rearrangements resulting in the fusion of TMPRSS2, an androgen-regulated gene, and the ETS family transcription factor ERG occur in over half of prostate cancers. However, the mechanism by which ERG promotes oncogenic gene expression and proliferation remains incompletely understood. Here, we identify a binding interaction between ERG and the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which is conserved among other oncogenic ETS factors, including ETV1, ETV4, and ETV5. We find that ERG drives genome-wide retargeting of BAF complexes in a manner dependent on binding of ERG to the ETS DNA motif. Moreover, ERG requires intact BAF complexes for chromatin occupancy and BAF complex ATPase activity for target gene regulation. In a prostate organoid model, BAF complexes are required for ERG-mediated basal-to-luminal transition, a hallmark of ERG activity in prostate cancer. These observations suggest a fundamental interdependence between ETS transcription factors and BAF chromatin remodeling complexes in cancer.
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Affiliation(s)
- Gabriel J Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - John L Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hubert Pakula
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - David Y Takeda
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marius Pop
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gaylor Boulay
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kaylyn E Williamson
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matthew J McBride
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Chemical Biology Program, Harvard Medical School, Boston, MA, USA
| | - Joshua Pan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roodolph St Pierre
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Chemical Biology Program, Harvard Medical School, Boston, MA, USA
| | - Emily Hartman
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Miguel N Rivera
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Zhe Li
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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A novel cross-talk between CXCR4 and PI4KIIIα in prostate cancer cells. Oncogene 2018; 38:332-344. [PMID: 30111818 PMCID: PMC6336684 DOI: 10.1038/s41388-018-0448-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/03/2018] [Accepted: 07/14/2018] [Indexed: 12/20/2022]
Abstract
Chemokine signaling regulates cell migration and tumor metastasis. CXCL12, a member of the chemokine family, and its receptor, CXCR4, a G protein coupled receptor (GPCR), are key mediators of prostate-cancer (PC) bone metastasis. In PC cells androgens activate CXCR4 gene expression and receptor signaling on lipid rafts, which induces protease expression and cancer cell invasion. To identify novel lipid-raft-associated CXCR4 regulators supporting invasion/metastasis, we performed a SILAC-based quantitative proteomic analysis of lipid-rafts derived from PC3 stable cell lines with overexpression or knockdown of CXCR4. This analysis identified the evolutionarily conserved phosphatidylinositol 4-kinase IIIα (PI4KIIIα), and SAC1 phosphatase that dephosphorylates phosphatidylinositol-4-phosphate as potential candidate CXCR4 regulators. CXCR4 interacted with PI4KIIIα membrane targeting machinery recruiting them to the plasma membrane for PI4P production. Consistent with this interaction, PI4KIIIα was found tightly linked to the CXCR4 induced PC cell invasion. Thus, ablation of PI4KIIIα in CXCR4-expressing PC3 cells reduced cellular invasion in response to a variety of chemokines. Immunofluorescence microscopy in CXCR4 expressing cells revealed localized production of PI4P on the invasive projections. Human tumor studies documented increased PI4KIIIα expression in metastatic tumors vs. the primary tumor counterparts, further supporting the PI4KIIIα role in tumor metastasis. Furthermore, we also identified an unexpected function of PI4KIIIα in GPCR signaling where CXCR4 regulates PI4KIIIα activity and mediate tumor metastasis. Together, our study identifies a novel cross-talk between PI4KIIIα and CXCR4 in promoting tumor metastasis and suggests that PI4KIIIα pharmacological targeting may have therapeutic benefit for advanced prostate cancer patients.
