1
|
Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. J Proteome Res 2024; 23:3235-3248. [PMID: 38412263 PMCID: PMC11301670 DOI: 10.1021/acs.jproteome.3c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface N-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories.
Collapse
Affiliation(s)
- Linda Berg Luecke
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Roneldine Mesidor
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Morgan Carpenter
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Melinda Wojtkiewicz
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L. Gundry
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| |
Collapse
|
2
|
Proof-of-principle studies on a strategy to enhance nucleotide imbalance specifically in cancer cells. Cell Death Dis 2022; 8:464. [PMID: 36424385 PMCID: PMC9691752 DOI: 10.1038/s41420-022-01254-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2022]
Abstract
Highly specific and potent inhibitors of dihydroorotate dehydrogenase (DHODH), an essential enzyme of the de novo pyrimidine ribonucleotide synthesis pathway, are in clinical trials for autoimmune diseases, viral infections and cancer. However, because DHODH inhibitors (DHODHi) are immunosuppressants they may reduce the anticancer activity of the immune system. Therefore, there may be a need to improve the therapeutic index of DHODHi in cancer patients. The aim of this study was to find strategies to protect activated T cells from DHODHi and to identify cancer types hypersensitive to these inhibitors. First, we observed that like uridine supplementation, adding cytidine to the culture medium protects T cells from DHODH blockage. Next, we identified tumor types with altered expression of pyrimidine ribonucleotide synthesis enzymes. In this regard, we detected that the expression of cytidine deaminase (CDA), which converts cytidine into uridine, is low in an important proportion of cancer cell lines and consistently low in neuroblastoma samples and in cell lines from neuroblastoma and small cell lung carcinoma. This suggested that in the presence of a DHODHi, an excess of cytidine would be deleterious for low CDA expressing cancer cell lines. We show that this was the case (as could be seen almost immediately after treatment) when cells were cultured with fetal bovine serum but, was significantly less evident when cultures contained human serum. One interesting feature of CDA is that aside from acting intracellularly, it is also present in human plasma/serum. Altogether, experiments using recombinant CDA, human serum, pharmacologic inhibition of CDA and T cell/cancer cell co-cultures suggest that the therapeutic index of DHODHi could be improved by selecting patients with low-CDA expressing cancers in combination with strategies to increase cytidine or the cytidine/uridine ratio in the extracellular environment. Collectively, this proof-of-principle study warrants the discovery of agents to deplete extracellular CDA.
Collapse
|
3
|
Packard TA, Schwarzer R, Herzig E, Rao D, Luo X, Egedal JH, Hsiao F, Widera M, Hultquist JF, Grimmett ZW, Messer RJ, Krogan NJ, Deeks SG, Roan NR, Dittmer U, Hasenkrug KJ, Greene WC. CCL2: a Chemokine Potentially Promoting Early Seeding of the Latent HIV Reservoir. mBio 2022; 13:e0189122. [PMID: 36073812 PMCID: PMC9600577 DOI: 10.1128/mbio.01891-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022] Open
Abstract
HIV infects long-lived CD4 memory T cells, establishing a latent viral reservoir that necessitates lifelong antiretroviral therapy (ART). How this reservoir is formed so quickly after infection remains unclear. We now show the innate inflammatory response to HIV infection results in CCL2 chemokine release, leading to recruitment of cells expressing the CCR2 receptor, including a subset of central memory CD4 T cells. Supporting a role for the CCL2/CCR2 axis in rapid reservoir formation, we find (i) treatment of humanized mice with anti-CCL2 antibodies during early HIV infection decreases reservoir seeding and preserves CCR2/5+ cells and (ii) CCR2/5+ cells from the blood of HIV-infected individuals on long-term ART contain significantly more integrated provirus than CCR2/5-negative memory or naive cells. Together, these studies support a model where the host's innate inflammatory response to HIV infection, including CCL2 production, leads to the recruitment of CCR2/5+ central memory CD4 T cells to zones of virus-associated inflammation, likely contributing to rapid formation of the latent HIV reservoir. IMPORTANCE There are currently over 35 million people living with HIV worldwide, and we still have no vaccine or scalable cure. One of the difficulties with HIV is its ability to rapidly establish a viral reservoir in lymphoid tissues that allows it to elude antivirals and the immune system. Thus, it is important to understand how HIV accomplishes this so we can develop preventive strategies. Our current results show that an early inflammatory response to HIV infection includes production of the chemokine CCL2, which recruits a unique subset of CCR2/5+ CD4+ T cells that become infected and form a significant reservoir for latent infection. Furthermore, we show that blockade of CCL2 in humanized mice significantly reduces persistent HIV infection. This information is relevant to the development of therapeutics to prevent and/or treat chronic HIV infections.
Collapse
Affiliation(s)
| | - Roland Schwarzer
- J. David Gladstone Institutes, San Francisco, California, USA
- Institute for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Eytan Herzig
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Deepashri Rao
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Xiaoyu Luo
- J. David Gladstone Institutes, San Francisco, California, USA
| | | | - Feng Hsiao
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Judd F. Hultquist
- J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | | | - Ronald J. Messer
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Nevan J. Krogan
- J. David Gladstone Institutes, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Steven G. Deeks
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Nadia R. Roan
- J. David Gladstone Institutes, San Francisco, California, USA
- Department of Urology, University of California San Francisco, San Francisco, California, USA
| | - Ulf Dittmer
- Institute for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Warner C. Greene
- J. David Gladstone Institutes, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
4
|
Heumos S, Dehn S, Bräutigam K, Codrea MC, Schürch CM, Lauer UM, Nahnsen S, Schindler M. Multiomics surface receptor profiling of the NCI-60 tumor cell panel uncovers novel theranostics for cancer immunotherapy. Cancer Cell Int 2022; 22:311. [PMID: 36221114 PMCID: PMC9555072 DOI: 10.1186/s12935-022-02710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Immunotherapy with immune checkpoint inhibitors (ICI) has revolutionized cancer therapy. However, therapeutic targeting of inhibitory T cell receptors such as PD-1 not only initiates a broad immune response against tumors, but also causes severe adverse effects. An ideal future stratified immunotherapy would interfere with cancer-specific cell surface receptors only. METHODS To identify such candidates, we profiled the surface receptors of the NCI-60 tumor cell panel via flow cytometry. The resulting surface receptor expression data were integrated into proteomic and transcriptomic NCI-60 datasets applying a sophisticated multiomics multiple co-inertia analysis (MCIA). This allowed us to identify surface profiles for skin, brain, colon, kidney, and bone marrow derived cell lines and cancer entity-specific cell surface receptor biomarkers for colon and renal cancer. RESULTS For colon cancer, identified biomarkers are CD15, CD104, CD324, CD326, CD49f, and for renal cancer, CD24, CD26, CD106 (VCAM1), EGFR, SSEA-3 (B3GALT5), SSEA-4 (TMCC1), TIM1 (HAVCR1), and TRA-1-60R (PODXL). Further data mining revealed that CD106 (VCAM1) in particular is a promising novel immunotherapeutic target for the treatment of renal cancer. CONCLUSION Altogether, our innovative multiomics analysis of the NCI-60 panel represents a highly valuable resource for uncovering surface receptors that could be further exploited for diagnostic and therapeutic purposes in the context of cancer immunotherapy.
