1
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Chang X, Zhu Y, Chen Y, Li L. DeepNphos: A deep-learning architecture for prediction of N-phosphorylation sites. Comput Biol Med 2024; 170:108079. [PMID: 38295472 DOI: 10.1016/j.compbiomed.2024.108079] [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: 08/17/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
Abstract
MOTIVATION Phosphorylation, a prevalent post-translational modification, plays a crucial role in regulating cellular activities. This process encompasses O-phosphorylation (e.g., phosphoserine) and N-phosphorylation (e.g., phospho-lysine (pK), phospho-arginine (pR), and phospho-histidine (pH)). While significant research has focused on O-phosphorylation, resulting in the development of various algorithms for predicting O-phosphorylation sites with commendable performance, there has been a notable absence of models designed to predict N-phosphorylation sites. This study introduces an integrated model named DeepNphos, designed to predict N-phosphorylation sites. This model is developed based on the analysis of thousands of experimentally identified pK, pR and pH sites. RESULTS Observing that the Convolutional Neural Network (CNN) model, incorporating the One-Hot encoding feature, demonstrates favorable performance in comparison to other models when predicting pK, pR, and pH sites. Additionally, pK exhibits similarities to other lysine modification types, and integrating the CNN model with a deep-transfer learning (DTL) strategy based on tens of thousands of known lysine modification sites could enhance pK prediction performance. In contrast, pR exhibits little similarity to other arginine modification types, and the integration of DTL has minimal impact on pR prediction performance. Furthermore, the decision was made to refrain from incorporating the DTL strategy in predicting pH sites, given the scarcity of histidine modification sites beyond those associated with pH. The final classifiers for predicting pK, pR, and pH sites achieve AUC values of 0.856, 0.805 and 0.802 for ten-fold cross-validation, respectively. Overall, DeepNphos is the first classifier for predicting N-phosphorylation sites, accessible at https://github.com/ChangXulinmessi/DeepNPhos.
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Affiliation(s)
- Xulin Chang
- College of Computer Science and Technology, Qingdao University, Qingdao, 266071, China
| | - Yafei Zhu
- College of Computer Science and Technology, Qingdao University, Qingdao, 266071, China
| | - Yu Chen
- College of Computer Science and Technology, Qingdao University, Qingdao, 266071, China
| | - Lei Li
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266000, China.
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2
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Smolen KA, Papke CM, Swingle MR, Musiyenko A, Li C, Salter EA, Camp AD, Honkanen RE, Kettenbach AN. Quantitative proteomics and phosphoproteomics of PP2A-PPP2R5D variants reveal deregulation of RPS6 phosphorylation via converging signaling cascades. J Biol Chem 2023; 299:105154. [PMID: 37572851 PMCID: PMC10485637 DOI: 10.1016/j.jbc.2023.105154] [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: 01/11/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/14/2023] Open
Abstract
Genetic germline variants of PPP2R5D (encoding: phosphoprotein phosphatase 2 regulatory protein 5D) result in PPP2R5D-related disorder (Jordan's Syndrome), which is characterized by intellectual disability, hypotonia, seizures, macrocephaly, autism spectrum disorder, and delayed motor skill development. The disorder originates from de novo single nucleotide mutations, generating missense variants that act in a dominant manner. Pathogenic mutations altering 13 different amino acids have been identified, with the E198K variant accounting for ∼40% of reported cases. However, the generation of a heterozygous E198K variant cell line to study the molecular effects of the pathogenic mutation has been challenging. Here, we use CRISPR-PRIME genomic editing to introduce a transition (c.592G>A) in a single PPP2R5D allele in HEK293 cells, generating E198K-heterozygous lines to complement existing E420K variant lines. We generate global protein and phosphorylation profiles of WT, E198K, and E420K cell lines and find unique and shared changes between variants and WT cells in kinase- and phosphatase-controlled signaling cascades. We observed ribosomal protein S6 (RPS6) hyperphosphorylation as a shared signaling alteration, indicative of increased ribosomal protein S6-kinase activity. Treatment with rapamycin or an RPS6-kinase inhibitor (LY2584702) suppressed RPS6 phosphorylation in both, suggesting upstream activation of mTORC1/p70S6K. Intriguingly, our data suggests ERK-dependent activation of mTORC1 in both E198K and E420K variant cells, with additional AKT-mediated mTORC1 activation in the E420K variant. Thus, although upstream activation of mTORC1 differs between PPP2R5D-related disorder genotypes, inhibition of mTORC1 or RPS6 kinases warrants further investigation as potential therapeutic strategies for patients.
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Affiliation(s)
- Kali A Smolen
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Cinta M Papke
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Chenchen Li
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - E Alan Salter
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Ashley D Camp
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA.
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA.
