1
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Alderman C, Anderson R, Zhang L, Hughes CJ, Li X, Ebmeier C, Wagley ME, Ahn NG, Ford HL, Zhao R. Biochemical characterization of the Eya and PP2A-B55α interaction. J Biol Chem 2024; 300:107408. [PMID: 38796066 DOI: 10.1016/j.jbc.2024.107408] [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] [Received: 12/15/2023] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
The eyes absent (Eya) proteins were first identified as co-activators of the six homeobox family of transcription factors and are critical in embryonic development. These proteins are also re-expressed in cancers after development is complete, where they drive tumor progression. We have previously shown that the Eya3 N-terminal domain (NTD) contains Ser/Thr phosphatase activity through an interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme and that this interaction increases the half-life of Myc through pT58 dephosphorylation. Here, we showed that Eya3 directly interacted with the NTD of Myc, recruiting PP2A-B55α to Myc. We also showed that Eya3 increased the Ser/Thr phosphatase activity of PP2A-B55α but not PP2A-B56α. Furthermore, we demonstrated that the NTD (∼250 amino acids) of Eya3 was completely disordered, and it used a 38-residue segment to interact with B55α. In addition, knockdown and phosphoproteomic analyses demonstrated that Eya3 and B55α affected highly similar phosphosite motifs with a preference for Ser/Thr followed by Pro, consistent with Eya3's apparent Ser/Thr phosphatase activity being mediated through its interaction with PP2A-B55α. Intriguingly, mutating this Pro to other amino acids in a Myc peptide dramatically increased dephosphorylation by PP2A. Not surprisingly, MycP59A, a naturally occurring mutation hotspot in several cancers, enhanced Eya3-PP2A-B55α-mediated dephosphorylation of pT58 on Myc, leading to increased Myc stability and cell proliferation, underscoring the critical role of this phosphosite in regulating Myc stability.
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Affiliation(s)
- Christopher Alderman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ryan Anderson
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Connor J Hughes
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chris Ebmeier
- Department of Biochemistry, University of Colorado-Boulder, Boulder, Colorado, USA
| | - Marisa E Wagley
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado-Boulder, Boulder, Colorado, USA
| | - Heide L Ford
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
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2
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Papaioannou G, Sato T, Houghton C, Kotsalidis PE, Strauss KE, Dean T, Nelson AJ, Stokes M, Gardella TJ, Wein MN. Regulation of intracellular cAMP levels in osteocytes by mechano-sensitive focal adhesion kinase via PDE8A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601153. [PMID: 38979143 PMCID: PMC11230356 DOI: 10.1101/2024.06.28.601153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Osteocytes are the primary mechano-sensitive cell type in bone. Mechanical loading is sensed across the dendritic projections of osteocytes leading to transient reductions in focal adhesion kinase (FAK) activity. Knowledge regarding the signaling pathways downstream of FAK in osteocytes is incomplete. We performed tyrosine-focused phospho-proteomic profiling in osteocyte-like Ocy454 cells to identify FAK substrates. Gsα, parathyroid hormone receptor (PTH1R), and phosphodiesterase 8A (PDE8A), all proteins associated with cAMP signaling, were found as potential FAK targets based on their reduced tyrosine phosphorylation in both FAK- deficient or FAK inhibitor treated cells. Real time monitoring of intracellular cAMP levels revealed that FAK pharmacologic inhibition or gene deletion increased basal and GPCR ligand-stimulated cAMP levels and downstream phosphorylation of protein kinase A substrates. Mutating FAK phospho-acceptor sites in Gsα and PTH1R had no effect on PTH- or FAK inhibitor-stimulated cAMP levels. Since FAK inhibitor treatment augmented cAMP levels even in the presence of forskolin, we focused on potential FAK substrates downstream of cAMP generation. Indeed, PDE8A inhibition mimicked FAK inhibition at the level of increased cAMP, PKA activity, and expression of cAMP-regulated target genes. In vitro kinase assay showed that PDE8A is directly phosphorylated by FAK while immunoprecipitation assays revealed intracellular association between FAK and PDE8A. Thus, FAK inhibition in osteocytes acts synergistically with signals that activate adenylate cyclase to increase intracellular cAMP. Mechanically-regulated FAK can modulate intracellular cAMP levels via effects on PDE8A. These data suggest a novel signal transduction mechanism that mediates crosstalk between mechanical and cAMP-linked hormonal signaling in osteocytes.
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He C, Xing X, Chen HY, Gao M, Shi J, Xiang B, Xiao X, Sun Y, Yu H, Xu G, Yao Y, Xie Z, Xing Y, Budiarto BR, Chen SY, Gao Y, Lee YR, Zhang J. UFL1 ablation in T cells suppresses PD-1 UFMylation to enhance anti-tumor immunity. Mol Cell 2024; 84:1120-1138.e8. [PMID: 38377992 DOI: 10.1016/j.molcel.2024.01.024] [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] [Received: 05/30/2023] [Revised: 11/10/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024]
Abstract
UFMylation is an emerging ubiquitin-like post-translational modification that regulates various biological processes. Dysregulation of the UFMylation pathway leads to human diseases, including cancers. However, the physiological role of UFMylation in T cells remains unclear. Here, we report that mice with conditional knockout (cKO) Ufl1, a UFMylation E3 ligase, in T cells exhibit effective tumor control. Single-cell RNA sequencing analysis shows that tumor-infiltrating cytotoxic CD8+ T cells are increased in Ufl1 cKO mice. Mechanistically, UFL1 promotes PD-1 UFMylation to antagonize PD-1 ubiquitination and degradation. Furthermore, AMPK phosphorylates UFL1 at Thr536, disrupting PD-1 UFMylation to trigger its degradation. Of note, UFL1 ablation in T cells reduces PD-1 UFMylation, subsequently destabilizing PD-1 and enhancing CD8+ T cell activation. Thus, Ufl1 cKO mice bearing tumors have a better response to anti-CTLA-4 immunotherapy. Collectively, our findings uncover a crucial role of UFMylation in T cells and highlight UFL1 as a potential target for cancer treatment.
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Affiliation(s)
- Chuan He
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xixin Xing
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Hsin-Yi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Minling Gao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jie Shi
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Bolin Xiang
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangling Xiao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yishuang Sun
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Haisheng Yu
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Gaoshan Xu
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yingmeng Yao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Zuosong Xie
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yujie Xing
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Bugi Ratno Budiarto
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Yang Gao
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yu-Ru Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan.
| | - Jinfang Zhang
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China.
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4
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Zhang Y, Li N, Li J, Fan M, Zhang Q, Dang F. Bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites for enrichment of phosphopeptides. Mikrochim Acta 2024; 191:211. [PMID: 38502246 DOI: 10.1007/s00604-024-06177-8] [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: 09/27/2023] [Accepted: 12/26/2023] [Indexed: 03/21/2024]
Abstract
A facile and mild method based on self-assembled lysozyme (LYZ) to fabricate bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites (CSSNCs) is reported for the high-efficiency enrichment of phosphopeptides. Under physiological conditions, LYZ rapidly self-assembled into a robust coating on Fe3O4@SiO2 magnetic nanoparticles (MNPs) with abundant surface functional groups, which effectively mediate heterogeneous nucleation and growth of UIO-66 nanocrystals. Well-defined MNPs@UIO-66 CSSNCs with stacked pores, showing high specific surface area (333.65 m2 g- 1) and low mass transfer resistance, were successfully fabricated by fine-tuning of the reaction conditions including reaction time and acetic acid content. Furthermore, the UIO-66 shells were further modified with arginine to obtain bifunctional MNPs@UIO-66-Arg CSSNCs. Thanks to the unique morphology and synergistic effect of Zr-O clusters and guanidine groups, the bifunctional MNPs@UIO-66-Arg CSSNCs exhibited outstanding enrichment performance for phosphopeptides, delivering a low limit of detection (0.1 fmol), high selectivity (β-casein/BSA, mass ratio 1:2000), and good capture capacity (120 mg g- 1). The mechanism for phosphopeptides capture may attribute to the hydrogen bonds, electrostatic interactions, and Zr-O-P bonds between phosphate groups in peptides and guanidyl/Zr-O clusters on bifunctional MNPs@UIO-66-Arg CSSNCs. In addition, the small stacking pores on the core-shell-satellite architecture may selectively capture phosphopeptides with low molecular weight, eliminating interference of other large molecular proteins in complex biological samples.