Collapse
Affiliation(s)
- Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany.,Biomedical Data Science, Dept. of Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Sandra Dehn
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Marius C Codrea
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany
| | - Christian M Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine VIII, Medical Oncology and Pneumology, Virotherapy Center Tübingen (VCT), Medical University Hospital Tübingen, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany.,Biomedical Data Science, Dept. of Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany.
| |
Collapse
|
5
|
Suomi T, Elo LL. Statistical and machine learning methods to study human CD4+ T cell proteome profiles. Immunol Lett 2022; 245:8-17. [DOI: 10.1016/j.imlet.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/05/2022]
|
6
|
Saha SS, Samanas NB, Miralda I, Shubin NJ, Niino K, Bhise G, Acharya M, Seo AJ, Camp N, Deutsch GH, James RG, Piliponsky AM. Mast cell surfaceome characterization reveals CD98 heavy chain is critical for optimal cell function. J Allergy Clin Immunol 2022; 149:685-697. [PMID: 34324892 PMCID: PMC8792104 DOI: 10.1016/j.jaci.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Mast cells are involved in many distinct pathologic conditions, suggesting that they recognize and respond to various stimuli and thus require a rich repertoire of cell surface proteins. However, mast cell surface proteomes have not been comprehensively characterized. OBJECTIVE We aimed to further characterize the mast cell surface proteome to obtain a better understanding of how mast cells function in health and disease. METHODS We enriched for glycosylated surface proteins expressed in mouse bone marrow-derived cultured mast cells (BMCMCs) and identified them using mass spectrometry analysis. The presence of novel surface proteins in mast cells was validated by real-time quantitative PCR and flow cytometry analysis in BMCMCs and peritoneal mast cells (PMCs). We developed a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing approach to disrupt genes of interest in BMCMCs. RESULTS The glycoprotein enrichment approach resulted in the identification of 1270 proteins in BMCMCs, 378 of which were localized to the plasma membrane. The most common protein classes among plasma membrane proteins were small GTPases, receptors, and transporters. One such cell surface protein was CD98 heavy chain (CD98hc), encoded by the Slc3a2 gene. Slc3a2 gene disruption resulted in a significant reduction in CD98hc expression, adhesion, and proliferation. CONCLUSIONS Glycoprotein enrichment coupled with mass spectrometry can be used to identify novel surface molecules in mast cells. Moreover, CD98hc plays an important role in mast cell function.
Collapse
Affiliation(s)
- Siddhartha S. Saha
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nyssa B. Samanas
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Irina Miralda
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nicholas J. Shubin
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Kerri Niino
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Gauri Bhise
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Manasa Acharya
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Albert J. Seo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nathan Camp
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Gail H. Deutsch
- Department of Laboratories, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Richard G. James
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Adrian M. Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America,Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America,Corresponding author: Adrian M. Piliponsky, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, 1900 9th Ave, Room 721, , Phone number: 206-884-7226, Fax number: 206-987-7310
| |
Collapse
|
7
|
Becht E, Tolstrup D, Dutertre CA, Morawski PA, Campbell DJ, Ginhoux F, Newell EW, Gottardo R, Headley MB. High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning. SCIENCE ADVANCES 2021; 7:eabg0505. [PMID: 34550730 PMCID: PMC8457665 DOI: 10.1126/sciadv.abg0505] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/14/2021] [Indexed: 06/03/2023]
Abstract
Modern immunologic research increasingly requires high-dimensional analyses to understand the complex milieu of cell types that comprise the tissue microenvironments of disease. To achieve this, we developed Infinity Flow combining hundreds of overlapping flow cytometry panels using machine learning to enable the simultaneous analysis of the coexpression patterns of hundreds of surface-expressed proteins across millions of individual cells. In this study, we demonstrate that this approach allows the comprehensive analysis of the cellular constituency of the steady-state murine lung and the identification of previously unknown cellular heterogeneity in the lungs of melanoma metastasis–bearing mice. We show that by using supervised machine learning, Infinity Flow enhances the accuracy and depth of clustering or dimensionality reduction algorithms. Infinity Flow is a highly scalable, low-cost, and accessible solution to single-cell proteomics in complex tissues.
Collapse
Affiliation(s)
- Etienne Becht
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Tolstrup
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles-Antoine Dutertre
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Program in Emerging Infectious Disease, Duke-NUS Medical School, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
| | - Peter A. Morawski
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Daniel J. Campbell
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Evan W. Newell
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark B. Headley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| |
Collapse
|
8
|
Soday L, Potts M, Hunter LM, Ravenhill BJ, Houghton JW, Williamson JC, Antrobus R, Wills MR, Matheson NJ, Weekes MP. Comparative Cell Surface Proteomic Analysis of the Primary Human T Cell and Monocyte Responses to Type I Interferon. Front Immunol 2021; 12:600056. [PMID: 33628210 PMCID: PMC7897682 DOI: 10.3389/fimmu.2021.600056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/13/2021] [Indexed: 12/28/2022] Open
Abstract
The cellular response to interferon (IFN) is essential for antiviral immunity, IFN-based therapy and IFN-related disease. The plasma membrane (PM) provides a critical interface between the cell and its environment, and is the initial portal of entry for viruses. Nonetheless, the effect of IFN on PM proteins is surprisingly poorly understood, and has not been systematically investigated in primary immune cells. Here, we use multiplexed proteomics to quantify IFNα2a-stimulated PM protein changes in primary human CD14+ monocytes and CD4+ T cells from five donors, quantifying 606 and 482 PM proteins respectively. Comparison of cell surface proteomes revealed a remarkable invariance between donors in the overall composition of the cell surface from each cell type, but a marked donor-to-donor variability in the effects of IFNα2a. Furthermore, whereas only 2.7% of quantified proteins were consistently upregulated by IFNα2a at the surface of CD4+ T cells, 6.8% of proteins were consistently upregulated in primary monocytes, suggesting that the magnitude of the IFNα2a response varies according to cell type. Among these differentially regulated proteins, we found the viral target Endothelin-converting enzyme 1 (ECE1) to be an IFNα2a-stimulated protein exclusively upregulated at the surface of CD4+ T cells. We therefore provide a comprehensive map of the cell surface of IFNα2a-stimulated primary human immune cells, including previously uncharacterized interferon stimulated genes (ISGs) and candidate antiviral factors.