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3
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KA S, CM P, Swingle MR, A M, C L, AD C, RE H, AN K. Quantitative proteomics and phosphoproteomics of PPP2R5D variants reveal deregulation of RPS6 phosphorylation through converging signaling cascades. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534397. [PMID: 37034727 PMCID: PMC10081281 DOI: 10.1101/2023.03.27.534397] [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: 06/19/2023]
Abstract
Variants in the phosphoprotein phosphatase-2 regulatory protein-5D gene ( PPP2R5D ) cause the clinical phenotype of Jordan's Syndrome (PPP2R5D-related disorder), which includes intellectual disability, hypotonia, seizures, macrocephaly, autism spectrum disorder and delayed motor skill development. The disorder originates from de novo single nucleotide mutations, generating missense variants that act in a dominant manner. Pathogenic mutations altering 13 different amino acids have been identified, with the E198K variant accounting for ∼40% of reported cases. Here, we use CRISPR-PRIME genomic editing to introduce a transition (c.592G>A) in the PPP2R5D allele in a heterozygous manner in HEK293 cells, generating E198K-heterozygous lines to complement existing E420K variant lines. We generate global protein and phosphorylation profiles of wild-type, E198K, and E420K cell lines and find unique and shared changes between variants and wild-type cells in kinase- and phosphatase-controlled signaling cascades. As shared signaling alterations, we observed ribosomal protein S6 (RPS6) hyperphosphorylation, indicative of increased ribosomal protein S6-kinase activity. Rapamycin treatment suppressed RPS6 phosphorylation in both, suggesting activation of mTORC1. Intriguingly, our data suggest AKT-dependent (E420K) and -independent (E198K) activation of mTORC1. Thus, although upstream activation of mTORC1 differs between PPP2R5D-related disorder genotypes, treatment with rapamycin or a p70S6K inhibitor warrants further investigation as potential therapeutic strategies for patients.
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Affiliation(s)
- Smolen KA
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Papke CM
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - MR Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Musiyenko A
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Li C
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Camp AD
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Honkanen RE
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Kettenbach AN
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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4
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Abstract
Cyclin A promotes Cdk activity in a cell cycle-dependent manner to facilitate specific cell cycle events and transitions with an established role for DNA replication in S phase. Recent evidence demonstrates that cyclin A also activates Cdk during early mitosis to promote faithful chromosome segregation by regulating the stability of kinetochore-microtubule (k-MT) attachments. Here we describe a methodology to identify protein substrates of cyclin A/Cdk during mitosis in human cells. The method combines selective cell cycle synchrony in mitosis with stable isotope labeling of amino acids in cell culture (SILAC) coupled to mass spectrometry. This strategy identified a catalogue of potential cyclin A/Cdk substrates in mitosis, as well as unveiled potential intersections between signaling regulated by Aurora, Polo-like, and Cdk mitotic kinases.
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Affiliation(s)
- Ana Maria G Dumitru
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Hanover, NH, USA
- Norris Cotton Cancer Center, Lebanon, NH, USA
- Department of Surgery, University of California San Diego, San Diego, CA, USA
| | - Duane A Compton
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Hanover, NH, USA.
- Norris Cotton Cancer Center, Lebanon, NH, USA.
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5
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Smith TG, Uzozie AC, Chen S, Lange PF. Robust unsupervised deconvolution of linear motifs characterizes 68 protein modifications at proteome scale. Sci Rep 2021; 11:22490. [PMID: 34795380 PMCID: PMC8602328 DOI: 10.1038/s41598-021-01971-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022] Open
Abstract
The local sequence context is the most fundamental feature determining the post-translational modification (PTM) of proteins. Recent technological improvements allow for the detection of new and less prevalent modifications. We found that established state-of-the-art algorithms for the detection of PTM motifs in complex datasets failed to keep up with this technological development and are no longer robust. To overcome this limitation, we developed RoLiM, a new linear motif deconvolution algorithm and webserver, that enables robust and unbiased identification of local amino acid sequence determinants in complex biological systems demonstrated here by the analysis of 68 modifications found across 30 tissues in the human draft proteome map. Furthermore, RoLiM analysis of a large-scale phosphorylation dataset comprising 30 kinase inhibitors of 10 protein kinases in the EGF signalling pathway identified prospective substrate motifs for PI3K and EGFR.