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Affiliation(s)
- Yuxiu Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Nan Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Biomedical Materials & Engineering (IBME), Xi'an Institute of Flexible Electronics (IFE), Northwestern Polytechnical University (NPU), Xi'an, 710072, China.
| | - Jianru Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Miao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Qiqi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China
| | - Fuquan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Street, Xi'an, 710119, China.
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5
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Ranjbarvaziri S, Zeng A, Wu I, Greer-Short A, Farshidfar F, Budan A, Xu E, Shenwai R, Kozubov M, Li C, Van Pell M, Grafton F, MacKay CE, Song X, Priest JR, Argast G, Mandegar MA, Hoey T, Yang J. Targeting HDAC6 to treat heart failure with preserved ejection fraction in mice. Nat Commun 2024; 15:1352. [PMID: 38409164 PMCID: PMC10897156 DOI: 10.1038/s41467-024-45440-7] [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] [Received: 05/29/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) poses therapeutic challenges due to the limited treatment options. Building upon our previous research that demonstrates the efficacy of histone deacetylase 6 (HDAC6) inhibition in a genetic cardiomyopathy model, we investigate HDAC6's role in HFpEF due to their shared mechanisms of inflammation and metabolism. Here, we show that inhibiting HDAC6 with TYA-018 effectively reverses established heart failure and its associated symptoms in male HFpEF mouse models. Additionally, in male mice lacking Hdac6 gene, HFpEF progression is delayed and they are resistant to TYA-018's effects. The efficacy of TYA-018 is comparable to a sodium-glucose cotransporter 2 (SGLT2) inhibitor, and the combination shows enhanced effects. Mechanistically, TYA-018 restores gene expression related to hypertrophy, fibrosis, and mitochondrial energy production in HFpEF heart tissues. Furthermore, TYA-018 also inhibits activation of human cardiac fibroblasts and enhances mitochondrial respiratory capacity in cardiomyocytes. In this work, our findings show that HDAC6 impacts on heart pathophysiology and is a promising target for HFpEF treatment.
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Affiliation(s)
| | - Aliya Zeng
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Iris Wu
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | | | - Ana Budan
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Emma Xu
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Reva Shenwai
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | - Cindy Li
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | | | | | - Xiaomei Song
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | | | | | - Timothy Hoey
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Jin Yang
- Tenaya Therapeutics, South San Francisco, CA, USA.
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6
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Koide E, Mohardt ML, Doctor ZM, Yang A, Hao M, Donovan KA, Kuismi CC, Nelson AJ, Abell K, Aguiar M, Che J, Stokes MP, Zhang T, Aguirre AJ, Fischer ES, Gray NS, Jiang B, Nabet B. Development and Characterization of Selective FAK Inhibitors and PROTACs with In Vivo Activity. Chembiochem 2023; 24:e202300141. [PMID: 37088717 PMCID: PMC10590827 DOI: 10.1002/cbic.202300141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Focal adhesion kinase (FAK) is an attractive drug target due to its overexpression in cancer. FAK functions as a non-receptor tyrosine kinase and scaffolding protein, coordinating several downstream signaling effectors and cellular processes. While drug discovery efforts have largely focused on targeting FAK kinase activity, FAK inhibitors have failed to show efficacy as single agents in clinical trials. Here, using structure-guided design, we report the development of a selective FAK inhibitor (BSJ-04-175) and degrader (BSJ-04-146) to evaluate the consequences and advantages of abolishing all FAK activity in cancer models. BSJ-04-146 achieves rapid and potent FAK degradation with high proteome-wide specificity in cancer cells and induces durable degradation in mice. Compared to kinase inhibition, targeted degradation of FAK exhibits pronounced improved activity on downstream signaling and cancer cell viability and migration. Together, BSJ-04-175 and BSJ-04-146 are valuable chemical tools to dissect the specific consequences of targeting FAK through small-molecule inhibition or degradation.
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Affiliation(s)
- Eriko Koide
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L. Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zainab M. Doctor
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Annan Yang
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Andrew J. Aguirre
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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7
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. J Proteome Res 2023; 22:1868-1880. [PMID: 37097255 PMCID: PMC10510590 DOI: 10.1021/acs.jproteome.2c00850] [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: 04/26/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding the fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY can handle up to 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic, and tyrosine-specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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8
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Zhang J, Simpson CM, Berner J, Chong HB, Fang J, Ordulu Z, Weiss-Sadan T, Possemato AP, Harry S, Takahashi M, Yang TY, Richter M, Patel H, Smith AE, Carlin AD, Hubertus de Groot AF, Wolf K, Shi L, Wei TY, Dürr BR, Chen NJ, Vornbäumen T, Wichmann NO, Mahamdeh MS, Pooladanda V, Matoba Y, Kumar S, Kim E, Bouberhan S, Oliva E, Rueda BR, Soberman RJ, Bardeesy N, Liau BB, Lawrence M, Stokes MP, Beausoleil SA, Bar-Peled L. Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. Cell 2023; 186:2361-2379.e25. [PMID: 37192619 PMCID: PMC10225361 DOI: 10.1016/j.cell.2023.04.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
Multiple anticancer drugs have been proposed to cause cell death, in part, by increasing the steady-state levels of cellular reactive oxygen species (ROS). However, for most of these drugs, exactly how the resultant ROS function and are sensed is poorly understood. It remains unclear which proteins the ROS modify and their roles in drug sensitivity/resistance. To answer these questions, we examined 11 anticancer drugs with an integrated proteogenomic approach identifying not only many unique targets but also shared ones-including ribosomal components, suggesting common mechanisms by which drugs regulate translation. We focus on CHK1 that we find is a nuclear H2O2 sensor that launches a cellular program to dampen ROS. CHK1 phosphorylates the mitochondrial DNA-binding protein SSBP1 to prevent its mitochondrial localization, which in turn decreases nuclear H2O2. Our results reveal a druggable nucleus-to-mitochondria ROS-sensing pathway-required to resolve nuclear H2O2 accumulation and mediate resistance to platinum-based agents in ovarian cancers.
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Affiliation(s)
- Junbing Zhang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | | | - Jacqueline Berner
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison B Chong
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Jiafeng Fang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Zehra Ordulu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Tommy Weiss-Sadan
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Stefan Harry
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Mariko Takahashi
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Tzu-Yi Yang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Marianne Richter
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Himani Patel
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Abby E Smith
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander D Carlin
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Konstantin Wolf
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Lei Shi
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Ting-Yu Wei
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt R Dürr
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas J Chen
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Tristan Vornbäumen
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Nina O Wichmann
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Mohammed S Mahamdeh
- Division of Cardiology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Venkatesh Pooladanda
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA; Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Yusuke Matoba
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA; Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Shaan Kumar
- Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Eugene Kim
- Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Sara Bouberhan
- Division of Hematology/Oncology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Bo R Rueda
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA; Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Roy J Soberman
- Division of Nephrology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nabeel Bardeesy
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Michael Lawrence
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | - Liron Bar-Peled
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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9
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Liu X, Rossio V, Gygi SP, Paulo JA. Enriching Cysteine-Containing Peptides Using a Sulfhydryl-Reactive Alkylating Reagent with a Phosphonic Acid Group and Immobilized Metal Affinity Chromatography. J Proteome Res 2023; 22:1270-1279. [PMID: 36971515 PMCID: PMC10311885 DOI: 10.1021/acs.jproteome.2c00806] [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: 03/29/2023]
Abstract
The reduction of disulfide bonds and their subsequent alkylation are commonplace in typical proteomics workflows. Here, we highlight a sulfhydryl-reactive alkylating reagent with a phosphonic acid group (iodoacetamido-LC-phosphonic acid, 6C-CysPAT) that facilitates the enrichment of cysteine-containing peptides for isobaric tag-based proteome abundance profiling. Specifically, we profile the proteome of the SH-SY5Y human cell line following 24 h treatments with two proteasome inhibitors (bortezomib and MG-132) in a tandem mass tag (TMT)pro9-plex experiment. We acquire three datasets─(1) Cys-peptide enriched, (2) the unbound complement, and (3) the non-depleted control─and compare the peptides and proteins quantified in each dataset, with emphasis on Cys-containing peptides. The data show that enrichment using 6C-Cys phosphonate adaptable tag (6C-CysPAT) can quantify over 38,000 Cys-containing peptides in 5 h with >90% specificity. In addition, our combined dataset provides the research community with a resource of over 9900 protein abundance profiles exhibiting the effects of two different proteasome inhibitors. Overall, the seamless incorporation of alkylation by 6C-CysPAT into a current TMT-based workflow permits the enrichment of a Cys-containing peptide subproteome. The acquisition of this "mini-Cys" dataset can be used to preview and assess the quality of a deep, fractionated dataset.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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10
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Zhang J, Simpson CM, Berner J, Chong HB, Fang J, Sahin ZO, Weiss-Sadan T, Possemato AP, Harry S, Takahashi M, Yang TY, Richter M, Patel H, Smith AE, Carlin AD, Hubertus de Groot AF, Wolf K, Shi L, Wei TY, Dürr BR, Chen NJ, Vornbäumen T, Wichmann NO, Pooladanda V, Matoba Y, Kumar S, Kim E, Bouberhan S, Olivia E, Rueda B, Bardeesy N, Liau B, Lawrence M, Stokes MP, Beausoleil SA, Bar-Peled L. Identification of chemotherapy targets reveals a nucleus-to-mitochondria ROS sensing pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532189. [PMID: 36945474 PMCID: PMC10028958 DOI: 10.1101/2023.03.11.532189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Multiple chemotherapies are proposed to cause cell death in part by increasing the steady-state levels of cellular reactive oxygen species (ROS). However, for most of these drugs exactly how the resultant ROS function and are sensed is poorly understood. In particular, it's unclear which proteins the ROS modify and their roles in chemotherapy sensitivity/resistance. To answer these questions, we examined 11 chemotherapies with an integrated proteogenomic approach identifying many unique targets for these drugs but also shared ones including ribosomal components, suggesting one mechanism by which chemotherapies regulate translation. We focus on CHK1 which we find is a nuclear H 2 O 2 sensor that promotes an anti-ROS cellular program. CHK1 acts by phosphorylating the mitochondrial-DNA binding protein SSBP1, preventing its mitochondrial localization, which in turn decreases nuclear H 2 O 2 . Our results reveal a druggable nucleus-to-mitochondria ROS sensing pathway required to resolve nuclear H 2 O 2 accumulation, which mediates resistance to platinum-based chemotherapies in ovarian cancers.