Collapse
Affiliation(s)
- Lior Soday
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Leah M. Hunter
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin J. Ravenhill
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Jack W. Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James C. Williamson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Mark R. Wills
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Nicholas J. Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
9
|
Joshi RN, Stadler C, Lehmann R, Lehtiö J, Tegnér J, Schmidt A, Vesterlund M. TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells. Front Immunol 2019; 10:2708. [PMID: 31849937 PMCID: PMC6902019 DOI: 10.3389/fimmu.2019.02708] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/04/2019] [Indexed: 01/07/2023] Open
Abstract
We have curated an in-depth subcellular proteomic map of primary human CD4+ T cells, divided into cytosolic, nuclear and membrane fractions generated by an optimized fractionation and HiRIEF-LC-MS/MS workflow for limited amounts of primary cells. The subcellular proteome of T cells was mapped under steady state conditions, as well as upon 15 min and 1 h of T cell receptor (TCR) stimulation, respectively. We quantified the subcellular distribution of 6,572 proteins and identified a subset of 237 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization, respectively. We further provide the data in an easy-to-use web platform to facilitate re-use, as the data can be relevant for basic research as well as for clinical exploitation of T cells as therapeutic targets.
Collapse
Affiliation(s)
- Rubin Narayan Joshi
- Unit of Computational Medicine, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital and Science for Life Laboratory, Stockholm, Sweden
| | - Charlotte Stadler
- Department of Protein Sciences, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Robert Lehmann
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital and Science for Life Laboratory, Stockholm, Sweden.,Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Angelika Schmidt
- Unit of Computational Medicine, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital and Science for Life Laboratory, Stockholm, Sweden
| | - Mattias Vesterlund
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| |
Collapse
|
10
|
Herster F, Bittner Z, Codrea MC, Archer NK, Heister M, Löffler MW, Heumos S, Wegner J, Businger R, Schindler M, Stegner D, Schäkel K, Grabbe S, Ghoreschi K, Miller LS, Weber ANR. Platelets Aggregate With Neutrophils and Promote Skin Pathology in Psoriasis. Front Immunol 2019; 10:1867. [PMID: 31474979 PMCID: PMC6706802 DOI: 10.3389/fimmu.2019.01867] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/23/2019] [Indexed: 12/13/2022] Open
Abstract
Psoriasis is a frequent systemic inflammatory autoimmune disease characterized primarily by skin lesions with massive infiltration of leukocytes, but frequently also presents with cardiovascular comorbidities. Especially polymorphonuclear neutrophils (PMNs) abundantly infiltrate psoriatic skin but the cues that prompt PMNs to home to the skin are not well-defined. To identify PMN surface receptors that may explain PMN skin homing in psoriasis patients, we screened 332 surface antigens on primary human blood PMNs from healthy donors and psoriasis patients. We identified platelet surface antigens as a defining feature of psoriasis PMNs, due to a significantly increased aggregation of neutrophils and platelets in the blood of psoriasis patients. Similarly, in the imiquimod-induced experimental in vivo mouse model of psoriasis, disease induction promoted PMN-platelet aggregate formation. In psoriasis patients, disease incidence directly correlated with blood platelet counts and platelets were detected in direct contact with PMNs in psoriatic but not healthy skin. Importantly, depletion of circulating platelets in mice in vivo ameliorated disease severity significantly, indicating that both PMNs and platelets may be relevant for psoriasis pathology and disease severity.
Collapse
Affiliation(s)
| | - Zsofia Bittner
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | - Nathan K Archer
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Martin Heister
- Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Department of Immunology, University of Tübingen, Tübingen, Germany.,Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
| | - Joanna Wegner
- Department of Dermatology, University Hospital Mainz, Mainz, Germany
| | - Ramona Businger
- Division of Molecular Virology, Institute of Virology, Tübingen, Germany
| | - Michael Schindler
- Division of Molecular Virology, Institute of Virology, Tübingen, Germany
| | - David Stegner
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Knut Schäkel
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Hospital Mainz, Mainz, Germany
| | - Kamran Ghoreschi
- Department of Dermatology, University Hospital Tübingen, Tübingen, Germany.,Department of Dermatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lloyd S Miller
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | |
Collapse
|
11
|
Boucau J, Madouasse J, Kourjian G, Carlin CS, Wambua D, Berberich MJ, Le Gall S. The Activation State of CD4 T Cells Alters Cellular Peptidase Activities, HIV Antigen Processing, and MHC Class I Presentation in a Sequence-Dependent Manner. THE JOURNAL OF IMMUNOLOGY 2019; 202:2856-2872. [PMID: 30936293 DOI: 10.4049/jimmunol.1700950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
CD4 T cell activation is critical to the initiation of adaptive immunity. CD4 T cells are also the main targets of HIV infection, and their activation status contributes to the maintenance and outcome of infection. Although the role of activation in the differentiation and proliferation of CD4 T cells is well studied, its impact on the processing and MHC class I (MHC-I) presentation of epitopes and immune recognition by CD8 T cells are not investigated. In this study, we show that the expression and hydrolytic activities of cellular peptidases are increased upon TCR-dependent and MHC-peptide activation of primary CD4 T cells from healthy or HIV-infected persons. Changes in peptidase activities altered the degradation patterns of HIV Ags analyzed by mass spectrometry, modifying the amount of MHC-I epitopes produced, the antigenicity of the degradation products, and the coverage of Ags by degradation peptides presentable by MHC-I. The computational analysis of 2237 degradation peptides generated during the degradation of various HIV-antigenic fragments in CD4 T cells identified cleavage sites that were predictably enhanced, reduced, or unchanged upon cellular activation. Epitope processing and presentation by CD4 T cells may be modulated by the activation state of cells in a sequence-dependent manner. Accordingly, cellular activation modified endogenous Ag processing and presentation and killing of HIV-infected CD4 T cells by CD8 T cells in a way that mirrored differences in in vitro epitope processing. The clearance of HIV-infected cells may rely on different immune responses according to activation state during HIV infection.