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Affiliation(s)
- Theodore G Smith
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Siyuan Chen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada. .,Department of Computer Science, University of British Columbia, Vancouver, BC, Canada. .,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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6
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Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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7
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Cheng A, Grant CE, Noble WS, Bailey TL. MoMo: discovery of statistically significant post-translational modification motifs. Bioinformatics 2019; 35:2774-2782. [PMID: 30596994 PMCID: PMC6691336 DOI: 10.1093/bioinformatics/bty1058] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/14/2018] [Accepted: 12/26/2018] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called 'motifs' that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. Accurate statistical confidence estimates for discovered motifs are critically important for proper interpretation and in the design of downstream experimental validation. RESULTS We describe a method for assigning statistical confidence estimates to PTM motifs, and we demonstrate that this method provides accurate P-values on both simulated and real data. Our methods are implemented in MoMo, a software tool for discovering motifs among sets of PTMs that we make available as a web server and as downloadable source code. MoMo re-implements the two most widely used PTM motif discovery algorithms-motif-x and MoDL-while offering many enhancements. Relative to motif-x, MoMo offers improved statistical confidence estimates and more accurate calculation of motif scores. The MoMo web server offers more proteome databases, more input formats, larger inputs and longer running times than the motif-x web server. Finally, our study demonstrates that the confidence estimates produced by motif-x are inaccurate. This inaccuracy stems in part from the common practice of drawing 'background' peptides from an unshuffled proteome database. Our results thus suggest that many of the papers that use motif-x to find motifs may be reporting results that lack statistical support. AVAILABILITY AND IMPLEMENTATION The MoMo web server and source code are provided at http://meme-suite.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alice Cheng
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Charles E Grant
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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8
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Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE. Phosphoproteomics Analysis Identifies Novel Candidate Substrates of the Nonreceptor Tyrosine Kinase, Src- related Kinase Lacking C-terminal Regulatory Tyrosine and N-terminal Myristoylation Sites (SRMS). Mol Cell Proteomics 2018; 17:925-947. [PMID: 29496907 DOI: 10.1074/mcp.ra118.000643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 01/23/2023] Open
Abstract
SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites), also known as PTK 70 (Protein tyrosine kinase 70), is a non-receptor tyrosine kinase that belongs to the BRK family of kinases (BFKs). To date less is known about the cellular role of SRMS primarily because of the unidentified substrates or signaling intermediates regulated by the kinase. In this study, we used phosphotyrosine antibody-based immunoaffinity purification in large-scale label-free quantitative phosphoproteomics to identify novel candidate substrates of SRMS. Our analyses led to the identification of 1258 tyrosine-phosphorylated peptides which mapped to 663 phosphoproteins, exclusively from SRMS-expressing cells. DOK1, a previously characterized SRMS substrate, was also identified in our analyses. Functional enrichment analyses revealed that the candidate SRMS substrates were enriched in various biological processes including protein ubiquitination, mitotic cell cycle, energy metabolism and RNA processing, as well as Wnt and TNF signaling. Analyses of the sequence surrounding the phospho-sites in these proteins revealed novel candidate SRMS consensus substrate motifs. We utilized customized high-throughput peptide arrays to validate a subset of the candidate SRMS substrates identified in our MS-based analyses. Finally, we independently validated Vimentin and Sam68, as bona fide SRMS substrates through in vitro and in vivo assays. Overall, our study identified a number of novel and biologically relevant SRMS candidate substrates, which suggests the involvement of the kinase in a vast array of unexplored cellular functions.
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Affiliation(s)
- Raghuveera Kumar Goel
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada
| | - Marta Paczkowska
- §Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto M5G 0A3, Ontario, Canada
| | - Jüri Reimand
- §Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto M5G 0A3, Ontario, Canada.,¶Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto M5G 1L7, Ontario, Canada
| | - Scott Napper
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada.,‖Vaccine and Infectious Disease Organization - International Vaccine Centre (VIDO-InterVac), 120 Veterinary Road, University of Saskatchewan, Saskatoon S7N 5E3, Saskatchewan, Canada
| | - Kiven Erique Lukong
- From the ‡Department of Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada;
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9
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Shee K, Yang W, Hinds JW, Hampsch RA, Varn FS, Traphagen NA, Patel K, Cheng C, Jenkins NP, Kettenbach AN, Demidenko E, Owens P, Faber AC, Golub TR, Straussman R, Miller TW. Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer. J Exp Med 2018; 215:895-910. [PMID: 29436393 PMCID: PMC5839765 DOI: 10.1084/jem.20171818] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/29/2017] [Accepted: 01/01/2018] [Indexed: 12/22/2022] Open
Abstract
Tumor microenvironment (TME) cytokine screening revealed FGF2 as a clinically relevant mechanism of resistance to anti-estrogens, mTORC1 inhibition, and PI3K inhibition in ER+ breast cancer. Shee et al. highlight an underdeveloped aspect of precision oncology: treating patients according to their TME constitution. Drug resistance to approved systemic therapies in estrogen receptor–positive (ER+) breast cancer remains common. We hypothesized that factors present in the human tumor microenvironment (TME) drive drug resistance. Screening of a library of recombinant secreted microenvironmental proteins revealed fibroblast growth factor 2 (FGF2) as a potent mediator of resistance to anti-estrogens, mTORC1 inhibition, and phosphatidylinositol 3-kinase inhibition in ER+ breast cancer. Phosphoproteomic analyses identified ERK1/2 as a major output of FGF2 signaling via FGF receptors (FGFRs), with consequent up-regulation of Cyclin D1 and down-regulation of Bim as mediators of drug resistance. FGF2-driven drug resistance in anti-estrogen–sensitive and –resistant models, including patient-derived xenografts, was reverted by neutralizing FGF2 or FGFRs. A transcriptomic signature of FGF2 signaling in primary tumors predicted shorter recurrence-free survival independently of age, grade, stage, and FGFR amplification status. These findings delineate FGF2 signaling as a ligand-based drug resistance mechanism and highlights an underdeveloped aspect of precision oncology: characterizing and treating patients according to their TME constitution.