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11
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Umfress A, Chakraborti A, Priya Sudarsana Devi S, Adams R, Epstein D, Massicano A, Sorace A, Singh S, Iqbal Hossian M, Andrabi SA, Crossman DK, Kumar N, Shahid Mukhtar M, Luo H, Simpson C, Abell K, Stokes M, Wiederhold T, Rosen C, Lu H, Natarajan A, Bibb JA. Cdk5 mediates rotational force-induced brain injury. Sci Rep 2023; 13:3394. [PMID: 36854738 PMCID: PMC9974974 DOI: 10.1038/s41598-023-29322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/02/2023] [Indexed: 03/02/2023] Open
Abstract
Millions of traumatic brain injuries (TBIs) occur annually. TBIs commonly result from falls, traffic accidents, and sports-related injuries, all of which involve rotational acceleration/deceleration of the brain. During these injuries, the brain endures a multitude of primary insults including compression of brain tissue, damaged vasculature, and diffuse axonal injury. All of these deleterious effects can contribute to secondary brain ischemia, cellular death, and neuroinflammation that progress for weeks, months, and lifetime after injury. While the linear effects of head trauma have been extensively modeled, less is known about how rotational injuries mediate neuronal damage following injury. Here, we developed a new model of repetitive rotational head trauma in rodents and demonstrated acute and prolonged pathological, behavioral, and electrophysiological effects of rotational TBI (rTBI). We identify aberrant Cyclin-dependent kinase 5 (Cdk5) activity as a principal mediator of rTBI. We utilized Cdk5-enriched phosphoproteomics to uncover potential downstream mediators of rTBI and show pharmacological inhibition of Cdk5 reduces the cognitive and pathological consequences of injury. These studies contribute meaningfully to our understanding of the mechanisms of rTBI and how they may be effectively treated.
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Affiliation(s)
- Alan Umfress
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ayanabha Chakraborti
- Department of Translational Neuroscience, University of Arizona College of Medicine in Phoeni, Biomedical Sciences Partnership Bldg, Phoenix, AZ, 85004 , USA
| | | | - Raegan Adams
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel Epstein
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adriana Massicano
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases University of Nebraska Medical Center, Omaha, NE, USA
| | - M Iqbal Hossian
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shaida A Andrabi
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Shahid Mukhtar
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | | | - Charles Rosen
- OSF Healthcare Illinois Neurological Institute, Peoria, IL, USA
| | - Hongbing Lu
- Department of Mechanical Engineering, University of Texas at Dallas, Dallas, TX, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases University of Nebraska Medical Center, Omaha, NE, USA
| | - James A Bibb
- Department of Translational Neuroscience, University of Arizona College of Medicine in Phoeni, Biomedical Sciences Partnership Bldg, Phoenix, AZ, 85004 , USA.
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12
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522335. [PMID: 36711935 PMCID: PMC9881991 DOI: 10.1101/2023.01.05.522335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY handles 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic and tyrosine specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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13
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Wu W, Tang R, Li Z, Shen Y, Ma S, Ou J. Fabrication of hydrophilic titanium (IV)-immobilized polydispersed microspheres via inverse suspension polymerization for enrichment of phosphopeptides in milk. Food Chem 2022; 395:133608. [DOI: 10.1016/j.foodchem.2022.133608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/29/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
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14
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Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Nat Commun 2022; 13:5948. [PMID: 36216816 PMCID: PMC9550814 DOI: 10.1038/s41467-022-33570-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
The steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different subcellular niches upon perturbation of the subcellular environment. Differential localisation, that is a change in the steady-state subcellular location of a protein, provides a step towards mechanistic insight of subcellular protein dynamics. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we describe a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to several datasets recovers well-studied translocations. In an application to cytomegalovirus infection, we obtain insights into the rewiring of the host proteome. Integration of other high-throughput datasets allows us to provide the functional context of these data.
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15
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Liu X, Rossio V, Thakurta SG, Flora A, Foster L, Bomgarden RD, Gygi SP, Paulo JA. Fe 3+-NTA magnetic beads as an alternative to spin column-based phosphopeptide enrichment. J Proteomics 2022; 260:104561. [PMID: 35331916 DOI: 10.1016/j.jprot.2022.104561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/05/2022] [Accepted: 03/12/2022] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a central mechanism of cellular signal transduction in living organisms. Phosphoproteomic studies systematically catalogue and characterize alterations in phosphorylation states across multiple cellular conditions and are often incorporated into global proteomics experiments. Previously, we found that spin column-based Fe3+-NTA enrichment integrated well with our workflow but remained a bottleneck for methods that require higher throughput or a scale that is beyond the capacity of these columns. Here, we compare our well-established spin column-based enrichment strategy with one encompassing magnetic beads. Our data show little difference when using either method in terms of the number of identified phosphopeptides as well as their physicochemical properties. In all, we illustrate how the potentially scalable and automation-friendly magnetic Fe3+-NTA beads can seamlessly substitute spin column-based Fe3+-NTA agarose beads for global phosphoproteome profiling. SIGNIFICANCE: Protein phosphorylation plays a key role in regulating a multitude of biological processes and can lead to insights into disease pathogenesis. Methodologies which can efficiently enrich phosphopeptides in a scalable and high-throughput manner are essential for profiling dynamic phosphoproteomes. Here we compare two phosphopeptide enrichment workflows, a well-established spin column-based strategy with agarose Fe3+-NTA beads and a strategy using magnetic Fe3+-NTA beads. Our data suggest that the scalable and automation-friendly magnetic bead-based workflow is an equivalent, but more flexible, enrichment strategy for phosphoproteome profiling experiments.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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16
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Chang M, Huhn S, Nelson L, Betenbaugh M, Du Z. Significant impact of mTORC1 and ATF4 pathways in CHO cell recombinant protein production induced by CDK4/6 inhibitor. Biotechnol Bioeng 2022; 119:1189-1206. [PMID: 35112712 DOI: 10.1002/bit.28050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/03/2022] [Accepted: 01/24/2022] [Indexed: 11/11/2022]
Abstract
The CDK4/6 inhibitor has been shown to increase recombinant protein productivity in Chinese hamster ovary cells (CHO). Therefore, we investigated the mechanism that couples cell cycle inhibitor (CCI) treatment with protein productivity utilizing proteomics and phosphoproteomics. We identified mTORC1 as a critical early signaling event that preceded boosted productivity. Following CCI treatment, mTOR exhibited a transient increase in phosphorylation at a novel site that is also conserved in human and mouse. Upstream of mTORC1, increased phosphorylation of AKT1S1 and decreased phosphorylation of RB1 may provide molecular links between CDK4/6 inhibition and mTORC1. Downstream, increased EIF4EBP phosphorylation was observed, which can mediate cap-dependent translation. In addition, the collective effect of increased phosphorylation of RPS6, increased phosphorylation of regulators of RNA polymerase I, and increased protein expression in tRNA-aminoacylation pathway may contribute to enhancing the translational apparatus for increased productivity. In concert, an elevated stress response via GCN2/EIF2AK4-ATF4 axis persisted over the treatment course, which may link mTOR to downstream responses including the unfolded protein response (UPR) and autophagy to enhance proper protein folding and secretion. Together, this comprehensive proteomics and phosphoproteomics characterization of CCI treated CHO cells offers insights into understanding multiple aspects of signaling events resulting from CDK4/CDK6 inhibition. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Meiping Chang
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Steven Huhn
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Luke Nelson
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Zhimei Du
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
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17
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Khbouz B, Rowart P, Poma L, Dahlke E, Bottner M, Stokes M, Bolen G, Rahmouni S, Theilig F, Jouret F. The genetic deletion of the Dual Specificity Phosphatase 3 (DUSP3) attenuates kidney damage and inflammation following ischaemia/reperfusion injury in mouse. Acta Physiol (Oxf) 2022; 234:e13735. [PMID: 34704357 DOI: 10.1111/apha.13735] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