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Šalovská B, Janečková H, Fabrik I, Karlíková R, Čecháková L, Ondrej M, Link M, Friedecký D, Tichý A. Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells. PLoS One 2018; 13:e0199349. [PMID: 30001349 PMCID: PMC6042708 DOI: 10.1371/journal.pone.0199349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/06/2018] [Indexed: 12/13/2022] Open
Abstract
Current anti-cancer strategy takes advantage of tumour specific abnormalities in DNA damage response to radio- or chemo-therapy. Inhibition of the ATR/Chk1 pathway has been shown to be synthetically lethal in cells with high levels of oncogene-induced replication stress and in p53- or ATM- deficient cells. In the presented study, we aimed to elucidate molecular mechanisms underlying radiosensitization of T-lymphocyte leukemic MOLT-4 cells by VE-821, a higly potent and specific inhibitor of ATR. We combined multiple approaches: cell biology techniques to reveal the inhibitor-induced phenotypes, and quantitative proteomics, phosphoproteomics, and metabolomics to comprehensively describe drug-induced changes in irradiated cells. VE-821 radiosensitized MOLT-4 cells, and furthermore 10 μM VE-821 significantly affected proliferation of sham-irradiated MOLT-4 cells. We detected 623 differentially regulated phosphorylation sites. We revealed changes not only in DDR-related pathways and kinases, but also in pathways and kinases involved in maintaining cellular metabolism. Notably, we found downregulation of mTOR, the main regulator of cellular metabolism, which was most likely caused by an off-target effect of the inhibitor, and we propose that mTOR inhibition could be one of the factors contributing to the phenotype observed after treating MOLT-4 cells with 10 μM VE-821. In the metabolomic analysis, 206 intermediary metabolites were detected. The data indicated that VE-821 potentiated metabolic disruption induced by irradiation and affected the response to irradiation-induced oxidative stress. Upon irradiation, recovery of damaged deoxynucleotides might be affected by VE-821, hampering DNA repair by their deficiency. Taken together, this is the first study describing a complex scenario of cellular events that might be ATR-dependent or triggered by ATR inhibition in irradiated MOLT-4 cells. Data are available via ProteomeXchange with identifier PXD008925.
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Affiliation(s)
- Barbora Šalovská
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Janečková
- Laboratory for Inherited Metabolic Disorders, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
- Department of Clinical Biochemistry, University Hospital Olomouc, Olomouc, Czech Republic
| | - Ivo Fabrik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
- Biomedical Research Center, University Hospital, Hradec Králové, Czech Republic
| | - Radana Karlíková
- Department of Clinical Biochemistry, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Lucie Čecháková
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
| | - Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
| | - David Friedecký
- Laboratory for Inherited Metabolic Disorders, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
- Department of Clinical Biochemistry, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Aleš Tichý
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
- Biomedical Research Center, University Hospital, Hradec Králové, Czech Republic
- * E-mail:
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Franchin C, Borgo C, Cesaro L, Zaramella S, Vilardell J, Salvi M, Arrigoni G, Pinna LA. Re-evaluation of protein kinase CK2 pleiotropy: new insights provided by a phosphoproteomics analysis of CK2 knockout cells. Cell Mol Life Sci 2018; 75:2011-2026. [PMID: 29119230 PMCID: PMC11105740 DOI: 10.1007/s00018-017-2705-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
CK2 denotes a ubiquitous and pleiotropic protein kinase whose holoenzyme is composed of two catalytic (α and/or α') and two regulatory β subunits. The CK2 consensus sequence, S/T-x-x-D/E/pS/pT is present in numerous phosphosites, but it is not clear how many of these are really generated by CK2. To gain information about this issue, advantage has been taken of C2C12 cells entirely deprived of both CK2 catalytic subunits by the CRISPR/Cas9 methodology. A comparative SILAC phosphoproteomics analysis reveals that, although about 30% of the quantified phosphosites do conform to the CK2 consensus, only one-third of these are substantially reduced in the CK2α/α'(-/-) cells, consistent with their generation by CK2. A parallel study with C2C12 cells deprived of the regulatory β subunit discloses a role of this subunit in determining CK2 targeting. We also find that phosphosites notoriously generated by CK2 are not fully abrogated in CK2α/α'(-/-) cells, while some phosphosites unrelated to CK2 are significantly altered. Collectively taken our data allow to conclude that the phosphoproteome generated by CK2 is not as ample and rigidly pre-determined as it was believed before. They also show that the lack of CK2 promotes phosphoproteomics perturbations attributable to kinases other than CK2.
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Affiliation(s)
- Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
| | - Luca Cesaro
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Silvia Zaramella
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy
| | - Jordi Vilardell
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, Padua, Italy.
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padua, Italy.
- CNR Institute of Neurosciences, Via U. Bassi 58/B, Padua, Italy.