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Affiliation(s)
- Kevin Shee
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Wei Yang
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - John W Hinds
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Riley A Hampsch
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Frederick S Varn
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Nicole A Traphagen
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Kishan Patel
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Chao Cheng
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Nicole P Jenkins
- Department of Biochemistry and Cell Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Eugene Demidenko
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Philip Owens
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN.,Research Medicine, Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN
| | - Anthony C Faber
- VCU Philips Institute for Oral Health Research, School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Todd W Miller
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH .,Comprehensive Breast Program, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
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10
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Dumitru AMG, Rusin SF, Clark AEM, Kettenbach AN, Compton DA. Cyclin A/Cdk1 modulates Plk1 activity in prometaphase to regulate kinetochore-microtubule attachment stability. eLife 2017; 6:e29303. [PMID: 29154753 PMCID: PMC5706962 DOI: 10.7554/elife.29303] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/10/2017] [Indexed: 12/24/2022] Open
Abstract
The fidelity of chromosome segregation in mitosis is safeguarded by the precise regulation of kinetochore microtubule (k-MT) attachment stability. Previously, we demonstrated that Cyclin A/Cdk1 destabilizes k-MT attachments to promote faithful chromosome segregation. Here, we use quantitative phosphoproteomics to identify 156 Cyclin A/Cdk1 substrates in prometaphase. One Cyclin A/Cdk1 substrate is myosin phosphatase targeting subunit 1 (MYPT1), and we show that MYPT1 localization to kinetochores depends on Cyclin A/Cdk1 activity and that MYPT1 destabilizes k-MT attachments by negatively regulating Plk1 at kinetochores. Thus, Cyclin A/Cdk1 phosphorylation primes MYPT1 for Plk1 binding. Interestingly, priming of PBIP1 by Plk1 itself (self-priming) increased in MYPT1-depleted cells showing that MYPT1 provides a molecular link between the processes of Cdk1-dependent priming and self-priming of Plk1 substrates. These data demonstrate cross-regulation between Cyclin A/Cdk1-dependent and Plk1-dependent phosphorylation of substrates during mitosis to ensure efficient correction of k-MT attachment errors necessary for high mitotic fidelity.
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Affiliation(s)
- Ana Maria G Dumitru
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at DartmouthHanoverUnited States
- Norris Cotton Cancer CenterLebanonUnited States
| | - Scott F Rusin
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at DartmouthHanoverUnited States
- Norris Cotton Cancer CenterLebanonUnited States
| | - Amber E M Clark
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at DartmouthHanoverUnited States
- Norris Cotton Cancer CenterLebanonUnited States
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at DartmouthHanoverUnited States
- Norris Cotton Cancer CenterLebanonUnited States
| | - Duane A Compton
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at DartmouthHanoverUnited States
- Norris Cotton Cancer CenterLebanonUnited States
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11
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He Z, Gu F, Zhao C, Liu X, Wu J, Wang J. Conditional discriminative pattern mining: Concepts and algorithms. Inf Sci (N Y) 2017. [DOI: 10.1016/j.ins.2016.09.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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von Stechow L, Francavilla C, Olsen JV. Recent findings and technological advances in phosphoproteomics for cells and tissues. Expert Rev Proteomics 2016; 12:469-87. [PMID: 26400465 PMCID: PMC4819829 DOI: 10.1586/14789450.2015.1078730] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.