AIM Dual Specificity Phosphatase 3 (DUSP3) regulates the innate immune response, with a putative role in angiogenesis. Modulating inflammation and perfusion contributes to renal conditioning against ischaemia/reperfusion (I/R). We postulate that the functional loss of DUSP3 is associated with kidney resistance to I/R. METHODS Ten C57BL/6 male WT and Dusp3-/- mice underwent right nephrectomy and left renal I/R (30 min/48 hours). Renal injury was assessed based on serum levels of urea (BUN) and Jablonski score. The expression of CD31 and VEGF vascular markers was quantified by RT-qPCR and immuno-staining. Renal resistivity index (RRI) was measured in vivo by Doppler ultrasound. Comparative phosphoproteomics was conducted using IMAC enrichment of phosphopeptides. Inflammatory markers were quantified at both mRNA and protein levels in ischaemic vs non-ischaemic kidneys in WT vs Dusp3-/- . RESULTS At baseline, we located DUSP3 in renal glomeruli and endothelial cells. CD31-positive vascular network was significantly larger in Dusp3-/- kidneys compared to WT, with a lower RRI in Dusp3-/- mice. Following I/R, BUN and Jablonski score were significantly lower in Dusp3-/- vs WT mice. Phosphoproteomics highlighted a down-regulation of inflammatory pathways and up-regulation of phospho-sites involved in cell metabolism and VEGF-related angiogenesis in Dusp3-/- vs WT ischaemic kidneys. Dusp3-/- ischaemic kidneys showed decreased mRNA levels of CD11b, TNF-α, KIM-1, IL-6, IL-1β and caspase-3 compared to controls. The numbers of PCNA-, F4-80- and CD11b-positive cells were reduced in Dusp3-/- vs WT kidneys post-I/R. CONCLUSION Genetic inactivation of Dusp3 is associated with kidney conditioning against I/R, possibly due to attenuated inflammation and improved perfusion.
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Affiliation(s)
- Badr Khbouz
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
| | - Pascal Rowart
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
- Department of Pharmacology and Chemical Biology School of Medicine University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Laurence Poma
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
| | - Eileen Dahlke
- Institute of Anatomy Christian Albrechts‐University Kiel Germany
| | - Martina Bottner
- Institute of Anatomy Christian Albrechts‐University Kiel Germany
| | - Matthew Stokes
- Cell Signaling Technology, Inc. Danvers Massachusetts USA
| | - Géraldine Bolen
- Department of Clinical Sciences Fundamental and Applied Research for Animals & Health (FARAH) Veterinary Faculty University of Liège (ULiège) Liège Belgium
| | - Souad Rahmouni
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Medical Genomics University of Liège (ULiège) Liège Belgium
| | - Franziska Theilig
- Institute of Anatomy Christian Albrechts‐University Kiel Germany
- Institute of Anatomy Department of Medicine University of Fribourg Fribourg Switzerland
| | - François Jouret
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
- Division of Nephrology CHU of Liège University of Liège (CHU ULiège) Liège Belgium
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18
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. CELL REPORTS METHODS 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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19
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Irfan A, Feng W, Liu K, Habib K, Qu Q, Yang L. TiO 2-modified fibrous core-shell mesoporous material to selectively enrich endogenous phosphopeptides with proteins exclusion prior to CE-MS analysis. Talanta 2021; 235:122737. [PMID: 34517605 DOI: 10.1016/j.talanta.2021.122737] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 02/01/2023]
Abstract
As an important post-translational modification of proteins, phosphorylation plays a key role in regulating a variety of complicated biological reactions. Owing to the fact that phosphopeptides are low abundant and the ionization efficiency could be suppressed in mass spectroscopic detection, highly efficient and selective enrichment methods are essential to identify protein phosphorylation by mass spectrometry. Here, we develop novel titanium oxide coated core shell mesoporous silica (CSMS@TiO2) nanocomposites for enrichment of phosphopeptides with simultaneous exclusion of massive proteins. The CSMS@TiO2 nanocomposites have essential features, including uniform 1.0 μm diameter, 120 nm thick shell, 7.0 nm mesopores perpendicular to the surface, large surface area of 77 m2/g and pore volume of 0.15 cm3/g, therefore can greatly improve the sensitivity for identifying phosphopeptides by capillary electrophoresis-mass spectrometry. The proposed CSMS@TiO2 nanocomposites are applied for analysis of β-casein tryptic digest and bovine serum albumin (BSA) protein mixture, respectively. The results show that the number of phosphopeptides detected is tremendously increased by using CSMS@TiO2 nanocomposite, proving selectively enriching phosphopeptides due to the size-exclusive and specific interaction of the TiO2-modified mesopores. The enrichment of the phosphopeptides is achieved even for the digests at very low concentration of β-casein (1 fmol/μL). This research would open up a promising idea to utilize mesoporous materials in peptidomics analysis.
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Affiliation(s)
- Azhar Irfan
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Wenxia Feng
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Kexin Liu
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Khan Habib
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Qishu Qu
- Key Laboratory of Functional Molecule Design and Interface Process, School of Materials and Chemical Engineering, Anhui Jianzhu University, Hefei, Anhui Province, 230601, China.
| | - Li Yang
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China.
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20
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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21
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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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Chen X, Sun Y, Zhang T, Shu L, Roepstorff P, Yang F. Quantitative Proteomics Using Isobaric Labeling: A Practical Guide. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:689-706. [PMID: 35007772 PMCID: PMC9170757 DOI: 10.1016/j.gpb.2021.08.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/19/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023]
Abstract
In the past decade, relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples. Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions, its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results. Here, we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method. We also discuss which precautions should be taken at each step of the isobaric labeling workflow, to obtain reliable quantification results in large-scale quantitative proteomics experiments. In the last section, we discuss the broad applications of the isobaric labeling technology in biological and clinical studies, with an emphasis on thermal proteome profiling and proteogenomics.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Lian Shu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
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23
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Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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24
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Ampudia-Mesias E, Puerta-Martinez F, Bridges M, Zellmer D, Janeiro A, Strokes M, Sham YY, Taher A, Castro MG, Moertel CL, Pluhar GE, Olin MR. CD200 Immune-Checkpoint Peptide Elicits an Anti-glioma Response Through the DAP10 Signaling Pathway. Neurotherapeutics 2021; 18:1980-1994. [PMID: 33829411 PMCID: PMC8609078 DOI: 10.1007/s13311-021-01038-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 02/08/2023] Open
Abstract
Numerous therapies aimed at driving an effective anti-glioma response have been employed over the last decade; nevertheless, survival outcomes for patients remain dismal. This may be due to the expression of immune-checkpoint ligands such as PD-L1 by glioblastoma (GBM) cells which interact with their respective receptors on tumor-infiltrating effector T cells curtailing the activation of anti-GBM CD8+ T cell-mediated responses. Therefore, a combinatorial regimen to abolish immunosuppression would provide a powerful therapeutic approach against GBM. We developed a peptide ligand (CD200AR-L) that binds an uncharacterized CD200 immune-checkpoint activation receptor (CD200AR). We sought to test the hypothesis that CD200AR-L/CD200AR binding signals via he DAP10&12 pathways through in vitro studies by analyzing transcription, protein, and phosphorylation, and in vivo loss of function studies using inhibitors to select signaling molecules. We report that CD200AR-L/CD200AR binding induces an initial activation of the DAP10&12 pathways followed by a decrease in activity within 30 min, followed by reactivation via a positive feedback loop. Further in vivo studies using DAP10&12KO mice revealed that DAP10, but not DAP12, is required for tumor control. When we combined CD200AR-L with an immune-stimulatory gene therapy, in an intracranial GBM model in vivo, we observed increased median survival, and long-term survivors. These studies are the first to characterize the signaling pathway used by the CD200AR, demonstrating a novel strategy for modulating immune checkpoints for immunotherapy currently being analyzed in a phase I adult trial.