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40
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Kaneva IN, Longworth J, Sudbery PE, Dickman MJ. Quantitative Proteomic Analysis in Candida albicans Using SILAC-Based Mass Spectrometry. Proteomics 2018; 18:e1700278. [PMID: 29280593 DOI: 10.1002/pmic.201700278] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/18/2017] [Indexed: 01/12/2023]
Abstract
Stable isotope labelling by amino acids in cell culture (SILAC) in conjunction with MS analysis is a sensitive and reliable technique for quantifying relative differences in protein abundance and posttranslational modifications between cell populations. We develop and utilise SILAC-MS workflows for quantitative proteomics in the fungal pathogen Candida albicans. Arginine metabolism provides important cues for escaping host defences during pathogenesis, which limits the use of auxotrophs in Candida research. Our strategy eliminates the need for engineering arginine auxotrophs for SILAC experiments and allows the use of ARG4 as selectable marker during strain construction. Cells that are auxotrophic for lysine are successfully labelled with both lysine and arginine stable isotopes. We find that prototrophic C. albicans preferentially uses exogenous arginine and down-regulates internal production, which allow it to achieve high incorporation rates. However, similar to other yeast, C. albicans is able to metabolise heavy arginine to heavy proline, which compromised the accuracy of protein quantification. A computational method is developed to correct for the incorporation of heavy proline. In addition, we utilise the developed SILAC labelling in C. albicans for the global quantitative proteomic analysis of a strain expressing a phosphatase-dead mutant Cdc14PD .
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Affiliation(s)
- Iliyana N Kaneva
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Joseph Longworth
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Peter E Sudbery
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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Williams JJL, Alotaiq N, Mullen W, Burchmore R, Liu L, Baillie GS, Schaper F, Pilch PF, Palmer TM. Interaction of suppressor of cytokine signalling 3 with cavin-1 links SOCS3 function and cavin-1 stability. Nat Commun 2018; 9:168. [PMID: 29330478 PMCID: PMC5766592 DOI: 10.1038/s41467-017-02585-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/11/2017] [Indexed: 11/09/2022] Open
Abstract
Effective suppression of JAK-STAT signalling by the inducible inhibitor "suppressor of cytokine signalling 3" (SOCS3) is essential for limiting signalling from cytokine receptors. Here we show that cavin-1, a component of caveolae, is a functionally significant SOCS3-interacting protein. Biochemical and confocal imaging demonstrate that SOCS3 localisation to the plasma membrane requires cavin-1. SOCS3 is also critical for cavin-1 stabilisation, such that deletion of SOCS3 reduces the expression of cavin-1 and caveolin-1 proteins, thereby reducing caveola abundance in endothelial cells. Moreover, the interaction of cavin-1 and SOCS3 is essential for SOCS3 function, as loss of cavin-1 enhances cytokine-stimulated STAT3 phosphorylation and abolishes SOCS3-dependent inhibition of IL-6 signalling by cyclic AMP. Together, these findings reveal a new functionally important mechanism linking SOCS3-mediated inhibition of cytokine signalling to localisation at the plasma membrane via interaction with and stabilisation of cavin-1.
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Affiliation(s)
- Jamie J L Williams
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, BD7 1DP, UK.
| | - Nasser Alotaiq
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Libin Liu
- Departments of Biochemistry and Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - George S Baillie
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Schaper
- Department of Systems Biology, Institute for Biology, Otto-von-Guericke-University Magdeburg, 39106, Magdeburg, Germany
| | - Paul F Pilch
- Departments of Biochemistry and Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Timothy M Palmer
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, BD7 1DP, UK.
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Abstract
Proteomics allows the simultaneous detection and identification of thousands of proteins within a sample. Here, we describe a quantitative method to compare protein expression and subcellular localization of different cell lines representative of different stages of colorectal cancer using stable isotope labeling with amino acids in culture, or SILAC. We also describe a biochemical fractionation approach to separate different cellular compartments and the necessary steps to obtain a specific proteomic profile of each cell line. This technique enables a comprehensive proteomic analysis of cancer cell lines and the identification of pathways that are deregulated in different cancer cell lines.
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43
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McMillan LJ, Hwang S, Farah RE, Koh J, Chen S, Maupin-Furlow JA. Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses. Environ Microbiol 2017; 20:385-401. [PMID: 29194950 DOI: 10.1111/1462-2920.14014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023]
Abstract
Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here, we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of 13 C/15 N-lysine and 13 C-arginine such that each peptide derived from trypsin digestion was labelled. This strain was found amenable to multiplex SILAC by case study of responses to oxidative stress by hypochlorite. A total of 2565 proteins was identified by LC-MS/MS analysis (q-value ≤ 0.01) that accounted for 64% of the theoretical proteome. Of these, 176 proteins were altered at least 1.5-fold (p-value < 0.05) in abundance during hypochlorite stress. Many of the differential proteins were of unknown function. Those of known function included transcription factor homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons. Thus, SILAC is found to be an ideal method for quantitative proteomics of archaea that holds promise to unravel gene function.