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Affiliation(s)
- Louise von Stechow
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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13
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Posch C, Sanlorenzo M, Vujic I, Oses-Prieto JA, Cholewa BD, Kim ST, Ma J, Lai K, Zekhtser M, Esteve-Puig R, Green G, Chand S, Burlingame AL, Panzer-Grümayer R, Rappersberger K, Ortiz-Urda S. Phosphoproteomic Analyses of NRAS(G12) and NRAS(Q61) Mutant Melanocytes Reveal Increased CK2α Kinase Levels in NRAS(Q61) Mutant Cells. J Invest Dermatol 2016; 136:2041-2048. [PMID: 27251789 DOI: 10.1016/j.jid.2016.05.098] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/21/2016] [Accepted: 05/18/2016] [Indexed: 01/20/2023]
Abstract
In melanoma, mutant and thereby constantly active neuroblastoma rat sarcoma (NRAS) affects 15-20% of tumors, contributing to tumor initiation, growth, invasion, and metastasis. Recent therapeutic approaches aim to mimic RAS extinction by interfering with critical signaling pathways downstream of the mutant protein. This study investigates the phosphoproteome of primary human melanocytes bearing mutations in the two hot spots of NRAS, NRAS(G12) and NRAS(Q61). Stable isotope labeling by amino acids in cell culture followed by mass spectrometry identified 14,155 spectra of 3,371 unique phosphopeptides mapping to 1,159 proteins (false discovery rate < 2%). Data revealed pronounced PI3K/AKT signaling in NRAS(G12V) mutant cells and pronounced mitogen-activated protein kinase (MAPK) signaling in NRAS(Q61L) variants. Computer-based prediction models for kinases involved, revealed that CK2α is significantly overrepresented in primary human melanocytes bearing NRAS(Q61L) mutations. Similar differences were found in human NRAS(Q61) mutant melanoma cell lines that were also more sensitive to pharmacologic CK2α inhibition compared with NRAS(G12) mutant cells. Furthermore, CK2α levels were pronounced in patient samples of NRAS(Q61) mutant melanoma at the mRNA and protein level. The preclinical findings of this study reveal that codon 12 and 61 mutant NRAS cells have distinct signaling characteristics that could allow for the development of more effective, mutation-specific treatment modalities.
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Affiliation(s)
- Christian Posch
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA; Department of Dermatology, The Rudolfstiftung Hospital, Academic Teaching Hospital, Medical University Vienna, Vienna, Austria; Leukemia Biology Group, Children's Cancer Research Institute, Vienna, Austria; School of Medicine, Sigmund Freud University, Vienna, Austria.
| | - Martina Sanlorenzo
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA; Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Igor Vujic
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA; Department of Dermatology, The Rudolfstiftung Hospital, Academic Teaching Hospital, Medical University Vienna, Vienna, Austria; School of Medicine, Sigmund Freud University, Vienna, Austria
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, California, USA
| | - Brian D Cholewa
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sarasa T Kim
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey Ma
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
| | - Kevin Lai
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
| | - Mitchell Zekhtser
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
| | - Rosaura Esteve-Puig
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
| | - Gary Green
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
| | - Shreya Chand
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, California, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, California, USA
| | | | - Klemens Rappersberger
- Department of Dermatology, The Rudolfstiftung Hospital, Academic Teaching Hospital, Medical University Vienna, Vienna, Austria
| | - Susana Ortiz-Urda
- Department of Dermatology, Mt. Zion Cancer Research Center, University of California San Francisco, San Francisco, California, USA
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Petrone A, Adamo ME, Cheng C, Kettenbach AN. Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics. Mol Cell Proteomics 2016; 15:2448-61. [PMID: 27134283 DOI: 10.1074/mcp.m116.059394] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 11/06/2022] Open
Abstract
Cyclin-dependent kinase 1 (Cdk1) is an essential regulator of many mitotic processes including the reorganization of the cytoskeleton, chromosome segregation, and formation and separation of daughter cells. Deregulation of Cdk1 activity results in severe defects in these processes. Although the role of Cdk1 in mitosis is well established, only a limited number of Cdk1 substrates have been identified in mammalian cells. To increase our understanding of Cdk1-dependent phosphorylation pathways in mitosis, we conducted a quantitative phosphoproteomics analysis in mitotic HeLa cells using two small molecule inhibitors of Cdk1, Flavopiridol and RO-3306. In these analyses, we identified a total of 24,840 phosphopeptides on 4,273 proteins, of which 1,215 phosphopeptides on 551 proteins were significantly reduced by 2.5-fold or more upon Cdk1 inhibitor addition. Comparison of phosphopeptide quantification upon either inhibitor treatment revealed a high degree of correlation (R(2) value of 0.87) between the different datasets. Motif enrichment analysis of significantly regulated phosphopeptides revealed enrichment of canonical Cdk1 kinase motifs. Interestingly, the majority of proteins identified in this analysis contained two or more Cdk1 inhibitor-sensitive phosphorylation sites, were highly connected with other candidate Cdk1 substrates, were enriched at specific subcellular structures, or were part of protein complexes as identified by the CORUM database. Furthermore, candidate Cdk1 substrates were enriched in G2 and M phase-specific genes. Finally, we validated a subset of candidate Cdk1 substrates by in vitro kinase assays. Our findings provide a valuable resource for the cell signaling and mitosis research communities and greatly increase our knowledge of Cdk1 substrates and Cdk1-dependent signaling pathways.
