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Singh A, Daemen A, Nickles D, Jeon SM, Foreman O, Sudini K, Gnad F, Lajoie S, Gour N, Mitzner W, Chatterjee S, Choi EJ, Ravishankar B, Rappaport A, Patil N, McCleland M, Johnson L, Acquaah-Mensah G, Gabrielson E, Biswal S, Hatzivassiliou G. NRF2 Activation Promotes Aggressive Lung Cancer and Associates with Poor Clinical Outcomes. Clin Cancer Res 2021; 27:877-888. [PMID: 33077574 PMCID: PMC10867786 DOI: 10.1158/1078-0432.ccr-20-1985] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/25/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Stabilization of the transcription factor NRF2 through genomic alterations in KEAP1 and NFE2L2 occurs in a quarter of patients with lung adenocarcinoma and a third of patients with lung squamous cell carcinoma. In lung adenocarcinoma, KEAP1 loss often co-occurs with STK11 loss and KRAS-activating alterations. Despite its prevalence, the impact of NRF2 activation on tumor progression and patient outcomes is not fully defined. EXPERIMENTAL DESIGN We model NRF2 activation, STK11 loss, and KRAS activation in vivo using novel genetically engineered mouse models. Furthermore, we derive a NRF2 activation signature from human non-small cell lung tumors that we use to dissect how these genomic events impact outcomes and immune contexture of participants in the OAK and IMpower131 immunotherapy trials. RESULTS Our in vivo data reveal roles for NRF2 activation in (i) promoting rapid-onset, multifocal intrabronchiolar carcinomas, leading to lethal pulmonary dysfunction, and (ii) decreasing elevated redox stress in KRAS-mutant, STK11-null tumors. In patients with nonsquamous tumors, the NRF2 signature is negatively prognostic independently of STK11 loss. Patients with lung squamous cell carcinoma with low NRF2 signature survive longer when receiving anti-PD-L1 treatment. CONCLUSIONS Our in vivo modeling establishes NRF2 activation as a critical oncogenic driver, cooperating with STK11 loss and KRAS activation to promote aggressive lung adenocarcinoma. In patients, oncogenic events alter the tumor immune contexture, possibly having an impact on treatment responses. Importantly, patients with NRF2-activated nonsquamous or squamous tumors have poor prognosis and show limited response to anti-PD-L1 treatment.
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Affiliation(s)
- Anju Singh
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Anneleen Daemen
- Oncology Bioinformatics, Genentech Inc., South San Francisco, California.
| | - Dorothee Nickles
- Oncology Bioinformatics, Genentech Inc., South San Francisco, California.
| | - Sang-Min Jeon
- Translational Oncology, Genentech Inc., South San Francisco, California
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology, Ajou University, Suwon, Gyeonggi-do, Republic of Korea
| | - Oded Foreman
- Pathology, Genentech Inc., South San Francisco, California
| | - Kuladeep Sudini
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Florian Gnad
- Oncology Bioinformatics, Genentech Inc., South San Francisco, California
| | - Stephane Lajoie
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Naina Gour
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Wayne Mitzner
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Samit Chatterjee
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Eun-Ji Choi
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology, Ajou University, Suwon, Gyeonggi-do, Republic of Korea
| | | | - Amy Rappaport
- Discovery Oncology, Genentech Inc., South San Francisco, California
| | - Namrata Patil
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Mark McCleland
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Leisa Johnson
- Discovery Oncology, Genentech Inc., South San Francisco, California
| | - George Acquaah-Mensah
- Department of Pharmaceutical Sciences, Massachusetts College of Pharmacy and Health Sciences, Worcester, Massachusetts
| | - Edward Gabrielson
- Department of Pathology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Shyam Biswal
- Department of Environmental Health Science and Engineering, Johns Hopkins University School of Public Health, Baltimore, Maryland.
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Simpson CM, Gnad F. Applying graph database technology for analyzing perturbed co-expression networks in cancer. Database (Oxford) 2020; 2020:6029398. [PMID: 33306799 PMCID: PMC7731929 DOI: 10.1093/database/baaa110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/20/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022]
Abstract
Graph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to design in relational databases. In contrast, graph databases store and represent complex interconnected data as nodes, edges and properties, making it fast and intuitive to query and analyze relationships. While graph-based database technologies are on their way from a fringe domain to going mainstream, there are only a few studies reporting their application to biological data. We used the graph database management system Neo4j to store and analyze co-expression networks derived from RNAseq data from The Cancer Genome Atlas. Comparing co-expression in tumors versus healthy tissues in six cancer types revealed significant perturbation tracing back to erroneous or rewired gene regulation. Applying centrality, community detection and pathfinding graph algorithms uncovered the destruction or creation of central nodes, modules and relationships in co-expression networks of tumors. Given the speed, accuracy and straightforwardness of managing these densely connected networks, we conclude that graph databases are ready for entering the arena of biological data.
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Affiliation(s)
- Claire M Simpson
- Department of Bioinformatics and Data Science, Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923, USA
| | - Florian Gnad
- Department of Bioinformatics and Data Science, Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923, USA
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3
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Vartanian S, Lee J, Klijn C, Gnad F, Bagniewska M, Schaefer G, Zhang D, Tan J, Watson SA, Liu L, Chen H, Liang Y, Watanabe C, Cuellar T, Kan D, Hartmaier RJ, Lau T, Costa MR, Martin SE, Merchant M, Haley B, Stokoe D. ERBB3 and IGF1R Signaling Are Required for Nrf2-Dependent Growth in KEAP1-Mutant Lung Cancer. Cancer Res 2019; 79:4828-4839. [PMID: 31416841 DOI: 10.1158/0008-5472.can-18-2086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 11/07/2018] [Accepted: 08/06/2019] [Indexed: 11/16/2022]
Abstract
Mutations in KEAP1 and NFE2L2 (encoding the protein Nrf2) are prevalent in both adeno and squamous subtypes of non-small cell lung cancer, as well as additional tumor indications. The consequence of these mutations is stabilized Nrf2 and chronic induction of a battery of Nrf2 target genes. We show that knockdown of Nrf2 caused modest growth inhibition of cells growing in two-dimension, which was more pronounced in cell lines expressing mutant KEAP1. In contrast, Nrf2 knockdown caused almost complete regression of established KEAP1-mutant tumors in mice, with little effect on wild-type (WT) KEAP1 tumors. The strong dependency on Nrf2 could be recapitulated in certain anchorage-independent growth environments and was not prevented by excess extracellular glutathione. A CRISPR screen was used to investigate the mechanism(s) underlying this dependence. We identified alternative pathways critical for Nrf2-dependent growth in KEAP1-mutant cell lines, including the redox proteins thioredoxin and peroxiredoxin, as well as the growth factor receptors IGF1R and ERBB3. IGF1R inhibition was effective in KEAP1-mutant cells compared with WT, especially under conditions of anchorage-independent growth. These results point to addiction of KEAP1-mutant tumor cells to Nrf2 and suggest that inhibition of Nrf2 or discrete druggable Nrf2 target genes such as IGF1R could be an effective therapeutic strategy for disabling these tumors. SIGNIFICANCE: This study identifies pathways activated by Nrf2 that are important for the proliferation and tumorigenicity of KEAP1-mutant non-small cell lung cancer.
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Affiliation(s)
| | | | | | - Florian Gnad
- Department of Bioinformatics and Computational Biology
| | | | | | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics
| | | | | | - Liling Liu
- Department of Drug Metabolism and Pharmacokinetics
| | - Honglin Chen
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
| | - Yuxin Liang
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
| | | | - Trinna Cuellar
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
| | | | | | - Ted Lau
- Department of Discovery Oncology
| | | | | | | | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
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Abstract
BACKGROUND Perturbed posttranslational modification (PTM) landscapes commonly cause pathological phenotypes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors allowing the identification of spontaneous cancer-driving mutations, while Uniprot and dbSNP manage genetic disease-associated variants in the human population. PhosphoSitePlus (PSP) is the most comprehensive resource for studying experimentally observed PTM sites and the only repository with daily updates on functional annotations for many of these sites. To elucidate altered PTM landscapes on a large scale, we integrated disease-associated mutations from TCGA, Uniprot, and dbSNP with PTM sites from PhosphoSitePlus. We characterized each dataset individually, compared somatic with germline mutations, and analyzed PTM sites intersecting directly with disease variants. To assess the impact of mutations in the flanking regions of phosphosites, we developed DeltaScansite, a pipeline that compares Scansite predictions on wild type versus mutated sequences. Disease mutations are also visualized in PhosphoSitePlus. RESULTS Characterization of somatic variants revealed oncoprotein-like mutation profiles of U2AF1, PGM5, and several other proteins, showing alteration patterns similar to germline mutations. The union of all datasets uncovered previously unknown losses and gains of PTM events in diseases unevenly distributed across different PTM types. Focusing on phosphorylation, our DeltaScansite workflow predicted perturbed signaling networks consistent with calculations by the machine learning method MIMP. CONCLUSIONS We discovered oncoprotein-like profiles in TCGA and mutations that presumably modify protein function by impacting PTM sites directly or by rewiring upstream regulation. The resulting datasets are enriched with functional annotations from PhosphoSitePlus and present a unique resource for potential biomarkers or disease drivers.
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Affiliation(s)
- Claire M Simpson
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA
| | - Peter V Hornbeck
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA.