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Affiliation(s)
- Lana J McMillan
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Sungmin Hwang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rawan E Farah
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Sixue Chen
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.,Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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44
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Kuljanin M, Bell GI, Sherman SE, Lajoie GA, Hess DA. Proteomic characterisation reveals active Wnt-signalling by human multipotent stromal cells as a key regulator of beta cell survival and proliferation. Diabetologia 2017; 60:1987-1998. [PMID: 28710530 DOI: 10.1007/s00125-017-4355-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/23/2017] [Indexed: 01/09/2023]
Abstract
AIMS/HYPOTHESIS Novel strategies to stimulate the expansion of beta cell mass in situ are warranted for diabetes therapy. The aim of this study was to elucidate the secretome of human bone marrow (BM)-derived multipotent stromal cells (MSCs) with documented islet regenerative paracrine function. We hypothesised that regenerative MSCs will secrete a unique combination of protein factors that augment islet regeneration. METHODS Human BM-derived MSCs were examined for glucose-lowering capacity after transplantation into streptozotocin-treated NOD/severe combined immunodeficiency (SCID) mice and segregated into samples with regenerative (MSCR) vs nonregenerative (MSCNR) capacity. Secreted proteins associated with islet regenerative function were identified using stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomics. To functionally validate the importance of active Wnt signalling, we stimulated the Wnt-signalling pathway in MSCNR samples during ex vivo expansion using glycogen synthase kinase 3 (GSK3) inhibition (CHIR99201), and the conditioned culture media (CM) generated was tested for the capacity to support cultured human islet cell survival and proliferation in vitro. RESULTS MSCR showed increased secretion of proteins associated with cell growth, matrix remodelling, immunosuppressive and proangiogenic properties. In contrast, MSCNR uniquely secreted proteins known to promote inflammation and negatively regulate angiogenesis. Most notably, MSCR maintained Wnt signalling via Wnt5A/B (~2.5-fold increase) autocrine activity during ex vivo culture, while MSCNR repressed Wnt signalling via Dickkopf-related protein (DKK)1 (~2.5-fold increase) and DKK3 secretion. Inhibition of GSK3 activity in MSCNR samples increased the accumulation of nuclear β-catenin and generated CM that augmented beta cell survival (13% increases) and proliferation when exposed to cultured human islets. CONCLUSIONS/INTERPRETATION Maintenance of active Wnt signalling within human MSCs promotes the secretion of matricellular and proangiogenic proteins that formulate a niche for islet regeneration.
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Affiliation(s)
- Miljan Kuljanin
- Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N5A 6C1, Canada
| | - Gillian I Bell
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Stephen E Sherman
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Molecular Medicine Laboratories, Krembil Centre for Stem Cell Biology, Robarts Research Institute, 100 Perth Drive, London, ON, N6A 5K8, Canada
| | - Gilles A Lajoie
- Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N5A 6C1, Canada.
| | - David A Hess
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
- Molecular Medicine Laboratories, Krembil Centre for Stem Cell Biology, Robarts Research Institute, 100 Perth Drive, London, ON, N6A 5K8, Canada.
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45
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Cho IT, Adelmant G, Lim Y, Marto JA, Cho G, Golden JA. Ascorbate peroxidase proximity labeling coupled with biochemical fractionation identifies promoters of endoplasmic reticulum-mitochondrial contacts. J Biol Chem 2017; 292:16382-16392. [PMID: 28760823 PMCID: PMC5625067 DOI: 10.1074/jbc.m117.795286] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/14/2017] [Indexed: 11/06/2022] Open
Abstract
To maintain cellular homeostasis, subcellular organelles communicate with each other and form physical and functional networks through membrane contact sites coupled by protein tethers. In particular, endoplasmic reticulum (ER)-mitochondrial contacts (EMC) regulate diverse cellular activities such as metabolite exchange (Ca2+ and lipids), intracellular signaling, apoptosis, and autophagy. The significance of EMCs has been highlighted by reports indicating that EMC dysregulation is linked to neurodegenerative diseases. Therefore, obtaining a better understanding of the physical and functional components of EMCs should provide new insights into the pathogenesis of several neurodegenerative diseases. Here, we applied engineered ascorbate peroxidase (APEX) to map the proteome at EMCs in live HEK293 cells. APEX was targeted to the outer mitochondrial membrane, and proximity-labeled proteins were analyzed by stable isotope labeling with amino acids in culture (SILAC)-LC/MS-MS. We further refined the specificity of the proteins identified by combining biochemical subcellular fractionation to the protein isolation method. We identified 405 proteins with a 2.0-fold cutoff ratio (log base 2) in SILAC quantification from replicate experiments. We performed validation screening with a Split-Rluc8 complementation assay that identified reticulon 1A (RTN1A), an ER-shaping protein localized to EMCs as an EMC promoter. Proximity mapping augmented with biochemical fractionation and additional validation methods reported here could be useful to discover other components of EMCs, identify mitochondrial contacts with other organelles, and further unravel their communication.