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Affiliation(s)
- Adam Petrone
- From the ‡Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - Mark E Adamo
- §Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756
| | - Chao Cheng
- ¶Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - Arminja N Kettenbach
- From the ‡Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755; §Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756;
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15
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Schwaid AG, Su C, Loos P, Wu J, Nguyen C, Stone KL, Kanyo J, Geoghegan KF, Bhattacharya SK, Dow RL, Buckbinder L, Carpino PA. MAP4K4 Is a Threonine Kinase That Phosphorylates FARP1. ACS Chem Biol 2015; 10:2667-71. [PMID: 26422651 DOI: 10.1021/acschembio.5b00679] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mitogen-activated protein kinase 4 (MAP4K4) regulates the MEK kinase cascade and is implicated in cytoskeletal rearrangement and migration; however, identifying MAP4K4 substrates has remained a challenge. To ascertain MAP4K4-dependent phosphorylation events, we combined phosphoproteomic studies of MAP4K4 inhibition with in vitro assessment of its kinase specificity. We identified 235 phosphosites affected by MAP4K4 inhibition in cells and found that pTP and pSP motifs were predominant among them. In contrast, in vitro assessment of kinase specificity showed that MAP4K4 favors a pTL motif. We showed that MAP4K4 directly phosphorylates and coimmunoprecipitates with FERM, RhoGEF, and pleckstrin domain-containing protein 1 (FARP1). MAP4K4 inhibition in SH-SY5Y cells increases neurite outgrowth, a process known to involve FARP1. As FARP1 and MAP4K4 both contribute to cytoskeletal rearrangement, the results suggest that MAP4K4 exerts some of its effects on the cytoskeleton via phosphorylation of FARP1.
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Affiliation(s)
| | | | | | - Jiang Wu
- Structural
Biology and Biophysics, Center for Chemistry Innovation and Excellence, Pfizer Pharmatherapeutics Research and Development, Groton, Connecticut 06340, United States
| | - Chuong Nguyen
- Structural
Biology and Biophysics, Center for Chemistry Innovation and Excellence, Pfizer Pharmatherapeutics Research and Development, Groton, Connecticut 06340, United States
| | - Kathryn L. Stone
- W.M.
Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Jean Kanyo
- W.M.
Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Kieran F. Geoghegan
- Structural
Biology and Biophysics, Center for Chemistry Innovation and Excellence, Pfizer Pharmatherapeutics Research and Development, Groton, Connecticut 06340, United States
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16
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Rusin SF, Schlosser KA, Adamo ME, Kettenbach AN. Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells. Sci Signal 2015; 8:rs12. [PMID: 26462736 DOI: 10.1126/scisignal.aab3138] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is an important regulatory mechanism controlling mitotic progression. Protein phosphatase 6 (PP6) is an essential enzyme with conserved roles in chromosome segregation and spindle assembly from yeast to humans. We applied a baculovirus-mediated gene silencing approach to deplete HeLa cells of the catalytic subunit of PP6 (PP6c) and analyzed changes in the phosphoproteome and proteome in mitotic cells by quantitative mass spectrometry-based proteomics. We identified 408 phosphopeptides on 272 proteins that increased and 298 phosphopeptides on 220 proteins that decreased in phosphorylation upon PP6c depletion in mitotic cells. Motif analysis of the phosphorylated sites combined with bioinformatics pathway analysis revealed previously unknown PP6c-dependent regulatory pathways. Biochemical assays demonstrated that PP6c opposed casein kinase 2-dependent phosphorylation of the condensin I subunit NCAP-G, and cellular analysis showed that depletion of PP6c resulted in defects in chromosome condensation and segregation in anaphase, consistent with dysregulation of condensin I function in the absence of PP6 activity.
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Affiliation(s)
- Scott F Rusin
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Kate A Schlosser
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Mark E Adamo
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Arminja N Kettenbach
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.
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17
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Frades I, Resjö S, Andreasson E. Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis. BMC Bioinformatics 2015. [PMID: 26224486 PMCID: PMC4520095 DOI: 10.1186/s12859-015-0657-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background How protein phosphorylation relates to kingdom/phylum divergence is largely unknown and the amino acid residues surrounding the phosphorylation site have profound importance on protein kinase–substrate interactions. Standard motif analysis is not adequate for large scale comparative analysis because each phophopeptide is assigned to a unique motif and perform poorly with the unbalanced nature of the input datasets. Results First the discriminative n-grams of five species from five different kingdom/phyla were identified. A signature with 5540 discriminative n-grams that could be found in other species from the same kingdoms/phyla was created. Using a test data set, the ability of the signature to classify species in their corresponding kingdom/phylum was confirmed using classification methods. Lastly, ortholog proteins among proteins with n-grams were identified in order to determine to what degree was the identity of the detected n-grams a property of phosphosites rather than a consequence of species-specific or kingdom/phylum-specific protein inventory. The motifs were grouped in clusters of equal physico-chemical nature and their distribution was similar between species in the same kingdom/phylum while clear differences were found among species of different kingdom/phylum. For example, the animal-specific top discriminative n-grams contained many basic amino acids and the plant-specific motifs were mainly acidic. Secondary structure prediction methods show that the discriminative n-grams in the majority of the cases lack from a regular secondary structure as on average they had 88 % of random coil compared to 66 % found in the phosphoproteins they were derived from. Conclusions The discriminative n-grams were able to classify organisms in their corresponding kingdom/phylum, they show different patterns among species of different kingdom/phylum and these regions can contribute to evolutionary divergence as they are in disordered regions that can evolve rapidly. The differences found possibly reflect group-specific differences in the kinomes of the different groups of species. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0657-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Itziar Frades
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.