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Hegde GV, de la Cruz C, Giltnane JM, Crocker L, Venkatanarayan A, Schaefer G, Dunlap D, Hoeck JD, Piskol R, Gnad F, Modrusan Z, de Sauvage FJ, Siebel CW, Jackson EL. NRG1 is a critical regulator of differentiation in TP63-driven squamous cell carcinoma. eLife 2019; 8:46551. [PMID: 31144617 PMCID: PMC6606022 DOI: 10.7554/elife.46551] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Squamous cell carcinomas (SCCs) account for the majority of cancer mortalities. Although TP63 is an established lineage-survival oncogene in SCCs, therapeutic strategies have not been developed to target TP63 or it’s downstream effectors. In this study we demonstrate that TP63 directly regulates NRG1 expression in human SCC cell lines and that NRG1 is a critical component of the TP63 transcriptional program. Notably, we show that squamous tumors are dependent NRG1 signaling in vivo, in both genetically engineered mouse models and human xenograft models, and demonstrate that inhibition of NRG1 induces keratinization and terminal squamous differentiation of tumor cells, blocking proliferation and inhibiting tumor growth. Together, our findings identify a lineage-specific function of NRG1 in SCCs of diverse anatomic origin.
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Affiliation(s)
- Ganapati V Hegde
- Discovery Oncology, Genentech, South San Francisco, United States
| | - Cecile de la Cruz
- Translational Oncology, Genentech, South San Francisco, United States
| | | | - Lisa Crocker
- Translational Oncology, Genentech, South San Francisco, United States
| | | | - Gabriele Schaefer
- Translational Oncology, Genentech, South San Francisco, United States
| | - Debra Dunlap
- Pathology, Genentech, South San Francisco, United States
| | - Joerg D Hoeck
- Molecular Oncology, Genentech, South San Francisco, United States
| | - Robert Piskol
- Bioinformatics, Genentech, South San Francisco, United States
| | - Florian Gnad
- Bioinformatics, Genentech, South San Francisco, United States
| | - Zora Modrusan
- Molecular Biology, Genentech, South San Francisco, United States
| | | | | | - Erica L Jackson
- Discovery Oncology, Genentech, South San Francisco, United States
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6
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Abstract
The concept of personalized medicine is predominantly been pursued through genomic and transcriptomic technologies, leading to the identification of multiple mutations in a large variety of cancers. However, it has proven challenging to distinguish driver and passenger mutations and to deal with tumor heterogeneity and resistant clonal populations. More generally, these heterogeneous mutation patterns do not in themselves predict the tumor phenotype. Analysis of the expressed proteins in a tumor and their modification states reveals if and how these mutations are translated to the functional level. It is already known that proteomic changes including posttranslational modifications are crucial drivers of oncogenesis, but proteomics technology has only recently become comparable in depth and accuracy to RNAseq. These advances also allow the rapid and highly sensitive analysis of formalin-fixed and paraffin-embedded biobank tissues, on both the proteome and phosphoproteome levels. In this perspective, pioneering mass spectrometry-based proteomic studies are highlighted that pave the way toward clinical implementation. It is argued that proteomics and phosphoproteomics could provide the missing link to make omics analysis actionable in the clinic.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Florian Gnad
- Department of Bioinformatics and Computational BiologyCell Signaling Technology Inc01923DanversMAUSA
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
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7
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Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N. iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. G3 (Bethesda) 2019; 9:1-11. [PMID: 30397019 PMCID: PMC6325894 DOI: 10.1534/g3.118.200637] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023]
Abstract
Post-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing their stability, interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, most commonly serine, threonine and tyrosine in metazoans. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that any given phosphorylation site might be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus tropicalis, Danio rerio, and Caenorhabditis elegans.
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Affiliation(s)
- Yanhui Hu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Richelle Sopko
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Verena Chung
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Marianna Foos
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Romain A Studer
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sean D Landry
- Department of Bioinformatics, Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923
| | - Daniel Liu
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Leonard Rabinow
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Florian Gnad
- Department of Bioinformatics, Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115
- Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115
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8
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Hornbeck PV, Kornhauser JM, Latham V, Murray B, Nandhikonda V, Nord A, Skrzypek E, Wheeler T, Zhang B, Gnad F. 15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. Nucleic Acids Res 2019; 47:D433-D441. [PMID: 30445427 PMCID: PMC6324072 DOI: 10.1093/nar/gky1159] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/26/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
For 15 years the mission of PhosphoSitePlus® (PSP, https://www.phosphosite.org) has been to provide comprehensive information and tools for the study of mammalian post-translational modifications (PTMs). The number of unique PTMs in PSP is now more than 450 000 from over 22 000 articles and thousands of MS datasets. The most important areas of growth in PSP are in disease and isoform informatics. Germline mutations associated with inherited diseases and somatic cancer mutations have been added to the database and can now be viewed along with PTMs and associated quantitative information on novel 'lollipop' plots. These plots enable researchers to interactively visualize the overlap between disease variants and PTMs, and to identify mutations that may alter phenotypes by rewiring signaling networks. We are expanding the sequence space to include over 30 000 human and mouse isoforms to enable researchers to explore the important but understudied biology of isoforms. This represents a necessary expansion of sequence space to accommodate the growing precision and depth of coverage enabled by ongoing advances in mass spectrometry. Isoforms are aligned using a new algorithm. Exploring the worlds of PTMs and disease mutations in the entire isoform space will hopefully lead to new biomarkers, therapeutic targets, and insights into isoform biology.
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Affiliation(s)
- Peter V Hornbeck
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Jon M Kornhauser
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Vaughan Latham
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Beth Murray
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Vidhisha Nandhikonda
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Alex Nord
- University of Montana, Missoula, MT, USA
| | - Elżbieta Skrzypek
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | | | - Bin Zhang
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
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Manning G, Lounsbury N, Hartmaier R, Trabucco S, Sokol E, Rinaldi J, Liu J, Gnad F. Abstract B37: Dissecting the playbook of cancer: Genomic analysis of 100,000 human tumors reveals elaborate patterns of activation of the RTK-RAS-MAPK pathway. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-b37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR03) of the Conference Proceedings.
Citation Format: Gerard Manning, Nicholas Lounsbury, Ryan Hartmaier, Sally Trabucco, Ethan Sokol, Jacob Rinaldi, Jinfeng Liu, Florian Gnad. Dissecting the playbook of cancer: Genomic analysis of 100,000 human tumors reveals elaborate patterns of activation of the RTK-RAS-MAPK pathway [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr B37.
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Manning G, Lounsbury N, Hartmaier R, Trabucco S, Sokol E, Rinaldi J, Liu J, Gnad F. Abstract PR03: Dissecting the playbook of cancer: Genomic analysis of 100,000 human tumors reveals elaborate patterns of activation of the RTK-RAS-MAPK pathway. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-pr03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Massive tumor sequencing allows us to progress beyond cataloging driver mutations, to discovery of the intricate patterns of genomic alterations that are required to enable a successful tumor. We used patterns of mutation co-occurrence to map activation of the RAS pathway in over 16,000 lung adenocarcinomas. This revealed a network of 40 highly mutually exclusive mutations in 19 genes, 18 of which are known RAS pathway genes (the RTKs EGFR, ERBB2, MET, ALK, RET, ROS1, KIT, FGFR2; NRAS and KRAS, BRAF and CRAF, MEK1/2, CBL, NF1, SOS1 and RIT1), indicating that each mutation is a strong pathway driver, and is redundant with other pathway mutations. Together, these mutations cover 71% of all lung adenocarcinomas, and include several previously uncharacterized mutations.
Analysis of the remaining tumors uncovers additional patterns of RAS pathway activation. Some have additional mutations in RAS pathway genes that have the opposite pattern—they are co-occurent with each other, either in an additive manner where several mutations are enriched with each other, such as rare RAF and RAS family mutations, or synergistic, where a particular pair of mutations is highly co-occurrent, often in the same gene. These pairs are exclusive of other pathway mutations, suggesting that they are also strong pathway activators.
We also see partially exclusive mutations, including amplifications of several genes and loss of function RAF family mutations that are likely to be weak activators of the RAS pathway in additional tumors. Finally, this approach also identifies recurrent mutations that are independent of other pathway mutations, giving clinical evidence that their function in human tumors is distinct from the common function of other RAS pathway mutations.
We validated these patterns of exclusivity, additivity, and synergy in 80,000 genomic profiles from 400 other tumor types, and identified additional exclusive RAS pathway alterations in several other tissues. Across all cancers, 30% of all tumors had exclusive mutations indicating that they were RAS pathway driven. The individual mutations varied greatly between tissues, suggesting that there exist extensive tissue-specific enhancers and inhibitors of each oncogenic mutation, which may be of great relevance to drug and biomarker development.
This initial foray into the future of massive tumor genomic datasets shows that we can transform genomic data from individual mutations into patterns of pathway activation, and distinguish pathway-driving mutations from other hotspots, providing a better understanding of the oncogenic strategies used by each human tumor. The degree of mutational exclusivity seen can predict the degree of oncogene addiction, and patterns of co-mutation can suggest strategies for combination therapies, as well as allow reverse translation to enable better matching of preclinical and basic research models to oncogenic strategies that are most relevant to human tumors.
This abstract is also being presented as Poster B37.
Citation Format: Gerard Manning, Nicholas Lounsbury, Ryan Hartmaier, Sally Trabucco, Ethan Sokol, Jacob Rinaldi, Jinfeng Liu, Florian Gnad. Dissecting the playbook of cancer: Genomic analysis of 100,000 human tumors reveals elaborate patterns of activation of the RTK-RAS-MAPK pathway [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr PR03.