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Affiliation(s)
- Il-Taeg Cho
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Guillaume Adelmant
- the Departments of Cancer Biology and Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Youngshin Lim
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Jarrod A Marto
- From the Department of Pathology, Brigham and Women's Hospital, and
- the Departments of Cancer Biology and Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Ginam Cho
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Jeffrey A Golden
- From the Department of Pathology, Brigham and Women's Hospital, and
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46
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Janouskova H, El Tekle G, Bellini E, Udeshi ND, Rinaldi A, Ulbricht A, Bernasocchi T, Civenni G, Losa M, Svinkina T, Bielski CM, Kryukov GV, Cascione L, Napoli S, Enchev RI, Mutch DG, Carney ME, Berchuck A, Winterhoff BJN, Broaddus RR, Schraml P, Moch H, Bertoni F, Catapano CV, Peter M, Carr SA, Garraway LA, Wild PJ, Theurillat JPP. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med 2017; 23:1046-1054. [PMID: 28805821 PMCID: PMC5592092 DOI: 10.1038/nm.4372] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations in the substrate recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancer. Their therapeutic implications remain incompletely understood. Here, we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer-specific SPOP mutants impaired degradation of BETs, promoting resistance against their pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations within the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat endometrial but not prostate cancer patients with SPOP mutations.
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Affiliation(s)
- Hana Janouskova
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Geniver El Tekle
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Elisa Bellini
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Namrata D Udeshi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anna Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Anna Ulbricht
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Tiziano Bernasocchi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Gianluca Civenni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Marco Losa
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Tanya Svinkina
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Craig M Bielski
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Luciano Cascione
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Radoslav I Enchev
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - David G Mutch
- Division of Gynecologic Oncology, Washington University, St. Louis, Missouri, USA
| | - Michael E Carney
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Duke Cancer Center, Durham, North Carolina, USA
| | - Boris J N Winterhoff
- Division of Gynecologic Oncology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Russell R Broaddus
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Matthias Peter
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Steven A Carr
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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47
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Jimenez L, Lim J, Burd B, Harris TM, Ow TJ, Kawachi N, Belbin TJ, Angeletti R, Prystowsky MB, Childs G, Segall JE. miR-375 Regulates Invasion-Related Proteins Vimentin and L-Plastin. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:1523-1536. [PMID: 28499703 PMCID: PMC5500828 DOI: 10.1016/j.ajpath.2017.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022]
Abstract
Invasion is a hallmark of advanced head and neck squamous cell carcinoma (HNSCC). We previously determined that low relative miR-375 expression was associated with poor patient prognosis. HNSCC cells with increased miR-375 expression have lower invasive properties and impaired invadopodium activity. Using stable isotope labeling with amino acids in cell culture and reverse-phase liquid chromatography mass spectrometry, we assessed the impact of miR-375 expression on protein levels in UM-SCC-1 cells. Increased miR-375 expression was associated with down-regulation of proteins involved in cellular assembly and organization, death and survival, and movement. Two invasion-associated proteins, vimentin and L-plastin, were strongly down-regulated by miR-375. Luciferase reporter assays demonstrated that high miR-375 expression reduced vimentin promoter activity, suggesting that vimentin is an indirect target of miR-375. Runt-related transcription factor 1 (RUNX1) is a potential miR-375 direct target, and its knockdown reduced vimentin and L-plastin expression. Data in The Cancer Genome Atlas HNSCC database showed a significant inverse correlation between miR-375 expression and RUNX1, vimentin, and L-plastin RNA expression. These clinical correlations validate our in vitro model findings and support a mechanism in which miR-375 suppresses RUNX1 levels, resulting in reduced vimentin and L-plastin expression. Furthermore, knockdown of RUNX1, L-plastin, and vimentin resulted in significant reductions in cell invasion in vitro, indicating the functional significance of miR-375 regulation of specific proteins involved in HNSCC invasion.