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Affiliation(s)
| | - Francisco Puerta-Martinez
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Miurel Bridges
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David Zellmer
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew Janeiro
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matt Strokes
- Cell Signaling Technology, Inc, Danvers, MA, 09123, USA
| | - Yuk Y Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ayman Taher
- Department of Neurosurgery and Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Maria G Castro
- Department of Neurosurgery and Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christopher L Moertel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - G Elizabeth Pluhar
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael R Olin
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
- University of Minnesota, 2-167 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.
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25
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Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics 2021; 21:e2000140. [PMID: 33455035 DOI: 10.1002/pmic.202000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.
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Affiliation(s)
- Joao A Paulo
- Harvard Medical School, Boston, Massachusetts, USA
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26
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Babur Ö, Melrose AR, Cunliffe JM, Klimek J, Pang J, Sepp ALI, Zilberman-Rudenko J, Tassi Yunga S, Zheng T, Parra-Izquierdo I, Minnier J, McCarty OJT, Demir E, Reddy AP, Wilmarth PA, David LL, Aslan JE. Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. Blood 2020; 136:2346-2358. [PMID: 32640021 PMCID: PMC7702475 DOI: 10.1182/blood.2020005496] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Platelets engage cues of pending vascular injury through coordinated adhesion, secretion, and aggregation responses. These rapid, progressive changes in platelet form and function are orchestrated downstream of specific receptors on the platelet surface and through intracellular signaling mechanisms that remain systematically undefined. This study brings together cell physiological and phosphoproteomics methods to profile signaling mechanisms downstream of the immunotyrosine activation motif (ITAM) platelet collagen receptor GPVI. Peptide tandem mass tag (TMT) labeling, sample multiplexing, synchronous precursor selection (SPS), and triple stage tandem mass spectrometry (MS3) detected >3000 significant (false discovery rate < 0.05) phosphorylation events on >1300 proteins over conditions initiating and progressing GPVI-mediated platelet activation. With literature-guided causal inference tools, >300 site-specific signaling relations were mapped from phosphoproteomics data among key and emerging GPVI effectors (ie, FcRγ, Syk, PLCγ2, PKCδ, DAPP1). Through signaling validation studies and functional screening, other less-characterized targets were also considered within the context of GPVI/ITAM pathways, including Ras/MAPK axis proteins (ie, KSR1, SOS1, STAT1, Hsp27). Highly regulated GPVI/ITAM targets out of context of curated knowledge were also illuminated, including a system of >40 Rab GTPases and associated regulatory proteins, where GPVI-mediated Rab7 S72 phosphorylation and endolysosomal maturation were blocked by TAK1 inhibition. In addition to serving as a model for generating and testing hypotheses from omics datasets, this study puts forth a means to identify hemostatic effectors, biomarkers, and therapeutic targets relevant to thrombosis, vascular inflammation, and other platelet-associated disease states.
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Affiliation(s)
- Özgün Babur
- Department of Molecular and Medical Genetics
- Computational Biology Program
| | | | | | | | | | | | | | | | | | | | | | | | - Emek Demir
- Department of Molecular and Medical Genetics
- Computational Biology Program
| | | | | | - Larry L David
- Proteomics Shared Resource
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR
| | - Joseph E Aslan
- Knight Cardiovascular Institute
- Department of Biomedical Engineering
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR
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27
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Sharma V, Sood R, Khlaifia A, Eslamizade MJ, Hung TY, Lou D, Asgarihafshejani A, Lalzar M, Kiniry SJ, Stokes MP, Cohen N, Nelson AJ, Abell K, Possemato AP, Gal-Ben-Ari S, Truong VT, Wang P, Yiannakas A, Saffarzadeh F, Cuello AC, Nader K, Kaufman RJ, Costa-Mattioli M, Baranov PV, Quintana A, Sanz E, Khoutorsky A, Lacaille JC, Rosenblum K, Sonenberg N. eIF2α controls memory consolidation via excitatory and somatostatin neurons. Nature 2020; 586:412-416. [PMID: 33029011 PMCID: PMC7874887 DOI: 10.1038/s41586-020-2805-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/06/2020] [Indexed: 12/19/2022]
Abstract
An important tenet of learning and memory is the notion of a molecular switch that promotes the formation of long-term memory1-4. The regulation of proteostasis is a critical and rate-limiting step in the consolidation of new memories5-10. One of the most effective and prevalent ways to enhance memory is by regulating the synthesis of proteins controlled by the translation initiation factor eIF211. Phosphorylation of the α-subunit of eIF2 (p-eIF2α), the central component of the integrated stress response (ISR), impairs long-term memory formation in rodents and birds11-13. By contrast, inhibiting the ISR by mutating the eIF2α phosphorylation site, genetically11 and pharmacologically inhibiting the ISR kinases14-17, or mimicking reduced p-eIF2α with the ISR inhibitor ISRIB11, enhances long-term memory in health and disease18. Here we used molecular genetics to dissect the neuronal circuits by which the ISR gates cognitive processing. We found that learning reduces eIF2α phosphorylation in hippocampal excitatory neurons and a subset of hippocampal inhibitory neurons (those that express somatostatin, but not parvalbumin). Moreover, ablation of p-eIF2α in either excitatory or somatostatin-expressing (but not parvalbumin-expressing) inhibitory neurons increased general mRNA translation, bolstered synaptic plasticity and enhanced long-term memory. Thus, eIF2α-dependent mRNA translation controls memory consolidation via autonomous mechanisms in excitatory and somatostatin-expressing inhibitory neurons.
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Affiliation(s)
- Vijendra Sharma
- Department of Biochemistry, McGill University, Montréal, Québec, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.
| | - Rapita Sood
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | | | - Mohammad Javad Eslamizade
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
- Department of Neurosciences, University of Montréal, Montréal, Québec, Canada
| | - Tzu-Yu Hung
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Danning Lou
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | | | - Maya Lalzar
- Bioinformatics Services Unit, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Matthew P Stokes
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923, USA
| | - Noah Cohen
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Alissa J Nelson
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923, USA
| | - Kathryn Abell
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923, USA
| | | | | | - Vinh T Truong
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Peng Wang
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Adonis Yiannakas
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Fatemeh Saffarzadeh
- Department of Neurosciences, University of Montréal, Montréal, Québec, Canada
| | - A Claudio Cuello
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Karim Nader
- Department of Psychology, McGill University, Montréal, Québec, Canada
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - Albert Quintana
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Neuroscience Institute, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elisenda Sanz
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Neuroscience Institute, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Arkady Khoutorsky
- Department of Anesthesia, McGill University, Montréal, Québec, Canada
- Faculty of Dentistry, McGill University, Montréal, Québec, Canada
| | - Jean-Claude Lacaille
- Department of Neurosciences, University of Montréal, Montréal, Québec, Canada
- Centre for Interdisciplinary Research on Brain and Learning, University of Montréal, Montréal, Québec, Canada
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel.
- Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel.
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.