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18
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McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A. Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Mol Cell Proteomics 2015; 14:2194-212. [PMID: 26055452 DOI: 10.1074/mcp.m114.046938] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/27/2022] Open
Abstract
Entry into mitosis is driven by the coordinated phosphorylation of thousands of proteins. For the cell to complete mitosis and divide into two identical daughter cells it must regulate dephosphorylation of these proteins in a highly ordered, temporal manner. There is currently a lack of a complete understanding of the phosphorylation changes that occur during the initial stages of mitotic exit in human cells. Therefore, we performed a large unbiased, global analysis to map the very first dephosphorylation events that occur as cells exit mitosis. We identified and quantified the modification of >16,000 phosphosites on >3300 unique proteins during early mitotic exit, providing up to eightfold greater resolution than previous studies. The data have been deposited to the ProteomeXchange with identifier PXD001559. Only a small fraction (∼ 10%) of phosphorylation sites were dephosphorylated during early mitotic exit and these occurred on proteins involved in critical early exit events, including organization of the mitotic spindle, the spindle assembly checkpoint, and reformation of the nuclear envelope. Surprisingly this enrichment was observed across all kinase consensus motifs, indicating that it is independent of the upstream phosphorylating kinase. Therefore, dephosphorylation of these sites is likely determined by the specificity of phosphatase/s rather than the activity of kinase/s. Dephosphorylation was significantly affected by the amino acids at and surrounding the phosphorylation site, with several unique evolutionarily conserved amino acids correlating strongly with phosphorylation status. These data provide a potential mechanism for the specificity of phosphatases, and how they co-ordinate the ordered events of mitotic exit. In summary, our results provide a global overview of the phosphorylation changes that occur during the very first stages of mitotic exit, providing novel mechanistic insight into how phosphatase/s specifically regulate this critical transition.
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Affiliation(s)
- Rachael A McCloy
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Benjamin L Parker
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Samuel Rogers
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Rima Chaudhuri
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Velimir Gayevskiy
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Nolan J Hoffman
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Naveid Ali
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - D Neil Watkins
- From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia; ¶St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, Australia; ‖Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Roger J Daly
- **Department of Biochemistry and Molecular Biology, School of Biomedical Sciences Monash University, Clatyon, VIC, 3800, Australia
| | - David E James
- §The Charles Perkins Center, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, NSW 2006, Australia
| | - Thierry Lorca
- ‡‡Equipe Labellisée Ligue Nationale Contre le Cancer, Universités Montpellier 2 et 1, Centre de Recherche de Biochimie Macromoléculaire, CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France
| | - Anna Castro
- ‡‡Equipe Labellisée Ligue Nationale Contre le Cancer, Universités Montpellier 2 et 1, Centre de Recherche de Biochimie Macromoléculaire, CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France
| | - Andrew Burgess
- ¶St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, Australia; From the ‡The Kinghorn Cancer Center, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia;
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19
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Oberstein A, Perlman DH, Shenk T, Terry LJ. Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome. Proteomics 2015; 15:2006-22. [PMID: 25867546 DOI: 10.1002/pmic.201400607] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/12/2015] [Accepted: 04/09/2015] [Indexed: 12/12/2022]
Abstract
Replication of human cytomegalovirus (HCMV) is regulated in part by cellular kinases and the single viral Ser/Thr kinase, pUL97. The virus-coded kinase augments the replication of HCMV by enabling nuclear egress and altering cell cycle progression. These roles are accomplished through direct phosphorylation of nuclear lamins and the retinoblastoma protein, respectively. In an effort to identify additional pUL97 substrates, we analyzed the phosphoproteome of SILAC-labeled human fibroblasts during infection with either wild-type HCMV or a pUL97 kinase-dead mutant virus. Phosphopeptides were enriched over a titanium dioxide matrix and analyzed by high-resolution MS. We identified 157 unambiguous phosphosites from 106 cellular and 17 viral proteins whose phosphorylation required UL97. Analysis of peptides containing these sites allowed the identification of several candidate pUL97 phosphorylation motifs, including a completely novel phosphorylation motif, LxSP. Substrates harboring the LxSP motif were enriched in nucleocytoplasmic transport functions, including a number of components of the nuclear pore complex. These results extend the known functions of pUL97 and suggest that modulation of nuclear pore function may be important during HCMV replication.