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Affiliation(s)
- Lizandra Jimenez
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Jihyeon Lim
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York; Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York
| | - Berta Burd
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York
| | - Thomas M Harris
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Thomas J Ow
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Nicole Kawachi
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Thomas J Belbin
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Ruth Angeletti
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York
| | | | - Geoffrey Childs
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Jeffrey E Segall
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York.
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48
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Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M. The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell 2017; 169:1051-1065.e18. [PMID: 28575669 PMCID: PMC5548193 DOI: 10.1016/j.cell.2017.05.022] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 03/13/2017] [Accepted: 05/14/2017] [Indexed: 11/19/2022]
Abstract
During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life's most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.
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Affiliation(s)
- Deniz Simsek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gerald C Tiu
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gun W Byeon
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Adele F Xu
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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49
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Maček B, Carpy A, Koch A, Bicho CC, Borek WE, Hauf S, Sawin KE. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Technology in Fission Yeast. Cold Spring Harb Protoc 2017; 2017:pdb.top079814. [PMID: 28572211 DOI: 10.1101/pdb.top079814] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Shotgun proteomics combined with stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach to quantify proteins and posttranslational modifications across the entire proteome. SILAC technology in Schizosaccharomyces pombe must cope with the "arginine conversion problem," in which isotope-labeled arginine is converted to other amino acids. This can be circumvented by either using stable isotope-marked lysine only (as opposed to the more standard lysine/arginine double labeling) or using yeast genetics to create strains that only very inefficiently convert arginine. Both strategies have been used successfully in large-scale (phospho)proteomics projects in S. pombe Here we introduce methods for performing a typical SILAC-based experiment in fission yeast, including generation of SILAC-compatible strains, sample preparation, and measurement by mass spectrometry.
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Affiliation(s)
- Boris Maček
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Alejandro Carpy
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - André Koch
- Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, 72076, Germany
| | - Claudia C Bicho
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Weronika E Borek
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Silke Hauf
- Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, 72076, Germany
| | - Kenneth E Sawin
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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50
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Borgo C, Franchin C, Scalco S, Bosello-Travain V, Donella-Deana A, Arrigoni G, Salvi M, Pinna LA. Generation and quantitative proteomics analysis of CK2α/α' (-/-) cells. Sci Rep 2017; 7:42409. [PMID: 28209983 PMCID: PMC5314375 DOI: 10.1038/srep42409] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 01/10/2017] [Indexed: 01/23/2023] Open
Abstract
CK2 is a ubiquitous, constitutively active, highly pleiotropic, acidophilic Ser/Thr protein kinase whose holoenzyme is composed of two catalytic (α and/or α’) subunits and a dimer of a non-catalytic β subunit. Abnormally high CK2 level/activity is often associated with malignancy and a variety of cancer cells have been shown to rely on it to escape apoptosis. To gain information about the actual “druggability” of CK2 and to dissect CK2 dependent cellular processes that are instrumental to the establishment and progression of neoplasia we have exploited the CRISPR/Cas9 genome editing technology to generate viable clones of C2C12 myoblasts devoid of either both the CK2 catalytic subunits or its regulatory β-subunit. Suppression of both CK2 catalytic subunits promotes the disappearance of the β-subunit as well, through its accelerated proteasomal degradation. A quantitative proteomics analysis of CK2α/α’(−/−) versus wild type cells shows that knocking out both CK2 catalytic subunits causes a rearrangement of the proteomics profile, with substantially altered level ( > 50%) of 240 proteins, 126 of which are up-regulated, while the other are down-regulated. A functional analysis reveals that up- and down-regulated proteins tend to be segregated into distinct sub-cellular compartments and play different biological roles, consistent with a global rewiring underwent by the cell to cope with the lack of CK2.
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Affiliation(s)
- Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, Padova, Italy
| | - Stefano Scalco
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, Padova, Italy
| | | | - Arianna Donella-Deana
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,CNR Institute of Neurosciences, Via U. Bassi 58/B, Padova, Italy
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