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Wertz I, Kategaya L, Lello PD, Rouge L, Pastor R, Clark KR, Drummond J, Kleinheinz T, Lin E, Upton JP, Prakash S, Heideker J, McCleland M, Ritorto MS, Alessi DR, Trost M, Bainbridge TW, Kwok MC, Ma TP, Stiffler Z, Brasher B, Tang Y, Jaishanker P, Hearn B, Renslo AR, Arkin MR, Cohen F, Yu K, Peale F, Gnad F, Chang MT, Klijn C, Blackwood E, Martin SE, Forrest WF, Ernst JA, Ndubaku C, Wang X, Beresini MH, Tsui V, Schwerdtfeger C, Blake RA, Murray J, Maurer T. Abstract SY23-03: Development and mechanistic characterization of USP7 deubiquitinase inhibitors. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-sy23-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The ubiquitin system regulates the majority of cellular processes in eukaryotes. Ubiquitin is ligated to substrate proteins as monomers or chains, and the topology of ubiquitin modifications regulates substrate interactions with specific proteins. Thus ubiquitination directs a variety of substrate fates, including proteasomal degradation. Deubiquitinase enzymes cleave ubiquitin from substrates and are implicated in disease; for example ubiquitin-specific protease-7 (USP7) regulates stability of the p53 tumor suppressor and other proteins critical for tumor cell survival. However, developing selective deubiquitinase inhibitors has been challenging and no co-crystal structures have been solved with small-molecule inhibitors. Here, using nuclear magnetic resonance (NMR)-based screening and structure-based design, we describe the development of selective USP7 inhibitors GNE-6640 and GNE-6776. These compounds induce tumor cell death and enhance cytotoxicity with chemotherapeutics and targeted compounds, including PIM kinase inhibitors. Structural studies reveal that GNE-6640 and GNE-6776 noncovalently target USP7 12Å distant from the catalytic cysteine. The compounds attenuate ubiquitin binding and thus inhibit USP7 deubiquitinase activity. GNE-6640 and GNE-6776 interact with acidic residues that mediate H-bond interactions with the ubiquitin Lys-48 side-chain, suggesting that USP7 preferentially interacts with and cleaves ubiquitin moieties having free Lys-48 side-chains. We investigated this idea by engineering di-ubiquitin chains containing differential proximal and distal isotopic labels and measuring USP7 binding via NMR, a study that substantiated our hypothesis. This preferential binding significantly protracted the depolymerization kinetics of Lys-48-linked ubiquitin chains relative to Lys-63-linked chains. In summary, engineering compounds that inhibit USP7 activity by attenuating ubiquitin binding suggests opportunities for developing other deubiquitinase inhibitors and may be a strategy more broadly applicable to inhibiting proteins that require ubiquitin binding for full functional activity.
[LK, PDL, and LR contributed equally to this work.]
Citation Format: Ingrid Wertz, Lorna Kategaya, Paola Di Lello, Lionel Rouge, Richard Pastor, Kevin R. Clark, Jason Drummond, Tracy Kleinheinz, Eva Lin, John-Paul Upton, Sumit Prakash, Johanna Heideker, Mark McCleland, Maria Stella Ritorto, Dario R. Alessi, Matthias Trost, Travis W. Bainbridge, Michael C. Kwok, Taylur P. Ma, Zachary Stiffler, Bradley Brasher, Yinyan Tang, Priya Jaishanker, Brian Hearn, Adam R. Renslo, Michelle R. Arkin, Frederick Cohen, Kebing Yu, Frank Peale, Florian Gnad, Matthew T. Chang, Christiaan Klijn, Elizabeth Blackwood, Scott E. Martin, William F. Forrest, James A. Ernst, Chudi Ndubaku, Xiaojing Wang, Maureen H. Beresini, Vickie Tsui, Carsten Schwerdtfeger, Robert A. Blake, Jeremy Murray, Till Maurer. Development and mechanistic characterization of USP7 deubiquitinase inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr SY23-03.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eva Lin
- 1Genentech, Inc., South San Francisco, CA
| | | | | | | | | | | | | | - Matthias Trost
- 3Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | | | | | | | - Yinyan Tang
- 5University of California San Francisco, San Francisco, CA
| | | | - Brian Hearn
- 5University of California San Francisco, San Francisco, CA
| | - Adam R. Renslo
- 5University of California San Francisco, San Francisco, CA
| | | | | | - Kebing Yu
- 1Genentech, Inc., South San Francisco, CA
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12
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Dogan T, Gnad F, Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP, Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G. Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling pathways to the cell cycle. J Biol Chem 2017; 292:14311-14324. [PMID: 28655764 PMCID: PMC5582827 DOI: 10.1074/jbc.m117.792754] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 11/23/2022] Open
Abstract
The interconnected PI3K and MAPK signaling pathways are commonly perturbed in cancer. Dual inhibition of these pathways by the small-molecule PI3K inhibitor pictilisib (GDC-0941) and the MEK inhibitor cobimetinib (GDC-0973) suppresses cell proliferation and induces cell death better than either single agent in several preclinical models. Using mass spectrometry-based phosphoproteomics, we have identified the RING finger E3 ubiquitin ligase RNF157 as a target at the intersection of PI3K and MAPK signaling. We demonstrate that RNF157 phosphorylation downstream of the PI3K and MAPK pathways influences the ubiquitination and stability of RNF157 during the cell cycle in an anaphase-promoting complex/cyclosome–CDH1-dependent manner. Deletion of these phosphorylation-targeted residues on RNF157 disrupts binding to CDH1 and protects RNF157 from ubiquitination and degradation. Expression of the cyclin-dependent kinase 2 (CDK2), itself a downstream target of PI3K/MAPK signaling, leads to increased phosphorylation of RNF157 on the same residues modulated by PI3K and MAPK signaling. Inhibition of PI3K and MEK in combination or of CDK2 by their respective small-molecule inhibitors reduces RNF157 phosphorylation at these residues and attenuates RNF157 interaction with CDH1 and its subsequent degradation. Knockdown of endogenous RNF157 in melanoma cells leads to late S phase and G2/M arrest and induces apoptosis, the latter further potentiated by concurrent PI3K/MEK inhibition, consistent with a role for RNF157 in the cell cycle. We propose that RNF157 serves as a novel node integrating oncogenic signaling pathways with the cell cycle machinery and promoting optimal cell cycle progression in transformed cells.
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Affiliation(s)
- Taner Dogan
- From the Departments of Translational Oncology
| | | | | | - Lilian Phu
- Microchemistry Proteomics and Lipidomics, and
| | - Amy Young
- From the Departments of Translational Oncology
| | | | - Sophia Doll
- Microchemistry Proteomics and Lipidomics, and
| | | | - Marcia Belvin
- From the Departments of Translational Oncology.,Cancer Immunology, Genentech, Inc., South San Francisco, California 94080 and
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Goldstein LD, Lee J, Gnad F, Klijn C, Schaub A, Reeder J, Daemen A, Bakalarski CE, Holcomb T, Shames DS, Hartmaier RJ, Chmielecki J, Seshagiri S, Gentleman R, Stokoe D. Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers. Cell Rep 2016; 16:2605-2617. [PMID: 27568559 DOI: 10.1016/j.celrep.2016.08.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 06/03/2016] [Accepted: 07/31/2016] [Indexed: 12/21/2022] Open
Abstract
The Nrf2 pathway is frequently activated in human cancers through mutations in Nrf2 or its negative regulator KEAP1. Using a cell-line-derived gene signature for Nrf2 pathway activation, we found that some tumors show high Nrf2 activity in the absence of known mutations in the pathway. An analysis of splice variants in oncogenes revealed that such tumors express abnormal transcript variants from the NFE2L2 gene (encoding Nrf2) that lack exon 2, or exons 2 and 3, and encode Nrf2 protein isoforms missing the KEAP1 interaction domain. The Nrf2 alterations result in the loss of interaction with KEAP1, Nrf2 stabilization, induction of a Nrf2 transcriptional response, and Nrf2 pathway dependence. In all analyzed cases, transcript variants were the result of heterozygous genomic microdeletions. Thus, we identify an alternative mechanism for Nrf2 pathway activation in human tumors and elucidate its functional consequences.
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Affiliation(s)
- Leonard D Goldstein
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA; Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - James Lee
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Christiaan Klijn
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Annalisa Schaub
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Jens Reeder
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Anneleen Daemen
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Corey E Bakalarski
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA; Department of Protein Chemistry, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thomas Holcomb
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | | | | | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Robert Gentleman
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - David Stokoe
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA.
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Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M. Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms. Proteomics 2016; 16:1998-2004. [DOI: 10.1002/pmic.201600119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/09/2016] [Accepted: 06/05/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology; Genentech Inc; South San Francisco CA USA
| | - Sophia Doll
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Kyung Song
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - John Moffat
- Department of Biochemical Pharmacology; Genentech Inc; South San Francisco CA USA
| | - Bonnie Liu
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - David Arnott
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Jeffrey Wallin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Lori S. Friedman
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - Marcia Belvin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
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Seshagiri S, Stawiski E, Goldstein L, Durinck S, Modrusan Z, Gnad F, Nguyen TT, Jaiswal B, De Rienzo A, Richards W, Bueno R. Abstract LB-331: Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive cancer arising from the mesothelial cells of the pleura. About 80% of mesothelioma cases are linked to asbestos exposure, while the remainder may be related to prior chest radiation, genetic predisposition or spontaneous occurrence.