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Affiliation(s)
- Adam Oberstein
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David H Perlman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Thomas Shenk
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laura J Terry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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20
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Analysis of the Candida albicans Phosphoproteome. EUKARYOTIC CELL 2015; 14:474-85. [PMID: 25750214 DOI: 10.1128/ec.00011-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/04/2015] [Indexed: 01/19/2023]
Abstract
Candida albicans is an important human fungal pathogen in both immunocompetent and immunocompromised individuals. C. albicans regulation has been studied in many contexts, including morphological transitions, mating competence, biofilm formation, stress resistance, and cell wall synthesis. Analysis of kinase- and phosphatase-deficient mutants has made it clear that protein phosphorylation plays an important role in the regulation of these pathways. In this study, to further our understanding of phosphorylation in C. albicans regulation, we performed a deep analysis of the phosphoproteome in C. albicans. We identified 19,590 unique peptides that corresponded to 15,906 unique phosphosites on 2,896 proteins. The ratios of serine, threonine, and tyrosine phosphosites were 80.01%, 18.11%, and 1.81%, respectively. The majority of proteins (2,111) contained at least two detected phosphorylation sites. Consistent with findings in other fungi, cytoskeletal proteins were among the most highly phosphorylated proteins, and there were differences in Gene Ontology (GO) terms for proteins with serine and threonine versus tyrosine phosphorylation sites. This large-scale analysis identified phosphosites in protein components of Mediator, an important transcriptional coregulatory protein complex. A targeted analysis of the phosphosites in Mediator complex proteins confirmed the large-scale studies, and further in vitro assays identified a subset of these phosphorylations that were catalyzed by Cdk8 (Ssn3), a kinase within the Mediator complex. These data represent the deepest single analysis of a fungal phosphoproteome and lay the groundwork for future analyses of the C. albicans phosphoproteome and specific phosphoproteins.
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21
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Silva-Sanchez C, Li H, Chen S. Recent advances and challenges in plant phosphoproteomics. Proteomics 2015; 15:1127-41. [PMID: 25429768 DOI: 10.1002/pmic.201400410] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/29/2014] [Accepted: 11/24/2014] [Indexed: 12/13/2022]
Abstract
Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
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22
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Liu X, Wu J, Gu F, Wang J, He Z. Discriminative pattern mining and its applications in bioinformatics. Brief Bioinform 2014; 16:884-900. [PMID: 25433466 DOI: 10.1093/bib/bbu042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Indexed: 11/13/2022] Open
Abstract
Discriminative pattern mining is one of the most important techniques in data mining. This challenging task is concerned with finding a set of patterns that occur with disproportionate frequency in data sets with various class labels. Such patterns are of great value for group difference detection and classifier construction. Research on finding interesting discriminative patterns in class-labeled data evolves rapidly and lots of algorithms have been proposed to specifically address this problem. Discriminative pattern mining techniques have proven their considerable value in biological data analysis. The archetypical applications in bioinformatics include phosphorylation motif discovery, differentially expressed gene identification, discriminative genotype pattern detection, etc. In this article, we present an overview of discriminative pattern mining and the corresponding effective methods, and subsequently we illustrate their applications to tackling the bioinformatics problems. In the end, we give a general discussion of potential challenges and future work for this task.
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23
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Liu X, Wu J, Gong H, Deng S, He Z. Mining Conditional Phosphorylation Motifs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:915-927. [PMID: 26356863 DOI: 10.1109/tcbb.2014.2321400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. Several algorithms have been proposed to uncover phosphorylation motifs, whereas the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. Here we present a novel notion called conditional phosphorylation motifs. Through this new concept, the motifs whose over-expressiveness mainly benefits from its constituting parts can be filtered out effectively. To discover conditional phosphorylation motifs, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. C-Motif is implemented under the Apriori framework, and it tests the statistical significance together with the frequency of candidate motifs in a single stage. Experiments demonstrate that C-Motif outperforms some current algorithms such as MMFPh and Motif-All in terms of coverage and non-redundancy of the results and efficiency of the execution. The source code of C-Motif is available at: https://sourceforge. net/projects/cmotif/.
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24
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van Wijk KJ, Friso G, Walther D, Schulze WX. Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs. THE PLANT CELL 2014; 26:2367-2389. [PMID: 24894044 PMCID: PMC4114939 DOI: 10.1105/tpc.114.125815] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 03/27/2014] [Accepted: 05/09/2014] [Indexed: 05/18/2023]
Abstract
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.
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Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Giulia Friso
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, 14476 Golm, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
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25
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He Z, Gong H. Comments on 'MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets'. Bioinformatics 2012; 28:2211-2; author reply 2213. [DOI: 10.1093/bioinformatics/bts346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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