Collapse
Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | | | | | - Daniel Wambua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| |
Collapse
|
12
|
Adriani M, Nytrova P, Mbogning C, Hässler S, Medek K, Jensen PEH, Creeke P, Warnke C, Ingenhoven K, Hemmer B, Sievers C, Lindberg Gasser RL, Fissolo N, Deisenhammer F, Bocskei Z, Mikol V, Fogdell-Hahn A, Kubala Havrdova E, Broët P, Dönnes P, Mauri C, Jury EC. Monocyte NOTCH2 expression predicts IFN-β immunogenicity in multiple sclerosis patients. JCI Insight 2018; 3:99274. [PMID: 29875313 DOI: 10.1172/jci.insight.99274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/24/2018] [Indexed: 01/25/2023] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by CNS inflammation leading to demyelination and axonal damage. IFN-β is an established treatment for MS; however, up to 30% of IFN-β-treated MS patients develop neutralizing antidrug antibodies (nADA), leading to reduced drug bioactivity and efficacy. Mechanisms driving antidrug immunogenicity remain uncertain, and reliable biomarkers to predict immunogenicity development are lacking. Using high-throughput flow cytometry, NOTCH2 expression on CD14+ monocytes and increased frequency of proinflammatory monocyte subsets were identified as baseline predictors of nADA development in MS patients treated with IFN-β. The association of this monocyte profile with nADA development was validated in 2 independent cross-sectional MS patient cohorts and a prospective cohort followed before and after IFN-β administration. Reduced monocyte NOTCH2 expression in nADA+ MS patients was associated with NOTCH2 activation measured by increased expression of Notch-responsive genes, polarization of monocytes toward a nonclassical phenotype, and increased proinflammatory IL-6 production. NOTCH2 activation was T cell dependent and was only triggered in the presence of serum from nADA+ patients. Thus, nADA development was driven by a proinflammatory environment that triggered activation of the NOTCH2 signaling pathway prior to first IFN-β administration.
Collapse
Affiliation(s)
- Marsilio Adriani
- Department of Rheumatology, University College Hospital, London, United Kingdom
| | - Petra Nytrova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Cyprien Mbogning
- CESP, Fac. De Médecine-Univ. Paris-Sud, Fac. De Médecine-UVSQ, INSERM, Université Paris-Saclay, Villejuif, France
| | - Signe Hässler
- CESP, Fac. De Médecine-Univ. Paris-Sud, Fac. De Médecine-UVSQ, INSERM, Université Paris-Saclay, Villejuif, France
| | - Karel Medek
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Poul Erik H Jensen
- Neuroimmunology Laboratory, DMSC, Department of Neurology, Rigshospitalet, Region H, Copenhagen, Denmark
| | - Paul Creeke
- Neuroimmunology Unit, Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Clemens Warnke
- Department of Neurology, Medical Faculty, Research Group for Clinical and Experimental Neuroimmunology, Heinrich-Heine-University, Düsseldorf, Germany.,University Hospital Koeln, Deptartment of Neurology, Koeln, Germany
| | - Kathleen Ingenhoven
- Department of Neurology, Medical Faculty, Research Group for Clinical and Experimental Neuroimmunology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Bernhard Hemmer
- Klinikum rechts der Isar, Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Claudia Sievers
- Laboratory of Clinical Neuroimmunology, Departments of Biomedicine and Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Raija Lp Lindberg Gasser
- Laboratory of Clinical Neuroimmunology, Departments of Biomedicine and Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Nicolas Fissolo
- Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Florian Deisenhammer
- Clinical Department of Neurology, Innsbruck Medical University, Innsbruck, Austria
| | - Zsolt Bocskei
- Translational Sciences Unit, Sanofi R&D, 91385 Chilly-Mazarin, Paris, France
| | - Vincent Mikol
- Translational Sciences Unit, Sanofi R&D, 91385 Chilly-Mazarin, Paris, France
| | - Anna Fogdell-Hahn
- Karolinska Institutet, Department of Clinical Neuroscience, Center for Molecular Medicine (CMM), Karolinska University Hospital, Sweden
| | - Eva Kubala Havrdova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Philippe Broët
- CESP, Fac. De Médecine-Univ. Paris-Sud, Fac. De Médecine-UVSQ, INSERM, Université Paris-Saclay, Villejuif, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Paul Brousse, Villejuif, France
| | | | - Claudia Mauri
- Department of Rheumatology, University College Hospital, London, United Kingdom
| | - Elizabeth C Jury
- Department of Rheumatology, University College Hospital, London, United Kingdom
| | | |
Collapse
|
13
|
T cells with low CD2 levels express reduced restriction factors and are preferentially infected in therapy naïve chronic HIV-1 patients. J Int AIDS Soc 2018; 20:21865. [PMID: 28953327 PMCID: PMC5964667 DOI: 10.7448/ias.20.1.21865] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Restriction factors (RFs) suppress HIV-1 in cell lines and primary cell models. Hence, RFs might be attractive targets for novel antiviral strategies, but their importance for virus control in vivo is controversial. METHODS We profiled the expression of RFs in primary blood-derived mononuclear cells (PBMC) from therapy-naïve HIV-1 patients and quantified infection. RESULTS Overall, there was no correlation between individual RF expression and HIV-1 status in total PBMC. However, we identified a T cell population with low levels of intracellular CD2 and reduced expression of SAMHD1, p21 and SerinC5. CD2low T cells with reduced RF expression were markedly positive for HIV-1 p24. In contrast, CD2+ T cells were less infected and expressed higher levels of RFs. CD2low T cell infection correlated with viral loads and was associated with HIV-1 disease progression. CONCLUSIONS In untreated therapy naïve chronic HIV-1 patients, RF expression in T cells is associated with CD2 expression and seems to influence viral loads. Our study suggests that RFs help to control HIV-1 infection in certain T cells in vivo and supports the potential for RFs as promising targets for therapeutic intervention.