We analyzed transcriptomes (n = 211), whole exomes (n = 99), and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Four distinct molecular subtypes, sarcomatoid (S), epithelioid (E), biphasic-E, and biphasic-S were identified using RNA-seq data. Using exome analysis we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1, and DDX51 to be significantly mutated MPM genes. We identified recurrent mutations in several genes including splice complex factor SF3B1 (∼2% [4/216]) and TRAF7 (∼2% [5/216]). SF3B1 mutant samples showed a distinct splicing profile compared to wild-type tumors. Mutations in TRAF7 occurred primarily in the WD40 domain and except in one case were mutually exclusive with NF2 mutations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. We analyzed the tumors for infiltrating immune cells and found that M2 macrophage to T-cell ratio was predictive of reduced overall survival. Further we found sarcomatoid subtype had a significantly higher level of PD-L1 expression suggesting that this group might be prioritized for checkpoint inhibitor therapy. Integrated analysis of alterations identified changes in Hippo, mTOR, Histone methylation, RNA helicase and p53 signaling pathways in MPMs.
Overall our study significantly expands on the previous genomic studies and provides a comprehensive genomics profile of mesothelioma and identifies several previously unknown alterations and biological pathways that are potential targets for drug discovery and treatment. Incorporating genomic analysis for detection of actionable alterations as part of MPM patient care will help in developing rational individualized therapy.
Citation Format: Somasekar Seshagiri, Eric Stawiski, Leonard Goldstein, Steffen Durinck, Zora Modrusan, Florian Gnad, Thong T. Nguyen, Bijay Jaiswal, Assunta De Rienzo, William Richards, Raphael Bueno. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-331.
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Firestein R, McCleland M, Mesh K, Gnad F. Abstract 406: Enhancer templated RNAs as predictors of therapeutic response to epigenetic therapy. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colon tumors arise in a stepwise fashion from either discrete genetic perturbations or epigenetic dysregulation. To uncover the key epigenetic regulators that drive colon cancer growth, we utilized a CRISPR loss of function screen and identified a number of essential genes, including the Bromodomain and Extraterminal (BET) protein, BRD4. We find BRD4 is critical for colon cancer proliferation and its loss leads to differentiation effects in vivo. JQ1, a BET inhibitor, preferentially reduced growth in a subset of epigenetically dysregulated colon cancers, characterized by the CpG island methylator phenotype (CIMP). Integrated transcriptomic and genomic analyses defined a distinct super-enhancer in CIMP(+) colon cancers that regulates cMYC transcription. We find that the CCAT1 long non-coding RNA (lncRNA) is transcribed from this super-enhancer and is exquisitely sensitive to BET inhibition. Concordantly, cMYC transcription and cell growth were tightly correlated with the presence of CCAT1 RNA in a variety of tumor types. Taken together, we propose CCAT1 as a clinically tractable biomarker for identifying patients likely to benefit from BET inhibitors.
Citation Format: Ron Firestein, Mark McCleland, Kathryn Mesh, Florian Gnad. Enhancer templated RNAs as predictors of therapeutic response to epigenetic therapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 406.
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Affiliation(s)
- Ron Firestein
- 1Hudson Institute of Medical Research, Clayton, Australia
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17
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Zimmerman KM, Lee B, Chung WJ, Gnad F, Lin E, Martin S, Lin K. Abstract LB-115: Mechanisms of acquired resistance to allosteric versus ATP-competitive AKT inhibition. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The PI3K/AKT signaling pathway mediates a variety of cellular processes including metabolism, glucose uptake, angiogenesis, growth, survival and proliferation. Increased activity of this pathway is observed in many cancer types and is associated with tumor invasiveness, survival, and proliferation. Various regulators of this pathway are being investigated as therapeutic targets in oncology, including the AKT kinases. Two distinct classes of AKT inhibitors (AKTi) are being evaluated as therapeutic agents in the clinic: allosteric inhibitors (e.g. MK-2206) and ATP-competitive inhibitors (e.g. Ipatasertib/GDC-0068). In an effort to elucidate pathway alterations in response to these inhibitors and, ultimately, to improve therapeutic outcome, we are currently evaluating mechanisms of acquired resistance to both AKT inhibitor classes. The establishment of clonal cell populations resistant to either MK-2206 or GDC-0068 and subsequent characterization of alterations in these lines revealed various genetic and non-genetic variations associated with AKTi resistance. Here, we will present findings on biological mechanisms that contribute to acquired AKTi resistance in prostate and ovarian cancer cell line models.
Citation Format: Kristin M. Zimmerman, Brian Lee, Wei-Jen Chung, Florian Gnad, Eva Lin, Scott Martin, Kui Lin. Mechanisms of acquired resistance to allosteric versus ATP-competitive AKT inhibition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-115.
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Affiliation(s)
| | - Brian Lee
- Genentech, Inc., South San Francisco, CA
| | | | | | - Eva Lin
- Genentech, Inc., South San Francisco, CA
| | | | - Kui Lin
- Genentech, Inc., South San Francisco, CA
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18
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Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M. Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network. Proteomics 2016; 16:1992-7. [DOI: 10.1002/pmic.201600118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/08/2016] [Accepted: 06/07/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology; Genentech Inc; South San Francisco CA USA
| | - Jeffrey Wallin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Kyle Edgar
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Sophia Doll
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - David Arnott
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Liliane Robillard
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | | | - Ulka Vijapurkar
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - Lori S. Friedman
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Marcia Belvin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
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19
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Anania VG, Yu K, Gnad F, Pferdehirt RR, Li H, Ma TP, Jeon D, Fortelny N, Forrest W, Ashkenazi A, Overall CM, Lill JR. Uncovering a Dual Regulatory Role for Caspases During Endoplasmic Reticulum Stress-induced Cell Death. Mol Cell Proteomics 2016; 15:2293-307. [PMID: 27125827 PMCID: PMC4937505 DOI: 10.1074/mcp.m115.055376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/13/2022] Open
Abstract
Many diseases are associated with endoplasmic reticulum (ER) stress, which results from an accumulation of misfolded proteins. This triggers an adaptive response called the "unfolded protein response" (UPR), and prolonged exposure to ER stress leads to cell death. Caspases are reported to play a critical role in ER stress-induced cell death but the underlying mechanisms by which they exert their effect continue to remain elusive. To understand the role caspases play during ER stress, a systems level approach integrating analysis of the transcriptome, proteome, and proteolytic substrate profile was employed. This quantitative analysis revealed transcriptional profiles for most human genes, provided information on protein abundance for 4476 proteins, and identified 445 caspase substrates. Based on these data sets many caspase substrates were shown to be downregulated at the protein level during ER stress suggesting caspase activity inhibits their cellular function. Additionally, RNA sequencing revealed a role for caspases in regulation of ER stress-induced transcriptional pathways and gene set enrichment analysis showed expression of multiple gene targets of essential transcription factors to be upregulated during ER stress upon inhibition of caspases. Furthermore, these transcription factors were degraded in a caspase-dependent manner during ER stress. These results indicate that caspases play a dual role in regulating the cellular response to ER stress through both post-translational and transcriptional regulatory mechanisms. Moreover, this study provides unique insight into progression of the unfolded protein response into cell death, which may help identify therapeutic strategies to treat ER stress-related diseases.
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Affiliation(s)
| | - Kebing Yu
- From the Departments of ‡Protein Chemistry
| | | | | | | | | | - Diana Jeon
- From the Departments of ‡Protein Chemistry
| | - Nikolaus Fortelny
- ‖Departments of Oral Biological and Medical Sciences, and University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Christopher M Overall
- ‖Departments of Oral Biological and Medical Sciences, and University of British Columbia, Vancouver, British Columbia, Canada
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20
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Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet 2016; 48:407-16. [PMID: 26928227 DOI: 10.1038/ng.3520] [Citation(s) in RCA: 600] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/04/2016] [Indexed: 02/06/2023]
Abstract
We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.
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Affiliation(s)
- Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric W Stawiski
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Leonard D Goldstein
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Steffen Durinck
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Assunta De Rienzo
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Florian Gnad
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Lucian R Chirieac
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniele Sciaranghella
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nhien Dao
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Corinne E Gustafson
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kiara J Munir
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason A Hackney
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Amitabha Chaudhuri
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Ravi Gupta
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Karen Toy
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Connie Ha
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Ying-Jiun Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Na Zhang
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thomas D Wu
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - David J Sugarbaker
- Division of Thoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Frederic J de Sauvage
- Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA
| | - William G Richards
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
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McCleland ML, Mesh K, Lorenzana E, Chopra VS, Segal E, Watanabe C, Haley B, Mayba O, Yaylaoglu M, Gnad F, Firestein R. CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer. J Clin Invest 2016; 126:639-52. [PMID: 26752646 DOI: 10.1172/jci83265] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/18/2015] [Indexed: 01/17/2023] Open
Abstract
Colon tumors arise in a stepwise fashion from either discrete genetic perturbations or epigenetic dysregulation. To uncover the key epigenetic regulators that drive colon cancer growth, we used a CRISPR loss-of-function screen and identified a number of essential genes, including the bromodomain and extraterminal (BET) protein BRD4. We found that BRD4 is critical for colon cancer proliferation, and its knockdown led to differentiation effects in vivo. JQ1, a BET inhibitor, preferentially reduced growth in a subset of epigenetically dysregulated colon cancers characterized by the CpG island methylator phenotype (CIMP). Integrated transcriptomic and genomic analyses defined a distinct superenhancer in CIMP+ colon cancers that regulates cMYC transcription. We found that the long noncoding RNA colon cancer-associated transcript 1 (CCAT1) is transcribed from this superenhancer and is exquisitely sensitive to BET inhibition. Concordantly, cMYC transcription and cell growth were tightly correlated with the presence of CCAT1 RNA in a variety of tumor types. Taken together, we propose that CCAT1 is a clinically tractable biomarker for identifying patients who are likely to benefit from BET inhibitors.