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28
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Cramer R. High-speed Analysis of Large Sample Sets - How Can This Key Aspect of the Omics Be Achieved? Mol Cell Proteomics 2020; 19:1760-1766. [PMID: 32796012 DOI: 10.1074/mcp.p120.001997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/29/2020] [Indexed: 01/25/2023] Open
Abstract
High-speed analysis of large (prote)omics sample sets at the rate of thousands or millions of samples per day on a single platform has been a challenge since the beginning of proteomics. For many years, ESI-based MS methods have dominated proteomics because of their high sensitivity and great depth in analyzing complex proteomes. However, despite improvements in speed, ESI-based MS methods are fundamentally limited by their sample introduction, which excludes off-line sample preparation/fractionation because of the time required to switch between individual samples/sample fractions, and therefore being dependent on the speed of on-line sample preparation methods such as liquid chromatography. Laser-based ionization methods have the advantage of moving from one sample to the next without these limitations, being mainly restricted by the speed of modern sample stages, i.e. 10 ms or less between samples. This speed matches the data acquisition speed of modern high-performing mass spectrometers whereas the pulse repetition rate of the lasers (>1 kHz) provides a sufficient number of desorption/ionization events for successful ion signal detection from each sample at the above speed of the sample stages. Other advantages of laser-based ionization methods include the generally higher tolerance to sample additives and contamination compared with ESI MS, and the contact-less and pulsed nature of the laser used for desorption, reducing the risk of cross-contamination. Furthermore, new developments in MALDI have expanded its analytical capabilities, now being able to fully exploit high-performing hybrid mass analyzers and their strengths in sensitivity and MS/MS analysis by generating an ESI-like stable yield of multiply charged analyte ions. Thus, these new developments and the intrinsically high speed of laser-based methods now provide a good basis for tackling extreme sample analysis speed in the omics.
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Affiliation(s)
- Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK.
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29
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Pérez-Mejías G, Velázquez-Cruz A, Guerra-Castellano A, Baños-Jaime B, Díaz-Quintana A, González-Arzola K, Ángel De la Rosa M, Díaz-Moreno I. Exploring protein phosphorylation by combining computational approaches and biochemical methods. Comput Struct Biotechnol J 2020; 18:1852-1863. [PMID: 32728408 PMCID: PMC7369424 DOI: 10.1016/j.csbj.2020.06.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications of proteins expand their functional diversity, regulating the response of cells to a variety of stimuli. Among these modifications, phosphorylation is the most ubiquitous and plays a prominent role in cell signaling. The addition of a phosphate often affects the function of a protein by altering its structure and dynamics. However, these alterations are often difficult to study and the functional and structural implications remain unresolved. New approaches are emerging to overcome common obstacles related to the production and manipulation of these samples. Here, we summarize the available methods for phosphoprotein purification and phosphomimetic engineering, highlighting the advantages and disadvantages of each. We propose a general workflow for protein phosphorylation analysis combining computational and biochemical approaches, building on recent advances that enable user-friendly and easy-to-access Molecular Dynamics simulations. We hope this innovative workflow will inform the best experimental approach to explore such post-translational modifications. We have applied this workflow to two different human protein models: the hemeprotein cytochrome c and the RNA binding protein HuR. Our results illustrate the usefulness of Molecular Dynamics as a decision-making tool to design the most appropriate phosphomimetic variant.
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Affiliation(s)
- Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Katiuska González-Arzola
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Miguel Ángel De la Rosa
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
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30
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Urick ME, Bell DW. Proteomic profiling of FBXW7-mutant serous endometrial cancer cells reveals upregulation of PADI2, a potential therapeutic target. Cancer Med 2020; 9:3863-3874. [PMID: 32248654 PMCID: PMC7286459 DOI: 10.1002/cam4.3013] [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: 02/04/2020] [Revised: 02/29/2020] [Accepted: 03/09/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite advancements over the past decade revealing molecular aberrations characteristic of endometrial cancer (EC) subtypes, serous ECs remain difficult to treat and associated with poor outcomes. This is due, in part, to the rarity of these tumors within clinical trials and the inability to directly target the most frequent genomic abnormalities. One of the most commonly somatically mutated genes in serous ECs is the tumor suppressor F-box and WD repeat domain containing 7 (FBXW7). METHODS To identify changes in protein expression associated with FBXW7 mutation, we clustered regularly interspaced short palindromic repeats (CRISPR)-edited ARK4 FBXW7 nonmutant serous EC cells to insert recurrent FBXW7 mutations. We then compared the liquid chromatography tandem mass spectrometry-based proteomic profiles of CRISPR-edited ARK1 and ARK4 serous EC cells to matched parental cells. RESULTS Among distinct total and phosphorylated proteins that were significantly differentially expressed in FBXW7-mutant cell lines compared to matched parental lines, we identified increased PADI2 (peptidyl arginine deiminase 2) expression in all ARK1 and ARK4 CRISPR-edited FBXW7-mutant cell lines. We further confirmed the correlation between FBXW7 mutation and increased PADI2 expression in a third biological background, JHUEM-1 endometrioid EC cells. Finally, we established that PADI2 protein is expressed in primary serous endometrial tumors. CONCLUSION Our findings provide novel insight into proteomic changes associated with FBXW7 mutation in serous ECs and identify PADI2 as a novel potential therapeutic target for these tumors.
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Affiliation(s)
- Mary Ellen Urick
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Daphne W. Bell
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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Chua XY, Mensah T, Aballo T, Mackintosh SG, Edmondson RD, Salomon AR. Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome. Mol Cell Proteomics 2020; 19:730-743. [PMID: 32071147 PMCID: PMC7124467 DOI: 10.1074/mcp.tir119.001865] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.
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Affiliation(s)
- Xien Yu Chua
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Theresa Mensah
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Timothy Aballo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
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Affinity chromatography assisted comprehensive phosphoproteomics analysis of human saliva for lung cancer. Anal Chim Acta 2020; 1111:103-113. [PMID: 32312387 DOI: 10.1016/j.aca.2020.03.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
Abstract
Affinity chromatography is a powerful technology for phosphopeptide enrichment from body fluids. Saliva is a non-invasive body fluid for disease diagnosis, while few studies applied affinity enrichment for saliva phosphoproteome. In this study, we tested two kinds of affinity chromatography materials, Ti4+-IMAC (immobilized metal affinity chromatography) and CaTiO3, for the enrichment of phosphopeptides. Through comparison, Ti4+-IMAC method was demonstrated as the superior one, which was utilized for the comprehensive analysis of salivary phosphoproteome. More than 360 phosphoproteins were specifically extracted and identified from human saliva. Ti4+-IMAC method was further applied to compare the phosphoprotein profiling in the saliva of lung cancer group and normal control group through label-free quantification. Accordingly, 477 and 699 phosphopeptides were enriched, respectively, which corresponded to 339 and 466 proteins. In total, 796 unique phosphopeptides were revealed for 517 saliva phosphoproteins. In particular, 709 phosphorylation sites were identified, among which 26 were up-regulated (>1.5) and 149 were down-regulated (<0.66) in lung cancer. Their corresponding proteins were mainly associated with cancer promotion, system disorder, and organismal injury. Our data collectively demonstrated that salivary phosphopeptides can be comprehensively characterized through Ti4+-IMAC method. These discovered phosphoprotein candidates might be used for lung cancer detection through salivary diagnostics.
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Schweppe DK, Rusin SF, Gygi SP, Paulo JA. Optimized Workflow for Multiplexed Phosphorylation Analysis of TMT-Labeled Peptides Using High-Field Asymmetric Waveform Ion Mobility Spectrometry. J Proteome Res 2019; 19:554-560. [PMID: 31799850 DOI: 10.1021/acs.jproteome.9b00759] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phosphorylation is a post-translational modification with a vital role in cellular signaling. Isobaric labeling-based strategies, such as tandem mass tags (TMT), can measure the relative phosphorylation states of peptides in a multiplexed format. However, the low stoichiometry of protein phosphorylation constrains the depth of phosphopeptide analysis by mass spectrometry. As such, robust and sensitive workflows are required. Here we evaluate and optimize high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS) coupled to Orbitrap Tribrid mass spectrometers for the analysis of TMT-labeled phosphopeptides. We determined that using FAIMS-MS3 with three compensation voltages (CV) in a single method (e.g., CV = -40/-60/-80 V) maximizes phosphopeptide coverage while minimizing inter-CV overlap. Furthermore, consecutive analyses using MSA-CID (multistage activation collision-induced dissociation) and HCD (higher-energy collisional dissociation) fragmentation at the MS2 stage increases the depth of phosphorylation analysis. The methodology and results outlined herein provide a template for tailoring optimized FAIMS-based methods.