Collapse
|
14
|
Landgraf-Rauf K, Boeck A, Siemens D, Klucker E, Vogelsang V, Schmidt S, Kunze S, Weissenbacher C, Graessel A, Schmidt-Weber C, von Mutius E, Schedel M, Schaub B. IRF-1 SNPs influence the risk for childhood allergic asthma: A critical role for pro-inflammatory immune regulation. Pediatr Allergy Immunol 2018; 29:34-41. [PMID: 29047170 DOI: 10.1111/pai.12821] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/15/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Allergic and non-allergic childhood asthma has been characterized by distinct immune mechanisms. While interferon regulating factor 1 (IRF-1) polymorphisms (SNPs) influence atopy risk, the effect of SNPs on asthma phenotype-specific immune mechanisms is unclear. We assessed whether IRF-1 SNPs modify distinct immune-regulatory pathways in allergic and non-allergic childhood asthma (AA/NA). METHODS In the CLARA study, asthma was characterized by doctor's diagnosis and AA vs NA by positive or negative specific IgE. Children were genotyped for four tagging SNPs within IRF-1 (n = 172). mRNA expression was measured with qRT-PCR. Gene expression was analyzed depending on genetic variants within IRF-1 and phenotype including haplotype estimation and an allelic risk score. RESULTS Carrying the risk alleles of IRF-1 in rs10035166, rs2706384, or rs2070721 was associated with increased risk for AA. Carrying the non-risk allele in rs17622656 was associated with lower risk for AA but not NA. In AA carrying the risk alleles, an increased pro-inflammatory expression of ICAM3, IRF-8, XBP-1, IFN-γ, RGS13, RORC, and TSC2 was observed. NOD2 expression was decreased in AA with risk alleles in rs2706384 and rs10035166 and with risk haplotype. Further, AA with risk haplotype showed increased IL-13 secretion. NA with risk allele in rs2070721 compared to non-risk allele in rs17622656 showed significantly upregulated calcium, innate, mTOR, neutrophil, and inflammatory-associated genes. CONCLUSION IRF-1 polymorphisms influence the risk for childhood allergic asthma being associated with increased pro-inflammatory gene regulation. Thus, it is critical to implement IRF-1 genetics in immune assessment for childhood asthma phenotypes.
Collapse
Affiliation(s)
- Katja Landgraf-Rauf
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Andreas Boeck
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany
| | - Diana Siemens
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany
| | - Elisabeth Klucker
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany
| | - Vanessa Vogelsang
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany
| | - Susanne Schmidt
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany
| | - Sonja Kunze
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Weissenbacher
- Department of Endocrinology, University Children's Hospital Munich, LMU Munich, Munich, Germany
| | - Anke Graessel
- ZAUM - Center of Allergy and Environment, Technische Universität and Helmholtz Center Munich, Munich, Germany
| | - Carsten Schmidt-Weber
- ZAUM - Center of Allergy and Environment, Technische Universität and Helmholtz Center Munich, Munich, Germany
| | - Erika von Mutius
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Michaela Schedel
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Bianca Schaub
- Department of Pulmonary & Allergy, University Children's Hospital Munich, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| |
Collapse
|
15
|
Huber MC, Falkenberg N, Hauck SM, Priller M, Braselmann H, Feuchtinger A, Walch A, Schmitt M, Aubele M. Cyr61 and YB-1 are novel interacting partners of uPAR and elevate the malignancy of triple-negative breast cancer. Oncotarget 2018; 7:44062-44075. [PMID: 27286449 PMCID: PMC5190079 DOI: 10.18632/oncotarget.9853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/16/2016] [Indexed: 11/29/2022] Open
Abstract
The triple-negative breast cancer (TNBC) is a very aggressive tumor type often occurring in young women and is associated with a bad prognosis for the patients. TNBC lacks established targets for breast cancer therapy, such as the estrogen receptor (ER), progesterone receptor (PR) and the human epidermal growth factor receptor 2 (HER2). Therefore, novel therapeutic targets and strategies are needed for an improved treatment of this breast cancer subtype. TNBC and respective cell lines often overexpress proteins of the urokinase plasminogen activator system (uPAS) including uPA, its receptor uPAR and inhibitor PAI-1, which together with co-factors contribute to the malignancy of TNBC. Here, two novel interacting partners of uPAR, the cysteine-rich angiogenic inducer 61 (Cyr61) and the Y-box-binding protein 1 (YB-1) were identified and their differential expression demonstrated in TNBC cells as well as in tumors. In the TNBC cohort, both interactors significantly correlated with expression levels of cathepsin B, c-Met and the tumor grade. In addition, expression levels of Cyr61 significantly correlated with cathepsin D (p=0.03), insulin receptor (p≤0.001), insulin-like growth factor receptor 1 (IGF1R, p=0.015) and also with YB-1 (p=0.0004) levels. The interactions of uPAR with Cyr61 significantly correlated with expression levels of tumor-promoting biomarkers including plasminogen (p=0.0014), cathepsin B (p=0.032), c-Met (p=0.0192) as well as with the tumor grade (p=0.02). In multivariate survival analysis, YB-1 showed independent prognostic value (p=0.01). As the novel interacting partners, also together with uPAR, contribute to tumor progression and metastasis, both may be potential therapeutic targets in breast cancer.
Collapse
Affiliation(s)
- Michaela C Huber
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Natalie Falkenberg
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Stefanie M Hauck
- Research Unit of Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Markus Priller
- Research Unit of Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Herbert Braselmann
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Annette Feuchtinger
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Axel Walch
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Manfred Schmitt
- Clinical Research Unit, Department of Obstetrics and Gynecology, Technische Universität München, München 81675, Germany
| | - Michaela Aubele
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| |
Collapse
|
16
|
Lepper MF, Ohmayer U, von Toerne C, Maison N, Ziegler AG, Hauck SM. Proteomic Landscape of Patient-Derived CD4+ T Cells in Recent-Onset Type 1 Diabetes. J Proteome Res 2017; 17:618-634. [PMID: 29182335 DOI: 10.1021/acs.jproteome.7b00712] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The pathophysiology underlying the autoimmune disease type 1 diabetes (T1D) is poorly understood. Obtaining an accurate proteomic profile of the T helper cell population is essential for understanding the pathogenesis of T1D. Here, we performed in-depth proteomic profiling of peripheral CD4+ T cells in a pediatric cohort to identify cellular signatures associated with the onset of T1D. Using only 250 000 CD4+ T cells per patient, isolated from biobanked PBMC samples, we identified nearly 6000 proteins using deep-proteome profiling with LC-MS/MS data-independent acquisition. Our analysis revealed an inflammatory signature in patients with T1D; this signature is characterized by circulating mediators of neutrophils, platelets, and the complement system. This signature likely reflects the inflammatory extracellular milieu, which suggests that activation of the innate immune system plays an important role in disease onset. Our results emphasize the potential value of using high-resolution LC-MS/MS to investigate limited quantities of biobanked samples to identify disease-relevant proteomic patterns. Proteomic profiles of 114 individuals have been deposited in a comprehensive portable repository serving as a unique resource for CD4+ T cell expression in the context of both health and T1D disease.