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MESH Headings
- Animals
- Azepines/pharmacology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Proliferation
- Colorectal Neoplasms
- CpG Islands
- DNA Methylation/drug effects
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Female
- Gene Knockdown Techniques
- Humans
- Mice
- Mice, Nude
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Triazoles/pharmacology
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22
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Gnad F, Zhang Z. Abstract B2-43: Bioinformatics analysis of TCGA tumors to identify cancer associated epigenetic regulators. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many cancer cells show distorted epigenetic landscapes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors, allowing the discovery of somatic alterations in the epigenetic machinery and the identification of potential cancer drivers among members of epigenetic protein families. We integrated mutation, expression, and copy number data from thousands of tumors from major cancer types to train a classification model that predicts the likelihood of being an oncogene (OG), tumor suppressor (TSG) or neutral gene (NG). Using classical driver genes to train an OG/TSG predictor, we determined mutation parameters as the most predictive features. We applied this predictor to epigenetic regulator genes (ERGs), and used differential expression and correlation network analysis to identify dysregulated ERGs along with co-expressed cancer genes. Mutation-based classifiers uncovered the TSG-like profiles for several ERGs, but did not detect any OG-like profile. Differential gene expression and correlation network analyses revealed that EZH2 is the most significantly over-expressed ERG in cancer and is co-regulated with a cell cycle network. Furthermore we quantified global proteomic changes by mass spectrometry after EZH2 inhibition. Proteomic analysis showed that EZH2 inhibition induced down-regulation of cell cycle regulators in lymphoma cells. We have now expanded our analysis to other types of proteins including kinases and secreted proteins.
Note: This abstract was not presented at the conference.
Citation Format: Florian Gnad, Zemin Zhang. Bioinformatics analysis of TCGA tumors to identify cancer associated epigenetic regulators. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-43.
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Gnad F, Doll S, Manning G, Arnott D, Zhang Z. Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics 2015; 16 Suppl 8:S5. [PMID: 26110843 PMCID: PMC4480953 DOI: 10.1186/1471-2164-16-s8-s5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Many cancer cells show distorted epigenetic landscapes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors, allowing the discovery of somatic alterations in the epigenetic machinery and the identification of potential cancer drivers among members of epigenetic protein families. Methods We integrated mutation, expression, and copy number data from 5943 tumors from 13 cancer types to train a classification model that predicts the likelihood of being an oncogene (OG), tumor suppressor (TSG) or neutral gene (NG). We applied this predictor to epigenetic regulator genes (ERGs), and used differential expression and correlation network analysis to identify dysregulated ERGs along with co-expressed cancer genes. Furthermore, we quantified global proteomic changes by mass spectrometry after EZH2 inhibition. Results Mutation-based classifiers uncovered the OG-like profile of DNMT3A and TSG-like profiles for several ERGs. Differential gene expression and correlation network analyses revealed that EZH2 is the most significantly over-expressed ERG in cancer and is co-regulated with a cell cycle network. Proteomic analysis showed that EZH2 inhibition induced down-regulation of cell cycle regulators in lymphoma cells. Conclusions Using classical driver genes to train an OG/TSG predictor, we determined the most predictive features at the gene level. Our predictor uncovered one OG and several TSGs among ERGs. Expression analyses elucidated multiple dysregulated ERGs including EZH2 as member of a co-expressed cell cycle network.
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24
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Zhou W, Jubb AM, Lyle K, Xiao Q, Ong CC, Desai R, Fu L, Gnad F, Song Q, Haverty PM, Aust D, Grützmann R, Romero M, Totpal K, Neve RM, Yan Y, Forrest WF, Wang Y, Raja R, Pilarsky C, de Jesus-Acosta A, Belvin M, Friedman LS, Merchant M, Jaffee EM, Zheng L, Koeppen H, Hoeflich KP. PAK1 mediates pancreatic cancer cell migration and resistance to MET inhibition. J Pathol 2014; 234:502-13. [PMID: 25074413 DOI: 10.1002/path.4412] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/25/2014] [Accepted: 07/18/2014] [Indexed: 12/19/2022]
Abstract
Pancreatic adenocarcinoma (PDAC) is a major unmet medical need and a deeper understanding of molecular drivers is needed to advance therapeutic options for patients. We report here that p21-activated kinase 1 (PAK1) is a central node in PDAC cells downstream of multiple growth factor signalling pathways, including hepatocyte growth factor (HGF) and MET receptor tyrosine kinase. PAK1 inhibition blocks signalling to cytoskeletal effectors and tumour cell motility driven by HGF/MET. MET antagonists, such as onartuzumab and crizotinib, are currently in clinical development. Given that even highly effective therapies have resistance mechanisms, we show that combination with PAK1 inhibition overcomes potential resistance mechanisms mediated either by activation of parallel growth factor pathways or by direct amplification of PAK1. Inhibition of PAK1 attenuated in vivo tumour growth and metastasis in a model of pancreatic adenocarcinoma. In human tissues, PAK1 is highly expressed in a proportion of PDACs (33% IHC score 2 or 3; n = 304) and its expression is significantly associated with MET positivity (p < 0.0001) and linked to a widespread metastatic pattern in patients (p = 0.067). Taken together, our results provide evidence for a functional role of MET/PAK1 signalling in pancreatic adenocarcinoma and support further characterization of therapeutic inhibitors in this indication.
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Affiliation(s)
- Wei Zhou
- Department of Translational Oncology, Genentech, Inc, South San Francisco, CA 94080, USA
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25
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Jhunjhunwala S, Jiang Z, Stawiski EW, Gnad F, Liu J, Mayba O, Du P, Diao J, Johnson S, Wong KF, Gao Z, Li Y, Wu TD, Kapadia SB, Modrusan Z, French DM, Luk JM, Seshagiri S, Zhang Z. Diverse modes of genomic alteration in hepatocellular carcinoma. Genome Biol 2014; 15:436. [PMID: 25159915 PMCID: PMC4189592 DOI: 10.1186/s13059-014-0436-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 08/11/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a heterogeneous disease with high mortality rate. Recent genomic studies have identified TP53, AXIN1, and CTNNB1 as the most frequently mutated genes. Lower frequency mutations have been reported in ARID1A, ARID2 and JAK1. In addition, hepatitis B virus (HBV) integrations into the human genome have been associated with HCC. RESULTS Here, we deep-sequence 42 HCC patients with a combination of whole genome, exome and transcriptome sequencing to identify the mutational landscape of HCC using a reasonably large discovery cohort. We find frequent mutations in TP53, CTNNB1 and AXIN1, and rare but likely functional mutations in BAP1 and IDH1. Besides frequent hepatitis B virus integrations at TERT, we identify translocations at the boundaries of TERT. A novel deletion is identified in CTNNB1 in a region that is heavily mutated in multiple cancers. We also find multiple high-allelic frequency mutations in the extracellular matrix protein LAMA2. Lower expression levels of LAMA2 correlate with a proliferative signature, and predict poor survival and higher chance of cancer recurrence in HCC patients, suggesting an important role of the extracellular matrix and cell adhesion in tumor progression of a subgroup of HCC patients. CONCLUSIONS The heterogeneous disease of HCC features diverse modes of genomic alteration. In addition to common point mutations, structural variations and methylation changes, there are several virus-associated changes, including gene disruption or activation, formation of chimeric viral-human transcripts, and DNA copy number changes. Such a multitude of genomic events likely contributes to the heterogeneous nature of HCC.
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Affiliation(s)
- Suchit Jhunjhunwala
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Zhaoshi Jiang
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Eric W Stawiski
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
- />Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Florian Gnad
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Jinfeng Liu
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Oleg Mayba
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Pan Du
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Jingyu Diao
- />Department of Infectious diseases, Genentech Inc., South San Francisco, CA 94080 USA
| | - Stephanie Johnson
- />Department of Pathology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Kwong-Fai Wong
- />Department of Surgery, University of Hong Kong, Pokfulam, Hong Kong
| | - Zhibo Gao
- />BGI-Shenzhen, Shenzhen, 518083 China
| | | | - Thomas D Wu
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Sharookh B Kapadia
- />Department of Infectious diseases, Genentech Inc., South San Francisco, CA 94080 USA
| | - Zora Modrusan
- />Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Dorothy M French
- />Department of Pathology, Genentech Inc., South San Francisco, CA 94080 USA
| | - John M Luk
- />Department of Surgery, University of Hong Kong, Pokfulam, Hong Kong
- />Department of Pharmacology, National University of Singapore, Singapore, 117597 Singapore
- />Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673 Singapore
| | - Somasekar Seshagiri
- />Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080 USA
| | - Zemin Zhang
- />Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080 USA
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26
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Jhunjhunwala S, Jiang Z, Stawiski EW, Gnad F, Liu J, Mayba O, Du P, Diao J, Johnson S, Wong KF, Gao Z, Li Y, Wu TD, Kapadia SB, Modrusan Z, French DM, Luk JM, Seshagiri S, Zhang Z. Diverse modes of genomic alterations in hepatocellular carcinoma. Genome Biol 2014. [DOI: 10.1186/preaccept-1790146428112469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Gnad F, Young A, Zhou W, Lyle K, Ong CC, Stokes MP, Silva JC, Belvin M, Friedman LS, Koeppen H, Minden A, Hoeflich KP. Systems-wide analysis of K-Ras, Cdc42, and PAK4 signaling by quantitative phosphoproteomics. Mol Cell Proteomics 2013; 12:2070-80. [PMID: 23608596 DOI: 10.1074/mcp.m112.027052] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although K-Ras, Cdc42, and PAK4 signaling are commonly deregulated in cancer, only a few studies have sought to comprehensively examine the spectrum of phosphorylation-mediated signaling downstream of each of these key signaling nodes. In this study, we completed a label-free quantitative analysis of oncogenic K-Ras, activated Cdc42, and PAK4-mediated phosphorylation signaling, and report relative quantitation of 2152 phosphorylated peptides on 1062 proteins. We define the overlap in phosphopeptides regulated by K-Ras, Cdc42, and PAK4, and find that perturbation of these signaling components affects phosphoproteins associated with microtubule depolymerization, cytoskeletal organization, and the cell cycle. These findings provide a resource for future studies to characterize novel targets of oncogenic K-Ras signaling and validate biomarkers of PAK4 inhibition.