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Affiliation(s)
- Devin K Schweppe
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Scott F Rusin
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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A polymer monolith composed of a perovskite and cucurbit[6]uril hybrid for highly selective enrichment of phosphopeptides prior to mass spectrometric analysis. Mikrochim Acta 2019; 187:68. [PMID: 31853651 DOI: 10.1007/s00604-019-4054-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
A hybrid monolith was prepared from perovskite and cucurbit[6]uril [poly(hydroxyethyl methacrylate-pentaerythritol triacrylate) monolith] for the enrichment of phosphopeptides. By coupling with mass spectrometry, three goals were simultaneously realized, viz. (a) selective enrichment of phosphopeptides from non-phosphopeptides, (b) identification of mono- and multi-phosphopeptides, and (c) recognition of tyrosine phosphopeptides. The perovskite introduced into the monolith warrants high selectivity for phosphopeptides even at a high (10,000:1) ratio of non-phosphopeptides to phosphopeptides, and and enables identification of eight mono- and multi-phosphopeptides from standard β-casein tryptic digests. Tyrosine phosphopeptides were specifically detected via the recognition capability of cucurbit[6]uril integrated into the monolith. The method has remarkably specific enrichment capacity for phosphopeptides from samples including human serum, nonfat milk, and human acute myelocytic leukemia cell lysate. Graphical abstractSchematic representation of a monolith integrated with perovskite and cucurbit[6]uril. The monolithic column was coupled with mass spectrometry and applied to the enrichment of phosphopeptides. The method has remarkably specific enrichment capacity for phosphopeptides from complex biological samples.
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Haymond A, Davis JB, Espina V. Proteomics for cancer drug design. Expert Rev Proteomics 2019; 16:647-664. [PMID: 31353977 PMCID: PMC6736641 DOI: 10.1080/14789450.2019.1650025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Introduction: Signal transduction cascades drive cellular proliferation, apoptosis, immune, and survival pathways. Proteins have emerged as actionable drug targets because they are often dysregulated in cancer, due to underlying genetic mutations, or dysregulated signaling pathways. Cancer drug development relies on proteomic technologies to identify potential biomarkers, mechanisms-of-action, and to identify protein binding hot spots. Areas covered: Brief summaries of proteomic technologies for drug discovery include mass spectrometry, reverse phase protein arrays, chemoproteomics, and fragment based screening. Protein-protein interface mapping is presented as a promising method for peptide therapeutic development. The topic of biosimilar therapeutics is presented as an opportunity to apply proteomic technologies to this new class of cancer drug. Expert opinion: Proteomic technologies are indispensable for drug discovery. A suite of technologies including mass spectrometry, reverse phase protein arrays, and protein-protein interaction mapping provide complimentary information for drug development. These assays have matured into well controlled, robust technologies. Recent regulatory approval of biosimilar therapeutics provides another opportunity to decipher the molecular nuances of their unique mechanisms of action. The ability to identify previously hidden protein hot spots is expanding the gamut of potential drug targets. Proteomic profiling permits lead compound evaluation beyond the one drug, one target paradigm.
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Affiliation(s)
- Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Justin B Davis
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
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Yao Y, Wang Y, Wang S, Liu X, Liu Z, Li Y, Fang Z, Mao J, Zheng Y, Ye M. One-Step SH2 Superbinder-Based Approach for Sensitive Analysis of Tyrosine Phosphoproteome. J Proteome Res 2019; 18:1870-1879. [PMID: 30875230 DOI: 10.1021/acs.jproteome.9b00045] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tyrosine phosphorylation plays a major role in regulating cell signaling pathways governing diverse biological functions such as proliferation and differentiation. Systemically mapping phosphotyrosine (pTyr) sites is the key to understanding molecular mechanisms underlining pTyr-dependent signaling. Although mass spectrometry-based technologies have been widely used for pTyr site profiling and quantification, their applications are often hindered by the poor efficiency in current multistep enrichment procedures for inherently low abundance pTyr peptides, especially under physiological conditions. Taking advantage of the sequence-independent high affinity of SH2 superbinder toward pTyr residues, we have developed a simplified one-step pTyr peptide enrichment method that uses immobilized SH2 superbinder for unbiased and robust enrichment of endogenous pTyr peptides from biological samples. By eliminating the prerequisite global phosphopeptide enrichment step in our previously developed two-step method, we minimized sample loss and improved peptide capture efficiency. Applying this method to Jurkat cells at resting state, where the tyrosine phosphorylation level is low, both the number of identified pTyr peptides and sites are increased by three folds compared to the two-step method. Specifically, we were able to identify 511 nonredundant pTyr peptides, corresponding to 403 high confidence pTyr sites, from Jurkat cells with high level technical reproducibility (Pearson's correlation coefficient as high as 0.94). Further applying this method to two human breast cancer cell lines, BT474 and HCC1954, before and after EGF stimulation, we demonstrated that this approach could be a powerful tool for illustrating pTyr-dependent signaling network controlling cellular behaviors such as drug resistance.
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Affiliation(s)
- Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Shujuan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhen Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yanan Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zheng Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yong Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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38
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Zhang H, Chingin K, Li J, Lu H, Huang K, Chen H. Selective Enrichment of Phosphopeptides and Phospholipids from Biological Matrixes on TiO2 Nanowire Arrays for Direct Molecular Characterization by Internal Extractive Electrospray Ionization Mass Spectrometry. Anal Chem 2018; 90:12101-12107. [DOI: 10.1021/acs.analchem.8b03022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hua Zhang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, P. R. China
| | - Jiajia Li
- Department of Obstetrics and Gynecology, First Hospital of Jilin University, Changchun 130021, P. R. China
| | - Haiyan Lu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Keke Huang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Huanwen Chen
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, P. R. China
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Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar F, Vizeacoumar F, Lam TT, Lukong KE. Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Proteome Sci 2018; 16:16. [PMID: 30140170 PMCID: PMC6098843 DOI: 10.1186/s12953-018-0143-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/19/2018] [Indexed: 01/27/2023] Open
Abstract
Background The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolutionarily conserved relative of the Src family kinases (SFKs). Tyrosine kinases are known to regulate a number of cellular processes and pathways via phosphorylating substrate proteins directly and/or by partaking in signaling cross-talks leading to the indirect modulation of various signaling intermediates. In a previous study, we profiled the tyrosine-phosphoproteome of SRMS and identified multiple candidate substrates of the kinase. The broader cellular signaling intermediates of SRMS are unknown. Methods In order to uncover the broader SRMS-regulated phosphoproteome and identify the SRMS-regulated indirect signaling intermediates, we performed label-free global phosphoproteomics analysis on cells expressing wild-type SRMS. Using computational database searching and bioinformatics analyses we characterized the dataset. Results Our analyses identified 60 hyperphosphorylated (phosphoserine/phosphothreonine) proteins mapped from 140 hyperphosphorylated peptides. Bioinfomatics analyses identified a number of significantly enriched biological and cellular processes among which DNA repair pathways were found to be upregulated while apoptotic pathways were found to be downregulated. Analyses of motifs derived from the upregulated phosphosites identified Casein kinase 2 alpha (CK2α) as one of the major potential kinases contributing to the SRMS-dependent indirect regulation of signaling intermediates. Conclusions Overall, our phosphoproteomics analyses identified serine/threonine phosphorylation dynamics as important secondary events of the SRMS-regulated phosphoproteome with implications in the regulation of cellular and biological processes. Electronic supplementary material The online version of this article (10.1186/s12953-018-0143-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raghuveera Kumar Goel
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - Mona Meyer
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Marta Paczkowska
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Jüri Reimand
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada.,3Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7 Canada
| | - Frederick Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Franco Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada.,5Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - TuKiet T Lam
- 6Department of Molecular Biophysics and Biochemistry and MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT USA
| | - Kiven Erique Lukong
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
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Paulo JA, Navarrete-Perea J, Erickson AR, Knott J, Gygi SP. An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1505-1511. [PMID: 29671274 PMCID: PMC6004253 DOI: 10.1007/s13361-018-1946-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
Phosphorylation-mediated signaling pathways have major implications in cellular regulation and disease. However, proteins with roles in these pathways are frequently less abundant and phosphorylation is often sub-stoichiometric. As such, the efficient enrichment, and subsequent recovery of phosphorylated peptides, is vital. Mass spectrometry-based proteomics is a well-established approach for quantifying thousands of phosphorylation events in a single experiment. We designed a peptide internal standard-based assay directed toward sample preparation strategies for mass spectrometry analysis to understand better phosphopeptide recovery from enrichment strategies. We coupled mass-differential tandem mass tag (mTMT) reagents (specifically, TMTzero and TMTsuper-heavy), nine mass spectrometry-amenable phosphopeptides (phos9), and peak area measurements from extracted ion chromatograms to determine phosphopeptide recovery. We showcase this mTMT/phos9 recovery assay by evaluating three phosphopeptide enrichment workflows. Our assay provides data on the recovery of phosphopeptides, which complement other metrics, namely the number of identified phosphopeptides and enrichment specificity. Our mTMT/phos9 assay is applicable to any enrichment protocol in a typical experimental workflow irrespective of sample origin or labeling strategy. Graphical Abstract ᅟ.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
| | - Jose Navarrete-Perea
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Alison R Erickson
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
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Grimes M, Hall B, Foltz L, Levy T, Rikova K, Gaiser J, Cook W, Smirnova E, Wheeler T, Clark NR, Lachmann A, Zhang B, Hornbeck P, Ma'ayan A, Comb M. Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. Sci Signal 2018; 11:eaaq1087. [PMID: 29789295 PMCID: PMC6822907 DOI: 10.1126/scisignal.aaq1087] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein posttranslational modifications (PTMs) have typically been studied independently, yet many proteins are modified by more than one PTM type, and cell signaling pathways somehow integrate this information. We coupled immunoprecipitation using PTM-specific antibodies with tandem mass tag (TMT) mass spectrometry to simultaneously examine phosphorylation, methylation, and acetylation in 45 lung cancer cell lines compared to normal lung tissue and to cell lines treated with anticancer drugs. This simultaneous, large-scale, integrative analysis of these PTMs using a cluster-filtered network (CFN) approach revealed that cell signaling pathways were outlined by clustering patterns in PTMs. We used the t-distributed stochastic neighbor embedding (t-SNE) method to identify PTM clusters and then integrated each with known protein-protein interactions (PPIs) to elucidate functional cell signaling pathways. The CFN identified known and previously unknown cell signaling pathways in lung cancer cells that were not present in normal lung epithelial tissue. In various proteins modified by more than one type of PTM, the incidence of those PTMs exhibited inverse relationships, suggesting that molecular exclusive "OR" gates determine a large number of signal transduction events. We also showed that the acetyltransferase EP300 appears to be a hub in the network of pathways involving different PTMs. In addition, the data shed light on the mechanism of action of geldanamycin, an HSP90 inhibitor. Together, the findings reveal that cell signaling pathways mediated by acetylation, methylation, and phosphorylation regulate the cytoskeleton, membrane traffic, and RNA binding protein-mediated control of gene expression.