Collapse
Affiliation(s)
- Marlen F Lepper
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | | | | | | | | | - Stefanie M Hauck
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| |
Collapse
|
17
|
Höper T, Mussotter F, Haase A, Luch A, Tralau T. Application of proteomics in the elucidation of chemical-mediated allergic contact dermatitis. Toxicol Res (Camb) 2017; 6:595-610. [PMID: 30090528 PMCID: PMC6062186 DOI: 10.1039/c7tx00058h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/07/2017] [Indexed: 12/23/2022] Open
Abstract
Allergic contact dermatitis (ACD) is a widespread hypersensitivity reaction of the skin. The cellular mechanisms underlying its development are complex and involve close interaction of different cell types of the immune system. It is this very complexity which has long prevented straightforward replacement of the corresponding regulatory in vivo tests. Recent efforts have already resulted in the development of several in vitro testing alternatives that address key steps of ACD. Yet identification of suitable biomarkers is still a subject of intense research. Search strategies for the latter encompass transcriptomics, proteomics as well as metabolomics approaches. The scope of this review shall be the application and use of proteomics in the context of ACD. This includes highlighting relevant aspects of the molecular and cellular mechanisms underlying ACD, the exploitation of these mechanisms for testing and biomarkers (e.g., in the context of the OECD's adverse outcome pathway initiative) as well as an outlook on emerging proteome targets, for example during the allergen-induced activation of dendritic cells (DCs).
Collapse
Affiliation(s)
- Tessa Höper
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Franz Mussotter
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Andrea Haase
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Andreas Luch
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Tewes Tralau
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| |
Collapse
|
18
|
Kalxdorf M, Gade S, Eberl HC, Bantscheff M. Monitoring Cell-surface N-Glycoproteome Dynamics by Quantitative Proteomics Reveals Mechanistic Insights into Macrophage Differentiation. Mol Cell Proteomics 2017; 16:770-785. [PMID: 28336715 DOI: 10.1074/mcp.m116.063859] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/17/2017] [Indexed: 11/06/2022] Open
Abstract
The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival, and cell identity. As such, it is a prominent target for pharmacological intervention. The relatively low abundance of this subproteome in conjunction with challenging extractability and solubility still hampers its comprehensive analysis. Here, we combined a chemical glycoprotein-tagging strategy with mass spectrometry to enable comprehensive analysis of the cell-surface glycoproteome. To benchmark this workflow and to provide guidance for cell line selection for functional experiments, we generated an inventory of the N-linked cell-surface glycoproteomes of 15 standard laboratory human cell lines and three primary lymphocytic cell types. On average, about 900 plasma membrane and secreted proteins were identified per experiment, including more than 300 transporters and ion channels. Primary cells displayed distinct expression of surface markers and transporters underpinning the importance of carefully validating model cell lines selected for the study of cell surface-mediated processes. To monitor dynamic changes of the cell-surface proteome in a highly multiplexed experiment, we employed an isobaric mass tag-based chemical labeling strategy. This enabled the time-resolved analysis of plasma membrane protein presentation during differentiation of the monocytic suspension cell line THP-1 into macrophage-like adherent cells. Time-dependent changes observed in membrane protein presentation reflect functional remodeling during the phenotypic transition in three distinct phases: rapid surface presentation and secretion of proteins from intracellular pools concurrent with rapid internalization of no longer needed proteins and finally delayed presentation of newly synthesized macrophage markers. Perturbation of this process using marketed receptor tyrosine kinase inhibitors revealed dasatinib to severely compromise macrophage differentiation due to an off-target activity. This finding suggests that dynamic processes can be highly vulnerable to drug treatment and should be monitored more rigorously to identify adverse drug effects.
Collapse
Affiliation(s)
- Mathias Kalxdorf
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - H Christian Eberl
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| |
Collapse
|
19
|
Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis. J Proteomics 2017; 154:102-108. [DOI: 10.1016/j.jprot.2016.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/22/2016] [Accepted: 12/27/2016] [Indexed: 12/27/2022]
|
20
|
von Toerne C, Laimighofer M, Achenbach P, Beyerlein A, de Las Heras Gala T, Krumsiek J, Theis FJ, Ziegler AG, Hauck SM. Peptide serum markers in islet autoantibody-positive children. Diabetologia 2017; 60:287-295. [PMID: 27815605 DOI: 10.1007/s00125-016-4150-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/05/2016] [Indexed: 01/13/2023]
Abstract
AIMS/HYPOTHESIS We sought to identify minimal sets of serum peptide signatures as markers for islet autoimmunity and predictors of progression rates to clinical type 1 diabetes in a case-control study. METHODS A double cross-validation approach was applied to first prioritise peptides from a shotgun proteomic approach in 45 islet autoantibody-positive and -negative children from the BABYDIAB/BABYDIET birth cohorts. Targeted proteomics for 82 discriminating peptides were then applied to samples from another 140 children from these cohorts. RESULTS A total of 41 peptides (26 proteins) enriched for the functional category lipid metabolism were significantly different between islet autoantibody-positive and autoantibody-negative children. Two peptides (from apolipoprotein M and apolipoprotein C-IV) were sufficient to discriminate autoantibody-positive from autoantibody-negative children. Hepatocyte growth factor activator, complement factor H, ceruloplasmin and age predicted progression time to type 1 diabetes with a significant improvement compared with age alone. CONCLUSION/INTERPRETATION Distinct peptide signatures indicate islet autoimmunity prior to the clinical manifestation of type 1 diabetes and enable refined staging of the presymptomatic disease period.
Collapse
Affiliation(s)
- Christine von Toerne
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764, München, Germany
| | - Michael Laimighofer
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching, Germany
| | - Peter Achenbach
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764, München, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
| | - Andreas Beyerlein
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764, München, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Tonia de Las Heras Gala
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching, Germany
| | - Anette G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764, München, Germany.