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Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California 94080, USA.
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28
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Liu J, Lee W, Jiang Z, Chen Z, Jhunjhunwala S, Haverty PM, Gnad F, Guan Y, Gilbert HN, Stinson J, Klijn C, Guillory J, Bhatt D, Vartanian S, Walter K, Chan J, Holcomb T, Dijkgraaf P, Johnson S, Koeman J, Minna JD, Gazdar AF, Stern HM, Hoeflich KP, Wu TD, Settleman J, de Sauvage FJ, Gentleman RC, Neve RM, Stokoe D, Modrusan Z, Seshagiri S, Shames DS, Zhang Z. Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Res 2012; 22:2315-27. [PMID: 23033341 PMCID: PMC3514662 DOI: 10.1101/gr.140988.112] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole-genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and three lung tumor/normal pairs. Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Smoker and never-smoker cancer samples exhibit distinguishable patterns of mutations. A number of epigenetic regulators, including KDM6A, ASH1L, SMARCA4, and ATAD2, are frequently altered by mutations or copy number changes. A systematic survey of splice-site mutations identified 106 splice site mutations associated with cancer specific aberrant splicing, including mutations in several known cancer-related genes. RAC1b, an isoform of the RAC1 GTPase that includes one additional exon, was found to be preferentially up-regulated in lung cancer. We further show that its expression is significantly associated with sensitivity to a MAP2K (MEK) inhibitor PD-0325901. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer-specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers. The detailed characterizations of the lung cancer cell lines also provide genomic context to the vast amount of experimental data gathered for these lines over the decades, and represent highly valuable resources for cancer biology.
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Affiliation(s)
- Jinfeng Liu
- Department of Bioinformatics and Computational Biology
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29
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Borchert N, Krug K, Gnad F, Sinha A, Sommer RJ, Macek B. Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models. Mol Cell Proteomics 2012; 11:1631-9. [PMID: 22923814 DOI: 10.1074/mcp.m112.022103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks.
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Affiliation(s)
- Nadine Borchert
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
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Zielinska DF, Gnad F, Schropp K, Wiśniewski JR, Mann M. Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery. Mol Cell 2012; 46:542-8. [PMID: 22633491 DOI: 10.1016/j.molcel.2012.04.031] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 01/18/2012] [Accepted: 04/27/2012] [Indexed: 11/26/2022]
Abstract
N-linked glycosylation is an important posttranslational modification in all eukaryotes, but little is known about the N-glycoproteomes in nonmammalian systems. Here, we measure N-glycoproteomes of the major model organisms Arabidopsis thaliana, Schizosaccharomyces pombe, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio, representatively spanning the eukaryotic domain of life. The number of detected N-glycosylation sites varied between 425 in fission yeast, 516 in budding yeast, 1,794 in worm, 2,186 in plant, 2,229 in fly, and 2,254 in zebrafish. We find that all eukaryotic N-glycoproteomes have invariant characteristics including sequence recognition patterns, structural constraints, and subcellular localization. However, a surprisingly large percentage of the N-glycoproteome evolved after the phylogenetic divergences between plants, fungi, nematodes, insects, and vertebrates. Many N-glycosylated proteins coevolved with the rise of extracellular processes that are specific within corresponding phylogenetic groups and essential for organismal development, body growth, and organ formation.
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Affiliation(s)
- Dorota F Zielinska
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried 82152, Germany
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31
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Abstract
SUMMARY Molecular networks are often studied in diverse cellular or experimental contexts, with highly context-specific details. Modelling introduces further choices as to levels of mathematical description. The resulting possibilities are difficult to explore rapidly, hampering the integration of modelling and experiment. We have developed Proteus, a web-based, context-specific tool for building compartmentalized, ordinary differential equation (ODE) models. It is inspired by the idea of a molecular 'toolkit' for Ca(2+) signalling. Toolkits in Proteus are context-independent representations of biological systems as sets of components, which may correspond to mechanisms of differing levels of complexity. Users pick and choose components from a toolkit and, for each component, pick and choose from different mechanisms, each of which describes a different instantiation of the component's mechanism. Proteus combines these choices into a system of ODEs, which may then be downloaded in SBML (Systems Biology Markup Language), Matlab or Fortran format and independently analyzed. Toolkits, components and mechanisms are user-constructible, either de novo or by cannibalizing existing models, including all those in the Biomodels database. A wide variety of context-specific models may thereby be rapidly built, modified and explored. AVAILABILITY AND IMPLEMENTATION Proteus, implemented in C#, and a prototype toolkit for modelling calcium signalling are freely and universally available at www.modularmodeling.com CONTACT gnad.florian@gene.com; jeremy@hms.harvard.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Florian Gnad
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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32
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Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Krüger M, Mann M. Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J Proteome Res 2011; 10:5275-84. [PMID: 22050367 DOI: 10.1021/pr101183k] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The turnover of each protein in the mammalian proteome is a functionally important characteristic. Here, we employed high-resolution mass spectrometry to quantify protein dynamics in nondividing mammalian cells. The ratio of externally supplied versus endogenous amino acids to de novo protein synthesis was about 17:1. Using subsaturating SILAC labeling, we obtained accurate turnover rates of 4106 proteins in HeLa and 3528 proteins in C2C12 cells. Comparison of these human and mouse cell lines revealed a highly significant turnover correlation of protein orthologs and thus high species conservation. Functionally, we observed statistically significant trends for the turnover of phosphoproteins and gene ontology categories that showed extensive covariation between mouse and human. Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover.
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Affiliation(s)
- Sidney B Cambridge
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Munich-Martinsried, Germany
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33
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Marchini FK, de Godoy LMF, Rampazzo RCP, Pavoni DP, Probst CM, Gnad F, Mann M, Krieger MA. Profiling the Trypanosoma cruzi phosphoproteome. PLoS One 2011; 6:e25381. [PMID: 21966514 PMCID: PMC3178638 DOI: 10.1371/journal.pone.0025381] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/02/2011] [Indexed: 12/30/2022] Open
Abstract
Protein phosphorylation is a reversible post-translational modification essential for the regulation of several signal transduction pathways and biological processes in the living cell. Therefore, the identification of protein phosphorylation sites is crucial to understand cell signaling control at the molecular level. Based on mass spectrometry, recent studies have reported the large-scale mapping of phosphorylation sites in various eukaryotes and prokaryotes. However, little is known about the impact of phosphorylation in protozoan parasites. To in depth characterize the phosphoproteome of Trypanosoma cruzi, a parasite of the Kinetoplastida class, protein samples from cells at different phases of the metacyclogenesis – differentiation process of the parasites from non-infective epimastigotes to infective metacyclic trypomastigotes - were enriched for phosphopeptides using TiO2 chromatography and analyzed on an LTQ-Orbitrap mass spectrometer. In total, 1,671 proteins were identified, including 753 phosphoproteins, containing a total of 2,572 phosphorylation sites. The distribution of phosphorylated residues was 2,162 (84.1%) on serine, 384 (14.9%) on threonine and 26 (1.0%) on tyrosine. Here, we also report several consensus phosphorylation sequence motifs and as some of these conserved groups have enriched biological functions, we can infer the regulation by protein kinases of this functions. To our knowledge, our phosphoproteome is the most comprehensive dataset identified until now for Kinetoplastida species. Here we also were able to extract biological information and infer groups of sites phosphorylated by the same protein kinase. To make our data accessible to the scientific community, we uploaded our study to the data repositories PHOSIDA, Proteome Commons and TriTrypDB enabling researchers to access information about the phosphorylation sites identified here.
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Affiliation(s)
| | - Lyris M. F. de Godoy
- Instituto Carlos Chagas, Fiocruz, Curitiba, Paraná, Brazil
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | - Florian Gnad
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marco A. Krieger
- Instituto Carlos Chagas, Fiocruz, Curitiba, Paraná, Brazil
- * E-mail:
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Xie X, Gong Z, Mansuy-Aubert V, Zhou QL, Tatulian SA, Sehrt D, Gnad F, Brill LM, Motamedchaboki K, Chen Y, Czech MP, Mann M, KrÜger M, Jiang ZY. C2 domain-containing phosphoprotein CDP138 regulates GLUT4 insertion into the plasma membrane. Cell Metab 2011; 14:378-89. [PMID: 21907143 PMCID: PMC3172579 DOI: 10.1016/j.cmet.2011.06.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 05/03/2011] [Accepted: 06/09/2011] [Indexed: 10/17/2022]
Abstract
The protein kinase B(β) (Akt2) pathway is known to mediate insulin-stimulated glucose transport through increasing glucose transporter GLUT4 translocation from intracellular stores to the plasma membrane (PM). Combining quantitative phosphoproteomics with RNAi-based functional analyses, we show that a previously uncharacterized 138 kDa C2 domain-containing phosphoprotein (CDP138) is a substrate for Akt2, and is required for optimal insulin-stimulated glucose transport, GLUT4 translocation, and fusion of GLUT4 vesicles with the PM in live adipocytes. The purified C2 domain is capable of binding Ca(2+) and lipid membranes. CDP138 mutants lacking the Ca(2+)-binding sites in the C2 domain or Akt2 phosphorylation site S197 inhibit insulin-stimulated GLUT4 insertion into the PM, a rate-limiting step of GLUT4 translocation. Interestingly, CDP138 is dynamically associated with the PM and GLUT4-containing vesicles in response to insulin stimulation. Together, these results suggest that CDP138 is a key molecule linking the Akt2 pathway to the regulation of GLUT4 vesicle-PM fusion.