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Affiliation(s)
- Mark Grimes
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA.
| | | | - Lauren Foltz
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Tyler Levy
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Jeremiah Gaiser
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - William Cook
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ekaterina Smirnova
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Travis Wheeler
- Division of Biological Sciences, and Department of Computer Science, Department of Mathematical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Neil R Clark
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS (Big Data to Knowledge Library of Integrated Network-based Cellular Signatures) Data Coordination and Integration Center, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS (Big Data to Knowledge Library of Integrated Network-based Cellular Signatures) Data Coordination and Integration Center, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS (Big Data to Knowledge Library of Integrated Network-based Cellular Signatures) Data Coordination and Integration Center, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Michael Comb
- Cell Signaling Technology, Danvers, MA 01923, USA
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Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res 2018; 17:2226-2236. [PMID: 29734811 DOI: 10.1021/acs.jproteome.8b00217] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol. We describe a universally applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step ("mini-phos") with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type Saccharomyces cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.
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Affiliation(s)
- José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Qing Yu
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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Paulo JA, Jedrychowski MP, Chouchani ET, Kazak L, Gygi SP. Multiplexed Isobaric Tag-Based Profiling of Seven Murine Tissues Following In Vivo Nicotine Treatment Using a Minimalistic Proteomics Strategy. Proteomics 2018; 18:e1700326. [PMID: 29660237 PMCID: PMC5992107 DOI: 10.1002/pmic.201700326] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/24/2017] [Indexed: 12/18/2022]
Abstract
Nicotine is a major addictive compound in tobacco and a component of smoking-related products, such as e-cigarettes. Once internalized, nicotine can perturb many cellular pathways and can induce alterations in proteins across different cell types; however, the mechanisms thereof remain undetermined. The authors hypothesize that both tissue-specific and global protein abundance alterations result from nicotine exposure. Presented here is the first proteomic profiling of multiple tissues from mice treated orally with nicotine. Proteins extracted from seven tissues (brain, heart, kidney, liver, lung, pancreas, and spleen) from treated (n = 5) and untreated control (n = 5) mice are assembled into a TMT10-plex experiment. A minimalistic proteomics strategy is employed using TMT reagents efficiently and centrifugation-based reversed-phase columns to streamline sample preparation. Combined, over 11 000 non-redundant proteins from over 138 000 different peptides are quantified in seven TMT10-plex experiments. Between 7 and 126 proteins are significantly altered in tissues from nicotine-exposed mice, 11 which are altered in two or more tissues. Our data showcase the vast extent of nicotine exposure across murine tissue.
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Affiliation(s)
- Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Mark P. Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Edward T. Chouchani
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Lawrence Kazak
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
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Kwon Y, Ju S, Kaushal P, Lee JW, Lee C. Neutralizing the Detrimental Effect of an N-Hydroxysuccinimide Quenching Reagent on Phosphopeptide in Quantitative Proteomics. Anal Chem 2018; 90:3019-3023. [PMID: 29406695 DOI: 10.1021/acs.analchem.7b04678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the most common chemistries used to label primary amines utilizes N-hydroxysuccinimide (NHS), which is also structurally incorporated in various quantitative proteomic reagents such as isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT). In this paper we report detrimental effect of hydroxylamine, a widely used quenching reagent for excess NHS, on phosphopeptides. We found an impairment in the degree of phosphopeptide identification when hydroxylamine-quenched TMT-labeled samples were vacuum-dried and desalted compared to the nondried (just diluted) and desalted ones prior to phosphoenrichment. We have also demonstrated that vacuum-drying in the presence of hydroxylamine promotes β-elimination of phosphate groups from phosphoserine and phosphothreonine while having a minimalistic effect on phosphotyrosine. Additionally, we herein report that this negative impact of hydroxylamine could be minimized by direct desalting after appropriate dilution of quenched samples. We also found a 1.6-fold increase in the number of phosphopeptide identifications after employing our optimized method. The above method was also successfully applied to human tumor tissues to quantify over 15000 phosphopeptides from 3 mg TMT 6-plex labeled-peptides.
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Affiliation(s)
- Yumi Kwon
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Shinyeong Ju
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Prashant Kaushal
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Cheolju Lee
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
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Adam K, Hunter T. Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. J Transl Med 2018; 98:233-247. [PMID: 29058706 PMCID: PMC5815933 DOI: 10.1038/labinvest.2017.118] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation is the most common type of post-translational modification in eukaryotes. The phosphoproteome is defined as the complete set of experimentally detectable phosphorylation sites present in a cell's proteome under various conditions. However, we are still far from identifying all the phosphorylation sites in a cell mainly due to the lack of information about phosphorylation events involving residues other than Ser, Thr and Tyr. Four types of phosphate-protein linkage exist and these generate nine different phosphoresidues-pSer, pThr, pTyr, pHis, pLys, pArg, pAsp, pGlu and pCys. Most of the effort in studying protein phosphorylation has been focused on Ser, Thr and Tyr phosphorylation. The recent development of 1- and 3-pHis monoclonal antibodies promises to increase our understanding of His phosphorylation and the kinases and phosphatases involved. Several His kinases are well defined in prokaryotes, especially those involved in two-component system (TCS) signaling. However, in higher eukaryotes, NM23, a protein originally characterized as a nucleoside diphosphate kinase, is the only characterized protein-histidine kinase. This ubiquitous and conserved His kinase autophosphorylates its active site His, and transfers this phosphate either onto a nucleoside diphosphate or onto a protein His residue. Studies of NM23 protein targets using newly developed anti-pHis antibodies will surely help illuminate the elusive His phosphorylation-based signaling pathways. This review discusses the role that the NM23/NME/NDPK phosphotransferase has, how the addition of the pHis phosphoproteome will expand the phosphoproteome and make His phosphorylation part of the global phosphorylation world. It also summarizes why our understanding of phosphorylation is still largely restricted to the acid stable phosphoproteome, and highlights the study of NM23 histidine kinase as an entrée into the world of histidine phosphorylation.
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Affiliation(s)
- Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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Dehghani A, Gödderz M, Winter D. Tip-Based Fractionation of Batch-Enriched Phosphopeptides Facilitates Easy and Robust Phosphoproteome Analysis. J Proteome Res 2017; 17:46-54. [DOI: 10.1021/acs.jproteome.7b00256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Alireza Dehghani
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
| | - Markus Gödderz
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
| | - Dominic Winter
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
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