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- Forschergruppe Diabetes e.V., Neuherberg, Germany.
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764, München, Germany.
| |
Collapse
|
21
|
Schäfer N, Grosche A, Reinders J, Hauck SM, Pouw RB, Kuijpers TW, Wouters D, Ehrenstein B, Enzmann V, Zipfel PF, Skerka C, Pauly D. Complement Regulator FHR-3 Is Elevated either Locally or Systemically in a Selection of Autoimmune Diseases. Front Immunol 2016; 7:542. [PMID: 27965669 PMCID: PMC5124756 DOI: 10.3389/fimmu.2016.00542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/16/2016] [Indexed: 12/30/2022] Open
Abstract
The human complement factor H-related protein-3 (FHR-3) is a soluble regulator of the complement system. Homozygous cfhr3/1 deletion is a genetic risk factor for the autoimmune form of atypical hemolytic-uremic syndrome (aHUS), while also found to be protective in age-related macular degeneration (AMD). The precise function of FHR-3 remains to be fully characterized. We generated four mouse monoclonal antibodies (mAbs) for FHR-3 (RETC) without cross-reactivity to the complement factor H (FH)-family. These antibodies detected FHR-3 from human serum with a mean concentration of 1 μg/mL. FHR-3 levels in patients were significantly increased in sera from systemic lupus erythematosus, rheumatoid arthritis, and polymyalgia rheumatica but remained almost unchanged in samples from AMD or aHUS patients. Moreover, by immunostaining of an aged human donor retina, we discovered a local FHR-3 production by microglia/macrophages. The mAb RETC-2 modulated FHR-3 binding to C3b but not the binding of FHR-3 to heparin. Interestingly, FHR-3 competed with FH for binding C3b and the mAb RETC-2 reduced the interaction of FHR-3 and C3b, resulting in increased FH binding. Our results unveil a previously unknown systemic involvement of FHR-3 in rheumatoid diseases and a putative local role of FHR-3 mediated by microglia/macrophages in the damaged retina. We conclude that the local FHR-3/FH equilibrium in AMD is a potential therapeutic target, which can be modulated by our specific mAb RETC-2.
Collapse
Affiliation(s)
- Nicole Schäfer
- Department of Ophthalmology, University Hospital Regensburg , Regensburg , Germany
| | - Antje Grosche
- Institute of Human Genetics, University of Regensburg , Regensburg , Germany
| | - Joerg Reinders
- Institute of Functional Genomics, University of Regensburg , Regensburg , Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) , Neuherberg , Germany
| | - Richard B Pouw
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Academic Medical Center, Emma Children's Hospital, Amsterdam, Netherlands; Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Diana Wouters
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands
| | - Boris Ehrenstein
- Klinik und Poliklinik für Rheumatologie und Klinische Immunologie, Asklepios Klinikum Bad Abbach , Bad Abbach , Germany
| | - Volker Enzmann
- Department of Ophthalmology, Inselspital, University of Bern , Bern , Switzerland
| | - Peter F Zipfel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany; Friedrich Schiller University, Jena, Germany
| | - Christine Skerka
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology , Jena , Germany
| | - Diana Pauly
- Department of Ophthalmology, University Hospital Regensburg , Regensburg , Germany
| |
Collapse
|
22
|
May JC, McLean JA. Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:387-409. [PMID: 27306312 PMCID: PMC5763907 DOI: 10.1146/annurev-anchem-071015-041734] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Hybrid analytical instrumentation constructed around mass spectrometry (MS) is becoming the preferred technique for addressing many grand challenges in science and medicine. From the omics sciences to drug discovery and synthetic biology, multidimensional separations based on MS provide the high peak capacity and high measurement throughput necessary to obtain large-scale measurements used to infer systems-level information. In this article, we describe multidimensional MS configurations as technologies that are big data drivers and review some new and emerging strategies for mining information from large-scale datasets. We discuss the information content that can be obtained from individual dimensions, as well as the unique information that can be derived by comparing different levels of data. Finally, we summarize some emerging data visualization strategies that seek to make highly dimensional datasets both accessible and comprehensible.
Collapse
Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235;
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235;
| |
Collapse
|
23
|
Heinzelmann K, Noskovičová N, Merl-Pham J, Preissler G, Winter H, Lindner M, Hatz R, Hauck SM, Behr J, Eickelberg O. Surface proteome analysis identifies platelet derived growth factor receptor-alpha as a critical mediator of transforming growth factor-beta-induced collagen secretion. Int J Biochem Cell Biol 2016; 74:44-59. [PMID: 26905437 DOI: 10.1016/j.biocel.2016.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/19/2016] [Accepted: 02/19/2016] [Indexed: 12/14/2022]
Abstract
Fibroblasts are extracellular matrix-producing cells in the lung. Fibroblast activation by transforming growth factor-beta leads to myofibroblast-differentiation and increased extracellular matrix deposition, a hallmark of pulmonary fibrosis. While fibroblast function with respect to migration, invasion, and extracellular matrix deposition has been well-explored, little is known about the surface proteome of lung fibroblasts in general and its specific response to fibrogenic growth factors, in particular transforming growth factor-beta. We thus performed a cell-surface proteome analysis of primary human lung fibroblasts in presence/absence of transforming growth factor-beta, followed by characterization of our findings using FACS analysis, Western blot, and siRNA-mediated knockdown experiments. We identified 213 surface proteins significantly regulated by transforming growth factor-beta, platelet derived growth factor receptor-alpha being one of the top down-regulated proteins. Transforming growth factor beta-induced downregulation of platelet derived growth factor receptor-alpha induced upregulation of platelet derived growth factor receptor-beta expression and phosphorylation of Akt, a downstream target of platelet derived growth factor signaling. Importantly, collagen type V expression and secretion was strongly increased after forced knockdown of platelet derived growth factor receptor-alpha, an effect that was potentiated by transforming growth factor-beta. We therefore show previously underappreciated cross-talk of transforming growth factor-beta and platelet derived growth factor signaling in human lung fibroblasts, resulting in increased extracellular matrix deposition in a platelet derived growth factor receptor-alpha dependent manner. These findings are of particular importance for the treatment of lung fibrosis patients with high pulmonary transforming growth factor-beta activity.