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Affiliation(s)
- Xiangyang Xie
- Metabolic Signaling and Disease Program, Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Zhenwei Gong
- Metabolic Signaling and Disease Program, Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Virginie Mansuy-Aubert
- Metabolic Signaling and Disease Program, Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Qiong L. Zhou
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Suren A. Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Daniel Sehrt
- Metabolic Signaling and Disease Program, Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Florian Gnad
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Laurence M. Brill
- Proteomic Core Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Khatereh Motamedchaboki
- Proteomic Core Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yu Chen
- Cell Biology and Metabolism Program, NICHD, NIH, Bethesda, MD 20892, USA
| | - Michael P. Czech
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marcus KrÜger
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Zhen Y. Jiang
- Metabolic Signaling and Disease Program, Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
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Wiśniewski JR, Nagaraj N, Zougman A, Gnad F, Mann M. Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology. J Proteome Res 2010; 9:3280-9. [PMID: 20415495 DOI: 10.1021/pr1002214] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Taking advantage of the recently developed Filter Assisted Sample Preparation (FASP) method for sample preparation, we performed an in-depth analysis of phosphorylation sites in mouse brain. To maximize the number of detected phosphorylation sites, we fractionated proteins by size exclusion chromatography (SEC) or separated tryptic peptides on an anion exchanger (SAX) prior or after the TiO(2)-based phosphopeptide enrichment, respectively. SEC allowed analysis of minute tissue samples (1 mg total protein), and resulted in identification of more than 4000 sites in a single experiment, comprising eight fractions. SAX in a pipet tip format offered a convenient and rapid way to fractionate phosphopeptides and mapped more than 5000 sites in a single six fraction experiment. To enrich peptides containing phosphotyrosine residues, we describe a filter aided antibody capturing and elution (FACE) method that requires only the uncoupled instead of resin-immobilized capture reagent. In total, we identified 12,035 phosphorylation sites on 4579 brain proteins of which 8446 are novel. Gene Ontology annotation reveals that 23% of identified sites are located on plasma membrane proteins, including a large number of ion channels and transporters. Together with the glycosylation sites from a recent large-scale study, they can confirm or correct predicted membrane topologies of these proteins, as we show for the examples calcium channels and glutamate receptors.
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Affiliation(s)
- Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried near Munich, Germany.
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Abstract
The primary purpose of PHOSIDA (http://www.phosida.com) is to manage posttranslational modification sites of various species ranging from bacteria to human. Since its last report, PHOSIDA has grown significantly in size and evolved in scope. It comprises more than 80,000 phosphorylated, N-glycosylated or acetylated sites from nine different species. All sites are obtained from high-resolution mass spectrometric data using the same stringent quality criteria. One of the main distinguishing features of PHOSIDA is the provision of a wide range of analysis tools. PHOSIDA is comprised of three main components: the database environment, the prediction platform and the toolkit section. The database environment integrates and combines high-resolution proteomic data with multiple annotations. High-accuracy species-specific phosphorylation and acetylation site predictors, trained on the modification sites contained in PHOSIDA, allow the in silico determination of modified sites on any protein on the basis of the primary sequence. The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets.
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Affiliation(s)
- Florian Gnad
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria. Mol Cell Proteomics 2010; 9:2642-53. [PMID: 20688971 DOI: 10.1074/mcp.m110.001594] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organisms, the prokaryotes, only a few hundred proteins have been found to be phosphorylated. Applying the same technology to eukaryotic species resulted in the detection of thousands of phosphorylation events. Evolutionary analysis shows that prokaryotic phosphoproteins are preferentially conserved in all living organisms, whereas-site specific phosphorylation is not. Eukaryotic phosphosites are generally more conserved than their non-phosphorylated counterparts (with similar structural constraints) throughout the eukaryotic domain. Yeast and Caenorhabditis elegans are two exceptions, indicating that the majority of phosphorylation events evolved after the divergence of higher eukaryotes from yeast and reflecting the unusually large number of nematode-specific kinases. Mitochondria present an interesting intermediate link between the prokaryotic and eukaryotic domains. Applying the same technology to this organelle yielded 174 phosphorylation sites mapped to 74 proteins. Thus, the mitochondrial phosphoproteome is similarly sparse as the prokaryotic phosphoproteomes. As expected from the endosymbiotic theory, phosphorylated as well as non-phosphorylated mitochondrial proteins are significantly conserved in prokaryotes. However, mitochondrial phosphorylation sites are not conserved throughout prokaryotes, consistent with the notion that serine/threonine phosphorylation in prokaryotes occurred relatively recently in evolution. Thus, the phosphoproteome reflects major events in the evolution of life.
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Affiliation(s)
- Florian Gnad
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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38
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Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC. Site-Specific Identification of SUMO-2 Targets in Cells Reveals an Inverted SUMOylation Motif and a Hydrophobic Cluster SUMOylation Motif. Mol Cell 2010; 39:641-52. [DOI: 10.1016/j.molcel.2010.07.026] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/22/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]
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Zielinska DF, Gnad F, Wiśniewski JR, Mann M. Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 2010; 141:897-907. [PMID: 20510933 DOI: 10.1016/j.cell.2010.04.012] [Citation(s) in RCA: 691] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 02/08/2010] [Accepted: 04/07/2010] [Indexed: 01/09/2023]
Abstract
N-linked glycosylation is a biologically important protein modification, but only a small fraction of modification sites have been mapped. We developed a "filter aided sample preparation" (FASP)-based method in which glycopeptides are enriched by binding to lectins on the top of a filter and mapped 6367 N-glycosylation sites on 2352 proteins in four mouse tissues and blood plasma using high-accuracy mass spectrometry. We found 74% of known mouse N-glycosites and discovered an additional 5753 sites on a diverse range of proteins. Sites almost always have the N-!P-[S|T]-!P (where !P is not proline) and rarely the N-X-C motif or nonconsensus sequences. Combining the FASP approach with analysis of subcellular glycosite localization reveals that the sites always orient toward the extracellular space or toward the lumen of ER, Golgi, lysosome, or peroxisome. The N-glycoproteome contains a plethora of modification sites on factors important in development, organ-specific functions, and disease.
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Affiliation(s)
- Dorota F Zielinska
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, Martinsried D-82152, Germany
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40
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Soufi B, Kumar C, Gnad F, Mann M, Mijakovic I, Macek B. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis. J Proteome Res 2010; 9:3638-46. [DOI: 10.1021/pr100150w] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Boumediene Soufi
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Chanchal Kumar
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Florian Gnad
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Matthias Mann
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Ivan Mijakovic
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Boris Macek
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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Abstract
Motivation: Lysine acetylation is a post-translational protein modification and a primary regulatory mechanism that controls many cell signaling processes. Lysine acetylation sites are recognized by acetyltransferases and deacetylases through sequence patterns (motifs). Recently, we used high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 human proteins covering most of the previously annotated sites and providing the most comprehensive acetylome so far. This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico prediction of acetylated lysine residues. Results: We developed a SVM to predict acetylated residues. The precision of our acetylation site predictor is 78% at 78% recall on input data containing equal numbers of modified and non-modified residues. Availability: The online predictor is available at http://www.phosida.com Contact:mmann@biochem.mpg.de
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Affiliation(s)
- Florian Gnad
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Gnad F, de Godoy LMF, Cox J, Neuhauser N, Ren S, Olsen JV, Mann M. High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics 2010; 9:4642-52. [PMID: 19795423 DOI: 10.1002/pmic.200900144] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protein phosphorylation is a fundamental regulatory mechanism that affects many cell signaling processes. Using high-accuracy MS and stable isotope labeling in cell culture-labeling, we provide a global view of the Saccharomyces cerevisiae phosphoproteome, containing 3620 phosphorylation sites mapped to 1118 proteins, representatively covering the yeast kinome and a multitude of transcription factors. We show that a single false discovery rate for all peptide identifications significantly overestimates occurrence of rare modifications, such as tyrosine phosphorylation in yeast. The identified phosphorylation sites are predominantly located on irregularly structured and accessible protein regions. We found high evolutionary conservation of phosphorylated proteins and a large overlap of significantly over-represented motifs with the human phosphoproteome. Nevertheless, phosphorylation events at the site level were not highly conserved between yeast and higher eukaryotes, which points to metazoan-specific kinase and substrate families. We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com).
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Affiliation(s)
- Florian Gnad
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Martinsried, Germany
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Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 2010; 3:ra3. [PMID: 20068231 DOI: 10.1126/scisignal.2000475] [Citation(s) in RCA: 1157] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.
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Affiliation(s)
- Jesper V Olsen
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried near Munich, Germany
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44
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Hilger M, Bonaldi T, Gnad F, Mann M. Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics. Mol Cell Proteomics 2009; 8:1908-20. [PMID: 19429919 PMCID: PMC2722773 DOI: 10.1074/mcp.m800559-mcp200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 03/26/2009] [Indexed: 12/11/2022] Open
Abstract
Signal transduction in metazoans regulates almost all aspects of biological function, and aberrant signaling is involved in many diseases. Perturbations in phosphorylation-based signaling networks are typically studied in a hypothesis-driven approach, using phospho-specific antibodies. Here we apply quantitative, high-resolution mass spectrometry to determine the systems response to the depletion of one signaling component. Drosophila cells were metabolically labeled using stable isotope labeling by amino acids in cell culture (SILAC) and the phosphatase Ptp61F, the ortholog of mammalian PTB1B, a drug target for diabetes, was knocked down by RNAi. In total we detected more than 10,000 phosphorylation sites in the phosphoproteome of Drosophila Schneider cells and trained a phosphorylation site predictor with this data. SILAC-based quantitation after phosphatase knock-down showed that apart from the phosphatase, the proteome was minimally affected whereas 288 of 6,478 high-confidence phosphorylation sites changed significantly. Responses at the phosphotyrosine level included the already described Ptp61F substrates Stat92E and Abi. Our analysis highlights a connection of Ptp61F to cytoskeletal regulation through GTPase regulating proteins and focal adhesion components.
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Affiliation(s)
- Maximiliane Hilger
- From the ‡Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany and
| | - Tiziana Bonaldi
- From the ‡Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany and
- §Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Florian Gnad
- From the ‡Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany and
| | - Matthias Mann
- From the ‡Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany and
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45
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Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009; 325:834-40. [PMID: 19608861 DOI: 10.1126/science.1175371] [Citation(s) in RCA: 3099] [Impact Index Per Article: 206.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lysine acetylation is a reversible posttranslational modification of proteins and plays a key role in regulating gene expression. Technological limitations have so far prevented a global analysis of lysine acetylation's cellular roles. We used high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins and quantified acetylation changes in response to the deacetylase inhibitors suberoylanilide hydroxamic acid and MS-275. Lysine acetylation preferentially targets large macromolecular complexes involved in diverse cellular processes, such as chromatin remodeling, cell cycle, splicing, nuclear transport, and actin nucleation. Acetylation impaired phosphorylation-dependent interactions of 14-3-3 and regulated the yeast cyclin-dependent kinase Cdc28. Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications.
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Affiliation(s)
- Chunaram Choudhary
- Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
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46
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Zielinska DF, Gnad F, Jedrusik-Bode M, Wiśniewski JR, Mann M. Caenorhabditis elegans Has a Phosphoproteome Atypical for Metazoans That Is Enriched in Developmental and Sex Determination Proteins. J Proteome Res 2009; 8:4039-49. [DOI: 10.1021/pr900384k] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Dorota F. Zielinska
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, and Laboratory of Chromatin Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Faβberg 11, D-37077 Göttingen, Germany
| | - Florian Gnad
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, and Laboratory of Chromatin Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Faβberg 11, D-37077 Göttingen, Germany
| | - Monika Jedrusik-Bode
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, and Laboratory of Chromatin Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Faβberg 11, D-37077 Göttingen, Germany
| | - Jacek R. Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, and Laboratory of Chromatin Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Faβberg 11, D-37077 Göttingen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, and Laboratory of Chromatin Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Faβberg 11, D-37077 Göttingen, Germany
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47
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Zanivan S, Gnad F, Wickström SA, Geiger T, Macek B, Cox J, Fässler R, Mann M. Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry. J Proteome Res 2009; 7:5314-26. [PMID: 19367708 DOI: 10.1021/pr800599n] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Kinases play a prominent role in tumor development, pointing to the presence of specific phosphorylation patterns in tumor tissues. Here, we investigate whether recently developed high resolution mass spectrometric (MS) methods for proteome and phosphoproteome analysis can also be applied to solid tumors. As tumor model, we used TG3 mutant mice carrying skin melanomas. At total of 100 microg of solid tumor lysate yielded a melanoma proteome of 4443 identified proteins, including at least 88 putative melanoma markers previously found by cDNA microarray technology. Analysis of 2 mg of lysate from dissected melanoma with titansphere chromatography and 8 mg with strong cation exchange together resulted in the identification of more than 5600 phosphorylation sites on 2250 proteins. The phosphoproteome included many hits from pathways important in melanoma. One-month storage at -80 degrees C did not significantly decrease the number of identified phosphorylation sites. Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies.
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Affiliation(s)
- Sara Zanivan
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Kéri G, Mann M, Daub H. Large-scale proteomics analysis of the human kinome. Mol Cell Proteomics 2009; 8:1751-64. [PMID: 19369195 DOI: 10.1074/mcp.m800588-mcp200] [Citation(s) in RCA: 239] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Members of the human protein kinase superfamily are the major regulatory enzymes involved in the activity control of eukaryotic signal transduction pathways. As protein kinases reside at the nodes of phosphorylation-based signal transmission, comprehensive analysis of their cellular expression and site-specific phosphorylation can provide important insights into the architecture and functionality of signaling networks. However, in global proteome studies, low cellular abundance of protein kinases often results in rather minor peptide species that are occluded by a vast excess of peptides from other cellular proteins. These analytical limitations create a rationale for kinome-wide enrichment of protein kinases prior to mass spectrometry analysis. Here, we employed stable isotope labeling by amino acids in cell culture (SILAC) to compare the binding characteristics of three kinase-selective affinity resins by quantitative mass spectrometry. The evaluated pre-fractionation tools possessed pyrido[2,3-d]pyrimidine-based kinase inhibitors as immobilized capture ligands and retained considerable subsets of the human kinome. Based on these results, an affinity resin displaying the broadly selective kinase ligand VI16832 was employed to quantify the relative expression of more than 170 protein kinases across three different, SILAC-encoded cancer cell lines. These experiments demonstrated the feasibility of comparative kinome profiling in a compact experimental format. Interestingly, we found high levels of cytoplasmic and low levels of receptor tyrosine kinases in MV4-11 leukemia cells compared with the adherent cancer lines HCT116 and MDA-MB-435S. The VI16832 resin was further exploited to pre-fractionate kinases for targeted phosphoproteomics analysis, which revealed about 1200 distinct phosphorylation sites on more than 200 protein kinases. This hitherto largest survey of site-specific phosphorylation across the kinome significantly expands the basis for functional follow-up studies on protein kinase regulation. In conclusion, the straightforward experimental procedures described here enable different implementations of kinase-selective proteomics with considerable potential for future signal transduction and kinase drug target analysis.
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Affiliation(s)
- Felix S Oppermann
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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Aivaliotis M, Macek B, Gnad F, Reichelt P, Mann M, Oesterhelt D. Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life. PLoS One 2009; 4:e4777. [PMID: 19274099 PMCID: PMC2652253 DOI: 10.1371/journal.pone.0004777] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 01/02/2009] [Indexed: 11/30/2022] Open
Abstract
In the quest for the origin and evolution of protein phosphorylation, the major regulatory post-translational modification in eukaryotes, the members of archaea, the “third domain of life”, play a protagonistic role. A plethora of studies have demonstrated that archaeal proteins are subject to post-translational modification by covalent phosphorylation, but little is known concerning the identities of the proteins affected, the impact on their functionality, the physiological roles of archaeal protein phosphorylation/dephosphorylation, and the protein kinases/phosphatases involved. These limited studies led to the initial hypothesis that archaea, similarly to other prokaryotes, use mainly histidine/aspartate phosphorylation, in their two-component systems representing a paradigm of prokaryotic signal transduction, while eukaryotes mostly use Ser/Thr/Tyr phosphorylation for creating highly sophisticated regulatory networks. In antithesis to the above hypothesis, several studies showed that Ser/Thr/Tyr phosphorylation is also common in the bacterial cell, and here we present the first genome-wide phosphoproteomic analysis of the model organism of archaea, Halobacterium salinarum, proving the existence/conservation of Ser/Thr/Tyr phosphorylation in the “third domain” of life, allowing a better understanding of the origin and evolution of the so-called “Nature's premier” mechanism for regulating the functional properties of proteins.
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Affiliation(s)
- Michalis Aivaliotis
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- * E-mail:
| | - Boris Macek
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Gnad
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter Reichelt
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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Pan C, Gnad F, Olsen JV, Mann M. Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors. Proteomics 2008; 8:4534-46. [PMID: 18846507 DOI: 10.1002/pmic.200800105] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The liver is a central organ involved in many aspects of physiology and disease. Signaling properties of hepatocytes, the main liver cell type, are of special interest in metabolic diseases and in regeneration. For this reason we investigated the phosphoproteome of the mouse liver cell line Hepa1-6 by stable isotope labeling by amino acids in cell culture (SILAC) and high resolution MS. Using stringent statistical evaluation criteria, we obtained 5433 phosphorylation sites on 1808 proteins. The phosphoproteome encompasses all major protein classes, including a large number of transcription factors. We compared control and phosphatase inhibitor treated cells by SILAC. This enabled ready identification of in vivo phosphorylation sites by sequencing the more abundant, inhibitor induced version of the peptide while still observing the endogenous version. We employed a mixture of pervanadate for blocking protein tyrosine phosphatases (PTPs) and calyculin A and deltamethrin for blocking the activities of serine/threonine phosphatases. Interestingly, these commonly used inhibitors in standard concentrations affected only 28% of the phosphopeptides by at least two-fold. The unaffected sites may be substrates of phosphatases that are not efficiently inhibited, have slow kinetic or sites that are almost stoichiometric in normally growing cells. Finally, we devised a triple labeling strategy comprising control cells, stimulated cells, and phosphatase treated cells to derive an upper bound on phosphorylation occupancy.
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Affiliation(s)
- Cuiping Pan
- Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Martinsried, Germany
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