Collapse
Affiliation(s)
- Katharina Heinzelmann
- Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Nina Noskovičová
- Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science/Helmholtz Zentrum München, Neuherberg, Germany
| | - Gerhard Preissler
- Thoraxchirurgisches Zentrum, Klinik für Allgemeine-, Viszeral-, Transplantations-, Gefäß- und Thoraxchirurgie, Klinikum Großhadern, Ludwig-Maximilians-Universität, Munich, Germany
| | - Hauke Winter
- Thoraxchirurgisches Zentrum, Klinik für Allgemeine-, Viszeral-, Transplantations-, Gefäß- und Thoraxchirurgie, Klinikum Großhadern, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Rudolf Hatz
- Thoraxchirurgisches Zentrum, Klinik für Allgemeine-, Viszeral-, Transplantations-, Gefäß- und Thoraxchirurgie, Klinikum Großhadern, Ludwig-Maximilians-Universität, Munich, Germany; Asklepios Fachkliniken München-Gauting, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science/Helmholtz Zentrum München, Neuherberg, Germany
| | - Jürgen Behr
- Asklepios Fachkliniken München-Gauting, Munich, Germany; Medizinische Klinik und Poliklinik V, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany.
| |
Collapse
|
24
|
O'Leary CE, Lewis EL, Oliver PM. Ubiquitylation as a Rheostat for TCR Signaling: From Targeted Approaches Toward Global Profiling. Front Immunol 2015; 6:618. [PMID: 26732666 PMCID: PMC4679856 DOI: 10.3389/fimmu.2015.00618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022] Open
Abstract
T cell receptor (TCR) signaling must be precisely tuned to limit collateral damage and prevent reactivity to self, while still allowing robust protective immune responses that control pathogen invasion. One process that can be used to promote, modify, or terminate TCR signaling is ubiquitylation. During ubiquitylation, ubiquitin is covalently attached to target proteins through a multistep process, in which E3 ubiquitin ligases promote the formation of ubiquitin chains on selected substrates. Ubiquitylation can facilitate protein–protein interactions, direct a protein to a specific subcellular location, or initiate protein destruction. Like phosphorylation, ubiquitylation is a reversible process – deubiquitylating enzymes counteract ligase function by removing ubiquitin chains. This reversibility also allows for ubiquitin chain “editing.” Based on an emerging wealth of information from genetic loss-of-function studies showing that deregulation of ubiquitylation pathways leads to immune dysfunction, it has become increasingly apparent that the dynamic process of ubiquitylation is critical for normal immune cell function. In this review, we will describe how ubiquitylation acts as a key modulator and integrator of signaling downstream of TCR engagement. Specifically, we highlight the known roles of the substrate-specific E3 ligases and deubiquitylating enzymes in TCR signaling and T cell activation. While it is clear that ubiquitin enzymes tune T cell signaling and T cell function, elucidating the molecular mechanisms by which these proteins modulate T cells has met with significant challenges. Identifying substrates of these enzymes has been a particular challenge, and thus substrates of many E3 ligases and deubiquitylating enzymes remain largely unknown. To that end, we discuss the promise, and some practical considerations, of using proteomics-based techniques for unbiased identification of putative substrates of ubiquitin cascade proteins within primary T cells. These methods provide an exciting opportunity for further defining how TCR signals are regulated and for identifying new targets for therapeutic modulation.
Collapse
Affiliation(s)
- Claire E O'Leary
- Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Emma L Lewis
- Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Paula M Oliver
- Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| |
Collapse
|
25
|
Grosche A, Hauser A, Lepper MF, Mayo R, von Toerne C, Merl-Pham J, Hauck SM. The Proteome of Native Adult Müller Glial Cells From Murine Retina. Mol Cell Proteomics 2015; 15:462-80. [PMID: 26324419 PMCID: PMC4739667 DOI: 10.1074/mcp.m115.052183] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Indexed: 12/26/2022] Open
Abstract
To date, the proteomic profiling of Müller cells, the dominant macroglia of the retina, has been hampered because of the absence of suitable enrichment methods. We established a novel protocol to isolate native, intact Müller cells from adult murine retinae at excellent purity which retain in situ morphology and are well suited for proteomic analyses. Two different strategies of sample preparation - an in StageTips (iST) and a subcellular fractionation approach including cell surface protein profiling were used for quantitative liquid chromatography-mass spectrometry (LC-MSMS) comparing Müller cell-enriched to depleted neuronal fractions. Pathway enrichment analyses on both data sets enabled us to identify Müller cell-specific functions which included focal adhesion kinase signaling, signal transduction mediated by calcium as second messenger, transmembrane neurotransmitter transport and antioxidant activity. Pathways associated with RNA processing, cellular respiration and phototransduction were enriched in the neuronal subpopulation. Proteomic results were validated for selected Müller cell genes by quantitative real time PCR, confirming the high expression levels of numerous members of the angiogenic and anti-inflammatory annexins and antioxidant enzymes (e.g. paraoxonase 2, peroxiredoxin 1, 4 and 6). Finally, the significant enrichment of antioxidant proteins in Müller cells was confirmed by measurements on vital retinal cells using the oxidative stress indicator CM-H2DCFDA. In contrast to photoreceptors or bipolar cells, Müller cells were most efficiently protected against H2O2-induced reactive oxygen species formation, which is in line with the protein repertoire identified in the proteomic profiling. Our novel approach to isolate intact glial cells from adult retina in combination with proteomic profiling enabled the identification of novel Müller glia specific proteins, which were validated as markers and for their functional impact in glial physiology. This provides the basis to allow the discovery of novel glial specializations and will enable us to elucidate the role of Müller cells in retinal pathologies — a topic still controversially discussed.
Collapse
Affiliation(s)
- Antje Grosche
- From the ‡Insitute of Human Genetics, University of Regensburg, D-93053 Regensburg, Germany;
| | - Alexandra Hauser
- From the ‡Insitute of Human Genetics, University of Regensburg, D-93053 Regensburg, Germany
| | - Marlen Franziska Lepper
- §Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), D-85764 Neuherberg, Germany
| | - Rebecca Mayo
- From the ‡Insitute of Human Genetics, University of Regensburg, D-93053 Regensburg, Germany
| | - Christine von Toerne
- §Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), D-85764 Neuherberg, Germany
| | - Juliane Merl-Pham
- §Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), D-85764 Neuherberg, Germany
| | - Stefanie M Hauck
- §Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), D-85764 Neuherberg, Germany
| |
Collapse
|